PCI-SS: MISO dynamic nonlinear protein secondary structure prediction
Directory of Open Access Journals (Sweden)
Aboul-Magd Mohammed O
2009-07-01
Full Text Available Abstract Background Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing α-helices, β-strands, and non-regular structures from primary sequence data which makes use of Parallel Cascade Identification (PCI, a powerful technique from the field of nonlinear system identification. Results Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs are applied in order to optimize the architectural parameters of the PCI models. The three-state prediction problem is broken down into a combination of three binary sub-problems and protein structure classifiers are built using 2 layers of PCI classifiers. Careful construction of the optimization, training, and test datasets ensures that no homology exists between any training and testing data. A detailed comparison between PCI and 9 contemporary methods is provided over a set of 125 new protein chains guaranteed to be dissimilar to all training data. Unlike other secondary structure prediction methods, here a web service is developed to provide both human- and machine-readable interfaces to PCI-based protein secondary structure prediction. This server, called PCI-SS, is available at http://bioinf.sce.carleton.ca/PCISS. In addition to a dynamic PHP-generated web interface for humans, a Simple Object Access Protocol (SOAP interface is added to permit invocation of the PCI-SS service remotely. This machine-readable interface facilitates incorporation of PCI-SS into multi-faceted systems biology analysis pipelines requiring protein secondary structure information, and greatly simplifies high-throughput analyses. XML is used to represent the input
Nonlinear Finite Strain Consolidation Analysis with Secondary Consolidation Behavior
Directory of Open Access Journals (Sweden)
Jieqing Huang
2014-01-01
Full Text Available This paper aims to analyze nonlinear finite strain consolidation with secondary consolidation behavior. On the basis of some assumptions about the secondary consolidation behavior, the continuity equation of pore water in Gibson’s consolidation theory is modified. Taking the nonlinear compressibility and nonlinear permeability of soils into consideration, the governing equation for finite strain consolidation analysis is derived. Based on the experimental data of Hangzhou soft clay samples, the new governing equation is solved with the finite element method. Afterwards, the calculation results of this new method and other two methods are compared. It can be found that Gibson’s method may underestimate the excess pore water pressure during primary consolidation. The new method which takes the secondary consolidation behavior, the nonlinear compressibility, and nonlinear permeability of soils into consideration can precisely estimate the settlement rate and the final settlement of Hangzhou soft clay sample.
Research on nonlinearity effect of secondary electron multiplier
International Nuclear Information System (INIS)
Wei Xingjian; Liao Junsheng; Deng Dachao; Yu Chunrong; Yuan Li
2007-01-01
The nonlinearity of secondary electron multiplier (SEM) of a thermal ionization mass spectrometer has been researched by using UTB-500 uranium isotope reference material and multi-collecting technique. The results show that the nonlinearity effect of SEM exists in the whole ion counting range, and there is an extreme point of the nonlinearity when the ion counting rate is about 20000 cps. The deviation between measured value of the extreme point and the reference value of the reference sample can be up to 3%, and the nonlinearity obeys logarithm linearity law on both sides of extreme point. A kind of mathematics model of nonlinearity calibration has been put forward. Using this model, the nonlinearity of SEM of TIMS can be calibrated. (authors)
Nonlinear Development and Secondary Instability of Traveling Crossflow Vortices
Li, Fei; Choudhari, Meelan M.; Duan, Lian; Chang, Chau-Lyan
2014-01-01
Transition research under NASA's Aeronautical Sciences Project seeks to develop a validated set of variable fidelity prediction tools with known strengths and limitations, so as to enable "sufficiently" accurate transition prediction and practical transition control for future vehicle concepts. This paper builds upon prior effort targeting the laminar breakdown mechanisms associated with stationary crossflow instability over a swept-wing configuration relevant to subsonic aircraft with laminar flow technology. Specifically, transition via secondary instability of traveling crossflow modes is investigated as an alternate scenario for transition. Results show that, for the parameter range investigated herein, secondary instability of traveling crossflow modes becomes insignificant in relation to the secondary instability of the stationary modes when the relative initial amplitudes of the traveling crossflow instability are lower than those of the stationary modes by approximately two orders of magnitudes or more. Linear growth predictions based on the secondary instability theory are found to agree well with those based on PSE and DNS, with the most significant discrepancies being limited to spatial regions of relatively weak secondary growth, i.e., regions where the primary disturbance amplitudes are smaller in comparison to its peak amplitude. Nonlinear effects on secondary instability evolution is also investigated and found to be initially stabilizing, prior to breakdown.
Amino acid code of protein secondary structure.
Shestopalov, B V
2003-01-01
The calculation of protein three-dimensional structure from the amino acid sequence is a fundamental problem to be solved. This paper presents principles of the code theory of protein secondary structure, and their consequence--the amino acid code of protein secondary structure. The doublet code model of protein secondary structure, developed earlier by the author (Shestopalov, 1990), is part of this theory. The theory basis are: 1) the name secondary structure is assigned to the conformation, stabilized only by the nearest (intraresidual) and middle-range (at a distance no more than that between residues i and i + 5) interactions; 2) the secondary structure consists of regular (alpha-helical and beta-structural) and irregular (coil) segments; 3) the alpha-helices, beta-strands and coil segments are encoded, respectively, by residue pairs (i, i + 4), (i, i + 2), (i, i = 1), according to the numbers of residues per period, 3.6, 2, 1; 4) all such pairs in the amino acid sequence are codons for elementary structural elements, or structurons; 5) the codons are divided into 21 types depending on their strength, i.e. their encoding capability; 6) overlappings of structurons of one and the same structure generate the longer segments of this structure; 7) overlapping of structurons of different structures is forbidden, and therefore selection of codons is required, the codon selection is hierarchic; 8) the code theory of protein secondary structure generates six variants of the amino acid code of protein secondary structure. There are two possible kinds of model construction based on the theory: the physical one using physical properties of amino acid residues, and the statistical one using results of statistical analysis of a great body of structural data. Some evident consequences of the theory are: a) the theory can be used for calculating the secondary structure from the amino acid sequence as a partial solution of the problem of calculation of protein three
Protein secondary structure: category assignment and predictability
DEFF Research Database (Denmark)
Andersen, Claus A.; Bohr, Henrik; Brunak, Søren
2001-01-01
In the last decade, the prediction of protein secondary structure has been optimized using essentially one and the same assignment scheme known as DSSP. We present here a different scheme, which is more predictable. This scheme predicts directly the hydrogen bonds, which stabilize the secondary......-forward neural network with one hidden layer on a data set identical to the one used in earlier work....
A Kernel for Protein Secondary Structure Prediction
Guermeur , Yann; Lifchitz , Alain; Vert , Régis
2004-01-01
http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=10338&mode=toc; International audience; Multi-class support vector machines have already proved efficient in protein secondary structure prediction as ensemble methods, to combine the outputs of sets of classifiers based on different principles. In this chapter, their implementation as basic prediction methods, processing the primary structure or the profile of multiple alignments, is investigated. A kernel devoted to the task is in...
Nonlinear deterministic structures and the randomness of protein sequences
Huang Yan Zhao
2003-01-01
To clarify the randomness of protein sequences, we make a detailed analysis of a set of typical protein sequences representing each structural classes by using nonlinear prediction method. No deterministic structures are found in these protein sequences and this implies that they behave as random sequences. We also give an explanation to the controversial results obtained in previous investigations.
Predicting Protein Secondary Structure with Markov Models
DEFF Research Database (Denmark)
Fischer, Paul; Larsen, Simon; Thomsen, Claus
2004-01-01
we are considering here, is to predict the secondary structure from the primary one. To this end we train a Markov model on training data and then use it to classify parts of unknown protein sequences as sheets, helices or coils. We show how to exploit the directional information contained...... in the Markov model for this task. Classifications that are purely based on statistical models might not always be biologically meaningful. We present combinatorial methods to incorporate biological background knowledge to enhance the prediction performance....
Molecular nonlinear dynamics and protein thermal uncertainty quantification
Xia, Kelin; Wei, Guo-Wei
2014-01-01
This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction. PMID:24697365
Detection of secondary binding sites in proteins using fragment screening.
Ludlow, R Frederick; Verdonk, Marcel L; Saini, Harpreet K; Tickle, Ian J; Jhoti, Harren
2015-12-29
Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.
Bayesian Inference using Neural Net Likelihood Models for Protein Secondary Structure Prediction
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Seong-Gon Kim
2011-06-01
Full Text Available Several techniques such as Neural Networks, Genetic Algorithms, Decision Trees and other statistical or heuristic methods have been used to approach the complex non-linear task of predicting Alpha-helicies, Beta-sheets and Turns of a proteins secondary structure in the past. This project introduces a new machine learning method by using an offline trained Multilayered Perceptrons (MLP as the likelihood models within a Bayesian Inference framework to predict secondary structures proteins. Varying window sizes are used to extract neighboring amino acid information and passed back and forth between the Neural Net models and the Bayesian Inference process until there is a convergence of the posterior secondary structure probability.
Combining neural networks for protein secondary structure prediction
DEFF Research Database (Denmark)
Riis, Søren Kamaric
1995-01-01
In this paper structured neural networks are applied to the problem of predicting the secondary structure of proteins. A hierarchical approach is used where specialized neural networks are designed for each structural class and then combined using another neural network. The submodels are designed...... by using a priori knowledge of the mapping between protein building blocks and the secondary structure and by using weight sharing. Since none of the individual networks have more than 600 adjustable weights over-fitting is avoided. When ensembles of specialized experts are combined the performance...
Deep recurrent conditional random field network for protein secondary prediction
DEFF Research Database (Denmark)
Johansen, Alexander Rosenberg; Sønderby, Søren Kaae; Sønderby, Casper Kaae
2017-01-01
Deep learning has become the state-of-the-art method for predicting protein secondary structure from only its amino acid residues and sequence profile. Building upon these results, we propose to combine a bi-directional recurrent neural network (biRNN) with a conditional random field (CRF), which...... of the labels for all time-steps. We condition the CRF on the output of biRNN, which learns a distributed representation based on the entire sequence. The biRNN-CRF is therefore close to ideally suited for the secondary structure task because a high degree of cross-talk between neighboring elements can...
Cascaded bidirectional recurrent neural networks for protein secondary structure prediction.
Chen, Jinmiao; Chaudhari, Narendra
2007-01-01
Protein secondary structure (PSS) prediction is an important topic in bioinformatics. Our study on a large set of non-homologous proteins shows that long-range interactions commonly exist and negatively affect PSS prediction. Besides, we also reveal strong correlations between secondary structure (SS) elements. In order to take into account the long-range interactions and SS-SS correlations, we propose a novel prediction system based on cascaded bidirectional recurrent neural network (BRNN). We compare the cascaded BRNN against another two BRNN architectures, namely the original BRNN architecture used for speech recognition as well as Pollastri's BRNN that was proposed for PSS prediction. Our cascaded BRNN achieves an overall three state accuracy Q3 of 74.38\\%, and reaches a high Segment OVerlap (SOV) of 66.0455. It outperforms the original BRNN and Pollastri's BRNN in both Q3 and SOV. Specifically, it improves the SOV score by 4-6%.
A genetic bistable switch utilizing nonlinear protein degradation.
Huang, Daniel; Holtz, William J; Maharbiz, Michel M
2012-07-09
Bistability is a fundamental property in engineered and natural systems, conferring the ability to switch and retain states. Synthetic bistable switches in prokaryotes have mainly utilized transcriptional components in their construction. Using both transcriptional and enzymatic components, creating a hybrid system, allows for wider bistable parameter ranges in a circuit. In this paper, we demonstrate a tunable family of hybrid bistable switches in E. coli using both transcriptional components and an enzymatic component. The design contains two linked positive feedback loops. The first loop utilizes the lambda repressor, CI, and the second positive feedback loop incorporates the Lon protease found in Mesoplasma florum (mf-Lon). We experimentally tested for bistable behavior in exponential growth phase, and found that our hybrid bistable switch was able to retain its state in the absence of an input signal throughout 40 cycles of cell division. We also tested the transient behavior of our switch and found that switching speeds can be tuned by changing the expression rate of mf-Lon. To our knowledge, this work demonstrates the first use of dynamic expression of an orthogonal and heterologous protease to tune a nonlinear protein degradation circuit. The hybrid switch is potentially a more robust and tunable topology for use in prokaryotic systems.
Parallel protein secondary structure prediction based on neural networks.
Zhong, Wei; Altun, Gulsah; Tian, Xinmin; Harrison, Robert; Tai, Phang C; Pan, Yi
2004-01-01
Protein secondary structure prediction has a fundamental influence on today's bioinformatics research. In this work, binary and tertiary classifiers of protein secondary structure prediction are implemented on Denoeux belief neural network (DBNN) architecture. Hydrophobicity matrix, orthogonal matrix, BLOSUM62 and PSSM (position specific scoring matrix) are experimented separately as the encoding schemes for DBNN. The experimental results contribute to the design of new encoding schemes. New binary classifier for Helix versus not Helix ( approximately H) for DBNN produces prediction accuracy of 87% when PSSM is used for the input profile. The performance of DBNN binary classifier is comparable to other best prediction methods. The good test results for binary classifiers open a new approach for protein structure prediction with neural networks. Due to the time consuming task of training the neural networks, Pthread and OpenMP are employed to parallelize DBNN in the hyperthreading enabled Intel architecture. Speedup for 16 Pthreads is 4.9 and speedup for 16 OpenMP threads is 4 in the 4 processors shared memory architecture. Both speedup performance of OpenMP and Pthread is superior to that of other research. With the new parallel training algorithm, thousands of amino acids can be processed in reasonable amount of time. Our research also shows that hyperthreading technology for Intel architecture is efficient for parallel biological algorithms.
Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.
Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo
2016-01-11
Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.
Wang, W. L.; Zhou, Z. R.; Yu, D. S.; Qin, Q. H.; Iwnicki, S.
2017-10-01
A full nonlinear physical 'in-service' model was built for a rail vehicle secondary suspension hydraulic damper with shim-pack-type valves. In the modelling process, a shim pack deflection theory with an equivalent-pressure correction factor was proposed, and a Finite Element Analysis (FEA) approach was applied. Bench test results validated the damper model over its full velocity range and thus also proved that the proposed shim pack deflection theory and the FEA-based parameter identification approach are effective. The validated full damper model was subsequently incorporated into a detailed vehicle dynamics simulation to study how its key in-service parameter variations influence the secondary-suspension-related vehicle system dynamics. The obtained nonlinear physical in-service damper model and the vehicle dynamic response characteristics in this study could be used in the product design optimization and nonlinear optimal specifications of high-speed rail hydraulic dampers.
Kamkar, Milad; Aliabadian, Ehsan; Shayesteh Zeraati, Ali; Sundararaj, Uttandaraman
2018-02-01
Carbon nanotube (CNT)/polymer nanocomposites exhibit excellent electrical properties by forming a percolated network. Adding a secondary filler can significantly affect the CNTs' network, resulting in changing the electrical properties. In this work, we investigated the effect of adding manganese dioxide nanowires (MnO2NWs) as a secondary nanofiller on the CNTs' network structure inside a poly(vinylidene fluoride) (PVDF) matrix. Incorporating MnO2NWs to PVDF/CNT samples produced a better state of dispersion of CNTs, as corroborated by light microscopy and transmission electron microscopy. The steady shear and oscillatory shear flows were employed to obtain a better insight into the nanofiller structure and viscoelastic behavior of the nanocomposites. The transient response under steady shear flow revealed that the stress overshoot of hybrid nanocomposites (two-fillers), PVDF/CNT/MnO2NWs, increased dramatically in comparison to binary nanocomposites (single-filler), PVDF/CNT and PVDF/MnO2NWs. This can be attributed to microstructural changes. Large amplitude oscillatory shear characterization was also performed to further investigate the effect of the secondary nanofiller on the nonlinear viscoelastic behavior of the samples. The nonlinear rheological observations were explained using quantitative nonlinear parameters [strain-stiffening ratio (S) and shear-thickening ratio (T)] and Lissajous-Bowditch plots. Results indicated that a more rigid nanofiller network was formed for the hybrid nanocomposites due to the better dispersion state of CNTs and this led to a more nonlinear viscoelastic behavior.
Protein 8-class secondary structure prediction using conditional neural fields.
Wang, Zhiyong; Zhao, Feng; Peng, Jian; Xu, Jinbo
2011-10-01
Compared with the protein 3-class secondary structure (SS) prediction, the 8-class prediction gains less attention and is also much more challenging, especially for proteins with few sequence homologs. This paper presents a new probabilistic method for 8-class SS prediction using conditional neural fields (CNFs), a recently invented probabilistic graphical model. This CNF method not only models the complex relationship between sequence features and SS, but also exploits the interdependency among SS types of adjacent residues. In addition to sequence profiles, our method also makes use of non-evolutionary information for SS prediction. Tested on the CB513 and RS126 data sets, our method achieves Q8 accuracy of 64.9 and 64.7%, respectively, which are much better than the SSpro8 web server (51.0 and 48.0%, respectively). Our method can also be used to predict other structure properties (e.g. solvent accessibility) of a protein or the SS of RNA. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Molkenthin, Nora; Hu, Shuangwei; Niemi, Antti J.
2011-02-01
We introduce a novel generalization of the discrete nonlinear Schrödinger equation. It supports solitons that we utilize to model chiral polymers in the collapsed phase and, in particular, proteins in their native state. As an example we consider the villin headpiece HP35, an archetypal protein for testing both experimental and theoretical approaches to protein folding. We use its backbone as a template to explicitly construct a two-soliton configuration. Each of the two solitons describe well over 7.000 supersecondary structures of folded proteins in the Protein Data Bank with sub-angstrom accuracy suggesting that these solitons are common in nature.
Rigatos, Gerasimos G; Rigatou, Efthymia G; Djida, Jean Daniel
2015-10-01
A method for early diagnosis of parametric changes in intracellular protein synthesis models (e.g. the p53 protein - mdm2 inhibitor model) is developed with the use of a nonlinear Kalman Filtering approach (Derivative-free nonlinear Kalman Filter) and of statistical change detection methods. The intracellular protein synthesis dynamic model is described by a set of coupled nonlinear differential equations. It is shown that such a dynamical system satisfies differential flatness properties and this allows to transform it, through a change of variables (diffeomorphism), to the so-called linear canonical form. For the linearized equivalent of the dynamical system, state estimation can be performed using the Kalman Filter recursion. Moreover, by applying an inverse transformation based on the previous diffeomorphism it becomes also possible to obtain estimates of the state variables of the initial nonlinear model. By comparing the output of the Kalman Filter (which is assumed to correspond to the undistorted dynamical model) with measurements obtained from the monitored protein synthesis system, a sequence of differences (residuals) is obtained. The statistical processing of the residuals with the use of x2 change detection tests, can provide indication within specific confidence intervals about parametric changes in the considered biological system and consequently indications about the appearance of specific diseases (e.g. malignancies).
Nonlinear analysis of sequence repeats of multi-domain proteins
Energy Technology Data Exchange (ETDEWEB)
Huang Yanzhao [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Li Mingfeng [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xiao Yi [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China)]. E-mail: lmf_bill@sina.com
2007-11-15
Many multi-domain proteins have repetitive three-dimensional structures but nearly-random amino acid sequences. In the present paper, by using a modified recurrence plot proposed by us previously, we show that these amino acid sequences have hidden repetitions in fact. These results indicate that the repetitive domain structures are encoded by the repetitive sequences. This also gives a method to detect the repetitive domain structures directly from amino acid sequences.
Amino Acid Molecular Units: Building Primary and Secondary Protein Structures
Directory of Open Access Journals (Sweden)
Aparecido R. Silva
2008-05-01
Full Text Available In order to guarantee the learning quality and suitable knowledge use about structural biology, it is fundamental to exist, since the beginning of students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring schematic drawings; even more elaborated figures and graphic computation do not permit the necessary interaction. The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to visualize such structures and correlate them to the real molecules. The design and applicability of the representative units were discussed with researchers and teachers before mould implementation. In this stage it will be presented the developed kit containing the representative plastic parts of the main amino acids. The kit can demonstrate the interaction among the amino acids functional groups (represented by colors, shapes, sizes and the peptidic bonds between them facilitating the assembly and visuali zation of the primary and secondary protein structure. The models were designed for Ca, amino, carboxyl groups and hydrogen. The lateral chains have well defined models that represent their geometrical shape. The completed kit set will be presented in this meeting (patent requested. In the last phase of the project will be realized an effective evaluation of the kit as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.
Density functional study of molecular interactions in secondary structures of proteins.
Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki
2016-01-01
Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.
Rigatos, Gerasimos G
2016-06-01
It is proven that the model of the p53-mdm2 protein synthesis loop is a differentially flat one and using a diffeomorphism (change of state variables) that is proposed by differential flatness theory it is shown that the protein synthesis model can be transformed into the canonical (Brunovsky) form. This enables the design of a feedback control law that maintains the concentration of the p53 protein at the desirable levels. To estimate the non-measurable elements of the state vector describing the p53-mdm2 system dynamics, the derivative-free non-linear Kalman filter is used. Moreover, to compensate for modelling uncertainties and external disturbances that affect the p53-mdm2 system, the derivative-free non-linear Kalman filter is re-designed as a disturbance observer. The derivative-free non-linear Kalman filter consists of the Kalman filter recursion applied on the linearised equivalent of the protein synthesis model together with an inverse transformation based on differential flatness theory that enables to retrieve estimates for the state variables of the initial non-linear model. The proposed non-linear feedback control and perturbations compensation method for the p53-mdm2 system can result in more efficient chemotherapy schemes where the infusion of medication will be better administered.
Protein Secondary Structure Prediction Using AutoEncoder Network and Bayes Classifier
Wang, Leilei; Cheng, Jinyong
2018-03-01
Protein secondary structure prediction is belong to bioinformatics,and it's important in research area. In this paper, we propose a new prediction way of protein using bayes classifier and autoEncoder network. Our experiments show some algorithms including the construction of the model, the classification of parameters and so on. The data set is a typical CB513 data set for protein. In terms of accuracy, the method is the cross validation based on the 3-fold. Then we can get the Q3 accuracy. Paper results illustrate that the autoencoder network improved the prediction accuracy of protein secondary structure.
International Nuclear Information System (INIS)
Lobashev, A.A.; Mostepanenko, V.M.
1993-01-01
Heisenberg formalism is developed for creation-annihilation operators of quantum fields propagating in nonstationary external fields. Quantum fields with spin 0,1/2, 1 are considered in the presence of such external fields as electromagnetic, scalar and the field of nonstationary dielectric properties of nonlinear medium. Elliptic operator parametrically depending on time is constructed. In Heisenberg representation field variables are decomposed over eigenfunction of this operator. The relation between Heisenberg creation-annihilation operators and the operators obtained in the frame of diagonalization of Hamiltonian with Bogoliubov transformations is set up
Schaefer, Christian
2010-01-16
MOTIVATION: The mutation of amino acids often impacts protein function and structure. Mutations without negative effect sustain evolutionary pressure. We study a particular aspect of structural robustness with respect to mutations: regular protein secondary structure and natively unstructured (intrinsically disordered) regions. Is the formation of regular secondary structure an intrinsic feature of amino acid sequences, or is it a feature that is lost upon mutation and is maintained by evolution against the odds? Similarly, is disorder an intrinsic sequence feature or is it difficult to maintain? To tackle these questions, we in silico mutated native protein sequences into random sequence-like ensembles and monitored the change in predicted secondary structure and disorder. RESULTS: We established that by our coarse-grained measures for change, predictions and observations were similar, suggesting that our results were not biased by prediction mistakes. Changes in secondary structure and disorder predictions were linearly proportional to the change in sequence. Surprisingly, neither the content nor the length distribution for the predicted secondary structure changed substantially. Regions with long disorder behaved differently in that significantly fewer such regions were predicted after a few mutation steps. Our findings suggest that the formation of regular secondary structure is an intrinsic feature of random amino acid sequences, while the formation of long-disordered regions is not an intrinsic feature of proteins with disordered regions. Put differently, helices and strands appear to be maintained easily by evolution, whereas maintaining disordered regions appears difficult. Neutral mutations with respect to disorder are therefore very unlikely.
Schaefer, Christian; Schlessinger, Avner; Rost, Burkhard
2010-01-01
MOTIVATION: The mutation of amino acids often impacts protein function and structure. Mutations without negative effect sustain evolutionary pressure. We study a particular aspect of structural robustness with respect to mutations: regular protein secondary structure and natively unstructured (intrinsically disordered) regions. Is the formation of regular secondary structure an intrinsic feature of amino acid sequences, or is it a feature that is lost upon mutation and is maintained by evolution against the odds? Similarly, is disorder an intrinsic sequence feature or is it difficult to maintain? To tackle these questions, we in silico mutated native protein sequences into random sequence-like ensembles and monitored the change in predicted secondary structure and disorder. RESULTS: We established that by our coarse-grained measures for change, predictions and observations were similar, suggesting that our results were not biased by prediction mistakes. Changes in secondary structure and disorder predictions were linearly proportional to the change in sequence. Surprisingly, neither the content nor the length distribution for the predicted secondary structure changed substantially. Regions with long disorder behaved differently in that significantly fewer such regions were predicted after a few mutation steps. Our findings suggest that the formation of regular secondary structure is an intrinsic feature of random amino acid sequences, while the formation of long-disordered regions is not an intrinsic feature of proteins with disordered regions. Put differently, helices and strands appear to be maintained easily by evolution, whereas maintaining disordered regions appears difficult. Neutral mutations with respect to disorder are therefore very unlikely.
Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps
Kumari, Amrita; Dorai, Kavita
2013-06-01
NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.
International Nuclear Information System (INIS)
Yu, P.
2007-01-01
Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the α-helix and β-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of β-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present study were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution (∼10 μm). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of α-helixes and β-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of α-helixes (from 47.1% to 36.1%: S-FTIR absorption intensity), increased the
Energy Technology Data Exchange (ETDEWEB)
Yu,P.
2007-01-01
Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the {alpha}-helix and {beta}-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of {beta}-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present study were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution ({approx}10 {mu}m). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of {alpha}-helixes and {beta}-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of {alpha}-helixes (from 47.1% to 36.1%: S
Protein Recovery from Secondary Paper Sludge and Its Potential Use as Wood Adhesive
Pervaiz, Muhammad
Secondary sludge is an essential part of biosolids produced through the waste treatment plant of paper mills. Globally paper mills generate around 3.0 million ton of biosolids and in the absence of beneficial applications, the handling and disposal of this residual biomass poses a serious environmental and economic proposition. Secondary paper sludges were investigated in this work for recovery of proteins and their use as wood adhesive. After identifying extracellular polymeric substances as adhesion pre-cursors through analytical techniques, studies were carried out to optimize protein recovery from SS and its comprehensive characterization. A modified physicochemical protocol was developed to recover protein from secondary sludge in substantial quantities. The combined effect of French press and sonication techniques followed by alkali treatment resulted in significant improvement of 44% in the yield of solubilized protein compared to chemical methods. The characterization studies confirmed the presence of common amino acids in recovered sludge protein in significant quantities and heavy metal concentration was reduced after recovery process. The sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis revealed the presence of both low and high molecular weight protein fractions in recovered sludge protein. After establishing the proof-of-concept in the use of recovered sludge protein as wood adhesive, the bonding mechanism of protein adhesives with cellulose substrate was further elucidated in a complementary protein-modification study involving soy protein isolate and its glycinin fractions. The results of this study validated the prevailing bonding theories by proving that surface wetting, protein structure, and type of wood play important role in determining final adhesive strength. Recovered sludge protein was also investigated for its compatibility to formulate hybrid adhesive blends with formaldehyde and bio-based polymers. Apart from chemical
Improving the accuracy of protein secondary structure prediction using structural alignment
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Gallin Warren J
2006-06-01
Full Text Available Abstract Background The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3 of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences, the probability of a newly identified sequence having a structural homologue is actually quite high. Results We have developed a method that performs structure-based sequence alignments as part of the secondary structure prediction process. By mapping the structure of a known homologue (sequence ID >25% onto the query protein's sequence, it is possible to predict at least a portion of that query protein's secondary structure. By integrating this structural alignment approach with conventional (sequence-based secondary structure methods and then combining it with a "jury-of-experts" system to generate a consensus result, it is possible to attain very high prediction accuracy. Using a sequence-unique test set of 1644 proteins from EVA, this new method achieves an average Q3 score of 81.3%. Extensive testing indicates this is approximately 4–5% better than any other method currently available. Assessments using non sequence-unique test sets (typical of those used in proteome annotation or structural genomics indicate that this new method can achieve a Q3 score approaching 88%. Conclusion By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible at http://wishart.biology.ualberta.ca/proteus. For high throughput or batch sequence analyses, the PROTEUS programs
Detection of secondary structure elements in proteins by hydrophobic cluster analysis.
Woodcock, S; Mornon, J P; Henrissat, B
1992-10-01
Hydrophobic cluster analysis (HCA) is a protein sequence comparison method based on alpha-helical representations of the sequences where the size, shape and orientation of the clusters of hydrophobic residues are primarily compared. The effectiveness of HCA has been suggested to originate from its potential ability to focus on the residues forming the hydrophobic core of globular proteins. We have addressed the robustness of the bidimensional representation used for HCA in its ability to detect the regular secondary structure elements of proteins. Various parameters have been studied such as those governing cluster size and limits, the hydrophobic residues constituting the clusters as well as the potential shift of the cluster positions with respect to the position of the regular secondary structure elements. The following results have been found to support the alpha-helical bidimensional representation used in HCA: (i) there is a positive correlation (clearly above background noise) between the hydrophobic clusters and the regular secondary structure elements in proteins; (ii) the hydrophobic clusters are centred on the regular secondary structure elements; (iii) the pitch of the helical representation which gives the best correspondence is that of an alpha-helix. The correspondence between hydrophobic clusters and regular secondary structure elements suggests a way to implement variable gap penalties during the automatic alignment of protein sequences.
Protein losing enteropathy secondary to a pulmonary artery stent
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Narayanswami Sreeram
2012-01-01
Full Text Available A 2-year-old patient with hypoplastic left heart syndrome presented 6 months following Fontan completion with protein-losing enteropathy (PLE. He had undergone stent implantation in the left pulmonary artery after the Norwood procedure, followed by redilation of the stent prior to Fontan completion. Combined bronchoscopic and catheterization studies during spontaneous breathing confirmed left bronchial stenosis behind the stent, and diastolic systemic ventricular pressure during expiration of 25 mm Hg. We postulate that the stent acts as a valve, against which the patient generates high expiratory pressures, which are reflected in the ventricular diastolic pressure. This may be the cause of PLE.
Nonlinear optical methods for the analysis of protein nanocrystals and biological tissues
Dow, Ximeng You
Structural biology underpins rational drug design and fundamental understanding of protein function. X-ray diffraction (XRD) has been the golden standard for solving for high-resolution protein structure. Second harmonic generation (SHG) microscopy has been developed by the Simpson lab as a sensitive, crystal-specific detection method for the identification of protein crystal and help optimize the crystallization condition. Protein nanocrystals has been widely used for structure determination of membrane proteins in serial femtosecond nanocrystallography. In this thesis work, novel nonlinear optical methods were developed to address the challenges associated with the detection and characterization of protein nanocrystals. SHG-correlation spectroscopy (SHG-CS) was developed to take advantage of the diffusing motion and retrieve the size distribution and crystal quality of the nanocrystals. Polarization-dependent SHG imaging technique was developed to measure the relative orientation as well as the internal structure of the sample. Two photon- excited fluorescence has been used in the Simpson lab as a complementary measurement besides the inherent SHG signal from the crystals. A novel instrumentation development was also introduced in this thesis work to greatly improve the speed of fluorescence lifetime imaging (FLIM).
Dynamics of protein aggregation and oligomer formation governed by secondary nucleation
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Michaels, Thomas C. T., E-mail: tctm3@cam.ac.uk; Lazell, Hamish W.; Arosio, Paolo; Knowles, Tuomas P. J., E-mail: tpjk2@cam.ac.uk [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)
2015-08-07
The formation of aggregates in many protein systems can be significantly accelerated by secondary nucleation, a process where existing assemblies catalyse the nucleation of new species. In particular, secondary nucleation has emerged as a central process controlling the proliferation of many filamentous protein structures, including molecular species related to diseases such as sickle cell anemia and a range of neurodegenerative conditions. Increasing evidence suggests that the physical size of protein filaments plays a key role in determining their potential for deleterious interactions with living cells, with smaller aggregates of misfolded proteins, oligomers, being particularly toxic. It is thus crucial to progress towards an understanding of the factors that control the sizes of protein aggregates. However, the influence of secondary nucleation on the time evolution of aggregate size distributions has been challenging to quantify. This difficulty originates in large part from the fact that secondary nucleation couples the dynamics of species distant in size space. Here, we approach this problem by presenting an analytical treatment of the master equation describing the growth kinetics of linear protein structures proliferating through secondary nucleation and provide closed-form expressions for the temporal evolution of the resulting aggregate size distribution. We show how the availability of analytical solutions for the full filament distribution allows us to identify the key physical parameters that control the sizes of growing protein filaments. Furthermore, we use these results to probe the dynamics of the populations of small oligomeric species as they are formed through secondary nucleation and discuss the implications of our work for understanding the factors that promote or curtail the production of these species with a potentially high deleterious biological activity.
Irradiation effects on secondary structure of protein induced by keV ions
International Nuclear Information System (INIS)
Cui, F.Z.; Lin, Y.B.; Zhang, D.M.; Tian, M.B.
2001-01-01
Protein secondary structure changes by low-energy ion irradiation are reported for the first time. The selected system is 30 keV N + irradiation on bovine serum albumin (BSA). After irradiation at increasing fluences from 1.0x10 15 to 2.5x10 16 ion/cm 2 , Fourier transform infrared spectra analysis was conducted. It was found that the secondary structures of BSA molecules were very sensitive to ion irradiation. Secondary conformations showed different trends of change during irradiation. With the increase of ion fluence from 0 to 2.5x10 16 ion/cm 2 , the fraction of α-helix and β-turns decreased from 17 to 12%, and from 40 to 31%, respectively, while that of random coil and β-sheet structure increased from 18 to 27%, and from 25 to 30%, respectively. Possible explanations for the secondary conformational changes of protein are proposed. (author)
Li, Sha Sha; Li, Bao Qiong; Liu, Jin Jin; Lu, Shao Hua; Zhai, Hong Lin
2018-04-20
Circular dichroism (CD) spectroscopy is a widely used technique for the evaluation of protein secondary structures that has a significant impact for the understanding of molecular biology. However, the quantitative analysis of protein secondary structures based on CD spectra is still a hard work due to the serious overlap of the spectra corresponding to different structural motifs. Here, Tchebichef image moment (TM) approach is introduced for the first time, which can effectively extract the chemical features in CD spectra for the quantitative analysis of protein secondary structures. The proposed approach was applied to analyze reference set. and the obtained results were evaluated by the strict statistical parameters such as correlation coefficient, cross-validation correlation coefficient and root mean squared error. Compared with several specialized prediction methods, TM approach provided satisfactory results, especially for turns and unordered structures. Our study indicates that TM approach can be regarded as a feasible tool for the analysis of the secondary structures of proteins based on CD spectra. An available TMs package is provided and can be used directly for secondary structures prediction. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.
Artificial Intelligence in Prediction of Secondary Protein Structure Using CB513 Database
Avdagic, Zikrija; Purisevic, Elvir; Omanovic, Samir; Coralic, Zlatan
2009-01-01
In this paper we describe CB513 a non-redundant dataset, suitable for development of algorithms for prediction of secondary protein structure. A program was made in Borland Delphi for transforming data from our dataset to make it suitable for learning of neural network for prediction of secondary protein structure implemented in MATLAB Neural-Network Toolbox. Learning (training and testing) of neural network is researched with different sizes of windows, different number of neurons in the hidden layer and different number of training epochs, while using dataset CB513. PMID:21347158
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Sze Sing-Hoi
2008-07-01
Full Text Available Abstract Background Since experimental determination of protein folding pathways remains difficult, computational techniques are often used to simulate protein folding. Most current techniques to predict protein folding pathways are computationally intensive and are suitable only for small proteins. Results By assuming that the native structure of a protein is known and representing each intermediate conformation as a collection of fully folded structures in which each of them contains a set of interacting secondary structure elements, we show that it is possible to significantly reduce the conformation space while still being able to predict the most energetically favorable folding pathway of large proteins with hundreds of residues at the mesoscopic level, including the pig muscle phosphoglycerate kinase with 416 residues. The model is detailed enough to distinguish between different folding pathways of structurally very similar proteins, including the streptococcal protein G and the peptostreptococcal protein L. The model is also able to recognize the differences between the folding pathways of protein G and its two structurally similar variants NuG1 and NuG2, which are even harder to distinguish. We show that this strategy can produce accurate predictions on many other proteins with experimentally determined intermediate folding states. Conclusion Our technique is efficient enough to predict folding pathways for both large and small proteins at the mesoscopic level. Such a strategy is often the only feasible choice for large proteins. A software program implementing this strategy (SSFold is available at http://faculty.cs.tamu.edu/shsze/ssfold.
MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction.
Fang, Chao; Shang, Yi; Xu, Dong
2018-05-01
Protein secondary structure prediction can provide important information for protein 3D structure prediction and protein functions. Deep learning offers a new opportunity to significantly improve prediction accuracy. In this article, a new deep neural network architecture, named the Deep inception-inside-inception (Deep3I) network, is proposed for protein secondary structure prediction and implemented as a software tool MUFOLD-SS. The input to MUFOLD-SS is a carefully designed feature matrix corresponding to the primary amino acid sequence of a protein, which consists of a rich set of information derived from individual amino acid, as well as the context of the protein sequence. Specifically, the feature matrix is a composition of physio-chemical properties of amino acids, PSI-BLAST profile, and HHBlits profile. MUFOLD-SS is composed of a sequence of nested inception modules and maps the input matrix to either eight states or three states of secondary structures. The architecture of MUFOLD-SS enables effective processing of local and global interactions between amino acids in making accurate prediction. In extensive experiments on multiple datasets, MUFOLD-SS outperformed the best existing methods and other deep neural networks significantly. MUFold-SS can be downloaded from http://dslsrv8.cs.missouri.edu/~cf797/MUFoldSS/download.html. © 2018 Wiley Periodicals, Inc.
Adhikari, Badri; Cheng, Jianlin
2017-08-29
Residue-residue contacts are key features for accurate de novo protein structure prediction. For the optimal utilization of these predicted contacts in folding proteins accurately, it is important to study the challenges of reconstructing protein structures using true contacts. Because contact-guided protein modeling approach is valuable for predicting the folds of proteins that do not have structural templates, it is necessary for reconstruction studies to focus on hard-to-predict protein structures. Using a data set consisting of 496 structural domains released in recent CASP experiments and a dataset of 150 representative protein structures, in this work, we discuss three techniques to improve the reconstruction accuracy using true contacts - adding secondary structures, increasing contact distance thresholds, and adding non-contacts. We find that reconstruction using secondary structures and contacts can deliver accuracy higher than using full contact maps. Similarly, we demonstrate that non-contacts can improve reconstruction accuracy not only when the used non-contacts are true but also when they are predicted. On the dataset consisting of 150 proteins, we find that by simply using low ranked predicted contacts as non-contacts and adding them as additional restraints, can increase the reconstruction accuracy by 5% when the reconstructed models are evaluated using TM-score. Our findings suggest that secondary structures are invaluable companions of contacts for accurate reconstruction. Confirming some earlier findings, we also find that larger distance thresholds are useful for folding many protein structures which cannot be folded using the standard definition of contacts. Our findings also suggest that for more accurate reconstruction using predicted contacts it is useful to predict contacts at higher distance thresholds (beyond 8 Å) and predict non-contacts.
Hafsa, Noor E; Arndt, David; Wishart, David S
2015-07-01
The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Zhou Yuan Wu
2013-07-01
Full Text Available In statistical methods of predicting protein secondary structure, many researchers focus on single amino acid frequencies in α-helices, β-sheets, and so on, or the impact near amino acids on an amino acid forming a secondary structure. But the paper considers a short sequence of amino acids (3, 4, 5 or 6 amino acids as integer, and statistics short sequence's probability forming secondary structure. Also, many researchers select low homologous sequences as statistical database. But this paper select whole PDB database. In this paper we propose a strategy to predict protein secondary structure using simple statistical method. Numerical computation shows that, short amino acids sequence as integer to statistics, which can easy see trend of short sequence forming secondary structure, and it will work well to select large statistical database (whole PDB database without considering homologous, and Q3 accuracy is ca. 74% using this paper proposed simple statistical method, but accuracy of others statistical methods is less than 70%.
Prediction of backbone dihedral angles and protein secondary structure using support vector machines
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Hirst Jonathan D
2009-12-01
Full Text Available Abstract Background The prediction of the secondary structure of a protein is a critical step in the prediction of its tertiary structure and, potentially, its function. Moreover, the backbone dihedral angles, highly correlated with secondary structures, provide crucial information about the local three-dimensional structure. Results We predict independently both the secondary structure and the backbone dihedral angles and combine the results in a loop to enhance each prediction reciprocally. Support vector machines, a state-of-the-art supervised classification technique, achieve secondary structure predictive accuracy of 80% on a non-redundant set of 513 proteins, significantly higher than other methods on the same dataset. The dihedral angle space is divided into a number of regions using two unsupervised clustering techniques in order to predict the region in which a new residue belongs. The performance of our method is comparable to, and in some cases more accurate than, other multi-class dihedral prediction methods. Conclusions We have created an accurate predictor of backbone dihedral angles and secondary structure. Our method, called DISSPred, is available online at http://comp.chem.nottingham.ac.uk/disspred/.
Shen, C.; Wu, C.; Gallet, S.; Cheng, H.; Edwards, R.; Hsieh, Y.; Lin, K.
2008-12-01
Contemporary multicollector-inductively coupled plasma mass spectrometry (MC-ICP-MS) with discrete dynode secondary electron multipliers (SEMs) can offer U-Th isotopic determinations with subpermil-permil- level precision in femtogram quantities. However, accurate isotopic measurement requires fully understanding SEM mass and intensity biases. In additional to dead-time effect, Richter et al (2001, Int. J. Mass Spectrom., 206, 105-127) reported a nonlinearity on SEMs produced by ETP and MasCom for count rates > 20 thousand counts per second (cps). We evaluated the possible biases for ion beams of 500- 1,600,000 cps on a latest MasCom SEM, SEV TE-Z/17, with more effective ion optical acceptance area (>50%) and better peak shape than previous models, used in a MC-ICP-MS, Thermo Fisher NEPTUNE. With the retarding potential quadruple lens (RPQ) turned off, ion beam intensity can be biased by only dead- time effect, which can be precisely corrected online or offline. With the RPQ on, two additional biases, an exponential-like increase of ion beam intensity from 100-100,000 s cps and an apparent dead-time effect (-2 to 2 ns) at high count rates, are observed. They are likely caused by the slightly defocused ions with a wide kinetic energy spread of ~5 eV, 10 times worse than that with thermal source, passing through the RPQ lens to the SEM, which is installed behind the focal plane. Fortunately, the two biases, which are stable during the daily measurements with the same settings of inlet system, source lenses, zoom optics, and RPQ, can be corrected effectively offline to earn accurate U-Th isotopic measurement.
ONIOM Investigation of the Second-Order Nonlinear Optical Responses of Fluorescent Proteins.
de Wergifosse, Marc; Botek, Edith; De Meulenaere, Evelien; Clays, Koen; Champagne, Benoît
2018-05-17
The first hyperpolarizability (β) of six fluorescent proteins (FPs), namely, enhanced green fluorescent protein, enhanced yellow fluorescent protein, SHardonnay, ZsYellow, DsRed, and mCherry, has been calculated to unravel the structure-property relationships on their second-order nonlinear optical properties, owing to their potential for multidimensional biomedical imaging. The ONIOM scheme has been employed and several of its refinements have been addressed to incorporate efficiently the effects of the microenvironment on the nonlinear optical responses of the FP chromophore that is embedded in a protective β-barrel protein cage. In the ONIOM scheme, the system is decomposed into several layers (here two) treated at different levels of approximation (method1/method2), from the most elaborated method (method1) for its core (called the high layer) to the most approximate one (method2) for the outer surrounding (called the low layer). We observe that a small high layer can already account for the variations of β as a function of the nature of the FP, provided the low layer is treated at an ab initio level to describe properly the effects of key H-bonds. Then, for semiquantitative reproduction of the experimental values obtained from hyper-Rayleigh scattering experiments, it is necessary to incorporate electron correlation as described at the second-order Møller-Plesset perturbation theory (MP2) level as well as implicit solvent effects accounted for using the polarizable continuum model (PCM). This led us to define the MP2/6-31+G(d):HF/6-31+G(d)/IEFPCM scheme as an efficient ONIOM approach and the MP2/6-31+G(d):HF/6-31G(d)/IEFPCM as a better compromise between accuracy and computational needs. Using these methods, we demonstrate that many parameters play a role on the β response of FPs, including the length of the π-conjugated segment, the variation of the bond length alternation, and the presence of π-stacking interactions. Then, noticing the small diversity
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models
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Borodovsky Mark
2006-03-01
Full Text Available Abstract Background The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of prediction algorithms: Single-sequence prediction algorithms imply that information about other (homologous proteins is not available, while algorithms of the second type imply that information about homologous proteins is available, and use it intensively. The single-sequence algorithms could make an important contribution to studies of proteins with no detected homologs, however the accuracy of protein secondary structure prediction from a single-sequence is not as high as when the additional evolutionary information is present. Results In this paper, we further refine and extend the hidden semi-Markov model (HSMM initially considered in the BSPSS algorithm. We introduce an improved residue dependency model by considering the patterns of statistically significant amino acid correlation at structural segment borders. We also derive models that specialize on different sections of the dependency structure and incorporate them into HSMM. In addition, we implement an iterative training method to refine estimates of HSMM parameters. The three-state-per-residue accuracy and other accuracy measures of the new method, IPSSP, are shown to be comparable or better than ones for BSPSS as well as for PSIPRED, tested under the single-sequence condition. Conclusions We have shown that new dependency models and training methods bring further improvements to single-sequence protein secondary structure prediction. The results are obtained under cross-validation conditions using a dataset with no pair of sequences having significant sequence similarity. As new sequences are added to the database it is possible to augment the dependency structure and obtain even higher accuracy. Current and future advances should contribute to the improvement of function prediction for orphan proteins inscrutable
Knowledge base and neural network approach for protein secondary structure prediction.
Patel, Maulika S; Mazumdar, Himanshu S
2014-11-21
Protein structure prediction is of great relevance given the abundant genomic and proteomic data generated by the genome sequencing projects. Protein secondary structure prediction is addressed as a sub task in determining the protein tertiary structure and function. In this paper, a novel algorithm, KB-PROSSP-NN, which is a combination of knowledge base and modeling of the exceptions in the knowledge base using neural networks for protein secondary structure prediction (PSSP), is proposed. The knowledge base is derived from a proteomic sequence-structure database and consists of the statistics of association between the 5-residue words and corresponding secondary structure. The predicted results obtained using knowledge base are refined with a Backpropogation neural network algorithm. Neural net models the exceptions of the knowledge base. The Q3 accuracy of 90% and 82% is achieved on the RS126 and CB396 test sets respectively which suggest improvement over existing state of art methods. Copyright © 2014 Elsevier Ltd. All rights reserved.
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de Brevern Alexandre G
2005-09-01
Full Text Available Abstract Background A number of methods are now available to perform automatic assignment of periodic secondary structures from atomic coordinates, based on different characteristics of the secondary structures. In general these methods exhibit a broad consensus as to the location of most helix and strand core segments in protein structures. However the termini of the segments are often ill-defined and it is difficult to decide unambiguously which residues at the edge of the segments have to be included. In addition, there is a "twilight zone" where secondary structure segments depart significantly from the idealized models of Pauling and Corey. For these segments, one has to decide whether the observed structural variations are merely distorsions or whether they constitute a break in the secondary structure. Methods To address these problems, we have developed a method for secondary structure assignment, called KAKSI. Assignments made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR, as well as secondary structures found in PDB files, on 4 datasets (X-ray structures with different resolution range, NMR structures. Results A detailed comparison of KAKSI assignments with those of STRIDE and PSEA reveals that KAKSI assigns slightly longer helices and strands than STRIDE in case of one-to-one correspondence between the segments. However, KAKSI tends also to favor the assignment of several short helices when STRIDE and PSEA assign longer, kinked, helices. Helices assigned by KAKSI have geometrical characteristics close to those described in the PDB. They are more linear than helices assigned by other methods. The same tendency to split long segments is observed for strands, although less systematically. We present a number of cases of secondary structure assignments that illustrate this behavior. Conclusion Our method provides valuable assignments which favor the regularity of secondary structure segments.
Babaei, Sepideh; Geranmayeh, Amir; Seyyedsalehi, Seyyed Ali
2010-12-01
The supervised learning of recurrent neural networks well-suited for prediction of protein secondary structures from the underlying amino acids sequence is studied. Modular reciprocal recurrent neural networks (MRR-NN) are proposed to model the strong correlations between adjacent secondary structure elements. Besides, a multilayer bidirectional recurrent neural network (MBR-NN) is introduced to capture the long-range intramolecular interactions between amino acids in formation of the secondary structure. The final modular prediction system is devised based on the interactive integration of the MRR-NN and the MBR-NN structures to arbitrarily engage the neighboring effects of the secondary structure types concurrent with memorizing the sequential dependencies of amino acids along the protein chain. The advanced combined network augments the percentage accuracy (Q₃) to 79.36% and boosts the segment overlap (SOV) up to 70.09% when tested on the PSIPRED dataset in three-fold cross-validation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.
Suresh, V; Parthasarathy, S
2014-01-01
We developed a support vector machine based web server called SVM-PB-Pred, to predict the Protein Block for any given amino acid sequence. The input features of SVM-PB-Pred include i) sequence profiles (PSSM) and ii) actual secondary structures (SS) from DSSP method or predicted secondary structures from NPS@ and GOR4 methods. There were three combined input features PSSM+SS(DSSP), PSSM+SS(NPS@) and PSSM+SS(GOR4) used to test and train the SVM models. Similarly, four datasets RS90, DB433, LI1264 and SP1577 were used to develop the SVM models. These four SVM models developed were tested using three different benchmarking tests namely; (i) self consistency, (ii) seven fold cross validation test and (iii) independent case test. The maximum possible prediction accuracy of ~70% was observed in self consistency test for the SVM models of both LI1264 and SP1577 datasets, where PSSM+SS(DSSP) input features was used to test. The prediction accuracies were reduced to ~53% for PSSM+SS(NPS@) and ~43% for PSSM+SS(GOR4) in independent case test, for the SVM models of above two same datasets. Using our method, it is possible to predict the protein block letters for any query protein sequence with ~53% accuracy, when the SP1577 dataset and predicted secondary structure from NPS@ server were used. The SVM-PB-Pred server can be freely accessed through http://bioinfo.bdu.ac.in/~svmpbpred.
Zhou, Jiyun; Wang, Hongpeng; Zhao, Zhishan; Xu, Ruifeng; Lu, Qin
2018-05-08
Protein secondary structure is the three dimensional form of local segments of proteins and its prediction is an important problem in protein tertiary structure prediction. Developing computational approaches for protein secondary structure prediction is becoming increasingly urgent. We present a novel deep learning based model, referred to as CNNH_PSS, by using multi-scale CNN with highway. In CNNH_PSS, any two neighbor convolutional layers have a highway to deliver information from current layer to the output of the next one to keep local contexts. As lower layers extract local context while higher layers extract long-range interdependencies, the highways between neighbor layers allow CNNH_PSS to have ability to extract both local contexts and long-range interdependencies. We evaluate CNNH_PSS on two commonly used datasets: CB6133 and CB513. CNNH_PSS outperforms the multi-scale CNN without highway by at least 0.010 Q8 accuracy and also performs better than CNF, DeepCNF and SSpro8, which cannot extract long-range interdependencies, by at least 0.020 Q8 accuracy, demonstrating that both local contexts and long-range interdependencies are indeed useful for prediction. Furthermore, CNNH_PSS also performs better than GSM and DCRNN which need extra complex model to extract long-range interdependencies. It demonstrates that CNNH_PSS not only cost less computer resource, but also achieves better predicting performance. CNNH_PSS have ability to extracts both local contexts and long-range interdependencies by combing multi-scale CNN and highway network. The evaluations on common datasets and comparisons with state-of-the-art methods indicate that CNNH_PSS is an useful and efficient tool for protein secondary structure prediction.
Rachel, Natalie M; Quaglia, Daniela; Lévesque, Éric; Charette, André B; Pelletier, Joelle N
2017-11-01
Microbial transglutaminase (MTG) is a practical tool to enzymatically form isopeptide bonds between peptide or protein substrates. This natural approach to crosslinking the side-chains of reactive glutamine and lysine residues is solidly rooted in food and textile processing. More recently, MTG's tolerance for various primary amines in lieu of lysine have revealed its potential for site-specific protein labeling with aminated compounds, including fluorophores. Importantly, MTG can label glutamines at accessible positions in the body of a target protein, setting it apart from most labeling enzymes that react exclusively at protein termini. To expand its applicability as a labeling tool, we engineered the B1 domain of Protein G (GB1) to probe the selectivity and enhance the reactivity of MTG toward its glutamine substrate. We built a GB1 library where each variant contained a single glutamine at positions covering all secondary structure elements. The most reactive and selective variants displayed a >100-fold increase in incorporation of a recently developed aminated benzo[a]imidazo[2,1,5-cd]indolizine-type fluorophore, relative to native GB1. None of the variants were destabilized. Our results demonstrate that MTG can react readily with glutamines in α-helical, β-sheet, and unstructured loop elements and does not favor one type of secondary structure. Introducing point mutations within MTG's active site further increased reactivity toward the most reactive substrate variant, I6Q-GB1, enhancing MTG's capacity to fluorescently label an engineered, highly reactive glutamine substrate. This work demonstrates that MTG-reactive glutamines can be readily introduced into a protein domain for fluorescent labeling. © 2017 The Protein Society.
DEFF Research Database (Denmark)
Rioseras, Beatriz; Sliaha, Pavel V; Gorshkov, Vladimir
2018-01-01
identified and quantified 3461 proteins corresponding to 44.3% of the S. coelicolor proteome across three developmental stages: vegetative hypha (MI); secondary metabolite producing hyphae (MII); and sporulating hyphae. A total of 1350 proteins exhibited more than 2-fold expression changes during....../Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor. We...... the bacterial differentiation process. These proteins include 136 regulators (transcriptional regulators, transducers, Ser/Thr/Tyr kinases, signalling proteins), as well as 542 putative proteins with no clear homology to known proteins which are likely to play a role in differentiation and secondary metabolism...
Correlation between protein secondary structure, backbone bond angles, and side-chain orientations
Lundgren, Martin; Niemi, Antti J.
2012-08-01
We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central Cα carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the Cβ carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the Cα-Cβ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.
Secondary Structure Prediction of Protein using Resilient Back Propagation Learning Algorithm
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Jyotshna Dongardive
2015-12-01
Full Text Available The paper proposes a neural network based approach to predict secondary structure of protein. It uses Multilayer Feed Forward Network (MLFN with resilient back propagation as the learning algorithm. Point Accepted Mutation (PAM is adopted as the encoding scheme and CB396 data set is used for the training and testing of the network. Overall accuracy of the network has been experimentally calculated with different window sizes for the sliding window scheme and by varying the number of units in the hidden layer. The best results were obtained with eleven as the window size and seven as the number of units in the hidden layer.
Exploiting the Past and the Future in Protein Secondary Structure Prediction
DEFF Research Database (Denmark)
Baldi, Pierre; Brunak, Søren; Frasconi, P
1999-01-01
predictions based on variable ranges of dependencies. These architectures extend recurrent neural networks, introducing non-causal bidirectional dynamics to capture both upstream and downstream information. The prediction algorithm is completed by the use of mixtures of estimators that leverage evolutionary......Motivation: Predicting the secondary structure of a protein (alpha-helix, beta-sheet, coil) is an important step towards elucidating its three-dimensional structure, as well as its function. Presently, the best predictors are based on machine learning approaches, in particular neural network...
International Nuclear Information System (INIS)
Bonwell, E.; Fisher, T.; Fritz, A.; Wetzel, D.
2008-01-01
One molecular aspect of mature hard wheat protein quality for breadmaking is the relative amount of endosperm protein in the a-helix form compared with that in other secondary structure forms including β-sheet. Modeling of a-helix and β-sheet absorption bands that contribute to the amide I band at 1650 cm-1 was applied to more than 1500 spectra in this study. The microscopic view of wheat endosperm is dominated by many large starch granules with protein in between. The spectrum produced from in situ microspectroscopy of this mixture is dominated by carbohydrate bands from the large starch granules that fill up the field. The high spatial resolution achievable with synchrotron infrared microspectroscopy enables revealing good in situ spectra of the protein located interstitially. Synchrotron infrared microspectroscopic mapping of 4 μm thick frozen sections of endosperm in the subaleurone region provides spectra from a large number of pixels. Pixels with protein-dominated spectra are sorted out from among adjacent pixels to minimize the starch absorption and scattering contributions. Subsequent data treatment to extract information from the amide I band requires a high signal to noise ratio. Although spectral interference of the carbohydrate band on the amide band is not a problem, the scattering produced by the large starch granules diminishes the signal to noise ratio throughout the spectrum. High density mapping was done on beamlines U2B and U10B at the National Synchrotron Light Source at Brookhaven National Laboratory, Upton, NY. Mapping with a single masked spot size of 5.5 μm diameter or confocal 5 μm x 5 μm spot size, respectively, on the two beamlines used produced spectra for new breeding lines under current consideration. Appropriate data treatment allows calculation of a numerical estimate of the a-helix population relative to other secondary protein structures from the position and shape of the amide I absorption band. Current breeding lines show a
Kashani-Amin, Elaheh; Tabatabaei-Malazy, Ozra; Sakhteman, Amirhossein; Larijani, Bagher; Ebrahim-Habibi, Azadeh
2018-02-27
Prediction of proteins' secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple secondary structure prediction (SSP) options is challenging. The current study is an insight onto currently favored methods and tools, within various contexts. A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of 209 studies were finally found eligible to extract data. Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating a SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. This study provides a comprehensive insight about the recent usage of SSP tools which could be helpful for selecting a proper tool's choice. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins
Directory of Open Access Journals (Sweden)
Tatyana Aleksandrovna Khrustaleva
2014-01-01
Full Text Available 3D structures of proteins with coordinated Mn2+ ions from bacteria with low, average, and high genomic GC-content have been analyzed (149 PDB files were used. Major Mn2+ binders are aspartic acid (6.82% of Asp residues, histidine (14.76% of His residues, and glutamic acid (3.51% of Glu residues. We found out that the motif of secondary structure “beta strand-major binder-random coil” is overrepresented around all the three major Mn2+ binders. That motif may be followed by either alpha helix or beta strand. Beta strands near Mn2+ binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn2+ ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. On the other hand, the percentage of Mn2+ sites with at least one amino acid in the “beta strand-major binder-random coil” motif of secondary structure (77.88% does not depend on genomic GC-content.
Yahyavi, Masoumeh; Falsafi-Zadeh, Sajad; Karimi, Zahra; Kalatarian, Giti; Galehdari, Hamid
2014-01-01
The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features. The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755.
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.
Spencer, Matt; Eickholt, Jesse; Jianlin Cheng
2015-01-01
Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent.
Directory of Open Access Journals (Sweden)
Al-Hakeim Hussein K
2015-12-01
Full Text Available Calcium phosphate nanoparticles (CaPNP have good biocompatibility and bioactivity inside human body. In this study, the interaction between CaPNP and human chorionic gonadotropin (hCG was analyzed to determine the changes in the protein structure in the presence of CaPNP and the quantity of protein adsorbed on the CaPNP surface. The results showed a significant adsorption of hCG on the CaPNP nanoparticle surface. The optimal fit was achieved using the Sips isotherm equation with a maximum adsorption capacity of 68.23 µg/mg. The thermodynamic parameters, including ∆H° and ∆G°, of the adsorption process are positive, whereas ∆S° is negative. The circular dichroism results of the adsorption of hCG on CaPNP showed the changes in its secondary structure; such changes include the decomposition of α-helix strand and the increase in β-pleated sheet and random coil percentages. Fluorescence study indicated minimal changes in the tertiary structure near the microenvironment of the aromatic amino acids such as tyrosine and phenyl alanine caused by the interaction forces between the CaPNP and hCG protein. The desorption process showed that the quantity of the hCG desorbed significantly increases as temperature increases, which indicates the weak forces between hCG and the surface.
Energy Technology Data Exchange (ETDEWEB)
Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States); Assadi, Amir [University of Wisconsin-Madison, Mathematics Department (United States); Markley, John L. [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)], E-mail: eghbalni@nmrfam.wisc.edu
2005-05-15
We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.
International Nuclear Information System (INIS)
Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash; Assadi, Amir; Markley, John L.
2005-01-01
We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states
Directory of Open Access Journals (Sweden)
Hajime Yamazaki
2017-06-01
Full Text Available Previously, we have shown that serine-16 phosphorylation in native full-length porcine amelogenin (P173 and the Leucine-Rich Amelogenin Peptide (LRAP(+P, an alternative amelogenin splice product, affects protein assembly and mineralization in vitro. Notably, P173 and LRAP(+P stabilize amorphous calcium phosphate (ACP and inhibit hydroxyapatite (HA formation, while non-phosphorylated counterparts (rP172, LRAP(−P guide the growth of ordered bundles of HA crystals. Based on these findings, we hypothesize that the phosphorylation of full-length amelogenin and LRAP induces conformational changes that critically affect its capacity to interact with forming calcium phosphate mineral phases. To test this hypothesis, we have utilized Fourier transform infrared spectroscopy (FTIR to determine the secondary structure of LRAP(−P and LRAP(+P in the absence/presence of calcium and selected mineral phases relevant to amelogenesis; i.e., hydroxyapatite (HA: an enamel crystal prototype and (ACP: an enamel crystal precursor phase. Aqueous solutions of LRAP(−P or LRAP(+P were prepared with or without 7.5 mM of CaCl2 at pH 7.4. FTIR spectra of each solution were obtained using attenuated total reflectance, and amide-I peaks were analyzed to provide secondary structure information. Secondary structures of LRAP(+P and LRAP(−P were similarly assessed following incubation with suspensions of HA and pyrophosphate-stabilized ACP. Amide I spectra of LRAP(−P and LRAP(+P were found to be distinct from each other in all cases. Spectra analyses showed that LRAP(−P is comprised mostly of random coil and β-sheet, while LRAP(+P exhibits more β-sheet and α-helix with little random coil. With added Ca, the random coil content increased in LRAP(−P, while LRAP(+P exhibited a decrease in α-helix components. Incubation of LRAP(−P with HA or ACP resulted in comparable increases in β-sheet structure. Notably, however, LRAP(+P secondary structure was more affected by
Palmero, Faustino; Lemos, M; Sánchez-Rey, Bernardo; Casado-Pascual, Jesús
2018-01-01
This book presents an overview of the most recent advances in nonlinear science. It provides a unified view of nonlinear properties in many different systems and highlights many new developments. While volume 1 concentrates on mathematical theory and computational techniques and challenges, which are essential for the study of nonlinear science, this second volume deals with nonlinear excitations in several fields. These excitations can be localized and transport energy and matter in the form of breathers, solitons, kinks or quodons with very different characteristics, which are discussed in the book. They can also transport electric charge, in which case they are known as polarobreathers or solectrons. Nonlinear excitations can influence function and structure in biology, as for example, protein folding. In crystals and other condensed matter, they can modify transport properties, reaction kinetics and interact with defects. There are also engineering applications in electric lattices, Josephson junction a...
Directory of Open Access Journals (Sweden)
Lees Jonathan G
2008-01-01
Full Text Available Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.
Directory of Open Access Journals (Sweden)
Ida Vaskova,
2012-01-01
Full Text Available Kraft pulping is the most commonly used pulping process in the pulp and paper industry. In this process wood chips are chemically delignified using sodium sulfide and sodium hydroxide. Delignification is usually followed by mechanical fiberization and a bleaching process of the resulting wood pulp. In addition to lignin-free wood pulp, this process also produces waste that contains residues of used chemicals, lignin, cellulose, hemicelluloses, and small amounts of other wood components. Because of the worldwide large-scale production of paper, the sludge from paper mills contributes significantly to environmental pollution. Although there have been great efforts being made to utilize this lignin-rich material, sludge is mostly disposed in landfills or incinerated in a boiler. This research project used secondary sludge as a substrate for 7 wood-decay fungi taxonomically belonging to the genus Trichoderma. The examined fungi expressed the capability of consuming sludge components as a carbon source to produce extracellular proteins. The proteins were separated by gel electrophoresis. Before and after fungi cultivation, the sludge was analyzed by Fourier transform infrared spectroscopy (FTIR.
Hossein-Zadeh, Navid Ghavi
2016-08-01
The aim of this study was to compare seven non-linear mathematical models (Brody, Wood, Dhanoa, Sikka, Nelder, Rook and Dijkstra) to examine their efficiency in describing the lactation curves for milk fat to protein ratio (FPR) in Iranian buffaloes. Data were 43 818 test-day records for FPR from the first three lactations of Iranian buffaloes which were collected on 523 dairy herds in the period from 1996 to 2012 by the Animal Breeding Center of Iran. Each model was fitted to monthly FPR records of buffaloes using the non-linear mixed model procedure (PROC NLMIXED) in SAS and the parameters were estimated. The models were tested for goodness of fit using Akaike's information criterion (AIC), Bayesian information criterion (BIC) and log maximum likelihood (-2 Log L). The Nelder and Sikka mixed models provided the best fit of lactation curve for FPR in the first and second lactations of Iranian buffaloes, respectively. However, Wood, Dhanoa and Sikka mixed models provided the best fit of lactation curve for FPR in the third parity buffaloes. Evaluation of first, second and third lactation features showed that all models, except for Dijkstra model in the third lactation, under-predicted test time at which daily FPR was minimum. On the other hand, minimum FPR was over-predicted by all equations. Evaluation of the different models used in this study indicated that non-linear mixed models were sufficient for fitting test-day FPR records of Iranian buffaloes.
Kent, J E
1987-03-01
The concentrations of haptoglobin, immunoglobin (Ig)G(T) and IgG were measured in the serum of four previously parasite-free pony yearlings following a single dose of 700 (Group H) or 200 (Group L) stage three Strongylus vulgaris larvae (L3) and following a reinfection with the same doses 34 weeks later. The results are compared with an uninfected control pony. The haptoglobin concentration increased during Weeks 1 to 6 and 14 to 17 after infection in the serum of the ponies receiving 200 L3, but in only one pony dosed with 700 L3 (during Weeks 1 to 16). The serum haptoglobin also increased during the first seven weeks after the second infection, in three of the four ponies following the second dose of larvae. The serum IgG(T) concentration started to increase from Week 6 or 9 in the ponies given 700 L3, reaching peaks of 44 and 32 g/litre respectively, eight to nine weeks later, compared with a peak of 16 g/litre 20 to 22 weeks after infection in ponies dosed with 200 L3. The IgG(T) concentration increased to a maximum of 25 g/litre in the serum of only one of the four ponies after the reinfection. The serum IgG concentration in all ponies increased nearly twofold during the first eight weeks after both the primary and secondary dose of larvae. It is concluded that the measurement of specific proteins is more reliable and quicker than the electrophoretic separation and quantitation of protein bands, in tracing changes in serum proteins following the artificial infection of ponies with S vulgaris larvae.
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Olga K Kamneva
Full Text Available A number of bacteria belonging to the PVC (Planctomycetes-Verrucomicrobia-Chlamydiae super-phylum contain unusual ribosome-bearing intracellular membranes. The evolutionary origins and functions of these membranes are unknown. Some proteins putatively associated with the presence of intracellular membranes in PVC bacteria contain signal peptides. Signal peptides mark proteins for translocation across the cytoplasmic membrane in prokaryotes, and the membrane of the endoplasmic reticulum in eukaryotes, by highly conserved Sec machinery. This suggests that proteins might be targeted to intracellular membranes in PVC bacteria via the Sec pathway. Here, we show that canonical signal peptides are significantly over-represented in proteins preferentially present in PVC bacteria possessing intracellular membranes, indicating involvement of Sec translocase in their cellular targeting. We also characterized Sec proteins using comparative genomics approaches, focusing on the PVC super-phylum. While we were unable to detect unique changes in Sec proteins conserved among membrane-bearing PVC species, we identified (1 SecA ATPase domain re-arrangements in some Planctomycetes, and (2 secondary SecA_DEAD domain proteins in the genomes of some Planctomycetes, Verrucomicrobia, Proteobacteria, Nitrospirae and Chlorobi. This is the first report of potentially duplicated SecA in Gram-negative bacteria. The phylogenetic distribution of secondary SecA_DEAD domain proteins suggests that the presence of these proteins is not related to the occurrence of PVC endomembranes. Further genomic analysis showed that secondary SecA_DEAD domain proteins are located within genomic neighborhoods that also encode three proteins possessing domains specific for the Type I secretion system.
Wang, Yuanze; van Oosterwijk, Niels; Ali, Ameena M; Adawy, Alaa; Anindya, Atsarina L; Dömling, Alexander S S; Groves, Matthew R
2017-08-24
Refolding of proteins derived from inclusion bodies is very promising as it can provide a reliable source of target proteins of high purity. However, inclusion body-based protein production is often limited by the lack of techniques for the detection of correctly refolded protein. Thus, the selection of the refolding conditions is mostly achieved using trial and error approaches and is thus a time-consuming process. In this study, we use the latest developments in the differential scanning fluorimetry guided refolding approach as an analytical method to detect correctly refolded protein. We describe a systematic buffer screen that contains a 96-well primary pH-refolding screen in conjunction with a secondary additive screen. Our research demonstrates that this approach could be applied for determining refolding conditions for several proteins. In addition, it revealed which "helper" molecules, such as arginine and additives are essential. Four different proteins: HA-RBD, MDM2, IL-17A and PD-L1 were used to validate our refolding approach. Our systematic protocol evaluates the impact of the "helper" molecules, the pH, buffer system and time on the protein refolding process in a high-throughput fashion. Finally, we demonstrate that refolding time and a secondary thermal shift assay buffer screen are critical factors for improving refolding efficiency.
Troshin, Peter V; Procter, James B; Sherstnev, Alexander; Barton, Daniel L; Madeira, Fábio; Barton, Geoffrey J
2018-06-01
JABAWS 2.2 is a computational framework that simplifies the deployment of web services for Bioinformatics. In addition to the five multiple sequence alignment (MSA) algorithms in JABAWS 1.0, JABAWS 2.2 includes three additional MSA programs (Clustal Omega, MSAprobs, GLprobs), four protein disorder prediction methods (DisEMBL, IUPred, Ronn, GlobPlot), 18 measures of protein conservation as implemented in AACon, and RNA secondary structure prediction by the RNAalifold program. JABAWS 2.2 can be deployed on a variety of in-house or hosted systems. JABAWS 2.2 web services may be accessed from the Jalview multiple sequence analysis workbench (Version 2.8 and later), as well as directly via the JABAWS command line interface (CLI) client. JABAWS 2.2 can be deployed on a local virtual server as a Virtual Appliance (VA) or simply as a Web Application Archive (WAR) for private use. Improvements in JABAWS 2.2 also include simplified installation and a range of utility tools for usage statistics collection, and web services querying and monitoring. The JABAWS CLI client has been updated to support all the new services and allow integration of JABAWS 2.2 services into conventional scripts. A public JABAWS 2 server has been in production since December 2011 and served over 800 000 analyses for users worldwide. JABAWS 2.2 is made freely available under the Apache 2 license and can be obtained from: http://www.compbio.dundee.ac.uk/jabaws. g.j.barton@dundee.ac.uk.
FT-IR spectroscopic studies of protein secondary structures for breast cancer diagnosis
International Nuclear Information System (INIS)
Karamancheva, I; Simonova, D.; Milev, A.
2013-01-01
Full text: Roughly 14 million new cancer cases and 8 million cancer deaths have occurred worldwide in 2012. At least 30 % of all cancer cases and 40 % of the cancer deaths should be avoided by improving the early detection. Fourier transform infrared (FT-IR) spectroscopy has shown many advantages as a tool for the detection of cancer over the traditional methods such as histopathological analysis, X-ray transmission, ultrasonic and computer tomography techniques. With the aim to establish the FT-IR spectroscopy as an alternative method for the diagnosis of human cancers, we have made several studies to examine in details the spectroscopic properties of normal and carcinomatous tissues. Human breast tissues were obtained immediately after surgical breast resection with the informed patient's consent. In our studies we made extensive use of Fourier self-deconvolution, second-order derivatization, difference spectra, curve-fitting procedures and quantitative determinations according to Beer's law. Cancer is a multi-step process. Characteristic differences in both the frequencies and the intensity ratios of several bands have been revealed. Considerable differences have been found in the spectral patterns. The most important and informative region in the mid-IR for determination of protein secondary structure is the amide I and amide II region. The bands between 1730 and 1600 cm -1 are highly sensitive to conformational changes. Considerable changes were observed in the A1735/A1652 absorbance ratio, which provides a measure for the content of a- helix and P-sheet domains. Our investigations have shown that the major biomarker peaks are in the amide I and amide II regions. In the so called 'fingerprint region' many molecular constituents such as lipids, phospholipids, proteins, DNA and RNA, carbohydrates and metabolites may overlap and the quantitative interpretation is impossible. The spectrum may therefore reflect only the average biochemical composition.; key words
Plant protein and secondary metabolites influence diet selection in a mammalian specialist herbivore
Ulappa, Amy C.; Kelsey, Rick G.; Frye, Graham G.; Rachlow, Janet L.; Shipley, Lisa A.; Bond, Laura; Pu, Xinzhu; Forbey, Jennifer Sorensen
2015-01-01
For herbivores, nutrient intake is limited by the relatively low nutritional quality of plants and high concentrations of potentially toxic defensive compounds (plant secondary metabolites, PSMs) produced by many plants. In response to phytochemical challenges, some herbivores selectively forage on plants with higher nutrient and lower PSM concentrations relative to other plants. Pygmy rabbits (Brachylagus idahoensis) are dietary specialists that feed on sagebrush (Artemisia spp.) and forage on specific plants more than others within a foraging patch. We predicted that the plants with evidence of heavy foraging (browsed plants) would be of higher dietary quality than plants that were not browsed (unbrowsed). We used model selection to determine which phytochemical variables best explained the difference between browsed and unbrowsed plants. Higher crude protein increased the odds that plants would be browsed by pygmy rabbits and the opposite was the case for certain PSMs. Additionally, because pygmy rabbits can occupy foraging patches (burrows) for consecutive years, their browsing may influence the nutritional and PSM constituents of plants at the burrows. In a post hoc analysis, we did not find a significant relationship between phytochemical concentrations, browse status and burrow occupancy length. We concluded that pygmy rabbits use nutritional and chemical cues while making foraging decisions. PMID:26366011
Lighezan, Liliana; Georgieva, Ralitsa; Neagu, Adrian
2016-09-01
Surface layer (S-layer) proteins have been identified in the cell envelope of many organisms, such as bacteria and archaea. They self-assemble, forming monomolecular crystalline arrays. Isolated S-layer proteins are able to recrystallize into regular lattices, which proved useful in biotechnology. Here we investigate the structure and thermal unfolding of the S-layer protein isolated from Lactobacillus salivarius 16 strain of human origin. Using circular dichroism (CD) spectroscopy, and the software CDSSTR from DICHROWEB, CONTINLL from CDPro, as well as CDNN, we assess the fractions of the protein's secondary structural elements at temperatures ranging between 10 and 90 °C, and predict the tertiary class of the protein. To study the thermal unfolding of the protein, we analyze the temperature dependence of the CD signal in the far- and near-UV domains. Fitting the experimental data by two- and three-state models of thermal unfolding, we infer the midpoint temperatures, the temperature dependence of the changes in Gibbs free energy, enthalpy, and entropy of the unfolding transitions in standard conditions, and the temperature dependence of the equilibrium constant. We also estimate the changes in heat capacity at constant pressure in standard conditions. The results indicate that the thermal unfolding of the S-layer protein from L. salivarius is highly cooperative, since changes in the secondary and tertiary structures occur simultaneously. The thermodynamic analysis predicts a "cold" transition, at about -3 °C, of both the secondary and tertiary structures. Our findings may be important for the use of S-layer proteins in biotechnology and in biomedical applications.
Nonlinear analysis of sequence symmetry of beta-trefoil family proteins
Energy Technology Data Exchange (ETDEWEB)
Li Mingfeng [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Huang Yanzhao [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xu Ruizhen [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xiao Yi [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China)]. E-mail: yxiao@mail.hust.edu.cn
2005-07-01
The tertiary structures of proteins of beta-trefoil family have three-fold quasi-symmetry while their amino acid sequences appear almost at random. In the present paper we show that these amino acid sequences have hidden symmetries in fact and furthermore the degrees of these hidden symmetries are the same as those of their tertiary structures. We shall present a modified recurrence plot to reveal hidden symmetries in protein sequences. Our results can explain the contradiction in sequence-structure relations of proteins of beta-trefoil family.
Zhao, Yu; Zhang, Li-Li; Ding, Fa-Xian; Cao, Ping; Qi, Yuan-Yuan; Wang, Jing
2017-11-01
Peptidyl-prolyl cis/trans isomerase NIMA-interacting 1 (Pin1) is a key regulator of PTH mRNA stability. Secondary hyperparathyroidism (SHPT), which is characterized by elevated serum PTH levels, is a common complication of CKD. We investigated the possible associations between CKD with SHPT (CKD SHPT) and single-nucleotide polymorphisms of the Pin1 gene and compared the levels of the Pin1 protein in the CKD SHPT patients with those of the controls. The study group included 251 CKD SHPT patients and 61 controls. One putative functional SNP (single nucleotide polymorphism) in the Pin1 promoter (rs2233679C > T: c.-667C > T) is the main object. Genotyping was performed on purified DNA using polymerase chain reaction-restriction (PCR) and restriction fragment length polymorphisms (RFLP). The levels of Pin1 were measured in serum using an enzyme-linked immunosorbent assay. Genotyping showed that CT + TT in the Pin1 promoter was significantly more common in the CKD SHPT group than in the control group (p<.05). The correlation analysis demonstrated that a significant difference in the C to T transition in the Pin1 promoter contributed to CKD SHPT (χ 2 =12.47, p<.05; Odds ratios (OR) = 1.26, 95% confidence (CI) intervals =1.06-1.49). The multivariate logistic regression analysis reported that the OR and 95%CI were 12.693 and 2.029-75.819 (p<.05), respectively, in the Pin1 gene promoter -667T variant genotypes (CT + TT) after adjusting for other factors, and those values in Pin1 were 0.310 and 0.122-0.792 (p<.05). The -667T genetic variants in the Pin1 promoter contribute to an increased risk of CKD SHPT and may be biomarkers of susceptibility to CKD SHPT.
Ye, Shuji; Li, Hongchun; Yang, Weilai; Luo, Yi
2014-01-29
Accurate determination of protein structures at the interface is essential to understand the nature of interfacial protein interactions, but it can only be done with a few, very limited experimental methods. Here, we demonstrate for the first time that sum frequency generation vibrational spectroscopy can unambiguously differentiate the interfacial protein secondary structures by combining surface-sensitive amide I and amide III spectral signals. This combination offers a powerful tool to directly distinguish random-coil (disordered) and α-helical structures in proteins. From a systematic study on the interactions between several antimicrobial peptides (including LKα14, mastoparan X, cecropin P1, melittin, and pardaxin) and lipid bilayers, it is found that the spectral profiles of the random-coil and α-helical structures are well separated in the amide III spectra, appearing below and above 1260 cm(-1), respectively. For the peptides with a straight backbone chain, the strength ratio for the peaks of the random-coil and α-helical structures shows a distinct linear relationship with the fraction of the disordered structure deduced from independent NMR experiments reported in the literature. It is revealed that increasing the fraction of negatively charged lipids can induce a conformational change of pardaxin from random-coil to α-helical structures. This experimental protocol can be employed for determining the interfacial protein secondary structures and dynamics in situ and in real time without extraneous labels.
A comparative method for finding and folding RNA secondary structures within protein-coding regions
DEFF Research Database (Denmark)
Pedersen, Jakob Skou; Meyer, Irmtraud Margret; Forsberg, Roald
2004-01-01
that RNA-DECODER's parameters can be automatically trained to successfully fold known secondary structures within the HCV genome. We scan the genomes of HCV and polio virus for conserved secondary-structure elements, and analyze performance as a function of available evolutionary information. On known...... secondary structures, RNA-DECODER shows a sensitivity similar to the programs MFOLD, PFOLD and RNAALIFOLD. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD....
Cannistraci, Carlo Vittorio
2015-01-26
Denoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet\\'s performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis.
Cannistraci, Carlo Vittorio; Abbas, Ahmed; Gao, Xin
2015-01-01
Denoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet's performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis.
Fan, Ming; Zheng, Bin; Li, Lihua
2015-10-01
Knowledge of the structural class of a given protein is important for understanding its folding patterns. Although a lot of efforts have been made, it still remains a challenging problem for prediction of protein structural class solely from protein sequences. The feature extraction and classification of proteins are the main problems in prediction. In this research, we extended our earlier work regarding these two aspects. In protein feature extraction, we proposed a scheme by calculating the word frequency and word position from sequences of amino acid, reduced amino acid, and secondary structure. For an accurate classification of the structural class of protein, we developed a novel Multi-Agent Ada-Boost (MA-Ada) method by integrating the features of Multi-Agent system into Ada-Boost algorithm. Extensive experiments were taken to test and compare the proposed method using four benchmark datasets in low homology. The results showed classification accuracies of 88.5%, 96.0%, 88.4%, and 85.5%, respectively, which are much better compared with the existing methods. The source code and dataset are available on request.
Volovelsky, Oded; Cohen, Gili; Kenig, Ariel; Wasserman, Gilad; Dreazen, Avigail; Meyuhas, Oded; Silver, Justin; Naveh-Many, Tally
2016-04-01
Secondary hyperparathyroidism is characterized by increased serum parathyroid hormone (PTH) level and parathyroid cell proliferation. However, the molecular pathways mediating the increased parathyroid cell proliferation remain undefined. Here, we found that the mTOR pathway was activated in the parathyroid of rats with secondary hyperparathyroidism induced by either chronic hypocalcemia or uremia, which was measured by increased phosphorylation of ribosomal protein S6 (rpS6), a downstream target of the mTOR pathway. This activation correlated with increased parathyroid cell proliferation. Inhibition of mTOR complex 1 by rapamycin decreased or prevented parathyroid cell proliferation in secondary hyperparathyroidism rats and in vitro in uremic rat parathyroid glands in organ culture. Knockin rpS6(p-/-) mice, in which rpS6 cannot be phosphorylated because of substitution of all five phosphorylatable serines with alanines, had impaired PTH secretion after experimental uremia- or folic acid-induced AKI. Uremic rpS6(p-/-) mice had no increase in parathyroid cell proliferation compared with a marked increase in uremic wild-type mice. These results underscore the importance of mTOR activation and rpS6 phosphorylation for the pathogenesis of secondary hyperparathyroidism and indicate that mTORC1 is a significant regulator of parathyroid cell proliferation through rpS6. Copyright © 2016 by the American Society of Nephrology.
Teaching Genetics in Secondary Classrooms: A Linguistic Analysis of Teachers' Talk about Proteins
Thörne, Karin; Gericke, Niklas
2014-01-01
This study investigates Swedish biology teachers' inclusion of proteins when teaching genetics in grade nine (students 15-16 years old). For some years, there has been a call to give attention to proteins when teaching genetics as a means of linking the concepts "gene" and "trait". Students are known to have problems with this…
Cavataio, F; Iacono, G; Montalto, G; Soresi, M; Tumminello, M; Carroccio, A
1996-01-01
AIMS: The primary aim was to assess whether there were differences in symptoms, laboratory data, and oesophageal pH-metry between infants with primary gastro-oesophageal reflux and those with reflux secondary to cows' milk protein allergy (CMPA). PATIENTS AND METHODS: 96 infants (mean(SD) age 7.8(2.0) months) with either primary gastro-oesophageal reflux, reflux with CMPA, CMPA only, or none of these (controls) were studied. Symptoms, immunochemical data, and oesophageal pH were compared between the four groups and the effect of a cows' milk protein-free diet on the severity of symptoms was also assessed. RESULTS: 14 out of 47(30%) infants with gastro-oesophageal reflux had CMPA. These infants had similar symptoms to those with primary gastro-oesophageal reflux but higher concentrations of total IgE and circulating eosinophils (p gastro-oesophageal reflux secondary to CMPA and in 24 of 25 infants with CMPA only. No infants with primary gastro-oesophageal reflux and none of the controls had this pattern. A cows' milk protein-free diet was associated with a significant improvement in symptoms only in infants with gastro-oesophageal reflux with CMPA. CONCLUSION: A characteristic oesophageal pH pattern is useful in distinguishing infants with gastro-oesophageal reflux associated with CMPA. PMID:8813871
Ultrasensitive probing of the protein resistance of PEG surfaces by secondary ion mass spectrometry
DEFF Research Database (Denmark)
Kingshott, P.; McArthur, S.; Thissen, H.
2002-01-01
The highly sensitive surface analytical techniques X-ray photoelectron spectroscopy (XPS) and time-of-flight static secondary ion mass spectrometry (ToF-SIMS) were used to test the resistance of poly(ethylene glycol) (PEG) coatings towards adsorption of lysozyme (LYS) and fibronectin (FN). PEG co...
Plant protein and secondary metabolites influence diet selection in a mammalian specialist herbivore
Amy C. Ulappa; Rick G. Kelsey; Graham G. Frye; Janet L. Rachlow; LIsa A. Shipley; Laura Bond; Xinzhu Pu; Jennifer Sorensen. Forbey
2014-01-01
For herbivores, nutrient intake is limited by the relatively low nutritional quality of plants and high concentrations of potentially toxic defensive compounds (plant secondary metabolites [PSMs]) produced by many plants. In response to phytochemical challenges, some herbivores selectively forage on plants with higher nutrient and lower PSM concentrations relative to...
Backbone assignment and secondary structure of the PsbQ protein from Photosystem II
Czech Academy of Sciences Publication Activity Database
Horničáková, M.; Kohoutová, Jaroslava; Schlagnitweit, J.; Wohlschlager, Ch.; Ettrich, Rüdiger; Fiala, R.; Schoefberger, W.; Müller, N.
2011-01-01
Roč. 5, č. 2 (2011), s. 169-175 ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LC06010 Institutional research plan: CEZ:AV0Z60870520 Keywords : Photosystem II * PsbQ * Missing link * NMR resonance assignment * Protein-protein interaction Subject RIV: BO - Biophysics Impact factor: 0.720, year: 2011 http://www.springerlink.com/content/3n38075w5h1l1082/fulltext.pdf
Yang, Qin; Zou, Hong-Yan; Zhang, Yan; Tang, Li-Juan; Shen, Guo-Li; Jiang, Jian-Hui; Yu, Ru-Qin
2016-01-15
Most of the proteins locate more than one organelle in a cell. Unmixing the localization patterns of proteins is critical for understanding the protein functions and other vital cellular processes. Herein, non-linear machine learning technique is proposed for the first time upon protein pattern unmixing. Variable-weighted support vector machine (VW-SVM) is a demonstrated robust modeling technique with flexible and rational variable selection. As optimized by a global stochastic optimization technique, particle swarm optimization (PSO) algorithm, it makes VW-SVM to be an adaptive parameter-free method for automated unmixing of protein subcellular patterns. Results obtained by pattern unmixing of a set of fluorescence microscope images of cells indicate VW-SVM as optimized by PSO is able to extract useful pattern features by optimally rescaling each variable for non-linear SVM modeling, consequently leading to improved performances in multiplex protein pattern unmixing compared with conventional SVM and other exiting pattern unmixing methods. Copyright © 2015 Elsevier B.V. All rights reserved.
International Nuclear Information System (INIS)
Swain, Monalisa; Atreya, Hanudatta S.
2009-01-01
Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1 H α and 13 C' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment
Bonvin, A.M.J.J.; Houben, K.; Guenneugues, M.N.L.; Kaptein, R.; Boelens, R.
2001-01-01
The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small alpha/beta protein
Jenkins, Janelle E.; Sampath, Sujatha; Butler, Emily; Kim, Jihyun; Henning, Robert W.; Holland, Gregory P.; Yarger, Jeffery L.
2013-01-01
This study provides a detailed secondary structural characterization of major ampullate dragline silk from Latrodectus hesperus (black widow) spiders. X-ray diffraction results show that the structure of black widow major ampullate silk fibers is comprised of stacked β-sheet nanocrystallites oriented parallel to the fiber axis and an amorphous region with oriented (anisotropic) and isotropic components. The combination of two-dimensional (2D) 13C-13C through-space and through-bond solid-state NMR experiments provide chemical shifts that are used to determine detailed information about amino acid motif secondary structure in black widow spider dragline silk. Individual amino acids are incorporated into different repetitive motifs that make up the majority of this protein-based biopolymer. From the solid-state NMR measurements, we assign distinct secondary conformations to each repetitive amino acid motif and hence to the amino acids that make up the motifs. Specifically, alanine is incorporated in β-sheet (poly(Alan) and poly(Gly-Ala)), 31-helix (poly(Gly-Gly-Xaa), and α-helix (poly(Gln-Gln-Ala-Tyr)) components. Glycine is determined to be in β-sheet (poly(Gly-Ala)) and 31-helical (poly(Gly-Gly-Xaa)) regions, while serine is present in β-sheet (poly(Gly-Ala-Ser)), 31-helix (poly(Gly-Gly-Ser)), and β-turn (poly(Gly-Pro-Ser)) structures. These various motif-specific secondary structural elements are quantitatively correlated to the primary amino acid sequence of major ampullate spidroin 1 and 2 (MaSp1 and MaSp2) and are shown to form a self-consistent model for black widow dragline silk. PMID:24024617
Cholestasis and protein-losing enteropathy secondary to hyperthyroidism in a 6-year-old girl.
Gargouri, Lamia; Charfi, Manel; Maalej, Bayen; Majdoub, Imen; Safi, Faiza; Fourati, Hela; Hentati, Yosr; Daoud, Emna; Mnif, Zeineb; Abid, Mohamed; Mahfoudh, Abdelmajid
2014-09-01
Hepatic dysfunctions are not infrequent in patients with hyperthyroidism. These disorders may be related to the effects of the excess thyroid hormone secretion, to the uses of antithyroid drugs, or to the presence of concomitant hepatic diseases. Our aim is to describe the clinical and biochemical features of liver dysfunction related to thyrotoxicosis. We report here a case of a 6-year-old girl who was admitted for jaundice and pruritus as a result of the development of hyperthyroidism due to Graves' disease. On physical examination at admission, she was found to have jaundice and hepatomegaly. Laboratory data show cholestasis and protein-losing enteropathy. Investigations exclude other causes of hepatic disorder. One month after the initiation of antithyroid drug, the patient became euthyroid with improvement in jaundice and pruritus and normalization of hepatic tests and alpha antitrypsine clearance. In conclusion, the diagnosis of hyperthyroidism may be delayed in patients in whom the primary manifestations were pruritus and jaundice. The physician should suspect thyrotoxicosis prior to hepatitis or skin manifestations.
Abe, Yuta; Kamiya, Koki; Osaki, Toshihisa; Sasaki, Hirotaka; Kawano, Ryuji; Miki, Norihisa; Takeuchi, Shoji
2015-08-21
This paper describes a simple microfluidic device that can generate nonlinear concentration gradients. We changed the "width" of channels that can drastically shorten the total microfluidic channel length and simplify the microfluidic network design rather than the "length" of channels. The logarithmic concentration gradients generated by the device were in good agreement with those obtained by simulation. Using this device, we evaluated a probable IC50 value of the ABC transporter proteins by the competitive transport assays at five different logarithmic concentrations. This probable IC50 value was in good agreement with an IC50 value (0.92 μM) obtained at the diluted concentrations of seven points.
Villanueva, Josep; Villegas, Virtudes; Querol, Enrique; Avilés, Francesc X; Serrano, Luis
2002-09-01
In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability. Copyright 2002 John Wiley & Sons, Ltd.
Takayama, Mitsuo; Osaka, Issey; Sakakura, Motoshi
2012-01-01
The susceptibility of the N-Cα bond of the peptide backbone to specific cleavage by in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was studied from the standpoint of the secondary structure of three proteins. A naphthalene derivative, 5-amino-1-naphtol (5,1-ANL), was used as the matrix. The resulting c'-ions, which originate from the cleavage at N-Cα bonds in flexible secondary structures such as turn and bend, and are free from intra-molecular hydrogen-bonded α-helix structure, gave relatively intense peaks. Furthermore, ISD spectra of the proteins showed that the N-Cα bonds of specific amino acid residues, namely Gly-Xxx, Xxx-Asp, and Xxx-Asn, were more susceptible to MALDI-ISD than other amino acid residues. This is in agreement with the observation that Gly, Asp and Asn residues usually located in turns, rather than α-helix. The results obtained indicate that protein molecules embedded into the matrix crystal in the MALDI experiments maintain their secondary structures as determined by X-ray crystallography, and that MALDI-ISD has the capability for providing information concerning the secondary structure of protein.
International Nuclear Information System (INIS)
Winkler, E.
1991-01-01
If nonlinear biological processes are investigated by means of tracer experiments they can be modelled with linear kinetic equations (compartment equations) as long as the total system is in a stationary state. But if nonstationary behaviour is included considerations on the kinetics of the individual processes are necessary. Within the range of biological and agricultural investigations especially first order reactions (constant fraction processes), zero order reactions (constant amount process) and saturation reactions (Michaelis-Menten-kinetics) are to be taken into account. A rigorous treatment of data based on system theory can be preceeded by graphic-algebraic procedure which may be more or less uncertain in its results but which can easily be handled. An example is given of methodological considerations concerning the combination of evaluation procedures and the discrimination between different reaction mechanisms. It treats protein turnover in 2 different parts of growing wheat plants investigated by means of an 15 N-tracer experiment. Whereas in a stationary system (upper stalk section) linear tracer equations were sufficient irrespective of the true reaction mechanism, for protein synthesis in the upper leaf as a nonstationary system it was necessary to decide between the hypotheses of a zero order and a first order reaction. In accordance with statements in the literature the unambiguous result was a combination of protein synthesis as a zero order process and of protein degradation as a first order process. (orig.) [de
López-Carrasco, Amparo; Flores, Ricardo
2017-07-01
Avocado sunblotch viroid (ASBVd), the type member of the family Avsunviroidae, replicates and accumulates in chloroplasts. Whether this minimal non-protein-coding circular RNA of 246-250 nt exists in vivo as a free nucleic acid or closely associated with host proteins remains unknown. To tackle this issue, the secondary structures of the monomeric circular (mc) (+) and (-) strands of ASBVd have been examined in silico by searching those of minimal free energy, and in vitro at single-nucleotide resolution by selective 2'-hydroxyl acylation analysed by primer extension (SHAPE). Both approaches resulted in predominant rod-like secondary structures without tertiary interactions, with the mc (+) RNA being more compact than its (-) counterpart as revealed by non-denaturing polyacryamide gel electrophoresis. Moreover, in vivo SHAPE showed that the mc ASBVd (+) form accumulates in avocado leaves as a free RNA adopting a similar rod-shaped conformation unprotected by tightly bound host proteins. Hence, the mc ASBVd (+) RNA behaves in planta like the previously studied mc (+) RNA of potato spindle tuber viroid, the type member of nuclear viroids (family Pospiviroidae), indicating that two different viroids replicating and accumulating in distinct subcellular compartments, have converged into a common structural solution. Circularity and compact secondary structures confer to these RNAs, and probably to all viroids, the intrinsic stability needed to survive in their natural habitats. However, in vivo SHAPE has not revealed the (possibly transient or loose) interactions of the mc ASBVd (+) RNA with two host proteins observed previously by UV irradiation of infected avocado leaves.
Bellio, Pierangelo; Di Pietro, Letizia; Mancini, Alisia; Piovano, Marisa; Nicoletti, Marcello; Brisdelli, Fabrizia; Tondi, Donatella; Cendron, Laura; Franceschini, Nicola; Amicosante, Gianfranco; Perilli, Mariagrazia; Celenza, Giuseppe
2017-06-15
RecA is a bacterial multifunctional protein essential to genetic recombination, error-prone replicative bypass of DNA damages and regulation of SOS response. The activation of bacterial SOS response is directly related to the development of intrinsic and/or acquired resistance to antimicrobials. Although recent studies directed towards RecA inactivation via ATP binding inhibition described a variety of micromolar affinity ligands, inhibitors of the DNA binding site are still unknown. Twenty-seven secondary metabolites classified as anthraquinones, depsides, depsidones, dibenzofurans, diphenyl-butenolides, paraconic acids, pseudo-depsidones, triterpenes and xanthones, were investigated for their ability to inhibit RecA from Escherichia coli. They were isolated in various Chilean regions from 14 families and 19 genera of lichens. The ATP hydrolytic activity of RecA was quantified detecting the generation of free phosphate in solution. The percentage of inhibition was calculated fixing at 100µM the concentration of the compounds. Deeper investigations were reserved to those compounds showing an inhibition higher than 80%. To clarify the mechanism of inhibition, the semi-log plot of the percentage of inhibition vs. ATP and vs. ssDNA, was evaluated. Only nine compounds showed a percentage of RecA inhibition higher than 80% (divaricatic, perlatolic, alpha-collatolic, lobaric, lichesterinic, protolichesterinic, epiphorellic acids, sphaerophorin and tumidulin). The half-inhibitory concentrations (IC 50 ) calculated for these compounds were ranging from 14.2µM for protolichesterinic acid to 42.6µM for sphaerophorin. Investigations on the mechanism of inhibition showed that all compounds behaved as uncompetitive inhibitors for ATP binding site, with the exception of epiphorellic acid which clearly acted as non-competitive inhibitor of the ATP site. Further investigations demonstrated that epiphorellic acid competitively binds the ssDNA binding site. Kinetic data were
International Nuclear Information System (INIS)
Boyd, R.W.
1992-01-01
Nonlinear optics is the study of the interaction of intense laser light with matter. This book is a textbook on nonlinear optics at the level of a beginning graduate student. The intent of the book is to provide an introduction to the field of nonlinear optics that stresses fundamental concepts and that enables the student to go on to perform independent research in this field. This book covers the areas of nonlinear optics, quantum optics, quantum electronics, laser physics, electrooptics, and modern optics
International Nuclear Information System (INIS)
Wang, Pan; Tian, Bo; Jiang, Yan; Wang, Yu-Feng
2013-01-01
For describing the dynamics of alpha helical proteins with internal molecular excitations, nonlinear couplings between lattice vibrations and molecular excitations, and spin excitations in one-dimensional isotropic biquadratic Heisenberg ferromagnetic spin with the octupole–dipole interactions, we consider an inhomogeneous generalized fourth-order nonlinear Schrödinger equation. Based on the Ablowitz–Kaup–Newell–Segur system, infinitely many conservation laws for the equation are derived. Through the auxiliary function, bilinear forms and N-soliton solutions for the equation are obtained. Interactions of solitons are discussed by means of the asymptotic analysis. Effects of linear inhomogeneity on the interactions of solitons are also investigated graphically and analytically. Since the inhomogeneous coefficient of the equation h=α x+β, the soliton takes on the parabolic profile during the evolution. Soliton velocity is related to the parameter α, distance scale coefficient and biquadratic exchange coefficient, but has no relation with the parameter β. Soliton amplitude and width are only related to α. Soliton position is related to β
Wang, Yuanze; van Oosterwijk, Niels; Ali, Ameena M; Adawy, Alaa; Anindya, Atsarina L; Dömling, Alexander S S; Groves, Matthew R
2017-01-01
Refolding of proteins derived from inclusion bodies is very promising as it can provide a reliable source of target proteins of high purity. However, inclusion body-based protein production is often limited by the lack of techniques for the detection of correctly refolded protein. Thus, the
International Nuclear Information System (INIS)
Shevtsov, Maxim A.; Nikolaev, Boris P.; Ryzhov, Vyacheslav A.; Yakovleva, Ludmila Y.; Dobrodumov, Anatolii V.; Marchenko, Yaroslav Y.; Margulis, Boris A.; Pitkin, Emil; Guzhova, Irina V.
2015-01-01
Brain tumor targeting efficiency and biodistribution of the superparamagnetic nanoparticles conjugated with heat shock protein Hsp70 (SPION–Hsp70) were evaluated in experimental glioma model. Synthesized conjugates were characterized using the method of longitudinal nonlinear response of magnetic nanoparticles to a weak ac magnetic field with measurements of second harmonic of magnetization (NLR-M 2 ). Cellular interaction of magnetic conjugates was analyzed in 9L glioma cell culture. The biodistribution of the nanoparticles and their accumulation in tumors was assessed by the latter approach as well. The efficacy of Hsp70-conjugates for contrast enhancement in the orthotopic model of 9L glioma was assessed by MR imaging (11 T). Magnetic nanoparticles conjugated with Hsp70 had the relaxivity properties of the MR-negative contrast agents. Morphological observation and cell viability test demonstrated good biocompatibility of Hsp70-conjugates. Analysis of the T 2 -weighted MR scans in tumor-bearing rats demonstrated the high efficacy of Hsp70-conjugates in contrast enhancement of the glioma in comparison to non-conjugated nanoparticles. High contrast enhancement of the glioma was provided by the accumulation of the SPION–Hsp70 particles in the glioma tissue (as shown by the histological assay). Biodistribution analysis by NLR-M 2 measurements evidenced the many-fold increase (~40) in the tumor-to-normal brain uptake ratio in the Hsp70-conjugates treated animals. Biodistribution pattern of Hsp70-decorated nanoparticles differed from that of non-conjugated SPIONs. Coating of the magnetic nanoparticles with Hsp70 protein enhances the tumor-targeting ability of the conjugates that could be applied in the MR imaging of the malignant brain tumors. - Highlights: • Second-harmonic nonlinear magnetic response is used for biodistribution analysis. • NLR-M 2 ensures high sensibility in detection of SPIONs in tissue. • SPION–Hsp70 conjugates effectively target the
Bloembergen, Nicolaas
1996-01-01
Nicolaas Bloembergen, recipient of the Nobel Prize for Physics (1981), wrote Nonlinear Optics in 1964, when the field of nonlinear optics was only three years old. The available literature has since grown by at least three orders of magnitude.The vitality of Nonlinear Optics is evident from the still-growing number of scientists and engineers engaged in the study of new nonlinear phenomena and in the development of new nonlinear devices in the field of opto-electronics. This monograph should be helpful in providing a historical introduction and a general background of basic ideas both for expe
Ladhani, Shamez N; Cordery, Rebecca; Mandal, Sema; Christensen, Hannah; Campbell, Helen; Borrow, Ray; Ramsay, Mary E
2014-11-01
To assess the potential use of a protein-based meningococcal group B (MenB) vaccine (Bexsero(®)) in addition to antibiotic chemoprophylaxis for preventing secondary cases. Published studies on the risk of secondary meningococcal infections were used to estimate the numbers needed to vaccinate (NNV) with Bexsero(®) to prevent a secondary case in household and educational settings. Most secondary cases occur within a few days of diagnosis in the index case. Unlike conjugate vaccines, early protection offered after a single dose of Bexsero(®) is likely to be low, particularly in young children, who are at higher risk of secondary infection. NNV was dependent on predicted meningococcal strain coverage, estimated onset of protection after one Bexsero(®) dose and estimated vaccine efficacy. Even in the most favourable scenario where we assume the vaccine is administered within 4 days of the index case and prevents 90% of cases occurring after 14 days, the NNV for household contacts was >1000. NNV in educational settings was much higher. The estimated NNV should be taken into account when deciding policy to recommend Bexsero(®) for close contacts of single cases in household or educational settings. Bexsero(®) may have a protective role in clusters and outbreaks. Copyright © 2014 The British Infection Association. Published by Elsevier Ltd. All rights reserved.
International Nuclear Information System (INIS)
Zhang Weici; Xiao Weihua; Wei Haiming; Zhang Jian; Tian Zhigang
2006-01-01
Codon usage and thermodynamic optimization of the 5'-end of mRNA have been applied to improve the efficiency of human protein production in Escherichia coli. However, high level expression of human protein in E. coli is still a challenge that virtually depends upon each individual target genes. Using human interleukin 10 (huIL-10) and interferon α (huIFN-α) coding sequences, we systematically analyzed the influence of several major factors on expression of human protein in E. coli. The results from huIL-10 and reinforced by huIFN-α showed that exposing AUG initiator codon from base-paired structure within mRNA itself significantly improved the translation of target protein, which resulted in a 10-fold higher protein expression than the wild-type genes. It was also noted that translation process was not affected by the retained short-range stem-loop structure at Shine-Dalgarno (SD) sequences. On the other hand, codon-optimized constructs of huIL-10 showed unimproved levels of protein expression, on the contrary, led to a remarkable RNA degradation. Our study demonstrates that exposure of AUG initiator codon from long-range intra-strand secondary structure at 5'-end of mRNA may be used as a general strategy for human protein production in E. coli
International Nuclear Information System (INIS)
Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei
2013-01-01
We introduce a Python-based program that utilizes the large database of 13 C and 15 N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13 C– 13 C, 15 N– 13 C, or 3D 15 N– 13 C– 13 C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13 C– 13 C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.
Energy Technology Data Exchange (ETDEWEB)
Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)
2013-06-15
We introduce a Python-based program that utilizes the large database of {sup 13}C and {sup 15}N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D {sup 13}C-{sup 13}C, {sup 15}N-{sup 13}C, or 3D {sup 15}N-{sup 13}C-{sup 13}C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D {sup 13}C-{sup 13}C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the C{alpha} and C{beta} chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-C{alpha}-C{beta} or N-C{alpha}-C{beta}), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.
Ching, Ada; Dhugga, Kanwarpal S; Appenzeller, Laura; Meeley, Robert; Bourett, Timothy M; Howard, Richard J; Rafalski, Antoni
2006-10-01
A spontaneous maize mutant, brittle stalk-2 (bk2-ref), exhibits dramatically reduced tissue mechanical strength. Reduction in mechanical strength in the stalk tissue was highly correlated with a reduction in the amount of cellulose and an uneven deposition of secondary cell wall material in the subepidermal and perivascular sclerenchyma fibers. Cell wall accounted for two-thirds of the observed reduction in dry matter content per unit length of the mutant stalk in comparison to the wildtype stalk. Although the cell wall composition was significantly altered in the mutant in comparison to the wildtype stalks, no compensation by lignin and cell wall matrix for reduced cellulose amount was observed. We demonstrate that Bk2 encodes a Cobra-like protein that is homologous to the rice Bc1 protein. In the bk2-ref gene, a 1 kb transposon-like element is inserted in the beginning of the second exon, disrupting the open reading frame. The Bk2 gene was expressed in the stalk, husk, root, and leaf tissues, but not in the embryo, endosperm, pollen, silk, or other tissues with comparatively few or no secondary cell wall containing cells. The highest expression was in the isolated vascular bundles. In agreement with its role in secondary wall formation, the expression pattern of the Bk2 gene was very similar to that of the ZmCesA10, ZmCesA11, and ZmCesA12 genes, which are known to be involved in secondary wall formation. We have isolated an independent Mutator-tagged allele of bk2, referred to as bk2-Mu7, the phenotype of which is similar to that of the spontaneous mutant. Our results demonstrate that mutations in the Bk2 gene affect stalk strength in maize by interfering with the deposition of cellulose in the secondary cell wall in fiber cells.
Yoshida, Zensho
2010-01-01
This book gives a general, basic understanding of the mathematical structure "nonlinearity" that lies in the depths of complex systems. Analyzing the heterogeneity that the prefix "non" represents with respect to notions such as the linear space, integrability and scale hierarchy, "nonlinear science" is explained as a challenge of deconstruction of the modern sciences. This book is not a technical guide to teach mathematical tools of nonlinear analysis, nor a zoology of so-called nonlinear phenomena. By critically analyzing the structure of linear theories, and cl
Nayfeh, Ali Hasan
1995-01-01
Nonlinear Oscillations is a self-contained and thorough treatment of the vigorous research that has occurred in nonlinear mechanics since 1970. The book begins with fundamental concepts and techniques of analysis and progresses through recent developments and provides an overview that abstracts and introduces main nonlinear phenomena. It treats systems having a single degree of freedom, introducing basic concepts and analytical methods, and extends concepts and methods to systems having degrees of freedom. Most of this material cannot be found in any other text. Nonlinear Oscillations uses sim
Energy Technology Data Exchange (ETDEWEB)
Wang Liya [Cold Spring Harbor Laboratory (United States); Markley, John L. [University of Wisconsin, Biochemistry Department (United States)], E-mail: markley@nmrfam.wisc.edu
2009-06-15
The linear analysis of chemical shifts (LACS) has provided a robust method for identifying and correcting {sup 13}C chemical shift referencing problems in data from protein NMR spectroscopy. Unlike other approaches, LACS does not require prior knowledge of the three-dimensional structure or inference of the secondary structure of the protein. It also does not require extensive assignment of the NMR data. We report here a way of extending the LACS approach to {sup 15}N NMR data from proteins, so as to enable the detection and correction of inconsistencies in chemical shift referencing for this nucleus. The approach is based on our finding that the secondary {sup 15}N chemical shift of the backbone nitrogen atom of residue i is strongly correlated with the secondary chemical shift difference (experimental minus random coil) between the alpha and beta carbons of residue i - 1. Thus once alpha and beta {sup 13}C chemical shifts are available (their difference is referencing error-free), the {sup 15}N referencing can be validated, and an appropriate offset correction can be derived. This approach can be implemented prior to a structure determination and can be used to analyze potential referencing problems in database data not associated with three-dimensional structure. Application of the LACS algorithm to the current BMRB protein chemical shift database, revealed that nearly 35% of the BMRB entries have {delta}{sup 15}N values mis-referenced by over 0.7 ppm and over 25% of them have {delta}{sup 1}H{sup N} values mis-referenced by over 0.12 ppm. One implication of the findings reported here is that a backbone {sup 15}N chemical shift provides a better indicator of the conformation of the preceding residue than of the residue itself.
International Nuclear Information System (INIS)
Kuzin, A.M.; Surkenova, G.N.; Revin, A.F.
1996-01-01
In is demonstrated that native protein of egg-white after being γ-irradiated with law doses is able to stimulate transition of cells of remote biological detector from non-cycling state to proliferation even if irradiated protein is separated from detector by quartz-glass. Animal tissues which have a high protein content (freshly cut hair, insect bodies) reveal the same ability. The role of natural background radiation in the maintenance excitation, state of living tissue proteins is discussed. 13 refs.; 1 figs.; 4 tabs
Energy Technology Data Exchange (ETDEWEB)
Shevtsov, Maxim A., E-mail: shevtsov-max@mail.ru [Institute of Cytology of the Russian Academy of Sciences (RAS), Tikhoretsky Ave. 4, St. Petersburg 194064 (Russian Federation); A.L. Polenov Russian Research Scientific Institute of Neurosurgery, Mayakovsky str. 12, St. Petersburg 191014 (Russian Federation); Nikolaev, Boris P. [Research Institute of Highly Pure Biopreparations, Pudozhskaya str. 12, St. Petersburg 197110 (Russian Federation); Ryzhov, Vyacheslav A. [Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina 188300 (Russian Federation); Yakovleva, Ludmila Y. [Research Institute of Highly Pure Biopreparations, Pudozhskaya str. 12, St. Petersburg 197110 (Russian Federation); Dobrodumov, Anatolii V. [Institute of Macromolecular Compounds of the Russian Academy of Sciences (RAS), Bolshoi pr. 31, St. Petersburg 199004 (Russian Federation); Marchenko, Yaroslav Y. [Research Institute of Highly Pure Biopreparations, Pudozhskaya str. 12, St. Petersburg 197110 (Russian Federation); Margulis, Boris A. [Institute of Cytology of the Russian Academy of Sciences (RAS), Tikhoretsky Ave. 4, St. Petersburg 194064 (Russian Federation); Pitkin, Emil [The Wharton School, University of Pennsylvania, 3730 Walnut St., Philadelphia, PA 19104 (United States); Guzhova, Irina V. [Institute of Cytology of the Russian Academy of Sciences (RAS), Tikhoretsky Ave. 4, St. Petersburg 194064 (Russian Federation)
2015-08-15
Brain tumor targeting efficiency and biodistribution of the superparamagnetic nanoparticles conjugated with heat shock protein Hsp70 (SPION–Hsp70) were evaluated in experimental glioma model. Synthesized conjugates were characterized using the method of longitudinal nonlinear response of magnetic nanoparticles to a weak ac magnetic field with measurements of second harmonic of magnetization (NLR-M{sub 2}). Cellular interaction of magnetic conjugates was analyzed in 9L glioma cell culture. The biodistribution of the nanoparticles and their accumulation in tumors was assessed by the latter approach as well. The efficacy of Hsp70-conjugates for contrast enhancement in the orthotopic model of 9L glioma was assessed by MR imaging (11 T). Magnetic nanoparticles conjugated with Hsp70 had the relaxivity properties of the MR-negative contrast agents. Morphological observation and cell viability test demonstrated good biocompatibility of Hsp70-conjugates. Analysis of the T{sub 2}-weighted MR scans in tumor-bearing rats demonstrated the high efficacy of Hsp70-conjugates in contrast enhancement of the glioma in comparison to non-conjugated nanoparticles. High contrast enhancement of the glioma was provided by the accumulation of the SPION–Hsp70 particles in the glioma tissue (as shown by the histological assay). Biodistribution analysis by NLR-M{sub 2} measurements evidenced the many-fold increase (~40) in the tumor-to-normal brain uptake ratio in the Hsp70-conjugates treated animals. Biodistribution pattern of Hsp70-decorated nanoparticles differed from that of non-conjugated SPIONs. Coating of the magnetic nanoparticles with Hsp70 protein enhances the tumor-targeting ability of the conjugates that could be applied in the MR imaging of the malignant brain tumors. - Highlights: • Second-harmonic nonlinear magnetic response is used for biodistribution analysis. • NLR-M{sub 2} ensures high sensibility in detection of SPIONs in tissue. • SPION–Hsp70 conjugates
Directory of Open Access Journals (Sweden)
Jia Yan
2012-07-01
Full Text Available Abstract Background Multiple sclerosis (MS is a chronic inflammatory disorder of the central nervous system (CNS. It involves damage to the myelin sheath surrounding axons and to the axons themselves. MS most often presents with a series of relapses and remissions but then evolves over a variable period of time into a slowly progressive form of neurological dysfunction termed secondary progressive MS (SPMS. The reasons for this change in clinical presentation are unclear. The absence of a diagnostic marker means that there is a lag time of several years before the diagnosis of SPMS can be established. At the same time, understanding the mechanisms that underlie SPMS is critical to the development of rational therapies for this untreatable stage of the disease. Results Using high performance liquid chromatography-coupled mass spectrometry (HPLC; we have established a highly specific and sensitive selected reaction monitoring (SRM assay. Our multiplexed SRM assay has facilitated the simultaneous detection of surrogate peptides originating from 26 proteins present in cerebrospinal fluid (CSF. Protein levels in CSF were generally ~200-fold lower than that in human sera. A limit of detection (LOD was determined to be as low as one femtomol. We processed and analysed CSF samples from a total of 22 patients with SPMS, 7 patients with SPMS treated with lamotrigine, 12 patients with non-inflammatory neurological disorders (NIND and 10 healthy controls (HC for the levels of these 26 selected potential protein biomarkers. Our SRM data found one protein showing significant difference between SPMS and HC, three proteins differing between SPMS and NIND, two proteins between NIND and HC, and 11 protein biomarkers showing significant difference between a lamotrigine-treated and untreated SPMS group. Principal component analysis (PCA revealed that these 26 proteins were correlated, and could be represented by four principal components. Overall, we established an
Directory of Open Access Journals (Sweden)
Lena Studt
Full Text Available The plant-pathogenic fungus Fusarium fujikuroi is a notorious rice pathogen causing hyper-elongation of infected plants due to the production of gibberellic acids (GAs. In addition to GAs, F. fujikuroi produces a wide range of other secondary metabolites, such as fusarins, fusaric acid or the red polyketides bikaverins and fusarubins. The recent availability of the fungal genome sequence for this species has revealed the potential of many more putative secondary metabolite gene clusters whose products remain to be identified. However, the complex regulation of secondary metabolism is far from being understood. Here we studied the impact of the heterotrimeric G protein and the cAMP-mediated signaling network, including the regulatory subunits of the cAMP-dependent protein kinase (PKA, to study their effect on colony morphology, sexual development and regulation of bikaverins, fusarubins and GAs. We demonstrated that fusarubin biosynthesis is negatively regulated by at least two Gα subunits, FfG1 and FfG3, which both function as stimulators of the adenylyl cyclase FfAC. Surprisingly, the primary downstream target of the adenylyl cyclase, the PKA, is not involved in the regulation of fusarubins, suggesting that additional, yet unidentified, cAMP-binding protein(s exist. In contrast, bikaverin biosynthesis is significantly reduced in ffg1 and ffg3 deletion mutants and positively regulated by FfAC and FfPKA1, while GA biosynthesis depends on the active FfAC and FfPKA2 in an FfG1- and FfG3-independent manner. In addition, we provide evidence that G Protein-mediated/cAMP signaling is important for growth in F. fujikuroi because deletion of ffg3, ffac and ffpka1 resulted in impaired growth on minimal and rich media. Finally, sexual crosses of ffg1 mutants showed the importance of a functional FfG1 protein for development of perithecia in the mating strain that carries the MAT1-1 idiomorph.
Directory of Open Access Journals (Sweden)
Chen Jiang
2017-01-01
Full Text Available Folliculogenesis is a progressive and highly regulated process, which is essential to provide ova for later reproductive life, requires the bidirectional communication between the oocyte and granulosa cells. This physical connection-mediated communication conveys not only the signals from the oocyte to granulosa cells that regulate their proliferation but also metabolites from the granulosa cells to the oocyte for biosynthesis. However, the underlying mechanism of establishing this communication is largely unknown. Here, we report that oocyte geranylgeranyl diphosphate (GGPP, a metabolic intermediate involved in protein geranylgeranylation, is required to establish the oocyte-granulosa cell communication. GGPP and geranylgeranyl diphosphate synthase (Ggpps levels in oocytes increased during early follicular development. The selective depletion of GGPP in mouse oocytes impaired the proliferation of granulosa cells, primary-secondary follicle transition and female fertility. Mechanistically, GGPP depletion inhibited Rho GTPase geranylgeranylation and its GTPase activity, which was responsible for the accumulation of cell junction proteins in the oocyte cytoplasm and the failure to maintain physical connection between oocyte and granulosa cells. GGPP ablation also blocked Rab27a geranylgeranylation, which might account for the impaired secretion of oocyte materials such as Gdf9. Moreover, GGPP administration restored the defects in oocyte-granulosa cell contact, granulosa cell proliferation and primary-secondary follicle transition in Ggpps depletion mice. Our study provides the evidence that GGPP-mediated protein geranylgeranylation contributes to the establishment of oocyte-granulosa cell communication and then regulates the primary-secondary follicle transition, a key phase of folliculogenesis essential for female reproductive function.
Boyd, Robert W
2013-01-01
Nonlinear Optics is an advanced textbook for courses dealing with nonlinear optics, quantum electronics, laser physics, contemporary and quantum optics, and electrooptics. Its pedagogical emphasis is on fundamentals rather than particular, transitory applications. As a result, this textbook will have lasting appeal to a wide audience of electrical engineering, physics, and optics students, as well as those in related fields such as materials science and chemistry.Key Features* The origin of optical nonlinearities, including dependence on the polarization of light* A detailed treatment of the q
National Research Council Canada - National Science Library
Drazin, P. G
1992-01-01
This book is an introduction to the theories of bifurcation and chaos. It treats the solution of nonlinear equations, especially difference and ordinary differential equations, as a parameter varies...
Gasinski, Leszek
2005-01-01
Hausdorff Measures and Capacity. Lebesgue-Bochner and Sobolev Spaces. Nonlinear Operators and Young Measures. Smooth and Nonsmooth Analysis and Variational Principles. Critical Point Theory. Eigenvalue Problems and Maximum Principles. Fixed Point Theory.
Directory of Open Access Journals (Sweden)
Laura Ramírez
2010-01-01
Full Text Available Leishmaniasis is an increasing public health problem and effective vaccines are not currently available. We have previously demonstrated that vaccination with ribosomal proteins extracts administered in combination of CpG oligodeoxynucleotides protects susceptible BALB/c mice against primary Leishmania major infection. Here, we evaluate the long-term immunity to secondary infection conferred by this vaccine. We show that vaccinated and infected BALB/c mice were able to control a secondary Leishmania major challenge, since no inflammation and very low number of parasites were observed in the site of reinfection. In addition, although an increment in the parasite burden was observed in the draining lymph nodes of the primary site of infection we did not detected inflammatory lesions at that site. Resistance against reinfection correlated to a predominant Th1 response against parasite antigens. Thus, cell cultures established from spleens and the draining lymph node of the secondary site of infection produced high levels of parasite specific IFN-γ in the absence of IL-4 and IL-10 cytokine production. In addition, reinfected mice showed a high IgG2a/IgG1 ratio for anti-Leishmania antibodies. Our results suggest that ribosomal vaccine, which prevents pathology in a primary challenge, in combination with parasite persistence might be effective for long-term maintenance of immunity.
Energy Technology Data Exchange (ETDEWEB)
Bonvin, Alexandre M.J.J.; Houben, Klaartje; Guenneugues, Marc; Kaptein, Robert; Boelens, Rolf [Utrecht University, Bijvoet Center for Biomolecular Research, NMR Spectroscopy (Netherlands)
2001-11-15
The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small {alpha}/{beta} protein chymotrypsin inhibitor 2. Dihedral angle restraints for the {phi} and {psi} angles of 32 out of 64 residues could be obtained from secondary chemical shift analysis with the TALOS program (Corneliscu et al., 1999a). This information was supplemented by 18 hydrogen-bond restraints derived from experimentally measured cross-hydrogen bond {sup 3hb}J{sub NC'} coupling constants. These experimental data were sufficient to generate structures that are as close as 1.0 A backbone rmsd from the crystal structure. The fold is, however, not uniquely defined and several solutions are generated that cannot be distinguished on the basis of violations or energetic considerations. Correct folds could be identified by combining clustering methods with knowledge-based potentials derived from structural databases.
Secondary hypertension Overview Secondary hypertension (secondary high blood pressure) is high blood pressure that's caused by another medical condition. Secondary hypertension can be caused by conditions that affect your kidneys, ...
Dietz, Andrea N; Villinger, Clarissa; Becker, Stefan; Frick, Manfred; von Einem, Jens
2018-01-01
The human cytomegalovirus (HCMV) tegument protein pUL71 is required for efficient secondary envelopment and accumulates at the Golgi compartment-derived viral assembly complex (vAC) during infection. Analysis of various C-terminally truncated pUL71 proteins fused to enhanced green fluorescent protein (eGFP) identified amino acids 23 to 34 as important determinants for its Golgi complex localization. Sequence analysis and mutational verification revealed the presence of an N-terminal tyrosine-based trafficking motif (YXXΦ) in pUL71. This led us to hypothesize a requirement of the YXXΦ motif for the function of pUL71 in infection. Mutation of both the tyrosine residue and the entire YXXΦ motif resulted in an altered distribution of mutant pUL71 at the plasma membrane and in the cytoplasm during infection. Both YXXΦ mutant viruses exhibited similarly decreased focal growth and reduced virus yields in supernatants. Ultrastructurally, mutant-virus-infected cells exhibited impaired secondary envelopment manifested by accumulations of capsids undergoing an envelopment process. Additionally, clusters of capsid accumulations surrounding the vAC were observed, similar to the ultrastructural phenotype of a UL71-deficient mutant. The importance of endocytosis and thus the YXXΦ motif for targeting pUL71 to the Golgi complex was further demonstrated when clathrin-mediated endocytosis was inhibited either by coexpression of the C-terminal part of cellular AP180 (AP180-C) or by treatment with methyl-β-cyclodextrin. Both conditions resulted in a plasma membrane accumulation of pUL71. Altogether, these data reveal the presence of a functional N-terminal endocytosis motif that is an important determinant for intracellular localization of pUL71 and that is furthermore required for the function of pUL71 during secondary envelopment of HCMV capsids at the vAC. IMPORTANCE Human cytomegalovirus (HCMV) is the leading cause of birth defects among congenital virus infections and can
Czech Academy of Sciences Publication Activity Database
Štys, Dalibor
2005-01-01
Roč. 43, č. 3 (2005), s. 421-424 ISSN 0300-3604 Institutional research plan: CEZ:AV0Z60870520; MSM6007665808 Keywords : protein Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.810, year: 2005
Samanta, Sudipta; Mukherjee, Sanchita
2018-01-28
The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.
Wu, Zhiyun; Bertram, Hanne Christine; Böcker, Ulrike; Ofstad, Ragni; Kohler, Achim
2007-05-16
The objective of this study was to investigate the influence of heating rate on myowater dynamics and protein secondary structures in three pork qualities by proton NMR T2 relaxation and Fourier transform infrared (FT-IR) microspectroscopy measurements. Two oven temperatures at 100 degrees C and 200 degrees C corresponding to slow and fast heating rates were applied on three pork qualities (DFD, PSE, and normal) to an internal center temperature of 65 degrees C. The fast heating induced a higher cooking loss, particularly for PSE meat. The water proton T21 distribution representing water entrapped within the myofibrillar network was influenced by heating rate and meat quality. Fast heating broadened the T21 distribution and decreased the relaxation times of the T21 peak position for three meat qualities. The changes in T21 relaxation times in meat can be interpreted in terms of chemical and diffusive exchange. FT-IR showed that fast heating caused a higher gain of random structures and aggregated beta-sheets at the expense of native alpha-helixes, and these changes dominate the fast-heating-induced broadening of T21 distribution and reduction in T21 times. Furthermore, of the three meat qualities, PSE meat had the broadest T21 distribution and the lowest T21 times for both heating rates, reflecting that the protein aggregation of PSE caused by heating is more extensive than those of DFD and normal, which is consistent with the IR data. The present study demonstrated that the changes in T2 relaxation times of water protons affected by heating rate and raw meat quality are well related to the protein secondary structural changes as probed by FT-IR microspectroscopy.
Samanta, Sudipta; Mukherjee, Sanchita
2018-01-01
The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.
Czech Academy of Sciences Publication Activity Database
Ulrych, Aleš; Goldová, Jana; Petříček, Miroslav; Benada, Oldřich; Kofroňová, Olga; Rampírová, Petra; Petříčková, Kateřina; Branny, Pavel
2013-01-01
Roč. 9, č. 6 (2013), s. 1453-1469 ISSN 1742-206X R&D Projects: GA MŠk LH12191; GA MŠk LH12055; GA MŠk 2B08064 Institutional support: RVO:61388971 Keywords : AERIAL MYCELIUM FORMATION * WD-REPEAT PROTEINS * BIOSYNTHESIS GENE-CLUSTER Subject RIV: EE - Microbiology, Virology Impact factor: 3.183, year: 2013
Ruszczynski, Andrzej
2011-01-01
Optimization is one of the most important areas of modern applied mathematics, with applications in fields from engineering and economics to finance, statistics, management science, and medicine. While many books have addressed its various aspects, Nonlinear Optimization is the first comprehensive treatment that will allow graduate students and researchers to understand its modern ideas, principles, and methods within a reasonable time, but without sacrificing mathematical precision. Andrzej Ruszczynski, a leading expert in the optimization of nonlinear stochastic systems, integrates the theory and the methods of nonlinear optimization in a unified, clear, and mathematically rigorous fashion, with detailed and easy-to-follow proofs illustrated by numerous examples and figures. The book covers convex analysis, the theory of optimality conditions, duality theory, and numerical methods for solving unconstrained and constrained optimization problems. It addresses not only classical material but also modern top...
International Nuclear Information System (INIS)
Bersch, Beate; Rossy, Emmanuel; Coves, Jacques; Brutscher, Bernhard
2003-01-01
NMR experiments are presented which allow backbone resonance assignment, secondary structure identification, and in favorable cases also molecular fold topology determination from a series of two-dimensional 1 H- 15 N HSQC-like spectra. The 1 H- 15 N correlation peaks are frequency shifted by an amount ± ω X along the 15 N dimension, where ω X is the C α , C β , or H α frequency of the same or the preceding residue. Because of the low dimensionality (2D) of the experiments, high-resolution spectra are obtained in a short overall experimental time. The whole series of seven experiments can be performed in typically less than one day. This approach significantly reduces experimental time when compared to the standard 3D-based methods. The here presented methodology is thus especially appealing in the context of high-throughput NMR studies of protein structure, dynamics or molecular interfaces
Barreto, Goncalo; Soininen, Antti; Sillat, Tarvo; Konttinen, Yrjö T; Kaivosoja, Emilia
2014-01-01
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is increasingly being used in analysis of biological samples. For example, it has been applied to distinguish healthy and osteoarthritic human cartilage. This chapter discusses ToF-SIMS principle and instrumentation including the three modes of analysis in ToF-SIMS. ToF-SIMS sets certain requirements for the samples to be analyzed; for example, the samples have to be vacuum compatible. Accordingly, sample processing steps for different biological samples, i.e., proteins, cells, frozen and paraffin-embedded tissues and extracellular matrix for the ToF-SIMS are presented. Multivariate analysis of the ToF-SIMS data and the necessary data preprocessing steps (peak selection, data normalization, mean-centering, and scaling and transformation) are discussed in this chapter.
Teilum, Kaare; Thormann, Thorsten; Caterer, Nigel R; Poulsen, Heidi I; Jensen, Peter H; Knudsen, Jens; Kragelund, Birthe B; Poulsen, Flemming M
2005-04-01
Comparison of the folding processes for homologue proteins can provide valuable information about details in the interactions leading to the formation of the folding transition state. Here the folding kinetics of 18 variants of yACBP and 3 variants of bACBP have been studied by Phi-value analysis. In combination with Phi-values from previous work, detailed insight into the transition states for folding of both yACBP and bACBP has been obtained. Of the 16 sequence positions that have been studied in both yACBP and bACBP, 5 (V12, I/L27, Y73, V77, and L80) have high Phi-values and appear to be important for the transition state formation in both homologues. Y31, A34, and A69 have high Phi-values only in yACBP, while F5, A9, and I74 have high Phi-values only in bACBP. Thus, additional interactions between helices A2 and A4 appear to be important for the transition state of yACBP, whereas additional interactions between helices A1 and A4 appear to be important for the transition state of bACBP. To examine whether these differences could be assigned to different packing of the residues in the native state, a solution structure of yACBP was determined by NMR. Small changes in the packing of the hydrophobic side-chains, which strengthen the interactions between helices A2 and A4, are observed in yACBP relative to bACBP. It is suggested that different structure elements serve as scaffolds for the folding of the 2 ACBP homologues. (c) 2005 Wiley-Liss, Inc.
Nonlinear Elliptic Differential Equations with Multivalued Nonlinearities
Indian Academy of Sciences (India)
In this paper we study nonlinear elliptic boundary value problems with monotone and nonmonotone multivalued nonlinearities. First we consider the case of monotone nonlinearities. In the first result we assume that the multivalued nonlinearity is defined on all R R . Assuming the existence of an upper and of a lower ...
Zeeshan, Farrukh; Tabbassum, Misbah; Jorgensen, Lene; Medlicott, Natalie J
2018-02-01
Protein drugs may encounter conformational perturbations during the formulation processing of lipid-based solid dosage forms. In aqueous protein solutions, attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopy can investigate these conformational changes following the subtraction of spectral interference of solvent with protein amide I bands. However, in solid dosage forms, the possible spectral contribution of lipid carriers to protein amide I band may be an obstacle to determine conformational alterations. The objective of this study was to develop an ATR FT-IR spectroscopic method for the analysis of protein secondary structure embedded in solid lipid matrices. Bovine serum albumin (BSA) was chosen as a model protein, while Precirol AT05 (glycerol palmitostearate, melting point 58 ℃) was employed as the model lipid matrix. Bovine serum albumin was incorporated into lipid using physical mixing, melting and mixing, or wet granulation mixing methods. Attenuated total reflection FT-IR spectroscopy and size exclusion chromatography (SEC) were performed for the analysis of BSA secondary structure and its dissolution in aqueous media, respectively. The results showed significant interference of Precirol ATO5 with BSA amide I band which was subtracted up to 90% w/w lipid content to analyze BSA secondary structure. In addition, ATR FT-IR spectroscopy also detected thermally denatured BSA solid alone and in the presence of lipid matrix indicating its suitability for the detection of denatured protein solids in lipid matrices. Despite being in the solid state, conformational changes occurred to BSA upon incorporation into solid lipid matrices. However, the extent of these conformational alterations was found to be dependent on the mixing method employed as indicated by area overlap calculations. For instance, the melting and mixing method imparted negligible effect on BSA secondary structure, whereas the wet granulation mixing method promoted
Fu, Y. B.; Ogden, R. W.
2001-05-01
This collection of papers by leading researchers in the field of finite, nonlinear elasticity concerns itself with the behavior of objects that deform when external forces or temperature gradients are applied. This process is extremely important in many industrial settings, such as aerospace and rubber industries. This book covers the various aspects of the subject comprehensively with careful explanations of the basic theories and individual chapters each covering a different research direction. The authors discuss the use of symbolic manipulation software as well as computer algorithm issues. The emphasis is placed firmly on covering modern, recent developments, rather than the very theoretical approach often found. The book will be an excellent reference for both beginners and specialists in engineering, applied mathematics and physics.
Rajasekar, Shanmuganathan
2016-01-01
This introductory text presents the basic aspects and most important features of various types of resonances and anti-resonances in dynamical systems. In particular, for each resonance, it covers the theoretical concepts, illustrates them with case studies, and reviews the available information on mechanisms, characterization, numerical simulations, experimental realizations, possible quantum analogues, applications and significant advances made over the years. Resonances are one of the most fundamental phenomena exhibited by nonlinear systems and refer to specific realizations of maximum response of a system due to the ability of that system to store and transfer energy received from an external forcing source. Resonances are of particular importance in physical, engineering and biological systems - they can prove to be advantageous in many applications, while leading to instability and even disasters in others. The book is self-contained, providing the details of mathematical derivations and techniques invo...
Fluctuations in Nonlinear Systems: A Short Review
International Nuclear Information System (INIS)
Rubia, F.J. de la; Buceta, J.; Cabrera, J.L.; Olarrea, J.; Parrondo, J.M.R.
2003-01-01
We review some results that illustrate the constructive role of noise in nonlinear systems. Several phenomena are briefly discussed: optimal localization of orbits in a system with limit cycle behavior and perturbed by colored noise; stochastic branch selection at secondary bifurcations; noise- induced order/disorder transitions and pattern formation in spatially extended systems. In all cases the presence of noise is crucial, and the results reinforce the modern view of the importance of noise in the evolution of nonlinear systems. (author)
International Nuclear Information System (INIS)
Dousseau, F.; Pezolet, M.
1990-01-01
A method for estimating protein secondary structure from infrared spectra has been developed. The infrared spectra of H 2 O solutions of 13 proteins of known crystal structure have been recorded and corrected for the spectral contribution of water in the amide I and II region by using the algorithm of Dousseau et al. This calibration set of proteins has been analyzed by using either a classical least-squares (CLS) method or the partial least-squares (PLS) method. The pure-structure spectra calculated by the classical least-squares method are in good agreement with spectra of poly(L-lysine) in the α-helix, β-sheet, and undefined conformations. The results show that the best agreement between the secondary structure determined by X-ray crystal-lography and that predicted by infrared spectroscopy is obtained when both the amide I and II bands are used to generate the calibration set, when the PLS method is used, and when it is assumed that the secondary structure of proteins is composed of only four types of structure: ordered and disordered α-helices, β-sheet, and undefined conformation. Attempts to include turns in the secondary structure estimation have led to a loss of accuracy. The spectra of the calibration proteins were also recorded in 2 H 2 O solution. After correction for the contribution of the combination band of 2 H 2 O in the amide I' band region, the spectra were analyzed with PLS, but the results were not as good as for the spectra obtained in H 2 O, especially for the α-helical conformation
[Nonlinear magnetohydrodynamics
International Nuclear Information System (INIS)
1994-01-01
Resistive MHD equilibrium, even for small resistivity, differs greatly from ideal equilibrium, as do the dynamical consequences of its instabilities. The requirement, imposed by Faraday's law, that time independent magnetic fields imply curl-free electric fields, greatly restricts the electric fields allowed inside a finite-resistivity plasma. If there is no flow and the implications of the Ohm's law are taken into account (and they need not be, for ideal equilibria), the electric field must equal the resistivity times the current density. The vanishing of the divergence of the current density then provides a partial differential equation which, together with boundary conditions, uniquely determines the scalar potential, the electric field, and the current density, for any given resistivity profile. The situation parallels closely that of driven shear flows in hydrodynamics, in that while dissipative steady states are somewhat more complex than ideal ones, there are vastly fewer of them to consider. Seen in this light, the vast majority of ideal MHD equilibria are just irrelevant, incapable of being set up in the first place. The steady state whose stability thresholds and nonlinear behavior needs to be investigated ceases to be an arbitrary ad hoc exercise dependent upon the whim of the investigator, but is determined by boundary conditions and choice of resistivity profile
Yoshida, Yuichi; Shibata, Hirotaka
2015-11-01
Hypertension is a common disease and a crucial predisposing factor of cardiovascular diseases. Approximately 10% of hypertensive patients are secondary hypertension, a pathogenetic factor of which can be identified. Secondary hypertension consists of endocrine, renal, and other diseases. Primary aldosteronism, Cushing's syndrome, pheochromocytoma, hyperthyroidism, and hypothyroidism result in endocrine hypertension. Renal parenchymal hypertension and renovascular hypertension result in renal hypertension. Other diseases such as obstructive sleep apnea syndrome are also very prevalent in secondary hypertension. It is very crucial to find and treat secondary hypertension at earlier stages since most secondary hypertension is curable or can be dramatically improved by specific treatment. One should keep in mind that screening of secondary hypertension should be done at least once in a daily clinical practice.
Nonlinear dynamics in biological systems
Carballido-Landeira, Jorge
2016-01-01
This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied math...
Ikeda, Shun; Abe, Takashi; Nakamura, Yukiko; Kibinge, Nelson; Hirai Morita, Aki; Nakatani, Atsushi; Ono, Naoaki; Ikemura, Toshimichi; Nakamura, Kensuke; Altaf-Ul-Amin, Md; Kanaya, Shigehiko
2013-05-01
Biology is increasingly becoming a data-intensive science with the recent progress of the omics fields, e.g. genomics, transcriptomics, proteomics and metabolomics. The species-metabolite relationship database, KNApSAcK Core, has been widely utilized and cited in metabolomics research, and chronological analysis of that research work has helped to reveal recent trends in metabolomics research. To meet the needs of these trends, the KNApSAcK database has been extended by incorporating a secondary metabolic pathway database called Motorcycle DB. We examined the enzyme sequence diversity related to secondary metabolism by means of batch-learning self-organizing maps (BL-SOMs). Initially, we constructed a map by using a big data matrix consisting of the frequencies of all possible dipeptides in the protein sequence segments of plants and bacteria. The enzyme sequence diversity of the secondary metabolic pathways was examined by identifying clusters of segments associated with certain enzyme groups in the resulting map. The extent of diversity of 15 secondary metabolic enzyme groups is discussed. Data-intensive approaches such as BL-SOM applied to big data matrices are needed for systematizing protein sequences. Handling big data has become an inevitable part of biology.
Westra, H.J.R.
2012-01-01
In this Thesis, nonlinear dynamics and nonlinear interactions are studied from a micromechanical point of view. Single and doubly clamped beams are used as model systems where nonlinearity plays an important role. The nonlinearity also gives rise to rich dynamic behavior with phenomena like
Cook, Thomas D.
Secondary evaluations, in which an investigator takes a body of evaluation data collected by a primary evaluation researcher and examines the data to see if the original conclusions about the program correspond with his own, are discussed. The different kinds of secondary evaluations and the advantages and disadvantages of each are pointed out,…
Directory of Open Access Journals (Sweden)
Jun-jie JING
2012-09-01
Full Text Available Objective To observe the changes of c-fos protein expression in brain and beta-endorphin (β-EP level in blood plasma in rats with diffuse brain injury (DBI and secondary brain insult (SBI after intraperitoneal injection of naloxone hydrochloride, and explore the role of c-fos andβ-EP in development of SBI in rats. Methods Seventy health male SD rats were enrolled in the present study and randomly divided into group A (intraperitoneally injected with 0.9% saline after DBI and SBI model was reproduced, group B (injected intraperitoneally with 1.0mg/kg naloxone hydrochloride after DBI and SBI model was reproduced, and group C (intraperitoneally injected with 1.0mg/kg naloxone hydrochloride after DBI and before SBI model was reproduced. The animals were sacrificed 3, 24 and 48 hours after injury, and the number of c-fos positive cells in brain and content of β-EP in blood plasma were determined by immunohistochemistry and radioimmunoassay respectively, the water content and number of injured neurons in brain tissue were measured by pathomorphological observation of the brain tissue. Results No significant difference was observed between group B and C for all the detection parameters. In group B and C, the water content in brain tissue at 3h and 24h was found to be decreased, while the number of injured neurons at 24h and 48h increased, number of c-fos positive cells in brain at 3h, 24h and 48h decreased, and content of β-EP in blood plasma at 3h and 24h decreased when compared with group A(P < 0.05. Conclusion Naloxone hydrochloride could decrease the c-fos expression in brain and β-EP level in blood plasma, alleviate the nerve injury, and protect neural function. The therapeutic effect of naloxone administered either after DBI and SBI or after DBI and before SBI was similar.
Nonlinear rheology of complex fluid-fluid interfaces
Sagis, L.M.C.; Fischer, P.
2014-01-01
Fluid–fluid interfaces stabilized by proteins, protein aggregates, polymers, or colloidal particles, tend to have a complex microstructure. Their response to an applied deformation is often highly nonlinear, even at small deformation (rates). The nonlinearity of the response is a result of changes
... in the medical history or examination to suggest secondary headache. Headache can be caused by general medical conditions such as severe hypertension, or by conditions that affect the brain and ...
Damianidi, L; Gruszfeld, D; Verduci, E; Vecchi, F; Xhonneux, A; Langhendries, J-P; Luque, V; Theurich, M A; Zaragoza-Jordana, M; Koletzko, B; Grote, V
2016-11-01
High protein intake in infancy affects future obesity risk and other health outcomes. We aim to describe total protein intake and its sources in a birth cohort in five European countries over the first 2 years of life. A total of 746 formula-fed infants were included. Three-day weighed dietary records at 6, 7, 8, 9, 12, 18 and 24 months of age were used. Kruskal-Wallis, ANOVA and Friedman's tests were used to assess possible differences in nutritional intake among countries and over time. Dairy products were the main components of the infants' diets. Cow's milk was rarely introduced before 12 months of age, whereas infants' formula was the main contributor of protein intake. Food choices and protein intake differed among countries (Pnutritional patterns were identified that were characterised by differences in energy, fat, protein and animal protein intake. Finally, food consumption was not always in line with protein intakes, and thus infants from some countries showed high consumption of specific food groups but relatively low protein intakes. During weaning, over-limited substitution of dairy products with other sources (especially meat) resulted in relatively high protein intakes in formula-fed infants. Differences in preferences of specific protein sources from complementary foods existed among European countries. Great opportunities in improving early nutrition were revealed, although cultural and geographical differences should always be considered.
On Poisson Nonlinear Transformations
Directory of Open Access Journals (Sweden)
Nasir Ganikhodjaev
2014-01-01
Full Text Available We construct the family of Poisson nonlinear transformations defined on the countable sample space of nonnegative integers and investigate their trajectory behavior. We have proved that these nonlinear transformations are regular.
Nonlinear Poisson equation for heterogeneous media.
Hu, Langhua; Wei, Guo-Wei
2012-08-22
The Poisson equation is a widely accepted model for electrostatic analysis. However, the Poisson equation is derived based on electric polarizations in a linear, isotropic, and homogeneous dielectric medium. This article introduces a nonlinear Poisson equation to take into consideration of hyperpolarization effects due to intensive charges and possible nonlinear, anisotropic, and heterogeneous media. Variational principle is utilized to derive the nonlinear Poisson model from an electrostatic energy functional. To apply the proposed nonlinear Poisson equation for the solvation analysis, we also construct a nonpolar solvation energy functional based on the nonlinear Poisson equation by using the geometric measure theory. At a fixed temperature, the proposed nonlinear Poisson theory is extensively validated by the electrostatic analysis of the Kirkwood model and a set of 20 proteins, and the solvation analysis of a set of 17 small molecules whose experimental measurements are also available for a comparison. Moreover, the nonlinear Poisson equation is further applied to the solvation analysis of 21 compounds at different temperatures. Numerical results are compared to theoretical prediction, experimental measurements, and those obtained from other theoretical methods in the literature. A good agreement between our results and experimental data as well as theoretical results suggests that the proposed nonlinear Poisson model is a potentially useful model for electrostatic analysis involving hyperpolarization effects. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Chen, Xianfeng; Zeng, Heping; Guo, Qi; She, Weilong
2015-01-01
This book presents an overview of the state of the art of nonlinear optics from weak light nonlinear optics, ultrafast nonlinear optics to electro-optical theory and applications. Topics range from the fundamental studies of the interaction between matter and radiation to the development of devices, components, and systems of tremendous commercial interest for widespread applications in optical telecommunications, medicine, and biotechnology.
A Model Predictive Algorithm for Active Control of Nonlinear Noise Processes
Directory of Open Access Journals (Sweden)
Qi-Zhi Zhang
2005-01-01
Full Text Available In this paper, an improved nonlinear Active Noise Control (ANC system is achieved by introducing an appropriate secondary source. For ANC system to be successfully implemented, the nonlinearity of the primary path and time delay of the secondary path must be overcome. A nonlinear Model Predictive Control (MPC strategy is introduced to deal with the time delay in the secondary path and the nonlinearity in the primary path of the ANC system. An overall online modeling technique is utilized for online secondary path and primary path estimation. The secondary path is estimated using an adaptive FIR filter, and the primary path is estimated using a Neural Network (NN. The two models are connected in parallel with the two paths. In this system, the mutual disturbances between the operation of the nonlinear ANC controller and modeling of the secondary can be greatly reduced. The coefficients of the adaptive FIR filter and weight vector of NN are adjusted online. Computer simulations are carried out to compare the proposed nonlinear MPC method with the nonlinear Filter-x Least Mean Square (FXLMS algorithm. The results showed that the convergence speed of the proposed nonlinear MPC algorithm is faster than that of nonlinear FXLMS algorithm. For testing the robust performance of the proposed nonlinear ANC system, the sudden changes in the secondary path and primary path of the ANC system are considered. Results indicated that the proposed nonlinear ANC system can rapidly track the sudden changes in the acoustic paths of the nonlinear ANC system, and ensure the adaptive algorithm stable when the nonlinear ANC system is time variable.
Hanamura, Eiichi; Yamanaka, Akio
2007-01-01
This graduate-level textbook gives an introductory overview of the fundamentals of quantum nonlinear optics. Based on the quantum theory of radiation, Quantum Nonlinear Optics incorporates the exciting developments in novel nonlinear responses of materials (plus laser oscillation and superradiance) developed over the past decade. It deals with the organization of radiation field, interaction between electronic system and radiation field, statistics of light, mutual manipulation of light and matter, laser oscillation, dynamics of light, nonlinear optical response, and nonlinear spectroscopy, as well as ultrashort and ultrastrong laser pulse. Also considered are Q-switching, mode locking and pulse compression. Experimental and theoretical aspects are intertwined throughout.
Nonlinear dynamics and complexity
Luo, Albert; Fu, Xilin
2014-01-01
This important collection presents recent advances in nonlinear dynamics including analytical solutions, chaos in Hamiltonian systems, time-delay, uncertainty, and bio-network dynamics. Nonlinear Dynamics and Complexity equips readers to appreciate this increasingly main-stream approach to understanding complex phenomena in nonlinear systems as they are examined in a broad array of disciplines. The book facilitates a better understanding of the mechanisms and phenomena in nonlinear dynamics and develops the corresponding mathematical theory to apply nonlinear design to practical engineering.
Distributed nonlinear optical response
DEFF Research Database (Denmark)
Nikolov, Nikola Ivanov
2005-01-01
of bound states of out of phase bright solitons and dark solitons. Also, the newly introduced analogy between the nonlocal cubic nonlinear and the quadratic nonlinear media, presented in paper B and Chapter 3 is discussed. In particular it supplies intuitive physical meaning of the formation of solitons...... in quadratic nonlinear media. In the second part of the report (Chapter 4), the possibility to obtain light with ultrabroad spectrum due to the interplay of many nonlinear effects based on cubic nonlinearity is investigated thoroughly. The contribution of stimulated Raman scattering, a delayed nonlinear...... a modified nonlinear Schroedinger model equation. Chapter 4 and papers D and E are dedicated to this part of the research....
Woerlen, Natalie; Allam, Gamalat; Popescu, Adina; Corrigan, Laura; Pautot, Véronique; Hepworth, Shelley R
2017-06-01
Repression of boundary genes by KNOTTED1-like homeodomain transcription factor BREVIPEDICELLUS promotes the differentiation of phase II secondary xylem in Arabidopsis roots. Plant growth and development relies on the activity of meristems. Boundaries are domains of restricted growth that separate forming organs and the meristem. Class I KNOX homeodomain transcription factors are important regulators of meristem maintenance. Members of this class including BREVIDICELLUS also called KNOTTED-LIKE FROM ARABIDOPSIS THALIANA1 (BP/KNAT1) fulfill this function in part by spatially regulating boundary genes. The vascular cambium is a lateral meristem that allows for radial expansion of organs during secondary growth. We show here that BP/KNAT1 repression of boundary genes plays a crucial role in root secondary growth. In particular, exclusion of BLADE-ON-PETIOLE1/2 (BOP1/2) and other members of this module from xylem is required for the differentiation of lignified fibers and vessels during the xylem expansion phase of root thickening. These data reveal a previously undiscovered role for boundary genes in the root and shed light on mechanisms controlling wood development in trees.
Energy Technology Data Exchange (ETDEWEB)
Yang, Jin-Wei; Gao, Yi-Tian, E-mail: gaoyt163@163.com; Wang, Qi-Min; Su, Chuan-Qi; Feng, Yu-Jie; Yu, Xin
2016-01-15
In this paper, a fourth-order variable-coefficient nonlinear Schrödinger equation is studied, which might describe a one-dimensional continuum anisotropic Heisenberg ferromagnetic spin chain with the octuple–dipole interaction or an alpha helical protein with higher-order excitations and interactions under continuum approximation. With the aid of auxiliary function, we derive the bilinear forms and corresponding constraints on the variable coefficients. Via the symbolic computation, we obtain the Lax pair, infinitely many conservation laws, one-, two- and three-soliton solutions. We discuss the influence of the variable coefficients on the solitons. With different choices of the variable coefficients, we obtain the parabolic, cubic, and periodic solitons, respectively. We analyse the head-on and overtaking interactions between/among the two and three solitons. Interactions between a bound state and a single soliton are displayed with different choices of variable coefficients. We also derive the quasi-periodic formulae for the three cases of the bound states.
Larocque, Sarah C; Kerstetter, Jane E; Cauley, Jane A; Insogna, Karl L; Ensrud, Kristine; Lui, Li-Yung; Allore, Heather G
2015-01-01
More than 90% of hip fractures in older Americans result from a fall. Inadequate intake of dietary protein and vitamin D are common in older adults, and diets in low these could contribute to loss of muscle mass and strength or coordination, in turn increasing the risk of falling. The objective of the study was to evaluate the relationship between protein and vitamin D intake with the occurrence of falls in older women in the Study of Osteoporotic Fracture, a prospective cohort of more than 4000 postmenopausal women participating from January 1997 to September 1998. Incident falls were ascertained for one year. Protein and vitamin D intake was assessed by a food frequency questionnaire; associations with a reported fall were estimated with logistic regression, adjusted for fall-related covariates and energy. Protein and vitamin D were modeled separately because of high correlation (rho = 0.55, P women reported a fall within one year. In separate, unadjusted models dietary protein (per 1 g/kg increase) and vitamin D (per 100 International Unit (IU) increase) significantly increased the odds ratio (OR) of falling (OR 1.35 95% CI 1.15-1.59, OR 1.11 95% CI 1.03-1.19, respectively). Once fall-related covariates were added to each model, dietary protein and vitamin D were noncontributory to falls. While we could find no direct association between vitamin D and protein intake and fall prevention, adequate intake of these two nutrients are critical for musculoskeletal health in older adults.
Energy Technology Data Exchange (ETDEWEB)
Bjeldanes, L F [Univ. of California, Berkeley; Morris, M M; Felton, J S; Healy, S; Stuermer, D; Berry, P; Timourian, H; Hatch, F T
1982-01-01
A survey of mutagen formation during the cooking of a variety of protein-rich foods that are minor sources of protein intake in the American diet is reported (see Bjeldanes, Morris, Felton et al. (1982) for survey of major protein foods). Milk, cheese, tofu and organ meats showed negligible mutagen formation except following high-temperature cooking for long periods of time. Even under the most extreme conditions, tofu, cheese and milk exhibited fewer than 500 Ames/Salmonella typhimurium revertants/100 g equivalents (wet weight of uncooked food), and organ meats only double that amount. Beans showed low mutagen formation after boiling followed by frying (with and without oil). Only boiling of beans followed by baking for 1 hr gave appreciable mutagenicity (3650 revertants/100 g equivalents). Seafood samples gave a variety of results: red snapper, salmon, trout, halibut and rock cod all gave more than 1000 revertants/100 g wet weight equivalents when pan-fried or griddle-fried for about 6 min/side. Baked or poached rock cod and deep-fried shrimp showed no significant mutagen formation. Broiled lamb chops showed mutagen formation similar to that in red meats tested in the preceding paper: 16,000 revertants/100 g equivalents. These findings show that as measured by bioassay in S. typhimurium, most of the food that are minor sources of protein in the American diet are also minor sources of cooking-induced mutagens.
Bjeldanes, L F; Morris, M M; Felton, J S; Healy, S; Stuermer, D; Berry, P; Timourian, H; Hatch, F T
1982-08-01
A survey of mutagen formation during the cooking of a variety of protein-rich foods that are minor sources of protein intake in the American diet is reported (see Bjeldanes, Morris, Felton et al. (1982) for survey of major protein foods). Milk, cheese, tofu and organ meats showed negligible mutagen formation except following high-temperature cooking for long periods of time. Even under the most extreme conditions, tofu, cheese and milk exhibited fewer than 500 Ames/Salmonella typhimurium revertants/100 g equivalents (wet weight of uncooked food), and organ meats only double that amount. Beans showed low mutagen formation after boiling and boiling followed by frying (with and without oil). Only boiling of beans followed by baking for 1 hr gave appreciable mutagenicity (3650 revertants/100g equivalents). Seafood samples gave a variety of results: red snapper, salmon, trout, halibut and rock cod all gave more than 1000 revertants/100 g wet weight equivalents when pan-fried or griddle-fried for about 6 min/side. Baked or poached rock and deep-fried shrimp showed no significant mutagen formation. Broiled lamb chops showed mutagen formation similar to that in red meats tested in the preceding paper: 16,000 revertants/100 g equivalents. These findings show that as measured by bioassay in S. typhimurium, most of the foods that are minor sources of protein in the American diet are also minor sources of cooking-induced mutagens.
Directory of Open Access Journals (Sweden)
Wei Khim Ng
2009-02-01
Full Text Available We construct nonlinear extensions of Dirac's relativistic electron equation that preserve its other desirable properties such as locality, separability, conservation of probability and Poincaré invariance. We determine the constraints that the nonlinear term must obey and classify the resultant non-polynomial nonlinearities in a double expansion in the degree of nonlinearity and number of derivatives. We give explicit examples of such nonlinear equations, studying their discrete symmetries and other properties. Motivated by some previously suggested applications we then consider nonlinear terms that simultaneously violate Lorentz covariance and again study various explicit examples. We contrast our equations and construction procedure with others in the literature and also show that our equations are not gauge equivalent to the linear Dirac equation. Finally we outline various physical applications for these equations.
Ooi, Kelvin J. A.; Tan, Dawn T. H.
2017-10-01
The rapid development of graphene has opened up exciting new fields in graphene plasmonics and nonlinear optics. Graphene's unique two-dimensional band structure provides extraordinary linear and nonlinear optical properties, which have led to extreme optical confinement in graphene plasmonics and ultrahigh nonlinear optical coefficients, respectively. The synergy between graphene's linear and nonlinear optical properties gave rise to nonlinear graphene plasmonics, which greatly augments graphene-based nonlinear device performance beyond a billion-fold. This nascent field of research will eventually find far-reaching revolutionary technological applications that require device miniaturization, low power consumption and a broad range of operating wavelengths approaching the far-infrared, such as optical computing, medical instrumentation and security applications.
Saenz, D T; Fiskus, W; Qian, Y; Manshouri, T; Rajapakshe, K; Raina, K; Coleman, K G; Crew, A P; Shen, A; Mill, C P; Sun, B; Qiu, P; Kadia, T M; Pemmaraju, N; DiNardo, C; Kim, M-S; Nowak, A J; Coarfa, C; Crews, C M; Verstovsek, S; Bhalla, K N
2017-09-01
The PROTAC (proteolysis-targeting chimera) ARV-825 recruits bromodomain and extraterminal (BET) proteins to the E3 ubiquitin ligase cereblon, leading to degradation of BET proteins, including BRD4. Although the BET-protein inhibitor (BETi) OTX015 caused accumulation of BRD4, treatment with equimolar concentrations of ARV-825 caused sustained and profound depletion (>90%) of BRD4 and induced significantly more apoptosis in cultured and patient-derived (PD) CD34+ post-MPN sAML cells, while relatively sparing the CD34+ normal hematopoietic progenitor cells. RNA-Seq, Reverse Phase Protein Array and mass cytometry 'CyTOF' analyses demonstrated that ARV-825 caused greater perturbations in messenger RNA (mRNA) and protein expressions than OTX015 in sAML cells. Specifically, compared with OTX015, ARV-825 treatment caused more robust and sustained depletion of c-Myc, CDK4/6, JAK2, p-STAT3/5, PIM1 and Bcl-xL, while increasing the levels of p21 and p27. Compared with OTX015, PROTAC ARV-771 treatment caused greater reduction in leukemia burden and further improved survival of NSG mice engrafted with luciferase-expressing HEL92.1.7 cells. Co-treatment with ARV-825 and JAK inhibitor ruxolitinib was synergistically lethal against established and PD CD34+ sAML cells. Notably, ARV-825 induced high levels of apoptosis in the in vitro generated ruxolitinib-persister or ruxolitinib-resistant sAML cells. These findings strongly support the in vivo testing of the BRD4-PROTAC based combinations against post-MPN sAML.
Stationary nonlinear Airy beams
International Nuclear Information System (INIS)
Lotti, A.; Faccio, D.; Couairon, A.; Papazoglou, D. G.; Panagiotopoulos, P.; Tzortzakis, S.; Abdollahpour, D.
2011-01-01
We demonstrate the existence of an additional class of stationary accelerating Airy wave forms that exist in the presence of third-order (Kerr) nonlinearity and nonlinear losses. Numerical simulations and experiments, in agreement with the analytical model, highlight how these stationary solutions sustain the nonlinear evolution of Airy beams. The generic nature of the Airy solution allows extension of these results to other settings, and a variety of applications are suggested.
Generalized Nonlinear Yule Models
Lansky, Petr; Polito, Federico; Sacerdote, Laura
2016-01-01
With the aim of considering models with persistent memory we propose a fractional nonlinear modification of the classical Yule model often studied in the context of macrovolution. Here the model is analyzed and interpreted in the framework of the development of networks such as the World Wide Web. Nonlinearity is introduced by replacing the linear birth process governing the growth of the in-links of each specific webpage with a fractional nonlinear birth process with completely general birth...
Gennari, C; Martini, G; Nuti, R
1998-06-01
Generalized osteoporosis currently represents a heterogeneous group of conditions with many different causes and pathogenetic mechanisms, that often are variably associated. The term "secondary" is applied to all patients with osteoporosis in whom the identifiable causal factors are other than menopause and aging. In this heterogeneous group of conditions, produced by many different pathogenetic mechanisms, a negative bone balance may be variably associated with low, normal or increased bone remodeling states. A consistent group of secondary osteoporosis is related to endocrinological or iatrogenic causes. Exogenous hypercortisolism may be considered an important risk factor for secondary osteoporosis in the community, and probably glucocorticoid-induced osteoporosis is the most common type of secondary osteoporosis. Supraphysiological doses of corticosteroids cause two abnormalities in bone metabolism: a relative increase in bone resorption, and a relative reduction in bone formation. Bone loss, mostly of trabecular bone, with its resultant fractures is the most incapacitating consequence of osteoporosis. The estimated incidence of fractures in patients prescribed corticosteroid is 30% to 50%. Osteoporosis is considered one of the potentially serious side effects of heparin therapy. The occurrence of heparin-induced osteoporosis appeared to be strictly related to the length of treatment (over 4-5 months), and the dosage (15,000 U or more daily), but the pathogenesis is poorly understood. It has been suggested that heparin could cause an increase in bone resorption by increasing the number of differentiated osteoclasts, and by enhancing the activity of individual osteoclasts. Hyperthyroidism is frequently associated with loss of trabecular and cortical bone; the enhanced bone turnover that develops in thyrotoxicosis is characterized by an increase in the number of osteoclasts and resorption sites, and an increase in the ratio of resorptive to formative bone
Uraltseva, N N
1995-01-01
This collection focuses on nonlinear problems in partial differential equations. Most of the papers are based on lectures presented at the seminar on partial differential equations and mathematical physics at St. Petersburg University. Among the topics explored are the existence and properties of solutions of various classes of nonlinear evolution equations, nonlinear imbedding theorems, bifurcations of solutions, and equations of mathematical physics (Navier-Stokes type equations and the nonlinear Schrödinger equation). The book will be useful to researchers and graduate students working in p
Kono, Mitsuo
2010-01-01
A nonlinearity is one of the most important notions in modern physics. A plasma is rich in nonlinearities and provides a variety of behaviors inherent to instabilities, coherent wave structures and turbulence. The book covers the basic concepts and mathematical methods, necessary to comprehend nonlinear problems widely encountered in contemporary plasmas, but also in other fields of physics and current research on self-organized structures and magnetized plasma turbulence. The analyses make use of strongly nonlinear models solved by analytical techniques backed by extensive simulations and available experiments. The text is written for senior undergraduates, graduate students, lecturers and researchers in laboratory, space and fusion plasmas.
Nonlinear optics at interfaces
International Nuclear Information System (INIS)
Chen, C.K.
1980-12-01
Two aspects of surface nonlinear optics are explored in this thesis. The first part is a theoretical and experimental study of nonlinear intraction of surface plasmons and bulk photons at metal-dielectric interfaces. The second part is a demonstration and study of surface enhanced second harmonic generation at rough metal surfaces. A general formulation for nonlinear interaction of surface plasmons at metal-dielectric interfaces is presented and applied to both second and third order nonlinear processes. Experimental results for coherent second and third harmonic generation by surface plasmons and surface coherent antiStokes Raman spectroscopy (CARS) are shown to be in good agreement with the theory
International Nuclear Information System (INIS)
Zelenyj, L.M.; Kuznetsova, M.M.
1989-01-01
Nonlinear study of magnetic perturbation development under single-mode conditions in collision-free plasma in configurations with the magnetic field shear is investigated. Results are obtained with regard of transverse component of electrical field and its effect on ion dynamics within wide range of ion Larmor radius value and values of magnetic field shear. Increments of nonlinear drift tearing mode are obtained and it is shown that excitation drastic conditions of even linearly stable modes are possible. Mechanism of instability nonlinear stabilization is considered and the value of magnetic island at the saturation threshold is estimeted. Energy of nonlinear drift tearing mode is discussed
Boyle, I T
1993-10-01
Osteoporosis with attendant increased fracture risk is a common complication of many other diseases. Indeed, almost all chronic diseases make some impact on life-style, usually by restricting physical activity and hence reducing the anabolic effect of exercise and gravitational strains on the skeleton. Restricted appetite and modified gastrointestinal tract function is another commonplace finding that has an impact on bone nutrition and synthesis, as on other systems. Sex hormone status is of particular importance for the maintenance of the normal skeleton, and the postmenopausal woman is at particular risk for most causes of secondary osteoporosis. In dealing with secondary osteoporosis in the hypo-oestrogenic woman, the question of giving hormone replacement therapy in addition to other disease-specific therapy should always be considered, as, for example, in a young amenorrhoeic woman with Crohn's disease. Similarly, in hypogonadal men the administration of testosterone is useful for bone conservation. The wider availability of bone densitometry ought to make us more aware of the presence of osteoporosis in the many disease states discussed above. This is particularly important as the life span of such patients is now increased by improved management of the underlying disease process in many instances. Even in steroid-induced osteoporosis--one of the commonest and most severe forms of osteoporosis--we now have some effective therapy in the form of the bisphosphonates and other anti-bone-resorbing drug classes. The possibility of prophylaxis against secondary osteoporosis has therefore become a possibility, although the very long-term effects of such drug regimens are still unknown. In some situations, such as thyrotoxicosis, Cushing's syndrome and immobilization, spontaneous resolution of at least part of the osteoporosis is possible after cure of the underlying problem. The shorter the existence of the basic problem, the more successful the restoration of the
Polarization Nonlinear Optics of Quadratically Nonlinear Azopolymers
International Nuclear Information System (INIS)
Konorov, S.O.; Akimov, D.A.; Ivanov, A.A.; Petrov, A.N.; Alfimov, M.V.; Yakimanskii, A.V.; Smirnov, N.N.; Ivanova, V.N.; Kudryavtsev, V.V.; Podshivalov, A.A.; Sokolova, I.M.; Zheltikov, A.M.
2005-01-01
The polarization properties of second harmonic and sum-frequency signals generated by femtosecond laser pulses in films of polymers containing covalent groups of an azobenzothiazole chromophore polarized by an external electric field are investigated. It is shown that the methods of polarization nonlinear optics make it possible to determine the structure of oriented molecular dipoles and reveal important properties of the motion of collectivized πelectrons in organic molecules with strong optical nonlinearities. The polarization measurements show that the tensor of quadratic nonlinear optical susceptibility of chromophore fragments oriented by an external field in macromolecules of the noted azopolymers has a degenerate form. This is indicative of a predominantly one-dimensional character of motion of collectivized π electrons along an extended group of atoms in such molecules
Nonlinear growth of strongly unstable tearing modes
International Nuclear Information System (INIS)
Waelbroeck, F.L.
1993-11-01
Rutherford's theory of the tearing instability is extended to cases where current nonlinearities are important, such as long wavelength modes in current slabs and the m = 1 instability in tokamaks with moderately large aspect-ratios. Of particular interest is the possibility that the associated magnetic islands, as a result of secondary instabilities, have a singular response to the Ohmic diffusion of the current. A family of islands is used to test this possibility; it is found that the response remains bounded
Nonlinear dynamics in Nuclotron
International Nuclear Information System (INIS)
Dinev, D.
1997-01-01
The paper represents an extensive study of the nonlinear beam dynamics in the Nuclotron. Chromatic effects, including the dependence of the betatron tunes on the amplitude, and chromatic perturbations have been investigated taking into account the measured field imperfections. Beam distortion, smear, dynamic aperture and nonlinear acceptance have been calculated for different particle energies and betatron tunes
Nonlinear Optics and Applications
Abdeldayem, Hossin A. (Editor); Frazier, Donald O. (Editor)
2007-01-01
Nonlinear optics is the result of laser beam interaction with materials and started with the advent of lasers in the early 1960s. The field is growing daily and plays a major role in emerging photonic technology. Nonlinear optics play a major role in many of the optical applications such as optical signal processing, optical computers, ultrafast switches, ultra-short pulsed lasers, sensors, laser amplifiers, and many others. This special review volume on Nonlinear Optics and Applications is intended for those who want to be aware of the most recent technology. This book presents a survey of the recent advances of nonlinear optical applications. Emphasis will be on novel devices and materials, switching technology, optical computing, and important experimental results. Recent developments in topics which are of historical interest to researchers, and in the same time of potential use in the fields of all-optical communication and computing technologies, are also included. Additionally, a few new related topics which might provoke discussion are presented. The book includes chapters on nonlinear optics and applications; the nonlinear Schrodinger and associated equations that model spatio-temporal propagation; the supercontinuum light source; wideband ultrashort pulse fiber laser sources; lattice fabrication as well as their linear and nonlinear light guiding properties; the second-order EO effect (Pockels), the third-order (Kerr) and thermo-optical effects in optical waveguides and their applications in optical communication; and, the effect of magnetic field and its role in nonlinear optics, among other chapters.
Directory of Open Access Journals (Sweden)
N. Anantasook
2013-06-01
Full Text Available The objective of this study was to determine the effect of rain tree pod meal with palm oil supplementation on feed intake, digestibility, microbial protein synthesis and microbial populations in dairy cows. Four, multiparous early-lactation Holstein-Friesian crossbred (75% lactating dairy cows with an initial body weight (BW of 405±40 kg and 36±8 DIM were randomly assigned to receive dietary treatments according to a 4×4 Latin square design. The four dietary treatments were un-supplementation (control, supplementation with rain tree pod meal (RPM at 60 g/kg, supplementation with palm oil (PO at 20 g/kg, and supplementation with RPM at 60 g/kg and PO at 20 g/kg (RPO, of total dry matter intake. The cows were offered concentrates, at a ratio of concentrate to milk production of 1:2, and chopped 30 g/kg of urea treated rice straw was fed ad libitum. The RPM contained condensed tannins and crude saponins at 88 and 141 g/kg of DM, respectively. It was found that supplementation with RPM and/or PO to dairy cows diets did not show negative effects on feed intake and ruminal pH and BUN at any times of sampling (p>0.05. However, RPM supplementation resulted in lower crude protein digestibility, NH3-N concentration and number of proteolytic bacteria. It resulted in greater allantoin absorption and microbial crude protein (p<0.05. In addition, dairy cows showed a higher efficiency of microbial N supply (EMNS in both RPM and RPO treatments. Moreover, NDF digestibility and cellulolytic bacteria numbers were highest in RPO supplementation (p<0.05 while, supplementation with RPM and/or PO decreased the protozoa population in dairy cows. Based on this study, supplementation with RPM and/or PO in diets could improve fiber digestibility, microbial protein synthesis in terms of quantity and efficiency and microbial populations in dairy cows.
DEFF Research Database (Denmark)
Zeeshan, Farrukh; Tabbassum, Misbah; Jorgensen, Lene
2018-01-01
encased in solid lipid matrices as a novel indicator of their stability upon in vitro release. Model proteins namely catalase and lysozyme were incorporated into lipid namely Precirol® AT05 (glycerol palmitostearate, melting point 58°C) at 30% w/w loading using melting and mixing and wet granulation...... aggregation for catalase which was increased using wet granulation. The biological activity of catalase was statistically different from that of control and was affected by the incorporation method and was found to be in alignment with ATR spectral changes and extent of aggregation. In conclusion, ATR...
Lugiato, Luigi; Brambilla, Massimo
2015-01-01
Guiding graduate students and researchers through the complex world of laser physics and nonlinear optics, this book provides an in-depth exploration of the dynamics of lasers and other relevant optical systems, under the umbrella of a unitary spatio-temporal vision. Adopting a balanced approach, the book covers traditional as well as special topics in laser physics, quantum electronics and nonlinear optics, treating them from the viewpoint of nonlinear dynamical systems. These include laser emission, frequency generation, solitons, optically bistable systems, pulsations and chaos and optical pattern formation. It also provides a coherent and up-to-date treatment of the hierarchy of nonlinear optical models and of the rich variety of phenomena they describe, helping readers to understand the limits of validity of each model and the connections among the phenomena. It is ideal for graduate students and researchers in nonlinear optics, quantum electronics, laser physics and photonics.
Directory of Open Access Journals (Sweden)
Jinhua Jiang
Full Text Available The velvet protein, VeA, is involved in the regulation of diverse cellular processes. In this study, we explored functions of FgVeA in the wheat head blight pathogen, Fusarium graminearum,using a gene replacement strategy. The FgVEA deletion mutant exhibited a reduction in aerial hyphae formation, hydrophobicity, and deoxynivalenol (DON biosynthesis. Deletion of FgVEA gene led to an increase in conidial production, but a delay in conidial germination. Pathogencity assays showed that the mutant was impaired in virulence on flowering wheat head. Sensitivity tests to various stresses exhibited that the FgVEA deletion mutant showed increased resistance to osmotic stress and cell wall-damaging agents, but increased sensitivity to iprodione and fludioxonil fungicides. Ultrastructural and histochemical analyses revealed that conidia of FgVeA deletion mutant contained an unusually high number of large lipid droplets, which is in agreement with the observation that the mutant accumulated a higher basal level of glycerol than the wild-type progenitor. Serial analysis of gene expression (SAGE in the FgVEA mutant confirmed that FgVeA was involved in various cellular processes. Additionally, six proteins interacting with FgVeA were identified by yeast two hybrid assays in current study. These results indicate that FgVeA plays a critical role in a variety of cellular processes in F. graminearum.
Nonlinear vs. linear biasing in Trp-cage folding simulations
Energy Technology Data Exchange (ETDEWEB)
Spiwok, Vojtěch, E-mail: spiwokv@vscht.cz; Oborský, Pavel; Králová, Blanka [Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, Prague 6 166 28 (Czech Republic); Pazúriková, Jana [Institute of Computer Science, Masaryk University, Botanická 554/68a, 602 00 Brno (Czech Republic); Křenek, Aleš [Institute of Computer Science, Masaryk University, Botanická 554/68a, 602 00 Brno (Czech Republic); Center CERIT-SC, Masaryk Univerzity, Šumavská 416/15, 602 00 Brno (Czech Republic)
2015-03-21
Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.
Energy nonlinearity in radiation detection materials: Causes and consequences
International Nuclear Information System (INIS)
Jaffe, J.E.; Jordan, D.V.; Peurrung, A.J.
2007-01-01
The phenomenology and present theoretical understanding of energy nonlinearity (nonproportionality) in radiation detection materials is reviewed, with emphasis on gamma-ray spectroscopy. Scintillators display varying degrees and patterns of nonlinearity, while semiconductor detectors are extremely linear, and gas detectors show a characteristic form of nonproportionality associated with core levels. The relation between nonlinear response (to both primary particles and secondary electrons) and spectrometer resolution is also discussed. We review the qualitative ideas about the origin of nonlinearity in scintillators that have been proposed to date, with emphasis on transport and recombination of electronic excitations. Recent computational and experimental work on the basic physics of scintillators is leading towards a better understanding of energy nonlinearity and should result in new, more linear scintillator materials in the near future
Nonlinear photonic metasurfaces
Li, Guixin; Zhang, Shuang; Zentgraf, Thomas
2017-03-01
Compared with conventional optical elements, 2D photonic metasurfaces, consisting of arrays of antennas with subwavelength thickness (the 'meta-atoms'), enable the manipulation of light-matter interactions on more compact platforms. The use of metasurfaces with spatially varying arrangements of meta-atoms that have subwavelength lateral resolution allows control of the polarization, phase and amplitude of light. Many exotic phenomena have been successfully demonstrated in linear optics; however, to meet the growing demand for the integration of more functionalities into a single optoelectronic circuit, the tailorable nonlinear optical properties of metasurfaces will also need to be exploited. In this Review, we discuss the design of nonlinear photonic metasurfaces — in particular, the criteria for choosing the materials and symmetries of the meta-atoms — for the realization of nonlinear optical chirality, nonlinear geometric Berry phase and nonlinear wavefront engineering. Finally, we survey the application of nonlinear photonic metasurfaces in optical switching and modulation, and we conclude with an outlook on their use for terahertz nonlinear optics and quantum information processing.
International Nuclear Information System (INIS)
Khoroshun, L.P.
1995-01-01
The characteristic features of the deformation and failure of actual materials in the vicinity of a crack tip are due to their physical nonlinearity in the stress-concentration zone, which is a result of plasticity, microfailure, or a nonlinear dependence of the interatomic forces on the distance. Therefore, adequate models of the failure mechanics must be nonlinear, in principle, although linear failure mechanics is applicable if the zone of nonlinear deformation is small in comparison with the crack length. Models of crack mechanics are based on analytical solutions of the problem of the stress-strain state in the vicinity of the crack. On account of the complexity of the problem, nonlinear models are bason on approximate schematic solutions. In the Leonov-Panasyuk-Dugdale nonlinear model, one of the best known, the actual two-dimensional plastic zone (the nonlinearity zone) is replaced by a narrow one-dimensional zone, which is then modeled by extending the crack with a specified normal load equal to the yield point. The condition of finite stress is applied here, and hence the length of the plastic zone is determined. As a result of this approximation, the displacement in the plastic zone at the abscissa is nonzero
Li, Tatsien
2017-01-01
This book focuses on nonlinear wave equations, which are of considerable significance from both physical and theoretical perspectives. It also presents complete results on the lower bound estimates of lifespan (including the global existence), which are established for classical solutions to the Cauchy problem of nonlinear wave equations with small initial data in all possible space dimensions and with all possible integer powers of nonlinear terms. Further, the book proposes the global iteration method, which offers a unified and straightforward approach for treating these kinds of problems. Purely based on the properties of solut ions to the corresponding linear problems, the method simply applies the contraction mapping principle.
The nonlinear dynamics of a spacecraft coupled to the vibration of a contained fluid
Peterson, Lee D.; Crawley, Edward F.; Hansman, R. John
1988-01-01
The dynamics of a linear spacecraft mode coupled to a nonlinear low gravity slosh of a fluid in a cylindrical tank is investigated. Coupled, nonlinear equations of motion for the fluid-spacecraft dynamics are derived through an assumed mode Lagrangian method. Unlike linear fluid slosh models, this nonlinear slosh model retains two fundamental slosh modes and three secondary modes. An approximate perturbation solution of the equations of motion indicates that the nonlinear coupled system response involves fluid-spacecraft modal resonances not predicted by either a linear, or a nonlinear, uncoupled slosh analysis. Experimental results substantiate the analytical predictions.
Energy Technology Data Exchange (ETDEWEB)
Zuo, Peng; Fan, Zheng, E-mail: ZFAN@ntu.edu.sg [School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798 (Singapore); Zhou, Yu [Advanced Remanufacturing and Technology Center (ARTC), 3 Clean Tech Loop, CleanTech Two, Singapore 637143 (Singapore)
2016-07-15
Nonlinear guided waves have been investigated widely in simple geometries, such as plates, pipe and shells, where analytical solutions have been developed. This paper extends the application of nonlinear guided waves to waveguides with arbitrary cross sections. The criteria for the existence of nonlinear guided waves were summarized based on the finite deformation theory and nonlinear material properties. Numerical models were developed for the analysis of nonlinear guided waves in complex geometries, including nonlinear Semi-Analytical Finite Element (SAFE) method to identify internal resonant modes in complex waveguides, and Finite Element (FE) models to simulate the nonlinear wave propagation at resonant frequencies. Two examples, an aluminum plate and a steel rectangular bar, were studied using the proposed numerical model, demonstrating the existence of nonlinear guided waves in such structures and the energy transfer from primary to secondary modes.
Hiragun, Makiko; Ishii, Kaori; Hiragun, Takaaki; Shindo, Hajime; Mihara, Shoji; Matsuo, Hiroaki; Hide, Michihiro
2013-09-01
Recently, an increasing number of patients with wheat-dependent exercise-induced anaphylaxis (WDEIA) have been reported in Japan. Most of them had developed this condition during or after using hydrolyzed wheat protein (HWP)-containing soap (HWP-WDEIA). To clarify the relation between WDEIA and HWP-containing soap and their prognosis, we retrospectively studied the patients who visited Hiroshima University Hospital and were diagnosed as WDEIA from January 2010 to June 2011. We took detailed clinical histories, performed skin prick tests, serum immunoassays for antigen-specific IgE and basophil histamine release test, and followed up their clinical courses after the diagnosis. Among 36 patients with WDEIA, 30 patients had used only one type of HWP-soap. The patients with HWP-WDEIA were mainly women and had developed facial symptoms and angioedema. They suffered from blood pressure reductions less frequently than patients with conventional WDEIA. The levels of gluten-specific IgE were higher than those of omega-5 gliadin in patients with HWP-WDEIA (P soap. The development of HWP-WDEIA is associated with the use of HWP-soap. The sensitivity to HWP that cross reacts with non-processed wheat may be reduced or possibly cured after the discontinuation of HWP-soap.
Heffernan, Rhys; Yang, Yuedong; Paliwal, Kuldip; Zhou, Yaoqi
2017-09-15
The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some 'short to intermediate' non-local interactions. Here, we employed Long Short-Term Memory (LSTM) Bidirectional Recurrent Neural Networks (BRNNs) which are capable of capturing long range interactions without using a window. We showed that the application of LSTM-BRNN to the prediction of protein structural properties makes the most significant improvement for residues with the most long-range contacts (|i-j| >19) over a previous window-based, deep-learning method SPIDER2. Capturing long-range interactions allows the accuracy of three-state secondary structure prediction to reach 84% and the correlation coefficient between predicted and actual solvent accessible surface areas to reach 0.80, plus a reduction of 5%, 10%, 5% and 10% in the mean absolute error for backbone ϕ , ψ , θ and τ angles, respectively, from SPIDER2. More significantly, 27% of 182724 40-residue models directly constructed from predicted C α atom-based θ and τ have similar structures to their corresponding native structures (6Å RMSD or less), which is 3% better than models built by ϕ and ψ angles. We expect the method to be useful for assisting protein structure and function prediction. The method is available as a SPIDER3 server and standalone package at http://sparks-lab.org . yaoqi.zhou@griffith.edu.au or yuedong.yang@griffith.edu.au. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email
Photostable nonlinear optical polycarbonates
Faccini, M.; Balakrishnan, M.; Diemeer, Mart; Torosantucci, Riccardo; Driessen, A.; Reinhoudt, David; Verboom, Willem
2008-01-01
Highly thermal and photostable nonlinear optical polymers were obtained by covalently incorporating the tricyanovinylidenediphenylaminobenzene (TCVDPA) chromophore to a polycarbonate backbone. NLO polycarbonates with different chromophore attachment modes and flexibilities were synthesized. In spite
Nonlinear singular elliptic equations
International Nuclear Information System (INIS)
Dong Minh Duc.
1988-09-01
We improve the Poincare inequality, the Sobolev imbedding theorem and the Trudinger imbedding theorem and prove a Mountain pass theorem. Applying these results we study a nonlinear singular mixed boundary problem. (author). 22 refs
Nonlinear Optical Terahertz Technology
National Aeronautics and Space Administration — We develop a new approach to generation of THz radiation. Our method relies on mixing two optical frequency beams in a nonlinear crystalline Whispering Gallery Mode...
Nonlinear differential equations
Struble, Raimond A
2017-01-01
Detailed treatment covers existence and uniqueness of a solution of the initial value problem, properties of solutions, properties of linear systems, stability of nonlinear systems, and two-dimensional systems. 1962 edition.
Terahertz semiconductor nonlinear optics
DEFF Research Database (Denmark)
Turchinovich, Dmitry; Hvam, Jørn Märcher; Hoffmann, Matthias
2013-01-01
In this proceedings we describe our recent results on semiconductor nonlinear optics, investigated using single-cycle THz pulses. We demonstrate the nonlinear absorption and self-phase modulation of strong-field THz pulses in doped semiconductors, using n-GaAs as a model system. The THz...... nonlinearity in doped semiconductors originates from the near-instantaneous heating of free electrons in the ponderomotive potential created by electric field of the THz pulse, leading to ultrafast increase of electron effective mass by intervalley scattering. Modification of effective mass in turn leads...... to a decrease of plasma frequency in semiconductor and produces a substantial modification of THz-range material dielectric function, described by the Drude model. As a result, the nonlinearity of both absorption coefficient and refractive index of the semiconductor is observed. In particular we demonstrate...
Leburn, Christopher; Reid, Derryck
2013-01-01
The field of ultrafast nonlinear optics is broad and multidisciplinary, and encompasses areas concerned with both the generation and measurement of ultrashort pulses of light, as well as those concerned with the applications of such pulses. Ultrashort pulses are extreme events – both in terms of their durations, and also the high peak powers which their short durations can facilitate. These extreme properties make them powerful experiment tools. On one hand, their ultrashort durations facilitate the probing and manipulation of matter on incredibly short timescales. On the other, their ultrashort durations can facilitate high peak powers which can drive highly nonlinear light-matter interaction processes. Ultrafast Nonlinear Optics covers a complete range of topics, both applied and fundamental in nature, within the area of ultrafast nonlinear optics. Chapters 1 to 4 are concerned with the generation and measurement of ultrashort pulses. Chapters 5 to 7 are concerned with fundamental applications of ultrasho...
Nonlinear surface Alfven waves
International Nuclear Information System (INIS)
Cramer, N.F.
1991-01-01
The problem of nonlinear surface Alfven waves propagating on an interface between a plasma and a vacuum is discussed, with dispersion provided by the finite-frequency effect, i.e. the finite ratio of the frequency to the ion-cyclotron frequency. A set of simplified nonlinear wave equations is derived using the method of stretched co-ordinates, and another approach uses the generation of a second-harmonic wave and its interaction with the first harmonic to obtain a nonlinear dispersion relation. A nonlinear Schroedinger equation is then derived, and soliton solutions found that propagate as solitary pulses in directions close to parallel and antiparallel to the background magnetic field. (author)
Indian Academy of Sciences (India)
The Structures Panel of the Aeronautics Research and Development Board of India ... A great variety of topics was covered, including themes such as nonlinear finite ... or shell structures, and three are on the composite form of construction, ...
A nonlinear oscillatory problem
International Nuclear Information System (INIS)
Zhou Qingqing.
1991-10-01
We have studied the nonlinear oscillatory problem of orthotropic cylindrical shell, we have analyzed the character of the oscillatory system. The stable condition of the oscillatory system has been given. (author). 6 refs
Degenerate nonlinear diffusion equations
Favini, Angelo
2012-01-01
The aim of these notes is to include in a uniform presentation style several topics related to the theory of degenerate nonlinear diffusion equations, treated in the mathematical framework of evolution equations with multivalued m-accretive operators in Hilbert spaces. The problems concern nonlinear parabolic equations involving two cases of degeneracy. More precisely, one case is due to the vanishing of the time derivative coefficient and the other is provided by the vanishing of the diffusion coefficient on subsets of positive measure of the domain. From the mathematical point of view the results presented in these notes can be considered as general results in the theory of degenerate nonlinear diffusion equations. However, this work does not seek to present an exhaustive study of degenerate diffusion equations, but rather to emphasize some rigorous and efficient techniques for approaching various problems involving degenerate nonlinear diffusion equations, such as well-posedness, periodic solutions, asympt...
Introduction to nonlinear science
Nicolis, G
1995-01-01
One of the most unexpected results in science in recent years is that quite ordinary systems obeying simple laws can give rise to complex, nonlinear or chaotic, behavior. In this book, the author presents a unified treatment of the concepts and tools needed to analyze nonlinear phenomena and to outline some representative applications drawn from the physical, engineering, and biological sciences. Some of the interesting topics covered include: dynamical systems with a finite number of degrees of freedom, linear stability analysis of fixed points, nonlinear behavior of fixed points, bifurcation analysis, spatially distributed systems, broken symmetries, pattern formation, and chaotic dynamics. The author makes a special effort to provide a logical connection between ordinary dynamical systems and spatially extended systems, and to balance the emphasis on chaotic behavior and more classical nonlinear behavior. He also develops a statistical approach to complex systems and compares it to traditional deterministi...
2015-05-07
associated with the lattice background; the nonlinearity is derived from the inclusion of cubic nonlinearity. Often the background potential is periodic...dispersion branch we can find discrete evolution equations for the envelope associated with the lattice NLS equation (1) by looking for solutions of...spatial operator in the above NLS equation can be elliptic, hyperbolic or parabolic . We remark that further reduction is possible by going into a moving
Nonlinear dynamics and astrophysics
International Nuclear Information System (INIS)
Vallejo, J. C.; Sanjuan, M. A. F.
2000-01-01
Concepts and techniques from Nonlinear Dynamics, also known as Chaos Theory, have been applied successfully to several astrophysical fields such as orbital motion, time series analysis or galactic dynamics, providing answers to old questions but also opening a few new ones. Some of these topics are described in this review article, showing the basis of Nonlinear Dynamics, and how it is applied in Astrophysics. (Author)
Elke, Gunnar; Wang, Miao; Weiler, Norbert; Day, Andrew G; Heyland, Daren K
2014-02-10
Current international sepsis guidelines recommend low-dose enteral nutrition (EN) for the first week. This contradicts other nutrition guidelines for heterogenous groups of ICU patients. Data on the optimal dose of EN in septic patients are lacking. Our aim was to evaluate the effect of energy and protein amount given by EN on clinical outcomes in a large cohort of critically ill septic patients. We conducted a secondary analysis of pooled data collected prospectively from international nutrition studies. Eligible patients had a diagnosis of sepsis and/or pneumonia and were admitted to the ICU for ≥3 days, mechanically ventilated within 48 hours of ICU admission and only receiving EN. Patients receiving parenteral nutrition were excluded. Data were collected from ICU admission up to a maximum of 12 days. Regression models were used to examine the impact of calorie and protein intake on 60-day mortality and ventilator-free days. Of the 13,630 patients included in the dataset, 2,270 met the study inclusion criteria. Patients received a mean amount of 1,057 kcal/d (14.5 kcal/kg/day) and 49 g protein/day (0.7 g/kg/d) by EN alone. Patients were mechanically ventilated for a median of 8.4 days and 60-day mortality was 30.5%. An increase of 1,000 kcal was associated with reduced 60-day mortality (odds ratio (OR) 0.61; 95% confidence interval (CI) 0.48 to 0.77, P <0.001) and more ventilator-free days (2.81 days, 95% CI 0.53 to 5.08, P = 0.02) as was an increase of 30 g protein per day (OR 0.76; 95% CI 0.65 to 0.87, P <0.001 and 1.92 days, 95% CI 0.58 to 3.27, P = 0.005, respectively). In critically ill septic patients, a calorie and protein delivery closer to recommended amounts by EN in the early phase of ICU stay was associated with a more favorable outcome.
Pescara benchmarks: nonlinear identification
Gandino, E.; Garibaldi, L.; Marchesiello, S.
2011-07-01
Recent nonlinear methods are suitable for identifying large systems with lumped nonlinearities, but in practice most structural nonlinearities are distributed and an ideal nonlinear identification method should cater for them as well. In order to extend the current NSI method to be applied also on realistic large engineering structures, a modal counterpart of the method is proposed in this paper. The modal NSI technique is applied on one of the reinforced concrete beams that have been tested in Pescara, under the project titled "Monitoring and diagnostics of railway bridges by means of the analysis of the dynamic response due to train crossing", financed by Italian Ministry of Research. The beam showed a softening nonlinear behaviour, so that the nonlinearity concerning the first mode is characterized and its force contribution is quantified. Moreover, estimates for the modal parameters are obtained and the model is validated by comparing the measured and the reconstructed output. The identified estimates are also used to accurately predict the behaviour of the same beam, when subject to different initial conditions.
Nonlinear Multiantenna Detection Methods
Directory of Open Access Journals (Sweden)
Chen Sheng
2004-01-01
Full Text Available A nonlinear detection technique designed for multiple-antenna assisted receivers employed in space-division multiple-access systems is investigated. We derive the optimal solution of the nonlinear spatial-processing assisted receiver for binary phase shift keying signalling, which we refer to as the Bayesian detector. It is shown that this optimal Bayesian receiver significantly outperforms the standard linear beamforming assisted receiver in terms of a reduced bit error rate, at the expense of an increased complexity, while the achievable system capacity is substantially enhanced with the advent of employing nonlinear detection. Specifically, when the spatial separation expressed in terms of the angle of arrival between the desired and interfering signals is below a certain threshold, a linear beamformer would fail to separate them, while a nonlinear detection assisted receiver is still capable of performing adequately. The adaptive implementation of the optimal Bayesian detector can be realized using a radial basis function network. Two techniques are presented for constructing block-data-based adaptive nonlinear multiple-antenna assisted receivers. One of them is based on the relevance vector machine invoked for classification, while the other on the orthogonal forward selection procedure combined with the Fisher ratio class-separability measure. A recursive sample-by-sample adaptation procedure is also proposed for training nonlinear detectors based on an amalgam of enhanced -means clustering techniques and the recursive least squares algorithm.
Pescara benchmarks: nonlinear identification
International Nuclear Information System (INIS)
Gandino, E; Garibaldi, L; Marchesiello, S
2011-01-01
Recent nonlinear methods are suitable for identifying large systems with lumped nonlinearities, but in practice most structural nonlinearities are distributed and an ideal nonlinear identification method should cater for them as well. In order to extend the current NSI method to be applied also on realistic large engineering structures, a modal counterpart of the method is proposed in this paper. The modal NSI technique is applied on one of the reinforced concrete beams that have been tested in Pescara, under the project titled M onitoring and diagnostics of railway bridges by means of the analysis of the dynamic response due to train crossing , financed by Italian Ministry of Research. The beam showed a softening nonlinear behaviour, so that the nonlinearity concerning the first mode is characterized and its force contribution is quantified. Moreover, estimates for the modal parameters are obtained and the model is validated by comparing the measured and the reconstructed output. The identified estimates are also used to accurately predict the behaviour of the same beam, when subject to different initial conditions.
Introduction to nonlinear acoustics
Bjørnø, Leif
2010-01-01
A brief review of the basic principles of fluid mechanics needed for development of linear and nonlinear ultrasonic concepts will be given. The fundamental equations of nonlinear ultrasonics will be derived and their physical properties explained. It will be shown how an originally monochromatic finite-amplitude ultrasonic wave, due to nonlinear effects, will distort during its propagation in time and space to form higher harmonics to its fundamental frequency. The concepts of shock formation will be presented. The material nonlinearity, described by the nonlinearity parameter B/A of the material, and the convective nonlinearity, described by the ultrasonic Mach Number, will be explained. Two procedures for determination of B/A will briefly be described and some B/A-values characterizing biological materials will be presented. Shock formation, described by use of the Goldberg Number,and Ultrasonic Saturation will be discussed.. An introduction to focused ultrasonic fields will be given and it will be shown how the ultrasonic intensity will vary axially and laterally in and near the focal region and how the field parameters of interest to biomedical applications may be described by use of the KZK-Model. Finally, an introduction will be given to the parametric acoustic array formed by mixing and interaction of two monochromatic, finite-amplitude ultrasonic waves in a liquid and the potentials of this mixing process in biomedical ultrasound will briefly be mentioned.
Fundamentals of nonlinear optical materials
Indian Academy of Sciences (India)
Nonlinear optics; nonlinear polarization; optical fiber communication; optical switch- ing. PACS Nos 42.65Tg; ... The importance of nonlinear optics is to understand the nonlinear behavior in the induced polarization and to ..... but much work in material development and characterization remains to be done. 16. Conclusion.
Nonlinear Approaches in Engineering Applications
Jazar, Reza
2012-01-01
Nonlinear Approaches in Engineering Applications focuses on nonlinear phenomena that are common in the engineering field. The nonlinear approaches described in this book provide a sound theoretical base and practical tools to design and analyze engineering systems with high efficiency and accuracy and with less energy and downtime. Presented here are nonlinear approaches in areas such as dynamic systems, optimal control and approaches in nonlinear dynamics and acoustics. Coverage encompasses a wide range of applications and fields including mathematical modeling and nonlinear behavior as applied to microresonators, nanotechnologies, nonlinear behavior in soil erosion,nonlinear population dynamics, and optimization in reducing vibration and noise as well as vibration in triple-walled carbon nanotubes. This book also: Provides a complete introduction to nonlinear behavior of systems and the advantages of nonlinearity as a tool for solving engineering problems Includes applications and examples drawn from the el...
Nonlinear amplitude dynamics in flagellar beating.
Oriola, David; Gadêlha, Hermes; Casademunt, Jaume
2017-03-01
The physical basis of flagellar and ciliary beating is a major problem in biology which is still far from completely understood. The fundamental cytoskeleton structure of cilia and flagella is the axoneme, a cylindrical array of microtubule doublets connected by passive cross-linkers and dynein motor proteins. The complex interplay of these elements leads to the generation of self-organized bending waves. Although many mathematical models have been proposed to understand this process, few attempts have been made to assess the role of dyneins on the nonlinear nature of the axoneme. Here, we investigate the nonlinear dynamics of flagella by considering an axonemal sliding control mechanism for dynein activity. This approach unveils the nonlinear selection of the oscillation amplitudes, which are typically either missed or prescribed in mathematical models. The explicit set of nonlinear equations are derived and solved numerically. Our analysis reveals the spatio-temporal dynamics of dynein populations and flagellum shape for different regimes of motor activity, medium viscosity and flagellum elasticity. Unstable modes saturate via the coupling of dynein kinetics and flagellum shape without the need of invoking a nonlinear axonemal response. Hence, our work reveals a novel mechanism for the saturation of unstable modes in axonemal beating.
International Nuclear Information System (INIS)
Shen Yuanrang
2011-01-01
This article presents a brief introduction to the birth and early investigations of nonlinear optics, such as second harmonic generation,sum and difference frequency generation, stimulated Raman scattering,and self-action of light etc. Several important research achievements and applications of nonlinear optics are presented as well, including nonlinear optical spectroscopy, phase conjugation and adaptive optics, coherent nonlinear optics, and high-order harmonic generation. In the end, current and future research topics in nonlinear optics are summarized. (authors)
A Teaching and Learning Sequence about the Interplay of Chance and Determinism in Nonlinear Systems
Stavrou, D.; Duit, R.; Komorek, M.
2008-01-01
A teaching and learning sequence aimed at introducing upper secondary school students to the interplay between chance and determinism in nonlinear systems is presented. Three experiments concerning nonlinear systems (deterministic chaos, self-organization and fractals) and one experiment concerning linear systems are introduced. Thirty upper…
Canonical structure of evolution equations with non-linear ...
Indian Academy of Sciences (India)
The dispersion produced is compensated by non-linear effects resulting in the formation of exponentially localized .... determining the values of Lagrange's multipliers αis. We postulate that a slightly .... c3 «w2x -v. (36). To include the effect of the secondary constraint c3 in the total Hamiltonian H we modify. (33) as. 104.
Nonlinear dynamics of structures
Oller, Sergio
2014-01-01
This book lays the foundation of knowledge that will allow a better understanding of nonlinear phenomena that occur in structural dynamics. This work is intended for graduate engineering students who want to expand their knowledge on the dynamic behavior of structures, specifically in the nonlinear field, by presenting the basis of dynamic balance in non‐linear behavior structures due to the material and kinematics mechanical effects. Particularly, this publication shows the solution of the equation of dynamic equilibrium for structure with nonlinear time‐independent materials (plasticity, damage and frequencies evolution), as well as those time dependent non‐linear behavior materials (viscoelasticity and viscoplasticity). The convergence conditions for the non‐linear dynamic structure solution are studied, and the theoretical concepts and its programming algorithms are presented.
Rodrigues, Nils; Weiskopf, Daniel
2018-01-01
Conventional dot plots use a constant dot size and are typically applied to show the frequency distribution of small data sets. Unfortunately, they are not designed for a high dynamic range of frequencies. We address this problem by introducing nonlinear dot plots. Adopting the idea of nonlinear scaling from logarithmic bar charts, our plots allow for dots of varying size so that columns with a large number of samples are reduced in height. For the construction of these diagrams, we introduce an efficient two-way sweep algorithm that leads to a dense and symmetrical layout. We compensate aliasing artifacts at high dot densities by a specifically designed low-pass filtering method. Examples of nonlinear dot plots are compared to conventional dot plots as well as linear and logarithmic histograms. Finally, we include feedback from an expert review.
Multidimensional nonlinear descriptive analysis
Nishisato, Shizuhiko
2006-01-01
Quantification of categorical, or non-numerical, data is a problem that scientists face across a wide range of disciplines. Exploring data analysis in various areas of research, such as the social sciences and biology, Multidimensional Nonlinear Descriptive Analysis presents methods for analyzing categorical data that are not necessarily sampled randomly from a normal population and often involve nonlinear relations. This reference not only provides an overview of multidimensional nonlinear descriptive analysis (MUNDA) of discrete data, it also offers new results in a variety of fields. The first part of the book covers conceptual and technical preliminaries needed to understand the data analysis in subsequent chapters. The next two parts contain applications of MUNDA to diverse data types, with each chapter devoted to one type of categorical data, a brief historical comment, and basic skills peculiar to the data types. The final part examines several problems and then concludes with suggestions for futu...
DEFF Research Database (Denmark)
Nguyen-Duy, Khiem
of a proposed NSE system with high dynamic performance. The goal of the work is to achieve a state-of-the art transient time of 10 µs. In order to produce the arbitrary nonlinear curve, the exponential function of a typical diode is used, but the diode can be replaced by other nonlinear curve reference...... of conductive common-mode current produced by the high rate of change of voltage over time (high dv/dt) at the NSE output. v/xvii The contributions of the thesis are based on the development of both units: the low Cio isolated power supply and the high dynamic performance NSE. Both units are investigated......-of-the-art dynamic performance among devices of the same kind. It also offers a complete solution for simulation of nonlinear source systems of different sizes, both in terrestrial and non-terrestrial applications. Key words: Current transformers, dc-dc power converters, hysteresis, parasitic capacitance, system...
Gu, Qin; Zhang, Chengqi; Yu, Fangwei; Yin, Yanni; Shim, Won-Bo; Ma, Zhonghua
2015-08-01
Saccharomyces cerevisiae protein kinase Sch9 is one of the downstream effectors of the target of rapamycin (TOR) complex 1 and plays multiple roles in stress resistance, longevity and nutrient sensing. However, the functions of Sch9 orthologs in filamentous fungi, particularly in pathogenic species, have not been characterized to date. Here, we investigated biological and genetic functions of FgSch9 in Fusarium graminearum. The FgSCH9 deletion mutant (ΔFgSch9) was defective in aerial hyphal growth, hyphal branching and conidial germination. The mutant exhibited increased sensitivity to osmotic and oxidative stresses, cell wall-damaging agents, and to rapamycin, while showing increased thermal tolerance. We identified FgMaf1 as one of the FgSch9-interacting proteins that plays an important role in regulating mycotoxin biosynthesis and virulence of F. graminearum. Co-immunoprecipitation and affinity capture-mass spectrometry assays showed that FgSch9 also interacts with FgTor and FgHog1. More importantly, both ΔFgSch9 and FgHog1 null mutant (ΔFgHog1) exhibited increased sensitivity to osmotic and oxidative stresses. This defect was more severe in the FgSch9/FgHog1 double mutant. Taken together, we propose that FgSch9 serves as a mediator of the TOR and high osmolarity glycerol pathways, and regulates vegetative differentiation, multiple stress responses and secondary metabolism in F. graminearum. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.
Nonlinear elastic waves in materials
Rushchitsky, Jeremiah J
2014-01-01
The main goal of the book is a coherent treatment of the theory of propagation in materials of nonlinearly elastic waves of displacements, which corresponds to one modern line of development of the nonlinear theory of elastic waves. The book is divided on five basic parts: the necessary information on waves and materials; the necessary information on nonlinear theory of elasticity and elastic materials; analysis of one-dimensional nonlinear elastic waves of displacement – longitudinal, vertically and horizontally polarized transverse plane nonlinear elastic waves of displacement; analysis of one-dimensional nonlinear elastic waves of displacement – cylindrical and torsional nonlinear elastic waves of displacement; analysis of two-dimensional nonlinear elastic waves of displacement – Rayleigh and Love nonlinear elastic surface waves. The book is addressed first of all to people working in solid mechanics – from the students at an advanced undergraduate and graduate level to the scientists, professional...
Nonlinear excitations in biomolecules
International Nuclear Information System (INIS)
Peyrard, M.
1995-01-01
The aim of the workshop entitled ''Nonlinear Excitations in Biomolecules'' is to attempt to bridge the gap between the physicists and biologists communities which is mainly due to language and cultural barriers. The progress of nonlinear science in the last few decades which have shown that the combination of nonlinearity, which characterize most biological phenomena, and cooperative effects in a system having a large number of degrees of freedom, can give rise to coherent excitations with remarkable properties. New concepts, such as solitons nd nonlinear energy localisation have become familiar to physicists and applied mathematicians. It is thus tempting to make an analogy between these coherent excitations and the exceptional stability of some biological processes, such as for instance DNA transcription, which require the coordination of many events in the ever changing environment of a cell. Physicists are now invoking nonlinear excitations to describe and explain many bio-molecular processes while biologists often doubt that the seemingly infinite variety of phenomena that they are attempting to classify can be reduced to such simple concepts. A large part of the meeting is devoted to tutorial lectures rather than to latest research results. The book provides a pedagogical introduction to the two topics forming the backbone of the meeting: the theory of nonlinear excitations and solitons, and their application in biology; and the structure and function of biomolecules, as well as energy and charge transport in biophysics. In order to emphasize the link between physics and biology, the volume is not divided along these two topics but according to biological subjects. Each chapter starts with a short introduction attempting to help the reader to find his way among the contributions and point out the connection between them. 23 lectures over the 32 presented have been selected and refers to quantum properties of macro-molecules. (J.S.)
Oscillations in nonlinear systems
Hale, Jack K
2015-01-01
By focusing on ordinary differential equations that contain a small parameter, this concise graduate-level introduction to the theory of nonlinear oscillations provides a unified approach to obtaining periodic solutions to nonautonomous and autonomous differential equations. It also indicates key relationships with other related procedures and probes the consequences of the methods of averaging and integral manifolds.Part I of the text features introductory material, including discussions of matrices, linear systems of differential equations, and stability of solutions of nonlinear systems. Pa
Nonlinearity in nanomechanical cantilevers
DEFF Research Database (Denmark)
Villanueva Torrijo, Luis Guillermo; Karabalin, R. B.; Matheny, M. H.
2013-01-01
Euler-Bernoulli beam theory is widely used to successfully predict the linear dynamics of micro-and nanocantilever beams. However, its capacity to characterize the nonlinear dynamics of these devices has not yet been rigorously assessed, despite its use in nanoelectromechanical systems developmen....... These findings underscore the delicate balance between inertial and geometric nonlinear effects in the fundamental mode, and strongly motivate further work to develop theories beyond the Euler-Bernoulli approximation. DOI: 10.1103/PhysRevB.87.024304...
Energy Technology Data Exchange (ETDEWEB)
Chandra, J; Scott, A C
1983-01-01
Topics discussed include transitions in weakly coupled nonlinear oscillators, singularly perturbed delay-differential equations, and chaos in simple laser systems. Papers are presented on truncated Navier-Stokes equations in a two-dimensional torus, on frequency locking in Josephson point contacts, and on soliton excitations in Josephson tunnel junctions. Attention is also given to the nonlinear coupling of radiation pulses to absorbing anharmonic molecular media, to aspects of interrupted coarse-graining in stimulated excitation, and to a statistical analysis of long-term dynamic irregularity in an exactly soluble quantum mechanical model.
DEFF Research Database (Denmark)
Clausen, Carl A. Balslev; Christiansen, Peter Leth; Torner, L.
1999-01-01
We show that with the quasi-phase-matching technique it is possible to fabricate stripes of nonlinearity that trap and guide light like waveguides. We investigate an array of such stripes and find that when the stripes are sufficiently narrow, the beam dynamics is governed by a quadratic nonlinear...... discrete equation. The proposed structure therefore provides an experimental setting for exploring discrete effects in a controlled manner. In particular, we show propagation of breathers that are eventually trapped by discreteness. When the stripes are wide the beams evolve in a structure we term...
Agrawal, Govind
2012-01-01
Since the 4e appeared, a fast evolution of the field has occurred. The 5e of this classic work provides an up-to-date account of the nonlinear phenomena occurring inside optical fibers, the basis of all our telecommunications infastructure as well as being used in the medical field. Reflecting the big developments in research, this new edition includes major new content: slow light effects, which offers a reduction in noise and power consumption and more ordered network traffic-stimulated Brillouin scattering; vectorial treatment of highly nonlinear fibers; and a brand new chapter o
Tsia, Kevin K.; Jalali, Bahram
2010-05-01
An intriguing optical property of silicon is that it exhibits a large third-order optical nonlinearity, with orders-ofmagnitude larger than that of silica glass in the telecommunication band. This allows efficient nonlinear optical interaction at relatively low power levels in a small footprint. Indeed, we have witnessed a stunning progress in harnessing the Raman and Kerr effects in silicon as the mechanisms for enabling chip-scale optical amplification, lasing, and wavelength conversion - functions that until recently were perceived to be beyond the reach of silicon. With all the continuous efforts developing novel techniques, nonlinear silicon photonics is expected to be able to reach even beyond the prior achievements. Instead of providing a comprehensive overview of this field, this manuscript highlights a number of new branches of nonlinear silicon photonics, which have not been fully recognized in the past. In particular, they are two-photon photovoltaic effect, mid-wave infrared (MWIR) silicon photonics, broadband Raman effects, inverse Raman scattering, and periodically-poled silicon (PePSi). These novel effects and techniques could create a new paradigm for silicon photonics and extend its utility beyond the traditionally anticipated applications.
Ritz, Christian; Parmigiani, Giovanni
2009-01-01
R is a rapidly evolving lingua franca of graphical display and statistical analysis of experiments from the applied sciences. This book provides a coherent treatment of nonlinear regression with R by means of examples from a diversity of applied sciences such as biology, chemistry, engineering, medicine and toxicology.
Borghi, M.; Castellan, C.; Signorini, S.; Trenti, A.; Pavesi, L.
2017-09-01
Silicon photonics is a technology based on fabricating integrated optical circuits by using the same paradigms as the dominant electronics industry. After twenty years of fervid development, silicon photonics is entering the market with low cost, high performance and mass-manufacturable optical devices. Until now, most silicon photonic devices have been based on linear optical effects, despite the many phenomenologies associated with nonlinear optics in both bulk materials and integrated waveguides. Silicon and silicon-based materials have strong optical nonlinearities which are enhanced in integrated devices by the small cross-section of the high-index contrast silicon waveguides or photonic crystals. Here the photons are made to strongly interact with the medium where they propagate. This is the central argument of nonlinear silicon photonics. It is the aim of this review to describe the state-of-the-art in the field. Starting from the basic nonlinearities in a silicon waveguide or in optical resonator geometries, many phenomena and applications are described—including frequency generation, frequency conversion, frequency-comb generation, supercontinuum generation, soliton formation, temporal imaging and time lensing, Raman lasing, and comb spectroscopy. Emerging quantum photonics applications, such as entangled photon sources, heralded single-photon sources and integrated quantum photonic circuits are also addressed at the end of this review.
Generalized Nonlinear Yule Models
Lansky, Petr; Polito, Federico; Sacerdote, Laura
2016-11-01
With the aim of considering models related to random graphs growth exhibiting persistent memory, we propose a fractional nonlinear modification of the classical Yule model often studied in the context of macroevolution. Here the model is analyzed and interpreted in the framework of the development of networks such as the World Wide Web. Nonlinearity is introduced by replacing the linear birth process governing the growth of the in-links of each specific webpage with a fractional nonlinear birth process with completely general birth rates. Among the main results we derive the explicit distribution of the number of in-links of a webpage chosen uniformly at random recognizing the contribution to the asymptotics and the finite time correction. The mean value of the latter distribution is also calculated explicitly in the most general case. Furthermore, in order to show the usefulness of our results, we particularize them in the case of specific birth rates giving rise to a saturating behaviour, a property that is often observed in nature. The further specialization to the non-fractional case allows us to extend the Yule model accounting for a nonlinear growth.
Intramolecular and nonlinear dynamics
Energy Technology Data Exchange (ETDEWEB)
Davis, M.J. [Argonne National Laboratory, IL (United States)
1993-12-01
Research in this program focuses on three interconnected areas. The first involves the study of intramolecular dynamics, particularly of highly excited systems. The second area involves the use of nonlinear dynamics as a tool for the study of molecular dynamics and complex kinetics. The third area is the study of the classical/quantum correspondence for highly excited systems, particularly systems exhibiting classical chaos.
Balancing for nonlinear systems
Scherpen, J.M.A.
1993-01-01
We present a method of balancing for nonlinear systems which is an extension of balancing for linear systems in the sense that it is based on the input and output energy of a system. It is a local result, but gives 'broader' results than we obtain by just linearizing the system. Furthermore, the
Intestinal Lymphangiectasia Secondary to Neuroblastoma
Directory of Open Access Journals (Sweden)
RM Reifen
1994-01-01
Full Text Available An eight month-old infant presented with a 10-day history of vomiting and diarrhea, and a one-week history of swelling of the lower extremities. Laboratory evaluations revealed hypoproteinemia and lymphocytopenia due to protein-losing enteropathy. Peroral small bowel biopsy showed intestinal lymphangiectasia. Subsequent onset of unexplained ecchymosis and obstructive jaundice resulted in additional studies which revealed an omental neuroblastoma as the underlying etiology of the infant’s symptoms. This report emphasizes the importance of considering secondary, obstructive causes for lymphangiectasia and protein-losing enteropathy.
Nonlinear Subincremental Method for Determination of Elastic-Plastic-Creep Behaviour
DEFF Research Database (Denmark)
Ottosen, N. Saabye; Gunneskov, O.
1985-01-01
to general elastic-plastic-creep behaviour including problems with a highly nonlinear total strain path caused by the occurrence of creep hardening. This nonlinear method degenerates to the linear approach for elastic-plastic behaviour and when secondary creep is present. It is also linear during step......The frequently used subincremental method has so far been used on a linear interpolation of the total strain path within each main step. This method has proven successful when elastic-plastic behaviour and secondary creep is involved. The authors propose a nonlinear subincremental method applicable...
A teaching and learning sequence about the interplay of chance and determinism in nonlinear systems
International Nuclear Information System (INIS)
Stavrou, D; Duit, R; Komorek, M
2008-01-01
A teaching and learning sequence aimed at introducing upper secondary school students to the interplay between chance and determinism in nonlinear systems is presented. Three experiments concerning nonlinear systems (deterministic chaos, self-organization and fractals) and one experiment concerning linear systems are introduced. Thirty upper secondary students' capabilities and difficulties in understanding the scientific point of view were investigated, using a teaching experiment design. The results show that most students were capable of sound explanations concerning the interplay of chance and determinism in nonlinear systems
Identification of nonlinear anelastic models
International Nuclear Information System (INIS)
Draganescu, G E; Bereteu, L; Ercuta, A
2008-01-01
A useful nonlinear identification technique applied to the anelastic and rheologic models is presented in this paper. First introduced by Feldman, the method is based on the Hilbert transform, and is currently used for identification of the nonlinear vibrations
Nonlinear chaos control and synchronization
Huijberts, H.J.C.; Nijmeijer, H.; Schöll, E.; Schuster, H.G.
2007-01-01
This chapter contains sections titled: Introduction Nonlinear Geometric Control Some Differential Geometric Concepts Nonlinear Controllability Chaos Control Through Feedback Linearization Chaos Control Through Input-Output Linearization Lyapunov Design Lyapunov Stability and Lyapunov's First Method
Nonlinearity and disorder: Classification and stability of nonlinear impurity modes
DEFF Research Database (Denmark)
Sukhorukov, Andrey A.; Kivshar, Yuri S.; Bang, Ole
2001-01-01
We study the effects produced by competition of two physical mechanisms of energy localization in inhomogeneous nonlinear systems. As an example, we analyze spatially localized modes supported by a nonlinear impurity in the generalized nonlinear Schrödinger equation and describe three types of no...... the case of a power-law nonlinearity in detail. We discuss several scenarios of the instability-induced dynamics of the nonlinear impurity modes, including the mode decay or switching to a new stable state, and collapse at the impurity site....
Terahertz Nonlinear Optics in Semiconductors
DEFF Research Database (Denmark)
Turchinovich, Dmitry; Hvam, Jørn Märcher; Hoffmann, Matthias C.
2013-01-01
We demonstrate the nonlinear optical effects – selfphase modulation and saturable absorption of a single-cycle THz pulse in a semiconductor. Resulting from THz-induced modulation of Drude plasma, these nonlinear optical effects, in particular, lead to self-shortening and nonlinear spectral...... breathing of a single-cycle THz pulse in a semiconductor....
FRF decoupling of nonlinear systems
Kalaycıoğlu, Taner; Özgüven, H. Nevzat
2018-03-01
Structural decoupling problem, i.e. predicting dynamic behavior of a particular substructure from the knowledge of the dynamics of the coupled structure and the other substructure, has been well investigated for three decades and led to several decoupling methods. In spite of the inherent nonlinearities in a structural system in various forms such as clearances, friction and nonlinear stiffness, all decoupling studies are for linear systems. In this study, decoupling problem for nonlinear systems is addressed for the first time. A method, named as FRF Decoupling Method for Nonlinear Systems (FDM-NS), is proposed for calculating FRFs of a substructure decoupled from a coupled nonlinear structure where nonlinearity can be modeled as a single nonlinear element. Depending on where nonlinear element is, i.e., either in the known or unknown subsystem, or at the connection point, the formulation differs. The method requires relative displacement information between two end points of the nonlinear element, in addition to point and transfer FRFs at some points of the known subsystem. However, it is not necessary to excite the system from the unknown subsystem even when the nonlinear element is in that subsystem. The validation of FDM-NS is demonstrated with two different case studies using nonlinear lumped parameter systems. Finally, a nonlinear experimental test structure is used in order to show the real-life application and accuracy of FDM-NS.
Rogue waves in nonlinear science
International Nuclear Information System (INIS)
Yan Zhenya
2012-01-01
Rogue waves, as a special type of solitary waves, play an important role in nonlinear optics, Bose-Einstein condensates, ocean, atmosphere, and even finance. In this report, we mainly review on the history of the rogue wave phenomenon and recent development of rogue wave solutions in some nonlinear physical models arising in the fields of nonlinear science.
H∞ Balancing for Nonlinear Systems
Scherpen, Jacquelien M.A.
1996-01-01
In previously obtained balancing methods for nonlinear systems a past and a future energy function are used to bring the nonlinear system in balanced form. By considering a different pair of past and future energy functions that are related to the H∞ control problem for nonlinear systems we define
Processes and problems in secondary star formation
International Nuclear Information System (INIS)
Klein, R.I.; Whitaker, R.W.; Sandford, M.T. II.
1984-03-01
Recent developments relating the conditions in molecular clouds to star formation triggered by a prior stellar generation are reviewed. Primary processes are those that lead to the formation of a first stellar generation. The secondary processes that produce stars in response to effects caused by existing stars are compared and evaluated in terms of the observational data presently available. We discuss the role of turbulence to produce clumpy cloud structures and introduce new work on colliding inter-cloud gas flows leading to non-linear inhomogeneous cloud structures in an intially smooth cloud. This clumpy morphology has important consequences for secondary formation. The triggering processes of supernovae, stellar winds, and H II regions are discussed with emphasis on the consequences for radiation driven implosion as a promising secondary star formation mechanism. Detailed two-dimensional, radiation-hydrodynamic calculations of radiation driven implosion are discussed. This mechanism is shown to be highly efficient in synchronizing the formation of new stars in congruent to 1-3 x 10 4 years and could account for the recent evidence for new massive star formation in several UCHII regions. It is concluded that, while no single theory adequately explains the variety of star formation observed, a uniform description of star formation is likely to involve several secondary processes. Advances in the theory of star formation will require multiple dimensional calculations of coupled processes. The important non-linear interactions include hydrodynamics, radiation transport, and magnetic fields
Processes and problems in secondary star formation
International Nuclear Information System (INIS)
Klein, R.I.; Whitaker, R.W.; Sandford, M.T. II
1985-01-01
Recent developments relating the conditions in molecular clouds to star formation triggered by a prior stellar generation are reviewed. Primary processes are those that lead to the formation of a first stellar generation. The secondary processes that produce stars in response to effects caused by existing stars are compared and evaluated in terms of observational data presently available. We discuss the role of turbulence to produce clumpy cloud structures and introduce new work on colliding intercloud gas flows leading to nonlinear inhomogeneous cloud structures in an initially smooth cloud. This clumpy morphology has important consequences for secondary formation. The triggering processes of supernovae, stellar winds, and H II regions are discussed with emphasis on the consequences for radiation-driven implosion as a promising secondary star formation mechanism. Detailed two-dimensional, radiation-hydrodynamic calculations of radiation-driven implosion are discussed. This mechanism is shown to be highly efficient in synchronizing the formation of new stars in -- 1-3 x 10/sup 4/ yr and could account for the recent evidence for new massive star formation in several ultracompact H II regions. It is concluded that, while no single theory adequately explains the variety of star formation observed, a uniform description of star formation is likely to involve several secondary processes. Advances in the theory of star formation will require multi-dimensional calculations of coupled processes. Important nonlinear interactions include hydrodynamics, radiation transport, and magnetic fields
Nonlinear differential equations
Energy Technology Data Exchange (ETDEWEB)
Dresner, L.
1988-01-01
This report is the text of a graduate course on nonlinear differential equations given by the author at the University of Wisconsin-Madison during the summer of 1987. The topics covered are: direction fields of first-order differential equations; the Lie (group) theory of ordinary differential equations; similarity solutions of second-order partial differential equations; maximum principles and differential inequalities; monotone operators and iteration; complementary variational principles; and stability of numerical methods. The report should be of interest to graduate students, faculty, and practicing scientists and engineers. No prior knowledge is required beyond a good working knowledge of the calculus. The emphasis is on practical results. Most of the illustrative examples are taken from the fields of nonlinear diffusion, heat and mass transfer, applied superconductivity, and helium cryogenics.
Nonlinear (Anharmonic Casimir Oscillator
Directory of Open Access Journals (Sweden)
Habibollah Razmi
2011-01-01
Full Text Available We want to study the dynamics of a simple linear harmonic micro spring which is under the influence of the quantum Casimir force/pressure and thus behaves as a (an nonlinear (anharmonic Casimir oscillator. Generally, the equation of motion of this nonlinear micromechanical Casimir oscillator has no exact solvable (analytical solution and the turning point(s of the system has (have no fixed position(s; however, for particular values of the stiffness of the micro spring and at appropriately well-chosen distance scales and conditions, there is (are approximately sinusoidal solution(s for the problem (the variable turning points are collected in a very small interval of positions. This, as a simple and elementary plan, may be useful in controlling the Casimir stiction problem in micromechanical devices.
DEFF Research Database (Denmark)
Mosegaard, Klaus
2012-01-01
For non-linear inverse problems, the mathematical structure of the mapping from model parameters to data is usually unknown or partly unknown. Absence of information about the mathematical structure of this function prevents us from presenting an analytical solution, so our solution depends on our......-heuristics are inefficient for large-scale, non-linear inverse problems, and that the 'no-free-lunch' theorem holds. We discuss typical objections to the relevance of this theorem. A consequence of the no-free-lunch theorem is that algorithms adapted to the mathematical structure of the problem perform more efficiently than...... pure meta-heuristics. We study problem-adapted inversion algorithms that exploit the knowledge of the smoothness of the misfit function of the problem. Optimal sampling strategies exist for such problems, but many of these problems remain hard. © 2012 Springer-Verlag....
Nonlinear Photonics 2014: introduction.
Akhmediev, N; Kartashov, Yaroslav
2015-01-12
International Conference "Nonlinear Photonics-2014" took place in Barcelona, Spain on July 27-31, 2014. It was a part of the "Advanced Photonics Congress" which is becoming a traditional notable event in the world of photonics. The current focus issue of Optics Express contains contributions from the participants of the Conference and the Congress. The articles in this focus issue by no means represent the total number of the congress contributions (around 400). However, it demonstrates wide range of topics covered at the event. The next conference of this series is to be held in 2016 in Australia, which is the home of many researchers working in the field of photonics in general and nonlinear photonics in particular.
Van Leeuwen, Peter Jan; Reich, Sebastian
2015-01-01
This book contains two review articles on nonlinear data assimilation that deal with closely related topics but were written and can be read independently. Both contributions focus on so-called particle filters. The first contribution by Jan van Leeuwen focuses on the potential of proposal densities. It discusses the issues with present-day particle filters and explorers new ideas for proposal densities to solve them, converging to particle filters that work well in systems of any dimension, closing the contribution with a high-dimensional example. The second contribution by Cheng and Reich discusses a unified framework for ensemble-transform particle filters. This allows one to bridge successful ensemble Kalman filters with fully nonlinear particle filters, and allows a proper introduction of localization in particle filters, which has been lacking up to now.
Essentials of nonlinear optics
Murti, Y V G S
2014-01-01
Current literature on Nonlinear Optics varies widely in terms of content, style, and coverage of specific topics, relative emphasis of areas and the depth of treatment. While most of these books are excellent resources for the researchers, there is a strong need for books appropriate for presenting the subject at the undergraduate or postgraduate levels in Universities. The need for such a book to serve as a textbook at the level of the bachelors and masters courses was felt by the authors while teaching courses on nonlinear optics to students of both science and engineering during the past two decades. This book has emerged from an attempt to address the requirement of presenting the subject at college level. A one-semester course covering the essentials can effectively be designed based on this.
Nonlinear differential equations
International Nuclear Information System (INIS)
Dresner, L.
1988-01-01
This report is the text of a graduate course on nonlinear differential equations given by the author at the University of Wisconsin-Madison during the summer of 1987. The topics covered are: direction fields of first-order differential equations; the Lie (group) theory of ordinary differential equations; similarity solutions of second-order partial differential equations; maximum principles and differential inequalities; monotone operators and iteration; complementary variational principles; and stability of numerical methods. The report should be of interest to graduate students, faculty, and practicing scientists and engineers. No prior knowledge is required beyond a good working knowledge of the calculus. The emphasis is on practical results. Most of the illustrative examples are taken from the fields of nonlinear diffusion, heat and mass transfer, applied superconductivity, and helium cryogenics
The forced nonlinear Schroedinger equation
International Nuclear Information System (INIS)
Kaup, D.J.; Hansen, P.J.
1985-01-01
The nonlinear Schroedinger equation describes the behaviour of a radio frequency wave in the ionosphere near the reflexion point where nonlinear processes are important. A simple model of this phenomenon leads to the forced nonlinear Schroedinger equation in terms of a nonlinear boundary value problem. A WKB analysis of the time evolution equations for the nonlinear Schroedinger equation in the inverse scattering transform formalism gives a crude order of magnitude estimation of the qualitative behaviour of the solutions. This estimation is compared with the numerical solutions. (D.Gy.)
Nonlinear electrodynamics and cosmology
International Nuclear Information System (INIS)
Breton, Nora
2010-01-01
Nonlinear electrodynamics (NLED) generalizes Maxwell's theory for strong fields. When coupled to general relativity NLED presents interesting features like the non-vanishing of the trace of the energy-momentum tensor that leads to the possibility of violation of some energy conditions and of acting as a repulsive contribution in the Raychaudhuri equation. This theory is worth to study in cosmological and astrophysical situations characterized by strong electromagnetic and gravitational fields.
Nonlinear fibre optics overview
DEFF Research Database (Denmark)
Travers, J. C.; Frosz, Michael Henoch; Dudley, J. M.
2010-01-01
The optical fiber based supercontinuum source has recently become a significant scientific and commercial success, with applications ranging from frequency comb production to advanced medical imaging. This one-of-a-kind book explains the theory of fiber supercontinuum broadening, describes......, provides a background to the associated nonlinear optical processes, treats the generation mechanisms from continuous wave to femtosecond pulse pump regimes and highlights the diverse applications. A full discussion of numerical methods and comprehensive computer code are also provided, enabling readers...
Damped nonlinear Schrodinger equation
International Nuclear Information System (INIS)
Nicholson, D.R.; Goldman, M.V.
1976-01-01
High frequency electrostatic plasma oscillations described by the nonlinear Schrodinger equation in the presence of damping, collisional or Landau, are considered. At early times, Landau damping of an initial soliton profile results in a broader, but smaller amplitude soliton, while collisional damping reduces the soliton size everywhere; soliton speeds at early times are unchanged by either kind of damping. For collisional damping, soliton speeds are unchanged for all time
Nonlinearity without superluminality
International Nuclear Information System (INIS)
Kent, Adrian
2005-01-01
Quantum theory is compatible with special relativity. In particular, though measurements on entangled systems are correlated in a way that cannot be reproduced by local hidden variables, they cannot be used for superluminal signaling. As Czachor, Gisin, and Polchinski pointed out, this is not generally true of general nonlinear modifications of the Schroedinger equation. Excluding superluminal signaling has thus been taken to rule out most nonlinear versions of quantum theory. The no-superluminal-signaling constraint has also been used for alternative derivations of the optimal fidelities attainable for imperfect quantum cloning and other operations. These results apply to theories satisfying the rule that their predictions for widely separated and slowly moving entangled systems can be approximated by nonrelativistic equations of motion with respect to a preferred time coordinate. This paper describes a natural way in which this rule might fail to hold. In particular, it is shown that quantum readout devices which display the values of localized pure states need not allow superluminal signaling, provided that the devices display the values of the states of entangled subsystems as defined in a nonstandard, although natural, way. It follows that any locally defined nonlinear evolution of pure states can be made consistent with Minkowski causality
Second-order nonlinear optical microscopy of spider silk
Zhao, Yue; Hien, Khuat Thi Thu; Mizutani, Goro; Rutt, Harvey N.
2017-06-01
Asymmetric β-sheet protein structures in spider silk should induce nonlinear optical interaction such as second harmonic generation (SHG) which is experimentally observed for a radial line and dragline spider silk using an imaging femtosecond laser SHG microscope. By comparing different spider silks, we found that the SHG signal correlates with the existence of the protein β-sheets. Measurements of the polarization dependence of SHG from the dragline indicated that the β-sheet has a nonlinear response depending on the direction of the incident electric field. We propose a model of what orientation the β-sheet takes in spider silk.
Lamb Wave Technique for Ultrasonic Nonlinear Characterization in Elastic Plates
International Nuclear Information System (INIS)
Lee, Tae Hun; Kim, Chung Seok; Jhang, Kyung Young
2010-01-01
Since the acoustic nonlinearity is sensitive to the minute variation of material properties, the nonlinear ultrasonic technique(NUT) has been considered as a promising method to evaluate the material degradation or fatigue. However, there are certain limitations to apply the conventional NUT using the bulk wave to thin plates. In case of plates, the use of Lamb wave can be considered, however, the propagation characteristics of Lamb wave are completely different with the bulk wave, and thus the separate study for the nonlinearity of Lamb wave is required. For this work, this paper analyzed first the conditions of mode pair suitable for the practical application as well as for the cumulative propagation of quadratic harmonic frequency and summarized the result in for conditions: phase matching, non-zero power flux, group velocity matching, and non-zero out-of-plane displacement. Experimental results in aluminum plates showed that the amplitude of the secondary Lamb wave and nonlinear parameter grew up with increasing propagation distance at the mode pair satisfying the above all conditions and that the ration of nonlinear parameters measured in Al6061-T6 and Al1100-H15 was closed to the ratio of the absolute nonlinear parameters
Nonlinear Dynamics of Carbon Nanotubes Under Large Electrostatic Force
Xu, Tiantian
2015-06-01
Because of the inherent nonlinearities involving the behavior of CNTs when excited by electrostatic forces, modeling and simulating their behavior is challenging. The complicated form of the electrostatic force describing the interaction of their cylindrical shape, forming upper electrodes, to lower electrodes poises serious computational challenges. This presents an obstacle against applying and using several nonlinear dynamics tools typically used to analyze the behavior of complicated nonlinear systems undergoing large motion, such as shooting, continuation, and integrity analysis techniques. This works presents an attempt to resolve this issue. We present an investigation of the nonlinear dynamics of carbon nanotubes when actuated by large electrostatic forces. We study expanding the complicated form of the electrostatic force into enough number of terms of the Taylor series. Then, we utilize this form along with an Euler-Bernoulli beam model to study for the first time the dynamic behavior of CNTs when excited by large electrostatic force. The geometric nonlinearity and the nonlinear electrostatic force are considered. An efficient reduced-order model (ROM) based on the Galerkin method is developed and utilized to simulate the static and dynamic responses of the CNTs. Several results are generated demonstrating softening and hardening behavior of the CNTs near their primary and secondary resonances. The effects of the DC and AC voltage loads on the behavior have been studied. The impacts of the initial slack level and CNT diameter are also demonstrated.
NONLINEAR DYNAMICS OF CARBON NANOTUBES UNDER LARGE ELECTROSTATIC FORCE
Xu, Tiantian
2015-06-01
Because of the inherent nonlinearities involving the behavior of CNTs when excited by electrostatic forces, modeling and simulating their behavior is challenging. The complicated form of the electrostatic force describing the interaction of their cylindrical shape, forming upper electrodes, to lower electrodes poises serious computational challenges. This presents an obstacle against applying and using several nonlinear dynamics tools typically used to analyze the behavior of complicated nonlinear systems undergoing large motion, such as shooting, continuation, and integrity analysis techniques. This works presents an attempt to resolve this issue. We present an investigation of the nonlinear dynamics of carbon nanotubes when actuated by large electrostatic forces. We study expanding the complicated form of the electrostatic force into enough number of terms of the Taylor series. Then, we utilize this form along with an Euler-Bernoulli beam model to study for the first time the dynamic behavior of CNTs when excited by large electrostatic force. The geometric nonlinearity and the nonlinear electrostatic force are considered. An efficient reduced-order model (ROM) based on the Galerkin method is developed and utilized to simulate the static and dynamic responses of the CNTs. Several results are generated demonstrating softening and hardening behavior of the CNTs near their primary and secondary resonances. The effects of the DC and AC voltage loads on the behavior have been studied. The impacts of the initial slack level and CNT diameter are also demonstrated.
Nonlinear robust hierarchical control for nonlinear uncertain systems
Directory of Open Access Journals (Sweden)
Leonessa Alexander
1999-01-01
Full Text Available A nonlinear robust control-system design framework predicated on a hierarchical switching controller architecture parameterized over a set of moving nominal system equilibria is developed. Specifically, using equilibria-dependent Lyapunov functions, a hierarchical nonlinear robust control strategy is developed that robustly stabilizes a given nonlinear system over a prescribed range of system uncertainty by robustly stabilizing a collection of nonlinear controlled uncertain subsystems. The robust switching nonlinear controller architecture is designed based on a generalized (lower semicontinuous Lyapunov function obtained by minimizing a potential function over a given switching set induced by the parameterized nominal system equilibria. The proposed framework robustly stabilizes a compact positively invariant set of a given nonlinear uncertain dynamical system with structured parametric uncertainty. Finally, the efficacy of the proposed approach is demonstrated on a jet engine propulsion control problem with uncertain pressure-flow map data.
Discrete nonlinear Schrodinger equations with arbitrarily high-order nonlinearities
DEFF Research Database (Denmark)
Khare, A.; Rasmussen, Kim Ø; Salerno, M.
2006-01-01
-Ladik equation. As a common property, these equations possess three kinds of exact analytical stationary solutions for which the Peierls-Nabarro barrier is zero. Several properties of these solutions, including stability, discrete breathers, and moving solutions, are investigated.......A class of discrete nonlinear Schrodinger equations with arbitrarily high-order nonlinearities is introduced. These equations are derived from the same Hamiltonian using different Poisson brackets and include as particular cases the saturable discrete nonlinear Schrodinger equation and the Ablowitz...
Diamond, Jared M.
1966-01-01
1. The relation between osmotic gradient and rate of osmotic water flow has been measured in rabbit gall-bladder by a gravimetric procedure and by a rapid method based on streaming potentials. Streaming potentials were directly proportional to gravimetrically measured water fluxes. 2. As in many other tissues, water flow was found to vary with gradient in a markedly non-linear fashion. There was no consistent relation between the water permeability and either the direction or the rate of water flow. 3. Water flow in response to a given gradient decreased at higher osmolarities. The resistance to water flow increased linearly with osmolarity over the range 186-825 m-osM. 4. The resistance to water flow was the same when the gall-bladder separated any two bathing solutions with the same average osmolarity, regardless of the magnitude of the gradient. In other words, the rate of water flow is given by the expression (Om — Os)/[Ro′ + ½k′ (Om + Os)], where Ro′ and k′ are constants and Om and Os are the bathing solution osmolarities. 5. Of the theories advanced to explain non-linear osmosis in other tissues, flow-induced membrane deformations, unstirred layers, asymmetrical series-membrane effects, and non-osmotic effects of solutes could not explain the results. However, experimental measurements of water permeability as a function of osmolarity permitted quantitative reconstruction of the observed water flow—osmotic gradient curves. Hence non-linear osmosis in rabbit gall-bladder is due to a decrease in water permeability with increasing osmolarity. 6. The results suggest that aqueous channels in the cell membrane behave as osmometers, shrinking in concentrated solutions of impermeant molecules and thereby increasing membrane resistance to water flow. A mathematical formulation of such a membrane structure is offered. PMID:5945254
Wu Zhuo Qun; Li Hui Lai; Zhao Jun Ning
2001-01-01
Nonlinear diffusion equations, an important class of parabolic equations, come from a variety of diffusion phenomena which appear widely in nature. They are suggested as mathematical models of physical problems in many fields, such as filtration, phase transition, biochemistry and dynamics of biological groups. In many cases, the equations possess degeneracy or singularity. The appearance of degeneracy or singularity makes the study more involved and challenging. Many new ideas and methods have been developed to overcome the special difficulties caused by the degeneracy and singularity, which
Bellman, Richard Ernest
1970-01-01
In this book, we study theoretical and practical aspects of computing methods for mathematical modelling of nonlinear systems. A number of computing techniques are considered, such as methods of operator approximation with any given accuracy; operator interpolation techniques including a non-Lagrange interpolation; methods of system representation subject to constraints associated with concepts of causality, memory and stationarity; methods of system representation with an accuracy that is the best within a given class of models; methods of covariance matrix estimation;methods for low-rank mat
Nonlinear optimal control theory
Berkovitz, Leonard David
2012-01-01
Nonlinear Optimal Control Theory presents a deep, wide-ranging introduction to the mathematical theory of the optimal control of processes governed by ordinary differential equations and certain types of differential equations with memory. Many examples illustrate the mathematical issues that need to be addressed when using optimal control techniques in diverse areas. Drawing on classroom-tested material from Purdue University and North Carolina State University, the book gives a unified account of bounded state problems governed by ordinary, integrodifferential, and delay systems. It also dis
DEFF Research Database (Denmark)
Mosekilde, Erik
Through a significant number of detailed and realistic examples this book illustrates how the insights gained over the past couple of decades in the fields of nonlinear dynamics and chaos theory can be applied in practice. Aomng the topics considered are microbiological reaction systems, ecological...... food-web systems, nephron pressure and flow regulation, pulsatile secretion of hormones, thermostatically controlled radiator systems, post-stall maneuvering of aircrafts, transfer electron devices for microwave generation, economic long waves, human decision making behavior, and pattern formation...... in chemical reaction-diffusion systems....
Nonlinear dynamics in psychology
Directory of Open Access Journals (Sweden)
Stephen J. Guastello
2001-01-01
Full Text Available This article provides a survey of the applications of nonlinear dynamical systems theory to substantive problems encountered in the full scope of psychological science. Applications are organized into three topical areas – cognitive science, social and organizational psychology, and personality and clinical psychology. Both theoretical and empirical studies are considered with an emphasis on works that capture the broadest scope of issues that are of substantive interest to psychological theory. A budding literature on the implications of NDS principles in professional practice is reported also.
DEFF Research Database (Denmark)
Jørgensen, Michael Finn
1995-01-01
It is generally very difficult to solve nonlinear systems, and such systems often possess chaotic solutions. In the rare event that a system is completely solvable, it is said to integrable. Such systems never have chaotic solutions. Using the Inverse Scattering Transform Method (ISTM) two...... particular configurations of the Discrete Self-Trapping (DST) system are shown to be completely solvable. One of these systems includes the Toda lattice in a certain limit. An explicit integration is carried through for this Near-Toda lattice. The Near-Toda lattice is then generalized to include singular...
Nonlinear surface electromagnetic phenomena
Ponath, H-E
1991-01-01
In recent years the physics of electromagnetic surface phenomena has developed rapidly, evolving into technologies for communications and industry, such as fiber and integrated optics. The variety of phenomena based on electromagnetism at surfaces is rich and this book was written with the aim of summarizing the available knowledge in selected areas of the field. The book contains reviews written by solid state and optical physicists on the nonlinear interaction of electromagnetic waves at and with surfaces and films. Both the physical phenomena and some potential applications are
Oscillators from nonlinear realizations
Kozyrev, N.; Krivonos, S.
2018-02-01
We construct the systems of the harmonic and Pais-Uhlenbeck oscillators, which are invariant with respect to arbitrary noncompact Lie algebras. The equations of motion of these systems can be obtained with the help of the formalism of nonlinear realizations. We prove that it is always possible to choose time and the fields within this formalism in such a way that the equations of motion become linear and, therefore, reduce to ones of ordinary harmonic and Pais-Uhlenbeck oscillators. The first-order actions, that produce these equations, can also be provided. As particular examples of this construction, we discuss the so(2, 3) and G 2(2) algebras.
Secondary Instability of Second Modes in Hypersonic Boundary Layers
Li, Fei; Choudhari, Meelan M.; Chang, Chau-Lyan; White, Jeffery A.
2012-01-01
Second mode disturbances dominate the primary instability stage of transition in a number of hypersonic flow configurations. The highest amplification rates of second mode disturbances are usually associated with 2D (or axisymmetric) perturbations and, therefore, a likely scenario for the onset of the three-dimensionality required for laminar-turbulent transition corresponds to the parametric amplification of 3D secondary instabilities in the presence of 2D, finite amplitude second mode disturbances. The secondary instability of second mode disturbances is studied for selected canonical flow configurations. The basic state for the secondary instability analysis is obtained by tracking the linear and nonlinear evolution of 2D, second mode disturbances using nonlinear parabolized stability equations. Unlike in previous studies, the selection of primary disturbances used for the secondary instability analysis was based on their potential relevance to transition in a low disturbance environment and the effects of nonlinearity on the evolution of primary disturbances was accounted for. Strongly nonlinear effects related to the self-interaction of second mode disturbances lead to an upstream shift in the upper branch neutral location. Secondary instability computations confirm the previously known dominance of subharmonic modes at relatively small primary amplitudes. However, for the Purdue Mach 6 compression cone configuration, it was shown that a strong fundamental secondary instability can exist for a range of initial amplitudes of the most amplified second mode disturbance, indicating that the exclusive focus on subharmonic modes in the previous applications of secondary instability theory to second mode primary instability may not have been fully justified.
Global Analysis of Nonlinear Dynamics
Luo, Albert
2012-01-01
Global Analysis of Nonlinear Dynamics collects chapters on recent developments in global analysis of non-linear dynamical systems with a particular emphasis on cell mapping methods developed by Professor C.S. Hsu of the University of California, Berkeley. This collection of contributions prepared by a diverse group of internationally recognized researchers is intended to stimulate interests in global analysis of complex and high-dimensional nonlinear dynamical systems, whose global properties are largely unexplored at this time. This book also: Presents recent developments in global analysis of non-linear dynamical systems Provides in-depth considerations and extensions of cell mapping methods Adopts an inclusive style accessible to non-specialists and graduate students Global Analysis of Nonlinear Dynamics is an ideal reference for the community of nonlinear dynamics in different disciplines including engineering, applied mathematics, meteorology, life science, computational science, and medicine.
Nonlinearity management in higher dimensions
International Nuclear Information System (INIS)
Kevrekidis, P G; Pelinovsky, D E; Stefanov, A
2006-01-01
In the present paper, we revisit nonlinearity management of the time-periodic nonlinear Schroedinger equation and the related averaging procedure. By means of rigorous estimates, we show that the averaged nonlinear Schroedinger equation does not blow up in the higher dimensional case so long as the corresponding solution remains smooth. In particular, we show that the H 1 norm remains bounded, in contrast with the usual blow-up mechanism for the focusing Schroedinger equation. This conclusion agrees with earlier works in the case of strong nonlinearity management but contradicts those in the case of weak nonlinearity management. The apparent discrepancy is explained by the divergence of the averaging procedure in the limit of weak nonlinearity management
Collapse of nonlinear Langmuir waves
International Nuclear Information System (INIS)
Malkin, V.M.
1986-01-01
The dispersion of sufficiently intensive Langmuir waves is determined by intrinsic (electron) nonlinearity. During Langmuir collapse the wave energy density required for the appearance of electron nonlinearity is attained, generally speaking, prior to the development of dissipative processes. Up to now, the effect of electron nonlinearity on the collapse dynamics and spectrum of strong Langmuir turbulence ( which may be very appreciable ) has not been studied extensively because of the difficulty of describing nonlinear Langmuir waves. In the present paper the positive determinacy of the electron nonlinear hamiltonian is proven, the increment of modulation instability of a nonlinear Langmuir wave cluster localized in a cavity is calculated, and the universal law of their collapse is found
Applications of nonlinear fiber optics
Agrawal, Govind
2008-01-01
* The only book describing applications of nonlinear fiber optics * Two new chapters on the latest developments: highly nonlinear fibers and quantum applications* Coverage of biomedical applications* Problems provided at the end of each chapterThe development of new highly nonlinear fibers - referred to as microstructured fibers, holey fibers and photonic crystal fibers - is the next generation technology for all-optical signal processing and biomedical applications. This new edition has been thoroughly updated to incorporate these key technology developments.The bo
Recent topics in nonlinear PDE
International Nuclear Information System (INIS)
Mimura, Masayasu; Nishida, Takaaki
1984-01-01
The meeting on the subject of nonlinear partial differential equations was held at Hiroshima University in February, 1983. Leading and active mathematicians were invited to talk on their current research interests in nonlinear pdes occuring in the areas of fluid dynamics, free boundary problems, population dynamics and mathematical physics. This volume contains the theory of nonlinear pdes and the related topics which have been recently developed in Japan. (Auth.)
Perspectives of nonlinear dynamics
International Nuclear Information System (INIS)
Jackson, E.A.
1985-03-01
Four lectures were given weekly in October and November, 1984, and some of the ideas presented here will be of use in the future. First, a brief survey of the historical development of nonlinear dynamics since about 1890 was given, and then, a few topics were discussed in detail. The objective was to introduce some of many concepts and methods which are presently used for describing nonlinear dynamics. The symbiotic relationship between sciences of all types and mathematics, two main categories of the models describing nature, the method for describing the dynamics of a system, the idea of control parameters and topological dimension, the asymptotic properties of dynamics, abstract dynamics, the concept of embedding, singular perturbation theory, strange attractor, Fermi-Pasta-Ulam phenomena, an example of computer heuristics, the idea of elementary catastrophe theory and so on were explained. The logistic map is the simplest introduction to complex dynamics. The complicated dynamics is referred to as strange attractors. Two-dimensional maps are the highest dimensional maps commonly studied. These were discussed in detail. (Kako, I.)
Nonlinearities in Behavioral Macroeconomics.
Gomes, Orlando
2017-07-01
This article undertakes a journey across the literature on behavioral macroeconomics, with attention concentrated on the nonlinearities that the behavioral approach typically suggests or implies. The emphasis is placed on thinking the macro economy as a living organism, composed of many interacting parts, each one having a will of its own, which is in sharp contrast with the mechanism of the orthodox view (well represented by the neoclassical or new Keynesian dynamic stochastic general equilibrium - DSGE - model). The paper advocates that a thorough understanding of individual behavior in collective contexts is the only possible avenue to further explore macroeconomic phenomena and the often observed 'anomalies' that the benchmark DSGE macro framework is unable to explain or justify. After a reflection on the role of behavioral traits as a fundamental component of a new way of thinking the economy, the article proceeds with a debate on some of the most relevant frameworks in the literature that somehow link macro behavior and nonlinearities; covered subjects include macro models with disequilibrium rules, agent-based models that highlight interaction and complexity, evolutionary switching frameworks, and inattention based decision problems. These subjects have, as a fundamental point in common, the use of behavioral elements to transform existing interpretations of the economic reality, making it more evident how irregular fluctuations emerge and unfold on the aggregate.
Nonlinear Waves in Complex Systems
DEFF Research Database (Denmark)
2007-01-01
The study of nonlinear waves has exploded due to the combination of analysis and computations, since the discovery of the famous recurrence phenomenon on a chain of nonlinearly coupled oscillators by Fermi-Pasta-Ulam fifty years ago. More than the discovery of new integrable equations, it is the ......The study of nonlinear waves has exploded due to the combination of analysis and computations, since the discovery of the famous recurrence phenomenon on a chain of nonlinearly coupled oscillators by Fermi-Pasta-Ulam fifty years ago. More than the discovery of new integrable equations...
Problems in nonlinear resistive MHD
International Nuclear Information System (INIS)
Turnbull, A.D.; Strait, E.J.; La Haye, R.J.; Chu, M.S.; Miller, R.L.
1998-01-01
Two experimentally relevant problems can relatively easily be tackled by nonlinear MHD codes. Both problems require plasma rotation in addition to the nonlinear mode coupling and full geometry already incorporated into the codes, but no additional physics seems to be crucial. These problems discussed here are: (1) nonlinear coupling and interaction of multiple MHD modes near the B limit and (2) nonlinear coupling of the m/n = 1/1 sawtooth mode with higher n gongs and development of seed islands outside q = 1
Nonlinear Response of Strong Nonlinear System Arisen in Polymer Cushion
Directory of Open Access Journals (Sweden)
Jun Wang
2013-01-01
Full Text Available A dynamic model is proposed for a polymer foam-based nonlinear cushioning system. An accurate analytical solution for the nonlinear free vibration of the system is derived by applying He's variational iteration method, and conditions for resonance are obtained, which should be avoided in the cushioning design.
Numerical study of jets secondary instabilities
International Nuclear Information System (INIS)
Brancher, Pierre
1996-01-01
The work presented in this dissertation is a contribution to the study of the transition to turbulence in open shear flows. Results from direct numerical simulations are interpreted within the framework of hydrodynamic stability theory. The first chapter is an introduction to the primary and secondary instabilities observed in jets and mixing layers. The numerical method used in the present study is detailed in the second chapter. The dynamics of homogeneous circular jets subjected to stream wise and azimuthal perturbations are investigated in the third chapter. A complete scenario describing the evolution of the jet is proposed with emphasis on the dynamics of vorticity within the flow. In the fourth chapter a parametric study reveals a three-dimensional secondary instability mainly controlled in the linear regime by the Strouhal number of the primary instability. In the nonlinear regime the dynamics of the azimuthal harmonies are described by means of model equations and are linked to the formation of stream wise vortices in the braid. The fifth chapter is dedicated to the convective or absolute nature of the secondary instabilities in plane shear layers. It is shown that there are flow configurations for which the two-dimensional secondary instability (pairing) is absolute even though the primary instability (Kelvin-Helmholtz) is convective. Some preliminary results concerning the three-dimensional secondary instabilities arc presented at the end of this chapter. The last chapter summarizes the main results and examines possible extensions of this work. (author) [fr
SECONDARY OSTEOARTHRITIS IN RHEUMATOID ARTHRITIS
Directory of Open Access Journals (Sweden)
I. A. Starodubtseva
2015-01-01
Full Text Available The paper considers the problems of comorbidities in patients with rheumatoid arthritis (RA. Two or more RA-related conditions were diagnosed according to the results of the QUEST-RA program implemented in 34 countries. Osteoarthritis along with hypertension, hyperlipidemia, and osteoporosis was detected among the most commonly diseases. Owing to expanded diagnostic capabilities, the recognition and treatment of the comorbidities have recently received much attention, as embodied in the draft Association of Rheumatologists of Russia Guidelines for RA management (2014; Part 1. The concept and major characteristics of secondary osteoarthritis in RA are analyzed. It is precisely the inflammatory process and underlying disease-related risk factors, including treatment, that have impact on the development of secondary osteoarthritis and patients’ quality of life as a whole. All this allows an inference about the mechanisms closely intertwined with the underlying disease for the development of secondary osteoarthritis, which initiates cartilage damage and further remodeling. Primary and secondary osteoarthritis was comparatively analyzed. Particular emphasis is placed on current cartilage biomarkers, their diagnostic value and role in monitoring the efficiency of treatment in clinical trials. The paper provides a comparative analysis of detectable serum and urine biomarkers according to the results of the complex analysis made by the National Institutes of Health. Particular attention is given to cartilage oligomeric matrix protein (COMP. Foreign authors’ investigations suggest that there is a relationship between serum COMP levels and disease severity and joint X-ray changes. There is evidence for the efficacy of hyaluronic acid used in the treatment of secondary osteoarthritis in patients with RA.
CFD modeling of secondary flows in fuel rod bundles
International Nuclear Information System (INIS)
Baglietto, Emilio; Ninokata, Hisashi
2004-01-01
An optimized non-linear eddy viscosity model is introduced, for calculations of detailed coolant velocity distribution in a tight lattice fuel bundle. The low Reynolds formulation has been optimized based on DNS data for channel flow. The non-linear stress-strain relationship has been modified in the coefficients to model the flow anisotropy, which causes the formation of turbulence driven secondary flows inside the bundle subchannels. Predictions of the model are first compared to experimental measurements of secondary flows in a triangularly arrayed rod bundle with p/d=1.3. Subsequently wall shear stress and velocity predictions are compared with different experimental data for a rod bundle with p/d=1.17. The model shows to be able to correctly reproduce the scale of the secondary motion, and to accurately reproduce both wall shear stress and velocity distributions inside the rod bundle subchannels. (author)
Design and implementation of a sensitive high-resolution nonlinear spectral imaging microscope
Palero, Jonathan A.; Latouche, Gwendal; de Bruijn, Henriëtte S.; van der Ploeg van den Heuvel, Angélique; Sterenborg, Henricus J. C. M.; Gerritsen, Hans C.
2008-01-01
Live tissue nonlinear microscopy based on multiphoton autofluorescence and second harmonic emission originating from endogenous fluorophores and noncentrosymmetric-structured proteins is rapidly gaining interest in biomedical applications. The advantage of this technique includes high imaging
Perspectives on Nonlinear Filtering
Law, Kody
2015-01-01
The solution to the problem of nonlinear filtering may be given either as an estimate of the signal (and ideally some measure of concentration), or as a full posterior distribution. Similarly, one may evaluate the fidelity of the filter either by its ability to track the signal or its proximity to the posterior filtering distribution. Hence, the field enjoys a lively symbiosis between probability and control theory, and there are plenty of applications which benefit from algorithmic advances, from signal processing, to econometrics, to large-scale ocean, atmosphere, and climate modeling. This talk will survey some recent theoretical results involving accurate signal tracking with noise-free (degenerate) dynamics in high-dimensions (infinite, in principle, but say d between 103 and 108 , depending on the size of your application and your computer), and high-fidelity approximations of the filtering distribution in low dimensions (say d between 1 and several 10s).
Nonlinear Photonic Crystal Fibers
DEFF Research Database (Denmark)
Hansen, Kim Per
2004-01-01
Despite the general recession in the global economy and the collapse of the optical telecommunication market, research within specialty fibers is thriving. This is, more than anything else, due to the technology transition from standard all-glass fibers to photonic crystal fibers, which, instead....... The freedom to design the dispersion profile of the fibers is much larger and it is possible to create fibers, which support only a single spatial mode, regardless of wavelength. In comparison, the standard dispersion-shifted fibers are limited by a much lower index-contrast between the core and the cladding...... in 1996, and are today on their way to become the dominating technology within the specialty fiber field. Whether they will replace the standard fiber in the more traditional areas like telecommunication transmission, is not yet clear, but the nonlinear photonic crystal fibers are here to stay....
Nonlinear estimation and classification
Hansen, Mark; Holmes, Christopher; Mallick, Bani; Yu, Bin
2003-01-01
Researchers in many disciplines face the formidable task of analyzing massive amounts of high-dimensional and highly-structured data This is due in part to recent advances in data collection and computing technologies As a result, fundamental statistical research is being undertaken in a variety of different fields Driven by the complexity of these new problems, and fueled by the explosion of available computer power, highly adaptive, non-linear procedures are now essential components of modern "data analysis," a term that we liberally interpret to include speech and pattern recognition, classification, data compression and signal processing The development of new, flexible methods combines advances from many sources, including approximation theory, numerical analysis, machine learning, signal processing and statistics The proposed workshop intends to bring together eminent experts from these fields in order to exchange ideas and forge directions for the future
2016-01-01
This volume brings together four lecture courses on modern aspects of water waves. The intention, through the lectures, is to present quite a range of mathematical ideas, primarily to show what is possible and what, currently, is of particular interest. Water waves of large amplitude can only be fully understood in terms of nonlinear effects, linear theory being not adequate for their description. Taking advantage of insights from physical observation, experimental evidence and numerical simulations, classical and modern mathematical approaches can be used to gain insight into their dynamics. The book presents several avenues and offers a wide range of material of current interest. Due to the interdisciplinary nature of the subject, the book should be of interest to mathematicians (pure and applied), physicists and engineers. The lectures provide a useful source for those who want to begin to investigate how mathematics can be used to improve our understanding of water wave phenomena. In addition, some of the...
Perspectives on Nonlinear Filtering
Law, Kody
2015-01-07
The solution to the problem of nonlinear filtering may be given either as an estimate of the signal (and ideally some measure of concentration), or as a full posterior distribution. Similarly, one may evaluate the fidelity of the filter either by its ability to track the signal or its proximity to the posterior filtering distribution. Hence, the field enjoys a lively symbiosis between probability and control theory, and there are plenty of applications which benefit from algorithmic advances, from signal processing, to econometrics, to large-scale ocean, atmosphere, and climate modeling. This talk will survey some recent theoretical results involving accurate signal tracking with noise-free (degenerate) dynamics in high-dimensions (infinite, in principle, but say d between 103 and 108 , depending on the size of your application and your computer), and high-fidelity approximations of the filtering distribution in low dimensions (say d between 1 and several 10s).
Solitons and protein folding: An In Silico experiment
International Nuclear Information System (INIS)
Ilieva, N.; Dai, J.; Sieradzan, A.; Niemi, A.
2015-01-01
Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics
Solitons and protein folding: An In Silico experiment
Energy Technology Data Exchange (ETDEWEB)
Ilieva, N., E-mail: nevena.ilieva@parallel.bas.bg [Institute of Information and Communication Technologies, Bulgarian Aacademy of Sciences, Sofia (Bulgaria); Dai, J., E-mail: daijing491@gmail.com [School of Physics, Beijing Institute of Technology, Beijing (China); Sieradzan, A., E-mail: adams86@wp.pl [Faculty of Chemistry, University of Gdańsk, Gdańsk (Poland); Niemi, A., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, Uppsala (Sweden); LMPT–CNRS, Université de Tours, Tours (France)
2015-10-28
Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.
Wave transmission in nonlinear lattices
International Nuclear Information System (INIS)
Hennig, D.; Tsironis, G.P.
1999-01-01
The interplay of nonlinearity with lattice discreteness leads to phenomena and propagation properties quite distinct from those appearing in continuous nonlinear systems. For a large variety of condensed matter and optics applications the continuous wave approximation is not appropriate. In the present review we discuss wave transmission properties in one dimensional nonlinear lattices. Our paradigmatic equations are discrete nonlinear Schroedinger equations and their study is done through a dynamical systems approach. We focus on stationary wave properties and utilize well known results from the theory of dynamical systems to investigate various aspects of wave transmission and wave localization. We analyze in detail the more general dynamical system corresponding to the equation that interpolates between the non-integrable discrete nonlinear Schroedinger equation and the integrable Albowitz-Ladik equation. We utilize this analysis in a nonlinear Kronig-Penney model and investigate transmission and band modification properties. We discuss the modifications that are effected through an electric field and the nonlinear Wannier-Stark localization effects that are induced. Several applications are described, such as polarons in one dimensional lattices, semiconductor superlattices and one dimensional nonlinear photonic band gap systems. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)
Solving Nonlinear Coupled Differential Equations
Mitchell, L.; David, J.
1986-01-01
Harmonic balance method developed to obtain approximate steady-state solutions for nonlinear coupled ordinary differential equations. Method usable with transfer matrices commonly used to analyze shaft systems. Solution to nonlinear equation, with periodic forcing function represented as sum of series similar to Fourier series but with form of terms suggested by equation itself.
Nonlinear Elasticity of Doped Semiconductors
2017-02-01
AFRL-RY-WP-TR-2016-0206 NONLINEAR ELASTICITY OF DOPED SEMICONDUCTORS Mark Dykman and Kirill Moskovtsev Michigan State University...2016 4. TITLE AND SUBTITLE NONLINEAR ELASTICITY OF DOPED SEMICONDUCTORS 5a. CONTRACT NUMBER FA8650-16-1-7600 5b. GRANT NUMBER 5c. PROGRAM...vibration amplitude. 15. SUBJECT TERMS semiconductors , microresonators, microelectromechanical 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF
Nonlinear evolution of MHD instabilities
International Nuclear Information System (INIS)
Bateman, G.; Hicks, H.R.; Wooten, J.W.; Dory, R.A.
1975-01-01
A 3-D nonlinear MHD computer code was used to study the time evolution of internal instabilities. Velocity vortex cells are observed to persist into the nonlinear evolution. Pressure and density profiles convect around these cells for a weak localized instability, or convect into the wall for a strong instability. (U.S.)
Nonlinear theory of elastic shells
International Nuclear Information System (INIS)
Costa Junior, J.A.
1979-08-01
Nonlinear theory of elastic shells is developed which incorporates both geometric and physical nonlinearities and which does not make use of the well known Love-Kirchhoff hypothesis. The resulting equations are formulated in tensorial notation and are reduced to the ones of common use when simplifying assumptions encountered in the especific litterature are taken. (Author) [pt
Balancing for Unstable Nonlinear Systems
Scherpen, J.M.A.
1993-01-01
A previously obtained method of balancing for stable nonlinear systems is extended to unstable nonlinear systems. The similarity invariants obtained by the concept of LQG balancing for an unstable linear system can also be obtained by considering a past and future energy function of the system. By
The enrichment secondary market
International Nuclear Information System (INIS)
Einbund, D.R.
1986-01-01
This paper will addresses two topics: the background to the present status of the enrichment secondary market and the future outlook of the secondary market in enrichment services, and the viability of the nuclear fuel brokerage industry. These two topics are inevitably connected, as most secondary market activity, not only in enrichment but also in natural uranium, has traditionally been conducted with the participation of brokers. Therefore, the author interrelates these topics
Nonlinear hyperbolic waves in multidimensions
Prasad, Phoolan
2001-01-01
The propagation of curved, nonlinear wavefronts and shock fronts are very complex phenomena. Since the 1993 publication of his work Propagation of a Curved Shock and Nonlinear Ray Theory, author Phoolan Prasad and his research group have made significant advances in the underlying theory of these phenomena. This volume presents their results and provides a self-contained account and gradual development of mathematical methods for studying successive positions of these fronts.Nonlinear Hyperbolic Waves in Multidimensions includes all introductory material on nonlinear hyperbolic waves and the theory of shock waves. The author derives the ray theory for a nonlinear wavefront, discusses kink phenomena, and develops a new theory for plane and curved shock propagation. He also derives a full set of conservation laws for a front propagating in two space dimensions, and uses these laws to obtain successive positions of a front with kinks. The treatment includes examples of the theory applied to converging wavefronts...
Cubication of conservative nonlinear oscillators
International Nuclear Information System (INIS)
Belendez, Augusto; Alvarez, Mariela L; Fernandez, Elena; Pascual, Inmaculada
2009-01-01
A cubication procedure of the nonlinear differential equation for conservative nonlinear oscillators is analysed and discussed. This scheme is based on the Chebyshev series expansion of the restoring force, and this allows us to approximate the original nonlinear differential equation by a Duffing equation in which the coefficients for the linear and cubic terms depend on the initial amplitude, A, while in a Taylor expansion of the restoring force these coefficients are independent of A. The replacement of the original nonlinear equation by an approximate Duffing equation allows us to obtain an approximate frequency-amplitude relation as a function of the complete elliptic integral of the first kind. Some conservative nonlinear oscillators are analysed to illustrate the usefulness and effectiveness of this scheme.
Quantitative secondary electron detection
Agrawal, Jyoti; Joy, David C.; Nayak, Subuhadarshi
2018-05-08
Quantitative Secondary Electron Detection (QSED) using the array of solid state devices (SSD) based electron-counters enable critical dimension metrology measurements in materials such as semiconductors, nanomaterials, and biological samples (FIG. 3). Methods and devices effect a quantitative detection of secondary electrons with the array of solid state detectors comprising a number of solid state detectors. An array senses the number of secondary electrons with a plurality of solid state detectors, counting the number of secondary electrons with a time to digital converter circuit in counter mode.
International Nuclear Information System (INIS)
Miyoshi, Takahiro; Becchaku, Masahiro; Kusano, Kanya
2008-01-01
Nonlinear dynamics of the resistive tearing instability in high magnetic Reynolds number (R m ) plasmas is studied by newly developing an accurate and robust resistive magnetohydrodynamic (MHD) scheme. The results show that reconnection processes strongly depend on R m . Particularly, in a high R m case, small-scale plasmoids induced by a secondary instability are intermittently generated and ejected accompanied by fast shocks. According to the intermittent processes, the reconnection rate increases intermittently at a later nonlinear stage. (author)
Nonlinear Ritz approximation for Fredholm functionals
Directory of Open Access Journals (Sweden)
Mudhir A. Abdul Hussain
2015-11-01
Full Text Available In this article we use the modify Lyapunov-Schmidt reduction to find nonlinear Ritz approximation for a Fredholm functional. This functional corresponds to a nonlinear Fredholm operator defined by a nonlinear fourth-order differential equation.
Breatherlike impurity modes in discrete nonlinear lattices
DEFF Research Database (Denmark)
Hennig, D.; Rasmussen, Kim; Tsironis, G. P.
1995-01-01
We investigate the properties of a disordered generalized discrete nonlinear Schrodinger equation, containing both diagonal and nondiagonal nonlinear terms. The equation models a Linear host lattice doped with nonlinear impurities. We find different types of impurity states that form itinerant...
Spatial solitons in nonlinear photonic crystals
DEFF Research Database (Denmark)
Corney, Joel Frederick; Bang, Ole
2000-01-01
We study solitons in one-dimensional quadratic nonlinear photonic crystals with periodic linear and nonlinear susceptibilities. We show that such crystals support stable bright and dark solitons, even when the effective quadratic nonlinearity is zero.......We study solitons in one-dimensional quadratic nonlinear photonic crystals with periodic linear and nonlinear susceptibilities. We show that such crystals support stable bright and dark solitons, even when the effective quadratic nonlinearity is zero....
International Nuclear Information System (INIS)
Rozenshtraukh, L.C.; Rybakova, N.I.; Vinner, M.G.
1987-01-01
Pathological changes, promoting the development of secondary pneumonias, are investigated. To this group belong: blood circulation disturbance in small circle, bronchial passability disturbance, aspiration of liquids, gases and vapors, infections and purulent processes, intoxications, injuries, operative interference. Roetgenologic symptomatics of each secondary acute pneumonia form is presented in detail
LDRD report nonlinear model reduction
Energy Technology Data Exchange (ETDEWEB)
Segalman, D.; Heinstein, M.
1997-09-01
The very general problem of model reduction of nonlinear systems was made tractable by focusing on the very large subclass consisting of linear subsystems connected by nonlinear interfaces. Such problems constitute a large part of the nonlinear structural problems encountered in addressing the Sandia missions. A synthesis approach to this class of problems was developed consisting of: detailed modeling of the interface mechanics; collapsing the interface simulation results into simple nonlinear interface models; constructing system models by assembling model approximations of the linear subsystems and the nonlinear interface models. These system models, though nonlinear, would have very few degrees of freedom. A paradigm problem, that of machine tool vibration, was selected for application of the reduction approach outlined above. Research results achieved along the way as well as the overall modeling of a specific machine tool have been very encouraging. In order to confirm the interface models resulting from simulation, it was necessary to develop techniques to deduce interface mechanics from experimental data collected from the overall nonlinear structure. A program to develop such techniques was also pursued with good success.
International Nuclear Information System (INIS)
Kaw, P.K.; Singh, R.; Weiland, J.G.
2001-01-01
Analytical investigations of several linear and nonlinear features of ETG turbulence are reported. The linear theory includes effects such as finite beta induced electromagnetic shielding, coupling to electron magnetohydrodynamic modes like whistlers etc. It is argued that nonlinearly, turbulence and transport are dominated by radially extended modes called 'streamers'. A nonlinear mechanism generating streamers based on a modulational instability theory of the ETG turbulence is also presented. The saturation levels of the streamers using a Kelvin Helmholtz secondary instability mechanism are calculated and levels of the electron thermal transport due to streamers are estimated. (author)
Secondary fuel delivery system
Parker, David M.; Cai, Weidong; Garan, Daniel W.; Harris, Arthur J.
2010-02-23
A secondary fuel delivery system for delivering a secondary stream of fuel and/or diluent to a secondary combustion zone located in the transition piece of a combustion engine, downstream of the engine primary combustion region is disclosed. The system includes a manifold formed integral to, and surrounding a portion of, the transition piece, a manifold inlet port, and a collection of injection nozzles. A flowsleeve augments fuel/diluent flow velocity and improves the system cooling effectiveness. Passive cooling elements, including effusion cooling holes located within the transition boundary and thermal-stress-dissipating gaps that resist thermal stress accumulation, provide supplemental heat dissipation in key areas. The system delivers a secondary fuel/diluent mixture to a secondary combustion zone located along the length of the transition piece, while reducing the impact of elevated vibration levels found within the transition piece and avoiding the heat dissipation difficulties often associated with traditional vibration reduction methods.
Secondary and tertiary hyperparathyroidism.
Jamal, Sophie A; Miller, Paul D
2013-01-01
We reviewed the etiology and management of secondary and tertiary hyperparathyroidism. Secondary hyperparathyroidism is characterized by an increase in parathyroid hormone (PTH) that is appropriate and in response to a stimulus, most commonly low serum calcium. In secondary hyperparathyroidism, the serum calcium is normal and the PTH level is elevated. Tertiary hyperparathyroidism is characterized by excessive secretion of PTH after longstanding secondary hyperparathyroidism, in which hypercalcemia has ensued. Tertiary hyperparathyroidism typically occurs in men and women with chronic kidney disease usually after kidney transplant. The etiology and treatment of secondary hyperparathyroidism is relatively straightforward whereas data on the management of tertiary hyperparathyroidism is limited to a few small trials with short follow-up. Copyright © 2013 The International Society for Clinical Densitometry. Published by Elsevier Inc. All rights reserved.
Nonlinear time heteronymous damping in nonlinear parametric planetary systems
Czech Academy of Sciences Publication Activity Database
Hortel, Milan; Škuderová, Alena
2014-01-01
Roč. 225, č. 7 (2014), s. 2059-2073 ISSN 0001-5970 Institutional support: RVO:61388998 Keywords : nonlinear dynamics * planetary systems * heteronymous damping Subject RIV: JT - Propulsion, Motors ; Fuels Impact factor: 1.465, year: 2014
Prediction of Protein Thermostability by an Efficient Neural Network Approach
Directory of Open Access Journals (Sweden)
Jalal Rezaeenour
2016-10-01
Full Text Available Introduction: Manipulation of protein stability is important for understanding the principles that govern protein thermostability, both in basic research and industrial applications. Various data mining techniques exist for prediction of thermostable proteins. Furthermore, ANN methods have attracted significant attention for prediction of thermostability, because they constitute an appropriate approach to mapping the non-linear input-output relationships and massive parallel computing. Method: An Extreme Learning Machine (ELM was applied to estimate thermal behavior of 1289 proteins. In the proposed algorithm, the parameters of ELM were optimized using a Genetic Algorithm (GA, which tuned a set of input variables, hidden layer biases, and input weights, to and enhance the prediction performance. The method was executed on a set of amino acids, yielding a total of 613 protein features. A number of feature selection algorithms were used to build subsets of the features. A total of 1289 protein samples and 613 protein features were calculated from UniProt database to understand features contributing to the enzymes’ thermostability and find out the main features that influence this valuable characteristic. Results:At the primary structure level, Gln, Glu and polar were the features that mostly contributed to protein thermostability. At the secondary structure level, Helix_S, Coil, and charged_Coil were the most important features affecting protein thermostability. These results suggest that the thermostability of proteins is mainly associated with primary structural features of the protein. According to the results, the influence of primary structure on the thermostabilty of a protein was more important than that of the secondary structure. It is shown that prediction accuracy of ELM (mean square error can improve dramatically using GA with error rates RMSE=0.004 and MAPE=0.1003. Conclusion: The proposed approach for forecasting problem
Design with Nonlinear Constraints
Tang, Chengcheng
2015-12-10
Most modern industrial and architectural designs need to satisfy the requirements of their targeted performance and respect the limitations of available fabrication technologies. At the same time, they should reflect the artistic considerations and personal taste of the designers, which cannot be simply formulated as optimization goals with single best solutions. This thesis aims at a general, flexible yet e cient computational framework for interactive creation, exploration and discovery of serviceable, constructible, and stylish designs. By formulating nonlinear engineering considerations as linear or quadratic expressions by introducing auxiliary variables, the constrained space could be e ciently accessed by the proposed algorithm Guided Projection, with the guidance of aesthetic formulations. The approach is introduced through applications in different scenarios, its effectiveness is demonstrated by examples that were difficult or even impossible to be computationally designed before. The first application is the design of meshes under both geometric and static constraints, including self-supporting polyhedral meshes that are not height fields. Then, with a formulation bridging mesh based and spline based representations, the application is extended to developable surfaces including origami with curved creases. Finally, general approaches to extend hard constraints and soft energies are discussed, followed by a concluding remark outlooking possible future studies.
Deimling, Klaus
1985-01-01
topics. However, only a modest preliminary knowledge is needed. In the first chapter, where we introduce an important topological concept, the so-called topological degree for continuous maps from subsets ofRn into Rn, you need not know anything about functional analysis. Starting with Chapter 2, where infinite dimensions first appear, one should be familiar with the essential step of consider ing a sequence or a function of some sort as a point in the corresponding vector space of all such sequences or functions, whenever this abstraction is worthwhile. One should also work out the things which are proved in § 7 and accept certain basic principles of linear functional analysis quoted there for easier references, until they are applied in later chapters. In other words, even the 'completely linear' sections which we have included for your convenience serve only as a vehicle for progress in nonlinearity. Another point that makes the text introductory is the use of an essentially uniform mathematical languag...
Scalable Nonlinear Compact Schemes
Energy Technology Data Exchange (ETDEWEB)
Ghosh, Debojyoti [Argonne National Lab. (ANL), Argonne, IL (United States); Constantinescu, Emil M. [Univ. of Chicago, IL (United States); Brown, Jed [Univ. of Colorado, Boulder, CO (United States)
2014-04-01
In this work, we focus on compact schemes resulting in tridiagonal systems of equations, specifically the fifth-order CRWENO scheme. We propose a scalable implementation of the nonlinear compact schemes by implementing a parallel tridiagonal solver based on the partitioning/substructuring approach. We use an iterative solver for the reduced system of equations; however, we solve this system to machine zero accuracy to ensure that no parallelization errors are introduced. It is possible to achieve machine-zero convergence with few iterations because of the diagonal dominance of the system. The number of iterations is specified a priori instead of a norm-based exit criterion, and collective communications are avoided. The overall algorithm thus involves only point-to-point communication between neighboring processors. Our implementation of the tridiagonal solver differs from and avoids the drawbacks of past efforts in the following ways: it introduces no parallelization-related approximations (multiprocessor solutions are exactly identical to uniprocessor ones), it involves minimal communication, the mathematical complexity is similar to that of the Thomas algorithm on a single processor, and it does not require any communication and computation scheduling.
Acoustic-gravity nonlinear structures
Directory of Open Access Journals (Sweden)
D. Jovanović
2002-01-01
Full Text Available A catalogue of nonlinear vortex structures associated with acoustic-gravity perturbations in the Earth's atmosphere is presented. Besides the previously known Kelvin-Stewart cat's eyes, dipolar and tripolar structures, new solutions having the form of a row of counter-rotating vortices, and several weakly two-dimensional vortex chains are given. The existence conditions for these nonlinear structures are discussed with respect to the presence of inhomogeneities of the shear flows. The mode-coupling mechanism for the nonlinear generation of shear flows in the presence of linearly unstable acoustic-gravity waves, possibly also leading to intermittency and chaos, is presented.
Nonlinear Dynamic Phenomena in Mechanics
Warminski, Jerzy; Cartmell, Matthew P
2012-01-01
Nonlinear phenomena should play a crucial role in the design and control of engineering systems and structures as they can drastically change the prevailing dynamical responses. This book covers theoretical and applications-based problems of nonlinear dynamics concerned with both discrete and continuous systems of interest in civil and mechanical engineering. They include pendulum-like systems, slender footbridges, shape memory alloys, sagged elastic cables and non-smooth problems. Pendulums can be used as a dynamic absorber mounted in high buildings, bridges or chimneys. Geometrical nonlinear
Saravanan, R
2018-01-01
Non-linear optical materials have widespread and promising applications, but the efforts to understand the local structure, electron density distribution and bonding is still lacking. The present work explores the structural details, the electron density distribution and the local bond length distribution of some non-linear optical materials. It also gives estimation of the optical band gap, the particle size, crystallite size, and the elemental composition from UV-Visible analysis, SEM, XRD and EDS of some non-linear optical materials respectively.
Nonlinear modulation of ionization waves
International Nuclear Information System (INIS)
Bekki, Naoaki
1981-01-01
In order to investigate the nonlinear characteristics of ionization waves (moving-striations) in the positive column of glow discharge, a nonlinear modulation of ionization waves in the region of the Pupp critical current is analysed by means of the reductive perturbation method. The modulation of ionization waves is described by a nonlinear Schroedinger type equation. The coefficients of the equation are evaluated using the data of the low pressure Argon-discharge, and the simple solutions (plane wave and envelope soliton type solutions) are presented. Under a certain condition an envelope soliton is propagated through the positive column. (author)
Single-shot measurement of nonlinear absorption and nonlinear refraction.
Jayabalan, J; Singh, Asha; Oak, Shrikant M
2006-06-01
A single-shot method for measurement of nonlinear optical absorption and refraction is described and analyzed. A spatial intensity variation of an elliptical Gaussian beam in conjugation with an array detector is the key element of this method. The advantages of this single-shot technique were demonstrated by measuring the two-photon absorption and free-carrier absorption in GaAs as well as the nonlinear refractive index of CS2 using a modified optical Kerr setup.
Cyanobacteria as Cell Factories to Produce Plant Secondary Metabolites
Xue, Yong; He, Qingfang
2015-01-01
Cyanobacteria represent a promising platform for the production of plant secondary metabolites. Their capacity to express plant P450 proteins, which have essential functions in the biosynthesis of many plant secondary metabolites, makes cyanobacteria ideal for this purpose, and their photosynthetic capability allows cyanobacteria to grow with simple nutrient inputs. This review summarizes the advantages of using cyanobacteria to transgenically produce plant secondary metabolites. Some techniq...
Nonlinear optics principles and applications
Li, Chunfei
2017-01-01
This book reflects the latest advances in nonlinear optics. Besides the simple, strict mathematical deduction, it also discusses the experimental verification and possible future applications, such as the all-optical switches. It consistently uses the practical unit system throughout. It employs simple physical images, such as "light waves" and "photons" to systematically explain the main principles of nonlinear optical effects. It uses the first-order nonlinear wave equation in frequency domain under the condition of “slowly varying amplitude approximation" and the classical model of the interaction between the light and electric dipole. At the same time, it also uses the rate equations based on the energy-level transition of particle systems excited by photons and the energy and momentum conservation principles to explain the nonlinear optical phenomenon. The book is intended for researchers, engineers and graduate students in the field of the optics, optoelectronics, fiber communication, information tech...
Nonlinear Dynamics in Spear Wigglers
International Nuclear Information System (INIS)
2002-01-01
BL11, the most recently installed wiggler in the SPEAR storage ring at SSRL, produces a large nonlinear perturbation of the electron beam dynamics, which was not directly evident in the integrated magnetic field measurements. Measurements of tune shifts with betatron oscillation amplitude and with closed orbit shifts were used to characterize the nonlinear fields of the SPEAR insertion devices (IDs). Because of the narrow pole width in BL11, the nonlinear fields seen along the wiggling electron trajectory are dramatically different than the flip coil measurements made along a straight line. This difference explains the tune shift measurements and the observed degradation in dynamic aperture. Corrector magnets to cancel the BL11 nonlinear fields are presently under construction
Device Applications of Nonlinear Dynamics
Baglio, Salvatore
2006-01-01
This edited book is devoted specifically to the applications of complex nonlinear dynamic phenomena to real systems and device applications. While in the past decades there has been significant progress in the theory of nonlinear phenomena under an assortment of system boundary conditions and preparations, there exist comparatively few devices that actually take this rich behavior into account. "Device Applications of Nonlinear Dynamics" applies and exploits this knowledge to make devices which operate more efficiently and cheaply, while affording the promise of much better performance. Given the current explosion of ideas in areas as diverse as molecular motors, nonlinear filtering theory, noise-enhanced propagation, stochastic resonance and networked systems, the time is right to integrate the progress of complex systems research into real devices.
Nonlinear programming analysis and methods
Avriel, Mordecai
2012-01-01
This text provides an excellent bridge between principal theories and concepts and their practical implementation. Topics include convex programming, duality, generalized convexity, analysis of selected nonlinear programs, techniques for numerical solutions, and unconstrained optimization methods.
Indian Academy of Sciences (India)
Home; Journals; Pramana – Journal of Physics; Volume 64; Issue 3 ... Keywords. Nonlinear dynamics; logistic map; -deformation; Tsallis statistics. ... As a specific example, a -deformation procedure is applied to the logistic map. Compared ...
Born-Infeld Nonlinear Electrodynamics
International Nuclear Information System (INIS)
Bialynicki-Birula, I.
1999-01-01
This is only a summary of a lecture delivered at the Infeld Centennial Meeting. In the lecture the history of the Born-Infeld nonlinear electrodynamics was presented and some general features of the theory were discussed. (author)
Nonlinear compression of optical solitons
Indian Academy of Sciences (India)
linear pulse propagation is the nonlinear Schrödinger (NLS) equation [1]. There are ... Optical pulse compression finds important applications in optical fibres. The pulse com ..... to thank CSIR, New Delhi for financial support in the form of SRF.
Nonlinear transformations of random processes
Deutsch, Ralph
2017-01-01
This concise treatment of nonlinear noise techniques encountered in system applications is suitable for advanced undergraduates and graduate students. It is also a valuable reference for systems analysts and communication engineers. 1962 edition.
Extreme Nonlinear Optics An Introduction
Wegener, Martin
2005-01-01
Following the birth of the laser in 1960, the field of "nonlinear optics" rapidly emerged. Today, laser intensities and pulse durations are readily available, for which the concepts and approximations of traditional nonlinear optics no longer apply. In this regime of "extreme nonlinear optics," a large variety of novel and unusual effects arise, for example frequency doubling in inversion symmetric materials or high-harmonic generation in gases, which can lead to attosecond electromagnetic pulses or pulse trains. Other examples of "extreme nonlinear optics" cover diverse areas such as solid-state physics, atomic physics, relativistic free electrons in a vacuum and even the vacuum itself. This book starts with an introduction to the field based primarily on extensions of two famous textbook examples, namely the Lorentz oscillator model and the Drude model. Here the level of sophistication should be accessible to any undergraduate physics student. Many graphical illustrations and examples are given. The followi...
Nonlinear dynamics: Challenges and perspectives
Indian Academy of Sciences (India)
fields such as economics, social dynamics and so on [6–10]. These nonlinear ..... developing all-optical computers in homogeneous bulk media such as pho- ... suggestions have been given to develop effective chaos-based cryptographic.
Teaching secondary mathematics
Rock, David
2013-01-01
Solidly grounded in up-to-date research, theory and technology,?Teaching Secondary Mathematics?is a practical, student-friendly, and popular text for secondary mathematics methods courses. It provides clear and useful approaches for mathematics teachers, and shows how concepts typically found in a secondary mathematics curriculum can be taught in a positive and encouraging way. The thoroughly revised fourth edition combines this pragmatic approach with truly innovative and integrated technology content throughout. Synthesized content between the book and comprehensive companion websi
Nonlinear Optics: Principles and Applications
DEFF Research Database (Denmark)
Rottwitt, Karsten; Tidemand-Lichtenberg, Peter
of applications, Nonlinear Optics: Principles and Applications effectively bridges physics and mathematics with relevant applied material for real-world use. The book progresses naturally from fundamental aspects to illustrative examples, and presents a strong theoretical foundation that equips the reader...... and matter, this text focuses on the physical understanding of nonlinear optics, and explores optical material response functions in the time and frequency domain....
Dynamics of nonlinear feedback control
Snippe, H.P.; Hateren, J.H. van
2007-01-01
Feedback control in neural systems is ubiquitous. Here we study the mathematics of nonlinear feedback control. We compare models in which the input is multiplied by a dynamic gain (multiplicative control) with models in which the input is divided by a dynamic attenuation (divisive control). The gain signal (resp. the attenuation signal) is obtained through a concatenation of an instantaneous nonlinearity and a linear low-pass filter operating on the output of the feedback loop. For input step...
On nonlinear periodic drift waves
International Nuclear Information System (INIS)
Kauschke, U.; Schlueter, H.
1990-09-01
Nonlinear periodic drift waves are investigated on the basis of a simple perturbation scheme for both the amplitude and inverse frequency. The coefficients for the generation of the forced harmonics are derived, a nonlinear dispersion relation is suggested and a criterion for the onset of the modulational instability is obtained. The results are compared with the ones obtained with the help of a standard KBM-treatment. Moreover cnoidal drift waves are suggested and compared to an experimental observation. (orig.)
Competitive nonlinear pricing and bundling
Armstrong, Mark; Vickers, John
2006-01-01
We examine the impact of multiproduct nonlinear pricing on profit, consumer surplus and welfare in a duopoly. When consumers buy all their products from one firm (the one-stop shopping model), nonlinear pricing leads to higher profit and welfare, but often lower consumer surplus, than linear pricing. By contrast, in a unit-demand model where consumers may buy one product from one firm and another product from another firm, bundling generally acts to reduce profit and welfare and to boost cons...
Nonlinear optics principles and applications
Rottwitt, Karsten
2014-01-01
IntroductionReview of linear opticsInduced polarizationHarmonic oscillator modelLocal field correctionsEstimated nonlinear responseSummaryTime-domain material responseThe polarization time-response functionThe Born-Oppenheimer approximationRaman scattering response function of silicaSummaryMaterial response in the frequency domain, susceptibility tensorsThe susceptibility tensorThe induced polarization in the frequency domainSum of monochromatic fieldsThe prefactor to the induced polarizationThird-order polarization in the Born-Oppenheimer approximation in the frequency domainKramers-Kronig relationsSummarySymmetries in nonlinear opticsSpatial symmetriesSecond-order materialsThird-order nonlinear materialsCyclic coordinate-systemContracted notation for second-order susceptibility tensorsSummaryThe nonlinear wave equationMono and quasi-monochromatic beamsPlane waves - the transverse problemWaveguidesVectorial approachNonlinear birefringenceSummarySecond-order nonlinear effectsGeneral theoryCoupled wave theoryP...
Modeling nonlinearities in MEMS oscillators.
Agrawal, Deepak K; Woodhouse, Jim; Seshia, Ashwin A
2013-08-01
We present a mathematical model of a microelectromechanical system (MEMS) oscillator that integrates the nonlinearities of the MEMS resonator and the oscillator circuitry in a single numerical modeling environment. This is achieved by transforming the conventional nonlinear mechanical model into the electrical domain while simultaneously considering the prominent nonlinearities of the resonator. The proposed nonlinear electrical model is validated by comparing the simulated amplitude-frequency response with measurements on an open-loop electrically addressed flexural silicon MEMS resonator driven to large motional amplitudes. Next, the essential nonlinearities in the oscillator circuit are investigated and a mathematical model of a MEMS oscillator is proposed that integrates the nonlinearities of the resonator. The concept is illustrated for MEMS transimpedance-amplifier- based square-wave and sine-wave oscillators. Closed-form expressions of steady-state output power and output frequency are derived for both oscillator models and compared with experimental and simulation results, with a good match in the predicted trends in all three cases.
BOOK REVIEW: Nonlinear Magnetohydrodynamics
Shafranov, V.
1998-08-01
Nonlinear magnetohydrodynamics by Dieter Biskamp is a thorough introduction to the physics of the most impressive non-linear phenomena that occur in conducting magnetoplasmas. The basic systems, in which non-trivial dynamic processes are observed, accompanied by changes of geometry of the magnetic field and the effects of energy transformation (magnetic energy into kinetic energy or the opposite effect in magnetic dynamos), are the plasma magnetic confinement systems for nuclear fusion and space plasmas, mainly the solar plasma. A significant number of the examples of the dynamic processes considered are taken from laboratory plasmas, for which an experimental check of the theory is possible. Therefore, though the book is intended for researchers and students interested in both laboratory, including nuclear fusion, and astrophysical plasmas, it is most probably closer to the first category of reader. In the Introduction the author notes that unlike the hydrodynamics of non-conducting fluids, where the phenomena caused by rapid fluid motions are the most interesting, for plasmas in a strong magnetic field the quasi-static configurations inside which the local dynamic processes occur are often the most important. Therefore, the reader will also find in this book rather traditional material on the theory of plasma equilibrium and stability in magnetic fields. In addition, it is notable that, as opposed to a linear theory, the non-linear theory, as a rule, cannot give quite definite explanations or predictions of phenomena, and consequently there are in the book many results obtained by consideration of numerical models with the use of supercomputers. The treatment of non-linear dynamics is preceded by Chapters 2 to 4, in which the basics of MHD theory are presented with an emphasis on the role of integral invariants of the magnetic helicity type, a derivation of the reduced MHD equations is given, together with examples of the exact solutions of the equilibrium
Secondary amenorrhea is the cessation of menstrual flow for a period of 6 months or more in the absence ... as anxiety can be the root cause of amenorrhea. Treatment can range from behavior modification for excessive ...
Nonlinear transport of dynamic system phase space
International Nuclear Information System (INIS)
Xie Xi; Xia Jiawen
1993-01-01
The inverse transform of any order solution of the differential equation of general nonlinear dynamic systems is derived, realizing theoretically the nonlinear transport for the phase space of nonlinear dynamic systems. The result is applicable to general nonlinear dynamic systems, with the transport of accelerator beam phase space as a typical example
A reliable treatment for nonlinear Schroedinger equations
International Nuclear Information System (INIS)
Khani, F.; Hamedi-Nezhad, S.; Molabahrami, A.
2007-01-01
Exp-function method is used to find a unified solution of nonlinear wave equation. Nonlinear Schroedinger equations with cubic and power law nonlinearity are selected to illustrate the effectiveness and simplicity of the method. It is shown that the Exp-function method, with the help of symbolic computation, provides a powerful mathematical tool for solving nonlinear equation
Towards secondary fingerprint classification
CSIR Research Space (South Africa)
Msiza, IS
2011-07-01
Full Text Available an accuracy figure of 76.8%. This small difference between the two figures is indicative of the validity of the proposed secondary classification module. Keywords?fingerprint core; fingerprint delta; primary classifi- cation; secondary classification I..., namely, the fingerprint core and the fingerprint delta. Forensically, a fingerprint core is defined as the innermost turning point where the fingerprint ridges form a loop, while the fingerprint delta is defined as the point where these ridges form a...
1981-09-01
Megaton Weapons and Secondary Ignition There are very few well documented data on fires initiated by physical damage (i.e., secondary ignitions). Those data...where significant physical damage to buildings and/or contents can occur. Where this outer bound is located relative to the primary ignition range is...maintenance 7.9 Busline facilities, including shops 3.0 Convalescent homes8 3.1 Hospitals 8.0 Radio and television transmitters Collges and universities
Identification of Nonlinear Dynamic Systems Possessing Some Non-linearities
Directory of Open Access Journals (Sweden)
Y. N. Pavlov
2015-01-01
Full Text Available The subject of this work is the problem of identification of nonlinear dynamic systems based on the experimental data obtained by applying test signals to the system. The goal is to determinate coefficients of differential equations of systems by experimental frequency hodographs and separate similar, but different, in essence, forces: dissipative forces with the square of the first derivative in the motion equations and dissipative force from the action of dry friction. There was a proposal to use the harmonic linearization method to approximate each of the nonlinearity of "quadratic friction" and "dry friction" by linear friction with the appropriate harmonic linearization coefficient.Assume that a frequency transfer function of the identified system has a known form. Assume as well that there are disturbances while obtaining frequency characteristics of the realworld system. As a result, the points of experimentally obtained hodograph move randomly. Searching for solution of the identification problem was in the hodograph class, specified by the system model, which has the form of the frequency transfer function the same as the form of the frequency transfer function of the system identified. Minimizing a proximity criterion (measure of the experimentally obtained system hodograph and the system hodograph model for all the experimental points described and previously published by one of the authors allowed searching for the unknown coefficients of the frequenc ransfer function of the system model. The paper shows the possibility to identify a nonlinear dynamic system with multiple nonlinearities, obtained on the experimental samples of the frequency system hodograph. The proposed algorithm allows to select the nonlinearity of the type "quadratic friction" and "dry friction", i.e. also in the case where the nonlinearity is dependent on the same dynamic parameter, in particular, on the derivative of the system output value. For the dynamic
Influence of Stationary Crossflow Modulation on Secondary Instability
Choudhari, Meelan M.; Li, Fei; Paredes, Pedro
2016-01-01
A likely scenario for swept wing transition on subsonic aircraft with natural laminar flow involves the breakdown of stationary crossflow vortices via high frequency secondary instability. A majority of the prior research on this secondary instability has focused on crossflow vortices with a single dominant spanwise wavelength. This paper investigates the effects of the spanwise modulation of stationary crossflow vortices at a specified wavelength by a subharmonic stationary mode. Secondary instability of the modulated crossflow pattern is studied using planar, partial-differential-equation based eigenvalue analysis. Computations reveal that weak modulation by the first subharmonic of the input stationary mode leads to mode splitting that is particularly obvious for Y-type secondary modes that are driven by the wall-normal shear of the basic state. Thus, for each Y mode corresponding to the fundamental wavelength of results in unmodulated train of crossflow vortices, the modulated flow supports a pair of secondary modes with somewhat different amplification rates. The mode splitting phenomenon suggests that a more complex stationary modulation such as that induced by natural surface roughness would yield a considerably richer spectrum of secondary instability modes. Even modest levels of subharmonic modulation are shown to have a strong effect on the overall amplification of secondary disturbances, particularly the Z-modes driven by the spanwise shear of the basic state. Preliminary computations related to the nonlinear breakdown of these secondary disturbances provide interesting insights into the process of crossflow transition in the presence of the first subharmonic of the dominant stationary vortex.
Final report. [Nonlinear magnetohydrodynamics
International Nuclear Information System (INIS)
Montgomery, D.C.
1998-01-01
This is a final report on the research activities carried out under the above grant at Dartmouth. During the period considered, the grant was identified as being for nonlinear magnetohydrodynamics, considered as the most tractable theoretical framework in which the plasma problems associated with magnetic confinement of fusion plasmas could be studied. During the first part of the grant's lifetime, the author was associated with Los Alamos National Laboratory as a consultant and the work was motivated by the reversed-field pinch. Later, when that program was killed at Los Alamos, the problems became ones that could be motivated by their relation to tokamaks. Throughout the work, the interest was always on questions that were as fundamental as possible, compatible with those motivations. The intent was always to contribute to plasma physics as a science, as well as to the understanding of mission-oriented confined fusion plasmas. Twelve Ph.D. theses were supervised during this period and a comparable number of postdoctoral research associates were temporarily supported. Many of these have gone on to distinguished careers, though few have done so in the context of the controlled fusion program. Their work was a combination of theory and numerical computation, in gradually less and less idealized settings, moving from rectangular periodic boundary conditions in two dimensions, through periodic straight cylinders and eventually, before the grant was withdrawn, to toroids, with a gradually more prominent role for electrical and mechanical boundary conditions. The author never had access to a situation where he could initiate experiments and relate directly to the laboratory data he wanted. Computers were the laboratory. Most of the work was reported in referred publications in the open literature, copies of which were transmitted one by one to DOE at the time they appeared. The Appendix to this report is a bibliography of published work which was carried out under the
Complex motions and chaos in nonlinear systems
Machado, José; Zhang, Jiazhong
2016-01-01
This book brings together 10 chapters on a new stream of research examining complex phenomena in nonlinear systems—including engineering, physics, and social science. Complex Motions and Chaos in Nonlinear Systems provides readers a particular vantage of the nature and nonlinear phenomena in nonlinear dynamics that can develop the corresponding mathematical theory and apply nonlinear design to practical engineering as well as the study of other complex phenomena including those investigated within social science.
Secondary instability and transition in three-dimensional boundary layers
Energy Technology Data Exchange (ETDEWEB)
Stolte, A.; Bertolotti, F.P.; Koch, W. (Deutsche Forschungsanstalt fuer Luft- und Raumfahrt e.V. (DLR), Goettingen (Germany). Inst. fuer Stroemungsmechanik)
1999-01-01
Stationary and traveling crossflow modes are the most prominent disturbances in the highly accelerated three-dimensional flow near the leading edge of a swept wing. Near transition onset, secondary three-dimensional instabilities of high frequency can be observed in such flows. A model flow on the basis of a DLR swept plate experiment allows a detailed study of transition scenarios triggered by crossflow instabilities, since the favorable pressure gradient over the whole plate inhibits instabilities of Tollmien-Schlichting type. In order to shed some light upon the role of the high-frequency secondary instabilities, the saturation characteristics of crossflow vortices in this model flow are investigated using the parabolized stability equations. In contrast to nonlinear equilibrium solutions of steady crossflow vortices, the nonlinear Polarized Stability Equations (PSE) results yield different maximal disturbance amplitudes for different initial amplitudes. (orig./AKF)
Secondary instability and transition in three-dimensional boundary layers
Energy Technology Data Exchange (ETDEWEB)
Stolte, A.; Bertolotti, F.P.; Koch, W. [Deutsche Forschungsanstalt fuer Luft- und Raumfahrt e.V. (DLR), Goettingen (Germany). Inst. fuer Stroemungsmechanik
1999-12-01
Stationary and traveling crossflow modes are the most prominent disturbances in the highly accelerated three-dimensional flow near the leading edge of a swept wing. Near transition onset, secondary three-dimensional instabilities of high frequency can be observed in such flows. A model flow on the basis of a DLR swept plate experiment allows a detailed study of transition scenarios triggered by crossflow instabilities, since the favorable pressure gradient over the whole plate inhibits instabilities of Tollmien-Schlichting type. In order to shed some light upon the role of the high-frequency secondary instabilities, the saturation characteristics of crossflow vortices in this model flow are investigated using the parabolized stability equations. In contrast to nonlinear equilibrium solutions of steady crossflow vortices, the nonlinear Polarized Stability Equations (PSE) results yield different maximal disturbance amplitudes for different initial amplitudes. (orig./AKF)
Cascaded nonlinearities for ultrafast nonlinear optical science and applications
DEFF Research Database (Denmark)
Bache, Morten
the cascading nonlinearity is investigated in detail, especially with focus on femtosecond energetic laser pulses being subjected to this nonlinear response. Analytical, numerical and experimental results are used to understand the cascading interaction and applications are demonstrated. The defocusing soliton...... observations with analogies in fiber optics are observed numerically and experimentally, including soliton self-compression, soliton-induced resonant radiation, supercontinuum generation, optical wavebreaking and shock-front formation. All this happens despite no waveguide being present, thanks...... is of particular interest here, since it is quite unique and provides the solution to a number of standing challenges in the ultrafast nonlinear optics community. It solves the problem of catastrophic focusing and formation of a filaments in bulk glasses, which even under controlled circumstances is limited...
Input saturation in nonlinear multivariable processes resolved by nonlinear decoupling
Directory of Open Access Journals (Sweden)
Jens G. Balchen
1995-04-01
Full Text Available A new method is presented for the resolution of the problem of input saturation in nonlinear multivariable process control by means of elementary nonlinear decoupling (END. Input saturation can have serious consequences particularly in multivariable control because it may lead to very undesirable system behaviour and quite often system instability. Many authors have searched for systematic techniques for designing multivariable control systems in which saturation may occur in any of the control variables (inputs, manipulated variables. No generally accepted method seems to have been presented so far which gives a solution in closed form. The method of elementary nonlinear decoupling (END can be applied directly to the case of saturation control variables by deriving as many control strategies as there are combinations of saturating control variables. The method is demonstrated by the multivariable control of a simulated Fluidized Catalytic Cracker (FCC with very convincing results.
Initiation of secondary ice production in clouds
Directory of Open Access Journals (Sweden)
S. C. Sullivan
2018-02-01
Full Text Available Disparities between the measured concentrations of ice-nucleating particles (INPs and in-cloud ice crystal number concentrations (ICNCs have led to the hypothesis that mechanisms other than primary nucleation form ice in the atmosphere. Here, we model three of these secondary production mechanisms – rime splintering, frozen droplet shattering, and ice–ice collisional breakup – with a six-hydrometeor-class parcel model. We perform three sets of simulations to understand temporal evolution of ice hydrometeor number (Nice, thermodynamic limitations, and the impact of parametric uncertainty when secondary production is active. Output is assessed in terms of the number of primarily nucleated ice crystals that must exist before secondary production initiates (NINP(lim as well as the ICNC enhancement from secondary production and the timing of a 100-fold enhancement. Nice evolution can be understood in terms of collision-based nonlinearity and the phasedness of the process, i.e., whether it involves ice hydrometeors, liquid ones, or both. Ice–ice collisional breakup is the only process for which a meaningful NINP(lim exists (0.002 up to 0.15 L−1. For droplet shattering and rime splintering, a warm enough cloud base temperature and modest updraft are the more important criteria for initiation. The low values of NINP(lim here suggest that, under appropriate thermodynamic conditions for secondary ice production, perturbations in cloud concentration nuclei concentrations are more influential in mixed-phase partitioning than those in INP concentrations.
Sane, Ramola; Agarwal, Sagar; Mittapalli, Rajendar K; Elmquist, William F
2013-04-01
The study objective was to investigate factors that affect the central nervous system (CNS) distribution of elacridar. Elacridar inhibits transport mediated by P-glycoprotein (P-gp) and breast cancer resistance protein (Bcrp) and has been used to study the influence of transporters on brain distribution of chemotherapeutics. Adequate distribution of elacridar across the blood-brain barrier (BBB) and into the brain parenchyma is necessary to target tumor cells in the brain that overexpress transporters and reside behind an intact BBB. We examined the role of P-gp and Bcrp on brain penetration of elacridar using Friend leukemia virus strain B wild-type, Mdr1a/b(-/-), Bcrp1(-/-), and Mdr1a/b(-/-)Bcrp1(-/-) mice. Initially, the mice were administered 2.5 mg/kg of elacridar intravenously, and the plasma and brain concentrations were determined. The brain-to-plasma partition coefficient of elacridar in the wild-type mice was 0.82, as compared with 3.5 in Mdr1a/b(-/-) mice, 6.6 in Bcrp1(-/-) mice, and 15 in Mdr1a/b(-/-)Bcrp1(-/-) mice, indicating that both P-gp and Bcrp limit the brain distribution of elacridar. The four genotypes were then administered increasing doses of elacridar, and the CNS distribution of elacridar was determined. The observed and model predicted maximum brain-to-plasma ratios (Emax) at the highest dose were not significantly different in all genotypes. However, the ED50 was lower for Mdr1a/b(-/-) mice compared with Bcrp1(-/-) mice. These findings correlate with the relative expression of P-gp and Bcrp at the BBB in these mice and demonstrate the quantitative enhancement in elacridar CNS distribution as a function of its dose. Overall, this study provides useful concepts for future applications of elacridar as an adjuvant therapy to improve targeting of chemotherapeutic agents to tumor cells in the brain parenchyma.
Nonlinear analysis of pupillary dynamics.
Onorati, Francesco; Mainardi, Luca Tommaso; Sirca, Fabiola; Russo, Vincenzo; Barbieri, Riccardo
2016-02-01
Pupil size reflects autonomic response to different environmental and behavioral stimuli, and its dynamics have been linked to other autonomic correlates such as cardiac and respiratory rhythms. The aim of this study is to assess the nonlinear characteristics of pupil size of 25 normal subjects who participated in a psychophysiological experimental protocol with four experimental conditions, namely “baseline”, “anger”, “joy”, and “sadness”. Nonlinear measures, such as sample entropy, correlation dimension, and largest Lyapunov exponent, were computed on reconstructed signals of spontaneous fluctuations of pupil dilation. Nonparametric statistical tests were performed on surrogate data to verify that the nonlinear measures are an intrinsic characteristic of the signals. We then developed and applied a piecewise linear regression model to detrended fluctuation analysis (DFA). Two joinpoints and three scaling intervals were identified: slope α0, at slow time scales, represents a persistent nonstationary long-range correlation, whereas α1 and α2, at middle and fast time scales, respectively, represent long-range power-law correlations, similarly to DFA applied to heart rate variability signals. Of the computed complexity measures, α0 showed statistically significant differences among experimental conditions (pnonlinear dynamics, (b) three well-defined and distinct long-memory processes exist at different time scales, and (c) autonomic stimulation is partially reflected in nonlinear dynamics. (c) autonomic stimulation is partially reflected in nonlinear dynamics.
Introduction to nonlinear dispersive equations
Linares, Felipe
2015-01-01
This textbook introduces the well-posedness theory for initial-value problems of nonlinear, dispersive partial differential equations, with special focus on two key models, the Korteweg–de Vries equation and the nonlinear Schrödinger equation. A concise and self-contained treatment of background material (the Fourier transform, interpolation theory, Sobolev spaces, and the linear Schrödinger equation) prepares the reader to understand the main topics covered: the initial-value problem for the nonlinear Schrödinger equation and the generalized Korteweg–de Vries equation, properties of their solutions, and a survey of general classes of nonlinear dispersive equations of physical and mathematical significance. Each chapter ends with an expert account of recent developments and open problems, as well as exercises. The final chapter gives a detailed exposition of local well-posedness for the nonlinear Schrödinger equation, taking the reader to the forefront of recent research. The second edition of Introdu...
Transient and chaotic low-energy transfers in a system with bistable nonlinearity
Energy Technology Data Exchange (ETDEWEB)
Romeo, F., E-mail: francesco.romeo@uniroma1.it [Department of Structural and Geotechnical Engineering, SAPIENZA University of Rome, Rome (Italy); Manevitch, L. I. [Institute of Chemical Physics, RAS, Moscow (Russian Federation); Bergman, L. A.; Vakakis, A. [College of Engineering, University of Illinois at Urbana–Champaign, Champaign, Illinois 61820 (United States)
2015-05-15
The low-energy dynamics of a two-dof system composed of a grounded linear oscillator coupled to a lightweight mass by means of a spring with both cubic nonlinear and negative linear components is investigated. The mechanisms leading to intense energy exchanges between the linear oscillator, excited by a low-energy impulse, and the nonlinear attachment are addressed. For lightly damped systems, it is shown that two main mechanisms arise: Aperiodic alternating in-well and cross-well oscillations of the nonlinear attachment, and secondary nonlinear beats occurring once the dynamics evolves solely in-well. The description of the former dissipative phenomenon is provided in a two-dimensional projection of the phase space, where transitions between in-well and cross-well oscillations are associated with sequences of crossings across a pseudo-separatrix. Whereas the second mechanism is described in terms of secondary limiting phase trajectories of the nonlinear attachment under certain resonance conditions. The analytical treatment of the two aformentioned low-energy transfer mechanisms relies on the reduction of the nonlinear dynamics and consequent analysis of the reduced dynamics by asymptotic techniques. Direct numerical simulations fully validate our analytical predictions.
Secondary metabolites from Ganoderma.
Baby, Sabulal; Johnson, Anil John; Govindan, Balaji
2015-06-01
Ganoderma is a genus of medicinal mushrooms. This review deals with secondary metabolites isolated from Ganoderma and their biological significance. Phytochemical studies over the last 40years led to the isolation of 431 secondary metabolites from various Ganoderma species. The major secondary compounds isolated are (a) C30 lanostanes (ganoderic acids), (b) C30 lanostanes (aldehydes, alcohols, esters, glycosides, lactones, ketones), (c) C27 lanostanes (lucidenic acids), (d) C27 lanostanes (alcohols, lactones, esters), (e) C24, C25 lanostanes (f) C30 pentacyclic triterpenes, (g) meroterpenoids, (h) farnesyl hydroquinones (meroterpenoids), (i) C15 sesquiterpenoids, (j) steroids, (k) alkaloids, (l) prenyl hydroquinone (m) benzofurans, (n) benzopyran-4-one derivatives and (o) benzenoid derivatives. Ganoderma lucidum is the species extensively studied for its secondary metabolites and biological activities. Ganoderma applanatum, Ganoderma colossum, Ganoderma sinense, Ganoderma cochlear, Ganoderma tsugae, Ganoderma amboinense, Ganoderma orbiforme, Ganoderma resinaceum, Ganoderma hainanense, Ganoderma concinna, Ganoderma pfeifferi, Ganoderma neo-japonicum, Ganoderma tropicum, Ganoderma australe, Ganoderma carnosum, Ganoderma fornicatum, Ganoderma lipsiense (synonym G. applanatum), Ganoderma mastoporum, Ganoderma theaecolum, Ganoderma boninense, Ganoderma capense and Ganoderma annulare are the other Ganoderma species subjected to phytochemical studies. Further phytochemical studies on Ganoderma could lead to the discovery of hitherto unknown biologically active secondary metabolites. Copyright © 2015 Elsevier Ltd. All rights reserved.
Neoclassical transport including collisional nonlinearity.
Candy, J; Belli, E A
2011-06-10
In the standard δf theory of neoclassical transport, the zeroth-order (Maxwellian) solution is obtained analytically via the solution of a nonlinear equation. The first-order correction δf is subsequently computed as the solution of a linear, inhomogeneous equation that includes the linearized Fokker-Planck collision operator. This equation admits analytic solutions only in extreme asymptotic limits (banana, plateau, Pfirsch-Schlüter), and so must be solved numerically for realistic plasma parameters. Recently, numerical codes have appeared which attempt to compute the total distribution f more accurately than in the standard ordering by retaining some nonlinear terms related to finite-orbit width, while simultaneously reusing some form of the linearized collision operator. In this work we show that higher-order corrections to the distribution function may be unphysical if collisional nonlinearities are ignored.
Nonlinear photoacoustic spectroscopy of hemoglobin.
Danielli, Amos; Maslov, Konstantin; Favazza, Christopher P; Xia, Jun; Wang, Lihong V
2015-05-18
As light intensity increases in photoacoustic imaging, the saturation of optical absorption and the temperature dependence of the thermal expansion coefficient result in a measurable nonlinear dependence of the photoacoustic (PA) signal on the excitation pulse fluence. Here, under controlled conditions, we investigate the intensity-dependent photoacoustic signals from oxygenated and deoxygenated hemoglobin at varied optical wavelengths and molecular concentrations. The wavelength and concentration dependencies of the nonlinear PA spectrum are found to be significantly greater in oxygenated hemoglobin than in deoxygenated hemoglobin. These effects are further influenced by the hemoglobin concentration. These nonlinear phenomena provide insights into applications of photoacoustics, such as measurements of average inter-molecular distances on a nm scale or with a tuned selection of wavelengths, a more accurate quantitative PA tomography.
Nonlinear photoacoustic spectroscopy of hemoglobin
International Nuclear Information System (INIS)
Danielli, Amos; Maslov, Konstantin; Favazza, Christopher P.; Xia, Jun; Wang, Lihong V.
2015-01-01
As light intensity increases in photoacoustic imaging, the saturation of optical absorption and the temperature dependence of the thermal expansion coefficient result in a measurable nonlinear dependence of the photoacoustic (PA) signal on the excitation pulse fluence. Here, under controlled conditions, we investigate the intensity-dependent photoacoustic signals from oxygenated and deoxygenated hemoglobin at varied optical wavelengths and molecular concentrations. The wavelength and concentration dependencies of the nonlinear PA spectrum are found to be significantly greater in oxygenated hemoglobin than in deoxygenated hemoglobin. These effects are further influenced by the hemoglobin concentration. These nonlinear phenomena provide insights into applications of photoacoustics, such as measurements of average inter-molecular distances on a nm scale or with a tuned selection of wavelengths, a more accurate quantitative PA tomography
Nonlinear Deformable-body Dynamics
Luo, Albert C J
2010-01-01
"Nonlinear Deformable-body Dynamics" mainly consists in a mathematical treatise of approximate theories for thin deformable bodies, including cables, beams, rods, webs, membranes, plates, and shells. The intent of the book is to stimulate more research in the area of nonlinear deformable-body dynamics not only because of the unsolved theoretical puzzles it presents but also because of its wide spectrum of applications. For instance, the theories for soft webs and rod-reinforced soft structures can be applied to biomechanics for DNA and living tissues, and the nonlinear theory of deformable bodies, based on the Kirchhoff assumptions, is a special case discussed. This book can serve as a reference work for researchers and a textbook for senior and postgraduate students in physics, mathematics, engineering and biophysics. Dr. Albert C.J. Luo is a Professor of Mechanical Engineering at Southern Illinois University, Edwardsville, IL, USA. Professor Luo is an internationally recognized scientist in the field of non...
NONLINEAR DYNAMICS OF ORGANIZATION DEVELOPMENT
Directory of Open Access Journals (Sweden)
Денис Антонович БУШУЕВ
2016-02-01
Full Text Available The nonlinear behavior of organizations in development projects is considered. The nonlinear behavior is initiated in the growth of organizations and requires a restructuring of governance in identifying dysfunctions. Such a restructuring is needed in the area of soft components, determining the organizational levels of competence in the management of projects, programs, portfolios and heads of the Project Management Office. An important component of the strategic development of the organization is the proposed concept for formation and management of development programs in the context according to their life cycle. It should take into account the non-linear behavior of the soft components of the system and violation of functional processes of the organization. The specific management syndromes of projects and programs are considered. Such as syndromes time management project linked to the singular points of the project. These syndromes are "shift to the right", "point of no return", "braking at the end of the project" and others.
Nonlinear operators and their propagators
International Nuclear Information System (INIS)
Schwartz, C.
1997-01-01
Mathematical physicists are familiar with a large set of tools designed for dealing with linear operators, which are so common in both the classical and quantum theories; but many of those tools are useless with nonlinear equations of motion. In this work a general algebra and calculus is developed for working with nonlinear operators: The basic new tool being the open-quotes slash product,close quotes defined by A(1+εB) =A+εA/B+O(ε 2 ). For a generic time development equation, the propagator is constructed and then there follows the formal version of time dependent perturbation theory, in remarkable similarity to the linear situation. A nonperturbative approximation scheme capable of producing high accuracy computations, previously developed for linear operators, is shown to be applicable as well in the nonlinear domain. A number of auxiliary mathematical properties and examples are given. copyright 1997 American Institute of Physics
Nonlinear optics an analytical approach
Mandel, Paul
2010-01-01
Based on the author's extensive teaching experience and lecture notes, this textbook provides a substantially analytical rather than descriptive presentation of nonlinear optics. Divided into five parts, with most chapters corresponding to a two-hour lecture, the book begins with a unique account of the historical development from Kirchhoff's law for the black-body radiation to Planck's quantum hypothesis and Einstein's discovery of spontaneous emission - providing all the explicit proofs. The subsequent sections deal with matter quantization, ultrashort pulse propagation in 2-level media, cavity nonlinear optics, chi(2) and chi(3) media. For graduate and PhD students in nonlinear optics or photonics, while also representing a valuable reference for researchers in these fields.
Nonlinear photoacoustic spectroscopy of hemoglobin
Energy Technology Data Exchange (ETDEWEB)
Danielli, Amos; Maslov, Konstantin; Favazza, Christopher P.; Xia, Jun; Wang, Lihong V., E-mail: LHWANG@WUSTL.EDU [Optical Imaging Laboratory, Department of Biomedical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130 (United States)
2015-05-18
As light intensity increases in photoacoustic imaging, the saturation of optical absorption and the temperature dependence of the thermal expansion coefficient result in a measurable nonlinear dependence of the photoacoustic (PA) signal on the excitation pulse fluence. Here, under controlled conditions, we investigate the intensity-dependent photoacoustic signals from oxygenated and deoxygenated hemoglobin at varied optical wavelengths and molecular concentrations. The wavelength and concentration dependencies of the nonlinear PA spectrum are found to be significantly greater in oxygenated hemoglobin than in deoxygenated hemoglobin. These effects are further influenced by the hemoglobin concentration. These nonlinear phenomena provide insights into applications of photoacoustics, such as measurements of average inter-molecular distances on a nm scale or with a tuned selection of wavelengths, a more accurate quantitative PA tomography.
Optimization for nonlinear inverse problem
International Nuclear Information System (INIS)
Boyadzhiev, G.; Brandmayr, E.; Pinat, T.; Panza, G.F.
2007-06-01
The nonlinear inversion of geophysical data in general does not yield a unique solution, but a single model, representing the investigated field, is preferred for an easy geological interpretation of the observations. The analyzed region is constituted by a number of sub-regions where the multi-valued nonlinear inversion is applied, which leads to a multi-valued solution. Therefore, combining the values of the solution in each sub-region, many acceptable models are obtained for the entire region and this complicates the geological interpretation of geophysical investigations. In this paper are presented new methodologies, capable to select one model, among all acceptable ones, that satisfies different criteria of smoothness in the explored space of solutions. In this work we focus on the non-linear inversion of surface waves dispersion curves, which gives structural models of shear-wave velocity versus depth, but the basic concepts have a general validity. (author)
Protein Structure Prediction by Protein Threading
Xu, Ying; Liu, Zhijie; Cai, Liming; Xu, Dong
The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on "the inverse protein folding problem" laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet profoundly novel approach to assessing if a protein sequence fits well with a given protein structural fold. Their follow-up work (Elofsson et al., 1996; Fischer and Eisenberg, 1996; Fischer et al., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et al., 1992) on protein fold recognition led to the development of a new brand of powerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many of the proteins encoded in the hundreds of genomes that have been sequenced up to now.
Nonlinear elasticity in resonance experiments
Li, Xun; Sens-Schönfelder, Christoph; Snieder, Roel
2018-04-01
Resonant bar experiments have revealed that dynamic deformation induces nonlinearity in rocks. These experiments produce resonance curves that represent the response amplitude as a function of the driving frequency. We propose a model to reproduce the resonance curves with observed features that include (a) the log-time recovery of the resonant frequency after the deformation ends (slow dynamics), (b) the asymmetry in the direction of the driving frequency, (c) the difference between resonance curves with the driving frequency that is swept upward and downward, and (d) the presence of a "cliff" segment to the left of the resonant peak under the condition of strong nonlinearity. The model is based on a feedback cycle where the effect of softening (nonlinearity) feeds back to the deformation. This model provides a unified interpretation of both the nonlinearity and slow dynamics in resonance experiments. We further show that the asymmetry of the resonance curve is caused by the softening, which is documented by the decrease of the resonant frequency during the deformation; the cliff segment of the resonance curve is linked to a bifurcation that involves a steep change of the response amplitude when the driving frequency is changed. With weak nonlinearity, the difference between the upward- and downward-sweeping curves depends on slow dynamics; a sufficiently slow frequency sweep eliminates this up-down difference. With strong nonlinearity, the up-down difference results from both the slow dynamics and bifurcation; however, the presence of the bifurcation maintains the respective part of the up-down difference, regardless of the sweep rate.
Periodic waves in nonlinear metamaterials
International Nuclear Information System (INIS)
Liu, Wen-Jun; Xiao, Jing-Hua; Yan, Jie-Yun; Tian, Bo
2012-01-01
Periodic waves are presented in this Letter. With symbolic computation, equations for monochromatic waves are studied, and analytic periodic waves are obtained. Factors affecting properties of periodic waves are analyzed. Nonlinear metamaterials, with the continuous distribution of the dielectric permittivity obtained, are different from the ones with the discrete distribution. -- Highlights: ► Equations for the monochromatic waves in transverse magnetic polarization have been studied. ► Analytic periodic waves for the equations have been obtained. ► Periodic waves are theoretically presented and studied in the nonlinear metamaterials.
Nonlinear Optics of Hexaphenyl Nanofibers
DEFF Research Database (Denmark)
Balzer, Frank; Al-Shamery, Katharina; Neuendorf, Rolf
2003-01-01
The nonlinear optical response of films of needle-shaped para-hexaphenyl nanoaggregates on mica surfaces is investigated. Two-photon luminescence as well as optical second harmonic generation (SHG) are observed following excitation with femtosecond pulses at 770 nm. Polarization dependent...... measurements reveal that the nonlinear optical transition dipole moment is oriented with an angle of 75° with respect to the needles long axes. The absolute value of the macroscopic second-order susceptibility, averaged over a size distribution of p-6P nanoaggregates, is estimated to be of the order of 6...
Nonlinear waves and weak turbulence
Zakharov, V E
1997-01-01
This book is a collection of papers on dynamical and statistical theory of nonlinear wave propagation in dispersive conservative media. Emphasis is on waves on the surface of an ideal fluid and on Rossby waves in the atmosphere. Although the book deals mainly with weakly nonlinear waves, it is more than simply a description of standard perturbation techniques. The goal is to show that the theory of weakly interacting waves is naturally related to such areas of mathematics as Diophantine equations, differential geometry of waves, Poincaré normal forms, and the inverse scattering method.
Nonlinear Control of Heartbeat Models
Directory of Open Access Journals (Sweden)
Witt Thanom
2011-02-01
Full Text Available This paper presents a novel application of nonlinear control theory to heartbeat models. Existing heartbeat models are investigated and modified by incorporating the control input as a pacemaker to provide the control channel. A nonlinear feedback linearization technique is applied to force the output of the systems to generate artificial electrocardiogram (ECG signal using discrete data as the reference inputs. The synthetic ECG may serve as a flexible signal source to assess the effectiveness of a diagnostic ECG signal-processing device.
Nonlinear phenomena at cyclotron resonance
International Nuclear Information System (INIS)
Subbarao, D.; Uma, R.
1986-01-01
Finite amplitude electromagnetic waves in a magnetoplasma which typically occur in situations as in present day wave heating, current drives and other schemes in magnetically confined fusion systems, can show qualitatively different absorption and emission characteristics around resonant frequencies of the plasma because of anharmonicity. Linear wave plasma coupling as well as weak nonlinear effects such as parametric instabilities generally overlook this important effect even though the thresholds for the two phenomena as shown here are comparable. Though the effects described here are relevant to a host of nonlinear resonance effects in fusion plasmas, the authors mainly limit themselves to ECRH
Field guide to nonlinear optics
Powers, Peter E
2013-01-01
Optomechanics is a field of mechanics that addresses the specific design challenges associated with optical systems. This [i]Field Guide [/i]describes how to mount optical components, as well as how to analyze a given design. It is intended for practicing optical and mechanical engineers whose work requires knowledge in both optics and mechanics. This Field Guide is designed for those looking for a condensed and concise source of key concepts, equations, and techniques for nonlinear optics. Topics covered include technologically important effects, recent developments in nonlinear optics
Time series with tailored nonlinearities
Räth, C.; Laut, I.
2015-10-01
It is demonstrated how to generate time series with tailored nonlinearities by inducing well-defined constraints on the Fourier phases. Correlations between the phase information of adjacent phases and (static and dynamic) measures of nonlinearities are established and their origin is explained. By applying a set of simple constraints on the phases of an originally linear and uncorrelated Gaussian time series, the observed scaling behavior of the intensity distribution of empirical time series can be reproduced. The power law character of the intensity distributions being typical for, e.g., turbulence and financial data can thus be explained in terms of phase correlations.
Finite elements of nonlinear continua
Oden, John Tinsley
1972-01-01
Geared toward undergraduate and graduate students, this text extends applications of the finite element method from linear problems in elastic structures to a broad class of practical, nonlinear problems in continuum mechanics. It treats both theory and applications from a general and unifying point of view.The text reviews the thermomechanical principles of continuous media and the properties of the finite element method, and then brings them together to produce discrete physical models of nonlinear continua. The mathematical properties of these models are analyzed, along with the numerical s
Stability analysis of nonlinear systems with slope restricted nonlinearities.
Liu, Xian; Du, Jiajia; Gao, Qing
2014-01-01
The problem of absolute stability of Lur'e systems with sector and slope restricted nonlinearities is revisited. Novel time-domain and frequency-domain criteria are established by using the Lyapunov method and the well-known Kalman-Yakubovich-Popov (KYP) lemma. The criteria strengthen some existing results. Simulations are given to illustrate the efficiency of the results.
Stability Analysis of Nonlinear Systems with Slope Restricted Nonlinearities
Directory of Open Access Journals (Sweden)
Xian Liu
2014-01-01
Full Text Available The problem of absolute stability of Lur’e systems with sector and slope restricted nonlinearities is revisited. Novel time-domain and frequency-domain criteria are established by using the Lyapunov method and the well-known Kalman-Yakubovich-Popov (KYP lemma. The criteria strengthen some existing results. Simulations are given to illustrate the efficiency of the results.
Nonlinear optical properties of silicon waveguides
International Nuclear Information System (INIS)
Tsang, H K; Liu, Y
2008-01-01
Recent work on two-photon absorption (TPA), stimulated Raman scattering (SRS) and optical Kerr effect in silicon-on-insulator (SOI) waveguides is reviewed and some potential applications of these optical nonlinearities, including silicon-based autocorrelation detectors, optical amplifiers, high speed optical switches, optical wavelength converters and self-phase modulation (SPM), are highlighted. The importance of free carriers generated by TPA in nonlinear devices is discussed, and a generalized definition of the nonlinear effective length to cater for nonlinear losses is proposed. How carrier lifetime engineering, and in particular the use of helium ion implantation, can enhance the nonlinear effective length for nonlinear devices is also discussed
Nonlinearity and nonclassicality in a nanomechanical resonator
Energy Technology Data Exchange (ETDEWEB)
Teklu, Berihu [Clermont Universite, Blaise Pascal University, CNRS, PHOTON-N2, Institut Pascal, Aubiere Cedex (France); Universita degli Studi di Milano, Dipartimento di Fisica, Milano (Italy); Ferraro, Alessandro; Paternostro, Mauro [Queen' s University, Centre for Theoretical Atomic, Molecular, and Optical Physics, School of Mathematics and Physics, Belfast (United Kingdom); Paris, Matteo G.A. [Universita degli Studi di Milano, Dipartimento di Fisica, Milano (Italy)
2015-12-15
We address quantitatively the relationship between the nonlinearity of a mechanical resonator and the nonclassicality of its ground state. In particular, we analyze the nonclassical properties of the nonlinear Duffing oscillator (being driven or not) as a paradigmatic example of a nonlinear nanomechanical resonator. We first discuss how to quantify the nonlinearity of this system and then show that the nonclassicality of the ground state, as measured by the volume occupied by the negative part of the Wigner function, monotonically increases with the nonlinearity in all the working regimes addressed in our study. Our results show quantitatively that nonlinearity is a resource to create nonclassical states in mechanical systems. (orig.)
Breugel, van M.
2007-01-01
The succession of tropical secondary forests on abandoned agricultural fields has been studied since long, most often by comparing stands of different age since abandonment. These so-called chronosequence studies have yielded much insight in general patterns of succession and the constraints and
Indian Academy of Sciences (India)
Figure shows formation of two secondary drops of unequal size and their merger. The process is same as the earlier process until t= 0.039 Tc with necking occurring at two places, one at the bottom of the column and the other at the middle. The necking at the middle of the liquid column is due to Raleigh instability.
[Primary and secondary encopresis].
Lang-Langer, Ellen
2007-01-01
While the difficulty of the child to part with its faeces in primary encopresis is linked to the incapability to experience the object as separated and independent from himself, secondary encopresis is a progressed psychical state of development. In this case we have to deal with regression caused by conflict. Two case-studies show clearly the differences.
[Secondary thrombotic microangiopathies].
Coppo, P
2017-11-01
Thrombotic microangiopathies (TMA) are termed secondary when associated to a specific context favouring their occurrence. They encompass mainly TMA associated with pregnancy, allogeneic hematopoietic stem cell transplantation, cancer, drugs, or HIV infection. Secondary TMA represent a heterogeneous group of diseases which clinical presentation largely depends on the associated context. It is therefore mandatory to recognize these conditions since they have a significant impact in TMA management and prognosis. A successful management still represents a challenge in secondary TMA. Significant progresses have been made in the understanding of pregnancy-associated TMA, allowing an improvement of prognosis; on the opposite, other forms of secondary TMA such as hematopoietic stem cell transplantation-associated TMA or TMA associated with chemotherapy remain of dismal prognosis. A better understanding of pathophysiology in these forms of TMA, in association with a more empirical approach through the use of new therapeutic agents that can also help in the understanding on new mechanisms a posteriori, should improve their prognosis. The preliminary encouraging results reported with complement blockers in this field could represent a convincing example. Copyright © 2017 Société Nationale Française de Médecine Interne (SNFMI). Published by Elsevier SAS. All rights reserved.
Secondary coolant purification system
International Nuclear Information System (INIS)
Stiteler, F.Z.; Donohue, J.P.
1978-01-01
The present invention combines the attributes of volatile chemical addition, continuous blowdown, and full flow condensate demineralization. During normal plant operation (defined as no primary to secondary leakage) condensate from the condenser is pumped through a full flow condensate demineralizer system by the condensate pumps. Volatile chemical additions are made. Dissolved and suspended solids are removed in the condensate polishers by ion exchange and/or filtration. At the same time a continuous blowdown of approximately 1 percent of the main steaming rate of the steam generators is maintained. Radiation detectors monitor the secondary coolant. If these monitors indicate no primary to secondary leakage, the blowdown is cooled and returned directly to the condensate pump discharge. If one of the radiation monitors should indicate a primary to secondary leak, when the temperature of the effluent exiting from the blowdown heat exchanger is compatible with the resin specifications of the ion exchangers, the bypass valve causes the blowdown flow to pass through the blowdown ion exchangers
Chemical shift homology in proteins
International Nuclear Information System (INIS)
Potts, Barbara C.M.; Chazin, Walter J.
1998-01-01
The degree of chemical shift similarity for homologous proteins has been determined from a chemical shift database of over 50 proteins representing a variety of families and folds, and spanning a wide range of sequence homologies. After sequence alignment, the similarity of the secondary chemical shifts of C α protons was examined as a function of amino acid sequence identity for 37 pairs of structurally homologous proteins. A correlation between sequence identity and secondary chemical shift rmsd was observed. Important insights are provided by examining the sequence identity of homologous proteins versus percentage of secondary chemical shifts that fall within 0.1 and 0.3 ppm thresholds. These results begin to establish practical guidelines for the extent of chemical shift similarity to expect among structurally homologous proteins
Nonlinear Impedance of Whole Cells Near an Electrode as a Probe of Mitochondrial Activity
Directory of Open Access Journals (Sweden)
John H. Miller Jr.
2011-04-01
Full Text Available By simultaneously measuring the bulk media and electrode interface voltages of a yeast (Saccharomyces cerevisiae suspension subjected to an AC voltage, a yeast-dependent nonlinear response was found only near the current injection electrodes. Computer simulation of yeast near a current injection electrode found an enhanced voltage drop across the yeast near the electrode due to slowed charging of the electrode interfacial capacitance. This voltage drop is sufficient to induce conformation change in membrane proteins. Disruption of the mitochondrial electron transport chain is found to significantly change the measured nonlinear current response, suggesting nonlinear impedance can be used as a non-invasive probe of cellular metabolic activity.
Statistical methods in nonlinear dynamics
Indian Academy of Sciences (India)
Sensitivity to initial conditions in nonlinear dynamical systems leads to exponential divergence of trajectories that are initially arbitrarily close, and hence to unpredictability. Statistical methods have been found to be helpful in extracting useful information about such systems. In this paper, we review briefly some statistical ...
Cosmological effects of nonlinear electrodynamics
International Nuclear Information System (INIS)
Novello, M; Goulart, E; Salim, J M; Bergliaffa, S E Perez
2007-01-01
It will be shown that a given realization of nonlinear electrodynamics, used as a source of Einstein's equations, generates a cosmological model with interesting features, namely a phase of current cosmic acceleration, and the absence of an initial singularity, thus pointing to a way of solving two important problems in cosmology
Nonlinearity, Conservation Law and Shocks
Indian Academy of Sciences (India)
However, genuine nonlinearity is always present in an ideal gas. The conservation form of the equation (25) brings in shocks which cut off the growing part of the amplitUde as shown in. Figure 15. Acknowledgements. The author sincerely thanks the two referees whose valuable comments led to an improvement of the ...
Impurity solitons with quadratic nonlinearities
DEFF Research Database (Denmark)
Clausen, Carl A. Balslev; Torres, Juan P-; Torner, Lluis
1998-01-01
We fmd families of solitary waves mediated by parametric mixing in quadratic nonlinear media that are localized at point-defect impurities. Solitons localized at attractive impurities are found to be dynamically stable. It is shown that localization at the impurity modifies strongly the soliton...
Nonlinear materials for frequency conversion
International Nuclear Information System (INIS)
Velsko, S.P.; Eimerl, D.
1988-01-01
Two figures of merit, the threshold power (P/sub th/) and the limiting volume (V/sub min/) can be used to compare the relative efficiency and economy of new harmonic generating crystals. The properties of barium metaborate and L-Arginine phosphate are used to illustrate the effect of nonlinearity, birefringence, and damage threshold on these figures of merit
Dynamics of nonlinear feedback control
Snippe, H.P.; Hateren, J.H. van
Feedback control in neural systems is ubiquitous. Here we study the mathematics of nonlinear feedback control. We compare models in which the input is multiplied by a dynamic gain (multiplicative control) with models in which the input is divided by a dynamic attenuation (divisive control). The gain
Nonlinear Markov processes: Deterministic case
International Nuclear Information System (INIS)
Frank, T.D.
2008-01-01
Deterministic Markov processes that exhibit nonlinear transition mechanisms for probability densities are studied. In this context, the following issues are addressed: Markov property, conditional probability densities, propagation of probability densities, multistability in terms of multiple stationary distributions, stability analysis of stationary distributions, and basin of attraction of stationary distribution
Nonlinear Dynamics of Nanomechanical Resonators
Ramakrishnan, Subramanian; Gulak, Yuiry; Sundaram, Bala; Benaroya, Haym
2007-03-01
Nanoelectromechanical systems (NEMS) offer great promise for many applications including motion and mass sensing. Recent experimental results suggest the importance of nonlinear effects in NEMS, an issue which has not been addressed fully in theory. We report on a nonlinear extension of a recent analytical model by Armour et al [1] for the dynamics of a single-electron transistor (SET) coupled to a nanomechanical resonator. We consider the nonlinear resonator motion in both (a) the Duffing and (b) nonlinear pendulum regimes. The corresponding master equations are derived and solved numerically and we consider moment approximations as well. In the Duffing case with hardening stiffness, we observe that the resonator is damped by the SET at a significantly higher rate. In the cases of softening stiffness and the pendulum, there exist regimes where the SET adds energy to the resonator. To our knowledge, this is the first instance of a single model displaying both negative and positive resonator damping in different dynamical regimes. The implications of the results for SET sensitivity as well as for, as yet unexplained, experimental results will be discussed. 1. Armour et al. Phys.Rev.B (69) 125313 (2004).
Oscillating solitons in nonlinear optics
Indian Academy of Sciences (India)
The study of solitons in those physical systems reveals some exciting .... With the following power series expansions for g(z,t) and f(z,t): g(z,t) = εg1(z,t) + ... If nonlinearity γ (z) is also taken as a function in figure 1b, the periodic and oscillation.
Oscillating solitons in nonlinear optics
Indian Academy of Sciences (India)
... are derived, and the relevant properties and features of oscillating solitons are illustrated. Oscillating solitons are controlled by the reciprocal of the group velocity and Kerr nonlinearity. Results of this paper will be valuable to the study of dispersion-managed optical communication system and mode-locked fibre lasers.
Nonlinear dynamics and plasma transport
International Nuclear Information System (INIS)
Antonsen, T.M. Jr.; Drake, J.F.; Finn, J.M.; Guzdar, P.N.; Hassam, A.B.; Sagdeev, R.Z.
1992-01-01
In this paper we summarize the progress made over the last year in three different areas of research: (a) shear flow generation and reduced transport in fluids and plasma, (b) nonlinear dynamics and visualization of 3D flows, and (c) application of wavelet analysis to the study of fractal dimensions in experimental and numerical data
Analysis of Nonlinear Dynamic Structures
African Journals Online (AJOL)
Bheema
work a two degrees of freedom nonlinear system with zero memory was ... FRF is the most widely used method in structural dynamics which gives information about the ..... 3.6, which is the waterfall diagram of the same response, as well.
Nonlinear Multigrid for Reservoir Simulation
DEFF Research Database (Denmark)
Christensen, Max la Cour; Eskildsen, Klaus Langgren; Engsig-Karup, Allan Peter
2016-01-01
efficiency for a black-oil model. Furthermore, the use of the FAS method enables a significant reduction in memory usage compared with conventional techniques, which suggests new possibilities for improved large-scale reservoir simulation and numerical efficiency. Last, nonlinear multilevel preconditioning...
Halo Mitigation Using Nonlinear Lattices
Sonnad, Kiran G
2005-01-01
This work shows that halos in beams with space charge effects can be controlled by combining nonlinear focusing and collimation. The study relies on Particle-in-Cell (PIC) simulations for a one dimensional, continuous focusing model. The PIC simulation results show that nonlinear focusing leads to damping of the beam oscillations thereby reducing the mismatch. It is well established that reduced mismatch leads to reduced halo formation. However, the nonlinear damping is accompanied by emittance growth causing the beam to spread in phase space. As a result, inducing nonlinear damping alone cannot help mitigate the halo. To compensate for this expansion in phase space, the beam is collimated in the simulation and further evolution of the beam shows that the halo is not regenerated. The focusing model used in the PIC is analysed using the Lie Transform perturbation theory showing that by averaging over a lattice period, one can reuduce the focusing force to a form that is identical to that used in the PIC simula...
Nonlinear laser-plasma interactions
Kaw, P. K.
2017-12-01
Soon after lasers were invented, there was tremendous curiosity on the nonlinear phenomena which would result in their interaction with a fully ionized plasma. Apart from the basic interest, it was realized that it could be used for the achievement of nuclear fusion in the laboratory. This led us to a paper on the propagation of a laser beam into an inhomogeneous fusion plasma, where it was first demonstrated that light would go up to the critical layer (where the frequency matches the plasma frequency) and get reflected from there with a reflection coefficient of order unity. The reflection coefficient was determined by collisional effects. Since the wave was expected to slow down to near zero group speed at the reflection point, the dominant collision frequency determining the reflection coefficient was the collision frequency at the reflection point. It turned out that the absorption of light was rather small for fusion temperatures. This placed a premium on investigation of nonlinear phenomena which might contribute to the absorption and penetration of the light into high-density plasma. An early investigation showed that electron jitter with respect to ions would be responsible for the excitation of decay instabilities which convert light waves into electrostatic plasma waves and ion waves near the critical frequency. These electrostatic waves would then get absorbed into the plasma even in the collisionless case and lead to plasma heating which is nonlinear. Detailed estimates of this heating were made. Similar nonlinear processes which could lead to stimulated scattering of light in the underdense region (ω >ω _p) were investigated together with a number of other workers. All these nonlinear processes need a critical threshold power for excitation. Another important process which was discovered around the same time had to do with filamentation and trapping of light when certain thresholds were exceeded. All of this work has been extensively verified in
Dynamics of nonlinear feedback control.
Snippe, H P; van Hateren, J H
2007-05-01
Feedback control in neural systems is ubiquitous. Here we study the mathematics of nonlinear feedback control. We compare models in which the input is multiplied by a dynamic gain (multiplicative control) with models in which the input is divided by a dynamic attenuation (divisive control). The gain signal (resp. the attenuation signal) is obtained through a concatenation of an instantaneous nonlinearity and a linear low-pass filter operating on the output of the feedback loop. For input steps, the dynamics of gain and attenuation can be very different, depending on the mathematical form of the nonlinearity and the ordering of the nonlinearity and the filtering in the feedback loop. Further, the dynamics of feedback control can be strongly asymmetrical for increment versus decrement steps of the input. Nevertheless, for each of the models studied, the nonlinearity in the feedback loop can be chosen such that immediately after an input step, the dynamics of feedback control is symmetric with respect to increments versus decrements. Finally, we study the dynamics of the output of the control loops and find conditions under which overshoots and undershoots of the output relative to the steady-state output occur when the models are stimulated with low-pass filtered steps. For small steps at the input, overshoots and undershoots of the output do not occur when the filtering in the control path is faster than the low-pass filtering at the input. For large steps at the input, however, results depend on the model, and for some of the models, multiple overshoots and undershoots can occur even with a fast control path.
Nonlinear Optical Fiber Arrays for Limiting Application
National Research Council Canada - National Science Library
Khoo, Iam-Choon
2006-01-01
.... Measurements show that they possess desirable nonlinear optical such as low-freezing pint, non-volatile, transparent for low light level and possess large effective nonlinear absorption coefficients...
Nonlinear dynamics between linear and impact limits
Pilipchuk, Valery N; Wriggers, Peter
2010-01-01
This book examines nonlinear dynamic analyses based on the existence of strongly nonlinear but simple counterparts to the linear models and tools. Discusses possible application to periodic elastic structures with non-smooth or discontinuous characteristics.
International Conference on Applications in Nonlinear Dynamics
Longhini, Patrick; Palacios, Antonio
2017-01-01
This book presents collaborative research works carried out by experimentalists and theorists around the world in the field of nonlinear dynamical systems. It provides a forum for applications of nonlinear systems while solving practical problems in science and engineering. Topics include: Applied Nonlinear Optics, Sensor, Radar & Communication Signal Processing, Nano Devices, Nonlinear Biomedical Applications, Circuits & Systems, Coupled Nonlinear Oscillator, Precision Timing Devices, Networks, and other contemporary topics in the general field of Nonlinear Science. This book provides a comprehensive report of the various research projects presented at the International Conference on Applications in Nonlinear Dynamics (ICAND 2016) held in Denver, Colorado, 2016. It can be a valuable tool for scientists and engineering interested in connecting ideas and methods in nonlinear dynamics with actual design, fabrication and implementation of engineering applications or devices.
SPARSE ELECTROMAGNETIC IMAGING USING NONLINEAR LANDWEBER ITERATIONS
Desmal, Abdulla; Bagci, Hakan
2015-01-01
minimization problem is solved using nonlinear Landweber iterations, where at each iteration a thresholding function is applied to enforce the sparseness-promoting L0/L1-norm constraint. The thresholded nonlinear Landweber iterations are applied to several two
Torres, Susan J; Robinson, Sian; Orellana, Liliana; O'Connell, Stella L; Grimes, Carley A; Mundell, Niamh L; Dunstan, David W; Nowson, Caryl A; Daly, Robin M
2017-06-01
Resistance training (RT) and increased dietary protein are recommended to attenuate age-related muscle loss in the elderly. This study examined the effect of a lean red meat protein-enriched diet combined with progressive resistance training (RT+Meat) on health-related quality of life (HR-QoL) in elderly women. In this 4-month cluster randomised controlled trial, 100 women aged 60-90 years (mean 73 years) from self-care retirement villages participated in RT twice a week and were allocated either 160 g/d (cooked) lean red meat consumed across 2 meals/d, 6 d/week or ≥1 serving/d (25-30 g) carbohydrates (control group, CRT). HR-QoL (SF-36 Health Survey questionnaire), lower limb maximum muscle strength and lean tissue mass (LTM) (dual-energy X-ray absorptiometry) were assessed at baseline and 4 months. In all, ninety-one women (91 %) completed the study (RT+Meat (n 48); CRT (n 43)). Mean protein intake was greater in RT+Meat than CRT throughout the study (1·3 (sd 0·3) v. 1·1 (sd 0·3) g/kg per d, P<0·05). Exercise compliance (74 %) was not different between groups. After 4 months there was a significant net benefit in the RT+Meat compared with CRT group for overall HR-QoL and the physical component summary (PCS) score (P<0·01), but there were no changes in either group in the mental component summary (MCS) score. Changes in lower limb muscle strength, but not LTM, were positively associated with changes in overall HR-QoL (muscle strength, β: 2·2 (95 % CI 0·1, 4·3), P<0·05). In conclusion, a combination of RT and increased dietary protein led to greater net benefits in overall HR-QoL in elderly women compared with RT alone, which was because of greater improvements in PCS rather than MCS.
Nonlinear diffraction from a virtual beam
DEFF Research Database (Denmark)
Saltiel, Solomon M.; Neshev, Dragomir N.; Krolikowski, Wieslaw
2010-01-01
We observe experimentally a novel type of nonlinear diffraction in the process of two-wave mixing on a nonlinear quadratic grating.We demonstrate that when the nonlinear grating is illuminated simultaneously by two noncollinear beams, a second-harmonic diffraction pattern is generated by a virtual...... beam propagating along the bisector of the two pump beams. The observed iffraction phenomena is a purely nonlinear effect that has no analogue in linear diffraction...
Nonlinear temporal modulation of pulsar radioemission
International Nuclear Information System (INIS)
Chian, A.C.-L.
1984-01-01
A nonlinear theory is discussed for self-modulation of pulsar radio pulses. A nonlinear Schroedinger equation is derived for strong electromagnetic waves propagating in an electron-positron plasma. The nonlinearities arising from wave intensity induced relativistic particle mass variation may excite the modulational instability of circularly and linearly polarized pulsar radiation. The resulting wave envelopes can take the form of periodic wave trains or solitons. These nonlinear stationary wave forms may account for the formation of pulsar microstructures. (Author) [pt
Nonlinear Michelson interferometer for improved quantum metrology
Luis, Alfredo; Rivas, Ángel
2015-01-01
We examine quantum detection via a Michelson interferometer embedded in a gas with Kerr nonlinearity. This nonlinear interferometer is illuminated by pulses of classical light. This strategy combines the robustness against practical imperfections of classical light with the improvement provided by nonlinear processes. Regarding ultimate quantum limits, we stress that, as a difference with linear schemes, the nonlinearity introduces pulse duration as a new variable into play along with the ene...
Solitons in quadratic nonlinear photonic crystals
DEFF Research Database (Denmark)
Corney, Joel Frederick; Bang, Ole
2001-01-01
We study solitons in one-dimensional quadratic nonlinear photonic crystals with modulation of both the linear and nonlinear susceptibilities. We derive averaged equations that include induced cubic nonlinearities, which can be defocusing, and we numerically find previously unknown soliton families....... Because of these induced cubic terms, solitons still exist even when the effective quadratic nonlinearity vanishes and conventional theory predicts that there can be no soliton. We demonstrate that both bright and dark forms of these solitons can propagate stably....
Nonlinear waves in solar plasmas - a review
International Nuclear Information System (INIS)
Ballai, I
2006-01-01
Nonlinearity is a direct consequence of large scale dynamics in the solar plasmas. When nonlinear steepening of waves is balanced by dispersion, solitary waves are generated. In the vicinity of resonances, waves can steepen into nonlinear waves influencing the efficiency of energy deposition. Here we review recent theoretical breakthroughs that have lead to a greater understanding of many aspects of nonlinear waves arising in homogeneous and inhomogeneous solar plasmas
Nonlinear finite element analysis of concrete structures
International Nuclear Information System (INIS)
Ottosen, N.S.
1980-05-01
This report deals with nonlinear finite element analysis of concrete structures loaded in the short-term up until failure. A profound discussion of constitutive modelling on concrete is performed; a model, applicable for general stress states, is described and its predictions are compared with experimental data. This model is implemented in the AXIPLANE-program applicable for axisymmetrick and plane structures. The theoretical basis for this program is given. Using the AXIPLANE-program various concrete structures are analysed up until failure and compared with experimental evidence. These analyses include panels pressure vessel, beams failing in shear and finally a specific pull-out test, the Lok-Test, is considered. In these analyses, the influence of different failure criteria, aggregate interlock, dowel action, secondary cracking, magnitude of compressive strenght, magnitude of tensile strenght and of different post-failure behaviours of the concrete are evaluated. Moreover, it is shown that a suitable analysis of the theoretical data results in a clear insight into the physical behaviour of the considered structures. Finally, it is demonstrated that the AXISPLANE-program for widely different structures exhibiting very delicate structural aspects gives predictions that are in close agreement with experimental evidence. (author)
On the secondary instability of three-dimensional boundary layers
Energy Technology Data Exchange (ETDEWEB)
Janke, E. [DLR Deutsches Zentrum fuer Luft- und Raumfahrt e.V., Goettingen (Germany). Inst. fuer Stroemungsmechanik; Balakumar, P. [Department of Aerospace Engineering, Old Dominion University, Norfolk, VA 23529 (United States)
2000-09-01
One of the possible transition scenarios in three-dimensional boundary layers, the saturation of stationary crossflow vortices and their secondary instability to high-frequency disturbances, is studied using the parabolized stability equations (PSE) and Floquet theory. Starting from nonlinear PSE solutions, we investigate the region where a purely stationary crossflow disturbance saturates for its secondary instability characteristics utilizing global and local eigenvalue solvers that are based on the implicitly restarted Arnoldi method and a Newton-Raphson technique, respectively. Results are presented for swept Hiemenz flow and the DLR swept flat plate experiment. The main focuses of this study are on the existence of multiple roots in the eigenvalue spectrum that could explain experimental observations of time-dependent occurrences of an explosive growth of traveling disturbances, on the origin of high-frequency disturbances, as well as on gaining more information about threshold amplitudes of primary disturbances necessary for the growth of secondary disturbances. (orig.)
Frequency response functions for nonlinear convergent systems
Pavlov, A.V.; Wouw, van de N.; Nijmeijer, H.
2007-01-01
Convergent systems constitute a practically important class of nonlinear systems that extends the class of asymptotically stable linear time-invariant systems. In this note, we extend frequency response functions defined for linear systems to nonlinear convergent systems. Such nonlinear frequency
Nonlinear dynamics aspects of particle accelerators
International Nuclear Information System (INIS)
Araki, H.; Ehlers, J.; Hepp, K.; Kippenhahn, R.; Weidenmuller, A.; Zittartz, J.
1986-01-01
This book contains 18 selections. Some of the titles are: Integrable and Nonintegrable Hamiltonian Systems; Nonlinear Dynamics Aspects of Modern Storage Rings; Nonlinear Beam-Beam Resonances; Synchro-Betatron Resonances; Review of Beam-Beam Simulations; and Perturbation Method in Nonlinear Dynamics
Nonlinear approaches in engineering applications 2
Jazar, Reza N
2013-01-01
Provides updated principles and applications of the nonlinear approaches in solving engineering and physics problems Demonstrates how nonlinear approaches may open avenues to better, safer, cheaper systems with less energy consumption Has a strong emphasis on the application, physical meaning, and methodologies of nonlinear approaches in different engineering and science problems
Averaging of nonlinearity-managed pulses
International Nuclear Information System (INIS)
Zharnitsky, Vadim; Pelinovsky, Dmitry
2005-01-01
We consider the nonlinear Schroedinger equation with the nonlinearity management which describes Bose-Einstein condensates under Feshbach resonance. By using an averaging theory, we derive the Hamiltonian averaged equation and compare it with other averaging methods developed for this problem. The averaged equation is used for analytical approximations of nonlinearity-managed solitons
Nonlinear science as a fluctuating research frontier
International Nuclear Information System (INIS)
He Jihuan
2009-01-01
Nonlinear science has had quite a triumph in all conceivable applications in science and technology, especially in high energy physics and nanotechnology. COBE, which was awarded the physics Nobel Prize in 2006, might be probably more related to nonlinear science than the Big Bang theory. Five categories of nonlinear subjects in research frontier are pointed out.
Variational principles for nonlinear piezoelectric materials
Energy Technology Data Exchange (ETDEWEB)
Rodriguez-Ramos, R.; Guinovart-Diaz, R. [Universidad de la Habana, Facultad de Matematica y Computacion, Vedado, Habana (Cuba); Pobedria, B.E. [Moscow State University M. V. Lomonosov, Composites Department, Moscow (Russian Federation); Padilla, P. [Universidad Nacional Autonoma de Mexico, Instituto de Investigaciones en Matematicas Aplicadas y en Sistemas (IIMAS), Cd. Universitaria, Mexico D.F. (Mexico); Bravo-Castillero, J. [Universidad de la Habana, Facultad de Matematica y Computacion, Vedado, Habana (Cuba); Campus Estado de Mexico. Division de Arquitectura e Ingenieria, Instituto Tecnologico de Estudios Superiores de Monterrey, Atizapan de Zaragoza, Estado de Mexico (Mexico); Maugin, G.A. [Universite Pierre et Marie Curie. Case 162, UMR 7607 CNRS, Laboratoire de Modelisation en Mecanique, Paris Cedex 05 (France)
2004-12-01
In the present paper, we consider the behavior of nonlinear piezoelectric materials by generalization for this case of the Hashin-Shtrikman variational principles. The new general formulation used here differs from others, because, it gives the possibility to evaluate the upper and lower Hashin-Shtrikman bounds for specific physical nonlinearities of piezoelectric materials. Geometrical nonlinearities are not considered. (orig.)
On secondary loops in LAOS via self-intersection of Lissajous–Bowditch curves
Ewoldt, Randy H.; McKinley, Gareth H.
2009-01-01
When the shear stress measured in large amplitude oscillatory shear (LAOS) deformation is represented as a 2-D Lissajous–Bowditch curve, the corresponding trajectory can appear to self-intersect and form secondary loops. This self-intersection is a general consequence of a strongly nonlinear material response to the imposed oscillatory forcing and can be observed for various material systems and constitutive models. We derive the mathematical criteria for the formation of secondary loops, qua...
Secondary hypertension in adults.
Puar, Troy Hai Kiat; Mok, Yingjuan; Debajyoti, Roy; Khoo, Joan; How, Choon How; Ng, Alvin Kok Heong
2016-05-01
Secondary hypertension occurs in a significant proportion of adult patients (~10%). In young patients, renal causes (glomerulonephritis) and coarctation of the aorta should be considered. In older patients, primary aldosteronism, obstructive sleep apnoea and renal artery stenosis are more prevalent than previously thought. Primary aldosteronism can be screened by taking morning aldosterone and renin levels, and should be considered in patients with severe, resistant or hypokalaemia-associated hypertension. Symptoms of obstructive sleep apnoea should be sought. Worsening of renal function after starting an angiotensin-converting enzyme inhibitor suggests the possibility of renal artery stenosis. Recognition, diagnosis and treatment of secondary causes of hypertension lead to good clinical outcomes and the possible reversal of end-organ damage, in addition to blood pressure control. As most patients with hypertension are managed at the primary care level, it is important for primary care physicians to recognise these conditions and refer patients appropriately. Copyright: © Singapore Medical Association.
Secondary combined suicide pact.
Jayanth, S H; Girish Chandra, Y P; Hugar, Basappa S; Kainoor, Sunilkumar
2014-03-01
This article reports a combined suicide pact, where in a young couple; a 26 year old male and a 20 year old female committed suicide by using two methods. The couple had resorted to hanging and self-immolation to prevent failure of single method alone. In secondary combined suicides, several other methods of suicide are tried after the first method chosen has failed. It is primary combined suicide only when two or more methods are used simultaneously. Both types of combined suicide by one individual is well reported in the literature whereas the same by two persons together is rare. In this report, the deceased were disappointed lovers, poor and the family members were against their marriage. The investigation of scene, methods employed to commit suicide, autopsy findings and the interview with their relatives altogether suggested that it was a secondary combined suicide pact. Copyright © 2014 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.
THE SECONDARY EXTINCTION CORRECTION
Energy Technology Data Exchange (ETDEWEB)
Zachariasen, W. H.
1963-03-15
It is shown that Darwin's formula for the secondary extinction correction, which has been universally accepted and extensively used, contains an appreciable error in the x-ray diffraction case. The correct formula is derived. As a first order correction for secondary extinction, Darwin showed that one should use an effective absorption coefficient mu + gQ where an unpolarized incident beam is presumed. The new derivation shows that the effective absorption coefficient is mu + 2gQ(1 + cos/sup 4/2 theta )/(1 plus or minus cos/sup 2/2 theta )/s up 2/, which gives mu + gQ at theta =0 deg and theta = 90 deg , but mu + 2gQ at theta = 45 deg . Darwin's theory remains valid when applied to neutron diffraction. (auth)
Secondary Breast Augmentation.
Brown, Mitchell H; Somogyi, Ron B; Aggarwal, Shagun
2016-07-01
After studying this article, the participant should be able to: 1. Assess common clinical problems in the secondary breast augmentation patient. 2. Describe a treatment plan to correct the most common complications of breast augmentation. 3. Provide surgical and nonsurgical options for managing complications of breast augmentation. 4. Decrease the incidence of future complications through accurate assessment, preoperative planning, and precise surgical technique. Breast augmentation has been increasing steadily in popularity over the past three decades. Many of these patients present with secondary problems or complications following their primary breast augmentation. Two of the most common complications are capsular contracture and implant malposition. Familiarity and comfort with the assessment and management of these complications is necessary for all plastic surgeons. An up-to-date understanding of current devices and techniques may decrease the need to manage future complications from the current cohort of breast augmentation patients.
Lie Symmetries and Solitons in Nonlinear Systems with Spatially Inhomogeneous Nonlinearities
International Nuclear Information System (INIS)
Belmonte-Beitia, Juan; Perez-Garcia, Victor M.; Vekslerchik, Vadym; Torres, Pedro J.
2007-01-01
Using Lie group theory and canonical transformations, we construct explicit solutions of nonlinear Schroedinger equations with spatially inhomogeneous nonlinearities. We present the general theory, use it to show that localized nonlinearities can support bound states with an arbitrary number solitons, and discuss other applications of interest to the field of nonlinear matter waves
DEFF Research Database (Denmark)
Christiansen, Dorte Mølgaard; Bak, Rikke; Elklit, Ask
2012-01-01
secondary victims, including family members, partners, and friends of male and female rape victims. We found that many respondents found it difficult to support the PV and that their relationship with the PV was often affected by the assault. Furthermore, the sample showed significant levels...... of social support for the respondent, and feeling let down by others. The respondents were generally interested in friend-, family-, and partner-focused interventions, particularly in receiving education about how best to support a rape victim...
International Nuclear Information System (INIS)
Shigeru Aoki
2005-01-01
The secondary system such as pipings, tanks and other mechanical equipment is installed in the primary system such as building. The important secondary systems should be designed to maintain their function even if they are subjected to destructive earthquake excitations. The secondary system has many nonlinear characteristics. Impact and friction characteristic, which are observed in mechanical supports and joints, are common nonlinear characteristics. As impact damper and friction damper, impact and friction characteristic are used for reduction of seismic response. In this paper, analytical methods of the first excursion probability of the secondary system with impact and friction, subjected to earthquake excitation are proposed. By using the methods, the effects of impact force, gap size and friction force on the first excursion probability are examined. When the tolerance level is normalized by the maximum response of the secondary system without impact or friction characteristics, variation of the first excursion probability is very small for various values of the natural period. In order to examine the effectiveness of the proposed method, the obtained results are compared with those obtained by the simulation method. Some estimation methods for the maximum response of the secondary system with nonlinear characteristics have been developed. (author)
Nonlinear PT-symmetric plaquettes
International Nuclear Information System (INIS)
Li Kai; Kevrekidis, P G; Malomed, Boris A; Günther, Uwe
2012-01-01
We introduce four basic two-dimensional (2D) plaquette configurations with onsite cubic nonlinearities, which may be used as building blocks for 2D PT-symmetric lattices. For each configuration, we develop a dynamical model and examine its PTsymmetry. The corresponding nonlinear modes are analyzed starting from the Hamiltonian limit, with zero value of the gain–loss coefficient, γ. Once the relevant waveforms have been identified (chiefly, in an analytical form), their stability is examined by means of linearization in the vicinity of stationary points. This reveals diverse and, occasionally, fairly complex bifurcations. The evolution of unstable modes is explored by means of direct simulations. In particular, stable localized modes are found in these systems, although the majority of identified solutions are unstable. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Quantum physics with non-Hermitian operators’. (paper)
Oscillating nonlinear acoustic shock waves
DEFF Research Database (Denmark)
Gaididei, Yuri; Rasmussen, Anders Rønne; Christiansen, Peter Leth
2016-01-01
We investigate oscillating shock waves in a tube using a higher order weakly nonlinear acoustic model. The model includes thermoviscous effects and is non isentropic. The oscillating shock waves are generated at one end of the tube by a sinusoidal driver. Numerical simulations show that at resona......We investigate oscillating shock waves in a tube using a higher order weakly nonlinear acoustic model. The model includes thermoviscous effects and is non isentropic. The oscillating shock waves are generated at one end of the tube by a sinusoidal driver. Numerical simulations show...... polynomial in the space and time variables, we find analytical approximations to the observed single shock waves in an infinitely long tube. Using perturbation theory for the driven acoustic system approximative analytical solutions for the off resonant case are determined....
An efficient nonlinear Feshbach engine
Li, Jing; Fogarty, Thomás; Campbell, Steve; Chen, Xi; Busch, Thomas
2018-01-01
We investigate a thermodynamic cycle using a Bose-Einstein condensate (BEC) with nonlinear interactions as the working medium. Exploiting Feshbach resonances to change the interaction strength of the BEC allows us to produce work by expanding and compressing the gas. To ensure a large power output from this engine these strokes must be performed on a short timescale, however such non-adiabatic strokes can create irreversible work which degrades the engine’s efficiency. To combat this, we design a shortcut to adiabaticity which can achieve an adiabatic-like evolution within a finite time, therefore significantly reducing the out-of-equilibrium excitations in the BEC. We investigate the effect of the shortcut to adiabaticity on the efficiency and power output of the engine and show that the tunable nonlinearity strength, modulated by Feshbach resonances, serves as a useful tool to enhance the system’s performance.
Simulating nonlinear neutrino flavor evolution
Duan, H.; Fuller, G. M.; Carlson, J.
2008-10-01
We discuss a new kind of astrophysical transport problem: the coherent evolution of neutrino flavor in core collapse supernovae. Solution of this problem requires a numerical approach which can simulate accurately the quantum mechanical coupling of intersecting neutrino trajectories and the associated nonlinearity which characterizes neutrino flavor conversion. We describe here the two codes developed to attack this problem. We also describe the surprising phenomena revealed by these numerical calculations. Chief among these is that the nonlinearities in the problem can engineer neutrino flavor transformation which is dramatically different to that in standard Mikheyev Smirnov Wolfenstein treatments. This happens even though the neutrino mass-squared differences are measured to be small, and even when neutrino self-coupling is sub-dominant. Our numerical work has revealed potential signatures which, if detected in the neutrino burst from a Galactic core collapse event, could reveal heretofore unmeasurable properties of the neutrinos, such as the mass hierarchy and vacuum mixing angle θ13.
New approaches to nonlinear waves
2016-01-01
The book details a few of the novel methods developed in the last few years for studying various aspects of nonlinear wave systems. The introductory chapter provides a general overview, thematically linking the objects described in the book. Two chapters are devoted to wave systems possessing resonances with linear frequencies (Chapter 2) and with nonlinear frequencies (Chapter 3). In the next two chapters modulation instability in the KdV-type of equations is studied using rigorous mathematical methods (Chapter 4) and its possible connection to freak waves is investigated (Chapter 5). The book goes on to demonstrate how the choice of the Hamiltonian (Chapter 6) or the Lagrangian (Chapter 7) framework allows us to gain a deeper insight into the properties of a specific wave system. The final chapter discusses problems encountered when attempting to verify the theoretical predictions using numerical or laboratory experiments. All the chapters are illustrated by ample constructive examples demonstrating the app...
A solution to nonlinearity problems
International Nuclear Information System (INIS)
Neuffer, D.V.
1989-01-01
New methods of correcting dynamic nonlinearities resulting from the multipole content of a synchrotron or transport line are presented. In a simplest form, correction elements are places at the center (C) of the accelerator half-cells as well as near the focusing (F) and defocusing (D) quadrupoles. In a first approximation, the corrector strengths follow Simpson's Rule, forming an accurate quasi-local canceling approximation to the nonlinearity. The F, C, and D correctors may also be used to obtain precise control of the horizontal, coupled, and vertical motion. Correction by three or more orders of magnitude can be obtained, and simple solutions to a fundamental problem in beam transport have been obtained. 13 refs., 1 fig., 1 tab
Nonlinear waves and pattern dynamics
Pelinovsky, Efim; Mutabazi, Innocent
2018-01-01
This book addresses the fascinating phenomena associated with nonlinear waves and spatio-temporal patterns. These appear almost everywhere in nature from sand bed forms to brain patterns, and yet their understanding still presents fundamental scientific challenges. The reader will learn here, in particular, about the current state-of-the art and new results in: Nonlinear water waves: resonance, solitons, focusing, Bose-Einstein condensation, as well as and their relevance for the sea environment (sea-wind interaction, sand bed forms, fiber clustering) Pattern formation in non-equilibrium media: soap films, chimera patterns in oscillating media, viscoelastic Couette-Taylor flow, flow in the wake behind a heated cylinder, other pattern formation. The editors and authors dedicate this book to the memory of Alexander Ezersky, Professor of Fluid Mechanics at the University of Caen Normandie (France) from September 2007 to July 2016. Before 2007, he had served as a Senior Scientist at the Institute of Applied Physi...
A programmable nonlinear acoustic metamaterial
Directory of Open Access Journals (Sweden)
Tianzhi Yang
2017-09-01
Full Text Available Acoustic metamaterials with specifically designed lattices can manipulate acoustic/elastic waves in unprecedented ways. Whereas there are many studies that focus on passive linear lattice, with non-reconfigurable structures. In this letter, we present the design, theory and experimental demonstration of an active nonlinear acoustic metamaterial, the dynamic properties of which can be modified instantaneously with reversibility. By incorporating active and nonlinear elements in a single unit cell, a real-time tunability and switchability of the band gap is achieved. In addition, we demonstrate a dynamic “editing” capability for shaping transmission spectra, which can be used to create the desired band gap and resonance. This feature is impossible to achieve in passive metamaterials. These advantages demonstrate the versatility of the proposed device, paving the way toward smart acoustic devices, such as logic elements, diode and transistor.
Some nonlinear space decomposition algorithms
Energy Technology Data Exchange (ETDEWEB)
Tai, Xue-Cheng; Espedal, M. [Univ. of Bergen (Norway)
1996-12-31
Convergence of a space decomposition method is proved for a general convex programming problem. The space decomposition refers to methods that decompose a space into sums of subspaces, which could be a domain decomposition or a multigrid method for partial differential equations. Two algorithms are proposed. Both can be used for linear as well as nonlinear elliptic problems and they reduce to the standard additive and multiplicative Schwarz methods for linear elliptic problems. Two {open_quotes}hybrid{close_quotes} algorithms are also presented. They converge faster than the additive one and have better parallelism than the multiplicative method. Numerical tests with a two level domain decomposition for linear, nonlinear and interface elliptic problems are presented for the proposed algorithms.
Nonlinear beam expander for ESNIT
International Nuclear Information System (INIS)
Rusthoi, D.P.; Blind, B.; Garnett, R.W.; Hanna, D.S.; Jason, A.J.; Kraus, R.H. Jr.; Neri, F.
1994-01-01
We describe the design of a beam-redistribution and expansion system for the Japanese Atomic Energy Research Institute (JAERI) Energy Selective Neutron Irradiation Test Facility (ESNIT). The system tailors the beam exiting a deuteron accelerator at energies from 20 to 35 MeV for deposition on a lithium neutron-production target. A uniform beam-intensity distribution in a well-defined irradiation area is inquired at the target and is achieved by the use of nonlinear elements. The design of the high-energy beam transport (HEBT) for ESNIT includes a 90 degree achromatic bend, a matching section with an energy-compacting cavity, a nonlinear beam expander, a target imager, a shielding dipole, and an rf-cavity system to add energy spread to the beam before it impinges on the target. The system meets performance requirements at multiple energies and currents, and for different spot sizes on target
Characteristics and generation of secondary jets and secondary gigantic jets
Lee, Li-Jou; Huang, Sung-Ming; Chou, Jung-Kung; Kuo, Cheng-Ling; Chen, Alfred B.; Su, Han-Tzong; Hsu, Rue-Rou; Frey, Harald U.; Takahashi, Yukihiro; Lee, Lou-Chuang
2012-06-01
Secondary transient luminous events (TLEs) recorded by the ISUAL-FORMOSAT2 mission can either be secondary jets or secondary gigantic jets (GJs), depending on their terminal altitudes. The secondary jets emerge from the cloud top beneath the preceding sprites and extend upward to the base of the sprites at ˜50 km. The secondary jets likely are negative electric discharges with vertically straight luminous columns, morphologically resembling the trailing jet of the type-I GJs. The number of luminous columns in a secondary jet seems to be affected by the size of the effective capacitor plate formed near the base of the preceding sprites and the charge distribution left behind by the sprite-inducing positive cloud-to-ground discharges. The secondary GJs originate from the cloud top under the shielding area of the preceding sprites, and develop upward to reach the lower ionosphere at ˜90 km. The observed morphology of the secondary GJs can either be the curvy shifted secondary GJs extending outside the region occupied by the preceding sprites or the straight pop-through secondary GJs developing through the center of the preceding circular sprites. A key factor in determining the terminal height of the secondary TLEs appears to be the local ionosphere boundary height that established by the preceding sprites. The abundance and the distribution of the negative charge in the thundercloud following the sprite-inducing positive cloud-to-ground discharges may play important role in the generation of the secondary TLEs.
Nonlinear electromagnetic susceptibilities of unmagnetized plasmas
International Nuclear Information System (INIS)
Yoon, Peter H.
2005-01-01
Fully electromagnetic nonlinear susceptibilities of unmagnetized plasmas are analyzed in detail. Concrete expressions of the second-order nonlinear susceptibility are found in various forms in the literature, usually in connection with the discussions of various three-wave decay processes, but the third-order susceptibilities are rarely discussed. The second-order susceptibility is pertinent to nonlinear wave-wave interactions (i.e., the decay/coalescence), whereas the third-order susceptibilities affect nonlinear wave-particle interactions (i.e., the induced scattering). In the present article useful approximate analytical expressions of these nonlinear susceptibilities that can be readily utilized in various situations are derived
Nonlinear plasma waves excited near resonance
International Nuclear Information System (INIS)
Cohen, B.I.; Kaufman, A.N.
1977-01-01
The nonlinear resonant response of a uniform plasma to an external plane-wave field is formulated in terms of the mismatch Δ/sub n l/ between the driving frequency and the time-dependent, complex, nonlinear normal mode frequency at the driving wavenumber. This formalism is applied to computer simulations of this process, yielding a deduced nonlinear frequency shift. The time dependence of the nonlinear phenomena, at frequency Δ/sub n l/ and at the bounce frequency of the resonant particles, is analyzed. The interdependence of the nonlinear features is described by means of energy and momentum relations
Generalized solutions of nonlinear partial differential equations
Rosinger, EE
1987-01-01
During the last few years, several fairly systematic nonlinear theories of generalized solutions of rather arbitrary nonlinear partial differential equations have emerged. The aim of this volume is to offer the reader a sufficiently detailed introduction to two of these recent nonlinear theories which have so far contributed most to the study of generalized solutions of nonlinear partial differential equations, bringing the reader to the level of ongoing research.The essence of the two nonlinear theories presented in this volume is the observation that much of the mathematics concernin
Nonlinear fiber optics formerly quantum electronics
Agrawal, Govind
1995-01-01
The field of nonlinear fiber optics has grown substantially since the First Edition of Nonlinear Fiber Optics, published in 1989. Like the First Edition, this Second Edition is a comprehensive, tutorial, and up-to-date account of nonlinear optical phenomena in fiber optics. It synthesizes widely scattered research material and presents it in an accessible manner for students and researchers already engaged in or wishing to enter the field of nonlinear fiber optics. Particular attention is paid to the importance of nonlinear effects in the design of optical fiber communication systems. This is
Nonlinear Pricing with Random Participation
Jean-Charles Rochet; Lars A. Stole
2002-01-01
The canonical selection contracting programme takes the agent's participation decision as deterministic and finds the optimal contract, typically satisfying this constraint for the worst type. Upon weakening this assumption of known reservation values by introducing independent randomness into the agents' outside options, we find that some of the received wisdom from mechanism design and nonlinear pricing is not robust and the richer model which allows for stochastic participation affords a m...
Nonlinear dynamics in cardiac conduction
Kaplan, D. T.; Smith, J. M.; Saxberg, B. E.; Cohen, R. J.
1988-01-01
Electrical conduction in the heart shows many phenomena familiar from nonlinear dynamics. Among these phenomena are multiple basins of attraction, phase locking, and perhaps period-doubling bifurcations and chaos. We describe a simple cellular-automation model of electrical conduction which simulates normal conduction patterns in the heart as well as a wide range of disturbances of heart rhythm. In addition, we review the application of percolation theory to the analysis of the development of complex, self-sustaining conduction patterns.
Nonlinear positron acoustic solitary waves
International Nuclear Information System (INIS)
Tribeche, Mouloud; Aoutou, Kamel; Younsi, Smain; Amour, Rabia
2009-01-01
The problem of nonlinear positron acoustic solitary waves involving the dynamics of mobile cold positrons is addressed. A theoretical work is presented to show their existence and possible realization in a simple four-component plasma model. The results should be useful for the understanding of the localized structures that may occur in space and laboratory plasmas as new sources of cold positrons are now well developed.
Статья Редакционная
2014-01-01
The workshop of the Nonlinear Dynamics scientific-educational center continued its work in 2014, focusing on methods of the dynamical system analysis and studies of their behavior. More than 30 talks in the field of scientific-educational center research have been made this year. The talk topics included numerical analysis of traveling waves in the Fisher–KPP equation with delay and simulations of the twophase heat distribution problem using heterogeneous computing architectures. In a number ...
Nonlinear Pricing to Produce Information
David J. Braden; Shmuel S. Oren
1994-01-01
We investigate the firm's dynamic nonlinear pricing problem when facing consumers whose tastes vary according to a scalar index. We relax the standard assumption that the firm knows the distribution of this index. In general the firm should determine its marginal price schedule as if it were myopic, and produce information by lowering the price schedule; “bunching” consumers at positive purchase levels should be avoided. As a special case we also consider a market characterized by homogeneous...
Nonlinear Relaxation in Population Dynamics
Cirone, Markus A.; de Pasquale, Ferdinando; Spagnolo, Bernardo
We analyze the nonlinear relaxation of a complex ecosystem composed of many interacting species. The ecological system is described by generalized Lotka-Volterra equations with a multiplicative noise. The transient dynamics is studied in the framework of the mean field theory and with random interaction between the species. We focus on the statistical properties of the asymptotic behaviour of the time integral of the ith population and on the distribution of the population and of the local field.
Nonlinear problems in theoretical physics
International Nuclear Information System (INIS)
Ranada, A.F.
1979-01-01
This volume contains the lecture notes and review talks delivered at the 9th GIFT international seminar on theoretical physics on the general subject 'Nonlinear Problems in Theoretical Physics'. Mist contributions deal with recent developments in the theory of the spectral transformation and solitons, but there are also articles from the field of transport theory and plasma physics and an unconventional view of classical and quantum electrodynamics. All contributions to this volume will appear under their corresponding subject categories. (HJ)
Scalable Nonlinear AUC Maximization Methods
Khalid, Majdi; Ray, Indrakshi; Chitsaz, Hamidreza
2017-01-01
The area under the ROC curve (AUC) is a measure of interest in various machine learning and data mining applications. It has been widely used to evaluate classification performance on heavily imbalanced data. The kernelized AUC maximization machines have established a superior generalization ability compared to linear AUC machines because of their capability in modeling the complex nonlinear structure underlying most real world-data. However, the high training complexity renders the kernelize...
Interactive Nonlinear Multiobjective Optimization Methods
Miettinen, Kaisa; Hakanen, Jussi; Podkopaev, Dmitry
2016-01-01
An overview of interactive methods for solving nonlinear multiobjective optimization problems is given. In interactive methods, the decision maker progressively provides preference information so that the most satisfactory Pareto optimal solution can be found for her or his. The basic features of several methods are introduced and some theoretical results are provided. In addition, references to modifications and applications as well as to other methods are indicated. As the...
Nonlinear filtering with particle filters
Haslehner, Mylène
2014-01-01
Convective phenomena in the atmosphere, such as convective storms, are characterized by very fast, intermittent and seemingly stochastic processes. They are thus difficult to predict with Numerical Weather Prediction (NWP) models, and difficult to estimate with data assimilation methods that combine prediction and observations. In this thesis, nonlinear data assimilation methods are tested on two idealized convective scale cloud models, developed in [58] and [59]. The aim of this work was to ...
Some nonlinear challenges in biology
International Nuclear Information System (INIS)
Mosconi, Francesco; Julou, Thomas; Desprat, Nicolas; Sinha, Deepak Kumar; Allemand, Jean-François; Croquette, Vincent; Bensimon, David
2008-01-01
Driven by a deluge of data, biology is undergoing a transition to a more quantitative science. Making sense of the data, building new models, asking the right questions and designing smart experiments to answer them are becoming ever more relevant. In this endeavour, nonlinear approaches can play a fundamental role. The biochemical reactions that underlie life are very often nonlinear. The functional features exhibited by biological systems at all levels (from the activity of an enzyme to the organization of a colony of ants, via the development of an organism or a functional module like the one responsible for chemotaxis in bacteria) are dynamically robust. They are often unaffected by order of magnitude variations in the dynamical parameters, in the number or concentrations of actors (molecules, cells, organisms) or external inputs (food, temperature, pH, etc). This type of structural robustness is also a common feature of nonlinear systems, exemplified by the fundamental role played by dynamical fixed points and attractors and by the use of generic equations (logistic map, Fisher–Kolmogorov equation, the Stefan problem, etc.) in the study of a plethora of nonlinear phenomena. However, biological systems differ from these examples in two important ways: the intrinsic stochasticity arising from the often very small number of actors and the role played by evolution. On an evolutionary time scale, nothing in biology is frozen. The systems observed today have evolved from solutions adopted in the past and they will have to adapt in response to future conditions. The evolvability of biological system uniquely characterizes them and is central to biology. As the great biologist T Dobzhansky once wrote: 'nothing in biology makes sense except in the light of evolution'. (open problem)
Nonlinear Single Spin Spectrum Analayzer
Kotler, Shlomi; Akerman, Nitzan; Glickman, Yinnon; Ozeri, Roee
2014-05-01
Qubits are excellent probes of their environment. When operating in the linear regime, they can be used as linear spectrum analyzers of the noise processes surrounding them. These methods fail for strong non-Gaussian noise where the qubit response is no longer linear. Here we solve the problem of nonlinear spectral analysis, required for strongly coupled environments. Our non-perturbative analytic model shows a nonlinear signal dependence on noise power, resulting in a spectral resolution beyond the Fourier limit as well as frequency mixing. We developed a noise characterization scheme adapted to this non-linearity. We then applied it using a single trapped 88Sr+ ion as the a sensitive probe of strong, non-Gaussian, discrete magnetic field noise. With this method, we attained a ten fold improvement over the standard Fourier limit. Finally, we experimentally compared the performance of equidistant vs. Uhrig modulation schemes for spectral analysis. Phys. Rev. Lett. 110, 110503 (2013), Synopsis at http://physics.aps.org/synopsis-for/10.1103/PhysRevLett.110.110503 Current position: National Institute of Standards and Tehcnology, Boulder, CO.
Focus issue introduction: nonlinear photonics.
Akhmediev, Nail; Rottwitt, Karsten
2012-11-19
It is now 23 years since the first Topical Meeting "Nonlinear Guided Wave Phenomena" (Houston, TX, February 2-4, 1989) has been organised by George Stegeman and Allan Boardman with support of the Optical Society of America. These series of the OSA conferences known as NLGW, continued under the name "Nonlinear Photonics" starting from 2007. The latest one, in Colorado Springs in June 17-21, 2012 has been a great success despite the fierce fires advancing around the city at the time of the conference. This Focus issue is a collection of several papers presented at the conference with extended content submitted to Optics Express. Although this collection is small in comparison to the total number of papers presented at the conference, it gives a flavor of the topics considered at the meeting. It is also worthy to mention here that the next meeting "Nonlinear Photonics" is planned to be held in Barcelona - one of the main European centers on this subject.
Nonlinear effects in water waves
International Nuclear Information System (INIS)
Janssen, P.A.E.M.
1989-05-01
This set of lecture notes on nonlinear effects in water waves was written on the occasion of the first ICTP course on Ocean Waves and Tides held from 26 September until 28 October 1988 in Trieste, Italy. It presents a summary and unification of my knowledge on nonlinear effects of gravity waves on an incompressible fluid without vorticity. The starting point of the theory is the Hamiltonian for water waves. The evolution equations of both weakly nonlinear, shallow water and deep water gravity waves are derived by suitable approximation of the energy of the waves, resulting in the Korteweg-de Vries equation and the Zakharov equation, respectively. Next, interesting properties of the KdV equation (solitons) and the Zakharov equation (instability of a finite amplitude wave train) are discussed in some detail. Finally, the evolution of a homogeneous, random wave field due to resonant four wave processes is considered and the importance of this process for ocean wave prediction is pointed out. 38 refs, 21 figs
Causes of secondary headache (image)
Temporomandibular joint, or TMJ, dysfunction, can be a cause of secondary headache. Secondary headaches result from underlying disorders which produce pain as a symptom. The TMJ may become painful and dysfunctional as a result ...
Adaptive regression for modeling nonlinear relationships
Knafl, George J
2016-01-01
This book presents methods for investigating whether relationships are linear or nonlinear and for adaptively fitting appropriate models when they are nonlinear. Data analysts will learn how to incorporate nonlinearity in one or more predictor variables into regression models for different types of outcome variables. Such nonlinear dependence is often not considered in applied research, yet nonlinear relationships are common and so need to be addressed. A standard linear analysis can produce misleading conclusions, while a nonlinear analysis can provide novel insights into data, not otherwise possible. A variety of examples of the benefits of modeling nonlinear relationships are presented throughout the book. Methods are covered using what are called fractional polynomials based on real-valued power transformations of primary predictor variables combined with model selection based on likelihood cross-validation. The book covers how to formulate and conduct such adaptive fractional polynomial modeling in the s...
Topology optimization of nonlinear optical devices
DEFF Research Database (Denmark)
Jensen, Jakob Søndergaard
2011-01-01
This paper considers the design of nonlinear photonic devices. The nonlinearity stems from a nonlinear material model with a permittivity that depends on the local time-averaged intensity of the electric field. A finite element model is developed for time-harmonic wave propagation and an incremen......This paper considers the design of nonlinear photonic devices. The nonlinearity stems from a nonlinear material model with a permittivity that depends on the local time-averaged intensity of the electric field. A finite element model is developed for time-harmonic wave propagation...... limiter. Here, air, a linear and a nonlinear material are distributed so that the wave transmission displays a strong sensitivity to the amplitude of the incoming wave....
Nonlinear filtering for LIDAR signal processing
Directory of Open Access Journals (Sweden)
D. G. Lainiotis
1996-01-01
Full Text Available LIDAR (Laser Integrated Radar is an engineering problem of great practical importance in environmental monitoring sciences. Signal processing for LIDAR applications involves highly nonlinear models and consequently nonlinear filtering. Optimal nonlinear filters, however, are practically unrealizable. In this paper, the Lainiotis's multi-model partitioning methodology and the related approximate but effective nonlinear filtering algorithms are reviewed and applied to LIDAR signal processing. Extensive simulation and performance evaluation of the multi-model partitioning approach and its application to LIDAR signal processing shows that the nonlinear partitioning methods are very effective and significantly superior to the nonlinear extended Kalman filter (EKF, which has been the standard nonlinear filter in past engineering applications.
Assessment of fibrotic liver disease with multimodal nonlinear optical microscopy
Lu, Fake; Zheng, Wei; Tai, Dean C. S.; Lin, Jian; Yu, Hanry; Huang, Zhiwei
2010-02-01
Liver fibrosis is the excessive accumulation of extracellular matrix proteins such as collagens, which may result in cirrhosis, liver failure, and portal hypertension. In this study, we apply a multimodal nonlinear optical microscopy platform developed to investigate the fibrotic liver diseases in rat models established by performing bile duct ligation (BDL) surgery. The three nonlinear microscopy imaging modalities are implemented on the same sectioned tissues of diseased model sequentially: i.e., second harmonic generation (SHG) imaging quantifies the contents of the collagens, the two-photon excitation fluorescence (TPEF) imaging reveals the morphology of hepatic cells, while coherent anti-Stokes Raman scattering (CARS) imaging maps the distributions of fats or lipids quantitatively across the tissue. Our imaging results show that during the development of liver fibrosis (collagens) in BDL model, fatty liver disease also occurs. The aggregated concentrations of collagen and fat constituents in liver fibrosis model show a certain correlationship between each other.
Nonlinear programming for classification problems in machine learning
Astorino, Annabella; Fuduli, Antonio; Gaudioso, Manlio
2016-10-01
We survey some nonlinear models for classification problems arising in machine learning. In the last years this field has become more and more relevant due to a lot of practical applications, such as text and web classification, object recognition in machine vision, gene expression profile analysis, DNA and protein analysis, medical diagnosis, customer profiling etc. Classification deals with separation of sets by means of appropriate separation surfaces, which is generally obtained by solving a numerical optimization model. While linear separability is the basis of the most popular approach to classification, the Support Vector Machine (SVM), in the recent years using nonlinear separating surfaces has received some attention. The objective of this work is to recall some of such proposals, mainly in terms of the numerical optimization models. In particular we tackle the polyhedral, ellipsoidal, spherical and conical separation approaches and, for some of them, we also consider the semisupervised versions.
International Nuclear Information System (INIS)
Eckstein, U.; Harte, R.; Kraetzig, W.B.; Wittek, U.
1983-01-01
In order to describe nonlinear response and instability behaviour the paper starts with the total potential energy considering the basic kinematic equations of a consistent nonlinear shell theory for large displacements and moderate rotations. The material behaviour is assumed to be hyperelastic and isotropic. The incrementation and discretization of the total potential energy leads to the tangent stiffness relation, which is the central equation of computational algorithms based on combined incremental and iterative techniques. Here a symmetrized form of the RIKS/WEMPNER-algorithm for positive and negative load incrementation represents the basis of the nonlinear solution technique. To detect secondary equilibrium branches at points of neutral equilibrium within nonlinear primary paths a quadratic eigenvalue-problem has to be solved. In order to follow those complicated nonlinear response phenomena the RIKS/WEMPNER incrementation/iteration process is combined with a simultaneous solution of the linearized quadratic eigenvalue-problem. Additionally the essentials of a recently derived family of arbitrarily curved shell elements for linear (LACS) and geometrically nonlinear (NACS) shell problems are presented. The main advantage of these elements is the exact description of all geometric properties as well as the energy-equivalent representation of the applied loads in combination with an efficient algorithm to form the stiffness submatrices. Especially the NACS-elements are designed to improve the accuracy of the solution in the deep postbuckling range including moderate rotations. The derived finite elements and solution strategies are applied to a certain number of typical shell problems to prove the precision of the shell elements and to demonstrate the possibilities of tracing linear and nonlinear bifurcation problems as well as snap-through phenomena with and without secondary bifurcation branches. (orig.)
International Nuclear Information System (INIS)
Doubre, H.
1992-01-01
GANIL, a user's facility since 1983, can deliver a broad spectrum of heavy-ion beams, from He to U, to well-equipped experimental areas. Their very large intensities are to be exploited to produce secondary beams, either using the fragmentation method (beams at energy per nucleon larger than 30 MeV/u), or the ISOL method. With the latter one, these ions have to be re-accelerated. The project of a cyclotron as a post-accelerator is described. (author) 11 refs.; 7 figs.; 3 tabs
Secondary Vertex Finder Algorithm
Heer, Sebastian; The ATLAS collaboration
2017-01-01
If a jet originates from a b-quark, a b-hadron is formed during the fragmentation process. In its dominant decay modes, the b-hadron decays into a c-hadron via the electroweak interaction. Both b- and c-hadrons have lifetimes long enough, to travel a few millimetres before decaying. Thus displaced vertices from b- and subsequent c-hadron decays provide a strong signature for a b-jet. Reconstructing these secondary vertices (SV) and their properties is the aim of this algorithm. The performance of this algorithm is studied with tt̄ events, requiring at least one lepton, simulated at 13 TeV.
SECONDARY (ENDOCRINE HYPERTENSION: LECTURE
Directory of Open Access Journals (Sweden)
M. Yu. Yukina
2016-01-01
Full Text Available Hypertension is a very common disease with high morbidity and reduction in quality of life. Endocrine disorders are the most common cause of secondary hypertension affecting ~3% of the population. Primary aldosteronism can be the cause of endocrine hypertension more often than other endocrine disorders. Other less common causes of endocrine hypertension include Cushing syndrome, pheochromocytoma, thyroid disorders, and hyperparathyroidism. Endocrine hypertension is potentially curable if the underlying cause is identified and treated accordingly. Younger age at manifestation of resistance to multiple antihypertensive drugs, together with other clinical signs of an endocrine disorder, should raise the suspicion and prompt the appropriate evaluation.
Evaluation of nonlinearity and validity of nonlinear modeling for complex time series.
Suzuki, Tomoya; Ikeguchi, Tohru; Suzuki, Masuo
2007-10-01
Even if an original time series exhibits nonlinearity, it is not always effective to approximate the time series by a nonlinear model because such nonlinear models have high complexity from the viewpoint of information criteria. Therefore, we propose two measures to evaluate both the nonlinearity of a time series and validity of nonlinear modeling applied to it by nonlinear predictability and information criteria. Through numerical simulations, we confirm that the proposed measures effectively detect the nonlinearity of an observed time series and evaluate the validity of the nonlinear model. The measures are also robust against observational noises. We also analyze some real time series: the difference of the number of chickenpox and measles patients, the number of sunspots, five Japanese vowels, and the chaotic laser. We can confirm that the nonlinear model is effective for the Japanese vowel /a/, the difference of the number of measles patients, and the chaotic laser.
Gurbatov, S N; Saichev, A I
2012-01-01
"Waves and Structures in Nonlinear Nondispersive Media: General Theory and Applications to Nonlinear Acoustics” is devoted completely to nonlinear structures. The general theory is given here in parallel with mathematical models. Many concrete examples illustrate the general analysis of Part I. Part II is devoted to applications to nonlinear acoustics, including specific nonlinear models and exact solutions, physical mechanisms of nonlinearity, sawtooth-shaped wave propagation, self-action phenomena, nonlinear resonances and engineering application (medicine, nondestructive testing, geophysics, etc.). This book is designed for graduate and postgraduate students studying the theory of nonlinear waves of various physical nature. It may also be useful as a handbook for engineers and researchers who encounter the necessity of taking nonlinear wave effects into account of their work. Dr. Gurbatov S.N. is the head of Department, and Vice Rector for Research of Nizhny Novgorod State University. Dr. Rudenko O.V. is...
Hammoudeh, Jeffrey A; Fahradyan, Artur; Gould, Daniel J; Liang, Fan; Imahiyerobo, Thomas; Urbinelli, Leo; Nguyen, JoAnna T; Magee, William; Yen, Stephen; Urata, Mark M
2017-08-01
Alveolar cleft reconstruction using iliac crest bone graft is considered standard of care for children with complete cleft lip and palate at the time of mixed dentition. Harvesting bone may result in donor-site morbidity and additional operating time and length of hospitalization. Recombinant human bone morphogenetic protein (rhBMP)-2 with a demineralized bone matrix is an alternative bone source for alveolar cleft reconstruction. The authors investigated the outcomes of rhBMP-2/demineralized bone matrix versus iliac crest bone graft for alveolar cleft reconstruction by reviewing postoperative surgical complications and cleft closure. A retrospective chart review was conducted for 258 rhBMP-2/demineralized bone matrix procedures (mean follow-up, 2.9 years) and 243 iliac crest bone graft procedures (mean follow-up, 4.1 years) on 414 patients over a 12-year period. The authors compared complications, canine eruption, and alveolar cleft closure between the two groups. In the rhBMP-2/demineralized bone matrix group, one patient required prolonged intubation because of intraoperative airway swelling not thought to be caused by rhBMP-2, 36 reported facial swelling and one required outpatient steroids as treatment, and 12 had dehiscence; however, half of these complications resolved without intervention. Twenty-three of the 228 rhBMP-2/demineralized bone matrix patients and 28 of the 242 iliac crest bone graft patients required repeated surgery for alveolar cleft repair. Findings for canine tooth eruption into the cleft site through the graft were similar between the groups. The rhBMP-2/demineralized bone matrix appears to be an acceptable alternative for alveolar cleft repair. The authors found no increase in serious adverse events with the use of this material. Local complications, such as swelling and minor wound dehiscence, predominantly improved without intervention. Therapeutic, III.
[Secondary osteoporosis in gynecology].
Taguchi, Y; Gorai, I
1998-06-01
Several diseases and medications are known to induce secondary osteoporosis. Among them, same situations are related to gynecological field. They include Turner's syndrome, anorexia nervosa, ovarian dysfunction, oophorectomy, GnRH agonist therapy, and osteoporosis associated with pregnancy. We briefly describe these secondary osteoporosis in this article as follows. Several studies have found osteoporosis to be a common complication of Turner's syndrome and hormone replacement therapy has been used as a possible management; in anorexic patient, low body weight, prolonged amenorrhea, early onset of anorexia nervosa, and hypercortisolism have been reported to be risks for bone demineralization; since oophorectomy which is a common intervention in gynecology leads osteoporosis, it is important to prevent osteoporosis caused by surgery as well as postmenopausal osteoporosis; GnRH agonist, which induces estrogen deficient state and affect bone mass, is commonly used as a management for endometriosis and leiomyoma of uterus; associated with pregnancy, post-pregnancy spinal osteoporosis and transient osteoporosis of the hip are clinically considered to be important and heparin therapy and magnesium sulfate therapy are commonly employed during pregnancy, affecting calcium homeostasis.
Radioactive heavy ion secondary beams
International Nuclear Information System (INIS)
Bimbot, R.
1987-01-01
The production of secondary radioactive beams at GANIL using the LISE spectrometer is reviewed. The experimental devices, and secondary beam characteristics are summarized. Production of neutron rich secondary beams was studied for the systems Ar40 + Be at 44 MeV/u, and 018 + Be at 45 and 65 MeV/u. Partial results were also obtained for the system Ne22 + Ta at 45 MeV/u. Experiments using secondary beams are classified into two categories: those which correspond to fast transfer of nuclei from the production target to a well shielded observation point; and those in which the radioactive beam interacts with a secondary target
Probing hysteretic elasticity in weakly nonlinear materials
Energy Technology Data Exchange (ETDEWEB)
Johnson, Paul A [Los Alamos National Laboratory; Haupert, Sylvain [UPMC UNIV PARIS; Renaud, Guillaume [UPMC UNIV PARIS; Riviere, Jacques [UPMC UNIV PARIS; Talmant, Maryline [UPMC UNIV PARIS; Laugier, Pascal [UPMC UNIV PARIS
2010-12-07
Our work is aimed at assessing the elastic and dissipative hysteretic nonlinear parameters' repeatability (precision) using several classes of materials with weak, intermediate and high nonlinear properties. In this contribution, we describe an optimized Nonlinear Resonant Ultrasound Spectroscopy (NRUS) measuring and data processing protocol applied to small samples. The protocol is used to eliminate the effects of environmental condition changes that take place during an experiment, and that may mask the intrinsic elastic nonlinearity. As an example, in our experiments, we identified external temperature fluctuation as a primary source of material resonance frequency and elastic modulus variation. A variation of 0.1 C produced a frequency variation of 0.01 %, which is similar to the expected nonlinear frequency shift for weakly nonlinear materials. In order to eliminate environmental effects, the variation in f{sub 0} (the elastically linear resonance frequency proportional to modulus) is fit with the appropriate function, and that function is used to correct the NRUS calculation of nonlinear parameters. With our correction procedure, we measured relative resonant frequency shifts of 10{sup -5} , which are below 10{sup -4}, often considered the limit to NRUS sensitivity under common experimental conditions. Our results show that the procedure is an alternative to the stringent control of temperature often applied. Applying the approach, we report nonlinear parameters for several materials, some with very small nonclassical nonlinearity. The approach has broad application to NRUS and other Nonlinear Elastic Wave Spectroscopy approaches.
Linearization of the Bradford Protein Assay
Ernst, Orna; Zor, Tsaffrir
2010-01-01
Determination of microgram quantities of protein in the Bradford Coomassie brilliant blue assay is accomplished by measurement of absorbance at 590 nm. This most common assay enables rapid and simple protein quantification in cell lysates, cellular fractions, or recombinant protein samples, for the purpose of normalization of biochemical measurements. However, an intrinsic nonlinearity compromises the sensitivity and accuracy of this method. It is shown that under standard assay conditions, t...
Augmented nonlinear differentiator design and application to nonlinear uncertain systems.
Shao, Xingling; Liu, Jun; Li, Jie; Cao, Huiliang; Shen, Chong; Zhang, Xiaoming
2017-03-01
In this paper, an augmented nonlinear differentiator (AND) based on sigmoid function is developed to calculate the noise-less time derivative under noisy measurement condition. The essential philosophy of proposed AND in achieving high attenuation of noise effect is established by expanding the signal dynamics with extra state variable representing the integrated noisy measurement, then with the integral of measurement as input, the augmented differentiator is formulated to improve the estimation quality. The prominent advantages of the present differentiation technique are: (i) better noise suppression ability can be achieved without appreciable delay; (ii) the improved methodology can be readily extended to construct augmented high-order differentiator to obtain multiple derivatives. In addition, the convergence property and robustness performance against noises are investigated via singular perturbation theory and describing function method, respectively. Also, comparison with several classical differentiators is given to illustrate the superiority of AND in noise suppression. Finally, the robust control problems of nonlinear uncertain systems, including a numerical example and a mass spring system, are addressed to demonstrate the effectiveness of AND in precisely estimating the disturbance and providing the unavailable differential estimate to implement output feedback based controller. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.
DROUGHT AFFECTS PROTEIN AND PHENOLIC CONTENT IN ...
African Journals Online (AJOL)
userpc
ABSTRACT. Bambara groundnut (Vigna subterranea L. Verdc.) is a legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in sub-Saharan. Africa. This study evaluates the effect of experimental water deficit stress on total protein concentration, secondary protein structure ...
Nonlinear Optimization with Financial Applications
Bartholomew-Biggs, Michael
2005-01-01
The book introduces the key ideas behind practical nonlinear optimization. Computational finance - an increasingly popular area of mathematics degree programs - is combined here with the study of an important class of numerical techniques. The financial content of the book is designed to be relevant and interesting to specialists. However, this material - which occupies about one-third of the text - is also sufficiently accessible to allow the book to be used on optimization courses of a more general nature. The essentials of most currently popular algorithms are described, and their performan
Jefrey, A
1964-01-01
In this book, we study theoretical and practical aspects of computing methods for mathematical modelling of nonlinear systems. A number of computing techniques are considered, such as methods of operator approximation with any given accuracy; operator interpolation techniques including a non-Lagrange interpolation; methods of system representation subject to constraints associated with concepts of causality, memory and stationarity; methods of system representation with an accuracy that is the best within a given class of models; methods of covariance matrix estimation;methods for low-rank mat
Modelling Loudspeaker Non-Linearities
DEFF Research Database (Denmark)
Agerkvist, Finn T.
2007-01-01
This paper investigates different techniques for modelling the non-linear parameters of the electrodynamic loudspeaker. The methods are tested not only for their accuracy within the range of original data, but also for the ability to work reasonable outside that range, and it is demonstrated...... that polynomial expansions are rather poor at this, whereas an inverse polynomial expansion or localized fitting functions such as the gaussian are better suited for modelling the Bl-factor and compliance. For the inductance the sigmoid function is shown to give very good results. Finally the time varying...
Nonlinear classical theory of electromagnetism
International Nuclear Information System (INIS)
Pisello, D.
1977-01-01
A topological theory of electric charge is given. Einstein's criteria for the completion of classical electromagnetic theory are summarized and their relation to quantum theory and the principle of complementarity is indicated. The inhibiting effect that this principle has had on the development of physical thought is discussed. Developments in the theory of functions on nonlinear spaces provide the conceptual framework required for the completion of electromagnetism. The theory is based on an underlying field which is a continuous mapping of space-time into points on the two-sphere. (author)
Nonlinear Pricing of Information Goods
Arun Sundararajan
2003-01-01
This paper analyzes optimal pricing for information goods under incomplete information, when both unlimited-usage (fixed-fee) pricing and usage-based pricing are feasible, and administering usage-based pricing may involve transaction costs. It is shown that offering fixed- fee pricing in addition to a non-linear usage-based pricing scheme is always profit-improving in the presence of any non-zero transaction costs, and there may be markets in which a pure fixed-fee is optimal. This implies th...
Nonlinear waves: some biomedical applications
International Nuclear Information System (INIS)
Rudenko, Oleg V
2007-01-01
The field of nonlinear physics, item No. 11 on Ginzburg's list of 'the most important and interesting problems', is reviewed. An example at the intersection of applied physics, medicine, and instrument engineering is discussed to illustrate the range and scope of the field and how deep the ideas and approaches it involves are incorporated in modern natural science and engineering. Results of relevant research and development, which has attracted much recent interest and financial support, are briefly examined. (oral issue of the journal 'uspekhi fizicheskikh nauk')
Beams on nonlinear elastic foundation
International Nuclear Information System (INIS)
Lukkassen, Dag; Meidell, Annette
2014-01-01
In order to determination vertical deflections and rail bending moments the Winkler model (1867) is often used. This linear model neglects several conditions. For example, by using experimental results, it has been observed that there is a substantial increase in the maximum rail deflection and rail bending moment when considering the nonlinearity of the track support system. A deeper mathematical analysis of the models is necessary in order to obtain better methods for more accurate numerical solutions in the determination of deflections and rail bending moments. This paper is intended to be a small step in this direction
Owens, RA; Hammel, S; Sheridan, KJ; Jones, GW; Doyle, S
2014-01-01
A combined proteomics and metabolomics approach was utilised to advance the identification and characterisation of secondary metabolites in Aspergillus fumigatus. Here, implementation of a shotgun proteomic strategy led to the identification of non-redundant mycelial proteins (n = 414) from A. fumigatus including proteins typically under-represented in 2-D proteome maps: proteins with multiple transmembrane regions, hydrophobic proteins and proteins with extremes of molecular mass and pI. Ind...
Transitions in Secondary Education
DEFF Research Database (Denmark)
Larsen, Britt Østergaard; Jensen, Leif; Pilegaard Jensen, Torben
2014-01-01
statistical model of educational progression. By using this method, we parcel educational attainment into a series of transitions and the model is able to control for educational selection and unobserved heterogeneity. We apply counterfactual analyses to allow a formal decomposition of the effects of social......The purpose of this article is to investigate educational choices and attainment of children who experience social problems during their upbringing. The study explores the extent to which social problems can help explain the gaps in entry and dropout rates in upper secondary education in Denmark...... between students from different socioeconomic backgrounds. Population-based registers are used to include information on family upbringing, e.g. alcohol abuse, criminality, use of psychopharmaca and out-of-home placement. We estimate a parsimonious version of Cameron and Heckman's (2001) dynamic...
Basanta, I; Sevillano, C; Álvarez, M D
2015-09-01
A case is presented of an 85 year-old Caucasian female with lymphoma that recurred in the orbit (secondary ocular adnexal lymphoma). The orbital tumour was a diffuse large B-cell lymphoma according to the REAL classification (Revised European-American Lymphoma Classification). Orbital lymphomas are predominantly B-cell proliferations of a variety of histological types, and most are low-grade tumours. Patients are usually middle-aged or elderly, and it is slightly more common in women. A palpable mass, proptosis and blepharoptosis are the most common signs of presentation. Copyright © 2011 Sociedad Española de Oftalmología. Published by Elsevier España, S.L.U. All rights reserved.
HANARO secondary coolant management
International Nuclear Information System (INIS)
Kim, Seon Duk.
1998-02-01
In this report, the basic theory for management of water quality, environmental factors influencing to the coolant, chemicals and its usage for quality control of coolant are mentioned, and water balance including the loss rate by evaporation (34.3 m 3 /hr), discharge rate (12.665 m 3 /hr), concentration ratio and feed rate (54.1 m 3 /hr) are calculated at 20 MW operation. Also, the analysis data of HANSU Limited for HANARO secondary coolant (feed water and circulating coolant) - turbidity, pH, conductivity, M-alkalinity, Ca-hardness, chloride ion, total iron ion, phosphoric ion and conversion rate are reviewed. It is confirmed that the feed water has good quality and the circulating coolant has been maintained within the control specification in general, but some items exceeded the control specification occasionally. Therefore it is judged that more regular discharge of coolant is needed. (author). 6 refs., 17 tabs., 18 figs
International Nuclear Information System (INIS)
Schulten, R.
1977-01-01
As an introduction, the FRG's energy industry situation is described, secondary energy systems to be taken into consideration are classified, and appropriate market requirements are analyzed. Dealt with is district heating, i.e. the direct transport of heat by means of circulating media, and long-distance energy, i.e. the long-distance energy transport by means of chemical conversion in closed- or open-cycle systems. In closed-cycle systems heat is transported in the form of chemical latent energy. In contrast to this, chemical energy is transported in open-cycle systems in the form of fuel gases produced by coal gasification or by thermochemical water splitting. (GG) [de
Nonlinear dynamics aspects of particle accelerators
International Nuclear Information System (INIS)
Jowett, J.M.; Turner, S.; Month, M.
1986-01-01
These proceedings contain the lectures presented at the named winter school. They deal with the application of dynamical systems to accelerator theory. Especially considered are the statistical description of charged-beam plasmas, integrable and nonintegrable Hamiltonian systems, single particle dynamics and nonlinear resonances in circular accelerators, nonlinear dynamics aspects of modern storage rings, nonlinear beam-beam resonances, synchro-betatron resonances, observations of the beam-beam interactions, the dynamics of the beam-beam interactions, beam-beam simulations, the perturbation method in nonlinear dynamics, theories of statistical equilibrium in electron-positron storage rings, nonlinear dissipative phenomena in electron storage rings, the dynamical aperture, the transition to chaos for area-preserving maps, special processors for particle tracking, algorithms for tracking of charged particles in circular accelerators, the breakdown of stability, and a personal perspective of nonlinear dynamics. (HSI)
Nonlinear optical crystals a complete survey
Nikogosyan, David N
2005-01-01
Nonlinear optical crystals are widely used in modern optical science and technology for frequency conversion of laser light, i.e. to generate laser radiation at any specific wavelength in visible, UV or IR spectral regions. This unrivalled reference book contains the most complete and up-to-date information on properties of nonlinear optical crystals. It includes: * Database of 63 common and novel nonlinear optical crystals * Periodically-poled and self-frequency-doubling materials * Full description of linear and nonlinear optical properties * Significant amount of crystallophysical, thermophysical, spectroscopic, electro-optic and magneto-optic information * 7 mini-reviews on novel applications, such as deep-UV light generation, terahertz-wave generation, ultrashort laser pulse compression, photonic band-gap crystals, x3 nonlinearity, etc. * More than 1500 different references with full titles It is a vital source of information for scientists and engineers dealing with modern applications of nonlinear opti...