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Single-molecule measurements of protein dynamics help unveil the complex conformational changes and transitions that occur during ligand binding and catalytic processes. Using high-resolution single-molecule nanocircuit techniques, we have investigated differences in the conformational dynamics and transitions of lysozyme interacting with three ligands: peptidoglycan substrate, substrate-based chitin analogue, and indole derivative inhibitors. While processing peptidoglycan, lysozyme followed one of the two mechanistic pathways for the hydrolysis of the glycosidic bonds: a concerted mechanism inducing direct conformational changes from open to fully closed conformations or a nonconcerted mechanism involving transient pauses in intermediate conformations between the open and closed conformations. In the presence of either chitin or an indole inhibitor, lysozyme was unable to access the fully closed conformation where catalysis occurs. Instead, lysozymes' conformational closures terminated at slightly closed, "excited" conformations that were approximately one-quarter of the full hinge-bending range. With the indole inhibitor, lysozyme reached this excited conformation in a single step without any evidence of rate-liming intermediates, but the same conformational motions with chitin involved three hidden, intermediate processes and features similar to the nonconcerted peptidoglycan mechanism. The similarities suggest that these hidden processes involve attempts to accommodate imperfectly aligned polysaccharides in the active site. The results provide a detailed glimpse of the enzyme-ligand interplay at the crux of molecular recognition, enzyme specificity, and catalysis.

Simple and fast methods for the detection of target genes with single-nucleotide specificity could open up genetic research and diagnostics beyond laboratory settings. We recently reported a biosensor for the electronic detection of unamplified target genes using liquid-gated graphene field-effect transistors employing an RNA-guided catalytically deactivated CRISPR-associated protein 9 (Cas9) anchored to a graphene monolayer. Here, using unamplified genomic samples from patients and by measuring multiple types of electrical response, we show that the biosensors can discriminate within one hour between wild-type and homozygous mutant alleles differing by a single nucleotide. We also show that biosensors using a guide RNA-Cas9 orthologue complex targeting genes within the protospacer-adjacent motif discriminated between homozygous and heterozygous DNA samples from patients with sickle cell disease, and that the biosensors can also be used to rapidly screen for guide RNA-Cas9 complexes that maximize gene-targeting efficiency.

Taq DNA polymerase functions at elevated temperatures with fast conformational dynamics—regimes previously inaccessible to mechanistic, single-molecule studies. Here, single-walled carbon nanotube transistors recorded the motions of Taq molecules processing matched or mismatched template–deoxynucleotide triphosphate pairs from 22° to 85°C. By using four enzyme orientations, the whole-enzyme closures of nucleotide incorporations were distinguished from more rapid, 20-μs closures of Taq’s fingers domain testing complementarity and orientation. On average, one transient closure was observed for every nucleotide binding event; even complementary substrate pairs averaged five transient closures between each catalytic incorporation at 72°C. The rate and duration of the transient closures and the catalytic events had almost no temperature dependence, leaving all of Taq’s temperature sensitivity to its rate-determining open state.

Nanoscale materials and devices provide new opportunities to monitor and understand biomolecules. This presentation will review novel devices in which single molecules of DNA polymerase have been joined to single-walled carbon nanotube (SWNT) transistors. DNA polymerases are the enzymes that convert single-stranded DNA into double-stranded helices. This biochemical process is the primary step in DNA replication, amplification, and most sequencing technologies. When one of these polymerases is attached to a SWNT transistor, the enzyme’s native activity is simultaneously transduced into a high-resolution electrical signal [1]. Each time the enzyme works its way down a DNA strand, it generates a nucleotide-by-nucleotide signal that encodes the DNA sequence. This hybrid, biofunctional device is the key element for developing a new, electronic DNA sequencing technology. As a solid-state, manufacturable element, the SWNT transistors provide exciting possibilities for high-density, high-throughput, and low cost sequencing solutions. In addition, the technique is easily generalized to DNA polymerases with specialized properties. Proof-of-principle measurements have been accomplished with DNA polymerases from five different organisms, including the highly processive polymerase of φ29 phage and the high-temperature polymerase Thermus aquaticus (Taq), which is the foundation of the polymerase chain reaction (PCR) and commercial DNA amplification. The SWNT transistor technique operates equally well at room temperature and the elevated PCR temperature of 72 °C, which opens opportunities for novel, high-temperature sequencing strategies with Taq or similar thermostable polymerases. [1] T. J. Olsen et. al., JACS 135, 7855 (2013); O. T. Gul et. al., Biosensors 6, 29 (2016)

Simple and fast methods for the detection of target genes with single-nucleotide specificity could open up genetic research and diagnostics beyond laboratory settings. We recently reported a biosensor for the electronic detection of unamplified target genes using liquid-gated graphene field-effect transistors employing an RNA-guided catalytically deactivated CRISPR-associated protein 9 (Cas9) anchored to a graphene monolayer. Here, using unamplified genomic samples from patients and by measuring multiple types of electrical response, we show that the biosensors can discriminate within one hour between wild-type and homozygous mutant alleles differing by a single nucleotide. We also show that biosensors using a guide RNA-Cas9 orthologue complex targeting genes within the protospacer-adjacent motif discriminated between homozygous and heterozygous DNA samples from patients with sickle cell disease, and that the biosensors can also be used to rapidly screen for guide RNA-Cas9 complexes that maximize gene-targeting efficiency.

Advances in bioconjugation, the ability to link biomolecules to each other, small molecules, surfaces, and more, can spur the development of advanced materials and therapeutics. We have discovered that pyrocinchonimide, the dimethylated analogue of maleimide, undergoes a surprising transformation with biomolecules. The reaction targets amines and involves an imide transfer, which has not been previously reported for bioconjugation purposes. Despite their similarity to maleimides, pyrocinchonimides do not react with free thiols. Though both lysine residues and the N-termini of proteins can receive the transferred imide, the reaction also exhibits a marked preference for certain amines that cannot solely be ascribed to solvent accessibility. This property is peculiar among amine-targeting reactions and can reduce combinatorial diversity when many available reactive amines are available, such as in the formation of antibody-drug conjugates. Unlike amides, the modification undergoes very slow reversion under high pH conditions. The reaction offers a thermodynamically controlled route to single or multiple modifications of proteins for a wide range of applications.

Large numbers of high quality graphene transistors with mobility approximately 5000 cm 2 /V*s were fabricated by chemical vapor deposition and packaged into ceramic carriers with an open cavity design. The ceramic carrier is compatible with standard electronics assembly, enabling the readout of graphene properties on the benchtop without large, expensive probing systems. After chemical functionalization, these sensors demonstrate sensitivity in the pM range and selectivity to many classes of biomolecules as a three terminal liquid-gated field effect transistor. High precision measurements of protein kinetics captured using this technology, commercially known as AGILE R100, are comparable and can exceed the capabilities of state-of-the-art biomolecule characterization tools.

Nanoscale materials provide new opportunities to interface solid-state electronics with biomolecules and biochemical activity. For example, single-walled carbon nanotubes (SWNTs) have the special property of electronic resistance that is sensitive to single electrons. We have exploited this sensitivity to build nanoelectronic biosensors that monitor the biochemical activity of individual proteins [1]. As an attached protein moves, binds, or performs catalysis, its charged amino acid sidechains induce resistance fluctuations in the SWNT device that may be monitored with microsecond resolution [2]. Recently, we have used this measurement platform for single-molecule measurements of DNA polymerases [3]. Polymerases are the key enzymes for converting single-stranded DNA to double-stranded helices, the primary step in DNA replication, amplification, and most sequencing technologies. When a polymerase processing DNA is also attached to a SWNT device, the electrical signal provides a high-resolution readout of single-nucleotide incorporations and exciting possibilities for high-density, high-throughput electronic DNA sequencing. To investigate the feasibility of electronic DNA sequencing, we have compared single-molecule transduction by DNA polymerases from three different organisms. By working with multiple families of DNA polymerases, we have tested the applicability of the electronic technique while also generating detailed records of differences among the enzymes. For example, we observe an anomalous rate variability when measuring the polymerase from the bacillus phage φ29. Base incorporation rates average 20 s-1 for most the enzymes processing single-stranded DNA templates, but rates up to 200 and 400 s-1 occurred when φ29 encountered homopolymeric sequences of poly(dT) or poly(dC), respectively. When processing poly(dA) and poly(dG) sequences, on the other hand, φ29 had bursts of activity interrupted by pauses lasting 50 to 300 s. This sequence-dependent activity illustrates one way that single-molecule methods reveal information hidden in ensemble-based techniques. Another workhorse protein in DNA sequencing technologies is the DNA polymerase derived from the thermophilic bacteria Thermus aquaticus (Taq). Anomalous stability at high temperatures makes Taq a unique enzyme for the polymerase chain reaction (PCR) and commercial amplification of DNA. In a first for single-molecule biophysics, SWNT devices have recorded Taq activity over a wide temperature range from 22 to 94 °C, including the typical PCR operating temperature of 72 °C. Even operating at this high temperature, the technique resolved Taq testing incoming nucleotides for complementarity and incorporating correct matches in the base-by-base construction of Watson-Crick pairs. The detailed recordings reveal the similarities of Taq’s operation to other, room temperature polymerases. [1] Y. Choi, et. al., Science 335, 319 (2012). [2] M. V. Akhterov, et. al., ACS Chem. Biol. 10, 1495 (2015). [3] T. J. Olsen et. al., JACS 135, 7855 (2013); O. T. Gul et. al., Biosensors 6, 29 (2016)

A single point defect surrounded on either side by quasi-ballistic, semimetallic carbon nanotube is a nearly ideal system for investigating disorder in one-dimensional (1D) conductors and comparing experiment to theory. Here, individual single-walled nanotubes (SWNTs) are investigated before and after the incorporation of single point defects. Transport and local Kelvin Probe force microscopy independently demonstrate high-resistance depletion regions over 1.0 μm wide surrounding one point defect in semimetallic SWNTs. Transport measurements show that conductance through such wide depletion regions occurs via a modified, 1D version of Poole-Frenkel field-assisted emission. Given the breadth of theory dedicated to the possible effects of disorder in 1D systems, it is surprising that a Poole-Frenkel mechanism appears to describe defect scattering and resistance in this semimetallic system.

DEFECTS AND DISORDER IN CARBON NANOTUBES Philip G. Collins University of California at Irvine, Irvine, USA 1. INTRODUCTION AND OUTLINE The presence of defects subtly alters all of a material’s properties. Chemical reactivity, mechanical strength, optical absorption, and electronic transport all vary with defect concentration. Despite these wide-ranging effects, however, it is very rare for defect control to be critical to a particular application. For example, electronic circuits perform perfectly well in the presence of defects. Even though a defect might trap or scatter charge carriers, a typical conductor will electrostatically screen such sites and still maintain a preponderance of unaffected carriers and conduction channels. In reduced dimensions these generalizations begin to fail. In one-dimensional (1-D) systems, defects play the most significant roles, and they can dominate physical property measurements. For example, the strength of a 1-D chain cannot exceed its weakest link. Charge carriers in 1-D are confined to a single trajectory and cannot avoid a scattering center nor scatter into nearby momentum states. Such consequences are critically important to the newly developing field of nanoscience, in which low dimensional materials are synthesized, characterized, and integrated into applications. To appear in Oxford Handbook of Nanoscience and Technology: Frontiers and Advances. A.V. Narlikar, & Y.Y. Fu, Eds. (Oxford Univ. Press, Oxford, 2009).

As biosensing devices shrink smaller and smaller, they approach a scale in which single molecule electronic sensing becomes possible. Here, we review the operation of single-enzyme transistors made using single-walled carbon nanotubes. These novel hybrid devices transduce the motions and catalytic activity of a single protein into an electronic signal for real-time monitoring of the protein’s activity. Analysis of these electronic signals reveals new insights into enzyme function and proves the electronic technique to be complementary to other single-molecule methods based on fluorescence. As one example of the nanocircuit technique, we have studied the Klenow Fragment (KF) of DNA polymerase I as it catalytically processes single-stranded DNA templates. The fidelity of DNA polymerases makes them a key component in many DNA sequencing techniques, and here we demonstrate that KF nanocircuits readily resolve DNA polymerization with single-base sensitivity. Consequently, template lengths can be directly counted from electronic recordings of KF’s base-by-base activity. After measuring as few as 20 copies, the template length can be determined with

We investigate interfacial charge transfer between a manganese oxide (MnO2) pseudocapacitor material and graphitic carbon supports in the limit where the graphitic carbon is defect free. We achieve this limit experimentally by fabricating model electrodes comprising MnO2 deposited on single, pristine, isolated single-walled carbon nanotubes. Li ion cyclic voltammetry of the composites gives a specific capacitance in accord with MnO2 storage capacities, but with kinetics limited by the poor electron transfer properties of defect free carbon. By fitting the data to an equivalent circuit model, we determine the charge transfer resistivity of MnO2-carbon interfaces to be 9 x 107 Ohm-cm when defects are absent, a limiting value for high power cathodes.

A variation of scanning gate microscopy (SGM) is demonstrated in which this imaging mode is extended into an electrostatic spectroscopy. Continuous variation of the SGM probe's electrostatic potential is used to directly resolve the energy spectrum of localized electronic scattering in functioning, molecular scale devices. The technique is applied to the energy-dependent carrier scattering that occurs at defect sites in carbon nanotube transistors, and fitting energy-resolved experimental data to a simple transmission model determines the electronic character of each defect site. For example, a phenolic type of covalent defect is revealed to produce a tunnel barrier 0.1 eV high and 0.5 nm wide.

Electronic conduction in one dimension is uniquely sensitive to single point perturbations. As quasi-one-dimensional conductors, single-walled carbon nanotubes are ideal examples of this sensitivity, and they can be exploited as single-molecule sensors in air, liquid, or vacuum. Even in complex physiological solutions, dynamic biochemical activity has been monitored with single-bond and microsecond resolution. However, past work along these lines was achieved on individual devices with low success rates of 10-20%. Here, we describe simultaneous progress on three fronts that has produced large-scale arrays of single-molecule devices. First, precise control of catalytic chemical vapor deposition has dramatically increased our yield of usable single-nanotube devices across 4” substrates. Second, contamination control methods have reduced charge-trap fluctuations that previously disqualified many transistors from single-molecule sensing experiments. Thirdly, new surface modification protocols have brought predictability and control to single-molecule biofunctionalization of the nanotube surfaces. When combined, these techniques scale up single-molecule dynamic sensing from single devices to large arrays. New research directions with these arrays include massively parallel sensing applications such as drug discovery and DNA sequencing.

Designing the next generation of high performance energy storage devices requires a deeper understanding of structural degradation. To this end, a wide variety of scanning probe microscopy techniques can help characterize charge transport and aging mechanisms in Li-ion battery materials and their interfaces. For example, we use in-situ probe microscopy and Kelvin probe force microscopy (KPFM) to investigate the mechanical and potentiostatic changes in MnO2 cathodes as they undergo charge cycling. Topography monitors mechanical expansion during charging, and the dependence of expansion on scan rate reveals the separate roles of Mn3+/4+ redox pseudocapacitance and faster, double-layer surface capacitance. On the same electrodes, KPFM observes the evolution of surface potentials with lateral resolution as low as 40 nm. At this length scale, inhomogeneous lithiation is clearly observed as a highly nonuniform, fractal growth or shrinkage of Mn3+ and Mn4+ phases. Via surface potential, KPFM also reveals "dead" zones that do not participate in charging, "hot" zones that charge or discharge most readily, and the evolution of each type as an electrode is repeatedly cycled. This work was supported as part of the Nanostructures for Electrical Energy Storage (NEES), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science.

While nanowires and nanotubes have been shown to be electrically sensitive to various chemicals, not enough is known about the underlying mechanisms to control or tailor this sensitivity. By limiting the chemically sensitive region of a nanostructure to a single binding site, single molecule precision can be obtained to study the chemoresistive response. We have developed techniques using single-walled- carbon-nanotube (SWCNT) circuits that enable single-site experimentation and illuminate the dynamics of chemical interactions. Discrete changes in the circuit conductance reveal chemical processes happening in real-time and allow SWCNT sidewalls to be deterministically broken, reformed, and conjugated to target species.

DNA polymerases exhibit a surprising tolerance for analogs of deoxyribonucleoside triphosphates (dNTPs), despite the enzymes' highly evolved mechanisms for the specific recognition and discrimination of native dNTPs. Here, individual DNA polymerase I Klenow fragment (KF) molecules were tethered to a single-walled carbon nanotube field-effect transistor (SWCNT-FET) to investigate accommodation of dNTP analogs with single-molecule resolution. Each base incorporation accompanied a change in current with its duration defined by τclosed. Under Vmax conditions, the average time of τclosed was similar for all analog and native dNTPs (0.2 to 0.4 ms), indicating no kinetic impact on this step due to analog structure. Accordingly, the average rates of dNTP analog incorporation were largely determined by durations with no change in current defined by τopen, which includes molecular recognition of the incoming dNTP. All α-thio-dNTPs were incorporated more slowly, at 40 to 65% of the rate for the corresponding native dNTPs. During polymerization with 6-Cl-2APTP, 2-thio-dTTP, or 2-thio-dCTP, the nanocircuit uncovered an alternative conformation represented by positive current excursions that does not occur with native dNTPs. A model consistent with these results invokes rotations by the enzyme's O-helix; this motion can test the stability of nascent base pairs using nonhydrophilic interactions and is allosterically coupled to charged residues near the site of SWCNT attachment. This model with two opposing O-helix motions differs from the previous report in which all current excursions were solely attributed to global enzyme closure and covalent-bond formation. The results suggest the enzyme applies a dynamic stability-checking mechanism for each nascent base pair.

© 2015 American Chemical Society. Single-molecule techniques can monitor the kinetics of transitions between enzyme open and closed conformations, but such methods usually lack the resolution to observe the underlying transition pathway or intermediate conformational dynamics. We have used a 1 MHz bandwidth carbon nanotube transistor to electronically monitor single molecules of the enzyme T4 lysozyme as it processes substrate. An experimental resolution of 2 μs allowed the direct recording of lysozymes opening and closing transitions. Unexpectedly, both motions required 37 μs, on average. The distribution of transition durations was also independent of the enzymes state: either catalytic or nonproductive. The observation of smooth, continuous transitions suggests a concerted mechanism for glycoside hydrolysis with lysozymes two domains closing upon the polysaccharide substrate in its active site. We distinguish these smooth motions from a nonconcerted mechanism, observed in approximately 10% of lysozyme openings and closings, in which the enzyme pauses for an additional 40-140 μs in an intermediate, partially closed conformation. During intermediate forming events, the number of rate-limiting steps observed increases to four, consistent with four steps required in the stepwise, arrow-pushing mechanism. The formation of such intermediate conformations was again independent of the enzymes state. Taken together, the results suggest lysozyme operates as a Brownian motor. In this model, the enzyme traces a single pathway for closing and the reverse pathway for enzyme opening, regardless of its instantaneous catalytic productivity. The observed symmetry in enzyme opening and closing thus suggests that substrate translocation occurs while the enzyme is closed.

Sunday, February 8, 2015 experiments with [U-15N,2H,13C]-BsPFK. The assignments allowed for the mapping of peaks representing isoleucine residues onto the crystal structure. This analysis has allowed specific regions of the enzyme involved in the bind- ing of allosteric ligands and the propagation of the allosteric effect to be iden- tified. Funding: NIH-GM33216, NIH-CBI, Welch-A1543. 148-Plat Microsecond-Resolution Recording of T4 Lysozyme Observes a Brownian Ratchet Maxim V. Akhterov 1 , Yongki Choi 2 , Tivoli J. Olsen 3 , Patrick C. Sims 1 , Mariam Iftikhar 3 , O. Tolga Gul 1 , Brad L. Corso 1 , Gregory A. Weiss 3 , Philip G. Collins 1 . Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, USA, 2 Department of Physics, North Dakota State University, Fargo, ND, USA, 3 Department of Chemistry, University of California, Irvine, Irvine, CA, USA. Single-molecule techniques can monitor the kinetics of transitions between enzyme open and closed conformations, but such methods usually lack the res- olution to directly observe the underlying transition pathway or any intermedi- ate conformational dynamics. We have recently described a single-molecule electronic technique that breaks this barrier (1-3). Using a 1 MHz-bandwidth carbon nanotube transistor, the transition dynamics of T4 lysozyme have been recorded with microsecond resolution. We directly resolve a smooth, continuous transition with an average duration of 37 microseconds that sug- gests a concerted mechanism for glycoside hydrolysis. Unexpectedly, the me- chanical closing and re-opening of the enzyme have identical distributions of transition durations, and the motions do not depend on whether the enzyme is in its catalytic or non-productive state. These results illustrate the principle of microscopic reversibility applied to a Brownian ratchet, with lysozyme tracing a single pathway for closing and the reverse pathway for enzyme open- ing, regardless of its instantaneous catalytic productivity. 1. Y. Choi, et. al., ‘‘Single-Molecule Lysozyme Dynamics Monitored by an Electronic Circuit,’’ Science 335, 319 (2012). 2. T.J. Olsen, et. al., ‘‘Electronic Measurements of Single-Molecule Processing by DNA polymerase I (Klenow fragment),’’ JACS 135, 7855 (2013). 3. P.C. Sims, et. al., ‘‘Electronic Measurements of Single-Molecule Catalysis by cAMP-Dependent Protein Kinase A,’’ JACS 135, 7861 (2013). 149-Plat Human Neuraminidase Enzymes alter the Lateral Mobility and Function of Integrin Receptors Christopher W. Cairo. Chemistry, University of Alberta, Edmonton, AB, Canada. Glycolipids and glycoproteins are important components of membrane struc- ture. Mechanisms which alter the structure of glycans at the membrane could influence cellular responses. For example, by removing an important binding epitope or else by unmasking a new one, protein-glycan interactions may be disrupted or reinforced. Our group has been working to understand the role of human neuraminidase enzymes (hNEU) in regulating cellular adhesion and migration through integrin receptors. Of the four hNEU isoenzymes, three have activity at the plasma membrane and lysosome; thus, these enzymes could regulate the composition of the plasma membrane by stripping neuraminic acid (Neu5Ac; also known as sialic acid) from membrane glycans. Using recombi- nant enzymes and selective hNEU inhibitors developed within our group, we can selectively probe increased or decreased activity of individual isoenzymes in vitro; allowing us to test the effect of specific enzymes. Previous studies have suggested that integrin-mediated adhesion may be altered through hNEU activ- ity. We measured the lateral mobility of integrins in cells treated with NEU3 and NEU4 using single-dye tracking (SDT) by total-internal-reflection fluores- cence microscopy (TIRF). We find that hNEU can dramatically change the diffusion of integrin receptors, and that the effect is dependent on the cell type and the isoenzyme used. Adhesion and cell migration assays of cells treated with chemical inhibitors of the enzymes reveal that hNEU activity is intimately involved in the regulation of integrin adhesion to their native li- gands. We will present lateral mobility and cell migration assays with enzyme and inhibitor conditions. Our results suggest an important role for hNEU as reg- ulators of membrane composition and the activity of adhesion receptors. Platform: Membrane Dynamics 150-Plat Nothing to Sneeze at: A Full-Scale Computational Model of the Human Influenza Virion Tyler Reddy 1 , David Shorthouse 1 , Daniel Parton 2 , Elizabeth Jefferys 1 , Philip W. Fowler 1 , Matthieu Chavent 1 , Marc Baaden 3 , Mark S.P. Sansom 1 . 31a SBCB Unit, Biochemistry, University of Oxford, Oxford, United Kingdom, Memorial Sloan Kettering Cancer Center, New York, NY, USA, 3 Institut de Biologie Physico-Chimique, Paris, France. Tackling the ongoing challenge of influenza infectivity would benefit greatly from a molecular understanding of why the influenza A virion exhibits seasonal patterns of infectivity and has wide-ranging survival times in different environ- ments. A computational approach to the study of the behaviour of the virion that focuses on the poorly-understood structural and dynamic role of the lipids is presented here. We have combined experimental data from X-ray crystallog- raphy, NMR spectroscopy, cryoelectron microscopy, and lipidomics to build a full-scale computational model of the influenza A virion. This represents the first set of microsecond-scale molecular dynamics simulations of an enveloped virion in explicit solvent that we are aware of. We report results for a set of simulations at different temperatures and with varying lipid compositions. The Forssman glycolipid, which is prevalent in the influenza A lipidome, influ- ences several biophysical characteristics of the virion model, including diffu- sion and clustering of proteins and lipids. The distribution of peplomers on the virion surface is consistent with accessibility to bivalent antibodies. The distances of binding sites for host cell sialic acid-containing receptors have been analyzed in the virion model for a variety of planar host cell membrane attack orientations. The relatively rigid membrane of the influenza A virion model exhibits a number of biophysical properties consistent with experimental measurements, and may serve as a useful platform for in silico assessment of virion behaviour. 151-Plat Role Of Membrane-Bending Proteins as Membrane Tension Sensors in Cell Migration Toshiki Itoh. Biosignal Research Center, Kobe University, Kobe, Japan. The plasma membrane (PM) tension has emerged as a key regulator for funda- mental cellular functions. However, a missing link between PM tension and biochemical reaction precludes our understanding of how PM tension is coupled to cellular events like directed migration. We found that FBP17, an F-BAR domain protein, acts as a membrane tension sensor that organizes cell polarity during cell migration. The mechanism is based on membrane- bending activity of the F-BAR domain that is counteracted by PM tension. Because FBP17 binds and activates WASP/N-WASP to promote actin poly- merization, it corresponds to the local activator of actin polymerization in the feedback loop regulated by PM tension for self-organized formation of the leading edge. These findings provide an important mechanistic insight into cell migration underpinning a wide variety of physiological events such as development, immune response, and cancer metastasis. 152-Plat Experiment and Simulation Reveal the Bending Properties of Nanoscopic Lipid Domains Jonathan D. Nickels 1 , Michael Ohl 2 , Xiaolin Cheng 1 , Christopher Stanley 3 , Frederick Heberle 3 , Robert Standaert 1 , John Katsaras 1 . Oak Ridge National Lab/Univ. of Tennessee, Knoxville, Oak Ridge, TN, USA, 2 Oak Ridge National Lab/ Julich Center for Neutron Science, Oak Ridge, TN, USA, 3 Oak Ridge National Lab, Oak Ridge, TN, USA. There has great interest in studying the mechanisms that support nanoscopic lipid domain size using model mixtures. To date, experimental studies have focused in large part on structural parameters such as thickness mismatch between phases, lacking access to mechanical properties in direct, experimental ways. The Neutron Spin Echo technique can directly measure the bending modulus of such bilayers systems by observing shape fluctuations. Furthermore, this method permits us to utilize hydrogen-deuterium contrast matching to make direct obser- vations of the mechanical properties of nanoscopic domains themselves. I will present results detailing for the first time the bending modulus of an in- dividual lipid domain. We have also measured both the structural and mechan- ical properties of each pure phase compositions of the three component lipid mixture which spontaneously forms these domains. Our results demonstrate that the liquid-ordered phase is more rigid than the liquid disordered phase. Interestingly, the value of the bending modulus in vesicles where these phases coexist as nanoscopic domains approaches that of the liquid ordered-phase, whereas our sample contrast matched so that we only probe the disordered phase in the coexisting system have a bending modulus similar to what is seen in the liquid-disordered only system. We analyze our results with the help of all atom MD simulations which accurately reproduce the structural properties of our system and agree with the trend in mechanical properties that we observe experimentally. These results have implications in deter- mination of important properties such as the line tension which may drive domain size.

The prevailing conception of carbon nanotubes and particularly single-walled carbon nanotubes (SWNTs) continues to be one of perfectly crystalline wires. Here, we demonstrate a selective electrochemical method that labels point defects and makes them easily visible for quantitative analysis. High-quality SWNTs are confirmed to contain one defect per 4 microm on average, with a distribution weighted towards areas of SWNT curvature. Although this defect density compares favourably to high-quality, silicon single-crystals, the presence of a single defect can have tremendous electronic effects in one-dimensional conductors such as SWNTs. We demonstrate a one-to-one correspondence between chemically active point defects and sites of local electronic sensitivity in SWNT circuits, confirming the expectation that individual defects may be critical to understanding and controlling variability, noise and chemical sensitivity in SWNT electronic devices. By varying the SWNT synthesis technique, we further show that the defect spacing can be varied over orders of magnitude. The ability to detect and analyse point defects, especially at very low concentrations, indicates the promise of this technique for quantitative process analysis, especially in nanoelectronics development.

The full electronic complexity of multiwalled carbon nanotubes may be explored by sequentially removing individual carbon shells. This technique is employed to directly measure the number of shells contributing to conduction at room temperature, as well as the contribution of each shell to the overall conductance. By exploring the gate dependence of the conductance, the random alternation between semiconducting and metallic shells can also be observed.

Recent work has demonstrated single-electron sensitivity in carbon nanotube transistors under a variety of conditions, including room temperature. In noncovalent cases like charged adsorbates or SiO2 imperfections, two-level fluctuators near the nanotube perturb the current electrostatically. In other cases, a sidewall defect or other covalent modification directly on the nanotube sidewall sensitizes a particular site. Comparative research has helped reveal differences in the transduction mechanisms of the two cases and provides design rules for maximizing reliable signals for electronic sensing. For example, noncovalent sensitization generally produces a smaller signal amplitude in a background of low-energy fluctuators at varying distances from the nanotube. Covalent modifications are far more sensitive than noncovalent perturbations, but the new degrees of freedom that accompany covalent disorder often have energy scales similar to the signal of interest, leading to multiple independent fluctuations that degrade the overall signal-to-noise for sensing. An outstanding compromise involves short, noncovalent linkers, which can produce highly predictable signal amplitudes without degradation of the device characteristics. Furthermore, noncovalent fabrication methods are scalable, so that wafer-scale arrays of molecular sensors are most likely to follow this path.

Uniform, conformal coating of MnO2 onto single walled carbon nanotubes is achieved with precise thickness control and without the introduction or utilization of defect sites. The resulting composite electrodes enable electrochemical testing of novel carbon–metal oxide composites in which rate-enhancing, fast-electron-transfer defect sites are completely absent. Such sites are ubiquitous and believed to be enormously consequential to the electron transfer properties of graphitic carbon systems, and the techniques described here provide an experimental route to quantitatively study such effects. For example, we immediately discern the enhanced interfacial resistance that occurs in the defect-free system. Keywords: Hybrid materials, Composite nanostructure, Carbon nanotube, Nanoelectrode

The inelastic mean free path ${\ensuremath{\lambda}}_{\mathrm{MFP}}$ is a critical parameter for electronic devices. Here, we demonstrate Kelvin probe force microscopy (KPFM) as a technique for studying ${\ensuremath{\lambda}}_{\mathrm{MFP}}$ in biased, semi-metallic single-walled carbon nanotubes (SWNTs). Having one of the longest room-temperature ${\ensuremath{\lambda}}_{\mathrm{MFP}}$ values of any known material, SWNTs provide a unique platform for probing mesoscopic transport. KPFM directly determined ${\ensuremath{\lambda}}_{\mathrm{MFP}}$ as a function of bias, quantitatively determined the contributions of different scattering mechanisms, and enabled comparative study of individual SWNTs with and without disorder. The room-temperature mean free paths for optical phonon and surface plasmon-polariton scattering were measured to be 62 \ifmmode\pm\else\textpm\fi{} 20 nm and 260 \ifmmode\pm\else\textpm\fi{} 50 nm, respectively. The optical phonon scattering length is significantly longer than inferred from previous measurements, and it resolves a longstanding discrepancy between SWNT theory and experiment, suggesting that KPFM could become a preferred quantitative technique for studying transport in nanoscale systems.

Carbon nanotubes display either metallic or semiconducting properties. Both large, multiwalled nanotubes (MWNTs), with many concentric carbon shells, and bundles or “ropes” of aligned single-walled nanotubes (SWNTs), are complex composite conductors that incorporate many weakly coupled nanotubes that each have a different electronic structure. Here we demonstrate a simple and reliable method for selectively removing single carbon shells from MWNTs and SWNT ropes to tailor the properties of these composite nanotubes. We can remove shells of MWNTs stepwise and individually characterize the different shells. By choosing among the shells, we can convert a MWNT into either a metallic or a semiconducting conductor, as well as directly address the issue of multiple-shell transport. With SWNT ropes, similar selectivity allows us to generate entire arrays of nanoscale field-effect transistors based solely on the fraction of semiconducting SWNTs.

The local density of electronic states N(E) has been measured on C{sub 36} thin films using scanning tunneling spectroscopy (STS). A 0.8thinspthinspeV energy gap and sharp features in N(E) with widths as small as 0.2thinspthinspeV can be ascribed to the discrete molecular energy levels predicted for the C{sub 36} molecule, broadened by intermolecular interactions. However, a more complete agreement between the experimental results and theoretical predictions occurs if the system is modeled as covalently bonded C{sub 36} dimers and trimers. These results confirm the molecular nature of C{sub 36} as well as its higher reactivity as compared to larger size fullerenes. {copyright} {ital 1998} {ital The American Physical Society}

Conductivity measurements were performed on bundles of single-walled carbon nanotubes with the aid of a scanning tunneling microscope (STM). Semimetallic current-voltage (I-V) characteristics generally indicated the bundles to be electronically similar to graphite. However, by moving the STM tip along the length of the nanotubes, sharp deviations in the I-V characteristics could also be observed. Well-defined positions were found at which the nanotube transport current changed abruptly from a graphitic response to one that is highly nonlinear and asymmetric, including near-perfect rectification. This abrupt change in the nanotube transport suggests that the STM tip had passed a region of the nanotube which acts less like a wire than it does a Schottky barrier or other heterojunction. Similar on-tube nanodevices have been theoretically predicted for point defects in individual carbon nanotubes and are consistent with our observations.

The attributes of electron field emission from disordered matrix arrays of carbon nanotubes are studied and found to be quite reproducible in spite of the disorder, density, and quality variations from sample to sample. At low applied electric fields, the electron field emission current-voltage characteristics qualitatively follow conventional Fowler-Nordheim behavior up to a critical current density. However, the current rise at low applied fields is anomalously steep, suggesting that the Fowler-Nordheim model is not sufficient to quantitatively characterize the emission. In the high-field region, the emission characteristics have a more complex behavior. In that regime, the instantaneous field emission is reminiscent of the low-field behavior, but discrete switching events lead to an overall current suppression. We attribute the sudden and well-defined onset of the switching events to interactions between neighboring nanotube tips. By correlating the switching behavior to the current-voltage characteristics, we rule out other physical processes that cause similar effects.

Nanoscale electronic devices like field-effect transistors have long promised to provide sensitive, label-free detection of biomolecules. In particular, single-walled carbon nanotubes have the requisite sensitivity to detect single molecule events and sufficient bandwidth to directly monitor single molecule dynamics in real time. Recent measurements have demonstrated this premise by monitoring the dynamic, single-molecule processivity of three different enzymes: lysozyme, protein Kinase A, and the Klenow fragment of DNA polymerase I. In each case, recordings resolved detailed trajectories of tens of thousands of individual chemical events and provided excellent statistics for single-molecule events. This electronic technique has a temporal resolution approaching 1 microsecond, which provides a new window for observing brief, intermediate transition states. In addition, the devices are indefinitely stable, so that the same molecule can be observed for minutes and hours. The extended recordings provide new insights into rare events like transitions to chemically-inactive conformations.

As electronic devices shrink to the one-dimensional limit, unusual device physics can result, even at room temperature. Nanoscale conductors like single-walled carbon nanotubes (SWNTs) are particularly useful tools for experimentally investigating these effects. Our characterization of point defects in SWNTs has focused on these electronic consequences. A single scattering site in an otherwise quasi-ballistic SWNT introduces resistance, transconductance, and chemical sensitivity, and here we investigate these contributions using a combination of transport and scanning probe techniques. The transport measurements determine the two-terminal contributions over a wide range of bias, temperature, and environmental conditions, while the scanning probe work provides complementary confirmation that the effects originate at a particular site along the conduction path in a SWNT. Together, the combination proves that single point defects behave like scattering barriers having Poole-Frenkel transport characteristics. The Poole-Frenkel barriers have heights of 10 – 30 meV and gate-dependent widths that grow as large as 1 μm due to the uniquely poor screening in one dimension. Poole-Frenkel characteristics suggest that the barriers contain at least one localized electronic state, and that this state primarily contributes to conduction under high bias or high temperature conditions. Because these localized states vary from one device to another, we hypothesize that each might be unique to a particular defect’s chemical type.

Single molecule bioelectronic circuits provide an opportunity to study chemical kinetics and kinetic variability with bond-by-bond resolution. To demonstrate this approach, we examined the catalytic activity of T4 lysozyme processing peptidoglycan substrates. Monitoring a single lysozyme molecule through changes in a circuit's conductance helped elucidate unexplored and previously invisible aspects of lysozyme's catalytic mechanism and demonstrated lysozyme to be a processive enzyme governed by 9 independent time constants. The variation of each time constant with pH or substrate crosslinking provided different insights into catalytic activity and dynamic disorder. Overall, ten lysozyme variants were synthesized and tested in single molecule circuits to dissect the transduction of chemical activity into electronic signals. Measurements show that a single amino acid with the appropriate properties is sufficient for good signal generation, proving that the single molecule circuit technique can be easily extended to other proteins.

For over a decade, researchers have pursued sensitive, label-free biosensing and biodetection using nanoscale electronic devices like field-effect transistors. Prototype devices made with single-walled carbon nanotubes proved to have enough sensitivity to detect single molecule events, as well as sufficient bandwidth to monitor real time dynamics. Combining these characteristics has led to novel electronic measurements where the bond-by-bond chemical activity of single enzyme molecules is monitored in real time. The high bandwidth of the nanotube transistors allow every individual chemical event to be clearly resolved, providing excellent statistics from tens of thousands of turnovers by a single molecule.

Single-molecule studies of enzymes open a window into their dynamics and kinetics. A single molecule of the catalytic domain of cAMP-dependent protein kinase A (PKA) was attached to a single-walled carbon nanotube device for long-duration monitoring. The electronic recording clearly resolves substrate binding, ATP binding, and cooperative formation of PKA's catalytically functional, ternary complex. Using recordings of a single PKA molecule extending over 10 min and tens of thousands of binding events, we determine the full transition probability matrix and conversion rates governing formation of the apo, intermediate, and closed enzyme configurations. We also observe kinetic rates varying over 2 orders of magnitude from one second to another. Anti-correlation of the on and off rates for PKA binding to the peptide substrate, but not ATP, demonstrates that regulation of enzyme activity results from altering the stability of the PKA-substrate complex, not its binding to ATP. The results depict a highly dynamic enzyme offering dramatic possibilities for regulated activity, an attribute useful for an enzyme with crucial roles in cell signaling. © 2013 American Chemical Society.

Bioconjugating single molecules of the Klenow fragment of DNA polymerase I into electronic nanocircuits allowed electrical recordings of enzymatic function and dynamic variability with the resolution of individual nucleotide incorporation events. Continuous recordings of DNA polymerase processing multiple homopolymeric DNA templates extended over 600 s and through >10,000 bond forming events. An enzymatic processivity of 42 nucleotides for a template of the same length was directly observed. Statistical analysis determined key kinetic parameters for the enzyme’s open and closed conformations. Consistent with these nanocircuit-based observations, the enzyme closed complex forms a phosphodiester bond in a highly efficient process >99.8% of the time with a mean duration of only 0.3 ms for all four dNTPs. The rate-limiting step for catalysis occurs during the enzyme open state, but with a nearly two-fold longer duration for dATP or dTTP incorporation than for dCTP or dGTP into complementary, homopolymeric DNA templates. Taken together, the results provide a wealth of new information complementing prior work on the mechanism and dynamics of DNA polymerase I.

Kelvin probe force microscopy (KPFM) should be a key tool for characterizing the device physics of nanoscale electronics because it can directly image electrostatic potentials. In practice, though, distant connective electrodes interfere with accurate KPFM potential measurements and compromise its applicability. A parameterized KPFM technique described here determines these influences empirically during imaging, so that accurate potential profiles can be deduced from arbitrary device geometries without additional modeling. The technique is demonstrated on current-carrying single-walled carbon nanotubes (SWNTs), directly resolving average resistances per unit length of 70 kΩ/μm in semimetallic SWNTs and 200 kΩ/μm in semiconducting SWNTs. © 2013 American Institute of Physics.

Single molecule experimental methods have provided new insights into biomolecular function, dynamic disorder, and transient states that are all invisible to conventional measurements. A novel, non-fluorescent single molecule technique involves attaching single molecules to single-walled carbon nanotube field-effective transistors (SWNT FETs). These ultrasensitive electronic devices provide long-duration, label-free monitoring of biomolecules and their dynamic motions. However, generalization of the SWNT FET technique first requires design rules that can predict the success and applicability of these devices. Here, we report on the transduction mechanism linking enzymatic processivity to electrical signal generation by a SWNT FET. The interaction between SWNT FETs and the enzyme lysozyme was systematically dissected using eight different lysozyme variants synthesized by protein engineering. The data prove that effective signal generation can be accomplished using a single charged amino acid, when appropriately located, providing a foundation to widely apply SWNT FET sensitivity to other biomolecular systems.

Nanoscale electronic devices like field-effect transistors (FETs) have long promised to provide sensitive, label-free detection of biomolecules. In particular, single-walled carbon nanotubes (SWNTs) have the requisite sensitivity to detect single molecule events, and have sufficient bandwidth to directly monitor single molecule dynamics in real time. Recent measurements have demonstrated this premise by monitoring the dynamic, single-molecule processivity of three different enzymes: lysozyme, protein kinase A, and the Klenow Fragment of polymerase I. Initial successes in each case indicated the generality and attractiveness of SWNT FETs as a new tool to complement other single molecule techniques. However, further generalization of the SWNT FET technique demands reliable design rules that can predict the success and applicability of these devices. Here, we address this need by focusing on the transduction mechanisms that link enzyme processivity to electrical signal generation in a SWNT FET. Using ten different lysozyme variants synthesized by mutagenesis, we systematically dissect the enzyme-SWNT interaction in order to understand this transduction. The data prove that mechanical displacements of charged functionalities near the SWNT attachment site are the primary sources of transduction, and that the resulting devices are sensitive enough to track the motions of just one charged amino acid. The purposeful incorporation of a charged group at a particular location allows the device to be designed to have sensitivity to particular chemical activities or allosterically-driven mechanical motions. The findings provide rules for the creation of similarly effective nanocircuits using a wide range of enzymes or proteins.

Single-molecule techniques eliminate ensemble averaging to reveal the mechanisms, timing, and energetics of individual chemical and biochemical events. Over the past decade, single-molecule science has flourished as new techniques have adopted fluorescent probes, optical traps, and scanning probe microscopy to access the single-molecule limit. Recently, carbon nanotube transistors have been added to this toolkit of single-molecule techniques. As electronic transducers, single-walled carbon nanotubes have the sensitivity to detect single molecular events [1] and the bandwidth to resolve microsecond-duration transients and intermediate states [2]. These characteristics provide exciting new opportunities to monitor and understand complex catalytic cycles such as the biochemical reactions of enzymes. For example, the single molecule kinetics of the Klenow fragment (KF) of polymerase I have recently been studied by bioconjugating KF to nanotube transistors. Continuous recordings of polymerase as it processes various DNA templates have extended through >10,000 bond-forming events, providing new insights into the processivity, kinetic variability, and tolerance of polymerase toward synthetic dNTP analogs [3,4]. In addition to the kinetics, signals generated with some analogs revealed conformational states that do not occur with native dNTPs, helping to explain polymerases’ tolerance for incorporating dNTP analogs. The high resolution of the electronic records illuminate new aspects of polymerase’s catalytic cycle and suggest new opportunities for all-electronic DNA sequencing. [1] Y. Choi, et. al., “Single-Molecule Lysozyme Dynamics Monitored by an Electronic Circuit,” Science 335, 319 (2012). [2] M.V. Akhterov, et. al., "Observing Lysozyme Closing and Opening Motions by High-Resolution Single Molecule Enzymology." ACS Chemical Biology 10, 1495 (2015). [3] T.J. Olsen, et. al., “Electronic Measurements of Single-Molecule Processing by DNA polymerase I (Klenow fragment),” JACS 135, 7855 (2013). [4] K.M. Pugliese, et. al., "Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits." JACS 137, 9587 (2015).

The faster kinetics of nanostructured charge-storage materials are often accompanied by accelerated degradation and failure, compromising the potential advantages of nanostructure and nanoporosity. Understanding and controlling the exact mechanisms of this degradation is a complex materials characterization challenge. The recent availability of in situ and in operando techniques allows new fundamental studies of these issues, including the failure of nanoscale porosity to fully accommodate the mechanical strains of charge insertion. Here, we use atomic force microscopy in liquid electrolytes to experimentally measure the mechanical expansion of porous, nanostructured Li-ion cathodes during charge cycling. Using thin films of LixMnO2 on Pt collectors, we analyze expansion as a function of scan rate, voltage window, and porosity. Comparative measurements in aqueous and nonaqueous electrolytes confirm the role of Li-ion species in the results. The rate dependent measurements of expansion can be separated into diffusion-limited, bulk components driven by Mn3+/4+ charging and faster, surface processes, in the same way that these contributions to capacitance are normally separated. Consequently, we have extracted the electrochemical-mechanical coupling coefficients ∂V/∂Q for surface and bulk processes separately. While the bulk coupling coefficient provides an excellent match to values predicted from first-principles theory, the surface coupling is surprisingly large. In fact, surface capacitance is responsible for a majority of the mechanical expansion at high rates, even when most of this capacitance would normally be attributed to double-layer charging mechanisms. The result demonstrates the importance of Mn3+/4+ species at the electrolyte interface and the inability of these species to take advantage of the film’s nanoporosity for accommodating expansion. In other words, fast surface charging processes do not involve mechanical relaxation of the material into adjacent pores, but rather drive expansion of the solid matrix.

Single-molecule techniques based on optical, electronic, and mechanical mechanisms have all proven useful for studying enzymes like DNA polymerases. Electronic devices, in particular, provide exciting new opportunities for understanding polymerase activity, especially with regard to improving DNA sequencing technologies. Recently, single molecule kinetics of the Klenow fragment (KF) of polymerase I have been studied by bioconjugating KF to single-walled carbon nanotube field-effect transistors. Continuous recordings of KF processing various DNA templates have extended over 600 seconds and through >10,000 bond-forming events, providing new insights into KF's processivity, kinetic variability, and tolerance of various dNTP analogs (1,2). For example, we show that the average duration of each incorporation event appears invariant across all analog and native dNTPs, indicating that analog structure has no impact on the timing of this step of the catalytic cycle. Despite similar timings, however, polymerization with some analogs have revealed alternate conformational states that do not occur with native dNTPs. The electronic technique's particular sensitivity to allosteric motions implicates a special role for KF's O-helix as it tests the stability of nascent base pairs with these analogs. The results help explain polymerases’ tolerance for dNTP analogs, despite having highly evolved mechanisms for specific recognition of and discrimination among dNTPs.1. T.J. Olsen, et. al., “Electronic Measurements of Single-Molecule Processing by DNA polymerase I (Klenow fragment),” JACS 135, 7855 (2013).2. K.M. Pugliese, et. al., “Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits.” JACS 137, 9587 (2015).

We review an extensive study of the factors that influence the intensity of coherent, nonlinear four-wave mixing (FWM) in carbon nanotubes, with particular attention to the variability inherent to single-walled carbon nanotubes (SWNTs). Through a combination of spatial imaging and spectroscopy applied to hundreds of individual SWNTs in optoelectronic devices, the FWM response is shown to vary systematically with free-carrier concentration. This dependence is manifested both in the intrinsic SWNT band structure and also by extrinsic and environmental effects. We demonstrate the sensitivity of the SWNT FWM signal by investigating SWNTs transferred from one substrate to another, before and after the introduction of chemical damage, and with chemical and electrostatic doping. The results demonstrate FWM as a sensitive technique for interrogating SWNT optoelectronic properties.

PHYSICAL REVIEW B 85, 235418 (2012) Distinguishing carbon nanotube defect chemistry using scanning gate spectroscopy Steven R. Hunt, Elliot J. Fuller, Brad L. Corso, and Philip G. Collins * Department of Physics and Astronomy, University of California, Irvine, Irvine, California 92697 USA (Received 25 April 2012; published 7 June 2012) Electronic scattering at individual defect sites is presumably sensitive to defect chemistry. Here, we combine advances in carbon nanotube device fabrication and scanning probe characterization to investigate this correspondence. Specifically, we apply scanning gate spectroscopy (SGS) to the study of defects introduced into single walled carbon nanotubes by point functionalization in water, sulfuric acid, or hydrochloric acid. SGS measures the energy-dependent transmission functions of defect sites, and by working in the dilute limit of individual, isolated defects we empirically distinguish the three chemical types. A preliminary analysis proposes a scattering model in order to motivate further theoretical investigations of this one-dimensional scattering system. DOI: 10.1103/PhysRevB.85.235418 PACS number(s): 73.63.Fg, 72.10.Fk, 85.35.Kt, 81.16.Pr I. INTRODUCTION Historically, optical spectroscopy has been the primary tool for characterizing point defects. 1,2 With the continued scaling of electronic devices, however, defect properties are now becoming directly accessible to electrical transport measurements. Various types of devices, including traditional Si field effect transistors (FETs), are now fabricated at scales for which the presence of a single atomic defect affects the device conductance, mobility, or fluctuations and noise. 3 Using high-purity devices made of Si, Ge, diamond, or compound semiconductors, a nascent field is growing around the concept of single atom electronics, sometimes termed “solotronics.” 4,5 Of the different low-dimensional conductors that are most sensitive to defects, the single walled carbon nanotube (SWNT) is an exceptional case. Pristine SWNTs are quasi- one-dimensional conductors with inelastic mean free paths that approach 1 μm at room temperature, 6–8 and these charac- teristics make their electronic properties unusually sensitive to individual defects. 9 The quasi-one-dimensionality of SWNT states means that every carrier propagating through the device is able to interact with the defect potential. The long mean-free path allows SWNT devices to be easily fabricated using conventional lithography, but still in a regime where other sources of inelastic scattering and dissipation are minimal. Besides these two advantages, the versatility afforded by carbon chemistry makes SWNTs a rich system where defect scattering sites can be chemically tailored to have many possible identities. Whereas traditional semiconductor defects are most likely to be atomic vacancies or interstitials, a SWNT defect site can incorporate an almost unlimited variety of covalently-bonded molecules, 10,11 and consequently, a range of scattering potentials. This versatility provides an oppor- tunity for precisely mapping the correspondence between chemical structure and electronic function in the challenging limit of dilute disorder. Near-field optical techniques can locate individual defects, but not distinguish the properties of different chemical types. 12–14 Transport measurements, on the other hand, are sensitive to individual defects, especially in the quasi-ballistic limit where one defect is the primary source of resistance. 8,15,16 This sensitivity provides a possible experimental method for identifying and categorizing different types of defects. In order to test this hypothesis and characterize SWNT defects electronically, we developed the electrochemical tech- nique of point functionalization 15 to add individual point defects to operational SWNT FETs. By measuring the same SWNT before and after deliberate chemical modification, we can directly observe the change in electrical characteristics caused by the added disorder. To spatially resolve these effects and more precisely investigate the role of the defect sites, we combine the electrical measurements with simultaneous scanning probe interrogation. 17 An electrostatic potential V tip on a conductive, scanning probe tip allows a SWNT to be locally gated, independently from the rest of the device. When performed using fixed biases, this scanning probe technique is known as scanning gate microscopy (SGM), and it creates a spatial image of the channel transconductance at particular bias conditions. 18–25 We have combined SGM with more traditional SWNT transport spectroscopy 7,8 by sweeping through multiple values of the backgate bias V bg , source-drain bias V sd , or V tip at each position along a SWNT. This technique generates a multidimensional data set referred to as scanning gate spectroscopy (SGS). The SGS data provides a detailed record of the gate-dependent scattering that occurs in the immediate vicinity of a defect site. 26 In this paper, we summarize the results of performing scanning gate spectroscopy on a variety of SWNT devices. A single defect has been analyzed in detail in a previous publication, 26 but here we describe the technique and apply it comparatively to SWNTs oxidized to different degrees in water or acids. Having oxidized multiple devices in each electrolyte, we demonstrate typical scattering characteristics for particular types of chemical modification. However, we also identify experimental variability that must be controlled before chemically distinct defects can be reliably categorized. II. EXPERIMENTAL METHODS A. SWNT synthesis and device fabrication For this work, SWNT FET devices were manufactured on 4 Si wafers using techniques common for the field, namely chemical vapor deposition (CVD) and conventional optical lithography. Numerous recipes are available for the CVD growth of dilute, high quality SWNTs on Si wafers. Our implementation used a monodisperse nanoparticle, Fe 30 Mo 84 , ©2012 American Physical Society

The dynamic processivity of individual T4 lysozyme molecules was monitored in the presence of either linear or cross-linked peptidoglycan substrates. Single-molecule monitoring was accomplished using a novel electronic technique in which lysozyme molecules were tethered to single-walled carbon nanotube field-effect transistors through pyrene linker molecules. The substrate-driven hinge-bending motions of lysozyme induced dynamic electronic signals in the underlying transistor, allowing long-term monitoring of the same molecule without the limitations of optical quenching or bleaching. For both substrates, lysozyme exhibited processive low turnover rates of 20-50 s(-1) and rapid (200-400 s(-1)) nonproductive motions. The latter nonproductive binding events occupied 43% of the enzyme's time in the presence of the cross-linked peptidoglycan but only 7% with the linear substrate. Furthermore, lysozyme catalyzed the hydrolysis of glycosidic bonds to the end of the linear substrate but appeared to sidestep the peptide cross-links to zigzag through the wild-type substrate.

When tailored to contain a single resistive defect, one dimensional nanocircuits can realize high dynamic range, high bandwidth transduction of single molecule chemical events. The physical mechanisms behind this sensitive transduction, however, remain poorly understood. Here, we complement ongoing sensing measurements with scanning probe characterization of the electronic properties of defects. The high sensitivity of defect sites is directly probed, and is found to be in excellent agreement with a finite element model containing realistic device parameters for the defect sites. The model illuminates the most likely sensing mechanisms of these single molecule circuits, and fully supports the premise that further tailoring of the defect sites could enable the chemically selective interrogation of a wide range of complex molecular interactions.

Carbon nanotubes display either metallic or semiconducting properties. Both large, multiwalled nanotubes (MWNTs), with many concentric carbon shells, and bundles or “ropes” of aligned single-walled nanotubes (SWNTs), are complex composite conductors that incorporate many weakly coupled nanotubes that each have a different electronic structure. Here we demonstrate a simple and reliable method for selectively removing single carbon shells from MWNTs and SWNT ropes to tailor the properties of these composite nanotubes. We can remove shells of MWNTs stepwise and individually characterize the different shells. By choosing among the shells, we can convert a MWNT into either a metallic or a semiconducting conductor, as well as directly address the issue of multiple-shell transport. With SWNT ropes, similar selectivity allows us to generate entire arrays of nanoscale field-effect transistors based solely on the fraction of semiconducting SWNTs.

Individual single-walled carbon nanotubes (SWCNTs) become sensitive to H(2) gas when their surfaces are decorated with Pd metal, and previous reports measure typical chemoresistive increases to be approximately 2-fold. Here, thousand-fold increases in resistance are demonstrated in the specific case where a Pd cluster decorates a SWCNT sidewall defect site. Measurements on single SWCNTs, performed both before and after defect incorporation, prove that defects have extraordinary consequences on the chemoresistive response, especially in the case of SWCNTs with metallic band structure. Undecorated defects do not contribute to H(2) chemosensitivity, indicating that this amplification is due to a specific but complex interdependence between a defect site's electronic transmission and the chemistry of the defect-Pd-H(2) system. Dosage experiments suggest a primary role is played by spillover of atomic H onto the defect site.

We investigate electronic devices consisting of individual, metallic, single-walled carbon nanotubes contacted by Pt electrodes in a field effect transistor configuration, focusing on improvements to the metal-nanotube contact resistance as the devices are annealed in inert environments including ultrahigh vacuum. At moderate temperatures (T880 K), thermal processing results in high resistance contacts with thermally activated barriers. Higher temperatures (T880 K) achieve nearly transparent contacts. In the latter case, analytical surface measurements reveal the catalytic decomposition of hydrocarbons into graphene layers on the Pt surface, suggesting that improved electronic behavior is primarily due to the formation of an all-carbon nanotube-graphite interface rather than to the improvement of the nanotube-Pt one.

Dual color four-wave-mixing (FWM) microscopy is used to spatially resolve the third-order optical response from individual carbon nanotubes. Good signal-to-noise is obtained from single-walled carbon nanotubes (SWNT) sitting on substrates, when the excitation beams are resonant with electronic transitions of the nanotube, by detecting the FWM response at the anti-Stokes frequency. Whereas the coherent anti-Stokes (CAS) signal is sensitive to both electronic and vibrational resonances of the material, it is shown that the signal from individual SWNTs is dominated by the electronic response. The CAS signal is strongly polarization dependent, with the highest signals found parallel with the enhanced electronic polarizibility along the long axis of the SWNT. © 2009 American Chemical Society.