Entropy and Barrier-Hopping Determine Conformational Viscoelasticity in Single Biomolecules

Biological macromolecules have complex and non-trivial energy landscapes, endowing them a unique conformational adaptability and diversity in function. Hence, understanding the processes of elasticity and dissipation at the nanoscale is important to molecular biology and also emerging fields such as nanotechnology. Here we analyse single molecule fluctuations in an atomic force microscope (AFM) experiment using a generic model of biopolymer viscoelasticity that importantly includes sources of local `internal' conformational dissipation. Comparing two biopolymers, dextran and cellulose, polysaccharides with and without the well-known `chair-to-boat' transition, reveals a signature of this simple conformational change as minima in both the elasticity and internal friction around a characteristic force. A calculation of two-state populations dynamics offers a simple explanation in terms of an elasticity driven by the entropy, and friction by barrier-controlled hopping, of populations on a landscape. The microscopic model, allows quantitative mapping of features of the energy landscape, revealing unexpectedly slow dynamics, suggestive of an underlying roughness to the free energy.Comment: 25 pages, 7 figures, naturemag.bst, modified nature.cls (naturemodified.cls

Real-time sliding mode observer scheme for shear force estimation in a transverse dynamic force microscope

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.This paper describes a sliding mode observer scheme for estimation of the shear force affecting the cantilever in a Transverse Dynamic Force Microscope (TDFM). The vertically oriented cantilever is oscillated in proximity to the specimen under investigation. The amplitude of oscillation of the cantilever tip is affected by these shear forces. They are created by the ordered-water layer above the specimen. The oscillation amplitude is therefore a measure of distance between the tip and the surface of the specimen. Consequently, the estimation of the shear forces provides useful information about the specimen characteristics. For estimating the shear forces, an approximate finite dimensional model of the cantilever is created using the method of lines. This model is subsequently reduced for its model order. An unknown input sliding mode observer has been used to reconstruct the unknown shear forces using only tip position measurements and the cantilever excitation. This paper describes the development of the sliding mode scheme and presents experimental results from the TDFM set up at the Centre for Nanoscience and Quantum Information (NSQI) at Bristol University

Estimation of the shear force in transverse dynamic force microscopy using a sliding mode observer

Open access journalIn this paper, the problem of estimating the shear force affecting the tip of the cantilever in a Transverse Dynamic Force Microscope (TDFM) using a real-time implementable sliding mode observer is addressed. The behaviour of a vertically oriented oscillated cantilever, in close proximity to a specimen surface, facilitates the imaging of the specimen at nano-metre scale. Distance changes between the cantilever tip and the specimen can be inferred from the oscillation amplitudes, but also from the shear force acting at the tip. Thus, the problem of accurately estimating the shear force is of significance when specimen images and mechanical properties need to be obtained at submolecular precision. A low order dynamic model of the cantilever is derived using the method of lines, for the purpose of estimating the shear force. Based on this model, an estimator using sliding mode techniques is presented to reconstruct the unknown shear force, from only tip position measurements and knowledge of the excitation signal applied to the top of the cantilever. Comparisons to methods assuming a quasi-static harmonic balance are made.Engineering and Physical Sciences Research Council (EPSRC

Optimisation of a nano-positioning stage for a Transverse Dynamic Force Microscope

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.This paper describes the optimisation of a nano-positioning stage for a Transverse Dynamic Force Microscope (TDFM). The nano-precision stage is required to move a specimen dish within a horizontal region of 1 μm × 1 μm and with a resolution of 0.3 nm. The design objective was to maximise positional accuracy during high speed actuation. This was achieved by minimising out-of-plane distortions and vibrations during actuation. Optimal performance was achieved through maximising out-of-plane stiffness through shape and material selection as well optimisation of the anchoring system. Several shape parameters were optimised including the shape of flexural beams and the shape of the dish holder. Physical prototype testing was an essential part of the design process to confirm the accuracy of modelling and also to reveal issues with manufacturing tolerances. An overall resonant frequency of 6 kHz was achieved allowing for a closed loop-control frequency of 1.73 kHz for precise horizontal motion control. This resonance represented a 12-fold increase from the original 500 Hz of a commercially available positioning stage. Experimental maximum out-of-plane distortions below the first resonance frequency were reduced from 0.3 μm for the first prototype to less than 0.05 μm for the final practical prototype

Characterization of magnetic nanostructures by magnetic force microscopy

Práce pojednává o mikroskopii magnetických sil magneticky měkkých nanostruktur, zejména NiFe nanodrátů a různě tvarovaných tenkých vrstev - například disků. Práce se zaměřuje na téměř vše, co s touto mikroskopickou technikou souvisí: přípravu měřicích sond a vzorků, samotná pozorování a mikromagnetické simulace magnetického stavu vzorků. Byla pozorována jádra magnetických vírů, jak s komerčními, tak s námi připravenými sondami. Podařilo se zobrazit i magnetické doménové stěny v nanodrátech o průměru pouhých 50 nm. Připravili jsme fungující sondy s různými magnetickými vrstvami: magneticky tvrdého kobaltu, slitiny CoCr a magneticky měkké slitiny NiFe. Magneticky tvrdé sondy poskytovaly lepší signál, zatímco magneticky měkké byly vhodnější pro pozorování magneticky měkkých vzorků, protože je příliš neovlivňují. Námi připravené sondy jsou přinejmenším srovnatelné se standardními komerčními sondami. Simulace se ve většině případů shodují jak s měřením, tak teorií. Dále představujeme také naše prvotní výsledky modelování interakce vzorku s magnetickou sondou, které mohou složit k simulaci měření pomocí mikroskopie magnetických sil, a to i v případě, kdy sonda ovlivňuje magnetický stav vzorku.The thesis deals with magnetic force microscopy of soft magnetic nanostructures, mainly NiFe nanowires and thin-film elements such as discs. The thesis covers almost all aspects related to this technique - i.e. from preparation of magnetic probes and magnetic nanowires, through the measurement itself to micromagnetic simulations of the investigated samples. We observed the cores of magnetic vortices, tiny objects, both with commercial and our home-coated probes. Even domain walls in nanowires 50 nm in diameter were captured with this technique. We prepared functional probes with various magnetic coatings: hard magnetic Co, CoCr and soft NiFe. Hard probes give better signal, whereas the soft ones are more suitable for the measurement of soft magnetic structures as they do not influence significantly the imaged sample. Our probes are at least comparable with the standard commercial probes. The simulations are in most cases in a good agreement with the measurement and the theory. Further, we present our preliminary results of the probe-sample interaction modelling, which can be exploited for the simulation of magnetic force microscopy image even in the case of probe induced perturbations of the sample.

Modal Characterization of Micron-Scale Structures

This thesis is mainly concerned with the application of Stochastic Subspace Identification algorithms to extract dynamic characteristics of smaller-scale structural elements. It also emphasizes the development of a suitable identification procedure for extracting modal characteristics of insect’s sensory systems, which are typically of the order of microns in length. The traditional way of extracting modal parameters by forming a transfer function is not practical for micron-scale structures owing to the practical limitations in applying a quantifiable input to excite such structures. Output-only identification and Stochastic Subspace Identification (SSI) methods attempt to extract modal parameters from the output response data and hence eliminate the need for quantifying the input. The input in this case is assumed as a broad band white noise and is assumed to arise from ambient sources. A program, Modal Analysis on Civil Engineering Structures (MACEC), is used as a modal analysis tool for extracting the modal parameters of macro as well as micron­ size structures. It provides a Graphical User Interface (GUI) for performing output-only system identification within the MATLAB programming environment. MACEC offers system identification via two different methods: SSI and Peak Picking Method (PPM) and provides animated visualization of mode shapes. As part of this thesis, a detailed verification for using this program for analysing micron-size structures is performed. An experiment is carried out on a meter long beam where data is collected using Laser Doppler Vibrometry (LDV) and mode shapes and modal frequencies are identified via MACEC. These results are also verified from the data collected using conventional system identification methods. The same methodology is then employed on further experiments which are carried out on submillimeter size beams. The data in this case is collected using Microscope Scanning Vibrometer (MSV). Frequencies are identified using SSI via MACEC. Based on the procedure used for submillimeter size beams, a preliminary experiment is carried out on micron-size mechanoreceptor hair on the cercus of a cricket and modal frequencies are identified using SSI via MACEC. The test procedures and methodology developed in this case is envisaged further work to be performed in the area of dynamic characterization of insect’s sensory systems

Dynamic analysis of submerged microscale plates: the effects of acoustic radiation and viscous dissipation

The aim of this paper is to study the dynamic characteristics of micromechanical rectangular plates used as sensing elements in a viscous compressible fluid. A novel modelling procedure for the plate–fluid interaction problem is developed on the basis of linearized Navier–Stokes equations and no-slip conditions. Analytical expression for the fluid-loading impedance is obtained using a double Fourier transform approach. This modelling work provides us an analytical means to study the effects of inertial loading, acoustic radiation and viscous dissipation of the fluid acting on the vibration of microplates. The numerical simulation is conducted on microplates with different boundary conditions and fluids with different viscosities. The simulation results reveal that the acoustic radiation dominates the damping mechanism of the submerged microplates. It is also proved that microplates offer better sensitivities (Q-factors) than the conventional beam type microcantilevers being mass sensing platforms in a viscous fluid environment. The frequency response features of microplates under highly viscous fluid loading are studied using the present model. The dynamics of the microplates with all edges clamped are less influenced by the highly viscous dissipation of the fluid than the microplates with other types of boundary conditions