The stretching of single poly-ubiquitin molecules: Static versus dynamic disorder in the non-exponential kinetics of chain unfolding

Static disorder has recently been implicated in the non-exponential kinetics of the unfolding of single molecules of poly-ubiquitin under a constant force Kuo, Garcia-Manyes, Li, Barel, Lu, Berne, Urbakh, Klafter, and Fernandez, Proc. Natl. Acad. Sci. U. S. A. 107, 11336 (2010)]. In the present paper, it is suggested that dynamic disorder may provide a plausible, alternative description of the experimental observations. This suggestion is made on the basis of a model in which the barrier to chain unfolding is assumed to be modulated by a control parameter r that evolves in a parabolic potential under the action of fractional Gaussian noise according to a generalized Langevin equation. The treatment of dynamic disorder within this model is pursued using Zwanzig's indirect approach to noise averaging Acc. Chem. Res. 23, 148 (1990)]. In conjunction with a self-consistent closure scheme developed by Wilemski and Fixman J. Chem. Phys. 58, 4009 (1973); ibid. 60, 866 (1974)], this approach eventually leads to an expression for the chain unfolding probability that can be made to fit the corresponding experimental data very closely. (C) 2011 American Institute of Physics.

Instability, intermittency, and multiscaling in discrete growth models of kinetic roughening

We show by numerical simulations that discretized versions of commonly studied continuum nonlinear growth equations (such as the Kardar-Parisi-Zhangequation and the Lai-Das Sarma-Villain equation) and related atomistic models of epitaxial growth have a generic instability in which isolated pillars (or grooves) on an otherwise flat interface grow in time when their height (or depth) exceeds a critical value. Depending on the details of the model, the instability found in the discretized version may or may not be present in the truly continuum growth equation, indicating that the behavior of discretized nonlinear growth equations may be very different from that of their continuum counterparts. This instability can be controlled either by the introduction of higher-order nonlinear terms with appropriate coefficients or by restricting the growth of pillars (or grooves) by other means. A number of such ''controlled instability'' models are studied by simulation. For appropriate choice of the parameters used for controlling the instability, these models exhibit intermittent behavior, characterized by multiexponent scaling of height fluctuations, over the time interval during which the instability is active. The behavior found in this regime is very similar to the ''turbulent'' behavior observed in recent simulations of several one- and two-dimensional atomistic models of epitaxial growth.

Statistical thermodynamics of lattice models in zeolites: Implications of local versus global mean field interactions

The statistical thermodynamics of adsorption in caged zeolites is developed by treating the zeolite as an ensemble of M identical cages or subsystems. Within each cage adsorption is assumed to occur onto a lattice of n identical sites. Expressions for the average occupancy per cage are obtained by minimizing the Helmholtz free energy in the canonical ensemble subject to the constraints of constant M and constant number of adsorbates N. Adsorbate-adsorbate interactions in the Brag-Williams or mean field approximation are treated in two ways. The local mean field approximation (LMFA) is based on the local cage occupancy and the global mean field approximation (GMFA) is based on the average coverage of the ensemble. The GMFA is shown to be equivalent in formulation to treating the zeolite as a collection of interacting single site subsystems. In contrast, the treatment in the LMFA retains the description of the zeolite as an ensemble of identical cages, whose thermodynamic properties are conveniently derived in the grand canonical ensemble. For a z coordinated lattice within the zeolite cage, with epsilon(aa) as the adsorbate-adsorbate interaction parameter, the comparisons for different values of epsilon(aa)(*)=epsilon(aa)z/2kT, and number of sites per cage, n, illustrate that for -1 0. We compare the isotherms predicted with the LMFA with previous GMFA predictions [K. G. Ayappa, C. R. Kamala, and T. A. Abinandanan, J. Chem. Phys. 110, 8714 (1999)] (which incorporates both the site volume reduction and a coverage-dependent epsilon(aa)) for xenon and methane in zeolite NaA. In all cases the predicted isotherms are very similar, with the exception of a small steplike feature present in the LMFA for xenon at higher coverages. (C) 1999 American Institute of Physics. [S0021-9606(99)70333-8].

Voltage and Temperature Scalable Standard Cell Leakage Models Based on Stacks for Statistical Leakage Characterization

With extensive use of dynamic voltage scaling (DVS) there is increasing need for voltage scalable models. Similarly, leakage being very sensitive to temperature motivates the need for a temperature scalable model as well. We characterize standard cell libraries for statistical leakage analysis based on models for transistor stacks. Modeling stacks has the advantage of using a single model across many gates there by reducing the number of models that need to be characterized. Our experiments on 15 different gates show that we needed only 23 models to predict the leakage across 126 input vector combinations. We investigate the use of neural networks for the combined PVT model, for the stacks, which can capture the effect of inter die, intra gate variations, supply voltage(0.6-1.2 V) and temperature (0 - 100degC) on leakage. Results show that neural network based stack models can predict the PDF of leakage current across supply voltage and temperature accurately with the average error in mean being less than 2% and that in standard deviation being less than 5% across a range of voltage, temperature.

Continuous-time Single Network Adaptive Critic for Regulator Design of Nonlinear Control Affine Systems

An optimal control law for a general nonlinear system can be obtained by solving Hamilton-Jacobi-Bellman equation. However, it is difficult to obtain an analytical solution of this equation even for a moderately complex system. In this paper, we propose a continuoustime single network adaptive critic scheme for nonlinear control affine systems where the optimal cost-to-go function is approximated using a parametric positive semi-definite function. Unlike earlier approaches, a continuous-time weight update law is derived from the HJB equation. The stability of the system is analysed during the evolution of weights using Lyapunov theory. The effectiveness of the scheme is demonstrated through simulation examples.

Improved parametric models and DPCM techniques for EGG data compiression

This paper presents a novel algorithm for compression of single lead Electrocardiogram (ECG) signals. The method is based on Pole-Zero modelling of the Discrete Cosine Transformed (DCT) signal. An extension is proposed to the well known Steiglitz-Hcbride algorithm, to model the higher frequency components of the input signal more accurately. This is achieved by weighting the error function minimized by the algorithm to estimate the model parameters. The data compression achieved by the parametric model is further enhanced by Differential Pulse Code Modulation (DPCM) of the model parameters. The method accomplishes a compression ratio in the range of 1:20 to 1:40, which far exceeds those achieved by most of the current methods.

Diffuse optical tomographic imager using a single light source

Near-infrared diffuse optical tomography (DOT) technique has the capability of providing good quantitative reconstruction of tissue absorption and scattering properties with additional inputs such as input and output modulation depths and correction for the photon leakage. We have calculated the two-dimensional (2D) input modulation depth from three-dimensional (3D) diffusion to model the 2D diffusion of photons. The photon leakage when light traverses from phantom to the fiber tip is estimated using a solid angle model. The experiments are carried for single (5 and 6 mm) as well as multiple inhomogeneities (6 and 8 mm) with higher absorption coefficient in a homogeneous phantom. Diffusion equation for photon transport is solved using finite element method and Jacobian is modeled for reconstructing the optical parameters. We study the development and performance of DOT system using modulated single light source and multiple detectors. The dual source methods are reported to have better reconstruction capabilities to resolve and localize single as well as multiple inhomogeneities because of its superior noise rejection capability. However, an experimental setup with dual sources is much more difficult to implement because of adjustment of two out of phase identical light probes symmetrically on either side of the detector during scanning time. Our work shows that with a relatively simpler system with a single source, the results are better in terms of resolution and localization. The experiments are carried out with 5 and 6 mm inhomogeneities separately and 6 and 8 mm inhomogeneities both together with absorption coefficient almost three times as that of the background. The results show that our experimental single source system with additional inputs such as 2D input/output modulation depth and air fiber interface correction is capable of detecting 5 and 6 mm inhomogeneities separately and can identify the size difference of multiple inhomogeneities such as 6 and 8 mm. The localization error is zero. The recovered absorption coefficient is 93% of inhomogeneity that we have embedded in experimental phantom.

A Revisit to Capture the Entire Behavior of Ultrasonic Wave Dispersion Characteristics of Single Walled Carbon Nanotubes Based on Nonlocal Elasticity Theory and Flugge Shell Model

In this paper, an ultrasonic wave propagation analysis in single-walled carbon nanotube (SWCNT) is re-studied using nonlocal elasticity theory, to capture the whole behaviour. The SWCNT is modeled using Flugge's shell theory, with the wall having axial, circumferential and radial degrees of freedom and also including small scale effects. Nonlocal governing equations for this system are derived and wave propagation analysis is also carried out. The revisited nonlocal elasticity calculation shows that the wavenumber tends to infinite at certain frequencies and the corresponding wave velocity tends to zero at those frequencies indicating localization and stationary behavior. This frequency is termed as escape frequency. This behavior is observed only for axial and radial waves in SWCNT. It has been shown that the circumferential waves will propagate dispersively at higher frequencies in nonlocality. The magnitudes of wave velocities of circumferential waves are smaller in nonlocal elasticity as compared to local elasticity. We also show that the explicit expressions of cut-off frequency depend on the nonlocal scaling parameter and the axial wavenumber. The effect of axial wavenumber on the ultrasonic wave behavior in SWCNTs is also discussed. The present results are compared with the corresponding results (for first mode) obtained from ab initio and 3-D elastodynamic continuum models. The acoustic phonon dispersion relation predicted by the present model is in good agreement with that obtained from literature. The results are new and can provide useful guidance for the study and design of the next generation of nanodevices that make use of the wave propagation properties of single-walled carbon nanotubes.

Thermodynamic Models for the Size-dependent Melting of Nanoparticles: Different Hypotheses

A careful comparison of the experimental results reported in the literature reveals different variations of the melting temperature even for the same materials. Though there are different theoretical models, thermodynamic model has been extensively used to understand different variations of size-dependent melting of nanoparticles. There are different hypotheses such as homogeneous melting (HMH), liquid nucleation and growth (LNG) and liquid skin melting (LSM) to resolve different variations of melting temperature as reported in the literature. HMH and LNG account for the linear variation where as LSM is applied to understand the nonlinear behaviour in the plot of melting temperature against reciprocal of particle size. However, a bird's eye view reveals that either HMH or LSM has been extensively used by experimentalists. It has also been observed that not a single hypothesis can explain the size-dependent melting in the complete range. Therefore we describe an approach which can predict the plausible hypothesis for a given data set of the size-dependent melting temperature. A variety of data have been analyzed to ascertain the hypothesis and to test the approach.

Inclusion of body doping in compact models for fully-depleted common double gate MOSFET adapted to gate-oxide thickness asymmetry

Since it is difficult to find the analytical solution of the governing Poisson equation for double gate MOSFETs with the body doping term included, the majority of the compact models are developed for undoped-body devices for which the analytical solution is available. Proposed is a simple technique to included a body doping term in such surface potential based common double gate MOSFET models also by taking into account any differences between the gate oxide thickness. The proposed technique is validated against TCAD simulation and found to be accurate as long as the channel is fully depleted.

Expanding universe: thermodynamical aspects from different models

The pivotal point of the paper is to discuss the behavior of temperature, pressure, energy density as a function of volume along with determination of caloric EoS from following two model: w(z)=w (0)+w (1)ln(1+z) & . The time scale of instability for this two models is discussed. In the paper we then generalize our result and arrive at general expression for energy density irrespective of the model. The thermodynamical stability for both of the model and the general case is discussed from this viewpoint. We also arrive at a condition on the limiting behavior of thermodynamic parameter to validate the third law of thermodynamics and interpret the general mathematical expression of integration constant U (0) (what we get while integrating energy conservation equation) physically relating it to number of micro states. The constraint on the allowed values of the parameters of the models is discussed which ascertains stability of universe. The validity of thermodynamical laws within apparent and event horizon is discussed.

Flux density calibration in diffuse optical tomographic systems

The solution of the forward equation that models the transport of light through a highly scattering tissue material in diffuse optical tomography (DOT) using the finite element method gives flux density (Phi) at the nodal points of the mesh. The experimentally measured flux (U-measured) on the boundary over a finite surface area in a DOT system has to be corrected to account for the system transfer functions (R) of various building blocks of the measurement system. We present two methods to compensate for the perturbations caused by R and estimate true flux density (Phi) from U-measured(cal). In the first approach, the measurement data with a homogeneous phantom (U-measured(homo)) is used to calibrate the measurement system. The second scheme estimates the homogeneous phantom measurement using only the measurement from a heterogeneous phantom, thereby eliminating the necessity of a homogeneous phantom. This is done by statistically averaging the data (U-measured(hetero)) and redistributing it to the corresponding detector positions. The experiments carried out on tissue mimicking phantom with single and multiple inhomogeneities, human hand, and a pork tissue phantom demonstrate the robustness of the approach. (C) 2013 Society of Photo-Optical Instrumentation Engineers (SPIE) DOI: 10.1117/1.JBO.18.2.026023]

Asymptotics of the invariant measure in mean field models with jumps

We consider the asymptotics of the invariant measure for the process of spatial distribution of N coupled Markov chains in the limit of a large number of chains. Each chain reflects the stochastic evolution of one particle. The chains are coupled through the dependence of transition rates on the spatial distribution of particles in the various states. Our model is a caricature for medium access interactions in wireless local area networks. Our model is also applicable in the study of spread of epidemics in a network. The limiting process satisfies a deterministic ordinary differential equation called the McKean-Vlasov equation. When this differential equation has a unique globally asymptotically stable equilibrium, the spatial distribution converges weakly to this equilibrium. Using a control-theoretic approach, we examine the question of a large deviation from this equilibrium.

Obtaining single document summaries using latent dirichlet allocation

In this paper, we present a novel approach that makes use of topic models based on Latent Dirichlet allocation(LDA) for generating single document summaries. Our approach is distinguished from other LDA based approaches in that we identify the summary topics which best describe a given document and only extract sentences from those paragraphs within the document which are highly correlated given the summary topics. This ensures that our summaries always highlight the crux of the document without paying any attention to the grammar and the structure of the documents. Finally, we evaluate our summaries on the DUC 2002 Single document summarization data corpus using ROUGE measures. Our summaries had higher ROUGE values and better semantic similarity with the documents than the DUC summaries.

Thermoelectric performance of a single-layer graphene sheet for energy harvesting

We investigate the thermoelectric (TE) figure-of-merit of a single-layer graphene (SLG) sheet by a physics-based analytical technique. We first develop analytical models of electrical and thermal resistances and the Seebeck coefficient of SLG by considering electron interactions with the in-plane and flexural phonons. Using those models, we show that both the figure-of-merit and the TE efficiency can be substantially increased with the addition of isotope doping as it significantly reduces the phonon-dominated thermal conductivity. In addition, we report that the TE open circuit output voltage and output power depends weakly on the SLG sheet dimensions and sheet concentration in the strongly diffusive regime. Proposed models agree well with the available experimental data and demonstrate the immense potential of graphene for waste-heat recovery application.