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Single-walled nanotubes (SWNT) have attracted significant attention because of the substance’s superior crystal quality, high thermal conductivity and current carrying capacity, thus emerging as an attractive material for nanoelectrics. To optimize the selection of SWNT structures in large-scale synthesis, an understanding of their growth mechanism is necessary. We report studies of the helicity distributions of SWNT using electron nanodiffraction. The overall statistical distribution of helicity has peaks at 0° and 30°. The peak evident at 0° was found to be a sharp local maximum, while the peak at 30° was broader. We also found that the helicity distribution varies from region to region of micrometer size. This observation indicates that local environment affects nanotube growth, resulting in different structural distributions. Keywords: carbon nanotube; helicity; growth mechanism 1. Introduction The unique physical properties and potential applications of single-walled carbon nanotubes (SWNT) have been well documented since their discovery, using both theory and experiment [1-6]. It is evident that the useful electronic properties of SWNT are largely dependent on the atomic structures of individual nanotubes, which can be accurately defined using the tube diameter

Single-molecule manipulation studies can provide quantitative information about the physical properties of complex biological molecules without ensemble artifacts obscuring the measurements. We demonstrate computational techniques which aim at more fully utilizing the wealth of information contained in noisy experimental time series. The "noise" comes from multiple sources e.g., inherent thermal motion, instrument measurement error, etc. The primary focus of this paper is a methodology that uses time domain based methods to extract the effective molecular friction from single-molecule pulling data. We studied molecules composed of eight tandem repeat titin I27 domains, but the modeling approaches have applicability to other single-molecule mechanical studies. The merits and challenges associated with applying such a computational approach to existing single-molecule manipulation data are also discussed.

We review recent work on DNA-linked gold nanoparticle assemblies. The synthesis, properties, and phase behavior of such DNA-gold nanoparticle assemblies are described. These nanoparticle assemblies have strong optical extinction in the ultraviolet and visible light regions; hence, the technique is used to study the kinetics and phase transitions of DNA-gold nanoparticle assemblies. The melting transition of DNA-gold nanoparticle assemblies shows unusual trends compared to those of free DNA. The phase transitions are influenced by many parameters, such as nanoparticle size, DNA sequence, DNA grafting density, DNA linker length, interparticle distance, base pairing defects, and disorders. The physics of the DNA-gold nanoparticle assemblies can be understood in terms of the phase behavior of complex fluids, with the colloidal gold interaction potential dominated by DNA hybridization energies.

We present direct evidence for a reversible phase transition of DNA-linked colloidal gold assemblies. Transmission electron microscopy and optical absorption spectroscopy are used to monitor the colloidal gold phase transition, whose behavior is dominated by DNA interactions. We use single-stranded DNA-capped colloidal gold that is linked by complementary linker DNA to form the assemblies. We found that, compared to free DNA, a sharp melting transition is observed for the DNA-linked colloidal gold assemblies. The structure of the assemblies is non-crystalline, much like a gel phase, consistent with theoretical predictions. Optical spectra and melting curves provide additional evidence of gelation of the colloidal system. The phase transition and separation are examples of percolation in a dilute solvent., 9 pages, 6 figures, Physica A (2005) to appear. Updated figures

Single-molecule manipulation techniques provide a unique tool for a close-up investigation of the complex biological properties and interactions. During the force measurement, a single molecule is pulled while its force response is monitored. However, quantifying these non-equilibrium data and using them to understand the structure-function relationship of biological systems have been challenging. We describe the mechanics of nanoscale biomolecules and the use of these force measurements for the free energy reconstruction using the recently derived non-equilibrium work theorem, i.e., Jarzynski’s equality. We also compare the results with those from other phenomenological approaches. Finally, mechanical characterization of systems such as overstretching transitions of DNA are presented, and the implications and challenges of these single-molecule force studies are discussed.

Single-molecule force measurement opens a new door for investigating detailed biomolecular interactions and their thermodynamic properties by pulling molecules apart while monitoring the force exerted on them. Recent advances in the nonequilibrium work theorem allows one to determine the free-energy landscapes of these events. Such information is valuable for understanding processes such as protein and RNA folding and receptor-ligand binding. Here, we used force as a physical parameter under the traditional chemical and temperature denaturing environment to alter the protein folding energy landscape and compared the change in the unfolding free-energy barrier of the I27 domain of human cardiac titin. We found that the trends in protein unfolding free-energy barriers are consistent for single-molecule force measurements and bulk chemical and temperature studies. The results suggest that the information from single-molecule pulling experiments are meaningful and useful for understanding the mechanism of folding of titin I27.

Single-molecule manipulation studies can provide quantitative information about the physical properties of complex biological molecules without ensemble artifacts obscuring the measurements. We demonstrate computational techniques which aim at more fully utilizing the wealth of information contained in noisy experimental time series. The "noise" comes from multiple sources e.g., inherent thermal motion, instrument measurement error, etc. The primary focus of this paper is a methodology that uses time domain based methods to extract the effective molecular friction from single-molecule pulling data. We studied molecules composed of eight tandem repeat titin I27 domains, but the modeling approaches have applicability to other single-molecule mechanical studies. The merits and challenges associated with applying such a computational approach to existing single-molecule manipulation data are also discussed.

When analyzing single-molecule data, a low-dimensional set of system observables typically serves as the observational data. We calibrate stochastic dynamical models from time series that record such observables. Numerical techniques for quantifying noise from multiple time scales in a single trajectory, including experimental instrument and inherent thermal noise, are demonstrated. The techniques are applied to study time series coming from both simulations and experiments associated with the nonequilibrium mechanical unfolding of titin's I27 domain. The estimated models can be used for several purposes, (1) detect dynamical signatures of "rare events" by analyzing the effective diffusion and force as a function of the monitored observable, (2) quantify the influence that conformational degrees of freedom, which are typically difficult to directly monitor experimentally, have on the dynamics of the monitored observable, (3) quantitatively compare the inherent thermal noise to other noise sources, for example, instrument noise, variation induced by conformational heterogeneity, and so forth, (4) simulate random quantities associated with repeated experiments, and (5) apply pathwise, that is, trajectory-wise, hypothesis tests to assess the goodness-of-fit of the models and even detect conformational transitions in noisy signals. These items are all illustrated with several examples.

We studied the velocity dependence of mechanical unfolding of single protein molecules with the atomic force microscope. We showed that with enough realizations, the free energy surfaces reconstructed from Jarzynski's equality converge with respect to pulling velocity, in good agreement with theory. Using the I27 domain of titin as an example, we estimated the required number of realizations for a given pulling velocity, and suggested the optimal range of velocities for single-molecule experiments. The results demonstrate that Jarzynski's equality is a powerful and practical tool for reconstructing free energy landscapes.

We used the atomic force microscope to manipulate and unfold individual molecules of the titin I27 domain and reconstructed its free energy surface using Jarzynski's equality. The free energy surface for both stretching and unfolding was reconstructed using an exact formula that relates the nonequilibrium work fluctuations to the molecular free energy. In addition, the unfolding free energy barrier, i.e. the activation energy, was directly obtained from experimental data for the first time. This work demonstrates that Jarzynski's equality can be used to analyze nonequilibrium single-molecule experiments, and to obtain the free energy surfaces for molecular systems, including interactions for which only nonequilibrium work can be measured., 4 pages, 3 figures. Phys. Rev. Lett. (2007) accepted

DNA-gold nanoparticle assemblies have shown promise as an alternative technology to DNA microarrays for DNA detection and RNA profiling. Understanding the effect of DNA sequences on the melting temperature of the system is central to developing reliable detection technology. We studied the effects of DNA base-pairing defects, such as mismatches and deletions, on the melting temperature of DNA-nanoparticle assemblies. We found that, contrary to the general assumption that defects lower the melting temperature of DNA, some defects increase the melting temperature of DNA-linked nanoparticle assemblies. The effects of mismatches and deletions were found to depend on the specific base pair, the sequence, and the location of the defects. Our results demonstrate that the surface-bound DNA exhibit hybridization behavior different from that of free DNA. Such findings indicate that a detailed understanding of DNA-nanoparticle assembly phase behavior is required for quantitative interpretation of DNA-nanoparticle aggregation., 12 pages, 3 figures

We report experimental observations on the effect of disorder on the phase behavior of DNA-linked nanoparticle assemblies. Variation in DNA linker lengths results in different melting temperatures of the DNA-linked nanoparticle assemblies. We observed an unusual trend of a non-monotonic ``zigzag'' pattern in the melting temperature as a function of DNAlinker length. Linker DNA resulting in unequal DNA duplex lengths introduces disorder and lowers the melting temperature of the nanoparticle system. Comparison with free DNA thermodynamics shows that such an anomalous zigzag pattern does not exist for free DNA duplex melting, which suggests that the disorder introduced by unequal DNA duplex lengths results in this unusual collective behavior of DNA-linked nanoparticle assemblies., 4 pages, 4 figures, Phys.Rev.Lett. (2005), to appear

DNA melting and hybridization is a fundamental biological process as well as a crucial step in many modern biotechnology applications. DNA confined on surfaces exhibits different behavior from that in free solutions. The system of DNA-capped gold nanoparticles exhibits unique phase transitions and represents a new class of complex fluids. Depending on the sequence of the DNA, particles can be linked to each other through direct complementary DNA sequences or via a ``linker'' DNA whose sequence is complementary to the sequence attached to the gold nanoparticles. We observed different melting transitions for these two distinct systems., Comment: 6 pages, 4 figures, Physica A (2005) to appear

Mechanical force is present in all aspects of living systems. It affects the conformation of molecules, the shape of cells, and the morphology of tissues. All of these are crucial in architecture-dependent biological functions. Nanoscience of advanced materials has provided knowledge and techniques that can be used to understand how mechanical force is involved in biological systems, as well as to open new avenues to tailor-made bio-mimetic materials with desirable properties. In this article, we describe models and show examples of how force is involved in molecular functioning, cell shape patterning, and tissue morphology.