Diffusion in an elastic medium: A model for macromolecule transport across the nuclear pore complex

Nuclear pore complexes (NPCs) are very selective filters that sit on the membrane of the nucleus and monitor the transport between the cytoplasm and the nucleoplasm. For the central plug of NPC two models have been suggested in the literature. The first suggests that the plug is a reversible hydrogel while the other suggests that it is a polymer brush. Here we propose a model for the transport of a protein through the plug, which is general enough to cover both the models. The protein stretches the plug and creates a local deformation, which together with the protein, we refer to as the bubble. We start with the free energy for creation of the bubble and consider its motion within the plug. The relevant coordinate is the center of the bubble which executes random walk. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. (C) 2014 Elsevier-B.V. All rights reserved.

Allosteric Transition Induced by Mg2+ Ion in a Transactivator Monitored by SERS

We demonstrate the utility of the surface-enhanced Raman spectroscopy (SERS) to monitor conformational transitions in protein upon ligand binding. The changes in protein's secondary and tertiary structures were monitored using amide and aliphatic/aromatic side chain vibrations. Changes in these bands are suggestive of the stabilization of the secondary and tertiary structure of transcription activator protein C in the presence of Mg2+ ion, whereas the spectral fingerprint remained unaltered in the case of a mutant protein, defective in Mg2+ binding. The importance of the acidic residues in Mg2+ binding, which triggers an overall allosteric transition in the protein, is visualized in the molecular model. The present study thus opens up avenues toward the application of SERS as a potential tool for gaining structural insights into the changes occurring during conformational transitions in proteins.

Organic fragments from graphene oxide: Isolation, characterization and solvent effects

As-prepared graphene oxide (GO) contains oxidative debris which can be washed using basic solutions. We present the isolation and characterization of these debris. Dynamic light scattering (DLS) is used to monitor the separation of the debris in various solvents in the presence of different protic and aprotic alkylamino bases. The study reveals that the debris are rich in carbonyl functional groups and water is an essential component for separation and removal of the debris from GO under oxidative reaction conditions.

Terbium(III)-cholate functionalized vesicles as luminescent indicators for the enzymatic conversion of dihydroxynaphthalene diesters

The phosphorescence intensity of unilamellar DOPC vesicles with embedded Tb3+-cholate complexes depends on the concentration of dihydroxynaphthalene (DHN) as sensitizer in solution. This was used to monitor the enzymatic conversion of DHN esters or DHN glucosides by enzymes in aqueous buffered solution.

In vitro exposure of tobacco specific nitrosamines decreases the rat lung phospholipids by enhanced phospholipase A(2) activity

Tobacco-specific nitrosamines (TSNA) have implications in the pathogenesis of various lung diseases and conditions are prevalent even in non-smokers. N-nitrosonornicotine (NNN) and 4-(methyl nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) are potent pulmonary carcinogens present in tobacco product and are mainly responsible for lung cancer. TSNA reacts with pulmonary surfactants, and alters the surfactant phospholipid. The present study was undertaken to investigate the in vitro exposure of rat lung tissue slices to NNK or NNN and to monitor the phospholipid alteration by P-32]orthophosphate labeling. Phospholipid content decreased significantly in the presence of either NNK or NNN with concentration and time dependent manner. Phosphatidylcholine (PC) is the main phospholipid of lung and significant reduction was observed in PC similar to 61%, followed by phosphatidylglycerol (PG) with 100 mu M of NNK, whereas NNN treated tissues showed a reduction in phosphatidylserine (PS) similar to 60% and PC at 250 mu M concentration. The phospholipase A(2) assays and expression studies reveal that both compounds enhanced phospholipid hydrolysis, thereby reducing the phospholipid content. Collectively, our data demonstrated that both NNK and NNN significantly influenced the surfactant phospholipid level by enhanced phospholipase A(2) activity. (C) 2014 Elsevier Ltd. All rights reserved.

Optimal error estimate using mesh equidistribution technique for singularly perturbed system of reaction-diffusion boundary-value problems

In this article, we study the problem of determining an appropriate grading of meshes for a system of coupled singularly perturbed reaction-diffusion problems having diffusion parameters with different magnitudes. The central difference scheme is used to discretize the problem on adaptively generated mesh where the mesh equation is derived using an equidistribution principle. An a priori monitor function is obtained from the error estimate. A suitable a posteriori analogue of this monitor function is also derived for the mesh construction which will lead to an optimal second-order parameter uniform convergence. We present the results of numerical experiments for linear and semilinear reaction-diffusion systems to support the effectiveness of our preferred monitor function obtained from theoretical analysis. (C) 2014 Elsevier Inc. All rights reserved.

Noise Detected NMR Spectroscopy

Spin noise phenomenon was predicted way back in 1946. However, experimental investigations regarding spin noise became possible only recently with major technological improvements in NMR hardware. These experiments have several potential novel applications and also demand refinements in the existing theoretical framework to explain the phenomenon. Elegance of noise spectroscopy in gathering information about the properties of a system lies in the fact that it does not require external perturbation, and the system remains in thermal equilibrium. Spin noise is intrinsic magnetic fluctuations, and both longitudinal and transverse components have been detected independently in many systems. Detection of fluctuating longitudinal magnetization leads to field of Magnetic Resonance Force Microscopy (MRFM) that can efficiently probe very few spins even down to the level of single spin utilizing ultrasensitive cantilevers. Transverse component of spin noise, which can simultaneously monitor different resonances over a given frequency range enabling one to distinguish between different chemical environments, has also received considerable attention, and found many novel applications. These experiments demand a detailed understanding of the underlying spin noise phenomenon in order to perform perturbation-free magnetic resonance and widen the highly promising application area. Detailed investigations of noise magnetization have been performed recently using force microscopy on equilibrium ensemble of paramagnetic alkali atoms. It was observed that random fluctuations generate spontaneous spin coherences which has similar characteristics as generated by macroscopic magnetization of polarized ensemble in terms of precession and relaxation properties. Several other intrinsic properties like g-factors, isotope-abundance ratios, hyperfine splitting, spin coherence lifetimes etc. also have been achieved without having to excite the sample. In contrast to MRFM-approaches, detection of transverse spin noise also offers novel applications, attracting considerable attention. This has unique advantage as different resonances over a given frequency range enable one to distinguish between different chemical environments. Since these noise signatures scale inversely with sample size, these approaches lead to the possibility of non-perturbative magnetic resonance of small systems down to nano-scale. In this review, these different approaches will be highlighted with main emphasis on transverse spin noise investigations.

Adaptive mesh generation for singularly perturbed fourth-order ordinary differential equations

In this paper, we consider a singularly perturbed boundary-value problem for fourth-order ordinary differential equation (ODE) whose highest-order derivative is multiplied by a small perturbation parameter. To solve this ODE, we transform the differential equation into a coupled system of two singularly perturbed ODEs. The classical central difference scheme is used to discretize the system of ODEs on a nonuniform mesh which is generated by equidistribution of a positive monitor function. We have shown that the proposed technique provides first-order accuracy independent of the perturbation parameter. Numerical experiments are provided to validate the theoretical results.

Design and Testing of a Control System for Supply Side Electrical Load Management

India's energy demand is increasing rapidly with the intensive growth of economy. The electricity demand in India exceeded the availability, both in terms of base load energy and peak availability. The efficient use of energy source and its conversion and utilizations are the viable alternatives available to the utilities or industry. There are essentially two approaches to electrical energy management. First at the supply / utility end (Supply Side Management or SSM) and the other at the consumer end (Demand Side Management or DSM). This work is based on Supply Side Management (SSM) protocol and consists of design, fabrication and testing of a control device that will be able to automatically regulate the power flow to an individual consumer's premise. This control device can monitor the overuse of electricity (above the connected load or contracted demand) by the individual consumers. The present project work specially emphasizes on contract demand of every consumer and tries to reduce the use beyond the contract demand. This control unit design includes both software and hardware work and designed for 0.5 kW contract demand. The device is tested in laboratory and reveals its potential use in the field.

Pulse transit time differential measurement by fiber Bragg grating pulse recorder

The present study reports a noninvasive technique for the measurement of the pulse transit time differential (PTTD) from the pulse pressure waveforms obtained at the carotid artery and radial artery using fiber Bragg grating pulse recorders (FBGPR). PTTD is defined as the time difference between the arrivals of a pulse pressure waveform at the carotid and radial arterial sites. The PTTD is investigated as an indicator of variation in the systolic blood pressure. The results are validated against blood pressure variation obtained from a Mindray Patient Monitor. Furthermore, the pulse wave velocity computed from the obtained PTTD is compared with the pulse wave velocity obtained from the color Doppler ultrasound system and is found to be in good agreement. The major advantage of the PTTD measurement via FBGPRs is that the data acquisition system employed can simultaneously acquire pulse pressure waveforms from both FBGPRs placed at carotid and radial arterial sites with a single time scale, which eliminates time synchronization complexity. (C) 2015 Society of Photo-Optical Instrumentation Engineers (SPIE)

Router Attack toward NoC-enabled MPSoC and Monitoring Countermeasures against such Threat

The growing number of applications and processing units in modern Multiprocessor Systems-on-Chips (MPSoCs) come along with reduced time to market. Different IP cores can come from different vendors, and their trust levels are also different, but typically they use Network-on-Chip (NoC) as their communication infrastructure. An MPSoC can have multiple Trusted Execution Environments (TEEs). Apart from performance, power, and area research in the field of MPSoC, robust and secure system design is also gaining importance in the research community. To build a secure system, the designer must know beforehand all kinds of attack possibilities for the respective system (MPSoC). In this paper we survey the possible attack scenarios on present-day MPSoCs and investigate a new attack scenario, i.e., router attack targeted toward NoC architecture. We show the validity of this attack by analyzing different present-day NoC architectures and show that they are all vulnerable to this type of attack. By launching a router attack, an attacker can control the whole chip very easily, which makes it a very serious issue. Both routing tables and routing logic-based routers are vulnerable to such attacks. In this paper, we address attacks on routing tables. We propose different monitoring-based countermeasures against routing table-based router attack in an MPSoC having multiple TEEs. Synthesis results show that proposed countermeasures, viz. Runtime-monitor, Restart-monitor, Intermediate manager, and Auditor, occupy areas that are 26.6, 22, 0.2, and 12.2 % of a routing table-based router area. Apart from these, we propose Ejection address checker and Local monitoring module inside a router that cause 3.4 and 10.6 % increase of a router area, respectively. Simulation results are also given, which shows effectiveness of proposed monitoring-based countermeasures.

After transition in a soft-walled microchannel

In comparison to the flow in a rigid channel, there is a multifold reduction in the transition Reynolds number for the flow in a microchannel when one of the walls is made sufficiently soft, due to a dynamical instability induced by the fluid-wall coupling, as shown by Verma & Kumaran (J. Fluid Mech., vol. 727, 2013, pp. 407-455). The flow after transition is characterised using particle image velocimetry in the x-y plane, where x is the streamwise direction and y is the cross-stream coordinate along the small dimension of the channel of height 0.2-0.3 mm. The flow after transition is characterised by a mean velocity profile that is flatter at the centre and steeper at the walls in comparison to that for a laminar flow. The root mean square of the streamwise fluctuating velocity shows a characteristic sharp increase away from the wall and a maximum close to the wall, as observed in turbulent flows in rigid-walled channels. However, the profile is asymmetric, with a significantly higher maximum close to the soft wall in comparison to that close to the hard wall, and the Reynolds stress is found to be non-zero at the soft wall, indicating that there is a stress exerted by fluid velocity fluctuations on the wall. The maximum of the root mean square of the velocity fluctuations and the Reynolds stress (divided by the fluid density) in the soft-walled microchannel for Reynolds numbers in the range 250-400, when scaled by suitable powers of the maximum velocity, are comparable to those in a rigid channel at Reynolds numbers in the range 5000-20 000. The near-wall velocity profile shows no evidence of a viscous sublayer for (y upsilon(*)/nu) as low as two, but there is a logarithmic layer for (y upsilon(*)/nu) up to approximately 30, where the von Karman constants are very different from those for a rigid-walled channel. Here, upsilon(*) is the friction velocity, nu is the kinematic viscosity and y is the distance from the soft surface. The surface of the soft wall in contact with the fluid is marked with dye spots to monitor the deformation and motion along the fluid-wall interface. Low-frequency oscillations in the displacement of the surface are observed after transition in both the streamwise and spanwise directions, indicating that the velocity fluctuations are dynamically coupled to motion in the solid.

Estimation of nonlinearities from pseudodynamic and dynamic responses of bridge structures using the Delay Vector Variance method

Analysis of the variability in the responses of large structural systems and quantification of their linearity or nonlinearity as a potential non-invasive means of structural system assessment from output-only condition remains a challenging problem. In this study, the Delay Vector Variance (DVV) method is used for full scale testing of both pseudo-dynamic and dynamic responses of two bridges, in order to study the degree of nonlinearity of their measured response signals. The DVV detects the presence of determinism and nonlinearity in a time series and is based upon the examination of local predictability of a signal. The pseudo-dynamic data is obtained from a concrete bridge during repair while the dynamic data is obtained from a steel railway bridge traversed by a train. We show that DVV is promising as a marker in establishing the degree to which a change in the signal nonlinearity reflects the change in the real behaviour of a structure. It is also useful in establishing the sensitivity of instruments or sensors deployed to monitor such changes. (C) 2015 Elsevier B.V. All rights reserved.

Study of H/D exchange rates to derive the strength of intramolecular hydrogen bonds in halo substituted organic building blocks: An NMR spectroscopic investigation

Rates of hydrogen/deuterium (H/D) exchange determined by H-1 NMR spectroscopy are utilized to derive the strength of hydrogen bonds and to monitor the electronic effects in the site-specific halogen substituted benzamides and anilines. The theoretical fitting of the time dependent variation of the integral areas of H-1 NMR resonances to the first order decay function permitted the determination of HID exchange rate constants (k) and their precise half-lives (t(1/2)) with high degree of reproducibility. The comparative study also permitted the unambiguous determination of relative strength of hydrogen bonds and the contribution from electronic effects on the HID exchange rate. (C) 2015 Elsevier B.V. All rights reserved.

Ultrasonic Guided Wave Sensor Network Optimization for Monitoring Rivet Line

Guided waves using piezo-electric wafer active sensors (PWAS) is one of the useful techniques of damage detection. Sensor network optimization with minimal network hardware footprint and maximal area of coverage remains a challenging problem. PWAS sensors are placed at discrete locations in order to inspect damages in plates and the idea has the potential to be extended to assembled structures. Various actuator-sensor configurations are possible within the network in order to identify and locate damages. In this paper we present a correlation based approach to monitor cracks emanating from rivet line using a simulated guided wave signal whose sensor is operating in pulse echo mode. Discussions regarding the identification of phase change due to reflections from the crack are also discussed in this paper.