Influence of electric field intensity, ionic strength, and migration distance on the mobility and diffusion in DNA surface electrophoresis

In order to increase the separation rate of surface electrophoresis while preserving the resolution for large DNA chains, e.g., genomic DNA, the mobility and diffusion of Lambda DNA chains adsorbed on flat silicon substrate under an applied electric field, as a function of migration distance, ionic strength, and field intensity, were studied using laser fluorescence microscope. The mobility was found to follow a power law with the field intensity beyond a certain threshold. The detected DNA peak width was shown to be constant with migration distance, slightly smaller with stronger field intensity, but significantly decreased with higher ionic strength. The molecular dynamics simulation demonstrated that the peak width was strongly related with the conformation of DNA chains adsorbed onto surface. The results also implied that there was no diffusion of DNA during migration on surface. Therefore, the Nernst-Einstein relation is not valid in the surface electrophoresis and the separation rate could be improved without losing resolution by decreasing separation distance, increasing buffer concentration, and field intensity. The results indicate the fast separation of genomic DNA chains by surface electrophoresis is possible.     

Two-dimensional spectral shearing interferometry for few-cycle pulse characterization

We present a new method for measuring the spectral phase of ultrashort pulses that utilizes spectral shearing interferometry with zero delay. Unlike conventional spectral phase interferometry for direct electric-field reconstruction, which encodes phase as a sensitively calibrated fringe in the spectral domain, two-dimensional spectral shearing interferometry robustly encodes phase along a second dimension. This greatly reduces demands on the spectrometer and allows for complex phase spectra to be measured over extremely large bandwidths, potentially exceeding 1.5 octaves.     

Impact of interstitial air holes on a wide-bandwidth rejection filter made from a photonic crystal fiber

We have investigated the spectral properties of a band rejection filter made with a long-period fiber grating written in photonic crystal fiber that has interstitial air holes. Experiments showed that only one mode was coupled strongly to the fundamental core mode over a 600 nm spectral range. The central wavelength of the filter could be tuned over that range without being appreciably affected by any other mode. By using the multipole method, we found that the interstitial air holes of the photonic crystal fiber played a critical role in limiting the number of modes that could strongly interact with the fundamental mode and in obtaining well-separated resonance peaks. Excellent agreement between theory and experiment was obtained.     

Measuring inter-pulse intervals in sperm whale clicks: consistency of automatic estimation methods

Sperm whale clicks are characterized by a multi-pulsed structure. The time lag between consecutive pulses, i.e., the inter-pulse interval (IPI), is related to the size of the sound production organ such that its measurement provides a means to acoustically estimate the size of individual whales. Due to off-axis effects the identification of pulses is, however, not always straightforward, and automatic measurement methods provide not only more objective estimation, but may also facilitate IPI estimation in cases where single click measurements are ambiguous. In particular, averaging measurements over a time series of clicks from the same whale could enhance the discrimination of time invariant pulses. The authors developed two automatic methods of automatic IPI measurement based on waveform and autocorrelation averaging and compared their accuracy and consistency with other previously used methods. Manual measurement by an experienced operator provided the most self-consistent estimates. The autocorrelation averaging technique had the best overall performance of the automated methods achieving a very similar performance to manual measurement. On some recordings cepstrum averaging methods converged when autocorrelation did not. Therefore, applying both of these automated methods and choosing the best of the two are recommended.     

Wave-modulated orbits in rate-and-state friction

A frictional spring-block system has been widely used historically as a model to display some of the features of two slabs in sliding frictional contact. Putelat et al. (2008) [7] demonstrated that equations governing the sliding of two slabs could be approximated by spring-block equations, and studied relaxation oscillations for two slabs driven by uniform relative motion at their outer surfaces, employing this approximation. The present work revisits this problem. The equations of motion are first formulated exactly, with full allowance for wave reflections. Since the sliding is restricted to be independent of position on the interface, this leads to a set of differential-difference equations in the time domain. Formal but systematic asymptotic expansions reduce the equations to differential equations. Truncation of the differential system at the lowest non-trivial order reproduces a classical spring-block system, but with a slightly different “equivalent mass” than was obtained in the earlier work. Retention of the next term gives a new system, of higher order, that contains also some explicit effects of wave reflections. The smooth periodic orbits that result from the spring-block system in the regime of instability of steady sliding are “decorated” by an oscillation whose period is related to the travel time of the waves across the slabs. The approximating differential system reproduces this effect with reasonable accuracy when the mean sliding velocity is not too far from the critical velocity for the steady state. The differential system also displays a period-doubling bifurcation as the mean sliding velocity is increased, corresponding to similar behaviour of the exact differential-difference system.     

Experimental validation of a dynamic resonant wall shear stress sensor

Experimental measurements are used to validate a numerical model of a dynamic resonant wall shear stress sensor. The numerical model consists of an unsteady two-dimensional boundary-layer model for the flow and a simple mechanical model for the sensor itself. The sensor’s sensitivity to wall shear stress is experimentally determined in a flat-plate boundary layer, and the results agree closely with those from the numerical simulations. Using the validated model, it is determined that the energy lost in each sensor oscillation due to the interaction between the sensor and fluid increases with increasing mean wall shear stress.     

Multi-scale interactions in a compressible boundary layer

The properties of spectral subranges of scales in a boundary layer at Mach=2.3 and friction Reynolds number Reτ = 570 are investigated by analysing DNS data. One major aim is to examine whether footprinting and modulation of small-scale near-wall motions by outer large structures, observed at high Reynolds numbers, also pertain to this low-Reynolds-number case, or whether the logarithmic layer simply contains a continuous hierarchy of motions without specific outer scales playing a distinctive role. To this end, the spectrum of scales is decomposed into modes by application of the “Empirical Mode Decomposition”. The properties of different scales are then investigated by means of spectra, maps of isotropy/anisotropy parameters, the premultiplied derivative of the second-order structure function, correlation coefficients and joint probability density function (PDF), the last constructed from conditionally sampled data for the small-scale motions within the large-scale footprints. A clear commonality is identified between interactions in high-Reynolds-number channel flow and the present low-Reynolds-number boundary layer.     

Statistical Examination of the <Emphasis Type="Italic">a</Emphasis> and <Emphasis Type="Italic">a</Emphasis> + 1 Fragment Ions from 193 nm Ultraviolet Photodissociation Reveals Local Hydrogen Bonding Interactions

Dissociation of proteins and peptides by 193 nm ultraviolet photodissociation (UVPD) has gained momentum in proteomic studies because of the diversity of backbone fragments that are produced and subsequent unrivaled sequence coverage obtained by the approach. The pathways that form the basis for the production of particular ion types are not completely understood. In this study, a statistical approach is used to probe hydrogen atom elimination from a + 1 radical ions, and different extents of elimination are found to vary as a function of the identity of the C-terminal residue of the a product ions and the presence or absence of hydrogen bonds to the cleaved residue.

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Negative Ions Enhance Survival of Membrane Protein Complexes

Membrane protein complexes are commonly introduced to the mass spectrometer solubilized in detergent micelles. The collisional activation used to remove the detergent, however, often causes protein unfolding and dissociation. As in the case for soluble proteins, electrospray in the positive ion mode is most commonly used for the study of membrane proteins. Here we show several distinct advantages of employing the negative ion mode. Negative polarity can yield lower average charge states for membrane proteins solubilized in saccharide detergents, with enhanced peak resolution and reduced adduct formation. Most importantly, we demonstrate that negative ion mode electrospray ionization (ESI) minimizes subunit dissociation in the gas phase, allowing access to biologically relevant oligomeric states. Together, these properties mean that intact membrane protein ions can be generated in a greater range of solubilizing detergents. The formation of negative ions, therefore, greatly expands the possibilities of using mass spectrometry on this intractable class of protein.

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Metallization of cyanide-modified Pt(111) electrodes with copper

Journal of Solid State Electrochemistry - The reduction of Cu2+ ions irreversibly attached to the surface of a cyanide-modified Pt(111) electrode via non-covalent or weakly covalent interactions...