Design, Synthesis, and DNA Binding Properties of Photoisomerizable Azobenzene−Distamycin Conjugates: An Experimental and Computational Study

Here, we present the synthesis, photochemical, and DNA binding properties of three photoisomerizable azobenzene−distamycin conjugates in which two distamycin units were linked via electron-rich alkoxy or electron-withdrawing carboxamido moieties with the azobenzene core. Like parent distamycin A, these molecules also demonstrated AT-specific DNA binding. Duplex DNA binding abilities of these conjugates were found to depend upon the nature and length of the spacer, the location of protonatable residues, and the isomeric state of the conjugate. The changes in the duplex DNA binding efficiency of the individual conjugates in the dark and with their respective photoirradiated forms were examined by circular dichroism, thermal denaturation of DNA, and Hoechst displacement assay with poly[d(A-T).d(T-A)] DNA in 150 mM NaCl buffer. Computational structural analyses of the uncomplexed ligands using ab initio HF and MP2 theory and molecular docking studies involving the conjugates with duplex d[(GC(AT)10CG)]2 DNA were performed to rationalize the nature of binding of these conjugates.

Computational analysis of proteome of H5N1 avian influenza virus to define T cell epitopes with vaccine potential

The existing vaccines against influenza are based on the generation of neutralizing antibody primarily directed against surface proteins-hernagglutinin and neuraminidase. In this work, we have computationally defined conserved T cell epitopes of proteins of influenza virus H5N1 to help in the design of a vaccine with haplotype specificity for a target population. The peptides from the proteome of H5NI irus which are predicted to bind to different HLAs, do not show similarity with peptides of human proteorne and are also identified to be generated by proteolytic cleavage. These peptides could be made use of in the design of either a DNA vaccine or a subunit vaccine against V influenza. (c) 2007 Elsevier Ltd. All rights reserved.

Testing and Modeling of MR Damper and Its Application to SDOF Systems Using Integral Backstepping Technique

Magnetorheological dampers are intrinsically nonlinear devices, which make the modeling and design of a suitable control algorithm an interesting and challenging task. To evaluate the potential of magnetorheological (MR) dampers in control applications and to take full advantages of its unique features, a mathematical model to accurately reproduce its dynamic behavior has to be developed and then a proper control strategy has to be taken that is implementable and can fully utilize their capabilities as a semi-active control device. The present paper focuses on both the aspects. First, the paper reports the testing of a magnetorheological damper with an universal testing machine, for a set of frequency, amplitude, and current. A modified Bouc-Wen model considering the amplitude and input current dependence of the damper parameters has been proposed. It has been shown that the damper response can be satisfactorily predicted with this model. Second, a backstepping based nonlinear current monitoring of magnetorheological dampers for semi-active control of structures under earthquakes has been developed. It provides a stable nonlinear magnetorheological damper current monitoring directly based on system feedback such that current change in magnetorheological damper is gradual. Unlike other MR damper control techniques available in literature, the main advantage of the proposed technique lies in its current input prediction directly based on system feedback and smooth update of input current. Furthermore, while developing the proposed semi-active algorithm, the dynamics of the supplied and commanded current to the damper has been considered. The efficiency of the proposed technique has been shown taking a base isolated three story building under a set of seismic excitation. Comparison with widely used clipped-optimal strategy has also been shown.

A Legendre spectral element model for sloshing and acoustic analysis in nearly incompressible fluids

A new spectral finite element formulation is presented for modeling the sloshing and the acoustic waves in nearly incompressible fluids. The formulation makes use of the Legendre polynomials in deriving the finite element interpolation shape functions in the Lagrangian frame of reference. The formulated element uses Gauss-Lobatto-Legendre quadrature scheme for integrating the volumetric stiffness and the mass matrices while the conventional Gauss-Legendre quadrature scheme is used on the rotational stiffness matrix to completely eliminate the zero energy modes, which are normally associated with the Lagrangian FE formulation. The numerical performance of the spectral element formulated here is examined by doing the inf-sup test oil a standard rectangular rigid tank partially filled with liquid The eigenvalues obtained from the formulated spectral element are compared with the conventional equally spaced node locations of the h-type Lagrangian finite element and the predicted results show that these spectral elements are more accurate and give superior convergence The efficiency and robustness of the formulated elements are demonstrated by solving few standard problems involving free vibration and dynamic response analysis with undistorted and distorted spectral elements. and the obtained results are compared with available results in the published literature (C) 2009 Elsevier Inc All rights reserved

Combined Atomic Force Microscopy and Modeling Study of The Evolution of Octadecylamine Films on a Mica Surface

The time evolution of the film thickness and domain formation of octadecylamine molecules adsorbed oil a mica surface is investigated Using atomic force microscopy. The adsorbed Film thickness is determined by measuring the height profile across the mica-amine interface of a mica surface partially immersed in a 15 mM solution of octadecylamine in chloroform. Using this novel procedure, adsorption of amine on mica is found to occur in three distinct stages, with morphologically distinct domain Formation and growth occurring during each stage. In the first stage, where adsorption is primarily in the thin-film regime, all average Film thickness of 0.2 (+/- 0.3) nm is formed for exposure times below 30 s and 0.8 (+/- 0.2) nm for 60 s of immersion time. During this stage, large sample spanning domains are observed. The second stage, which occurs between 60-300 s, is associated with it regime of rapid film growth, and the film thickness increases from about 0.8 to 25 nm during this stage. Once the thick-film regime is established, further exposure to the amine solution results in all increase in the domain area, and it regime of lateral domain growth is observed. In this stage, the domain area coverage grows from 38 to 75%, and the FTIR spectra reveal an increased level of crystallinity in the film. Using it diffusion-controlled model and it two-step Langmuir isotherm, the time evolution of the film growth is quantitatively captured. The model predicts the time at which the thin to thick film transition occurs as well its the time required for complete film growth at longer times. The Ward-Tordai equation is also solved to determine the model parameters in the monolayer (thin-film) regime, which occurs during the initial stages of film growth.

Electromechanical interactions in a carbon nanotube based thin film field emitting diode

Carbon nanotubes (CNTs) have emerged as promising candidates for biomedical x-ray devices and other applications of field emission. CNTs grown/deposited in a thin film are used as cathodes for field emission. In spite of the good performance of such cathodes, the procedure to estimate the device current is not straightforward and the required insight towards design optimization is not well developed. In this paper, we report an analysis aided by a computational model and experiments by which the process of evolution and self-assembly (reorientation) of CNTs is characterized and the device current is estimated. The modeling approach involves two steps: (i) a phenomenological description of the degradation and fragmentation of CNTs and (ii) a mechanics based modeling of electromechanical interaction among CNTs during field emission. A computational scheme is developed by which the states of CNTs are updated in a time incremental manner. Finally, the device current is obtained by using the Fowler–Nordheim equation for field emission and by integrating the current density over computational cells. A detailed analysis of the results reveals the deflected shapes of the CNTs in an ensemble and the extent to which the initial state of geometry and orientation angles affect the device current. Experimental results confirm these effects.

Modeling and analysis of a tunable piezoelectric structure for transverse shear wave generation

An analytical investigation of the transverse shear wave mode tuning with a resonator mass (packing mass) on a Lead Zirconium Titanate (PZT) crystal bonded together with a host plate and its equivalent electric circuit parameters are presented. The energy transfer into the structure for this type of wave modes are much higher in this new design. The novelty of the approach here is the tuning of a single wave mode in the thickness direction using a resonator mass. First, a one-dimensional constitutive model assuming the strain induced only in the thickness direction is considered. As the input voltage is applied to the PZT crystal in the thickness direction, the transverse normal stress distribution induced into the plate is assumed to have parabolic distribution, which is presumed as a function of the geometries of the PZT crystal, packing mass, substrate and the wave penetration depth of the generated wave. For the PZT crystal, the harmonic wave guide solution is assumed for the mechanical displacement and electric fields, while for the packing mass, the former is solved using the boundary conditions. The electromechanical characteristics in terms of the stress transfer, mechanical impedance, electrical displacement, velocity and electric field are analyzed. The analytical solutions for the aforementioned entities are presented on the basis of varying the thickness of the PZT crystal and the packing mass. The results show that for a 25% increase in the thickness of the PZT crystal, there is ~38% decrease in the first resonant frequency, while for the same change in the thickness of the packing mass, the decrease in the resonant frequency is observed as ~35%. Most importantly the tuning of the generated wave can be accomplished with the packing mass at lower frequencies easily. To the end, an equivalent electric circuit, for tuning the transverse shear wave mode is analyzed.

Modeling of magnetostrictive materials and structures

The constitutive model for a magnetostrictive material and its effect on the structural response is presented in this article. The example of magnetostrictive material considered is the TERFENOL-D. As like the piezoelectric material, this material has two constitutive laws, one of which is the sensing law and the other is the actuation law, both of which are highly coupled and non-linear. For the purpose of analysis, the constitutive laws can be characterized as coupled or uncoupled and linear or non linear. Coupled model is studied without assuming any explicit direct relationship with magnetic field. In the linear coupled model, which is assumed to preserve the magnetic flux line continuity, the elastic modulus, the permeability and magneto-elastic constant are assumed as constant. In the nonlinear-coupled model, the nonlinearity is decoupled and solved separately for the magnetic domain and the mechanical domain using two nonlinear curves, namely the stress vs. strain curve and the magnetic flux density vs. magnetic field curve. This is performed by two different methods. In the first, the magnetic flux density is computed iteratively, while in the second, the artificial neural network is used, where in the trained network will give the necessary strain and magnetic flux density for a given magnetic field and stress level. The effect of nonlinearity is demonstrated on a simple magnetostrictive rod.

Modeling and Analysis of Noise Margin in SET Logic

In this paper the static noise margin for SET (single electron transistor) logic is defined and compact models for the noise margin are developed by making use of the MIB (Mahapatra-Ionescu-Banerjee) model. The variation of the noise margin with temperature and background charge is also studied. A chain of SET inverters is simulated to validate the definition of various logic levels (like VIH, VOH, etc.) and noise margin. Finally the noise immunity of SET logic is compared with current CMOS logic.

Prediction of flame liftoff height of diffusion/partially premixed jet flames and modeling of mild combustion burners

In this article, a new flame extinction model based on the k/epsilon turbulence time scale concept is proposed to predict the flame liftoff heights over a wide range of coflow temperature and O-2 mass fraction of the coflow. The flame is assumed to be quenched, when the fluid time scale is less than the chemical time scale ( Da < 1). The chemical time scale is derived as a function of temperature, oxidizer mass fraction, fuel dilution, velocity of the jet and fuel type. The present extinction model has been tested for a variety of conditions: ( a) ambient coflow conditions ( 1 atm and 300 K) for propane, methane and hydrogen jet flames, ( b) highly preheated coflow, and ( c) high temperature and low oxidizer concentration coflow. Predicted flame liftoff heights of jet diffusion and partially premixed flames are in excellent agreement with the experimental data for all the simulated conditions and fuels. It is observed that flame stabilization occurs at a point near the stoichiometric mixture fraction surface, where the local flow velocity is equal to the local flame propagation speed. The present method is used to determine the chemical time scale for the conditions existing in the mild/ flameless combustion burners investigated by the authors earlier. This model has successfully predicted the initial premixing of the fuel with combustion products before the combustion reaction initiates. It has been inferred from these numerical simulations that fuel injection is followed by intense premixing with hot combustion products in the primary zone and combustion reaction follows further downstream. Reaction rate contours suggest that reaction takes place over a large volume and the magnitude of the combustion reaction is lower compared to the conventional combustion mode. The appearance of attached flames in the mild combustion burners at low thermal inputs is also predicted, which is due to lower average jet velocity and larger residence times in the near injection zone.

Computational fluid dynamics simulations in aerosol and nucleation studies

Nucleation is the first step in the formation of a new phase inside a mother phase. Two main forms of nucleation can be distinguished. In homogeneous nucleation, the new phase is formed in a uniform substance. In heterogeneous nucleation, on the other hand, the new phase emerges on a pre-existing surface (nucleation site). Nucleation is the source of about 30% of all atmospheric aerosol which in turn has noticeable health effects and a significant impact on climate. Nucleation can be observed in the atmosphere, studied experimentally in the laboratory and is the subject of ongoing theoretical research. This thesis attempts to be a link between experiment and theory. By comparing simulation results to experimental data, the aim is to (i) better understand the experiments and (ii) determine where the theory needs improvement. Computational fluid dynamics (CFD) tools were used to simulate homogeneous onecomponent nucleation of n-alcohols in argon and helium as carrier gases, homogeneous nucleation in the water-sulfuric acid-system, and heterogeneous nucleation of water vapor on silver particles. In the nucleation of n-alcohols, vapor depletion, carrier gas effect and carrier gas pressure effect were evaluated, with a special focus on the pressure effect whose dependence on vapor and carrier gas properties could be specified. The investigation of nucleation in the water-sulfuric acid-system included a thorough analysis of the experimental setup, determining flow conditions, vapor losses, and nucleation zone. Experimental nucleation rates were compared to various theoretical approaches. We found that none of the considered theoretical descriptions of nucleation captured the role of water in the process at all relative humidities. Heterogeneous nucleation was studied in the activation of silver particles in a TSI 3785 particle counter which uses water as its working fluid. The role of the contact angle was investigated and the influence of incoming particle concentrations and homogeneous nucleation on counting efficiency determined.

Geant4 Hadronic Cascade Models and CMS Data Analysis : Computational Challenges in the LHC era

This work belongs to the field of computational high-energy physics (HEP). The key methods used in this thesis work to meet the challenges raised by the Large Hadron Collider (LHC) era experiments are object-orientation with software engineering, Monte Carlo simulation, the computer technology of clusters, and artificial neural networks. The first aspect discussed is the development of hadronic cascade models, used for the accurate simulation of medium-energy hadron-nucleus reactions, up to 10 GeV. These models are typically needed in hadronic calorimeter studies and in the estimation of radiation backgrounds. Various applications outside HEP include the medical field (such as hadron treatment simulations), space science (satellite shielding), and nuclear physics (spallation studies). Validation results are presented for several significant improvements released in Geant4 simulation tool, and the significance of the new models for computing in the Large Hadron Collider era is estimated. In particular, we estimate the ability of the Bertini cascade to simulate Compact Muon Solenoid (CMS) hadron calorimeter HCAL. LHC test beam activity has a tightly coupled cycle of simulation-to-data analysis. Typically, a Geant4 computer experiment is used to understand test beam measurements. Thus an another aspect of this thesis is a description of studies related to developing new CMS H2 test beam data analysis tools and performing data analysis on the basis of CMS Monte Carlo events. These events have been simulated in detail using Geant4 physics models, full CMS detector description, and event reconstruction. Using the ROOT data analysis framework we have developed an offline ANN-based approach to tag b-jets associated with heavy neutral Higgs particles, and we show that this kind of NN methodology can be successfully used to separate the Higgs signal from the background in the CMS experiment.

Process variability-aware statistical hybrid modeling of dynamic power dissipation in 65 nm CMOS designs

A generalized technique is proposed for modeling the effects of process variations on dynamic power by directly relating the variations in process parameters to variations in dynamic power of a digital circuit. The dynamic power of a 2-input NAND gate is characterized by mixed-mode simulations, to be used as a library element for 65mn gate length technology. The proposed methodology is demonstrated with a multiplier circuit built using the NAND gate library, by characterizing its dynamic power through Monte Carlo analysis. The statistical technique of Response. Surface Methodology (RSM) using Design of Experiments (DOE) and Least Squares Method (LSM), are employed to generate a "hybrid model" for gate power to account for simultaneous variations in multiple process parameters. We demonstrate that our hybrid model based statistical design approach results in considerable savings in the power budget of low power CMOS designs with an error of less than 1%, with significant reductions in uncertainty by atleast 6X on a normalized basis, against worst case design.

Theoretical modeling of ionospheric electrodynamics including induction effects

This thesis deals with theoretical modeling of the electrodynamics of auroral ionospheres. In the five research articles forming the main part of the thesis we have concentrated on two main themes: Development of new data-analysis techniques and study of inductive phenomena in the ionospheric electrodynamics. The introductory part of the thesis provides a background for these new results and places them in the wider context of ionospheric research. In this thesis we have developed a new tool (called 1D SECS) for analysing ground based magnetic measurements from a 1-dimensional magnetometer chain (usually aligned in the North-South direction) and a new method for obtaining ionospheric electric field from combined ground based magnetic measurements and estimated ionospheric electric conductance. Both these methods are based on earlier work, but contain important new features: 1D SECS respects the spherical geometry of large scale ionospheric electrojet systems and due to an innovative way of implementing boundary conditions the new method for obtaining electric fields can be applied also at local scale studies. These new calculation methods have been tested using both simulated and real data. The tests indicate that the new methods are more reliable than the previous techniques. Inductive phenomena are intimately related to temporal changes in electric currents. As the large scale ionospheric current systems change relatively slowly, in time scales of several minutes or hours, inductive effects are usually assumed to be negligible. However, during the past ten years, it has been realised that induction can play an important part in some ionospheric phenomena. In this thesis we have studied the role of inductive electric fields and currents in ionospheric electrodynamics. We have formulated the induction problem so that only ionospheric electric parameters are used in the calculations. This is in contrast to previous studies, which require knowledge of the magnetospheric-ionosphere coupling. We have applied our technique to several realistic models of typical auroral phenomena. The results indicate that inductive electric fields and currents are locally important during the most dynamical phenomena (like the westward travelling surge, WTS). In these situations induction may locally contribute up to 20-30% of the total ionospheric electric field and currents. Inductive phenomena do also change the field-aligned currents flowing between the ionosphere and magnetosphere, thus modifying the coupling between the two regions.