面向可视化纳米操作的DNA分子运动学建模研究

利用原子力显微镜(AFM:Atomic Force Microscopy)对DNA进行单分子纳米操作对生命科学的发展具有特别重要的意义,但是AFM纳米操作缺乏实时视觉反馈的问题依然制约着生物操纵技术的发展.虚拟现实技术是解决该问题的有效方法之一,但是必须预先建立起被操作物体的运动学模型.目前面向可视化纳米操作的建模研究多针对纳米棒、纳米颗粒等刚性物体展开,很少涉及到柔性DNA分子的运动建模方法。针对该问题,本文以弹簧-质点模型为基础,借鉴统计力学在DNA机械特性上的研究成果,提出了一种具有较强物理意义和实际可信度的柔性DNA分子运动学建模方法,并进行了相关仿真实验研究,从而为实现DNA分子的可视化纳米操作提供了理论依据。

机器人化纳米操作中任务空间的实时反馈方法研究

纳米科技的最终目标是在原子、分子尺度上，制造具有新颖物理、化学和生物特性的器件和系统，而实现这个目标最为关键的使能技术便是纳米尺度下进行观测、操作和装配的科学方法与相关技术手段。原子力显微镜（AFM：Atomic Force Microscopy）的发明为实现这一目标提供了可行途径，AFM除了能够在常态下实现对原子、分子尺度大小物体的观测，并且由于其超高的分辨率和运动精度，可控、可重复的运动方式，独特的机械力作用机理，任意环境的可适应性而广泛应用于纳米操作。然而AFM的主要功能是进行纳米观测，应用于纳米操作时面临着许多挑战性的难题，尽管随着近十年的深入研究，一些问题已经得到了部分解决，但是缺乏高可信度的实时视觉反馈、无法实现任务空间内探针的精确定位依然阻碍着AFM纳米操作的效率。以目前最为先进的AFM纳米操作方法—增强现实技术为例，尽管该技术可以为操作者提供实时的视觉反馈，但是这种视觉反馈并不代表纳米操作场景的真实变化，而是根据离线模型计算得到的一种图形仿真，因而视觉反馈是否可信取决于模型的准确程度，然而受纳米尺度下各种非线性力的影响，如毛细力、范德华力、静电力等等，很难建立完全精确的物理模型，模型误差将导致错误的视觉反馈并引起纳米操作的失败。此外，受PZT非线性和温漂的影响，基于AFM的纳米操作还缺乏在任务空间内对探针进行精确定位的能力，导致操作过程中AFM探针无法有效接触到纳米物体，使得机器人学中“从A点运动到B点”最为基本的任务难以实现，这些缺点都严重阻碍着AFM纳米操作的效率和效果。本论文针对上述问题，以机器人学中的感知、决策、行为理论和监控方法为基础，具体开展了以下几方面的工作： 1、视觉反馈缺乏可信度是基于增强现实AFM纳米操作面临的主要问题，由于操作者无法对视觉反馈可信度作出评断，经常会在错误视觉反馈的指引下进行无效的纳米操作，从而浪费大量的时间，降低了AFM纳米操作的效率。为了克服上述问题，本文在研究信息诊断与反馈理论基础上，提出了基于Kalman滤波的视觉反馈可信度在线监控方法，实现了视觉反馈错误的实时检测，避免了无效纳米操作的发生，提高了AFM纳米操作的效率。 2、错误视觉反馈被检测出后，需要对其修正以保证纳米操作任务的成功完成。然而传统修正方法需要中断纳米操作进行重新扫描成像，这往往需要耗费几分钟的时间，严重降低了AFM纳米操作的效率。针对该问题，本文提出一种基于局部扫描的在线修正方法，通过扫描轨迹的优化，该方法能够对真实纳米操作结果进行实时感知，从而不需要中断纳米操作就能实现错误视觉反馈的修正，并使得整个修正过程对于操作者透明。这保证了实时可视监控信息的真实性，显著提升了AFM纳米操作的效率。 3、PZT非线性和随机漂移是影响AFM探针精确定位的主要因素，针对该问题本文提出了一种基于路标的探针定位方法，其核心思想是不再采用距离为测度方式进行探针位置描述，而是将作业区域的特定形貌特征定义为参考路标，通过探针对特征形貌的主动感知实现基于路标地图的探针定位，有效消除PZT非线性和随机漂移引起的定位误差，提高探针在任务空间内的定位精度。 4、研究了机器人化纳米操作系统任务空间实时反馈的构建技术，具体包括高灵敏度纳米操作力的感知方法，系统结构误差的产生原因和补偿策略，面向探针实时运动控制的系统结构设计，系统的软硬件实现方案等内容，并利用该实验平台开展了大量实验研究，验证了本论文所提出理论方法的正确性，同时演示性地组建了基于单根CNT和DNA的纳电子器件，实验结果表明AFM纳米操作的效率和效果得到了极大提升。本文的研究工作丰富了基于AFM的机器人化纳米操作理论，为基于AFM的纳米制造技术发展提供了具有一定指导意义的理论方法和研究途径。

Ultrasonic synthesis of silica-alumina nanomaterials with controlled mesopore distribution without using surfactants

A novel sol-gel process has been developed for the synthesis of amorphous silica-aluminas with controlled mesopore distribution without the use of organic templating agents, e.g., surfactant molecules. Ultrasonic treatment during the synthesis enables production of precursor sols with narrow particle size distribution. Atomic force microscopy analysis shows that these sol particles are spherical in shape with a narrow size distribution (i.e., 13-25 nm) and their aggregation during the gelation creates clusters containing similar sized interparticle mesopores. A nitrogen physiadsorption study indicates that the mesoporous materials containing different Si/Al ratios prepared by the new synthesis method has a large specific surface area (i.e., 587-692 m(2)/g) and similar pore sizes of 2-11 nm. Solid-state Al-27 magic angle spinning (MAS) NMR shows that most of the aluminum is located in the tetrahedral position. A transmission electron microscopy (TEM) image shows that the mesoporous silica-alumina consists of 12-25 nm spheres. Additionally, high-resolution TEM and electron diffraction indicate that some nanoparticles are characteristic of a crystal, although X-ray diffraction and Si-29 MAS NMR analysis show an amorphous material.

Internal structure of copper(II)-phthalocyanine thin films on SiO2/Si substrates investigated by grazing incidence x-ray reflectometry

Jenkins, Tudor; Brieva, A.C.; Jones, D.G.; Evans, D.A., (2006) 'Internal structure of copper(II)-phthalocyanine thin films on SiO2/Si substrates investigated by grazing incidence x-ray reflectometry', Journal of Applied Physics 99 pp.73504 RAE2008

Pressure induced anisotropy of electrical conductivity in polycrystalline molybdenum disulfide

Anisotropic specimens of MoS2 are obtained by pressing the microcrystalline powder into special die. This inelastic compression results in a rearrangement of the disulfide micro platelets observed by Atomic Force Microscopy and reflected in the macroscopic anisotropy in electrical conductivity in these samples. The conductivity measured parallel and perpendicular to the direction of applied pressure exhibits an anisotropy factor of ∼10 at 1 GPa. This behaviour of the conductivity as a function of applied pressure is explained as the result of the simultaneous influence of a rearrangement of the micro platelets in the solid and the change of the inter-grain distances.

Nanoscale electronic properties of conjugated polymers and nanocrystals

The objective of this thesis is the exploration and characterisation of the nanoscale electronic properties of conjugated polymers and nanocrystals. In Chapter 2, the first application of conducting-probe atomic force microscopy (CP-AFM)-based displacement-voltage (z-V) spectroscopy to local measurement of electronic properties of conjugated polymer thin films is reported. Charge injection thresholds along with corresponding single particle gap and exciton binding energies are determined for a poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] thin film. By performing measurements across a grid of locations on the film, a series of exciton binding energy distributions are identified. The variation in measured exciton binding energies is in contrast to the smoothness of the film suggesting that the variation may be attributable to differences in the nano-environment of the polymer molecules within the film at each measurement location. In Chapter 3, the CP-AFM-based z-V spectroscopy method is extended for the first time to local, room temperature measurements of the Coulomb blockade voltage thresholds arising from sequential single electron charging of 28 kDa Au nanocrystal arrays. The fluid-like properties of the nanocrystal arrays enable reproducible formation of nanoscale probe-array-substrate junctions, allowing the influence of background charge on the electronic properties of the array to be identified. CP-AFM also allows complementary topography and phase data to be acquired before and after spectroscopy measurements, enabling comparison of local array morphology with local measurements of the Coulomb blockade thresholds. In Chapter 4, melt-assisted template wetting is applied for the first time to massively parallel fabrication of poly-(3-hexylthiophene) nanowires. The structural characteristics of the wires are first presented. Two-terminal electrical measurements of individual nanowires, utilising a CP-AFM tip as the source electrode, are then used to obtain the intrinsic nanowire resistivity and the total nanowire-electrode contact resistance subsequently allowing single nanowire hole mobility and mean nanowire-electrode barrier height values to be estimated. In Chapter 5, solution-assisted template wetting is used for fabrication of fluorene-dithiophene co-polymer nanowires. The structural characteristics of these wires are also presented. Two-terminal electrical measurements of individual nanowires indicate barrier formation at the nanowire-electrode interfaces and measured resistivity values suggest doping of the nanowires, possibly due to air exposure. The first report of single conjugated polymer nanowires as ultra-miniature photodetectors is presented, with single wire devices yielding external quantum efficiencies ~ 0.1 % and responsivities ~ 0.4 mA/W under monochromatic illumination.

Development of inversion-mode and junctionless Indium-Gallium-Arsenide MOSFETs

This PhD covers the development of planar inversion-mode and junctionless Al2O3/In0.53Ga0.47As metal-oxidesemiconductor field-effect transistors (MOSFETs). An implant activation anneal was developed for the formation of the source and drain (S/D) of the inversionmode MOSFET. Fabricated inversion-mode devices were used as test vehicles to investigate the impact of forming gas annealing (FGA) on device performance. Following FGA, the devices exhibited a subthreshold swing (SS) of 150mV/dec., an ION/IOFF of 104 and the transconductance, drive current and peak effective mobility increased by 29%, 25% and 15%, respectively. An alternative technique, based on the fitting of the measured full-gate capacitance vs gate voltage using a selfconsistent Poisson-Schrödinger solver, was developed to extract the trap energy profile across the full In0.53Ga0.47As bandgap and beyond. A multi-frequency inversion-charge pumping approach was proposed to (1) study the traps located at energy levels aligned with the In0.53Ga0.47As conduction band and (2) separate the trapped charge and mobile charge contributions. The analysis revealed an effective mobility (μeff) peaking at ~2850cm2/V.s for an inversion-charge density (Ninv) = 7*1011cm2 and rapidly decreasing to ~600cm2/V.s for Ninv = 1*1013 cm2, consistent with a μeff limited by surface roughness scattering. Atomic force microscopy measurements confirmed a large surface roughness of 1.95±0.28nm on the In0.53Ga0.47As channel caused by the S/D activation anneal. In order to circumvent the issue relative to S/D formation, a junctionless In0.53Ga0.47As device was developed. A digital etch was used to thin the In0.53Ga0.47As channel and investigate the impact of channel thickness (tInGaAs) on device performance. Scaling of the SS with tInGaAs was observed for tInGaAs going from 24 to 16nm, yielding a SS of 115mV/dec. for tInGaAs = 16nm. Flat-band μeff values of 2130 and 1975cm2/V.s were extracted on devices with tInGaAs of 24 and 20nm, respectively

Electrochemical biosensor based on microfabricated electrode arrays for life sciences applications

In developing a biosensor, the utmost important aspects that need to be emphasized are the specificity and selectivity of the transducer. These two vital prerequisites are of paramount in ensuring a robust and reliable biosensor. Improvements in electrochemical sensors can be achieved by using microelectrodes and to modify the electrode surface (using chemical or biological recognition layers to improve the sensitivity and selectivity). The fabrication and characterisations of silicon-based and glass-based gold microelectrode arrays with various geometries (band and disc) and dimension (ranging from 10 μm-100 nm) were reported. It was found that silicon-based transducers of 10 μm gold microelectrode array exhibited the most stable and reproducible electrochemical measurements hence this dimension was selected for further study. Chemical electrodeposition on both 10 μm microband and microdisc were found viable by electro-assisted self-assembled sol-gel silica film and nanoporous-gold electrodeposition respectively. The fabrication and characterisations of on-chip electrochemical cell was also reported with a fixed diameter/width dimension and interspacing variation. With this regard, the 10 μm microelectrode array with interspacing distance of 100 μm exhibited the best electrochemical response. Surface functionalisations on single chip of planar gold macroelectrodes were also studied for the immobilisation of histidine-tagged protein and antibody. Imaging techniques such as atomic force microscopy, fluorescent microscopy or scanning electron microscope were employed to complement the electrochemical characterisations. The long-chain thiol of self-assembled monolayer with NTA-metal ligand coordination was selected for the histidine-tagged protein while silanisation technique was selected for the antibody immobilisation. The final part of the thesis described the development of a T-2 labelless immunosensor using impedimetric approach. Good antibody calibration curve was obtained for both 10 μm microband and 10 μm microdisc array. For the establishment of the T-2/HT-2 toxin calibration curve, it was found that larger microdisc array dimension was required to produce better calibration curve. The calibration curves established in buffer solution show that the microelectrode arrays were sensitive and able to detect levels of T-2/HT-2 toxin as low as 25 ppb (25 μg kg-1) with a limit of quantitation of 4.89 ppb for a 10 μm microband array and 1.53 ppb for the 40 μm microdisc array.

Bonds between fibronectin and fibronectin-binding proteins on Staphylococcus aureus and Lactococcus lactis.

Bacterial cell-wall-associated fibronectin binding proteins A and B (FnBPA and FnBPB) form bonds with host fibronectin. This binding reaction is often the initial step in prosthetic device infections. Atomic force microscopy was used to evaluate binding interactions between a fibronectin-coated probe and laboratory-derived Staphylococcus aureus that are (i) defective in both FnBPA and FnBPB (fnbA fnbB double mutant, DU5883), (ii) capable of expressing only FnBPA (fnbA fnbB double mutant complemented with pFNBA4), or (iii) capable of expressing only FnBPB (fnbA fnbB double mutant complemented with pFNBB4). These experiments were repeated using Lactococcus lactis constructs expressing fnbA and fnbB genes from S. aureus. A distinct force signature was observed for those bacteria that expressed FnBPA or FnBPB. Analysis of this force signature with the biomechanical wormlike chain model suggests that parallel bonds form between fibronectin and FnBPs on a bacterium. The strength and covalence of bonds were evaluated via nonlinear regression of force profiles. Binding events were more frequent (p < 0.01) for S. aureus expressing FnBPA or FnBPB than for the S. aureus double mutant. The binding force, frequency, and profile were similar between the FnBPA and FnBPB expressing strains of S. aureus. The absence of both FnBPs from the surface of S. aureus removed its ability to form a detectable bond with fibronectin. By contrast, ectopic expression of FnBPA or FnBPB on the surface of L. lactis conferred fibronectin binding characteristics similar to those of S. aureus. These measurements demonstrate that fibronectin-binding adhesins FnBPA and FnBPB are necessary and sufficient for the binding of S. aureus to prosthetic devices that are coated with host fibronectin.

Phase transfer catalysts drive diverse organic solvent solubility of single-walled carbon nanotubes helically wrapped by ionic, semiconducting polymers.

Use of phase transfer catalysts such as 18-crown-6 enables ionic, linear conjugated poly[2,6-{1,5-bis(3-propoxysulfonicacidsodiumsalt)}naphthylene]ethynylene (PNES) to efficiently disperse single-walled carbon nanotubes (SWNTs) in multiple organic solvents under standard ultrasonication methods. Steady-state electronic absorption spectroscopy, atomic force microscopy (AFM), and transmission electron microscopy (TEM) reveal that these SWNT suspensions are composed almost exclusively of individualized tubes. High-resolution TEM and AFM data show that the interaction of PNES with SWNTs in both protic and aprotic organic solvents provides a self-assembled superstructure in which a PNES monolayer helically wraps the nanotube surface with periodic and constant morphology (observed helical pitch length = 10 ± 2 nm); time-dependent examination of these suspensions indicates that these structures persist in solution over periods that span at least several months. Pump-probe transient absorption spectroscopy reveals that the excited state lifetimes and exciton binding energies of these well-defined nanotube-semiconducting polymer hybrid structures remain unchanged relative to analogous benchmark data acquired previously for standard sodium dodecylsulfate (SDS)-SWNT suspensions, regardless of solvent. These results demonstrate that the use of phase transfer catalysts with ionic semiconducting polymers that helically wrap SWNTs provide well-defined structures that solubulize SWNTs in a wide range of organic solvents while preserving critical nanotube semiconducting and conducting properties.

Inkless microcontact printing on SAMs of Boc- and TBS-protected thiols.

We report a new inkless catalytic muCP technique that achieves accurate, fast, and complete pattern reproduction on SAMs of Boc- and TBS-protected thiols immobilized on gold using a polyurethane-acrylate stamp functionalized with covalently bound sulfonic acids. Pattern transfer is complete at room temperature just after one minute of contact and renders sub-200 nm size structures of chemically differentiated SAMs.

Photoelectrocatalysis: Principles, nanoemitter applications and routes to bio-inspired systems

An overview on processes that are relevant in light-induced fuel generation, such as water photoelectrolysis or carbon dioxide reduction, is given. Considered processes encompass the photophysics of light absorption, excitation energy transfer to catalytically active sites and interfacial reactions at the catalyst/solution phase boundary. The two major routes envisaged for realization of photoelectrocatalytic systems, e.g. bio-inspired single photon catalysis and multiple photon inorganic or hybrid tandem cells, are outlined. For development of efficient tandem cell structures that are based on non-oxidic semiconductors, stabilization strategies are presented. Physical surface passivation is described using the recently introduced nanoemitter concept which is also applicable in photovoltaic (solid state or electrochemical) solar cells and first results with p-Si and p-InP thin films are presented. Solar-to-hydrogen efficiencies reach 12.1% for homoepitaxial InP thin films covered with Rh nanoislands. In the pursuit to develop biologically inspired systems, enzyme adsorption onto electrochemically nanostructured silicon surfaces is presented and tapping mode atomic force microscopy images of heterodimeric enzymes are shown. An outlook towards future envisaged systems is given. © 2010 The Royal Society of Chemistry.

Nanotopography-induced changes in focal adhesions, cytoskeletal organization, and mechanical properties of human mesenchymal stem cells.

The growth of stem cells can be modulated by physical factors such as extracellular matrix nanotopography. We hypothesize that nanotopography modulates cell behavior by changing the integrin clustering and focal adhesion (FA) assembly, leading to changes in cytoskeletal organization and cell mechanical properties. Human mesenchymal stem cells (hMSCs) cultured on 350 nm gratings of tissue-culture polystyrene (TCPS) and polydimethylsiloxane (PDMS) showed decreased expression of integrin subunits alpha2, alpha , alpha V, beta2, beta 3 and beta 4 compared to the unpatterned controls. On gratings, the elongated hMSCs exhibited an aligned actin cytoskeleton, while on unpatterned controls, spreading cells showed a random but denser actin cytoskeleton network. Expression of cytoskeleton and FA components was also altered by the nanotopography as reflected in the mechanical properties measured by atomic force microscopy (AFM) indentation. On the rigid TCPS, hMSCs on gratings exhibited lower instantaneous and equilibrium Young's moduli and apparent viscosity. On the softer PDMS, the effects of nanotopography were not significant. However, hMSCs cultured on PDMS showed lower cell mechanical properties than those on TCPS, regardless of topography. These suggest that both nanotopography and substrate stiffness could be important in determining mechanical properties, while nanotopography may be more dominant in determining the organization of the cytoskeleton and FAs.

Diameter-selective solubilization of carbon nanotubes by lipid micelles

The one-step dispersion of HiPco single-walled carbon nanotubes in aqueous media with the use of a synthetic lyso-phosphatidylcholine was studied. Solubilization occurs through wrapping of lipid molecules around the circumference of the tubes, yielding lipid monolayers on the graphitic sidewalls as evidenced by atomic force microscopy imaging and dynamic light scattering measurements. Raman spectroscopy showed that the dispersion and centrifugation process leads to an effective enrichment of the stable aqueous suspension in carbon nanostructures with smaller diameters.

Delamination of oil paints from acrylic grounds

Many modern artists paint in oil or oil-modified alkyd paints over acrylic grounds. In some cases the oil based paints do not remain adhered to the ground. In a set of composite samples of oil or alkyd paints, over acrylic grounds, naturally aged for nine years, some of the samples delaminated. Samples were analyzed with X-ray fluorescence (XRF), inductively coupled plasma (ICP), Fourier transform infrared - attenuated total reflectance (FTIR-ATR), scanning electron microscopy (SEM), pyrolysis gas-chromatography mass-spectrometry (PY-GC/MS), laser desorption/ionization mass-spectrometry (LDI-MS), atomic force microscopy (AFM) and other methods, in order to find what the delaminating ones have in common. In addition, two examples of severely delaminating paintings were examined, to confirm the results from the laboratory-prepared samples. Results indicate the main cause of delamination is metal soaps in the oil paint and particularly zinc soaps. There is some evidence that metal soaps were more concentrated at the interface between the layers and this disrupted the adhesion. The ground is a minor consideration as well, rougher grounds providing better adhesion than smooth ones.