Stretching DNA using the electric field in a synthetic nanopore

The mechanical properties of DNA over segments comparable to the size of a protein-binding site (3-10 nm) are examined using an electric-field-induced translocation of single molecules through a nanometer diameter pore. DNA, immersed in an electrolyte, is forced through synthetic pores ranging from 0.5 to 1.5 nm in radius in a 10 nm thick Si(3)N(4) membrane using an electric field. To account for the stretching and bending, we use molecular dynamics to simulate the translocation. We have found a threshold for translocation that depends on both the dimensions of the pore and the applied transmembrane bias. The voltage threshold coincides with the stretching transition that occurs in double-stranded DNA near 60 pN.     

The effect of document types and sizes on the scaling relationship between citations and co-authorship patterns in management journals

The aim of this paper is to explore the power-law relationship between citation-based performance (CBP) and co-authorship patterns for papers in management journals by analyzing its behavior according to the type of documents (articles and reviews) and the number of pages of documents. We analyzed 36,241 papers that received 239,172 citations. The scaling exponent of CBP for article papers was larger than for reviews. Citations to articles increased 2^1.67 or 3.18 times each time the number of article papers published in a year in management journals doubled. The citations to reviews increased 2^1.29 or 2.45 times each time the number of reviews published in a year in management journals doubled. The scaling exponent for the power-law relationship of citation-based performance according to number of pages of papers was 1.44 ± 0.05 for articles and 1.25 ± 0.05 for reviews. The citations to articles increased faster than citation to reviews. The scaling exponent for the power-law of citation-based performance to co-authored articles was higher than single-authored articles. For reviews the scaling exponent was the same for the relationship between citation based performance and the number of reviews. Citations increased faster in single authored reviews than co-authored reviews.     

Controlling DNA Tug‐of‐War in a Dual Nanopore Device

Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence‐specific features. A method is created for reducing and controlling the speed of DNA that uses two independently controllable nanopores operated with an active control logic. The pores are positioned sufficiently close to permit cocapture of a single DNA by both pores. Once cocapture occurs, control logic turns on constant competing voltages at the pores leading to a “tug‐of‐war” whereby opposing forces are applied to regions of the molecules threading through the pores. These forces exert both conformational and speed control over the cocaptured molecule, removing folds and reducing the translocation rate. When the voltages are tuned so that the electrophoretic force applied to both pores comes into balance, the life time of the tug‐of‐war state is limited purely by diffusive sliding of the DNA between the pores. A tug‐of‐war state is produced on 76.8% of molecules that are captured with a maximum two‐order of magnitude increase in average pore translocation time relative to the average time for single‐pore translocation. Moreover, the translocation slow‐down is quantified as a function of voltage tuning and it is shown that the slow‐down is well described by a first passage analysis for a 1D subdiffusive process. The ionic current of each nanopore provides an independent sensor that synchronously measures a different region of the same molecule, enabling sequential detection of physical labels, such as monostreptavidin tags. With advances in devices and control logic, future dual‐pore applications include genome mapping and enzyme‐free sequencing.     

Frictionless sliding of single-stranded DNA in a carbon nanotube pore observed by single molecule force spectroscopy

Smooth inner pores of carbon nanotubes (CNT) provide a fascinating model for studying biological transport. We used an atomic force microscope to pull a single-stranded DNA oligomer from a carbon nanotube pore. DNA extraction from CNT pores occurs at a nearly constant force, which is drastically different from the elastic profile commonly observed during polymer stretching with atomic force microscopy. We show that a combination of the frictionless nanotube pore walls and an unfavorable DNA solvation energy produces this constant force profiles.     

Single-strand DNA molecule translocation through nanoelectrode gaps

Molecular dynamics simulations were performed to investigate the translocation of single-strand DNA through nanoscale electrode gaps under the action of a constant driving force. The application behind this theoretical study is a proposal to use nanoelectrodes as a screening gap as part of a rapid genomic sequencing device. Preliminary results from a series of simulations using various gap widths and driving forces suggest that the narrowest electrode gap that a single-strand DNA can pass is ～1.5?nm. The minimum force required to initiate the translocation within nanoseconds is ～0.3?nN. Simulations using DNA segments of various lengths indicate that the minimum initiation force is insensitive to the length of DNA. However, the average threading velocity of DNA varies appreciably from short to long DNA segments. We attribute such variation to the different nature of drag force experienced by the short and long DNA segments in the environment. It?is found that DNA molecules deform significantly to fit in the shape of the nanogap during the translocation.     

Creep of Driven Flux Lines in Type-II Superconductors

The creep motions of flux lines in both Bragg glass (BrG) and vortex glass (VG) are studied. The power-law dependence of the creep activation barrier on the driving force is obtained. Two universal classes of creep motion are found with the exponent μ=0.5±0.02 for the BrG and μ=0.28±0.02 for the VG. The former is in good agreement with the prediction by the scaling theory and the functional-renormalization-group theory on creep, while the latter is a new estimate. The different dynamics of flux lines in the VG and in the BrG are investigated accordingly.     

Nanopore translocation dynamics of a single DNA-bound protein

We study the translocation dynamics of a single protein molecule attached to a double-stranded DNA that is threaded through a solid-state nanopore by optical tweezers and an electric field (nanopore force spectroscopy). We find distinct asymmetric and retarded force signals that depend on the protein charge, the DNA elasticity and its counterionic screening in the buffer. A theoretical model where an isolated charge on an elastic, polyelectrolyte strand is experiencing an anharmonic nanopore potential was developed. Its results compare very well with the measured force curves and explain the experimental findings that the force depends linearly on the applied electric field and exhibits a small hysteresis during back and forth translocation cycles. Moreover, the translocation dynamics reflects the stochastic nature of the thermally activated hopping between two adjacent states in the nanopore that can be adequately described by Kramers rate theory.     

The scaling relationship between degree centrality of countries and their citation-based performance on Management Information Systems

The aim of this paper is to explore the power-law relationship between the degree centrality of countries and their citation-based performance in Management Information Systems research. We analyzed 27,662 articles that received 127,974 citations. The distribution of the citation-based performance follows a power law with exponent of ?2.46 ± 0.05. The distribution of the centrality degree of countries follows a power law with exponent of ?2.26 ± 0.24. The citation-based performance and degree centrality exhibited a power-law correlation with a scaling exponent of 1.22 ± 0.04. Citations to the articles of a country in MIS tend to increase 2^1.22 or 2.33 times each time it doubles its degree centrality in the international collaborative network. Policies that encourage a country to increase its degree centrality in a collaboration network can disproportionately increase the impact of its research.     

Salt dependence of ion transport and DNA translocation through solid-state nanopores

We report experimental measurements of the salt dependence of ion transport and DNA translocation through solid-state nanopores. The ionic conductance shows a three-order-of-magnitude decrease with decreasing salt concentrations from 1 M to 1 muM, strongly deviating from bulk linear behavior. The data are described by a model that accounts for a salt-dependent surface charge of the pore. Subsequently, we measure translocation of 16.5-mum-long dsDNA for 50 mM to 1 M salt concentrations. DNA translocation is shown to result in either a decrease ([KCl] > 0.4 M) or increase of the ionic current ([KCl] < 0.4 M). The data are described by a model where current decreases result from the partial blocking of the pore and current increases are attributed to motion of the counterions that screen the charge of the DNA backbone. We demonstrate that the two competing effects cancel at a KCl concentration of 370 +/- 40 mM.     

Structural geometry effect on the size-scaling of strength

The sensitivity of the empirical exponent of Bazant's size-effect scaling law on structural geometry is clarified through numerical experiments. For large centre- cracked tension panels, made of a linearly softening material, the best-fitting exponent is 0.90, whereas for large edge-cracked panels it is 0.75. For edge-cracked panels, the value of the exponent increases as a function of increasing crack-length-to-width-ratio. The results indicate that with structures of brittleness numbers below unity, reliable predictions of strength require the size-effect scaling law to be fitted for any particular structural geometry.     

Effects of occlusion, edges, and scaling on the power spectra of natural images

The circularly averaged power spectra of natural image ensembles tend to have a power-law dependence on spatial frequency with an exponent of approximately -2. This phenomenon has been attributed to object occlusion, the presence of edges, and scaling of object sizes (self-similarity) in natural scenes, although the relative importance of these properties is still unclear. A detailed examination of the effects of occlusion, edges, and self-similarity on the behavior of the power spectrum is conducted using a simple model of natural images. Numerical simulations show that edges and self-similarity are necessary for a power-law power spectrum over a wide range of spatial frequencies. Object occlusion is not an essential factor. A theoretical analysis for images containing nonoccluding objects supports these results.     

Ultrasonic attenuation based on the Roney generalized theory andmultiple power-law grain-size distributions

We investigate ultrasonic attenuation as a nondestructive determination of grain-size distributions. Previous work showed power-law relationships between the wavelength dependence of ultrasonic attenuation and a single power-law grain-size distribution, along with experimental verification. The work presented here further validates the previously reported relationship for single power-law grain-size distributions, and generalizes the relationships to cases where the grain-size distribution follows multiple power-laws. Roney's generalized approach to ultrasonic attenuation is used. Numerical results are presented for the single power-law and multiple power-law cases. The attenuation exponents computed from the numerical calculations correspond well with theoretical expectations. For wavelengths greater than all the grain sizes, Rayleigh scattering dominates and the attenuation exponent approaches 4. For single power-laws and wavelengths between the smallest and largest grain size, the attenuation exponent equals the grain-size distribution exponent. When multiple power-laws are used to describe the grain-size distribution, the attenuation exponent is a combination of the grain-size distribution exponent, and therefore cannot be directly measured from the attenuation curve     

A Low-Field Scaling Rule of Minor Hysteresis Loops in Plastically Deformed Steels

A scaling rule of magnetic minor hysteresis loops at low applied fields has been examined in plastically deformed low carbon steel and pure Ni. It was found that a power law between hysteresis loss and remanence of a minor loop holds true over the wide range of magnetization from the very low to intermediate range unlike the well-known Steinmetz law. The power-law exponent was an almost constant value of 1.35 being independent of the types of magnetic materials, the level of plastic deformation, and sample shape. The coefficient of the scaling rule increases with deformation and is in linear proportion to coercivity. This behavior was qualitatively explained on the basis of the Rayleigh law and NÉel theory.      

Self-avoiding flexible polymers under spherical confinement

We compute the free energy of confinement for a flexible self-avoiding polymer inside a spherical cavity. Accurate numerical results allow us to arbitrate between three competing scaling predictions. For moderate confinement, the free energy exhibits a power-law dependence on cavity size that is different from what is observed for planar and cylindrical confinement. At high monomer concentrations, crossover to a different scaling regime is observed, consistent with the screening of the excluded-volume interactions. We demonstrate how our findings lead to a revised prediction for the escape time of a polymer from a spherical confinement.     

Fundamental mechanism of translocation across liquidlike membranes: toward control over nanoparticle behavior

We envision and theoretically investigate a novel behavior of a functionalized nanoparticle designed to translocate through a liquidlike membrane. We develop a statistical-mechanical approach to such a system. We predict a new mechanism for the opening of a circular energy-dominated pore on the membrane by a nanoparticle functionalized with a peptide aggregate. Following fluctuations in the position and orientation of the nanoparticle, the peptide aggregate incorporates into the membrane and locally destabilizes it. The nucleation of a pore centered at the peptide aggregate attached to the particle is a precursor to particle translocation. The subsequent opening of the pore is assisted by adhesion of the membrane to the particle. We determine the conditions in which thermal fluctuations in the membrane shape and the pore size can induce translocation of the particle. For different system parameters quantities such as the free energy, entropy, pore size, degree of particle wrapping, and the probability of spontaneous translocation are obtained.     

Lattice gas simulations of dynamical geometry in one dimension

We present numerical results obtained using a lattice gas model with dynamical geometry. The (irreversible) macroscopic behaviour of the geometry (size) of the lattice is discussed in terms of a simple scaling theory and obtained numerically. The emergence of irreversible behaviour from the reversible microscopic lattice gas rules is discussed in terms of the constraint that the macroscopic evolution be reproducible. The average size of the lattice exhibits power-law growth with exponent at late times. The deviation of the macroscopic behaviour from reproducibility for particular initial conditions ('rogue states') is investigated as a function of system size. The number of such 'rogue states' is observed to decrease with increasing system size. Two mean-field analyses of the macroscopic behaviour are also presented.     

Recapturing and trapping single molecules with a solid-state nanopore

The development of solid-state nanopores, inspired by their biological counterparts, shows great potential for the study of single macromolecules. Applications such as DNA sequencing and the exploration of protein folding require control of the dynamics of the molecule's interaction with the pore, but DNA capture by a solid-state nanopore is not well understood. By recapturing individual molecules soon after they pass through a nanopore, we reveal the mechanism by which double-stranded DNA enters the pore. The observed recapture rates and times agree with solutions of a drift-diffusion model. Electric forces draw DNA to the pore over micrometer-scale distances, and upon arrival at the pore, molecules begin translocation almost immediately. Repeated translocation of the same molecule improves measurement accuracy, offers a way to probe the chemical transformations and internal dynamics of macromolecules on sub-millisecond time and sub-micrometre length scales, and demonstrates the ability to trap, study and manipulate individual macromolecules in solution.     

Hybrid pore formation by directed insertion of α-haemolysin into solid-state nanopores

Most experiments on nanopores have concentrated on the pore-forming protein α-haemolysin (αHL) and on artificial pores in solid-state membranes. While biological pores offer an atomically precise structure and the potential for genetic engineering, solid-state nanopores offer durability, size and shape control, and are also better suited for integration into wafer-scale devices. However, each system has significant limitations: αHL is difficult to integrate because it relies on delicate lipid bilayers for mechanical support, and the fabrication of solid-state nanopores with precise dimensions remains challenging. Here we show that these limitations may be overcome by inserting a single αHL pore into a solid-state nanopore. A double-stranded DNA attached to the protein pore is threaded into a solid-state nanopore by electrophoretic translocation. Protein insertion is observed in 30-40% of our attempts, and translocation of single-stranded DNA demonstrates that the hybrid nanopore remains functional. The hybrid structure offers a platform to create wafer-scale device arrays for genomic analysis, including sequencing.     

Experimental and computational study of the effect of the system size on rough surfaces formed by sedimenting particles in quasi-two-dimensions

The roughness exponent of surfaces obtained by dispersing silica spheres through a viscous fluid in a quasi-two-dimensional cell is examined using experimental and computational methods. The cell consists of two glass plates separated by a gap which is comparable in size to the diameter of the beads. We have studied the effect of changing the gap between the plates to a limit of about twice the diameter of the beads. If a conventional scaling analysis is performed, the roughness exponent is found to be robust against changes in the gap between the plates. The surfaces formed have two roughness exponents in two length scales, which have a crossover length of about 1 cm.; however, the computational results do not show the same crossover behavior. The single exponent obtained from the simulations stays between the two roughness exponents obtained in the experiments.     

Controlled translocation of individual DNA molecules through protein nanopores with engineered molecular brakes

Protein nanopores may provide a cheap and fast technology to sequence individual DNA molecules. However, the electrophoretic translocation of ssDNA molecules through protein nanopores has been too rapid for base identification. Here, we show that the translocation of DNA molecules through the α-hemolysin protein nanopore can be slowed controllably by introducing positive charges into the lumen of the pore by site directed mutagenesis. Although the residual ionic current during DNA translocation is insufficient for direct base identification, we propose that the engineered pores might be used to slow down DNA in hybrid systems, for example, in combination with solid-state nanopores.