Sudden stoppage of rotor in a thermally driven rotary motor made from double-walled carbon nanotubes

In a thermally driven rotary motor made from double-walled carbon nanotubes, the rotor (inner tube) can be actuated to rotate within the stator (outer tube) when the environmental temperature is high enough. A sudden stoppage of the rotor can occur when the inner tube has been actuated to rotate at a stable high speed. To find the mechanisms of such sudden stoppages, eight motor models with the same rotor but different stators are built and simulated in the canonical NVT ensembles. Numerical results demonstrate that the sudden stoppage of the rotor occurs when the difference between radii is near 0.34 nm at a high environmental temperature. A smaller difference between radii does not imply easier activation of the sudden rotor stoppage. During rotation, the positions and electron density distribution of atoms at the ends of the motor show that a sp(1) bonded atom on the rotor is attracted by the sp(1) atom with the biggest deviation of radial position on the stator, after which they become two sp(2) atoms. The strong bond interaction between the two atoms leads to the loss of rotational speed of the rotor within 1 ps. Hence, the sudden stoppage is attributed to two factors: the deviation of radial position of atoms at the stator's ends and the drastic thermal vibration of atoms on the rotor in rotation. For a stable motor, sudden stoppage could be avoided by reducing deviation of the radial position of atoms at the stator's ends. A nanobrake can be, thus, achieved by adjusting a sp(1) atom at the ends of stator to stop the rotation of rotor quickly.The authors are grateful for financial support from the National Natural-Science-Foundation of China (Grant Nos. 50908190, 11372100)

A method for measuring rotation of a thermal carbon nanomotor using centrifugal effect

A thermal nanomotor is relatively easy to fabricate and regulate as it contains just a few or even no accessory devices. Since the double-wall carbon nanotube (CNT)-based rotary nanomotor was established in a thermostat, assessment of the rotation of the rotor (inner tube) in the stator (outer tube) of the nanomotor has been critical, but remains challenging due to two factors: the small size of the rotor (only a few nanometers) and the high rotational frequency (»1 GHz). To measure the rotation of the nanomotor, in the present study, a probe test method is proposed. Briefly, the rotor is connected to an end-tube (CNT) through a graphene (GN) nanoribbon. As the CNT-probe is on the trajectory of the end-tube which rotates with the rotor, it will collide with the end-tube. The sharp fluctuation indicating the probe tip deflection can be observed and recorded. As a curly GN by hydrogenation is adopted for connecting the rotor and the end-tube, collision between the end-tube and the probe tip occurs only when the centrifugal force is higher than a threshold which can be considered as the rotational frequency of the rotor being measured by the present method.The authors are grateful for financial support from the National Natural-Science-Foundation of China (Grant No. 11372100) and the Australian Research Council (Grant No. DP140103137)

The Effect of Defects and Surface Modification on Biomolecular Assembly and Transport

Nanoscale transport using the kinesin-microtubule (MT) biomolecular system has been successfully used in a wide range of nanotechnological applications including self-assembly, nanofluidic transport, and biosensing. Most of these applications use the ‘gliding motility geometry’, in which surface-adhered kinesin motors attach and propel MT filaments across the surface, a process driven by ATP hydrolysis. It has been demonstrated that active assembly facilitated by these biomolecular motors results in complex, non-equilibrium nanostructures currently unattainable through conventional self-assembly methods. In particular, MTs functionalized with biotin assemble into rings and spools upon introduction of streptavidin and/or streptavidin-coated nanoparticles. Upon closer examination of these structures using fluorescence and electron microscopy, the structures revealed a level of irregularity including kinked and coiled domains, as well as in- and out- of -plane loops. In this work, we describe the effects of large scale “defective” segments (i.e. non-biotinylated MTs) on active assembly of nanocomposite spools. We demonstrate the preferential removal of the defective portions from spools during assembly to overcome structurally induced strain in regions that lack biotin-streptavidin bonds. Additionally, we show how the level of defective MTs affect the morphology and physical properties of the resulting nanostructures.Further, we explore alternative nanostructures for controlling transport using the kinesin-MT biomolecular system. Guiding MT transport has been achieved using lithographically patterning physical and chemical features, which have been shown to limit the MT trajectories, causing MTs to escape the barriers and lead to stalling or complete loss of MTs. Here, we demonstrate reliable guiding and transport of MTs on three different chemically modified, and structurally varying surfaces using 1) self-assembled monolayers (SAMs) with varying functional groups, 2) Fetal-bovine serum (FBS) coated SAMs to generate protein patterns, and 3) silicification of the FBS coated SAMs to preserve the surface. Overall, the work presented in this dissertation provides crucial insights for future development of dynamic and adaptable hybrid nanostructures, as well as provides biocompatible patterns to modulate MT motility with the goal of advancing self-regulating, multi-functional materials

APPROACHING EFFICIENT NANOMOTORS VIA BIOMIMICKING MECHANISMS

Ph.DDOCTOR OF PHILOSOPH

Transmembrane molecular machines

Transmembrane molecular machines are ubiquitous in nature. These evolved systems demonstrate superlative elegance and efficiency of operation. Imitation and hijacking of biological components such as proteins and DNA has emerged as a means of imparting desirable characteristics to rationally designed synthetic molecular machines. This thesis presents work towards various synthetic transmembrane molecular machines based on alpha-haemolysin (α-HL). Chapter One reviews progress towards synthetic transmembrane machines, introducing natural examples, defining criteria for being ‘a molecular machine’ cataloguing examples and trends in synthetic molecular machines in solution, on surfaces and in membranes. Examples are evaluated in terms of their machine like behaviour and α-HL emerges as a particularly promising component in the development of synthetic transmembrane molecular machines. Chapter Two examines solvent isotope effects resulting from substitution of hydrogen by deuterium in water at the nanoscale – on the rates of transmembrane ion transport and transmembrane translocation of ssDNA through α-HL, both of which are of concern in the context of building molecular machines which use α-HL as a component. Chapters Three to Six look at different machine applications of related transmembrane architectures based on individual transmembrane rotaxanes constructed in α-HL from DNA/PEG copolymer ‘thread’ strands and DNA ‘primer’ strands. Chapter Three uses this approach to observe translational motion of the thread strand in both directions along the z-axis due to nucleotide incorporation and pyrophosphorolysis in real-time with single-nucleotide resolution. Chapter Four provides the first demonstration of asymmetrical, hysteretic cyclical behaviour in the translational motion of the thread strand by incorporation of a nicking site which resets the system after nucleotide incorporations have occurred. Chapter Five introduces a novel variant of the rotaxane architecture using a circularised primer strand which allows real time observation of rolling circle amplification at the single molecule level by coupling the process to the unidirectional translocation of the thread strand. Chapter Six considers the use of the vestibule of α-HL as a transmembrane DNA ligase mimic with the DNA thread/primer complex as substrate

Controlling the motion of molecular machines at the nanoscale

Geïnspireerd door biologische systemen hebben wetenschappers geprobeerd om kunstmatige, machine-achtige complexen werk te laten uitvoeren. Het ontwerpen en construeren van kunstmatige nanomachines behoort hierbij tot de grootste uitdagingen. Om deze uitdagingen aan te gaan, wordt er intensief samengewerkt tussen chemie en verschillende, verwante gebieden, zoals beschreven in hoofdstuk 1. Mijn onderzoek richtte zich op ontwerp, synthese en ontwikkeling van moleculaire motoren en hun toepassingen. Hoofdstuk 2 concentreert zich op het ontwerp van hybride motoren, met als doel: 1) het bestuderen van het aggregatiegedrag van porphyrine hybride motoren bij verschillende standen van de motor en 2) het onderzoeken van de dynamiek van hybride motoren gebaseerd op een molecuul dat zowel motor- als rotor-functies bevat. Hoofstuk 3 verhaalt over de ontwikkeling van een oscillerende biaryl-allylester. De oscillatie wordt geïnduceerd door een Pd-gekatalyseerde, allylische omlegging. Op deze manier werd een katalytisch proces gekoppeld aan de mechanische beweging van een moleculair systeem. Hoofdstuk 4 betreft de synthese van moleculaire motoren die in staat zijn tot unidirectionele rotatie, in twee richtingen, door middel van base-gekatalyseerde epimerisatie. Een reversibele motor, waarbij de rotatie zowel met de klok mee als tegen de klok in kan plaatsvinden, werd gesynthetiseerd. Hoofdstukken 5 en 6 beschrijven het ontwerp van moleculen met vierwielaandrijving, gevolgd door hun synthese en een complete spectroscopische karakterisatie van de fotochemische processen. Met één van deze systemen is voor de eerste keer een autonome, gerichte, translationele beweging op een oppervlak bereikt. Inspired by biological systems, scientists have attempted to manipulate artificial machine-like complexes to perform work. Designing and building artificial nanoscale machines are one of the major challenges. In order to address these challenges, recent research has been focused on molecular machines as described in chapter 1. My research was aiming at the design, synthesis and development of molecular motors and their applications. In chapter 2 the design of hybrid-motors is discussed. The goal of this research was 1) study the aggregation behavior of porphyrin hybrid-motors under controlled by the molecular motors and 2) investigate the dynamic properties of hybrid-motors based on a molecule which comprises motor and rotor functions. In chapter 3, we described the development of an oscillating biaryl-allyl ester driven by catalysis and utilized this property to initiate movement. In order to achieve this, we designed a molecule in which oscillation can be induced by a catalytic event, via Pd-catalyzed allylic rearrangement. This catalytic process was then coupled with a dynamic function in molecular systems to induce mechanical motion. Our aim of chapter 4 was to synthesize molecular motors capable of unidirectional rotation, in either direction, using base-catalyzed epimerization. The synthesis of a reversible motor, with the ability to rotate clockwise and counter-clockwise, depending on the initial trigger used, was achieved. Chapters 5 and 6 described the design of the four-wheeled drive molecules, followed by synthesis and full spectroscopic characterization of their photochemistry. One of these compounds was further more used to demonstrate autonomous directed translational movement, upon fuelling on the surface, for the first time.

Insights into hydrogen bonded systems: from single molecule to the bulk

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Química Orgánica. Fecha de lectura: 23-03-201