Cybernetic modeling of adaptive prediction of environmental changes by microorganisms

Microorganisms exhibit varied regulatory strategies such as direct regulation, symmetric anticipatory regulation, asymmetric anticipatory regulation, etc. Current mathematical modeling frameworks for the growth of microorganisms either do not incorporate regulation or assume that the microorganisms utilize the direct regulation strategy. In the present study, we extend the cybernetic modeling framework to account for asymmetric anticipatory regulation strategy. The extended model accurately captures various experimental observations. We use the developed model to explore the fitness advantage provided by the asymmetric anticipatory regulation strategy and observe that the optimal extent of asymmetric regulation depends on the selective pressure that the microorganisms experience. We also explore the importance of timing the response in anticipatory regulation and find that there is an optimal time, dependent on the extent of asymmetric regulation, at which microorganisms should respond anticipatorily to maximize their fitness. We then discuss the advantages offered by the cybernetic modeling framework over other modeling frameworks in modeling the asymmetric anticipatory regulation strategy. (C) 2013 Published by Elsevier Inc.

Threshold-Independent QRS Detection Using the Dynamic Plosion Index

Detection of QRS serves as a first step in many automated ECG analysis techniques. Motivated by the strong similarities between the signal structures of an ECG signal and the integrated linear prediction residual (ILPR) of voiced speech, an algorithm proposed earlier for epoch detection from ILPR is extended to the problem of QRS detection. The ECG signal is pre-processed by high-pass filtering to remove the baseline wandering and by half-wave rectification to reduce the ambiguities. The initial estimates of the QRS are iteratively obtained using a non-linear temporal feature, named the dynamic plosion index suitable for detection of transients in a signal. These estimates are further refined to obtain a higher temporal accuracy. Unlike most of the high performance algorithms, this technique does not make use of any threshold or differencing operation. The proposed algorithm is validated on the MIT-BIH database using the standard metrics and its performance is found to be comparable to the state-of-the-art algorithms, despite its threshold independence and simple decision logic.

Nonlinear gravity-wave interactions in stratified turbulence

To investigate the dynamics of gravity waves in stratified Boussinesq flows, a model is derived that consists of all three-gravity-wave-mode interactions (the GGG model), excluding interactions involving the vortical mode. The GGG model is a natural extension of weak turbulence theory that accounts for exact three-gravity-wave resonances. The model is examined numerically by means of random, large-scale, high-frequency forcing. An immediate observation is a robust growth of the so-called vertically sheared horizontal flow (VSHF). In addition, there is a forward transfer of energy and equilibration of the nonzero-frequency (sometimes called ``fast'') gravity-wave modes. These results show that gravity-wave-mode interactions by themselves are capable of systematic interscale energy transfer in a stratified fluid. Comparing numerical simulations of the GGG model and the full Boussinesq system, for the range of Froude numbers (Fr) considered (0.05 a parts per thousand currency sign Fr a parts per thousand currency sign 1), in both systems the VSHF is hardest to resolve. When adequately resolved, VSHF growth is more vigorous in the GGG model. Furthermore, a VSHF is observed to form in milder stratification scenarios in the GGG model than the full Boussinesq system. Finally, fully three-dimensional nonzero-frequency gravity-wave modes equilibrate in both systems and their scaling with vertical wavenumber follows similar power-laws. The slopes of the power-laws obtained depend on Fr and approach -2 (from above) at Fr = 0.05, which is the strongest stratification that can be properly resolved with our computational resources.

Studies on an improved indigenous pressure wave generator and its testing with a pulse tube cooler

Earlier version of an indigenously developed Pressure Wave Generator (PWG) could not develop the necessary pressure ratio to satisfactorily operate a pulse tube cooler, largely due to high blow by losses in the piston cylinder seal gap and due to a few design deficiencies. Effect of different parameters like seal gap, piston diameter, piston stroke, moving mass and the piston back volume on the performance is studied analytically. Modifications were done to the PWG based on analysis and the performance is experimentally measured. A significant improvement in PWG performance is seen as a result of the modifications. The improved PWG is tested with the same pulse tube cooler but with different inertance tube configurations. A no load temperature of 130 K is achieved with an inertance tube configuration designed using Sage software. The delivered PV power is estimated to be 28.4 W which can produce a refrigeration of about 1 W at 80 K.

Anomalous power law decay in solvation dynamics of DNA: a mode coupling theory analysis of ion contribution

Several time dependent fluorescence Stokes shift (TDFSS) experiments have reported a slow power law decay in the hydration dynamics of a DNA molecule. Such a power law has neither been observed in computer simulations nor in some other TDFSS experiments. Here we observe that a slow decay may originate from collective ion contribution because in experiments DNA is immersed in a buffer solution, and also from groove bound water and lastly from DNA dynamics itself. In this work we first express the solvation time correlation function in terms of dynamic structure factors of the solution. We use mode coupling theory to calculate analytically the time dependence of collective ionic contribution. A power law decay in seen to originate from an interplay between long-range probe-ion direct correlation function and ion-ion dynamic structure factor. Although the power law decay is reminiscent of Debye-Falkenhagen effect, yet solvation dynamics is dominated by ion atmosphere relaxation times at longer length scales (small wave number) than in electrolyte friction. We further discuss why this power law may not originate from water motions which have been computed by molecular dynamics simulations. Finally, we propose several experiments to check the prediction of the present theoretical work.

Nonequilibrium ``Melting'' of a Charge Density Wave Insulator via an Ultrafast Laser Pulse

We employ an exact solution of the simplest model for pump-probe time-resolved photoemission spectroscopy in charge-density-wave systems to show how, in nonequilibrium, the gap in the density of states disappears while the charge density remains modulated, and then the gap reforms after the pulse has passed. This nonequilibrium scenario qualitatively describes the common short-time experimental features in TaS2 and TbTe3, indicating a quasiuniversality for nonequilibrium ``melting'' with qualitative features that can be easily understood within a simple picture.

Ultrasonic guided wave sensing properties of PVDF thin film with inter digital electrodes

Ultrasonic strain sensing performance of the large area PVDF with Inter Digital Electrodes (IDE) is studied in this work. Procedure to obtain IDE on a beta-phase PVDF is explained. PVDF film with IDE is bonded on a plate structure and is characterized for its directional sensitivity at different frequencies. Guided waves are induced on the IDE-PVDF sensor from different directions by placing a piezoelectric wafer actuator at different angles. Strain induced on the IDE-PVDF sensor by the guided waves in estimated by using a Laser Doppler Vibrometer (LDV) and a wave propagation model. Using measured voltage response from IDE-PVDF sensor and the strain measurements from LDV the piezoelectric coefficient is estimated in various directions. The variation of 11 e at different angles shows directional sensitivity of the IDE-PVDF sensor to the incident guided waves. The present study provides an effective technique to characterize thin film piezoelectric sensors for ultrasonic strain sensing at very high frequencies of 200 kHz. Often frequency of the guided wave is changed to alter the wavelength to interrogate damages of different sizes in Structural Health Monitoring (SHM) applications. The unique property of directional sensitivity combined with frequency tunability makes the IDE-PVDF sensor most suitable for SHM of structures.

Spectral finite element based on an efficient layerwise theory for wave propagation analysis of composite and sandwich beams

In this paper, we present a spectral finite element model (SFEM) using an efficient and accurate layerwise (zigzag) theory, which is applicable for wave propagation analysis of highly inhomogeneous laminated composite and sandwich beams. The theory assumes a layerwise linear variation superimposed with a global third-order variation across the thickness for the axial displacement. The conditions of zero transverse shear stress at the top and bottom and its continuity at the layer interfaces are subsequently enforced to make the number of primary unknowns independent of the number of layers, thereby making the theory as efficient as the first-order shear deformation theory (FSDT). The spectral element developed is validated by comparing the present results with those available in the literature. A comparison of the natural frequencies of simply supported composite and sandwich beams obtained by the present spectral element with the exact two-dimensional elasticity and FSDT solutions reveals that the FSDT yields highly inaccurate results for the inhomogeneous sandwich beams and thick composite beams, whereas the present element based on the zigzag theory agrees very well with the exact elasticity solution for both thick and thin, composite and sandwich beams. A significant deviation in the dispersion relations obtained using the accurate zigzag theory and the FSDT is also observed for composite beams at high frequencies. It is shown that the pure shear rotation mode remains always evanescent, contrary to what has been reported earlier. The SFEM is subsequently used to study wavenumber dispersion, free vibration and wave propagation time history in soft-core sandwich beams with composite faces for the first time in the literature. (C) 2014 Elsevier Ltd. All rights reserved.

Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: Implications for three-dimensional modeling

With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naive Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (approximate to 85%) and specific (approximate to 95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions. Proteins 2014; 82:1219-1234. (c) 2013 Wiley Periodicals, Inc.

Frequency Domain Based Solution for Certain Class of Wave Equations: An exhaustive study of Numerical Solutions

The paper discusses the frequency domain based solution for a certain class of wave equations such as: a second order partial differential equation in one variable with constant and varying coefficients (Cantilever beam) and a coupled second order partial differential equation in two variables with constant and varying coefficients (Timoshenko beam). The exact solution of the Cantilever beam with uniform and varying cross-section and the Timoshenko beam with uniform cross-section is available. However, the exact solution for Timoshenko beam with varying cross-section is not available. Laplace spectral methods are used to solve these problems exactly in frequency domain. The numerical solution in frequency domain is done by discretisation in space by approximating the unknown function using spectral functions like Chebyshev polynomials, Legendre polynomials and also Normal polynomials. Different numerical methods such as Galerkin Method, Petrov- Galerkin method, Method of moments and Collocation method or the Pseudo-spectral method in frequency domain are studied and compared with the available exact solution. An approximate solution is also obtained for the Timoshenko beam with varying cross-section using Laplace Spectral Element Method (LSEM). The group speeds are computed exactly for the Cantilever beam and Timoshenko beam with uniform cross-section and is compared with the group speeds obtained numerically. The shear mode and the bending modes of the Timoshenko beam with uniform cross-section are separated numerically by applying a modulated pulse as the shear force and the corresponding group speeds for varying taper parameter in are obtained numerically by varying the frequency of the input pulse. An approximate expression for calculating group speeds corresponding to the shear mode and the bending mode, and also the cut-off frequency is obtained. Finally, we show that the cut-off frequency disappears for large in, for epsilon > 0 and increases for large in, for epsilon < 0.

Wave propagation analysis in laminated composite plates with transverse cracks using the wavelet spectral finite element method

This paper presents a newly developed wavelet spectral finite element (WFSE) model to analyze wave propagation in anisotropic composite laminate with a transverse surface crack penetrating part-through the thickness. The WSFE formulation of the composite laminate, which is based on the first-order shear deformation theory, produces accurate and computationally efficient results for high frequency wave motion. Transverse crack is modeled in wavenumber-frequency domain by introducing bending flexibility of the plate along crack edge. Results for tone burst and impulse excitations show excellent agreement with conventional finite element analysis in Abaqus (R). Problems with multiple cracks are modeled by assembling a number of spectral elements with cracks in frequency-wavenumber domain. Results show partial reflection of the excited wave due to crack at time instances consistent with crack locations. (C) 2014 Elsevier B.V. All rights reserved.

Diffusing-wave spectroscopy in an inhomogeneous object: Local viscoelastic spectra from ultrasound-assisted measurement of correlation decay arising from the ultrasound focal volume

We demonstrate diffusing-wave spectroscopy (DWS) in a localized region of a viscoelastically inhomogeneous object by measurement of the intensity autocorrelation g(2)(tau)] that captures only the decay introduced by the temperature-induced Brownian motion in the region. The region is roughly specified by the focal volume of an ultrasound transducer which introduces region specific mechanical vibration owing to insonification. Essential characteristics of the localized non-Markovian dynamics are contained in the decay of the modulation depth M(tau)], introduced by the ultrasound forcing in the focal volume selected, on g(2)(tau). The modulation depth M(tau(i)) at any delay time tau(i) can be measured by short-time Fourier transform of g(2)(tau) and measurement of the magnitude of the spectrum at the ultrasound drive frequency. By following the established theoretical framework of DWS, we are able to connect the decay in M(tau) to the mean-squared displacement (MSD) of scattering centers and the MSD to G*(omega), the complex viscoelastic spectrum. A two-region composite polyvinyl alcohol phantom with different viscoelastic properties is selected for demonstrating local DWS-based recovery of G*(omega) corresponding to these regions from the measured region specific M(tau(i))vs tau(i). The ultrasound-assisted measurement of MSD is verified by simulating, using a generalized Langevin equation (GLE), the dynamics of the particles in the region selected as well as by the usual DWS experiment without the ultrasound. It is shown that whereas the MSD obtained by solving the GLE without the ultrasound forcing agreed with its experimental counterpart covering small and large values of tau, the match was good only in the initial transients in regard to experimental measurements with ultrasound.

Role of Vertex Index in Substructure Identification and Activity Prediction: A Study on Antitubercular Activity of a Series of Acid Alkyl Ester Derivatives

Tuberculosis (TB) is a life threatening disease caused due to infection from Mycobacterium tuberculosis (Mtb). That most of the TB strains have become resistant to various existing drugs, development of effective novel drug candidates to combat this disease is a need of the day. In spite of intensive research world-wide, the success rate of discovering a new anti-TB drug is very poor. Therefore, novel drug discovery methods have to be tried. We have used a rule based computational method that utilizes a vertex index, named `distance exponent index (D-x)' (taken x = -4 here) for predicting anti-TB activity of a series of acid alkyl ester derivatives. The method is meant to identify activity related substructures from a series a compounds and predict activity of a compound on that basis. The high degree of successful prediction in the present study suggests that the said method may be useful in discovering effective anti-TB compound. It is also apparent that substructural approaches may be leveraged for wide purposes in computer-aided drug design.

A spectral multiscale method for wave propagation analysis: Atomistic-continuum coupled simulation

In this paper, we present a new multiscale method which is capable of coupling atomistic and continuum domains for high frequency wave propagation analysis. The problem of non-physical wave reflection, which occurs due to the change in system description across the interface between two scales, can be satisfactorily overcome by the proposed method. We propose an efficient spectral domain decomposition of the total fine scale displacement along with a potent macroscale equation in the Laplace domain to eliminate the spurious interfacial reflection. We use Laplace transform based spectral finite element method to model the macroscale, which provides the optimum approximations for required dynamic responses of the outer atoms of the simulated microscale region very accurately. This new method shows excellent agreement between the proposed multiscale model and the full molecular dynamics (MD) results. Numerical experiments of wave propagation in a 1D harmonic lattice, a 1D lattice with Lennard-Jones potential, a 2D square Bravais lattice, and a 2D triangular lattice with microcrack demonstrate the accuracy and the robustness of the method. In addition, under certain conditions, this method can simulate complex dynamics of crystalline solids involving different spatial and/or temporal scales with sufficient accuracy and efficiency. (C) 2014 Elsevier B.V. All rights reserved.

Isotropic finite volume discretization

Finite volume methods traditionally employ dimension by dimension extension of the one-dimensional reconstruction and averaging procedures to achieve spatial discretization of the governing partial differential equations on a structured Cartesian mesh in multiple dimensions. This simple approach based on tensor product stencils introduces an undesirable grid orientation dependence in the computed solution. The resulting anisotropic errors lead to a disparity in the calculations that is most prominent between directions parallel and diagonal to the grid lines. In this work we develop isotropic finite volume discretization schemes which minimize such grid orientation effects in multidimensional calculations by eliminating the directional bias in the lowest order term in the truncation error. Explicit isotropic expressions that relate the cell face averaged line and surface integrals of a function and its derivatives to the given cell area and volume averages are derived in two and three dimensions, respectively. It is found that a family of isotropic approximations with a free parameter can be derived by combining isotropic schemes based on next-nearest and next-next-nearest neighbors in three dimensions. Use of these isotropic expressions alone in a standard finite volume framework, however, is found to be insufficient in enforcing rotational invariance when the flux vector is nonlinear and/or spatially non-uniform. The rotationally invariant terms which lead to a loss of isotropy in such cases are explicitly identified and recast in a differential form. Various forms of flux correction terms which allow for a full recovery of rotational invariance in the lowest order truncation error terms, while preserving the formal order of accuracy and discrete conservation of the original finite volume method, are developed. Numerical tests in two and three dimensions attest the superior directional attributes of the proposed isotropic finite volume method. Prominent anisotropic errors, such as spurious asymmetric distortions on a circular reaction-diffusion wave that feature in the conventional finite volume implementation are effectively suppressed through isotropic finite volume discretization. Furthermore, for a given spatial resolution, a striking improvement in the prediction of kinetic energy decay rate corresponding to a general two-dimensional incompressible flow field is observed with the use of an isotropic finite volume method instead of the conventional discretization. (C) 2014 Elsevier Inc. All rights reserved.