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.

Density Functional Theoretical Modeling, Electrostatic Surface Potential and Surface Enhanced Raman Spectroscopic Studies on Biosynthesized Silver Nanoparticles: Observation of 400 pM Sensitivity to Explosives

Interaction of adsorbate on charged surfaces, orientation of the analyte on the surface, and surface enhancement aspects have been studied. These aspects have been explored in details to explain the surface-enhanced Raman spectroscopic (SERS) spectra of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (HNIW or CL-20), a well-known explosive, and 2,4,6-trinitrotoluene (TNT) using one-pot synthesis of silver nanoparticles via biosynthetic route using natural precursor extracts of clove and pepper. The biosynthesized silver nanoparticles (bio Ag Nps) have been characterized using UV-vis spectroscopy, scanning electron microscopy and atomic force microscopy. SERS studies conducted using bio Ag Nps on different water insoluble analytes, such as CL-20 and TNT, lead to SERS signals at concentration levels of 400 pM. The experimental findings have been corroborated with density functional computational results, electrostatic surface potential calculations, Fukui functions and potential measurements.

Theoretical modeling of photon and electron-stimulated Na and K desorption from SiO2

The mechanism of generation of atomic Na and K from SiO2 samples has been studied using explicitly correlated wave function and density functional theory cluster calculations. Possible pathways for the photon and electron stimulated desorption of Na and K atoms from silicates are proposed, thus providing new insight on the generation of the tenuous Na and K atmosphere of the Moon.

Implementation and application of basis set superposition error-correction schemes to the theoretical modeling of weak intermolecular interactions

This thesis deals with the so-called Basis Set Superposition Error (BSSE) from both a methodological and a practical point of view. The purpose of the present thesis is twofold: (a) to contribute step ahead in the correct characterization of weakly bound complexes and, (b) to shed light the understanding of the actual implications of the basis set extension effects in the ab intio calculations and contribute to the BSSE debate. The existing BSSE-correction procedures are deeply analyzed, compared, validated and, if necessary, improved. A new interpretation of the counterpoise (CP) method is used in order to define counterpoise-corrected descriptions of the molecular complexes. This novel point of view allows for a study of the BSSE-effects not only in the interaction energy but also on the potential energy surface and, in general, in any property derived from the molecular energy and its derivatives A program has been developed for the calculation of CP-corrected geometry optimizations and vibrational frequencies, also using several counterpoise schemes for the case of molecular clusters. The method has also been implemented in Gaussian98 revA10 package. The Chemical Hamiltonian Approach (CHA) methodology has been also implemented at the RHF and UHF levels of theory for an arbitrary number interacting systems using an algorithm based on block-diagonal matrices. Along with the methodological development, the effects of the BSSE on the properties of molecular complexes have been discussed in detail. The CP and CHA methodologies are used for the determination of BSSE-corrected molecular complexes properties related to the Potential Energy Surfaces and molecular wavefunction, respectively. First, the behaviour of both BSSE-correction schemes are systematically compared at different levels of theory and basis sets for a number of hydrogen-bonded complexes. The Complete Basis Set (CBS) limit of both uncorrected and CP-corrected molecular properties like stabilization energies and intermolecular distances has also been determined, showing the capital importance of the BSSE correction. Several controversial topics of the BSSE correction are addressed as well. The application of the counterpoise method is applied to internal rotational barriers. The importance of the nuclear relaxation term is also pointed out. The viability of the CP method for dealing with charged complexes and the BSSE effects on the double-well PES blue-shifted hydrogen bonds is also studied in detail. In the case of the molecular clusters the effect of high-order BSSE effects introduced with the hierarchical counterpoise scheme is also determined. The effect of the BSSE on the electron density-related properties is also addressed. The first-order electron density obtained with the CHA/F and CHA/DFT methodologies was used to assess, both graphically and numerically, the redistribution of the charge density upon BSSE-correction. Several tools like the Atoms in Molecules topologycal analysis, density difference maps, Quantum Molecular Similarity, and Chemical Energy Component Analysis were used to deeply analyze, for the first time, the BSSE effects on the electron density of several hydrogen bonded complexes of increasing size. The indirect effect of the BSSE on intermolecular perturbation theory results is also pointed out It is shown that for a BSSE-free SAPT study of hydrogen fluoride clusters, the use of a counterpoise-corrected PES is essential in order to determine the proper molecular geometry to perform the SAPT analysis.

Theoretical modeling and experimental validation of surface stress in thrombin aptasensor

Adsorption of target molecules on the immobilized microcantilever surface produced beam displacement due to the differential surface stress generated between the immobilized and non-immobilized surface. Surface stress is caused by the intermolecular forces between the molecules. Van der Waals, electrostatic forces, hydrogen bonding, hydrophobic effect and steric hindrance are some of the intermolecular forces involved. A theoretical framework describing the adsorption-induced microcantilever displacement is derived in this paper. Experimental displacement of thrombin aptamer-thrombin interactions was carried out. The relation between the electrostatic interactions involved between adsorbates (thrombin) as well as adsorbates and substrates (thrombin aptamer) and the microcantilever beam displacement utilizing the proposed mathematical model was quantified and compared to the experimental value. This exercise is important to aid the designers in microcantilever sensing performance optimization.

Photoluminescence of crystalline and disordered BTO : Mn powder: Experimental and theoretical modeling

Disordered and crystalline Mn-doped BaTiO3 (BTO:Mn) powders were synthesized by the polymeric precursor method. After heat treatment, the nature of visible photoluminescence (PL) at room temperature in amorphous BTO:Mn was discussed, considering results of experimental and theoretical studies. X-ray diffraction (XRD), PL, and UV-vis were used to characterize this material. Rietveld refinement of the BTO:Mn from XRD data was used to built two models, which represent the crystalline BTO:Mn (BTO:Mn,) and disordered BTO:Mn (BTO:Mn-d) structures. Theses models were analyzed by the periodic ab initio quantum mechanical calculations using the CRYSTAL98 package within the framework of density functional theory at the B3LYP level. The experimental and theoretical results indicated that PL is related with the degree of disorder in the BTO:Mn powders and also suggests the presence of localized states in the disordered structure. (c) 2006 Elsevier B.V. All rights reserved.

Blood flow and oxygen delivery to human brain during functional activity: Theoretical modeling and experimental data

Coupling of cerebral blood flow (CBF) and cerebral metabolic rate for oxygen (CMRO2) in physiologically activated brain states remains the subject of debates. Recently it was suggested that CBF is tightly coupled to oxidative metabolism in a nonlinear fashion. As part of this hypothesis, mathematical models of oxygen delivery to the brain have been described in which disproportionately large increases in CBF are necessary to sustain even small increases in CMRO2 during activation. We have explored the coupling of CBF and oxygen delivery by using two complementary methods. First, a more complex mathematical model was tested that differs from those recently described in that no assumptions were made regarding tissue oxygen level. Second, [15O] water CBF positron emission tomography (PET) studies in nine healthy subjects were conducted during states of visual activation and hypoxia to examine the relationship of CBF and oxygen delivery. In contrast to previous reports, our model showed adequate tissue levels of oxygen could be maintained without the need for increased CBF or oxygen delivery. Similarly, the PET studies demonstrated that the regional increase in CBF during visual activation was not affected by hypoxia. These findings strongly indicate that the increase in CBF associated with physiological activation is regulated by factors other than local requirements in oxygen.

Theoretical modeling and experimental validation of fluid-loaded micro rectangular plates

This paper presents a theoretical model on the vibration analysis of micro scale fluid-loaded rectangular isotropic plates, based on the Lamb's assumption of fluid-structure interaction and the Rayleigh-Ritz energy method. An analytical solution for this model is proposed, which can be applied to most cases of boundary conditions. The dynamical experimental data of a series of microfabricated silicon plates are obtained using a base-excitation dynamic testing facility. The natural frequencies and mode shapes in the experimental results are in good agreement with the theoretical simulations for the lower order modes. The presented theoretical and experimental investigations on the vibration characteristics of the micro scale plates are of particular interest in the design of microplate based biosensing devices. Copyright © 2009 by ASME.

Ray-theoretical modeling of secondary microseism P-waves

Secondary microseism sources are pressure fluctuations close to the ocean surface. They generate acoustic P-waves that propagate in water down to the ocean bottom where they are partly reflected, and partly transmitted into the crust to continue their propagation through the Earth. We present the theory for computing the displacement power spectral density of secondary microseism P-waves recorded by receivers in the far field. In the frequency domain, the P-wave displacement can be modeled as the product of (1) the pressure source, (2) the source site effect that accounts for the constructive interference of multiply reflected P-waves in the ocean, (3) the propagation from the ocean bottom to the stations, (4) the receiver site effect. Secondary microseism P-waves have weak amplitudes, but they can be investigated by beamforming analysis. We validate our approach by analyzing the seismic signals generated by Typhoon Ioke (2006) and recorded by the Southern California Seismic Network. Back projecting the beam onto the ocean surface enables to follow the source motion. The observed beam centroid is in the vicinity of the pressure source derived from the ocean wave model WAVEWATCH IIIR. The pressure source is then used for modeling the beam and a good agreement is obtained between measured and modeled beam amplitude variation over time. This modeling approach can be used to invert P-wave noise data and retrieve the source intensity and lateral extent.

Purification, characterization, crystallization and theoretical molecular modeling of gyroxin fraction from Crotalus durissus terrificus venom (Laurenti, 1768)

The venom of Crotalus durissus terrificus snakes presents various substances, including a serine protease with thrombin-like activity, called gyroxin, that clots plasmatic fibrinogen and promote the fibrin formation. The aim of this study was to purify and structurally characterize the gyroxin enzyme from Crotalus durissus terrificus venom. For isolation and purification, the following methods were employed: gel filtration on Sephadex G75 column and affinity chromatography on benzamidine Sepharose 6B; 12% SDS-PAGE under reducing conditions; N-terminal sequence analysis; cDNA cloning and expression through RT-PCR and crystallization tests. Theoretical molecular modeling was performed using bioinformatics tools based on comparative analysis of other serine proteases deposited in the NCBI (National Center for Biotechnology Information) database. Protein N-terminal sequencing produced a single chain with a molecular mass of similar to 30 kDa while its full-length cDNA had 714 bp which encoded a mature protein containing 238 amino acids. Crystals were obtained from the solutions 2 and 5 of the Crystal Screen Kit (R), two and one respectively, that reveal the protein constitution of the sample. For multiple sequence alignments of gyroxin-like B2.1 with six other serine proteases obtained from snake venoms (SVSPs), the preservation of cysteine residues and their main structural elements (alpha-helices, beta-barrel and loops) was indicated. The localization of the catalytic triad in His57, Asp102 and Ser198 as well as S1 and S2 specific activity sites in Thr193 and Gli215 amino acids was pointed. The area of recognition and cleavage of fibrinogen in SVSPs for modeling gyroxin B2.1 sequence was located at Arg60, Arg72, Gln75, Arg81, Arg82, Lis85, Glu86 and Lis87 residues. Theoretical modeling of gyroxin fraction generated a classical structure consisting of two alpha-helices, two beta-barrel structures, five disulfide bridges and loops in positions 37, 60, 70, 99, 148, 174 and 218. These results provided information about the functional structure of gyroxin allowing its application in the design of new drugs.

Progress In Modeling Of Fluid Flows In Crystal Growth Processes

Modeling of fluid flows in crystal growth processes has become an important research area in theoretical and applied mechanics. Most crystal growth processes involve fluid flows, such as flows in the melt, solution or vapor. Theoretical modeling has played an important role in developing technologies used for growing semiconductor crystals for high performance electronic and optoelectronic devices. The application of devices requires large diameter crystals with a high degree of crystallographic perfection, low defect density and uniform dopant distribution. In this article, the flow models developed in modeling of the crystal growth processes such as Czochralski, ammonothermal and physical vapor transport methods are reviewed. In the Czochralski growth modeling, the flow models for thermocapillary flow, turbulent flow and MHD flow have been developed. In the ammonothermal growth modeling, the buoyancy and porous media flow models have been developed based on a single-domain and continuum approach for the composite fluid-porous layer systems. In the physical vapor transport growth modeling, the Stefan flow model has been proposed based on the flow-kinetics theory for the vapor growth. In addition, perspectives for future studies on crystal growth modeling are proposed. (c) 2008 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Theoretical insights into bacterial chemotaxis

Research into understanding bacterial chemotactic systems has become a paradigm for Systems Biology. Experimental and theoretical researchers have worked hand-in-hand for over 40 years to understand the intricate behavior driving bacterial species, in particular how such small creatures, usually not more than 5 µm in length, detect and respond to small changes in their extracellular environment. In this review we highlight the importance that theoretical modeling has played in providing new insight and understanding into bacterial chemotaxis. We begin with an overview of the bacterial chemotaxis sensory response, before reviewing the role of theoretical modeling in understanding elements of the system on the single cell scale and features underpinning multiscale extensions to population models. WIREs Syst Biol Med 2012 doi: 10.1002/wsbm.1168 For further resources related to this article, please visit the WIREs website.

Dye incorporation in polyphosphate gels: synthesis and theoretical calculations

ABSTRACT: In this work we described theoretical calculations on the electronic structure and optical properties of the dyes crystal violet and malachite green based in semiempirical methods (Parametric Method 3 and Intermediate Neglect of Differential Overlap / Spectroscopic - Configuration Interaction) and the synthesis of a new hybrid material based upon the incorporation of these dyes in an aluminum polyphosphate gel network. The samples are nearly transparent, free-standing thick films. The optical properties of the entrapped dyes are sensitive to chemical changes within the matrix caused either by gel aging or external stimulli such as exposition to acidic and basic vapors that can percolate within the matrix. Our theoretical modeling is in good agreement with the experimental results for the dyes.

Development and evolution of caste dimorphism in honeybees - a modeling approach

The difference in phenotypes of queens and workers is a hallmark of the highly eusocial insects. The caste dimorphism is often described as a switch-controlled polyphenism, in which environmental conditions decide an individual's caste. Using theoretical modeling and empirical data from honeybees, we show that there is no discrete larval developmental switch. Instead, a combination of larval developmental plasticity and nurse worker feeding behavior make up a colony-level social and physiological system that regulates development and produces the caste dimorphism. Discrete queen and worker phenotypes are the result of discrete feeding regimes imposed by nurses, whereas a range of experimental feeding regimes produces a continuous range of phenotypes. Worker ovariole numbers are reduced through feeding-regime-mediated reduction in juvenile hormone titers, involving reduced sugar in the larval food. Based on the mechanisms identified in our analysis, we propose a scenario of the evolutionary history of honeybee development and feeding regimes.