Confined dynamics of a single DNA molecule

The effect of a slit-like confinement on the relaxation dynamics of DNA is studied via a mesoscale model in which a bead and spring model for the polymer is coupled to a particle-based Navier-Stokes solver (multi-particle collision dynamics). The confinement is found to affect the equilibrium stretch of the chain when the bulk gyration radius is comparable to or smaller than the channel height and our data are in agreement with the (R(g,bulk)/h)(1/4) scaling of the polymer extension in the wall tangential direction. Relaxation simulation at different confinements indicates that, while the overall behaviour of the relaxation dynamics is similar for low and strong confinements, a small, but significant, slowing of the far-equilibrium relaxation is found as the confinement increases.     

Experimental techniques for single cell and single molecule biomechanics

Stresses and strains that act on the human body can arise either from external physical forces or internal physiological environmental conditions. These biophysical interactions can occur not only at the musculoskeletal but also cellular and molecular levels and can determine the health and function of the human body. Here, we seek to investigate the structure-property-function relationship of cells and biomolecules so as to understand their important physiological functions as well as establish possible connections to human diseases. With the recent advancements in cell and molecular biology, biophysics and nanotechnology, several innovative and state-of-the-art experimental techniques and equipment have been developed to probe the structural and mechanical properties of biostructures from the micro- down to picoscale. Some of these experimental techniques include the optical or laser trap method, micropipette aspiration, step-pressure technique, atomic force microscopy and molecular force spectroscopy. In this article, we will review the basic principles and usage of these techniques to conduct single cell and single molecule biomechanics research.     

Electrical readouts of single and few molecule systems in metal-molecule-metal device structures

Electrical conduction through molecular junctions are measured in different local environments through two test beds that are ideal for single/few molecule and molecular monolayer systems. A technique has been developed to realize Au films with approximately 1.5 A surface roughness comparable to the best available techniques and suitable for formation of patterned device structures. The technique utilizes room temperature e-beam evaporated Au films over oxidized Si substrates silanized with (3-mercaptopropyl)trimethoxysilane (MPTMS). The lateral (single/few molecule) and vertical (many molecules) device structures are both enabled by the process for realizing ultraflat Au layer. Lateral metal-molecule-metal (M-M-M) device structures are fabricated by forming pairs of Au electrodes with nanometer separation (nano-gap) through an electromigration-induced break-junction (EIBJ) technique at room temperature and conductivity measurements are carried out for dithiol functionalized single molecules. We have used the flat Au layer (using the current technique) as the bottom contact in vertical M-M-M device structures. Here, molecular self-assembly are formed on the Au surface, and patterned (20 x 20 microm2) top Au contacts were successfully transferred on to the device using a stamping technique (where the Au is deposited on a polydimethylsiloxane (PDMS) pad and following a physical contact on the thiolated Au layer). The single molecular property of XYL, a highly conductive molecule and many molecular property of HS-C9-SH, an insulating molecule in its molecular monolayer form are measured. Observation of enhanced conduction following molecular deposition, and comparison of conductance-voltage characteristics to those predicted theoretically, confirms the success of trapping single/few molecules in the nano-gap. The observed approximately 10(2) less conductance through the molecular monolayer of HS-C9-SH compared to the estimation of a linear sum of single molecule conductances over large area indicate that either all the molecules are not in physical contact with the top stamping electrode or electrode-molecule coupling has a less broadening in presence of it own environment or both.     

Nanochannel-based single molecule recycling

We present a method for measuring the fluorescence from a single molecule hundreds of times without surface immobilization. The approach is based on the use of electroosmosis to repeatedly drive a single target molecule in a fused silica nanochannel through a stationary laser focus. Single molecule fluorescence detected during the transit time through the laser focus is used to repeatedly reverse the electrical potential controlling the flow direction. Our method does not rely on continuous observation and therefore is less susceptible to fluorescence blinking than existing fluorescence-based trapping schemes. The variation in the turnaround times can be used to measure the diffusion coefficient on a single molecule level. We demonstrate the ability to recycle both proteins and DNA in nanochannels and show that the procedure can be combined with single-pair F?rster energy transfer. Nanochannel-based single molecule recycling holds promise for studying conformational dynamics on the same single molecule in solution and without surface tethering.     

Universal superelasticity characteristic for polymer systems

The superelastic strain is represented in universal form as a function of the product shear rate times maximum relaxation time in the relaxation spectrum for a polymer system. A relation is established between the superelastic strain and the relaxation spectrum as well as the change of the latter due to the shear rate.Translated from In zhenerno-Fizicheskii Zhurnal, Vol. 24, No. 1, pp. 91–96, January, 1973.     

SEM-induced shrinking of solid-state nanopores for single molecule detection

We have investigated the mechanism by which the diameter of solid-state nanopores is reduced by a scanning electron microscope. The process depends on beam parameters such as the accelerating voltage and electron flux and does not involve simple electron-beam-induced deposition of hydrocarbon contaminants. Instead, it is an energy-dependent process that involves material flow along the surface of the nanopore membrane. We also show that pores fabricated in this manner can detect double stranded DNA.     

Giant magnetoresistance through a single molecule

Magnetoresistance is a change in the resistance of a material system caused by an applied magnetic field. Giant magnetoresistance occurs in structures containing ferromagnetic contacts separated by a metallic non-magnetic spacer, and is now the basis of read heads for hard drives and for new forms of random access memory. Using an insulator (for example, a molecular thin film) rather than a metal as the spacer gives rise to tunnelling magnetoresistance, which typically produces a larger change in resistance for a given magnetic field strength, but also yields higher resistances, which are a disadvantage for real device operation. Here, we demonstrate giant magnetoresistance across a single, non-magnetic hydrogen phthalocyanine molecule contacted by the ferromagnetic tip of a scanning tunnelling microscope. We measure the magnetoresistance to be 60% and the conductance to be 0.26G(0), where G(0) is the quantum of conductance. Theoretical analysis identifies spin-dependent hybridization of molecular and electrode orbitals as the cause of the large magnetoresistance.     

Non-planar nanofluidic devices for single molecule analysis fabricated using nanoglassblowing

A method termed 'nanoglassblowing' is presented for fabricating integrated microfluidic and nanofluidic devices with gradual depth changes and wide, shallow nanochannels. This method was used to construct fused silica channels with out-of-plane curvature of channel covers from over ten micrometers to a few nanometers, nanochannel aspect ratios smaller than 2 × 10(-5):1 (depth:width), and nanochannel depths as shallow as 7?nm. These low aspect ratios and shallow channel depths would be difficult to form otherwise without collapse of the channel cover, and the gradual changes in channel depth eliminate abrupt free energy barriers at the transition from microfluidic to nanofluidic regions. Devices were characterized with atomic force microscopy (AFM), white light interferometry, scanned height measurements, fluorescence intensity traces, and single molecule analysis of double-stranded deoxyribonucleic acid (DNA) velocity and conformation. Nanochannel depths and aspect ratios formed by nanoglassblowing allowed measurements of the radius of gyration, R(g), of single λ?DNA molecules confined to slit-like nanochannels with depths, d, ranging from 11?nm to 507?nm. Measurements of R(g) as a function of d agreed qualitatively with the scaling law R(g)∝d(-0.25) predicted by Brochard for nanochannel depths from 36?nm to 156?nm, while measurements of R(g) in 11?nm and 507?nm deep nanochannels deviated from this prediction.     

High density single-molecule-bead arrays for parallel single molecule force spectroscopy

The assembly of a highly parallel force spectroscopy tool requires careful placement of single-molecule targets on the substrate and the deliberate manipulation of a multitude of force probes. Since the probe must approach the target biomolecule for covalent attachment, while avoiding irreversible adhesion to the substrate, the use of polymer microspheres as force probes to create the tethered bead array poses a problem. Therefore, the interactions between the force probe and the surface must be repulsive at very short distances (<5 nm) and attractive at long distances. To achieve this balance, the chemistry of the substrate, force probe, and solution must be tailored to control the probe-surface interactions. In addition to an appropriately designed chemistry, it is necessary to control the surface density of the target molecule in order to ensure that only one molecule is interrogated by a single force probe. We used gold-thiol chemistry to control both the substrate's surface chemistry and the spacing of the studied molecules, through binding of the thiol-terminated DNA and an inert thiol forming a blocking layer. For our single molecule array, we modeled the forces between the probe and the substrate using DLVO theory and measured their magnitude and direction with colloidal probe microscopy. The practicality of each system was tested using a probe binding assay to evaluate the proportion of the beads remaining adhered to the surface after application of force. We have translated the results specific for our system to general guiding principles for preparation of tethered bead arrays and demonstrated the ability of this system to produce a high yield of active force spectroscopy probes in a microwell substrate. This study outlines the characteristics of the chemistry needed to create such a force spectroscopy array.     

The theory of polymer dynamics

Recent years have brought exciting theoretical advances to understanding the behavior of macromolecular systems under nonequilibrium conditions. Developments in diffusion-controlled reactions of polymers are bringing molecular insights to reactive blending technologies, and improved theories relating to associating polymers should aid in the design of thickening agents and coatings. Recent progress in molecular theories of flow and deformation may facilitate the design of branched polymers with tailored rheological properties and improved adhesives.     

Zero-birefringence polymer by the anisotropic molecule dope method

We propose using the anisotropic molecule dope method for synthesizing a zero-birefringence polymer that showed no orientational birefringence at any orientation degree of polymer chains. In this method a rodlike molecule with polarizability anisotropy was chosen to compensate orientational birefringence. The zero-birefringence polymer was synthesized by doping of 3-wt.% trans-stilbene as an anisotropic molecule into poly(methyl methacrylate). The zero-birefringence at the 590-nm wavelength in the drawn film and the injection-molded plate made from the zero-birefringence polymer was confirmed by the rotating parallel nicols method. Furthermore, high transparency (37.2 dB/km) of the zero-birefringence polymer at the 633-nm wavelength was confirmed by the light-scattering measurement.     

Force spectroscopy on single polymer incorporated into polymer gels

We conducted the extraction experiments of single polymer incorporated into hydrogels with an atomic force microscope (AFM) as a model for investigating nonspecific intermolecular interactions between macromolecules in a semidilute region at the single molecule level. Small amount of poly(ethylene glycol) (PEG) terminated with a thiol group was inserted in poly(acrylamide) gels, and a part of PEG polymer segments on the gel surface was attempted to pull out of the gels with a gold-coated AFM tip. The observed force-distance curves were classified into two kinds of extraction force profiles: a plateau force, which is almost constant irrespective of the tip-surface distance and a nonlinear force, which nonlinearly increases with the extraction length. Characteristic interaction length, L, and force, F, of these extraction force profiles were measured with changing the crosslinker concentration of gels which strongly affects the network structures. As a result, L of these extraction profiles significantly decreased at crosslinker concentrations higher than a standard one at which most gels have been prepared for investigating their physical properties. On the other hand, F showed no obvious difference on the change in crosslinker concentrations both on the plateau and the nonlinear force profiles. The origin of the observed forces was discussed in terms of gel network structures.     

Controlling quantum transport through a single molecule

We investigate multiterminal quantum transport through single monocyclic aromatic annulene molecules, and their derivatives, using the nonequilibrium Green function approach within the self-consistent Hartree-Fock approximation. We propose a new device concept, the quantum interference effect transistor, that exploits perfect destructive interference stemming from molecular symmetry and controls current flow by introducing decoherence and/or elastic scattering that break the symmetry. This approach overcomes the fundamental problems of power dissipation and environmental sensitivity that beset nanoscale device proposals.     

Shot noise measurements on a single molecule

We report measurements of shot noise in the current through a single D2 molecule. The molecular junctions were formed by means of the mechanically controllable break junction technique. The configuration of the D2 molecule bridging the gap between two Pt tips is verified by use of point contact spectroscopy. Maintaining the same junction shot noise measurements were performed and the observed quantum suppression shows that conductance is carried dominantly by a single, almost fully transparent conductance channel. This observation allows us to decide between conflicting model calculations for this system, and this may serve as a benchmark for further computations on molecular junctions.     

Plasmon-enhanced colorimetric ELISA with single molecule sensitivity

Robust but ultrasensitive biosensors with a capability of detecting low abundance biomarkers could revolutionize clinical diagnostics and enable early detection of cancer, neurological diseases, and infections. We utilized a combination of localized surface plasmon resonance (LSPR) refractive index sensing and the well-known enzyme-linked immunosorbent assay to develop a simple colorimetric biosensing methodology with single molecule sensitivity. The technique is based on spectral imaging of a large number of isolated gold nanoparticles. Each particle binds a variable number of horseradish peroxidase (HRP) enzyme molecules that catalyze a localized precipitation reaction at the particle surface. The enzymatic reaction dramatically amplifies the shift of the LSPR scattering maximum, λ(max), and makes it possible to detect the presence of only one or a few HRP molecules per particle.     

Manipulating Kondo temperature via single molecule switching

Two conformations of isolated single TBrPP-Co molecules on a Cu(111) surface are switched by applying +2.2 V voltage pulses from a scanning tunneling microscope tip at 4.6 K. The TBrPP-Co has a spin-active cobalt atom caged at its center, and the interaction between the spin of this cobalt atom and free electrons from the Cu(111) substrate can cause a Kondo resonance. Tunneling spectroscopy data reveal that switching from the saddle to a planar molecular conformation enhances spin-electron coupling, which increases the associated Kondo temperature from 130 to 170 K. This result demonstrates that the Kondo temperature can be manipulated just by changing molecular conformation without altering chemical composition of the molecule.     

Simulation of polymer systems

The present paper describes an algorithm which can generate, even on a small computer, arbitrarily long polymer chains, making sure that the configurations generated do not suffer from boundary effects. This has been achieved by employing the concept of a window, which is an analogue of virtual memory scheme. The algorithm has been tested for the case of dilute polymer solution.     

Materials systems for interleave toughening in polymer composites

We review the literature describing the use of interleaves to increase interlaminar fracture toughness in fibre-reinforced polymer composites and hence to improve damage tolerance. From an analysis of data provided in the literature from the use of microfibre and nanofibre interleaves, we show that the performance of these widely researched systems is clearly differentiated when plotted against the mean coverage of the interleaf. Using a simple analysis, we suggest that this can be attributed to the influence of their porous architectures on the infusion of resin. We show also that the superior toughening performance of microfibre interleaves is only weakly influenced by the choice of fibre. We find also that the inclusion of carbon nanotubes within interleaves to deliver multifunctional composites can be optimised by using a hybrid system with microfibres.

Graphical abstract

     

Imaging the charge distribution within a single molecule

Scanning tunnelling microscopy and atomic force microscopy can be used to study the electronic and structural properties of surfaces, as well as molecules and nanostructures adsorbed on surfaces, with atomic precision, but they cannot directly probe the distribution of charge in these systems. However, another form of scanning probe microscopy, Kelvin probe force microscopy, can be used to measure the local contact potential difference between the scanning probe tip and the surface, a quantity that is closely related to the charge distribution on the surface. Here, we use a combination of scanning tunnelling microscopy, atomic force microscopy and Kelvin probe force microscopy to examine naphthalocyanine molecules (which have been used as molecular switches) on a thin insulating layer of NaCl on Cu(111). We show that Kelvin probe force microscopy can map the local contact potential difference of this system with submolecular resolution, and we use density functional theory calculations to verify that these maps reflect the intramolecular distribution of charge. This approach could help to provide fundamental insights into single-molecule switching and bond formation, processes that are usually accompanied by the redistribution of charge within or between molecules.