Protein Secondary Structure Prediction Using AutoEncoder Network and Bayes Classifier

Science.gov (United States)

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.

Protein Secondary Structures (α-helix and β-sheet) at a Cellular Level and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach

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

Protein Secondary Structures (alpha-helix and beta-sheet) at a Cellular Levle and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach

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

Knowledge base and neural network approach for protein secondary structure prediction.

Science.gov (United States)

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.

Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be.

KAUST Repository

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.

Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be.

KAUST Repository

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.

Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks.

Science.gov (United States)

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.

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.

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)

A Kernel for Protein Secondary Structure Prediction

OpenAIRE

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...

MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction.

Science.gov (United States)

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.

Artificial Intelligence in Prediction of Secondary Protein Structure Using CB513 Database

Science.gov (United States)

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

Discrete Nonlinear Schrödinger Equation and Polygonal Solitons with Applications to Collapsed Proteins

Science.gov (United States)

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.

Tchebichef image moment approach to the prediction of protein secondary structures based on circular dichroism.

Science.gov (United States)

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.

Quantitative proteome and phosphoproteome analyses of Streptomyces coelicolor reveal proteins and phosphoproteins modulating differentiation and secondary metabolism

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...

Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

Science.gov (United States)

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.

Protein Recovery from Secondary Paper Sludge and Its Potential Use as Wood Adhesive

Science.gov (United States)

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

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....

Cascaded bidirectional recurrent neural networks for protein secondary structure prediction.

Science.gov (United States)

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%.

Parallel protein secondary structure prediction based on neural networks.

Science.gov (United States)

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.

Prediction of backbone dihedral angles and protein secondary structure using support vector machines

Directory of Open Access Journals (Sweden)

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/.

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...

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.

Science.gov (United States)

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.

VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program.

Science.gov (United States)

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.

Nonlinear optical methods for the analysis of protein nanocrystals and biological tissues

Science.gov (United States)

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).

Protein secondary structure prediction for a single-sequence using hidden semi-Markov models

Directory of Open Access Journals (Sweden)

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

SAAS: Short Amino Acid Sequence - A Promising Protein Secondary Structure Prediction Method of Single Sequence

Directory of Open Access Journals (Sweden)

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%.

Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

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.

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

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.

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

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

Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts.

Science.gov (United States)

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.

Multiplex protein pattern unmixing using a non-linear variable-weighted support vector machine as optimized by a particle swarm optimization algorithm.

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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.

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...

Nonlinear rheology of complex fluid-fluid interfaces

NARCIS (Netherlands)

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

The secondary structure and the thermal unfolding parameters of the S-layer protein from Lactobacillus salivarius.

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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 systems

CERN Document Server

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...

CNNH_PSS: protein 8-class secondary structure prediction by convolutional neural network with highway.

Science.gov (United States)

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.

Influence of secondary structure on in-source decay of protein in matrix-assisted laser desorption/ionization mass spectrometry.

Science.gov (United States)

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.

Secondary Instability of Second Modes in Hypersonic Boundary Layers

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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.

CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

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

ONIOM Investigation of the Second-Order Nonlinear Optical Responses of Fluorescent Proteins.

Science.gov (United States)

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

Proteins Related to the Type I Secretion System Are Associated with Secondary SecA_DEAD Domain Proteins in Some Species of Planctomycetes, Verrucomicrobia, Proteobacteria, Nitrospirae and Chlorobi.

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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.

Protein 8-class secondary structure prediction using conditional neural fields.

Science.gov (United States)

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.

Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

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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.

Protein secondary structure assignment revisited: a detailed analysis of different assignment methods

Directory of Open Access Journals (Sweden)

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.

A novel Multi-Agent Ada-Boost algorithm for predicting protein structural class with the information of protein secondary structure.

Science.gov (United States)

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.

Correlation between protein secondary structure, backbone bond angles, and side-chain orientations

Science.gov (United States)

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.

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...

SVM-PB-Pred: SVM based protein block prediction method using sequence profiles and secondary structures.

Science.gov (United States)

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.

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Science.gov (United States)

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.

A genetic bistable switch utilizing nonlinear protein degradation.

Science.gov (United States)

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.

Engineered, highly reactive substrates of microbial transglutaminase enable protein labeling within various secondary structure elements.

Science.gov (United States)

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.

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

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

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.

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)

A Systematic Protein Refolding Screen Method using the DGR Approach Reveals that Time and Secondary TSA are Essential Variables.

Science.gov (United States)

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.

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.

Secondary Structure Prediction of Protein using Resilient Back Propagation Learning Algorithm

Directory of Open Access Journals (Sweden)

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.

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)

Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C’ scalar couplings (3hbJNC’)

NARCIS (Netherlands)

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

Clinical and pH-metric characteristics of gastro-oesophageal reflux secondary to cows' milk protein allergy.

Science.gov (United States)

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

Accurate determination of interfacial protein secondary structure by combining interfacial-sensitive amide I and amide III spectral signals.

Science.gov (United States)

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.

The nonlinear dynamics of a spacecraft coupled to the vibration of a contained fluid

Science.gov (United States)

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.

Second-order nonlinear optical microscopy of spider silk

Science.gov (United States)

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.

A Teaching and Learning Sequence about the Interplay of Chance and Determinism in Nonlinear Systems

Science.gov (United States)

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…

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.

Science.gov (United States)

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.

Estimation method for first excursion probability of secondary system with impact and friction using maximum response

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)

Directional nonlinear guided wave mixing: Case study of counter-propagating shear horizontal waves

Science.gov (United States)

Hasanian, Mostafa; Lissenden, Cliff J.

2018-04-01

While much nonlinear ultrasonics research has been conducted on higher harmonic generation, wave mixing provides the potential for sensitive measurements of incipient damage unencumbered by instrumentation nonlinearity. Studies of nonlinear ultrasonic wave mixing, both collinear and noncollinear, for bulk waves have shown the robust capability of wave mixing for early damage detection. One merit of bulk wave mixing lies in their non-dispersive nature, but guided waves enable inspection of otherwise inaccessible material and a variety of mixing options. Co-directional guided wave mixing was studied previously, but arbitrary direction guided wave mixing has not been addressed until recently. Wave vector analysis is applied to study variable mixing angles to find wave mode triplets (two primary waves and a secondary wave) resulting in the phase matching condition. As a case study, counter-propagating Shear Horizontal (SH) guided wave mixing is analyzed. SH wave interactions generate a secondary Lamb wave mode that is readily receivable. Reception of the secondary Lamb wave mode is compared for an angle beam transducer, an air coupled transducer, and a laser Doppler vibrometer (LDV). Results from the angle beam and air coupled transducers are quite consistent, while the LDV measurement is plagued by variability issues.

Nonlinear Poisson equation for heterogeneous media.

Science.gov (United States)

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.

Numerical studies of nonlinear ultrasonic guided waves in uniform waveguides with arbitrary cross sections

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.

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

Signaling governed by G proteins and cAMP is crucial for growth, secondary metabolism and sexual development in Fusarium fujikuroi.

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.

Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements

Directory of Open Access Journals (Sweden)

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.

A Tyrosine-Based Trafficking Motif of the Tegument Protein pUL71 Is Crucial for Human Cytomegalovirus Secondary Envelopment.

Science.gov (United States)

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

A systematic review on popularity, application and characteristics of protein secondary structure prediction tools.

Science.gov (United States)

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 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)

Nonlinear dynamics in biological systems

CERN Document Server

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...

Attenuated Total Reflection Fourier Transform Infrared (ATR FT-IR) Spectroscopy as an Analytical Method to Investigate the Secondary Structure of a Model Protein Embedded in Solid Lipid Matrices.

Science.gov (United States)

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

Solution strategies for linear and nonlinear instability phenomena for arbitrarily thin shell structures

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.)

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.

Determination of Endosperm Protein Secondary Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy

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

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 features of the electron temperature gradient mode and electron thermal transport in tokamaks

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)

Nonlinear amplitude dynamics in flagellar beating.

Science.gov (United States)

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.

Modelling lactation curve for milk fat to protein ratio in Iranian buffaloes (Bubalus bubalis) using non-linear mixed models.

Science.gov (United States)

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.

Monomer-dependent secondary nucleation in amyloid formation.

Science.gov (United States)

Linse, Sara

2017-08-01

Secondary nucleation of monomers on the surface of an already existing aggregate that is formed from the same kind of monomers may lead to autocatalytic amplification of a self-assembly process. Such monomer-dependent secondary nucleation occurs during the crystallization of small molecules or proteins and self-assembled materials, as well as in protein self-assembly into fibrous structures. Indications of secondary nucleation may come from analyses of kinetic experiments starting from pure monomers or monomers supplemented with a low concentration of pre-formed aggregates (seeds). More firm evidence requires additional experiments, for example those employing isotope labels to distinguish new aggregates arising from the monomer from those resulting from fragmentation of the seed. In cases of amyloid formation, secondary nucleation leads to the formation of toxic oligomers, and inhibitors of secondary nucleation may serve as starting points for therapeutic developments. Secondary nucleation displays a high degree of structural specificity and may be enhanced by mutations or screening of electrostatic repulsion.

Flutter analysis of an airfoil with nonlinear damping using equivalent linearization

Directory of Open Access Journals (Sweden)

Chen Feixin

2014-02-01

Full Text Available The equivalent linearization method (ELM is modified to investigate the nonlinear flutter system of an airfoil with a cubic damping. After obtaining the linearization quantity of the cubic nonlinearity by the ELM, an equivalent system can be deduced and then investigated by linear flutter analysis methods. Different from the routine procedures of the ELM, the frequency rather than the amplitude of limit cycle oscillation (LCO is chosen as an active increment to produce bifurcation charts. Numerical examples show that this modification makes the ELM much more efficient. Meanwhile, the LCOs obtained by the ELM are in good agreement with numerical solutions. The nonlinear damping can delay the occurrence of secondary bifurcation. On the other hand, it has marginal influence on bifurcation characteristics or LCOs.

Intermittent dynamics of nonlinear resistive tearing modes at extremely high magnetic Reynolds number

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)

Determination of the secondary structure content of proteins in aqueous solutions from their amide I and amide II infrared bands. Comparison between classical and partial least-squares methods

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

Novel nonlinear knowledge-based mean force potentials based on machine learning.

Science.gov (United States)

Dong, Qiwen; Zhou, Shuigeng

2011-01-01

The prediction of 3D structures of proteins from amino acid sequences is one of the most challenging problems in molecular biology. An essential task for solving this problem with coarse-grained models is to deduce effective interaction potentials. The development and evaluation of new energy functions is critical to accurately modeling the properties of biological macromolecules. Knowledge-based mean force potentials are derived from statistical analysis of proteins of known structures. Current knowledge-based potentials are almost in the form of weighted linear sum of interaction pairs. In this study, a class of novel nonlinear knowledge-based mean force potentials is presented. The potential parameters are obtained by nonlinear classifiers, instead of relative frequencies of interaction pairs against a reference state or linear classifiers. The support vector machine is used to derive the potential parameters on data sets that contain both native structures and decoy structures. Five knowledge-based mean force Boltzmann-based or linear potentials are introduced and their corresponding nonlinear potentials are implemented. They are the DIH potential (single-body residue-level Boltzmann-based potential), the DFIRE-SCM potential (two-body residue-level Boltzmann-based potential), the FS potential (two-body atom-level Boltzmann-based potential), the HR potential (two-body residue-level linear potential), and the T32S3 potential (two-body atom-level linear potential). Experiments are performed on well-established decoy sets, including the LKF data set, the CASP7 data set, and the Decoys “R”Us data set. The evaluation metrics include the energy Z score and the ability of each potential to discriminate native structures from a set of decoy structures. Experimental results show that all nonlinear potentials significantly outperform the corresponding Boltzmann-based or linear potentials, and the proposed discriminative framework is effective in developing knowledge

NONLINEAR DYNAMICS OF CARBON NANOTUBES UNDER LARGE ELECTROSTATIC FORCE

KAUST Repository

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

KAUST Repository

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 Dynamic Behavior of a Bi-Axial Torsional MEMS Mirror with Sidewall Electrodes

Directory of Open Access Journals (Sweden)

Mehmet Ozdogan

2016-03-01

Full Text Available Nonlinear dynamic responses of a Micro-Electro-Mechanical Systems (MEMS mirror with sidewall electrodes are presented that are in close agreement with previously-reported experimental data. An analysis of frequency responses reveals softening behavior, and secondary resonances originated from the dominant quadratic nonlinearity. The quadratic nonlinearity is an electromechanical coupling effect caused by the electrostatic force. This effect is reflected in our mathematical model used to simulate the dynamic response of the micro-mirror. The effects of increased forcing and decreased damping on the frequency response are investigated as the mirrors are mostly used in vacuum packages. The results can predict MEMS mirror behaviors in optical devices better than previously-reported models.

Deciphering the shape and deformation of secondary structures through local conformation analysis

Directory of Open Access Journals (Sweden)

Camproux Anne-Claude

2011-02-01

Full Text Available Abstract Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

Deciphering the shape and deformation of secondary structures through local conformation analysis.

Science.gov (United States)

Baussand, Julie; Camproux, Anne-Claude

2011-02-01

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

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 ...

On secondary loops in LAOS via self-intersection of Lissajous–Bowditch curves

OpenAIRE

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...

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

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

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

Pulse reshaping in photonic crystal waveguides and microcavities with Kerr nonlinearity: Critical issues for all-optical switching

International Nuclear Information System (INIS)

Vujic, Dragan; John, Sajeev

2005-01-01

We delineate critical issues for 'controlling light with light' in photonic crystal (PC) waveguides coupled to Kerr-nonlinear microresonators. These arise from (a) fundamental trade-off between switching speed and switching intensity threshold inherent in high-quality Q-factor cavities and (b) the dynamical nonlinear oscillation of such cavities in response to incident light pulses. Using finite-difference time-domain simulations of electromagnetic pulse propagation, we consider both (i) a nonlinear Fabry-Perot microresonator (embedded within a PC waveguide) exhibiting a narrow transmission resonance and (ii) a nonlinear point defect (side-coupled to a PC waveguide) exhibiting a narrow reflection spectrum. We describe self-induced switching from transmission to reflection induced by pulse intensity tuning as well as control of pulse transmission induced by the secondary, continuous (cw) laser field propagating through the same PC waveguide. For the Fabry-Perot microresonator, a well-defined self-switching threshold is obtained. However, this is accompanied by considerable temporal and spectral distortion of the pulse caused by the oscillatory nonlinear response of the microresonator. When the quality factor of the microresonator is increased, the switching intensity threshold can be lowered but the pulse transit (switching) time and the pulse distortion are increased. For the side-coupled microresonator, a gradual (not sharp) self-switching behavior as a function of incident intensity is obtained. For both the Fabry-Perot and side-coupled nonlinear microresonators, control of pulse transmission can be achieved by means of a secondary cw laser field. The cw power required for switching with realistic Kerr nonlinearities is in excess of 1 W/μm 2 and may cause optical damage to the semiconducting PC backbone. Both instantaneous and noninstantaneous Kerr-response models are considered. Our results underscore the limitations and trade-offs inherent in the possible

Study of a nonlinear system with shocks under broadband excitation. Application to a steam generator tube

International Nuclear Information System (INIS)

Thenint, Th.

2011-01-01

The steam generator is a heat exchanger and participates to the nuclear safety. Energy is transferred from the primary to the secondary fluid through many U-tubes maintained vertically by support plates. A sludge deposit tends to modify the boundary conditions and the secondary fluid flow. A fluid-elastic instability can then occur and lead to quick tube ruin. This thesis seeks a better understanding of the effect of contact nonlinearity on the dynamics of a tube in-air intermittently impacting the support plates and its consequences in regards with instability. The use of discretized contact conditions with circular obstacles distributed over the thickness of the plates and the use of enriched reduction bases allow quick and relevant nonlinear numerical simulations. These simulations are well correlated with experimental measurements and valid even with strong nonlinearity or negative modal damping. The evolution of power spectral densities (PSD) with growing excitation amplitude is analyzed: padding of the anti-resonances, peak shift and spread. It is then shown that an apparent stiffness associated with a permanent bilateral contact is pertinent to describe these transitions. In the case of an unstable linear system, one demonstrates that the nonlinearity keeps the responses bounded or stabilised, thus paving the way for future work with real or simulated fluid flows. (author)

BLAST-based structural annotation of protein residues using Protein Data Bank.

Science.gov (United States)

Singh, Harinder; Raghava, Gajendra P S

2016-01-25

In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of the biggest challenges for the computational biologist. Although, it is easy to perform BLAST search against Protein Data Bank (PDB) but it is difficult for a biologist to annotate protein residues from BLAST search. A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures. It uses standard BLAST software for performing similarity search of a query protein against protein structures in PDB. This server integrates wide range modules for assigning different types of annotation that includes, Secondary-structure, Accessible surface area, Tight-turns, DNA-RNA and Ligand modules. Secondary structure module allows users to predict regular secondary structure states to each residue in a protein. Accessible surface area predict the exposed or buried residues in a protein. Tight-turns module is designed to predict tight turns like beta-turns in a protein. DNA-RNA module developed for predicting DNA and RNA interacting residues in a protein. Similarly, Ligand module of server allows one to predicted ligands, metal and nucleotides ligand interacting residues in a protein. In summary, this manuscript presents a web server for comprehensive annotation of a protein based on similarity search. It integrates number of visualization tools that facilitate users to understand structure and function of protein residues. This web server is available freely for scientific community from URL http://crdd.osdd.net/raghava/starpdb .

Interaction Of Calcium Phosphate Nanoparticles With Human Chorionic Gonadotropin Modifies Secondary And Tertiary Protein Structure

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.

mRNA secondary structure at start AUG codon is a key limiting factor for human protein expression in Escherichia coli

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

CMB anisotropies at all orders: the non-linear Sachs-Wolfe formula

International Nuclear Information System (INIS)

Roldan, Omar

2017-01-01

We obtain the non-linear generalization of the Sachs-Wolfe + integrated Sachs-Wolfe (ISW) formula describing the CMB temperature anisotropies. Our formula is valid at all orders in perturbation theory, is also valid in all gauges and includes scalar, vector and tensor modes. A direct consequence of our results is that the maps of the logarithmic temperature anisotropies are much cleaner than the usual CMB maps, because they automatically remove many secondary anisotropies. This can for instance, facilitate the search for primordial non-Gaussianity in future works. It also disentangles the non-linear ISW from other effects. Finally, we provide a method which can iteratively be used to obtain the lensing solution at the desired order.

CMB anisotropies at all orders: the non-linear Sachs-Wolfe formula

Energy Technology Data Exchange (ETDEWEB)

Roldan, Omar, E-mail: oaroldan@if.ufrj.br [Instituto de Física, Universidade Federal do Rio de Janeiro, 21941-972, Rio de Janeiro, RJ (Brazil)

2017-08-01

We obtain the non-linear generalization of the Sachs-Wolfe + integrated Sachs-Wolfe (ISW) formula describing the CMB temperature anisotropies. Our formula is valid at all orders in perturbation theory, is also valid in all gauges and includes scalar, vector and tensor modes. A direct consequence of our results is that the maps of the logarithmic temperature anisotropies are much cleaner than the usual CMB maps, because they automatically remove many secondary anisotropies. This can for instance, facilitate the search for primordial non-Gaussianity in future works. It also disentangles the non-linear ISW from other effects. Finally, we provide a method which can iteratively be used to obtain the lensing solution at the desired order.

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.

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

Empirical correlation between protein backbone {sup 15}N and {sup 13}C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

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.

Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C' scalar couplings (3hbJNC')

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.

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.

Nonlinear concentration gradients regulated by the width of channels for observation of half maximal inhibitory concentration (IC50) of transporter proteins.

Science.gov (United States)

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.

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

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.

Characterizing the Secondary Protein Structure of Black Widow Dragline Silk Using Solid-State NMR & X-ray Diffraction

Science.gov (United States)

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

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

GGPP-Mediated Protein Geranylgeranylation in Oocyte Is Essential for the Establishment of Oocyte-Granulosa Cell Communication and Primary-Secondary Follicle Transition in Mouse Ovary.

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.

Protein Phosphorylation and Mineral Binding Affect the Secondary Structure of the Leucine-Rich Amelogenin Peptide

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

EXTRACELLULAR PROTEINS PRODUCED BY DIFFERENT SPECIES OF THE FUNGUS TRICHODERMA ON SECONDARY PAPER MILL SLUDGE SUBSTRATE

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.

Nonlinear optics

CERN Document Server

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

A universal DNA-based protein detection system.

Science.gov (United States)

Tran, Thua N N; Cui, Jinhui; Hartman, Mark R; Peng, Songming; Funabashi, Hisakage; Duan, Faping; Yang, Dayong; March, John C; Lis, John T; Cui, Haixin; Luo, Dan

2013-09-25

Protein immune detection requires secondary antibodies which must be carefully selected in order to avoid interspecies cross-reactivity, and is therefore restricted by the limited availability of primary/secondary antibody pairs. Here we present a versatile DNA-based protein detection system using a universal adapter to interface between IgG antibodies and DNA-modified reporter molecules. As a demonstration of this capability, we successfully used DNA nano-barcodes, quantum dots, and horseradish peroxidase enzyme to detect multiple proteins using our DNA-based labeling system. Our system not only eliminates secondary antibodies but also serves as a novel method platform for protein detection with modularity, high capacity, and multiplexed capability.

Influence of Stationary Crossflow Modulation on Secondary Instability

Science.gov (United States)

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.

The predominant circular form of avocado sunblotch viroid accumulates in planta as a free RNA adopting a rod-shaped secondary structure unprotected by tightly bound host proteins.

Science.gov (United States)

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.

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

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.

Estimated risk for secondary cancer in the contra-lateral breast following radiation therapy of breast cancer

International Nuclear Information System (INIS)

Johansen, Safora; Danielsen, Turi; Olsen, Dag Rune

2008-01-01

Purpose. To facilitate a discussion about the impact of dose heterogeneity on the risk for secondary contralateral breast (CB) cancer predicted with linear and non linear models associated with primary breast irradiation. Methods and materials. Dose volume statistics of the CB calculated for eight patients using a collapsed cone algorithm were used to predict the excess relative risk (ERR) for cancer induction in CB. Both linear and non-linear models were employed. A sensitivity analysis demonstrating the impact of different parameter values on calculated ERR for the eight patients was also included in this study. Results. A proportionality assumption was established to make the calculations with a linear and non-linear model comparable. ERR of secondary cancer predicted by the linear model varied considerably between the patients, while the predicted ERR for the same patients using the non-linear model showed very small variation. The predicted ERRs by the two models were indistinguishable for small doses, i.e. below ∼3 Gy. The sensitivity analysis showed that the quadratic component of the radiation-induction pre-malignant cell term is negligible for lower dose level. The ERR is highly sensitive to the value of agr1 and agr2. Conclusions. Optimization of breast cancer radiation therapy, where also the risk for radiation induced secondary malignancies in the contralateral breast is taken into account, requires robust and valid risk assessment. The linear dose-risk model does not account for the complexity in the mechanisms underlying the development of secondary malignancies following exposure to radiation; this is particularly important when estimating risk associated with highly heterogeneous dose distributions as is the case in the contralateral breast of women receiving breast cancer irradiation

Limitation of secondary electron multiplier non-linearity on accurate U-Th isotopic determination by MC-ICP-MS

Science.gov (United States)

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.

Phosphorylation of Ribosomal Protein S6 Mediates Mammalian Target of Rapamycin Complex 1-Induced Parathyroid Cell Proliferation in Secondary Hyperparathyroidism.

Science.gov (United States)

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.

Cyanobacteria as Cell Factories to Produce Plant Secondary Metabolites

OpenAIRE

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

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

Design and implementation of a sensitive high-resolution nonlinear spectral imaging microscope

NARCIS (Netherlands)

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

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....

A 'periodic table' for protein structures.

Science.gov (United States)

Taylor, William R

2002-04-11

Current structural genomics programs aim systematically to determine the structures of all proteins coded in both human and other genomes, providing a complete picture of the number and variety of protein structures that exist. In the past, estimates have been made on the basis of the incomplete sample of structures currently known. These estimates have varied greatly (between 1,000 and 10,000; see for example refs 1 and 2), partly because of limited sample size but also owing to the difficulties of distinguishing one structure from another. This distinction is usually topological, based on the fold of the protein; however, in strict topological terms (neglecting to consider intra-chain cross-links), protein chains are open strings and hence are all identical. To avoid this trivial result, topologies are determined by considering secondary links in the form of intra-chain hydrogen bonds (secondary structure) and tertiary links formed by the packing of secondary structures. However, small additions to or loss of structure can make large changes to these perceived topologies and such subjective solutions are neither robust nor amenable to automation. Here I formalize both secondary and tertiary links to allow the rigorous and automatic definition of protein topology.

Nonlinear Science

CERN Document Server

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

Nonlinear beam mechanics

NARCIS (Netherlands)

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

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.)

Nonlinear oscillations

CERN Document Server

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

Correlation between ultrasonic nonlinearity and elastic nonlinearity in heat-treated aluminum alloy

Energy Technology Data Exchange (ETDEWEB)

Kim, Jong Beom; Jhang, Kyung Young [Hanyang University, Seoul (Korea, Republic of)

2017-04-15

The nonlinear ultrasonic technique is a potential nondestructive method to evaluate material degradation, in which the ultrasonic nonlinearity parameter is usually measured. The ultrasonic nonlinearity parameter is defined by the elastic nonlinearity coefficients of the nonlinear Hooke’s equation. Therefore, even though the ultrasonic nonlinearity parameter is not equal to the elastic nonlinearity parameter, they have a close relationship. However, there has been no experimental verification of the relationship between the ultrasonic and elastic nonlinearity parameters. In this study, the relationship is experimentally verified for a heat-treated aluminum alloy. Specimens of the aluminum alloy were heat-treated at 300°C for different periods of time (0, 1, 2, 5, 10, 20, and 50 h). The relative ultrasonic nonlinearity parameter of each specimen was then measured, and the elastic nonlinearity parameter was determined by fitting the stress-strain curve obtained from a tensile test to the 5th-order-polynomial nonlinear Hooke’s equation. The results showed that the variations in these parameters were in good agreement with each other.

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.

Integrability and soliton solutions for an inhomogeneous generalized fourth-order nonlinear Schrödinger equation describing the inhomogeneous alpha helical proteins and Heisenberg ferromagnetic spin chains

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

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

A Reference Database for Circular Dichroism Spectroscopy Covering Fold and Secondary Structure Space

International Nuclear Information System (INIS)

Lees, J.; Miles, A.; Wien, F.; Wallace, B.

2006-01-01

Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined. This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology

Modularity in protein structures: study on all-alpha proteins.

Science.gov (United States)

Khan, Taushif; Ghosh, Indira

2015-01-01

Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

Evaluation of nonlinearity and validity of nonlinear modeling for complex time series.

Science.gov (United States)

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.

Nonlinear graphene plasmonics

Science.gov (United States)

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.

Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database.

Science.gov (United States)

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.

Non-linear sputtering effects induced by MeV energy gold clusters

International Nuclear Information System (INIS)

Boussofiane-Baudin, K.; Brunelle, A.; Chaurand, P.; Della-Negra, S.; Depauw, J.; Le Beyec, Y.; Hakansson, P.

1993-09-01

Gold clusters Au n + with 1 < n ≤ 4, accelerated to MeV energies at the Orsay tandem accelerator, have been used to induce secondary ion emission from the surface of thin organic and inorganic films. A non-linear enhancement of the secondary ion yields is observed when cluster impacts are compared to single atom impacts at the same velocity. It has been shown that the collective effects propagate in the solid over a depth larger than 2000 A. The equilibrium charge state of cluster constituents after their passage through a thin carbon foil (1000 A) has been measured. The mean value for the cluster constituents is the same as for single atoms at the same velocity. (authors). 41 refs., 8 figs., 1 tab

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

Tracer kinetics: Modelling of tracer behaviour in nonlinear and nonsteady state systems exemplified by the evaluation of protein turnover in plant organs

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

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.

Linearization of the Bradford Protein Assay

OpenAIRE

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...

Specific serum protein changes associated with primary and secondary Strongylus vulgaris infections in pony yearlings.

Science.gov (United States)

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.

Heisenberg representation for secondary-quantized fields in nonstationary external fields and dielectric nonlinear medium

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

Preventing secondary cases of invasive meningococcal capsular group B (MenB) disease using a recently-licensed, multi-component, protein-based vaccine (Bexsero(®)).

Science.gov (United States)

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.

Approaches to link RNA secondary structures with splicing regulation

DEFF Research Database (Denmark)

Plass, Mireya; Eyras, Eduardo

2014-01-01

In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either by facilitat...... describes the steps in the analysis of the secondary structure of the pre-mRNA and its possible relation to splicing. As a working example, we use the case of yeast and the problem of the recognition of the 3' splice site (3'ss).......In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either...

Nonlinear Dirac Equations

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.

CMB anisotropies at all orders: the non-linear Sachs-Wolfe formula

OpenAIRE

Roldan, Omar

2017-01-01

We obtain the non-linear generalization of the Sachs-Wolfe + integrated Sachs-Wolfe (ISW) formula describing the CMB temperature anisotropies. Our formula is valid at all orders in perturbation theory, is also valid in all gauges and includes scalar, vector and tensor modes. A direct consequence of our results is that the maps of the logarithmic temperature anisotropies are much cleaner than the usual CMB maps, because they automatically remove many secondary anisotropies. This can for instan...

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

Brittle stalk 2 encodes a putative glycosylphosphatidylinositol-anchored protein that affects mechanical strength of maize tissues by altering the composition and structure of secondary cell walls.

Science.gov (United States)

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.

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 photonic metasurfaces

Science.gov (United States)

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.

Plasma Homocysteine is Not Related to the Severity of Microangiopathy in Secondary Raynaud Phenomenon

Science.gov (United States)

Jacomella, Vincenzo; Wasila, Monika; Husmann, Marc; Gitzelmann, Gabriela; Meier, Thomas; Amann-Vesti, Beatrice

2011-01-01

Introduction: The role of elevated homocysteine in primary and secondary Raynaud phenomenon (RP) and in patients with atherosclerosis has been reported controversially. In secondary RP due to connective tissue disease specific alterations of nailfold capillaries might be present. An association between these microvascular changes and homocysteine has been suggested. Aim: The aim of this study was to determine whether homocysteine level differs between patients with primary and secondary RP and to test the hypothesis that homocysteine or other cardiovascular risk factors are associated with specific features of microangiopathy in secondary RP. Patients and Methods Eighty-one consecutive patients with RP referred for vascular assessment were studied by nailfold capillaroscopy. Homocysteine, C-reactive protein and cholesterol were measured and other cardiovascular risk factors and comorbidities assessed. Results: Homocysteine, C-reactive-protein and cholesterol levels did not differ between patients with primary (n=60) and secondary RP (n=21). Likewise, no differences in the prevalence of cardiovascular risk factors and comorbidities were found. In secondary RP no correlation was found between microvascular involvement and homocysteine or C-reactive protein. Conclusion: Plasma homocysteine is not different in patients with either primary or secondary RP and is therefore not a marker for the distinction of these diseases. The extent of microvascular involvement in secondary RP does not correlate with plasma homocysteine. PMID:22216066

Quantum Nonlinear Optics

CERN Document Server

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 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.

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....

Unidirectional reflection and invisibility in nonlinear media with an incoherent nonlinearity

Science.gov (United States)

Mostafazadeh, Ali; Oflaz, Neslihan

2017-11-01

We give explicit criteria for the reflectionlessness, transparency, and invisibility of a finite-range potential in the presence of an incoherent (intensity-dependent) nonlinearity that is confined to the range of the potential. This allows us to conduct a systematic study of the effects of such a nonlinearity on a locally periodic class of finite-range potentials that display perturbative unidirectional invisibility. We use our general results to examine the effects of a weak Kerr nonlinearity on the behavior of these potentials and show that the presence of nonlinearity destroys the unidirectional invisibility of these potentials. If the strength of the Kerr nonlinearity is so weak that the first-order perturbation theory is reliable, the presence of nonlinearity does not affect the unidirectional reflectionlessness and transmission reciprocity of the potential. We show that the expected violation of the latter is a second order perturbative effect.

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...

Nonlinear network model analysis of vibrational energy transfer and localisation in the Fenna-Matthews-Olson complex

Science.gov (United States)

Morgan, Sarah E.; Cole, Daniel J.; Chin, Alex W.

2016-11-01

Collective protein modes are expected to be important for facilitating energy transfer in the Fenna-Matthews-Olson (FMO) complex of photosynthetic green sulphur bacteria, however to date little work has focussed on the microscopic details of these vibrations. The nonlinear network model (NNM) provides a computationally inexpensive approach to studying vibrational modes at the microscopic level in large protein structures, whilst incorporating anharmonicity in the inter-residue interactions which can influence protein dynamics. We apply the NNM to the entire trimeric FMO complex and find evidence for the existence of nonlinear discrete breather modes. These modes tend to transfer energy to the highly connected core pigments, potentially opening up alternative excitation energy transfer routes through their influence on pigment properties. Incorporating localised modes based on these discrete breathers in the optical spectra calculations for FMO using ab initio site energies and excitonic couplings can substantially improve their agreement with experimental results.

Nonlinear evolution equations

CERN Document Server

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

A Simple FEM Formulation Applied to Nonlinear Problems of Impact with Thermomechanical Coupling

Directory of Open Access Journals (Sweden)

João Paulo de Barros Cavalcante

Full Text Available Abstract The thermal effects of problems involving deformable structures are essential to describe the behavior of materials in feasible terms. Verifying the transformation of mechanical energy into heat it is possible to predict the modifications of mechanical properties of materials due to its temperature changes. The current paper presents the numerical development of a finite element method suitable for nonlinear structures coupled with thermomechanical behavior; including impact problems. A simple and effective alternative formulation is presented, called FEM positional, to deal with the dynamic nonlinear systems. The developed numerical is based on the minimum potential energy written in terms of nodal positions instead of displacements. The effects of geometrical, material and thermal nonlinearities are considered. The thermodynamically consistent formulation is based on the laws of thermodynamics and the Helmholtz free-energy, used to describe the thermoelastic and the thermoplastic behaviors. The coupled thermomechanical model can result in secondary effects that cause redistributions of internal efforts, depending on the history of deformation and material properties. The numerical results of the proposed formulation are compared with examples found in the literature.

Graphene oxide as a protein matrix: influence on protein biophysical properties.

Science.gov (United States)

Hernández-Cancel, Griselle; Suazo-Dávila, Dámaris; Ojeda-Cruzado, Axel J; García-Torres, Desiree; Cabrera, Carlos R; Griebenow, Kai

2015-10-19

This study provides fundamental information on the influence of graphene oxide (GO) nanosheets and glycans on protein catalytic activity, dynamics, and thermal stability. We provide evidence of protein stabilization by glycans and how this strategy could be implemented when GO nanosheets is used as protein immobilization matrix. A series of bioconjugates was constructed using two different strategies: adsorbing or covalently attaching native and glycosylated bilirubin oxidase (BOD) to GO. Bioconjugate formation was followed by FT-IR, zeta-potential, and X-ray photoelectron spectroscopy measurements. Enzyme kinetic parameters (k(m) and k(cat)) revealed that the substrate binding affinity was not affected by glycosylation and immobilization on GO, but the rate of enzyme catalysis was reduced. Structural analysis by circular dichroism showed that glycosylation did not affect the tertiary or the secondary structure of BOD. However, GO produced slight changes in the secondary structure. To shed light into the biophysical consequence of protein glycosylation and protein immobilization on GO nanosheets, we studied structural protein dynamical changes by FT-IR H/D exchange and thermal inactivation. It was found that glycosylation caused a reduction in structural dynamics that resulted in an increase in thermostability and a decrease in the catalytic activity for both, glycoconjugate and immobilized enzyme. These results establish the usefulness of chemical glycosylation to modulate protein structural dynamics and stability to develop a more stable GO-protein matrix.

On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking

DEFF Research Database (Denmark)

Feliu, Elisenda; Aloy, Patrick; Oliva, Baldo

2011-01-01

Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions for s...... and with independence of the partner. This information is encoded at the residue level and could be easily incorporated in the initial grid scoring for Fast Fourier Transform rigid-body docking methods.......Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions...... for selecting rigid-body docking poses. These potentials include the energetic component that provides the residues with a particular secondary structure and surface accessibility. These scoring functions have been tested on a state-of-art benchmark dataset and on a decoy dataset of permanent interactions. Our...

Nonlinear optics

CERN Document Server

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

Ultrafast nonlinear dynamics of thin gold films due to an intrinsic delayed nonlinearity

Science.gov (United States)

Bache, Morten; Lavrinenko, Andrei V.

2017-09-01

Using long-range surface plasmon polaritons light can propagate in metal nano-scale waveguides for ultracompact opto-electronic devices. Gold is an important material for plasmonic waveguides, but although its linear optical properties are fairly well understood, the nonlinear response is still under investigation. We consider the propagation of pulses in ultrathin gold strip waveguides, modeled by the nonlinear Schrödinger equation. The nonlinear response of gold is accounted for by the two-temperature model, revealing it as a delayed nonlinearity intrinsic in gold. The consequence is that the measured nonlinearities are strongly dependent on pulse duration. This issue has so far only been addressed phenomenologically, but we provide an accurate estimate of the quantitative connection as well as a phenomenological theory to understand the enhanced nonlinear response as the gold thickness is reduced. In comparison with previous works, the analytical model for the power-loss equation has been improved, and can be applied now to cases with a high laser peak power. We show new fits to experimental data from the literature and provide updated values for the real and imaginary parts of the nonlinear susceptibility of gold for various pulse durations and gold layer thicknesses. Our simulations show that the nonlinear loss is inhibiting efficient nonlinear interaction with low-power laser pulses. We therefore propose to design waveguides suitable for the mid-IR, where the ponderomotive instantaneous nonlinearity can dominate over the delayed hot-electron nonlinearity and provide a suitable plasmonics platform for efficient ultrafast nonlinear optics.

Few-cycle nonlinear mid-IR pulse generated with cascaded quadratic nonlinearities

DEFF Research Database (Denmark)

Bache, Morten; Liu, Xing; Zhou, Binbin

Generating few-cycle energetic and broadband mid-IR pulses is an urgent current challenge in nonlinear optics. Cascaded second-harmonic generation (SHG) gives access to an ultrafast and octave-spanning self-defocusing nonlinearity: when ΔkL >> 2π the pump experiences a Kerr-like nonlinear index...

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

Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

Science.gov (United States)

Kinjo, Akira R; Nakamura, Haruki

2013-01-01

Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

Nonlinear crack mechanics

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

JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure.

Science.gov (United States)

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.

Nonlinear dynamics and complexity

CERN Document Server

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.

Waves and Structures in Nonlinear Nondispersive Media General Theory and Applications to Nonlinear Acoustics

CERN Document Server

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...

Nonlinear programming for classification problems in machine learning

Science.gov (United States)

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.

Nonlinear Approaches in Engineering Applications

CERN Document Server

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 modelling of polymer electrolyte membrane fuel cell stack using nonlinear cancellation technique

Energy Technology Data Exchange (ETDEWEB)

Barus, R. P. P., E-mail: rismawan.ppb@gmail.com [Engineering Physics, Faculty of Industrial Technology, Institut Teknologi Bandung, Jalan Ganesa 10 Bandung and Centre for Material and Technical Product, Jalan Sangkuriang No. 14 Bandung (Indonesia); Tjokronegoro, H. A.; Leksono, E. [Engineering Physics, Faculty of Industrial Technology, Institut Teknologi Bandung, Jalan Ganesa 10 Bandung (Indonesia); Ismunandar [Chemistry Study, Faculty of Mathematics and Science, Institut Teknologi Bandung, Jalan Ganesa 10 Bandung (Indonesia)

2014-09-25

Fuel cells are promising new energy conversion devices that are friendly to the environment. A set of control systems are required in order to operate a fuel cell based power plant system optimally. For the purpose of control system design, an accurate fuel cell stack model in describing the dynamics of the real system is needed. Currently, linear model are widely used for fuel cell stack control purposes, but it has limitations in narrow operation range. While nonlinear models lead to nonlinear control implemnetation whos more complex and hard computing. In this research, nonlinear cancellation technique will be used to transform a nonlinear model into a linear form while maintaining the nonlinear characteristics. The transformation is done by replacing the input of the original model by a certain virtual input that has nonlinear relationship with the original input. Then the equality of the two models is tested by running a series of simulation. Input variation of H2, O2 and H2O as well as disturbance input I (current load) are studied by simulation. The error of comparison between the proposed model and the original nonlinear model are less than 1 %. Thus we can conclude that nonlinear cancellation technique can be used to represent fuel cell nonlinear model in a simple linear form while maintaining the nonlinear characteristics and therefore retain the wide operation range.

Nonlinear modelling of polymer electrolyte membrane fuel cell stack using nonlinear cancellation technique

International Nuclear Information System (INIS)

Barus, R. P. P.; Tjokronegoro, H. A.; Leksono, E.; Ismunandar

2014-01-01

Fuel cells are promising new energy conversion devices that are friendly to the environment. A set of control systems are required in order to operate a fuel cell based power plant system optimally. For the purpose of control system design, an accurate fuel cell stack model in describing the dynamics of the real system is needed. Currently, linear model are widely used for fuel cell stack control purposes, but it has limitations in narrow operation range. While nonlinear models lead to nonlinear control implemnetation whos more complex and hard computing. In this research, nonlinear cancellation technique will be used to transform a nonlinear model into a linear form while maintaining the nonlinear characteristics. The transformation is done by replacing the input of the original model by a certain virtual input that has nonlinear relationship with the original input. Then the equality of the two models is tested by running a series of simulation. Input variation of H2, O2 and H2O as well as disturbance input I (current load) are studied by simulation. The error of comparison between the proposed model and the original nonlinear model are less than 1 %. Thus we can conclude that nonlinear cancellation technique can be used to represent fuel cell nonlinear model in a simple linear form while maintaining the nonlinear characteristics and therefore retain the wide operation range

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.

FTIR study of secondary structure of bovine serum albumin and ovalbumin

International Nuclear Information System (INIS)

Abrosimova, K V; Shulenina, O V; Paston, S V

2016-01-01

Proteins structure is the critical factor for their functioning. Fourier transform infrared spectroscopy provides a possibility to obtain information about secondary structure of proteins in different states and also in a whole biological samples. Infrared spectra of egg white from the untreated and hard-boiled hen's egg, and also of chicken ovalbumin and bovine serum albumin in lyophilic form and in aqueous solution were studied. Lyophilization of investigated globular proteins is accompanied by the decrease of a-helix structures and the increase in amount of intermolecular β-sheets. Analysis of infrared spectrum of egg white allowed to make an estimation of OVA secondary structure and to observe α-to-β structural transformation as a result of the heat denaturation. (paper)

Nonlinear behaviour of cantilevered carbon nanotube resonators based on a new nonlinear electrostatic load model

Science.gov (United States)

Farokhi, Hamed; Païdoussis, Michael P.; Misra, Arun K.

2018-04-01

The present study examines the nonlinear behaviour of a cantilevered carbon nanotube (CNT) resonator and its mass detection sensitivity, employing a new nonlinear electrostatic load model. More specifically, a 3D finite element model is developed in order to obtain the electrostatic load distribution on cantilevered CNT resonators. A new nonlinear electrostatic load model is then proposed accounting for the end effects due to finite length. Additionally, a new nonlinear size-dependent continuum model is developed for the cantilevered CNT resonator, employing the modified couple stress theory (to account for size-effects) together with the Kelvin-Voigt model (to account for nonlinear damping); the size-dependent model takes into account all sources of nonlinearity, i.e. geometrical and inertial nonlinearities as well as nonlinearities associated with damping, small-scale, and electrostatic load. The nonlinear equation of motion of the cantilevered CNT resonator is obtained based on the new models developed for the CNT resonator and the electrostatic load. The Galerkin method is then applied to the nonlinear equation of motion, resulting in a set of nonlinear ordinary differential equations, consisting of geometrical, inertial, electrical, damping, and size-dependent nonlinear terms. This high-dimensional nonlinear discretized model is solved numerically utilizing the pseudo-arclength continuation technique. The nonlinear static and dynamic responses of the system are examined for various cases, investigating the effect of DC and AC voltages, length-scale parameter, nonlinear damping, and electrostatic load. Moreover, the mass detection sensitivity of the system is examined for possible application of the CNT resonator as a nanosensor.

Protein Structure Prediction by Protein Threading

Science.gov (United States)

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.

Time history nonlinear earthquake response analysis considering materials and geometrical nonlinearity

International Nuclear Information System (INIS)

Kobayashi, T.; Yoshikawa, K.; Takaoka, E.; Nakazawa, M.; Shikama, Y.

2002-01-01

A time history nonlinear earthquake response analysis method was proposed and applied to earthquake response prediction analysis for a Large Scale Seismic Test (LSST) Program in Hualien, Taiwan, in which a 1/4 scale model of a nuclear reactor containment structure was constructed on sandy gravel layer. In the analysis both of strain-dependent material nonlinearity, and geometrical nonlinearity by base mat uplift, were considered. The 'Lattice Model' for the soil-structure interaction model was employed. An earthquake record on soil surface at the site was used as control motion, and deconvoluted to the input motion of the analysis model at GL-52 m with 300 Gal of maximum acceleration. The following two analyses were considered: (A) time history nonlinear, (B) equivalent linear, and the advantage of time history nonlinear earthquake response analysis method is discussed

Geometrically Nonlinear Transient Response of Laminated Plates with Nonlinear Elastic Restraints

Directory of Open Access Journals (Sweden)

Shaochong Yang

2017-01-01

Full Text Available To investigate the dynamic behavior of laminated plates with nonlinear elastic restraints, a varied constraint force model and a systematic numerical procedure are presented in this work. Several kinds of typical relationships of force-displacement for spring are established to simulate the nonlinear elastic restraints. In addition, considering the restraining moments of flexible pads, the pads are modeled by translational and rotational springs. The displacement- dependent constraint forces are added to the right-hand side of equations of motion and treated as additional applied loads. These loads can be explicitly defined, via an independent set of nonlinear load functions. The time histories of transverse displacements at typical points of the laminated plate are obtained through the transient analysis. Numerical examples show that the present method can effectively treat the geometrically nonlinear transient response of plates with nonlinear elastic restraints.

Nonlinear optical systems

CERN Document Server

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.

Development of protein biomarkers in cerebrospinal fluid for secondary progressive multiple sclerosis using selected reaction monitoring mass spectrometry (SRM-MS

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

Nonlinear elastic waves in materials

CERN Document Server

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...

Plant protein and secondary metabolites influence diet selection in a mammalian specialist herbivore

Science.gov (United States)

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

Nonlinear correlations in the hydrophobicity and average flexibility along the glycolytic enzymes sequences

Energy Technology Data Exchange (ETDEWEB)

Ciorsac, Alecu, E-mail: aleciorsac@yahoo.co [Politehnica University of Timisoara, Department of Physical Education and Sport, 2 P-ta Victoriei, 300006, Timisoara (Romania); Craciun, Dana, E-mail: craciundana@gmail.co [Teacher Training Department, West University of Timisoara, 4 Boulevard V. Pirvan, Timisoara, 300223 (Romania); Ostafe, Vasile, E-mail: vostafe@cbg.uvt.r [Department of Chemistry, West University of Timisoara, 16 Pestallozi, 300115, Timisoara (Romania); Laboratory of Advanced Researches in Environmental Protection, Nicholas Georgescu-Roegen Interdisciplinary Research and Formation Platform, 4 Oituz, Timisoara, 300086 (Romania); Isvoran, Adriana, E-mail: aisvoran@cbg.uvt.r [Department of Chemistry, West University of Timisoara, 16 Pestallozi, 300115, Timisoara (Romania); Laboratory of Advanced Researches in Environmental Protection, Nicholas Georgescu-Roegen Interdisciplinary Research and Formation Platform, 4 Oituz, Timisoara, 300086 (Romania)

2011-04-15

Research highlights: lights: We focus our study on the glycolytic enzymes. We reveal correlation of hydrophobicity and flexibility along their chains. We also reveal fractal aspects of the glycolytic enzymes structures and surfaces. The glycolytic enzyme sequences are not random. Creation of fractal structures requires the operation of nonlinear dynamics. - Abstract: Nonlinear methods widely used for time series analysis were applied to glycolytic enzyme sequences to derive information concerning the correlation of hydrophobicity and average flexibility along their chains. The 20 sequences of different types of the 10 human glycolytic enzymes were considered as spatial series and were analyzed by spectral analysis, detrended fluctuations analysis and Hurst coefficient calculation. The results agreed that there are both short range and long range correlations of hydrophobicity and average flexibility within investigated sequences, the short range correlations being stronger and indicating that local interactions are the most important for the protein folding. This correlation is also reflected by the fractal nature of the structures of investigated proteins.

FRF decoupling of nonlinear systems

Science.gov (United States)

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.

Elements of a dialogue between nonlinear models in condensed matter and biophysics

International Nuclear Information System (INIS)

Bishop, A.R.; Lomdahl, P.S.; Kerr, W.C.

1985-01-01

We indicate some of the emerging thematic connections between strongly nonlinear effects in condensed matter and biological materials. These are illustrated with model studies of: (1) structural phase transitions in anisotropic lattices; and (2) finite temperature effects on self-trapped states in vibron-phonon models of α-helix proteins. 13 refs., 8 figs

Nonlinear behavior in the time domain in argon atmospheric dielectric-barrier discharges

International Nuclear Information System (INIS)

Shi Hong; Wang Yanhui; Wang Dezhen

2008-01-01

A vast majority of nonlinear behavior in atmospheric pressure discharges has so far been studied in the space domain, and their time-domain characters are often believed to exact the periodicity of the externally applied voltage. In this paper, based on one-dimensional fluid mode, we study complex nonlinear behavior in the time domain in argon atmospheric dielectric-barrier discharges at very broad frequency range from kilohertz to megahertz. Under certain conditions, the discharge not only can be driven to chaos from time-periodic state through period-doubling bifurcation, but also can return stable periodic motion from chaotic state through an inverse period-doubling bifurcation sequence. Upon changing the parameter the discharge undergoes alternatively chaotic and periodic behavior. Some periodic windows embedded in chaos, as well as the secondary bifurcation occurring in the periodic windows can also be observed. The corresponding discharge characteristics are investigated.

Analytical and numerical studies of approximate phase velocity matching based nonlinear S0 mode Lamb waves for the detection of evenly distributed microstructural changes

International Nuclear Information System (INIS)

Wan, X; Xu, G H; Tao, T F; Zhang, Q; Tse, P W

2016-01-01

Most previous studies on nonlinear Lamb waves are conducted using mode pairs that satisfying strict phase velocity matching and non-zero power flux criteria. However, there are some limitations in existence. First, strict phase velocity matching is not existed in the whole frequency bandwidth; Second, excited center frequency is not always exactly equal to the true phase-velocity-matching frequency; Third, mode pairs are isolated and quite limited in number; Fourth, exciting a single desired primary mode is extremely difficult in practice and the received signal is quite difficult to process and interpret. And few attention has been paid to solving these shortcomings. In this paper, nonlinear S0 mode Lamb waves at low-frequency range satisfying approximate phase velocity matching is proposed for the purpose of overcoming these limitations. In analytical studies, the secondary amplitudes with the propagation distance considering the fundamental frequency, the maximum cumulative propagation distance (MCPD) with the fundamental frequency and the maximum linear cumulative propagation distance (MLCPD) using linear regression analysis are investigated. Based on analytical results, approximate phase velocity matching is quantitatively characterized as the relative phase velocity deviation less than a threshold value of 1%. Numerical studies are also conducted using tone burst as the excitation signal. The influences of center frequency and frequency bandwidth on the secondary amplitudes and MCPD are investigated. S1–S2 mode with the fundamental frequency at 1.8 MHz, the primary S0 mode at the center frequencies of 100 and 200 kHz are used respectively to calculate the ratios of nonlinear parameter of Al 6061-T6 to Al 7075-T651. The close agreement of the computed ratios to the actual value verifies the effectiveness of nonlinear S0 mode Lamb waves satisfying approximate phase velocity matching for characterizing the material nonlinearity. Moreover, the ratios derived

Solution of linear and nonlinear matrix systems. Application to a nonlinear diffusion equation

International Nuclear Information System (INIS)

Bonnet, M.; Meurant, G.

1978-01-01

Different methods of solution of linear and nonlinear algebraic systems are applied to the nonlinear system obtained by discretizing a nonlinear diffusion equation. For linear systems, methods in general use of alternating directions type or Gauss Seidel's methods are compared to more recent ones of the type of generalized conjugate gradient; the superiority of the latter is shown by numerical examples. For nonlinear systems, a method on nonlinear conjugate gradient is studied as also Newton's method and some of its variants. It should be noted, however that Newton's method is found to be more efficient when coupled with a good method for solution of the linear system. To conclude, such methods are used to solve a nonlinear diffusion problem and the numerical results obtained are to be compared [fr

Solution of linear and nonlinear matrix systems. Application to a nonlinear diffusion equation

International Nuclear Information System (INIS)

Bonnet, M.; Meurant, G.

1978-01-01

The object of this study is to compare different methods of solving linear and nonlinear algebraic systems and to apply them to the nonlinear system obtained by discretizing a nonlinear diffusion equation. For linear systems the conventional methods of alternating direction type or Gauss Seidel's methods are compared to more recent ones of the type of generalized conjugate gradient; the superiority of the latter is shown by numerical examples. For nonlinear systems, a method of nonlinear conjugate gradient is studied together with Newton's method and some of its variants. It should be noted, however, that Newton's method is found to be more efficient when coupled with a good method for solving the linear system. As a conclusion, these methods are used to solve a nonlinear diffusion problem and the numerical results obtained are compared [fr

The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins.

Science.gov (United States)

Ponce de Leon, Miguel; de Miranda, Antonio Basilio; Alvarez-Valin, Fernando; Carels, Nicolas

2014-01-01

For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a regularity (the codon structure) resulting from physicochemical constraints on proteins and thermodynamic constraints on ribosomal machinery. The physicochemical constraints on proteins mainly come from the hydropathy and molecular weight (MW) of secondary structures as well as the energy cost of amino acid synthesis. These constraints appear through a network of statistical correlations, such as (i) the cost of amino acid synthesis, which is in favor of a higher level of guanine in the first codon position, (ii) the constructive contribution of hydropathy alternation in proteins, (iii) the spatial organization of secondary structure in proteins according to solvent accessibility, (iv) the spatial organization of secondary structure according to amino acid hydropathy, (v) the statistical correlation of MW with protein secondary structures and their overall hydropathy, (vi) the statistical correlation of thymine in the second codon position with hydropathy and the energy cost of amino acid synthesis, and (vii) the statistical correlation of adenine in the second codon position with amino acid complexity and the MW of secondary protein structures. Amino acid physicochemical properties and functional constraints on proteins constitute a code that is translated into a purine bias within the coding DNA via tRNAs. In that sense, the Rrr pattern within coding DNA is the effect of information transfer on nucleotide composition from protein to DNA by selection according to the codon positions. Thus, coding DNA structure and ribosomal machinery co-evolved to minimize the energy cost of protein coding given the functional

ProteinShop: A tool for interactive protein manipulation and steering

Energy Technology Data Exchange (ETDEWEB)

Crivelli, Silvia; Kreylos, Oliver; Max, Nelson; Hamann, Bernd; Bethel, Wes

2004-05-25

We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing secondary structures specified by the user. Second, it can interactively manipulate protein fragments to achieve desired folds by adjusting the dihedral angles of selected coil regions using an Inverse Kinematics method. Last, it serves as a visual framework to monitor and steer a protein structure prediction process that may be running on a remote machine. ProteinShop was used to create initial configurations for a protein structure prediction method developed by a team that competed in CASP5. ProteinShop's use accelerated the process of generating initial configurations, reducing the time required from days to hours. This paper describes the structure of ProteinShop and discusses its main features.

Unraveling the meaning of chemical shifts in protein NMR.

Science.gov (United States)

Berjanskii, Mark V; Wishart, David S

2017-11-01

Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

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....

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 Dielectric Spectroscopy as an Indirect Probe of Metabolic Activity in Thylakoid Membrane

Directory of Open Access Journals (Sweden)

John H. Miller

2011-01-01

Full Text Available Nonlinear dielectric spectroscopy (NDS is a non-invasive probe of cellular metabolic activity with potential application in the development of whole-cell biosensors. However, the mechanism of NDS interaction with metabolic membrane proteins is poorly understood, partly due to the inherent complexity of single cell organisms. Here we use the light-activated electron transport chain of spinach thylakoid membrane as a model system to study how NDS interacts with metabolic activity. We find protein modification, as opposed to membrane pump activity, to be the dominant source of NDS signal change in this system. Potential mechanisms for such protein modifications include reactive oxygen species generation and light-activated phosphorylation.

50 years of nonlinear optics

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)

Nonlinear Optics and Applications

Science.gov (United States)

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.

Diffusion of a protein in configuration space

Energy Technology Data Exchange (ETDEWEB)

Garcia, A.E.; Blumenfeld, R.; Hummer, G.; Sobehart, J.

1995-09-01

Simulations of biomolecular dynamics are commonly interpreted in terms of harmonic or quasi-harmonic models for the dynamics of the system. These models assume that biomolecules exhibit oscillations around a single energy minimum. However, spectroscopic data on myoglobin suggest that proteins sample multiple minima. Transitions between minima reveal a broad distribution of energy barriers. This behavior has been observed in other biomolecular systems. To elucidate the nature of protein dynamics the authors have studied a 1.2ns molecular dynamics trajectory of crambin in aqueous solution. This trajectory samples multiple local energy minima. Transitions between minima involve collective motions of amino acids over long distances. The authors show that nonlinear motions are responsible for most of the atomic fluctuations of the protein. These atomic fluctuations are not well described by large motions of individual atoms or a small group of atoms, but rather by concerted motions of many atoms. These nonlinear motions describe transitions between different basins of attraction. The signature of these motions manifests in local and global structural variables. A method for extracting Molecule Optimal Dynamic Coordinates (MODC) is presented.

A Nonlinear Model of Mix Coil Spring – Rubber for Vertical Suspension of Railway Vehicle

Directory of Open Access Journals (Sweden)

Dumitriu Mădălina

2016-03-01

Full Text Available The paper focuses on a nonlinear model to represent the mechanical behaviour of a mix coil spring - rubber used in the secondary suspension of passenger rail vehicles. The principle of the model relies on overlapping of the forces corresponding to three components - the elastic component, the viscous component and the dry friction component. The model has two sources on non-linearity, in the elastic force and the friction force, respectively. The main attributes of the model are made visible by its response to an imposed displacement-type harmonic excitation. The results thus obtained from the applications of numerical simulation show a series of basic properties of the model, namely the dependence on amplitude and the excitation frequency of the model response, as well as of its stiffness and damping.

Nestin upregulation characterizes vascular remodeling secondary to hypertension in the rat.

Science.gov (United States)

Tardif, Kim; Hertig, Vanessa; Duquette, Natacha; Villeneuve, Louis; El-Hamamsy, Ismail; Tanguay, Jean-François; Calderone, Angelino

2015-05-15

Proliferation and hypertrophy of vascular smooth muscle cells represent hallmark features of vessel remodeling secondary to hypertension. The intermediate filament protein nestin was recently identified in vascular smooth muscle cells and in other cell types directly participated in proliferation. The present study tested the hypothesis that vessel remodeling secondary to hypertension was characterized by nestin upregulation in vascular smooth muscle cells. Two weeks after suprarenal abdominal aorta constriction of adult male Sprague-Dawley rats, elevated mean arterial pressure increased the media area and thickness of the carotid artery and aorta and concomitantly upregulated nestin protein levels. In the normal adult rat carotid artery, nestin immunoreactivity was observed in a subpopulation of vascular smooth muscle cells, and the density significantly increased following suprarenal abdominal aorta constriction. Filamentous nestin was detected in cultured rat carotid artery- and aorta-derived vascular smooth muscle cells and an analogous paradigm observed in human aorta-derived vascular smooth muscle cells. ANG II and EGF treatment of vascular smooth muscle cells stimulated DNA and protein synthesis and increased nestin protein levels. Lentiviral short-hairpin RNA-mediated nestin depletion of carotid artery-derived vascular smooth muscle cells inhibited peptide growth factor-stimulated DNA synthesis, whereas protein synthesis remained intact. These data have demonstrated that vessel remodeling secondary to hypertension was characterized in part by nestin upregulation in vascular smooth muscle cells. The selective role of nestin in peptide growth factor-stimulated DNA synthesis has revealed that the proliferative and hypertrophic responses of vascular smooth muscle cells were mediated by divergent signaling events. Copyright © 2015 the American Physiological Society.

Engineering the Oryza sativa cell wall with rice NAC transcription factors regulating secondary wall formation

Directory of Open Access Journals (Sweden)

Kouki eYoshida

2013-10-01

Full Text Available Plant tissues that require structural rigidity synthesize a thick, strong secondary cell wall of lignin, cellulose and hemicelluloses in a complicated bridged structure. Master regulators of secondary wall synthesis were identified in dicots, and orthologs of these regulators have been identified in monocots, but regulation of secondary cell wall formation in monocots has not been extensively studied. Here we demonstrate that the rice transcription factors SECONDARY WALL NAC DOMAIN PROTEINs (SWNs can regulate secondary wall formation in rice (Oryza sativa and are potentially useful for engineering the monocot cell wall. The OsSWN1 promoter is highly active in sclerenchymatous cells of the leaf blade and less active in xylem cells. By contrast, the OsSWN2 promoter is highly active in xylem cells and less active in sclerenchymatous cells. OsSWN2 splicing variants encode two proteins; the shorter protein (OsSWN2S has very low transcriptional activation ability, but the longer protein (OsSWN2L and OsSWN1 have strong transcriptional activation ability. In rice, expression of an OsSWN2S chimeric repressor, driven by the OsSWN2 promoter, resulted in stunted growth and para-wilting (leaf rolling and browning under normal water conditions due to impaired vascular vessels. The same OsSWN2S chimeric repressor, driven by the OsSWN1 promoter, caused a reduction of cell wall thickening in sclerenchymatous cells, a drooping leaf phenotype, reduced lignin and xylose contents and increased digestibility as forage. These data suggest that OsSWNs regulate secondary wall formation in rice and manipulation of OsSWNs may enable improvements in monocotyledonous crops for forage or biofuel applications.

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

Pescara benchmarks: nonlinear identification

Science.gov (United States)

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.

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.

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....

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...

Neural Networks for protein Structure Prediction

DEFF Research Database (Denmark)

Bohr, Henrik

1998-01-01

This is a review about neural network applications in bioinformatics. Especially the applications to protein structure prediction, e.g. prediction of secondary structures, prediction of surface structure, fold class recognition and prediction of the 3-dimensional structure of protein backbones...

Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations

Energy Technology Data Exchange (ETDEWEB)

Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

2012-06-15

NMR is ideally suited for the analysis of protein-protein and protein ligand interactions with dissociation constants ranging from {approx}2 {mu}M to {approx}1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K{sub D}) of 1:1 protein-protein or protein-ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K{sub D}, and nonlinear least squares analysis of chemical shift changes as a function of ligand concentration is employed to determine estimates for the parameters K{sub D} and the maximum chemical shift change ({Delta}{delta}{sub max}). During a typical NMR titration, the initial protein concentration, [P{sub 0}], is held nearly constant. For this condition, to determine the most accurate parameters for K{sub D} and {Delta}{delta}{sub max} from nonlinear least squares analyses requires initial protein concentrations that are {approx}0.5 Multiplication-Sign K{sub D}, and a maximum concentration for the ligand, or titrant, of {approx}10 Multiplication-Sign [P{sub 0}]. From a practical standpoint, these requirements are often difficult to achieve. Using Monte Carlo simulations, we demonstrate that co-variation of the ligand and protein concentrations during a titration leads to an increase in the precision of the fitted K{sub D} and {Delta}{delta}{sub max} values when [P{sub 0}] > K{sub D}. Importantly, judicious choice of protein and ligand concentrations for a given NMR titration, combined with nonlinear least squares analyses using two independent variables (ligand and protein concentrations) and two parameters (K{sub D} and {Delta}{delta}{sub max}) is a straightforward approach to increasing the accuracy of measured dissociation constants for 1:1 protein-ligand interactions.

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.)

Blow-Up Time for Nonlinear Heat Equations with Transcendental Nonlinearity

Directory of Open Access Journals (Sweden)

Hee Chul Pak

2012-01-01

Full Text Available A blow-up time for nonlinear heat equations with transcendental nonlinearity is investigated. An upper bound of the first blow-up time is presented. It is pointed out that the upper bound of the first blow-up time depends on the support of the initial datum.

Exploring inductive linearization for pharmacokinetic-pharmacodynamic systems of nonlinear ordinary differential equations.

Science.gov (United States)

Hasegawa, Chihiro; Duffull, Stephen B

2018-02-01

Pharmacokinetic-pharmacodynamic systems are often expressed with nonlinear ordinary differential equations (ODEs). While there are numerous methods to solve such ODEs these methods generally rely on time-stepping solutions (e.g. Runge-Kutta) which need to be matched to the characteristics of the problem at hand. The primary aim of this study was to explore the performance of an inductive approximation which iteratively converts nonlinear ODEs to linear time-varying systems which can then be solved algebraically or numerically. The inductive approximation is applied to three examples, a simple nonlinear pharmacokinetic model with Michaelis-Menten elimination (E1), an integrated glucose-insulin model and an HIV viral load model with recursive feedback systems (E2 and E3, respectively). The secondary aim of this study was to explore the potential advantages of analytically solving linearized ODEs with two examples, again E3 with stiff differential equations and a turnover model of luteinizing hormone with a surge function (E4). The inductive linearization coupled with a matrix exponential solution provided accurate predictions for all examples with comparable solution time to the matched time-stepping solutions for nonlinear ODEs. The time-stepping solutions however did not perform well for E4, particularly when the surge was approximated by a square wave. In circumstances when either a linear ODE is particularly desirable or the uncertainty in matching the integrator to the ODE system is of potential risk, then the inductive approximation method coupled with an analytical integration method would be an appropriate alternative.

Nonlocal and nonlinear dispersion in a nonlinear Schrodinger-type equation: exotic solitons and short-wavelength instabilities

DEFF Research Database (Denmark)

Oster, Michael; Gaididei, Yuri B.; Johansson, Magnus

2004-01-01

We study the continuum limit of a nonlinear Schrodinger lattice model with both on-site and inter-site nonlinearities, describing weakly coupled optical waveguides or Bose-Einstein condensates. The resulting continuum nonlinear Schrodinger-type equation includes both nonlocal and nonlinear...

Extreme nonlinear energy exchanges in a geometrically nonlinear lattice oscillating in the plane

Science.gov (United States)

Zhang, Zhen; Manevitch, Leonid I.; Smirnov, Valeri; Bergman, Lawrence A.; Vakakis, Alexander F.

2018-01-01

We study the in-plane damped oscillations of a finite lattice of particles coupled by linear springs under distributed harmonic excitation. Strong nonlinearity in this system is generated by geometric effects due to the in-plane stretching of the coupling spring elements. The lattice has a finite number of nonlinear transverse standing waves (termed nonlinear normal modes - NNMs), and an equal number of axial linear modes which are nonlinearly coupled to the transverse ones. Nonlinear interactions between the transverse and axial modes under harmonic excitation give rise to unexpected and extreme nonlinear energy exchanges in the lattice. In particular, we directly excite a transverse NNM by harmonic forcing (causing simulataneous indirect excitation of a corresponding axial linear mode due to nonlinear coupling), and identify three energy transfer mechanisms in the lattice. First, we detect the stable response of the directly excited transverse NNM (despite its instability in the absence of forcing), with simultaneous stability of the indirectly excited axial linear mode. Second, by changing the system and forcing parameters we report extreme nonlinear "energy explosions," whereby, after an initial regime of stability, the directly excited transverse NNM loses stability, leading to abrupt excitation of all transverse and axial modes of the lattice, at all possible wave numbers. This strong instability is triggered by the parametric instability of an indirectly excited axial mode which builds energy until the explosion. This is proved through theoretical analysis. Finally, in other parameter ranges we report intermittent, intense energy transfers from the directly excited transverse NNM to a small set of transverse NNMs with smaller wavelengths, and from the indirectly excited axial mode to a small set of axial modes, but with larger wavelengths. These intermittent energy transfers resemble energy cascades occurring in turbulent flows. Our results show that

Brain tumor magnetic targeting and biodistribution of superparamagnetic iron oxide nanoparticles linked with 70-kDa heat shock protein study by nonlinear longitudinal response

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

Brain tumor magnetic targeting and biodistribution of superparamagnetic iron oxide nanoparticles linked with 70-kDa heat shock protein study by nonlinear longitudinal response

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

Nonlinear correlations in the hydrophobicity and average flexibility along the glycolytic enzymes sequences

International Nuclear Information System (INIS)

Ciorsac, Alecu; Craciun, Dana; Ostafe, Vasile; Isvoran, Adriana

2011-01-01

Research highlights: → We focus our study on the glycolytic enzymes. → We reveal correlation of hydrophobicity and flexibility along their chains. → We also reveal fractal aspects of the glycolytic enzymes structures and surfaces. → The glycolytic enzyme sequences are not random. → Creation of fractal structures requires the operation of nonlinear dynamics. - Abstract: Nonlinear methods widely used for time series analysis were applied to glycolytic enzyme sequences to derive information concerning the correlation of hydrophobicity and average flexibility along their chains. The 20 sequences of different types of the 10 human glycolytic enzymes were considered as spatial series and were analyzed by spectral analysis, detrended fluctuations analysis and Hurst coefficient calculation. The results agreed that there are both short range and long range correlations of hydrophobicity and average flexibility within investigated sequences, the short range correlations being stronger and indicating that local interactions are the most important for the protein folding. This correlation is also reflected by the fractal nature of the structures of investigated proteins.

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.

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 ...

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.)

Advances in nonlinear optics

CERN Document Server

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.

Protein folding and the organization of the protein topology universe

DEFF Research Database (Denmark)

Lindorff-Larsen,, Kresten; Røgen, Peter; Paci, Emanuele

2005-01-01

residues and, in addition, that the topology of the transition state is closer to that of the native state than to that of any other fold in the protein universe. Here, we review the evidence for these conclusions and suggest a molecular mechanism that rationalizes these findings by presenting a view...... of protein folds that is based on the topological features of the polypeptide backbone, rather than the conventional view that depends on the arrangement of different types of secondary-structure elements. By linking the folding process to the organization of the protein structure universe, we propose...

Nonlinear optics principles and applications

CERN Document Server

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...

PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs

Directory of Open Access Journals (Sweden)

Greenblatt Jack

2006-07-01

Full Text Available Abstract Background Identification of protein interaction networks has received considerable attention in the post-genomic era. The currently available biochemical approaches used to detect protein-protein interactions are all time and labour intensive. Consequently there is a growing need for the development of computational tools that are capable of effectively identifying such interactions. Results Here we explain the development and implementation of a novel Protein-Protein Interaction Prediction Engine termed PIPE. This tool is capable of predicting protein-protein interactions for any target pair of the yeast Saccharomyces cerevisiae proteins from their primary structure and without the need for any additional information or predictions about the proteins. PIPE showed a sensitivity of 61% for detecting any yeast protein interaction with 89% specificity and an overall accuracy of 75%. This rate of success is comparable to those associated with the most commonly used biochemical techniques. Using PIPE, we identified a novel interaction between YGL227W (vid30 and YMR135C (gid8 yeast proteins. This lead us to the identification of a novel yeast complex that here we term vid30 complex (vid30c. The observed interaction was confirmed by tandem affinity purification (TAP tag, verifying the ability of PIPE to predict novel protein-protein interactions. We then used PIPE analysis to investigate the internal architecture of vid30c. It appeared from PIPE analysis that vid30c may consist of a core and a secondary component. Generation of yeast gene deletion strains combined with TAP tagging analysis indicated that the deletion of a member of the core component interfered with the formation of vid30c, however, deletion of a member of the secondary component had little effect (if any on the formation of vid30c. Also, PIPE can be used to analyse yeast proteins for which TAP tagging fails, thereby allowing us to predict protein interactions that are not

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)

Nonlinear Physics of Plasmas

CERN Document Server

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

Nonlinear drift tearing mode

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

On the dynamics of Airy beams in nonlinear media with nonlinear losses.

Science.gov (United States)

Ruiz-Jiménez, Carlos; Nóbrega, K Z; Porras, Miguel A

2015-04-06

We investigate on the nonlinear dynamics of Airy beams in a regime where nonlinear losses due to multi-photon absorption are significant. We identify the nonlinear Airy beam (NAB) that preserves the amplitude of the inward Hänkel component as an attractor of the dynamics. This attractor governs also the dynamics of finite-power (apodized) Airy beams, irrespective of the location of the entrance plane in the medium with respect to the Airy waist plane. A soft (linear) input long before the waist, however, strongly speeds up NAB formation and its persistence as a quasi-stationary beam in comparison to an abrupt input at the Airy waist plane, and promotes the formation of a new type of highly dissipative, fully nonlinear Airy beam not described so far.

Nonlinear optimization

CERN Document Server

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...

NAPS: Network Analysis of Protein Structures

Science.gov (United States)

Chakrabarty, Broto; Parekh, Nita

2016-01-01

Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue–residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in Å) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein–protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/. PMID:27151201

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade.

Science.gov (United States)

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.

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade

Science.gov (United States)

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.

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. 

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.

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.

Global Analysis of Nonlinear Dynamics

CERN Document Server

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.  

Effective-medium theory for nonlinear magneto-optics in magnetic granular alloys: cubic nonlinearity

International Nuclear Information System (INIS)

Granovsky, Alexander B.; Kuzmichov, Michail V.; Clerc, J.-P.; Inoue, Mitsuteru

2003-01-01

We propose a simple effective-medium approach for calculating the effective dielectric function of a magnetic metal-insulator granular alloy in which there is a weakly nonlinear relation between electric displacement D and electric field E for both constituent materials of the form D i =ε i (0) E i +χ i (3) |E i | 2 E i . We assume that linear ε i (0) and cubic nonlinear χ i (3) dielectric functions are diagonal and linear with magnetization non-diagonal components. For such metal-insulator composite magneto-optical effects depend on a light intensity and the effective cubic dielectric function χ eff (3) can be significantly greater (up to 10 3 times) than that for constituent materials. The calculation scheme is based on the Bergman and Stroud-Hui theory of nonlinear optical properties of granular matter. The giant cubic magneto-optical nonlinearity is found for composites with metallic volume fraction close to the percolation threshold and at a resonance of optical conductivity. It is shown that a composite may exhibit nonlinear magneto-optics even when both constituent materials have no cubic magneto-optical nonlinearity

Ultrafast nonlinear optics

CERN Document Server

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...

Wave propagation in a strongly nonlinear locally resonant granular crystal

Science.gov (United States)

Vorotnikov, K.; Starosvetsky, Y.; Theocharis, G.; Kevrekidis, P. G.

2018-02-01

In this work, we study the wave propagation in a recently proposed acoustic structure, the locally resonant granular crystal. This structure is composed of a one-dimensional granular crystal of hollow spherical particles in contact, containing linear resonators. The relevant model is presented and examined through a combination of analytical approximations (based on ODE and nonlinear map analysis) and of numerical results. The generic dynamics of the system involves a degradation of the well-known traveling pulse of the standard Hertzian chain of elastic beads. Nevertheless, the present system is richer, in that as the primary pulse decays, secondary ones emerge and eventually interfere with it creating modulated wavetrains. Remarkably, upon suitable choices of parameters, this interference "distills" a weakly nonlocal solitary wave (a "nanopteron"). This motivates the consideration of such nonlinear structures through a separate Fourier space technique, whose results suggest the existence of such entities not only with a single-side tail, but also with periodic tails on both ends. These tails are found to oscillate with the intrinsic oscillation frequency of the out-of-phase motion between the outer hollow bead and its internal linear attachment.

Referencing cross-reactivity of detection antibodies for protein array experiments [version 1; referees: 1 approved, 2 approved with reservations

Directory of Open Access Journals (Sweden)

Darragh Lemass

2016-01-01

Full Text Available Protein arrays are frequently used to profile antibody repertoires in humans and animals. High-throughput protein array characterisation of complex antibody repertoires requires a platform-dependent, lot-to-lot validation of secondary detection antibodies. This article details the validation of an affinity-isolated anti-chicken IgY antibody produced in rabbit and a goat anti-rabbit IgG antibody conjugated with alkaline phosphatase using protein arrays consisting of 7,390 distinct human proteins. Probing protein arrays with secondary antibodies in absence of chicken serum revealed non-specific binding to 61 distinct human proteins. The cross-reactivity of the tested secondary detection antibodies points towards the necessity of platform-specific antibody characterisation studies for all secondary immunoreagents. Secondary antibody characterisation using protein arrays enables generation of reference lists of cross-reactive proteins, which can be then excluded from analysis in follow-up experiments. Furthermore, making such cross-reactivity lists accessible to the wider research community may help to interpret data generated by the same antibodies in applications not related to protein arrays such as immunoprecipitation, Western blots or other immunoassays.

A Proteomic Approach to Investigating Gene Cluster Expression and Secondary Metabolite Functionality in Aspergillus fumigatus

Science.gov (United States)

Owens, Rebecca A.; Hammel, Stephen; Sheridan, Kevin J.; Jones, Gary W.; Doyle, Sean

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. Indirect identification of secondary metabolite cluster expression was also achieved, with proteins (n = 18) from LaeA-regulated clusters detected, including GliT encoded within the gliotoxin biosynthetic cluster. Biochemical analysis then revealed that gliotoxin significantly attenuates H2O2-induced oxidative stress in A. fumigatus (p>0.0001), confirming observations from proteomics data. A complementary 2-D/LC-MS/MS approach further elucidated significantly increased abundance (pproteome and experimental strategies, plus mechanistic data pertaining to gliotoxin functionality in the organism. PMID:25198175

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.

Cloud prediction of protein structure and function with PredictProtein for Debian.

Science.gov (United States)

Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Staniewski, Cedric; Rost, Burkhard

2013-01-01

We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome.

Fitness Effects of Network Non-Linearity Induced by Gene Expression Noise

Science.gov (United States)

Ray, Christian; Cooper, Tim; Balazsi, Gabor

2012-02-01

In the non-equilibrium dynamics of growing microbial cells, metabolic enzymes can create non-linearities in metabolite concentration because of non-linear degradation (utilization): an enzyme can saturate in the process of metabolite utilization. Increasing metabolite production past the saturation point then results in an ultrasensitive metabolite response. If the production rate of a metabolite depends on a second enzyme or other protein-mediated process, uncorrelated gene expression noise can thus cause transient metabolite concentration bursts. Such bursts are physiologically unnecessary and may represent a source of selection against the ultrasensitive switch, especially if the fluctuating metabolic intermediate is toxic. Selection may therefore favor correlated gene expression fluctuations for enzymes in the same pathway, such as by same-operon membership in bacteria. Using a modified experimental lac operon system, we are undertaking a combined theoretical-experimental approach to demonstrate that (i) the lac operon has an implicit ultrasensitive switch that we predict is avoided by gene expression correlations induced by same-operon membership; (ii) bacterial growth rates are sensitive to crossing the ultrasensitive threshold. Our results suggest that correlations in intrinsic gene expression noise are exploited by evolution to ameliorate the detrimental effects of nonlinearities in metabolite concentrations.

Evans functions and bifurcations of nonlinear waves of some nonlinear reaction diffusion equations

Science.gov (United States)

Zhang, Linghai

2017-10-01

The main purposes of this paper are to accomplish the existence, stability, instability and bifurcation of the nonlinear waves of the nonlinear system of reaction diffusion equations ut =uxx + α [ βH (u - θ) - u ] - w, wt = ε (u - γw) and to establish the existence, stability, instability and bifurcation of the nonlinear waves of the nonlinear scalar reaction diffusion equation ut =uxx + α [ βH (u - θ) - u ], under different conditions on the model constants. To establish the bifurcation for the system, we will study the existence and instability of a standing pulse solution if 0 1; the existence and instability of two standing wave fronts if 2 (1 + αγ) θ = αβγ and 0 traveling wave front as well as the existence and instability of a standing pulse solution if 0 traveling wave front as well as the existence and instability of an upside down standing pulse solution if 0 traveling wave back of the nonlinear scalar reaction diffusion equation ut =uxx + α [ βH (u - θ) - u ] -w0, where w0 = α (β - 2 θ) > 0 is a positive constant, if 0 motivation to study the existence, stability, instability and bifurcations of the nonlinear waves is to study the existence and stability/instability of infinitely many fast/slow multiple traveling pulse solutions of the nonlinear system of reaction diffusion equations. The existence and stability of infinitely many fast multiple traveling pulse solutions are of great interests in mathematical neuroscience.

Nonlinear wave equations

CERN Document Server

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.

Interactive protein manipulation

International Nuclear Information System (INIS)

2003-01-01

We describe an interactive visualization and modeling program for the creation of protein structures ''from scratch''. The input to our program is an amino acid sequence -decoded from a gene- and a sequence of predicted secondary structure types for each amino acid-provided by external structure prediction programs. Our program can be used in the set-up phase of a protein structure prediction process; the structures created with it serve as input for a subsequent global internal energy minimization, or another method of protein structure prediction. Our program supports basic visualization methods for protein structures, interactive manipulation based on inverse kinematics, and visualization guides to aid a user in creating ''good'' initial structures

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

Effective-medium theory for nonlinear magneto-optics in magnetic granular alloys: cubic nonlinearity

Energy Technology Data Exchange (ETDEWEB)

Granovsky, Alexander B. E-mail: granov@magn.ru; Kuzmichov, Michail V.; Clerc, J.-P.; Inoue, Mitsuteru

2003-03-01

We propose a simple effective-medium approach for calculating the effective dielectric function of a magnetic metal-insulator granular alloy in which there is a weakly nonlinear relation between electric displacement D and electric field E for both constituent materials of the form D{sub i}={epsilon}{sub i}{sup (0)}E{sub i} +{chi}{sub i}{sup (3)}|E{sub i}|{sup 2}E{sub i}. We assume that linear {epsilon}{sub i}{sup (0)} and cubic nonlinear {chi}{sub i}{sup (3)} dielectric functions are diagonal and linear with magnetization non-diagonal components. For such metal-insulator composite magneto-optical effects depend on a light intensity and the effective cubic dielectric function {chi}{sub eff}{sup (3)} can be significantly greater (up to 10{sup 3} times) than that for constituent materials. The calculation scheme is based on the Bergman and Stroud-Hui theory of nonlinear optical properties of granular matter. The giant cubic magneto-optical nonlinearity is found for composites with metallic volume fraction close to the percolation threshold and at a resonance of optical conductivity. It is shown that a composite may exhibit nonlinear magneto-optics even when both constituent materials have no cubic magneto-optical nonlinearity.

Gradient-based optimization in nonlinear structural dynamics

DEFF Research Database (Denmark)

Dou, Suguang

The intrinsic nonlinearity of mechanical structures can give rise to rich nonlinear dynamics. Recently, nonlinear dynamics of micro-mechanical structures have contributed to developing new Micro-Electro-Mechanical Systems (MEMS), for example, atomic force microscope, passive frequency divider......, frequency stabilization, and disk resonator gyroscope. For advanced design of these structures, it is of considerable value to extend current optimization in linear structural dynamics into nonlinear structural dynamics. In this thesis, we present a framework for modelling, analysis, characterization......, and optimization of nonlinear structural dynamics. In the modelling, nonlinear finite elements are used. In the analysis, nonlinear frequency response and nonlinear normal modes are calculated based on a harmonic balance method with higher-order harmonics. In the characterization, nonlinear modal coupling...

Chaos and Structures in Nonlinear Plasmas

Science.gov (United States)

Chen, James

In recent decades, the concepts and applications of chaos, complexity, and nonlinear dynamics have profoundly influenced scientific as well as literary thinking. Some aspects of these concepts are used in almost all of the geophysical disciplines. Chaos and Structures in Nonlinear Plasmas, written by two respected plasma physicists, focuses on nonlinear phenomena in laboratory and space plasmas, which are rich in nonlinear and complex collective effects. Chaos is treated only insofar as it relates to some aspects of nonlinear plasma physics.At the outset, the authors note that plasma physics research has made fundamental contributions to modern nonlinear sciences. For example, the Poincare surface of section technique was extensively used in studies of stochastic field lines in magnetically confined plasmas and turbulence. More generally, nonlinearity in plasma waves and wave-wave and wave-particle interactions critically determines the propagation of energy through a plasma medium. The book also makes it clear that the importance of understanding nonlinear waves goes beyond plasma physics, extending to such diverse fields as solid state physics, fluid dynamics, atmospheric physics, and optics. In space physics, non-linear plasma physics is essential for interpreting in situ as well as remote-sensing data.

Modeling nonlinearities in MEMS oscillators.

Science.gov (United States)

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.

Nonlinear Elliptic Boundary Value Problems at Resonance with Nonlinear Wentzell Boundary Conditions

Directory of Open Access Journals (Sweden)

Ciprian G. Gal

2017-01-01

Full Text Available Given a bounded domain Ω⊂RN with a Lipschitz boundary ∂Ω and p,q∈(1,+∞, we consider the quasilinear elliptic equation -Δpu+α1u=f in Ω complemented with the generalized Wentzell-Robin type boundary conditions of the form bx∇up-2∂nu-ρbxΔq,Γu+α2u=g on ∂Ω. In the first part of the article, we give necessary and sufficient conditions in terms of the given functions f, g and the nonlinearities α1, α2, for the solvability of the above nonlinear elliptic boundary value problems with the nonlinear boundary conditions. In other words, we establish a sort of “nonlinear Fredholm alternative” for our problem which extends the corresponding Landesman and Lazer result for elliptic problems with linear homogeneous boundary conditions. In the second part, we give some additional results on existence and uniqueness and we study the regularity of the weak solutions for these classes of nonlinear problems. More precisely, we show some global a priori estimates for these weak solutions in an L∞-setting.

Theory and design of nonlinear metamaterials

Science.gov (United States)

Rose, Alec Daniel

If electronics are ever to be completely replaced by optics, a significant possibility in the wake of the fiber revolution, it is likely that nonlinear materials will play a central and enabling role. Indeed, nonlinear optics is the study of the mechanisms through which light can change the nature and properties of matter and, as a corollary, how one beam or color of light can manipulate another or even itself within such a material. However, of the many barriers preventing such a lofty goal, the narrow and limited range of properties supported by nonlinear materials, and natural materials in general, stands at the forefront. Many industries have turned instead to artificial and composite materials, with homogenizable metamaterials representing a recent extension of such composites into the electromagnetic domain. In particular, the inclusion of nonlinear elements has caused metamaterials research to spill over into the field of nonlinear optics. Through careful design of their constituent elements, nonlinear metamaterials are capable of supporting an unprecedented range of interactions, promising nonlinear devices of novel design and scale. In this context, I cast the basic properties of nonlinear metamaterials in the conventional formalism of nonlinear optics. Using alternately transfer matrices and coupled mode theory, I develop two complementary methods for characterizing and designing metamaterials with arbitrary nonlinear properties. Subsequently, I apply these methods in numerical studies of several canonical metamaterials, demonstrating enhanced electric and magnetic nonlinearities, as well as predicting the existence of nonlinear magnetoelectric and off-diagonal nonlinear tensors. I then introduce simultaneous design of the linear and nonlinear properties in the context of phase matching, outlining five different metamaterial phase matching methods, with special emphasis on the phase matching of counter propagating waves in mirrorless parametric amplifiers

Single-shot measurement of nonlinear absorption and nonlinear refraction.

Science.gov (United States)

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.

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

Generalized Nonlinear Yule Models

OpenAIRE

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...

Measurement and fitting techniques for the assessment of material nonlinearity using nonlinear Rayleigh waves

Energy Technology Data Exchange (ETDEWEB)

Torello, David [GW Woodruff School of Mechanical Engineering, Georgia Tech (United States); Kim, Jin-Yeon [School of Civil and Environmental Engineering, Georgia Tech (United States); Qu, Jianmin [Department of Civil and Environmental Engineering, Northwestern University (United States); Jacobs, Laurence J. [School of Civil and Environmental Engineering, Georgia Tech and GW Woodruff School of Mechanical Engineering, Georgia Tech (United States)

2015-03-31

This research considers the effects of diffraction, attenuation, and the nonlinearity of generating sources on measurements of nonlinear ultrasonic Rayleigh wave propagation. A new theoretical framework for correcting measurements made with air-coupled and contact piezoelectric receivers for the aforementioned effects is provided based on analytical models and experimental considerations. A method for extracting the nonlinearity parameter β{sub 11} is proposed based on a nonlinear least squares curve-fitting algorithm that is tailored for Rayleigh wave measurements. Quantitative experiments are conducted to confirm the predictions for the nonlinearity of the piezoelectric source and to demonstrate the effectiveness of the curve-fitting procedure. These experiments are conducted on aluminum 2024 and 7075 specimens and a β{sub 11}{sup 7075}/β{sub 11}{sup 2024} measure of 1.363 agrees well with previous literature and earlier work.

H∞ Balancing for Nonlinear Systems

NARCIS (Netherlands)

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

Dynamic one-dimensional modeling of secondary settling tanks and system robustness evaluation.

Science.gov (United States)

Li, Ben; Stenstrom, M K

2014-01-01

One-dimensional secondary settling tank models are widely used in current engineering practice for design and optimization, and usually can be expressed as a nonlinear hyperbolic or nonlinear strongly degenerate parabolic partial differential equation (PDE). Reliable numerical methods are needed to produce approximate solutions that converge to the exact analytical solutions. In this study, we introduced a reliable numerical technique, the Yee-Roe-Davis (YRD) method as the governing PDE solver, and compared its reliability with the prevalent Stenstrom-Vitasovic-Takács (SVT) method by assessing their simulation results at various operating conditions. The YRD method also produced a similar solution to the previously developed Method G and Enquist-Osher method. The YRD and SVT methods were also used for a time-to-failure evaluation, and the results show that the choice of numerical method can greatly impact the solution. Reliable numerical methods, such as the YRD method, are strongly recommended.

Multiscale character of the nonlinear coherent dynamics in the Rayleigh-Taylor instability

International Nuclear Information System (INIS)

Abarzhi, S.I.; Nishihara, K.; Rosner, R.

2006-01-01

We report nonlinear solutions for a system of conservation laws describing the dynamics of the large-scale coherent structure of bubbles and spikes in the Rayleigh-Taylor instability (RTI) for fluids with a finite density ratio. Three-dimensional flows are considered with general type of symmetry in the plane normal to the direction of gravity. The nonlocal properties of the interface evolution are accounted for on the basis of group theory. It is shown that isotropic coherent structures are stable. For anisotropic structures, secondary instabilities develop with the growth rate determined by the density ratio. For stable structures, the curvature and velocity of the nonlinear bubble have nontrivial dependencies on the density ratio, yet their mutual dependence on one another has an invariant form independent of the density ratio. The process of bubble merge is not considered. Based on the obtained results we argue that the large-scale coherent dynamics in RTI has a multiscale character and is governed by two length scales: the period of the coherent structure and the bubble (spike) position

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.

A proteomic approach to investigating gene cluster expression and secondary metabolite functionality in Aspergillus fumigatus.

OpenAIRE

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...

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.

Introduction to nonlinear acoustics

Science.gov (United States)

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.

Assessment of fibrotic liver disease with multimodal nonlinear optical microscopy

Science.gov (United States)

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.

Non-linear optical materials

CERN Document Server

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 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...

Single-ion nonlinear mechanical oscillator

International Nuclear Information System (INIS)

Akerman, N.; Kotler, S.; Glickman, Y.; Dallal, Y.; Keselman, A.; Ozeri, R.

2010-01-01

We study the steady-state motion of a single trapped ion oscillator driven to the nonlinear regime. Damping is achieved via Doppler laser cooling. The ion motion is found to be well described by the Duffing oscillator model with an additional nonlinear damping term. We demonstrate here the unique ability of tuning both the linear as well as the nonlinear damping coefficients by controlling the laser-cooling parameters. Our observations pave the way for the investigation of nonlinear dynamics on the quantum-to-classical interface as well as mechanical noise squeezing in laser-cooling dynamics.

Nonlinear wave equation in frequency domain: accurate modeling of ultrafast interaction in anisotropic nonlinear media

DEFF Research Database (Denmark)

Guo, Hairun; Zeng, Xianglong; Zhou, Binbin

2013-01-01

We interpret the purely spectral forward Maxwell equation with up to third-order induced polarizations for pulse propagation and interactions in quadratic nonlinear crystals. The interpreted equation, also named the nonlinear wave equation in the frequency domain, includes quadratic and cubic...... nonlinearities, delayed Raman effects, and anisotropic nonlinearities. The full potential of this wave equation is demonstrated by investigating simulations of solitons generated in the process of ultrafast cascaded second-harmonic generation. We show that a balance in the soliton delay can be achieved due...

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.

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

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....

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...

Nonlinear saturation controller for vibration supersession of a nonlinear composite beam

Energy Technology Data Exchange (ETDEWEB)

Hamed, Y. S. [Menofia University, Menouf (Egypt); Amer, Y. A. [Zagazig University, Zagazig (Egypt)

2014-08-15

In this paper, a study for nonlinear saturation controller (NSC) is presented that used to suppress the vibration amplitude of a structural dynamic model simulating nonlinear composite beam at simultaneous sub-harmonic and internal resonance excitation. The absorber exploits the saturation phenomenon that is known to occur in dynamical systems with quadratic non-linearities of the feedback gain and a two-to-one internal resonance. The analytical solution for the system and the nonlinear saturation controller are obtained using method of multiple time scales perturbation up to the second order approximation. All possible resonance cases were extracted at this approximation order and studied numerically. The stability of the system at the worst resonance case (Ω = 2ω{sub s} and ω{sub s} =2ω{sub C}) is investigated using both frequency response equations and phase-plane trajectories. The effects of different parameters on the system and the controller are studied numerically. The effect of some types of controller on the system is investigated numerically. The simulation results are achieved using Matlab and Maple programs.

Solitons in proteins at non-zero temperatures with allowance for the fluctuations of polarization

International Nuclear Information System (INIS)

Simo, E.; Caputo, J.G.

2007-06-01

A model for the nonlinear transfer of vibrational energy in molecular chains is derived at temperatures of realistic interest for transport in proteins. The study includes the influence of the fluctuations of polarization in the chain. This theory exhibits a new form of temperature-dependence in intrinsic parameters of alpha-helix, and consequently in the coefficients of the nonlinear Schroedinger equation governing the system and in the solitons' parameters. Thermal fluctuations are analysed in the basis of the non-Gaussian approximation and the total free-energy of the alpha-helix is determined to elucidate the denaturation process of the protein. (author)

Adaptive regression for modeling nonlinear relationships

CERN Document Server

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...

A generalized auxiliary equation method and its application to nonlinear Klein-Gordon and generalized nonlinear Camassa-Holm equations

International Nuclear Information System (INIS)

Yomba, Emmanuel

2008-01-01

With the aid of symbolic computation, a generalized auxiliary equation method is proposed to construct more general exact solutions to two types of NLPDEs. First, we present new family of solutions to a nonlinear Klein-Gordon equation, by using this auxiliary equation method including a new first-order nonlinear ODE with six-degree nonlinear term proposed by Sirendaoreji. Then, we apply an indirect F-function method very close to the F-expansion method to solve the generalized Camassa-Holm equation with fully nonlinear dispersion and fully nonlinear convection C(l,n,p). Taking advantage of the new first-order nonlinear ODE with six degree nonlinear term, this indirect F-function method is used to map the solutions of C(l,n,p) equations to those of that nonlinear ODE. As a result, we can successfully obtain in a unified way, many exact solutions

Nonlinear fiber optics formerly quantum electronics

CERN Document Server

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

Interactive protein manipulation

Energy Technology Data Exchange (ETDEWEB)

SNCrivelli@lbl.gov

2003-07-01

We describe an interactive visualization and modeling program for the creation of protein structures ''from scratch''. The input to our program is an amino acid sequence -decoded from a gene- and a sequence of predicted secondary structure types for each amino acid-provided by external structure prediction programs. Our program can be used in the set-up phase of a protein structure prediction process; the structures created with it serve as input for a subsequent global internal energy minimization, or another method of protein structure prediction. Our program supports basic visualization methods for protein structures, interactive manipulation based on inverse kinematics, and visualization guides to aid a user in creating ''good'' initial structures.

Use of secondary structural information and Cα-Cα distance ...

Indian Academy of Sciences (India)

PRAKASH KUMAR

2007-06-21

Jun 21, 2007 ... Model evolution; protein modelling; residue contact prediction; secondary structure prediction. Abbreviations used: ... set of sequence data (NR) and calculated conservation index of each ... evaluators (Moult et al 2003) to evaluate these model ... (Siew et al 2000), is a measure aims at identifying the largest.

Impact of secondary metabolites and related enzymes in flax ...

African Journals Online (AJOL)

Changes in various physiological defenses including secondary metabolites, proline, total soluble protein and antioxidant enzymes were investigated in leaves and stems of 18 flax lines either resistant or susceptible to powdery mildew. The results showed that the total alkaloids content in flax stems was significantly ...

Multiphoton microscopy of ECM proteins in baboon aortic leaflet

Science.gov (United States)

Gonzalez, Mariacarla; Saytashev, Ilyas; Luna, Camila; Gonzalez, Brittany; Pinero, Alejandro; Perez, Manuel; Ramaswamy, Sharan; Ramella-Roman, Jessica

2018-02-01

The extracellular matrix (ECM) plays crucial role in defining mechanical properties of a heart valve yet the mechanobiological role of the ECM proteins - collagen and elastin - in living heart valve leaflets is still poorly understood. In this study, non-linear microscopy was used to obtain three dimensional images of collagen and elastin arrangement in aortic leaflets under combined steady flow (850 ml/min) and cyclic flexure (1 Hz) mechanical (dynamic) training. A novel bioreactor capable of mimicking the flow conditions in a living heart was used in this study and was optimized for microscopic imagery. A custom made non-linear microscope was used in this study to provide Second Harmonic Generation (SHG) imaging of collagen arrangement and two-photon imaging of elastin. Two control and three trained leaflet samples from static and dynamic tissue culture were imaged to observe protein changes in the tissue for a period of seven days. Dynamic training led to a decrease in alignment index of the protein fibers compared to the static treatment.

A Secondary Antibody-Detecting Molecular Weight Marker with Mouse and Rabbit IgG Fc Linear Epitopes for Western Blot Analysis.

Science.gov (United States)

Lin, Wen-Wei; Chen, I-Ju; Cheng, Ta-Chun; Tung, Yi-Ching; Chu, Pei-Yu; Chuang, Chih-Hung; Hsieh, Yuan-Chin; Huang, Chien-Chiao; Wang, Yeng-Tseng; Kao, Chien-Han; Roffler, Steve R; Cheng, Tian-Lu

2016-01-01

Molecular weight markers that can tolerate denaturing conditions and be auto-detected by secondary antibodies offer great efficacy and convenience for Western Blotting. Here, we describe M&R LE protein markers which contain linear epitopes derived from the heavy chain constant regions of mouse and rabbit immunoglobulin G (IgG Fc LE). These markers can be directly recognized and stained by a wide range of anti-mouse and anti-rabbit secondary antibodies. We selected three mouse (M1, M2 and M3) linear IgG1 and three rabbit (R1, R2 and R3) linear IgG heavy chain epitope candidates based on their respective crystal structures. Western blot analysis indicated that M2 and R2 linear epitopes are effectively recognized by anti-mouse and anti-rabbit secondary antibodies, respectively. We fused the M2 and R2 epitopes (M&R LE) and incorporated the polypeptide in a range of 15-120 kDa auto-detecting markers (M&R LE protein marker). The M&R LE protein marker can be auto-detected by anti-mouse and anti-rabbit IgG secondary antibodies in standard immunoblots. Linear regression analysis of the M&R LE protein marker plotted as gel mobility versus the log of the marker molecular weights revealed good linearity with a correlation coefficient R2 value of 0.9965, indicating that the M&R LE protein marker displays high accuracy for determining protein molecular weights. This accurate, regular and auto-detected M&R LE protein marker may provide a simple, efficient and economical tool for protein analysis.

Global Analysis of RNA Secondary Structure in Two Metazoans

Directory of Open Access Journals (Sweden)

Fan Li

2012-01-01

Full Text Available The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA] and unpaired (single-stranded RNA [ssRNA] components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals.

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.

The new protein topology graph library web server.

Science.gov (United States)

Schäfer, Tim; Scheck, Andreas; Bruneß, Daniel; May, Patrick; Koch, Ina

2016-02-01

We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology. The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net. tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Nonlinearities in modified gravity cosmology: Signatures of modified gravity in the nonlinear matter power spectrum

International Nuclear Information System (INIS)

Cui Weiguang; Zhang Pengjie; Yang Xiaohu

2010-01-01

A large fraction of cosmological information on dark energy and gravity is encoded in the nonlinear regime. Precision cosmology thus requires precision modeling of nonlinearities in general dark energy and modified gravity models. We modify the Gadget-2 code and run a series of N-body simulations on modified gravity cosmology to study the nonlinearities. The modified gravity model that we investigate in the present paper is characterized by a single parameter ζ, which determines the enhancement of particle acceleration with respect to general relativity (GR), given the identical mass distribution (ζ=1 in GR). The first nonlinear statistics we investigate is the nonlinear matter power spectrum at k < or approx. 3h/Mpc, which is the relevant range for robust weak lensing power spectrum modeling at l < or approx. 2000. In this study, we focus on the relative difference in the nonlinear power spectra at corresponding redshifts where different gravity models have the same linear power spectra. This particular statistics highlights the imprint of modified gravity in the nonlinear regime and the importance of including the nonlinear regime in testing GR. By design, it is less susceptible to the sample variance and numerical artifacts. We adopt a mass assignment method based on wavelet to improve the power spectrum measurement. We run a series of tests to determine the suitable simulation specifications (particle number, box size, and initial redshift). We find that, the nonlinear power spectra can differ by ∼30% for 10% deviation from GR (|ζ-1|=0.1) where the rms density fluctuations reach 10. This large difference, on one hand, shows the richness of information on gravity in the corresponding scales, and on the other hand, invalidates simple extrapolations of some existing fitting formulae to modified gravity cosmology.

A Multi-technique Characterization of Adsorbed Protein Films: Orientation and Structure by ToF-SIMS, NEXAFS, SFG, and XPS

Science.gov (United States)

Baio, Joseph E.

There are many techniques that allow surface scientists to study interfaces. However, few are routinely applied to probe biological surfaces. The work presented here demonstrates how detailed information about the conformation, orientation, chemical state, and molecular structure of biological molecules immobilized onto a surface can be assessed by electron spectroscopy, mass spectrometry, and nonlinear vibrational spectroscopy techniques. This investigation began with the development of simple model systems (small proteins, and peptides) and evolved into a study of more complex --- real world systems. Initially, two model systems based on the chemical and electrostatic immobilization of a small rigid protein (Protein G B1 domain, 6kDa) were built to develop the capabilities of time-of-flight secondary ion mass spectrometry (ToFSIMS), near edge X-ray absorption fine structure spectroscopy (NEXAFS) and sum frequency generation (SFG) spectroscopy as tools to probe the structure of surface immobilized proteins. X-ray photoelectron spectroscopy (XPS) was used to measure the amount of immobilized protein and ToF-SIMS sampled the amino acid composition of the exposed surface of the protein film. Within the ToF-SIMS spectra, an enrichment of secondary ions from amino acids located at opposite ends of the proteins were used to describe protein orientation. SFG spectral peaks characteristic of ordered alpha-helix and beta-sheet elements were observed for both systems and the phase of the peaks indicated a predominantly upright orientation for both the covalent and electrostatic configurations. Polarization dependence of the NEXAFS signal from the N 1s to pi* transition of the peptide bonds that make up the beta-sheets also indicated protein ordering at the surface. Building upon the Protein G B1 studies, the orientation and structure of a surface immobilized antibody (HuLys Fv: variant of humanized anti-lysozyme variable fragment, 26kDa) was characterized across two

International Conference on Applications in Nonlinear Dynamics

CERN Document Server

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.

STABILITY, BIFURCATIONS AND CHAOS IN UNEMPLOYMENT NON-LINEAR DYNAMICS

Directory of Open Access Journals (Sweden)

Pagliari Carmen

2013-07-01

Full Text Available The traditional analysis of unemployment in relation to real output dynamics is based on some empirical evidences deducted from Okun’s studies. In particular the so called Okun’s Law is expressed in a linear mathematical formulation, which cannot explain the fluctuation of the variables involved. Linearity is an heavy limit for macroeconomic analysis and especially for every economic growth study which would consider the unemployment rate among the endogenous variables. This paper deals with an introductive study about the role of non-linearity in the investigation of unemployment dynamics. The main idea is the existence of a non-linear relation between the unemployment rate and the gap of GDP growth rate from its trend. The macroeconomic motivation of this idea moves from the consideration of two concatenate effects caused by a variation of the unemployment rate on the real output growth rate. These two effects are concatenate because there is a first effect that generates a secondary one on the same variable. When the unemployment rate changes, the first effect is the variation in the level of production in consequence of the variation in the level of such an important factor as labour force; the secondary effect is a consecutive variation in the level of production caused by the variation in the aggregate demand in consequence of the change of the individual disposal income originated by the previous variation of production itself. In this paper the analysis of unemployment dynamics is carried out by the use of the logistic map and the conditions for the existence of bifurcations (cycles are determined. The study also allows to find the range of variability of some characteristic parameters that might be avoided for not having an absolute unpredictability of unemployment dynamics (deterministic chaos: unpredictability is equivalent to uncontrollability because of the total absence of information about the future value of the variable to

Unidirectional transmission in 1D nonlinear photonic crystal based on topological phase reversal by optical nonlinearity

OpenAIRE

Chong Li; Xiaoyong Hu; Hong Yang; Qihuang Gong

2017-01-01

We propose a scheme of unidirectional transmission in a 1D nonlinear topological photonic crystal based on the topological edge state and three order optical nonlinearity. The 1D photonic crystals consists of a nonlinear photonic crystal L and a linear photonic crystal R. In the backward direction, light is totally reflected for the photons transmission prohibited by the bandgap. While in the forward direction, light interacts with the nonlinear photonic crystal L by optical Kerr effect, brin...

Nonlinear silicon photonics

Science.gov (United States)

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.

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.

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

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 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)

Key Roles for MYC, KIT and RET signaling in secondary angiosarcomas

DEFF Research Database (Denmark)

Styring, E; Seinen, J; Dominguez-Valentin, M

2014-01-01

of the gene signature to an external data set. RESULTS: In total, 103 genes were significantly deregulated between primary and secondary angiosarcomas. Secondary angiosarcomas showed upregulation of MYC, KIT and RET and downregulation of CDKN2C. Functional annotation analysis identified multiple target genes...... in the receptor protein tyrosine kinase pathway. The results were validated using RT-qPCR and immunohistochemistry. Further, the gene signature was applied to an external data set and, herein, distinguished primary from secondary angiosarcomas. CONCLUSIONS: Upregulation of MYC, KIT and RET and downregulation......BACKGROUND: Angiosarcomas may develop as primary tumours of unknown cause or as secondary tumours, most commonly following radiotherapy to the involved field. The different causative agents may be linked to alternate tumorigenesis, which led us to investigate the genetic profiles of morphologically...

Essential multimeric enzymes in kinetoplastid parasites: A host of potentially druggable protein-protein interactions.

Science.gov (United States)

Wachsmuth, Leah M; Johnson, Meredith G; Gavenonis, Jason

2017-06-01

Parasitic diseases caused by kinetoplastid parasites of the genera Trypanosoma and Leishmania are an urgent public health crisis in the developing world. These closely related species possess a number of multimeric enzymes in highly conserved pathways involved in vital functions, such as redox homeostasis and nucleotide synthesis. Computational alanine scanning of these protein-protein interfaces has revealed a host of potentially ligandable sites on several established and emerging anti-parasitic drug targets. Analysis of interfaces with multiple clustered hotspots has suggested several potentially inhibitable protein-protein interactions that may have been overlooked by previous large-scale analyses focusing solely on secondary structure. These protein-protein interactions provide a promising lead for the development of new peptide and macrocycle inhibitors of these enzymes.

Blow-Up Analysis for a Quasilinear Degenerate Parabolic Equation with Strongly Nonlinear Source

Directory of Open Access Journals (Sweden)

Pan Zheng

2012-01-01

Full Text Available We investigate the blow-up properties of the positive solution of the Cauchy problem for a quasilinear degenerate parabolic equation with strongly nonlinear source ut=div(|∇um|p−2∇ul+uq,  (x,t∈RN×(0,T, where N≥1, p>2 , and m, l,  q>1, and give a secondary critical exponent on the decay asymptotic behavior of an initial value at infinity for the existence and nonexistence of global solutions of the Cauchy problem. Moreover, under some suitable conditions we prove single-point blow-up for a large class of radial decreasing solutions.

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 generalization of the Kallen-Welton formula

International Nuclear Information System (INIS)

Kargin, A.Yu.

1982-01-01

Nonlinear dissipative-fluctuation relations permitting to find spectral correlation functions of (n+1) order for fluctuations of different electrodynamic values in plasma using the given value of tensor of nonlinear response of n order have been obtained for equilibrium plasma. At n=1 the relations obtained transform to the Kallen-Welton dissipative-fluctuation relation. Transformation of the nonlinear dissipative-fluctuation relation for cubical nonlinearity permitting to find nonlinear electric plasma susceptibility from the Known spectral correlation function of fourth order for charge density fluctUations in the absence of particle interaction is considered as an example. A compact expression for tensor of nonlinear plasma response has been obtained for an arbitrary order of nonlinearity

A multivariate nonlinear mixed effects method for analyzing energy partitioning in growing pigs

DEFF Research Database (Denmark)

Strathe, Anders Bjerring; Danfær, Allan Christian; Chwalibog, André

2010-01-01

to the multivariate nonlinear regression model because the MNLME method accounted for correlated errors associated with PD and LD measurements and could also include the random effect of animal. It is recommended that multivariate models used to quantify energy metabolism in growing pigs should account for animal......Simultaneous equations have become increasingly popular for describing the effects of nutrition on the utilization of ME for protein (PD) and lipid deposition (LD) in animals. The study developed a multivariate nonlinear mixed effects (MNLME) framework and compared it with an alternative method...... for estimating parameters in simultaneous equations that described energy metabolism in growing pigs, and then proposed new PD and LD equations. The general statistical framework was implemented in the NLMIXED procedure in SAS. Alternative PD and LD equations were also developed, which assumed...

Exact solutions for the higher-order nonlinear Schoerdinger equation in nonlinear optical fibres

International Nuclear Information System (INIS)

Liu Chunping

2005-01-01

First, by using the generally projective Riccati equation method, many kinds of exact solutions for the higher-order nonlinear Schoerdinger equation in nonlinear optical fibres are obtained in a unified way. Then, some relations among these solutions are revealed

Nonlinear Mechanics of MEMS Rectangular Microplates under Electrostatic Actuation

KAUST Repository

Saghir, Shahid

2016-12-01

The first objective of the dissertation is to develop a suitable reduced order model capable of investigating the nonlinear mechanical behavior of von-Karman plates under electrostatic actuation. The second objective is to investigate the nonlinear static and dynamic behavior of rectangular microplates under small and large actuating forces. In the first part, we present and compare various approaches to develop reduced order models for the nonlinear von-Karman rectangular microplates actuated by nonlinear electrostatic forces. The reduced-order models aim to investigate the static and dynamic behavior of the plate under small and large actuation forces. A fully clamped microplate is considered. Different types of basis functions are used in conjunction with the Galerkin method to discretize the governing equations. First we investigate the convergence with the number of modes retained in the model. Then for validation purpose, a comparison of the static results is made with the results calculated by a nonlinear finite element model. The linear eigenvalue problem for the plate under the electrostatic force is solved for a wide range of voltages up to pull-in. In the second part, we present an investigation of the static and dynamic behavior of a fully clamped microplate. We investigate the effect of different non-dimensional design parameters on the static response. The forced-vibration response of the plate is then investigated when the plate is excited by a harmonic AC load superimposed to a DC load. The dynamic behavior is examined near the primary and secondary (superharmonic and subharmonic) resonances. The microplate shows a strong hardening behavior due to the cubic nonlinearity of midplane stretching. However, the behavior switches to softening as the DC load is increased. Next, near-square plates are studied to understand the effect of geometric imperfections of microplates. In the final part of the dissertation, we investigate the mechanical behavior of

Degenerate nonlinear diffusion equations

CERN Document Server

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

CERN Document Server

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...

Nonlinear Ion Harmonics in the Paul Trap with Added Octopole Field: Theoretical Characterization and New Insight into Nonlinear Resonance Effect.

Science.gov (United States)

Xiong, Caiqiao; Zhou, Xiaoyu; Zhang, Ning; Zhan, Lingpeng; Chen, Yongtai; Nie, Zongxiu

2016-02-01

The nonlinear harmonics within the ion motion are the fingerprint of the nonlinear fields. They are exclusively introduced by these nonlinear fields and are responsible to some specific nonlinear effects such as nonlinear resonance effect. In this article, the ion motion in the quadrupole field with a weak superimposed octopole component, described by the nonlinear Mathieu equation (NME), was studied by using the analytical harmonic balance (HB) method. Good accuracy of the HB method, which was comparable with that of the numerical fourth-order Runge-Kutta (4th RK), was achieved in the entire first stability region, except for the points at the stability boundary (i.e., β = 1) and at the nonlinear resonance condition (i.e., β = 0.5). Using the HB method, the nonlinear 3β harmonic series introduced by the octopole component and the resultant nonlinear resonance effect were characterized. At nonlinear resonance, obvious resonant peaks were observed in the nonlinear 3β series of ion motion, but were not found in the natural harmonics. In addition, both resonant excitation and absorption peaks could be observed, simultaneously. These are two unique features of the nonlinear resonance, distinguishing it from the normal resonance. Finally, an approximation equation was given to describe the corresponding working parameter, q nr , at nonlinear resonance. This equation can help avoid the sensitivity degradation due to the operation of ion traps at the nonlinear resonance condition.

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.

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.

Naturally stable Sagnac-Michelson nonlinear interferometer.

Science.gov (United States)

Lukens, Joseph M; Peters, Nicholas A; Pooser, Raphael C

2016-12-01

Interferometers measure a wide variety of dynamic processes by converting a phase change into an intensity change. Nonlinear interferometers, making use of nonlinear media in lieu of beamsplitters, promise substantial improvement in the quest to reach the ultimate sensitivity limits. Here we demonstrate a new nonlinear interferometer utilizing a single parametric amplifier for mode mixing-conceptually, a nonlinear version of the conventional Michelson interferometer with its arms collapsed together. We observe up to 99.9% interference visibility and find evidence for noise reduction based on phase-sensitive gain. Our configuration utilizes fewer components than previous demonstrations and requires no active stabilization, offering new capabilities for practical nonlinear interferometric-based sensors.

Dynamic model evaluation for secondary inorganic aerosol and its precursors over Europe between 1990 and 2009

OpenAIRE

Banzhaf, S.; Schaap, M.; Kraneburg, R.; Manders, A.M.M.; Segers, A.J.; Visschedijk, A.H.J.; Denier van der on, H.A.C.; Kuenen, J.P.P.; van Meijgaard, E.; van Ulft, L.H.; Cofala, J.; Builtjes, P.J.H.

2015-01-01

In this study we present a dynamic model evaluation of the chemistry transport model LOTOS-EUROS to analyse the ability of the model to reproduce observed non-linear responses to emission changes and interannual variability of secondary inorganic aerosol (SIA) and its precursors over Europe from 1990 to 2009. The 20 year simulation was performed using a consistent set of meteorological data provided by the regional climate model RACMO2. Observations at Europ...

Useful tools for non-linear systems: Several non-linear integral inequalities

Czech Academy of Sciences Publication Activity Database

Agahi, H.; Mohammadpour, A.; Mesiar, Radko; Vaezpour, M. S.

2013-01-01

Roč. 49, č. 1 (2013), s. 73-80 ISSN 0950-7051 R&D Projects: GA ČR GAP402/11/0378 Institutional support: RVO:67985556 Keywords : Monotone measure * Comonotone functions * Integral inequalities * Universal integral Subject RIV: BA - General Mathematics Impact factor: 3.058, year: 2013 http://library.utia.cas.cz/separaty/2013/E/mesiar-useful tools for non-linear systems several non-linear integral inequalities.pdf

Spike-layer solutions to nonlinear fractional Schrodinger equations with almost optimal nonlinearities

Directory of Open Access Journals (Sweden)

Jinmyoung Seok

2015-07-01

Full Text Available In this article, we are interested in singularly perturbed nonlinear elliptic problems involving a fractional Laplacian. Under a class of nonlinearity which is believed to be almost optimal, we construct a positive solution which exhibits multiple spikes near any given local minimum components of an exterior potential of the problem.

Characterization of primary and secondary metabolites of leaf and ...

African Journals Online (AJOL)

This study evaluates the primary and secondary metabolite profiles of Eurycoma longifolia Jack (EL) stems and leaves to determine whether it can be utilized for therapeutic purposes as the roots. A total of six types of extracts were tested. The extracts showed high content of glycosaponins, polysaccharides, proteins and ...

Self-induced parametric amplification arising from nonlinear elastic coupling in a micromechanical resonating disk gyroscope.

Science.gov (United States)

Nitzan, Sarah H; Zega, Valentina; Li, Mo; Ahn, Chae H; Corigliano, Alberto; Kenny, Thomas W; Horsley, David A

2015-03-12

Parametric amplification, resulting from intentionally varying a parameter in a resonator at twice its resonant frequency, has been successfully employed to increase the sensitivity of many micro- and nano-scale sensors. Here, we introduce the concept of self-induced parametric amplification, which arises naturally from nonlinear elastic coupling between the degenerate vibration modes in a micromechanical disk-resonator, and is not externally applied. The device functions as a gyroscope wherein angular rotation is detected from Coriolis coupling of elastic vibration energy from a driven vibration mode into a second degenerate sensing mode. While nonlinear elasticity in silicon resonators is extremely weak, in this high quality-factor device, ppm-level nonlinear elastic effects result in an order-of-magnitude increase in the observed sensitivity to Coriolis force relative to linear theory. Perfect degeneracy of the primary and secondary vibration modes is achieved through electrostatic frequency tuning, which also enables the phase and frequency of the parametric coupling to be varied, and we show that the resulting phase and frequency dependence of the amplification follow the theory of parametric resonance. We expect that this phenomenon will be useful for both fundamental studies of dynamic systems with low dissipation and for increasing signal-to-noise ratio in practical applications such as gyroscopes.

Nonlinear Wave Propagation

Science.gov (United States)

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 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

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.

Intermediates and the folding of proteins L and G

Energy Technology Data Exchange (ETDEWEB)

Brown, Scott; Head-Gordon, Teresa

2003-07-01

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

An iterative kernel based method for fourth order nonlinear equation with nonlinear boundary condition

Science.gov (United States)

Azarnavid, Babak; Parand, Kourosh; Abbasbandy, Saeid

2018-06-01

This article discusses an iterative reproducing kernel method with respect to its effectiveness and capability of solving a fourth-order boundary value problem with nonlinear boundary conditions modeling beams on elastic foundations. Since there is no method of obtaining reproducing kernel which satisfies nonlinear boundary conditions, the standard reproducing kernel methods cannot be used directly to solve boundary value problems with nonlinear boundary conditions as there is no knowledge about the existence and uniqueness of the solution. The aim of this paper is, therefore, to construct an iterative method by the use of a combination of reproducing kernel Hilbert space method and a shooting-like technique to solve the mentioned problems. Error estimation for reproducing kernel Hilbert space methods for nonlinear boundary value problems have yet to be discussed in the literature. In this paper, we present error estimation for the reproducing kernel method to solve nonlinear boundary value problems probably for the first time. Some numerical results are given out to demonstrate the applicability of the method.

LDV measurement of small nonlinearities in flat and curved membranes. A model for eardrum nonlinear acoustic behaviour

Science.gov (United States)

Kilian, Gladiné; Pieter, Muyshondt; Joris, Dirckx

2016-06-01

Laser Doppler Vibrometry is an intrinsic highly linear measurement technique which makes it a great tool to measure extremely small nonlinearities in the vibration response of a system. Although the measurement technique is highly linear, other components in the experimental setup may introduce nonlinearities. An important source of artificially introduced nonlinearities is the speaker, which generates the stimulus. In this work, two correction methods to remove the effects of stimulus nonlinearity are investigated. Both correction methods were found to give similar results but have different pros and cons. The aim of this work is to investigate the importance of the conical shape of the eardrum as a source of nonlinearity in hearing. We present measurements on flat and indented membranes. The data shows that the curved membrane exhibit slightly higher levels of nonlinearity compared to the flat membrane.

Introduction to nonlinear dispersive equations

CERN Document Server

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...

Nonlinear hyperbolic waves in multidimensions

CERN Document Server

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...

Complex motions and chaos in nonlinear systems

CERN Document Server

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.

Second-order nonlinearity induced transparency.

Science.gov (United States)

Zhou, Y H; Zhang, S S; Shen, H Z; Yi, X X

2017-04-01

In analogy to electromagnetically induced transparency, optomechanically induced transparency was proposed recently in [Science330, 1520 (2010)SCIEAS0036-807510.1126/science.1195596]. In this Letter, we demonstrate another form of induced transparency enabled by second-order nonlinearity. A practical application of the second-order nonlinearity induced transparency is to measure the second-order nonlinear coefficient. Our scheme might find applications in quantum optics and quantum information processing.

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.)

Nonlinear signaling on biological networks: The role of stochasticity and spectral clustering

Science.gov (United States)

Hernandez-Hernandez, Gonzalo; Myers, Jesse; Alvarez-Lacalle, Enrique; Shiferaw, Yohannes

2017-03-01

Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different conformational states. Signaling is typically a cooperative process which requires the occurrence of multiple binding events so that reaction rates have a nonlinear dependence on the amount of signaling molecule. It is this nonlinearity that endows biological signaling networks with robust switchlike properties which are critical to their biological function. In this study we investigate how the properties of these signaling systems depend on the network architecture. Our main result is that these nonlinear networks exhibit bistability where the network activity can switch between states that correspond to a low and high activity level. We show that this bistable regime emerges at a critical coupling strength that is determined by the spectral structure of the network. In particular, the set of nodes that correspond to large components of the leading eigenvector of the adjacency matrix determines the onset of bistability. Above this transition the eigenvectors of the adjacency matrix determine a hierarchy of clusters, defined by its spectral properties, which are activated sequentially with increasing network activity. We argue further that the onset of bistability occurs either continuously or discontinuously depending upon whether the leading eigenvector is localized or delocalized. Finally, we show that at low network coupling stochastic transitions to the active branch are also driven by the set of nodes that contribute more strongly to the leading eigenvector. However, at high coupling, transitions are insensitive to network structure since the network can be activated by stochastic transitions of a few nodes. Thus this work identifies important features of biological signaling networks that may underlie their biological

Nonlinear Schrödinger equations with single power nonlinearity and harmonic potential

Science.gov (United States)

Cipolatti, R.; de Macedo Lira, Y.; Trallero-Giner, C.

2018-03-01

We consider a generalized nonlinear Schrödinger equation (GNLS) with a single power nonlinearity of the form λ ≤ft\\vert \\varphi \\right\\vert p , with p  >  0 and λ\\in{R} , in the presence of a harmonic confinement. We report the conditions that p and λ must fulfill for the existence and uniqueness of ground states of the GNLS. We discuss the Cauchy problem and summarize which conditions are required for the nonlinear term λ ≤ft\\vert \\varphi \\right\\vert p to render the ground state solutions orbitally stable. Based on a new variational method we provide exact formulæ for the minimum energy for each index p and the changing range of values of the nonlinear parameter λ. Also, we report an approximate close analytical expression for the ground state energy, performing a comparative analysis of the present variational calculations with those obtained by a generalized Thomas-Fermi approach, and soliton solutions for the respective ranges of p and λ where these solutions can be implemented to describe the minimum energy.

Drought affects protein and phenolic content in bambara groundnut ...

African Journals Online (AJOL)

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 and the total ...

Nonlinear optical crystals a complete survey

CERN Document Server

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...

A nonlinear plate control without linearization

Directory of Open Access Journals (Sweden)

Yildirim Kenan

2017-03-01

Full Text Available In this paper, an optimal vibration control problem for a nonlinear plate is considered. In order to obtain the optimal control function, wellposedness and controllability of the nonlinear system is investigated. The performance index functional of the system, to be minimized by minimum level of control, is chosen as the sum of the quadratic 10 functional of the displacement. The velocity of the plate and quadratic functional of the control function is added to the performance index functional as a penalty term. By using a maximum principle, the nonlinear control problem is transformed to solving a system of partial differential equations including state and adjoint variables linked by initial-boundary-terminal conditions. Hence, it is shown that optimal control of the nonlinear systems can be obtained without linearization of the nonlinear term and optimal control function can be obtained analytically for nonlinear systems without linearization.

Nonlinear silicon photonics

Science.gov (United States)

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.

Nonlinear Damping Identification in Nonlinear Dynamic System Based on Stochastic Inverse Approach

Directory of Open Access Journals (Sweden)

S. L. Han

2012-01-01

Full Text Available The nonlinear model is crucial to prepare, supervise, and analyze mechanical system. In this paper, a new nonparametric and output-only identification procedure for nonlinear damping is studied. By introducing the concept of the stochastic state space, we formulate a stochastic inverse problem for a nonlinear damping. The solution of the stochastic inverse problem is designed as probabilistic expression via the hierarchical Bayesian formulation by considering various uncertainties such as the information insufficiency in parameter of interests or errors in measurement. The probability space is estimated using Markov chain Monte Carlo (MCMC. The applicability of the proposed method is demonstrated through numerical experiment and particular application to a realistic problem related to ship roll motion.

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

Nonlinear optics of liquid crystalline materials

International Nuclear Information System (INIS)

Khoo, Iam Choon

2009-01-01

Liquid crystals occupy an important niche in nonlinear optics as a result of their unique physical and optical properties. Besides their broadband birefringence and transparency, abilities to self-assemble into various crystalline phases and to conform to various flexible forms and shapes, liquid crystals are compatible with almost all other optoelectronic materials and technology platforms. In both isotropic and ordered phases, liquid crystals possess extraordinarily large optical nonlinearities that stretch over multiple time scales. To date, almost all conceivable nonlinear optical phenomena have been observed in a very broad spectrum spanning the entire visible to infrared and beyond. In this review, we present a self-contained complete discussion of the optical nonlinearities of liquid crystals, and a thorough review of a wide range of nonlinear optical processes and phenomena enabled by these unique properties. Starting with a brief historical account of the development of nonlinear optical studies of the mesophases of liquid crystals, we then review various liquid crystalline materials and structures, and their nonlinear optical properties. Emphasis is placed on the nematic phase, which best exemplifies the dual nature of liquid crystals, although frequent references to other phases are also made. We also delve into recent work on novel structures such as photonic crystals, metamaterials and nanostructures and their special characteristics and emergent properties. The mechanisms and complex nonlocal dynamics of optical nonlinearities associated with laser induced director axis reorientation, thermal, density, and order parameter fluctuations, space charge field formation and photorefractivity are critically reviewed as a foundation for the discussions of various nonlinear optical processes detailed in this paper

Exact solutions of the two-dimensional discrete nonlinear Schrodinger equation with saturable nonlinearity

DEFF Research Database (Denmark)

Khare, A.; Rasmussen, K. O.; Samuelsen, Mogens Rugholm

2010-01-01

We show that the two-dimensional, nonlinear Schrodinger lattice with a saturable nonlinearity admits periodic and pulse-like exact solutions. We establish the general formalism for the stability considerations of these solutions and give examples of stability diagrams. Finally, we show that the e...

Nonlinear Dot Plots.

Science.gov (United States)

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.

Nonlinear and stochastic dynamics of coherent structures

DEFF Research Database (Denmark)

Rasmussen, Kim

1997-01-01

This Thesis deals with nonlinear and stochastic dynamics in systems which can be described by nonlinear Schrödinger models. Basically three different models are investigated. The first is the continuum nonlinear Schröndinger model in one and two dimensions generalized by a tunable degree of nonli......This Thesis deals with nonlinear and stochastic dynamics in systems which can be described by nonlinear Schrödinger models. Basically three different models are investigated. The first is the continuum nonlinear Schröndinger model in one and two dimensions generalized by a tunable degree...... introduces the nonlinear Schrödinger model in one and two dimensions, discussing the soliton solutions in one dimension and the collapse phenomenon in two dimensions. Also various analytical methods are described. Then a derivation of the nonlinear Schrödinger equation is given, based on a Davydov like...... system described by a tight-binding Hamiltonian and a harmonic lattice coupled b y a deformation-type potential. This derivation results in a two-dimensional nonline ar Schrödinger model, and considering the harmonic lattice to be in thermal contact with a heat bath w e show that the nonlinear...

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.)

Nonlinear magnetohydrodynamics of edge localized mode precursors

Energy Technology Data Exchange (ETDEWEB)

Guo, Z. B., E-mail: guozhipku@gmail.com [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing (China); WCI Center for Fusion Theory, NFRI, Gwahangno 113, Yusung-gu, Daejeon 305-333 (Korea, Republic of); Wang, Lu [SEEE, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Wang, X. G. [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing (China)

2015-02-15

A possible origin of edge-localized-mode (ELM) precursors based on nonlinear ideal peeling-ballooning mode is reported. Via nonlinear variational principle, a nonlinear evolution equation of the radial displacement is derived and solved, analytically. Besides an explosive growth in the initial nonlinear phase, it is found that the local displacement evolves into an oscillating state in the developed nonlinear phase. The nonlinear frequency of the ELM precursors scales as ω{sub pre}∼x{sup 1/3}ξ{sup ^}{sub ψ,in}{sup 2/3}n, with x position in radial direction, ξ{sup ^}{sub ψ,in} strength of initial perturbation, and n toroidal mode number.

Solitary wave for a nonintegrable discrete nonlinear Schrödinger equation in nonlinear optical waveguide arrays

Science.gov (United States)

Ma, Li-Yuan; Ji, Jia-Liang; Xu, Zong-Wei; Zhu, Zuo-Nong

2018-03-01

We study a nonintegrable discrete nonlinear Schrödinger (dNLS) equation with the term of nonlinear nearest-neighbor interaction occurred in nonlinear optical waveguide arrays. By using discrete Fourier transformation, we obtain numerical approximations of stationary and travelling solitary wave solutions of the nonintegrable dNLS equation. The analysis of stability of stationary solitary waves is performed. It is shown that the nonlinear nearest-neighbor interaction term has great influence on the form of solitary wave. The shape of solitary wave is important in the electric field propagating. If we neglect the nonlinear nearest-neighbor interaction term, much important information in the electric field propagating may be missed. Our numerical simulation also demonstrates the difference of chaos phenomenon between the nonintegrable dNLS equation with nonlinear nearest-neighbor interaction and another nonintegrable dNLS equation without the term. Project supported by the National Natural Science Foundation of China (Grant Nos. 11671255 and 11701510), the Ministry of Economy and Competitiveness of Spain (Grant No. MTM2016-80276-P (AEI/FEDER, EU)), and the China Postdoctoral Science Foundation (Grant No. 2017M621964).

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

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....

Identification of Tobacco Topping Responsive Proteins in Roots

Directory of Open Access Journals (Sweden)

Hongxiang eGuo

2016-04-01

Full Text Available Tobacco plant has many responses to topping, such as the increase in ability of nicotine synthesis and secondary growth of roots. Some topping responsive miRNAs and genes had been identified in our previous work, but it is not enough to elaborate mechanism of tobacco response to topping. Here, topping responsive proteins were screened from tobacco roots with two-dimensional electrophoresis. Of these proteins, calretulin (CRT and Auxin-responsive protein IAA9 were related to the secondary growth of roots, LRR disease resistance, heat shock protein 70 and farnesyl pyrophosphate synthase 1（FPPS）were involved in wounding stress response, and F-box protein played an important role in promoting the ability of nicotine synthesis after topping. In addition, there were five tobacco bHLH proteins (NtbHLH, NtMYC1a, NtMYC1b, NtMYC2a and NtMYC2b related to nicotine synthesis. It was suggested that NtMYC2 might be the main positive transcription factor and NtbHLH protein is a negative regulator in the JA-mediating activation of nicotine synthesis after topping. Tobacco topping activates some comprehensive biology processes involving IAA and JA signaling pathway, and the identification of these proteins will be helpful to understand the process of topping response.

Introduction to nonlinear finite element analysis

CERN Document Server

Kim, Nam-Ho

2015-01-01

This book introduces the key concepts of nonlinear finite element analysis procedures. The book explains the fundamental theories of the field and provides instructions on how to apply the concepts to solving practical engineering problems. Instead of covering many nonlinear problems, the book focuses on three representative problems: nonlinear elasticity, elastoplasticity, and contact problems. The book is written independent of any particular software, but tutorials and examples using four commercial programs are included as appendices: ANSYS, NASTRAN, ABAQUS, and MATLAB. In particular, the MATLAB program includes all source codes so that students can develop their own material models, or different algorithms. This book also: ·         Presents clear explanations of nonlinear finite element analysis for elasticity, elastoplasticity, and contact problems ·         Includes many informative examples of nonlinear analyses so that students can clearly understand the nonlinear theory ·    ...

Fractional analysis for nonlinear electrical transmission line and nonlinear Schroedinger equations with incomplete sub-equation

Science.gov (United States)

Fendzi-Donfack, Emmanuel; Nguenang, Jean Pierre; Nana, Laurent

2018-02-01

We use the fractional complex transform with the modified Riemann-Liouville derivative operator to establish the exact and generalized solutions of two fractional partial differential equations. We determine the solutions of fractional nonlinear electrical transmission lines (NETL) and the perturbed nonlinear Schroedinger (NLS) equation with the Kerr law nonlinearity term. The solutions are obtained for the parameters in the range (0<α≤1) of the derivative operator and we found the traditional solutions for the limiting case of α =1. We show that according to the modified Riemann-Liouville derivative, the solutions found can describe physical systems with memory effect, transient effects in electrical systems and nonlinear transmission lines, and other systems such as optical fiber.

Multi-frequency Defect Selective Imaging via Nonlinear Ultrasound

Science.gov (United States)

Solodov, Igor; Busse, Gerd

The concept of defect-selective ultrasonic nonlinear imaging is based on visualization of strongly nonlinear inclusions in the form of localized cracked defects. For intense excitation, the ultrasonic response of defects is affected by mechanical constraint between their fragments that makes their vibrations extremely nonlinear. The cracked flaws, therefore, efficiently generate multiple new frequencies, which can be used as a nonlinear "tag" to detect and image them. In this paper, the methodologies of nonlinear scanning laser vibrometry (NSLV) and nonlinear air-coupled emission (NACE) are applied for nonlinear imaging of various defects in hi-tech and constructional materials. A broad database obtained demonstrates evident advantages of the nonlinear approach over its linear counterpart. The higher-order nonlinear frequencies provide increase in signal-to-noise ratio and enhance the contrast of imaging. Unlike conventional ultrasonic instruments, the nonlinear approach yields abundant multi-frequency information on defect location. The application of image recognition and processing algorithms is described and shown to improve reliability and quality of ultrasonic imaging.

Design and static simulation of secondary loop of small PWR nuclear power plants

International Nuclear Information System (INIS)

Martin Lopez, L.A.N.

1989-01-01

A computer program that has been developed with the purpose of making easier the decisions concerning the design of the secondary loop of small PWR nuclear power plants through numerical experiments of low running costs and short time is presented. Initially, the first part of the computer program is described. It aims to preliminarily design several major components of the secondary circuit from user-defined design conditions. Next, the second part of the computer program is presented. It simulates the steady state operation at part-load conditions of the preliminary design of the plant by generating and solving systems of simultaneous nonlinear algebraic equations, their number varying from 17 to 107. The computer program has been tested for several application cases. The program results are discussed in the last part of the work, along with several aspects to be added to the program in future works. (author)

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

BALB/c Mice Vaccinated with Leishmania major Ribosomal Proteins Extracts Combined with CpG Oligodeoxynucleotides Become Resistant to Disease Caused by a Secondary Parasite Challenge

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.

Homogenized description and retrieval method of nonlinear metasurfaces

Science.gov (United States)

Liu, Xiaojun; Larouche, Stéphane; Smith, David R.

2018-03-01

A patterned, plasmonic metasurface can strongly scatter incident light, functioning as an extremely low-profile lens, filter, reflector or other optical device. When the metasurface is patterned uniformly, its linear optical properties can be expressed using effective surface electric and magnetic polarizabilities obtained through a homogenization procedure. The homogenized description of a nonlinear metasurface, however, presents challenges both because of the inherent anisotropy of the medium as well as the much larger set of potential wave interactions available, making it challenging to assign effective nonlinear parameters to the otherwise inhomogeneous layer of metamaterial elements. Here we show that a homogenization procedure can be developed to describe nonlinear metasurfaces, which derive their nonlinear response from the enhanced local fields arising within the structured plasmonic elements. With the proposed homogenization procedure, we are able to assign effective nonlinear surface polarization densities to a nonlinear metasurface, and link these densities to the effective nonlinear surface susceptibilities and averaged macroscopic pumping fields across the metasurface. These effective nonlinear surface polarization densities are further linked to macroscopic nonlinear fields through the generalized sheet transition conditions (GSTCs). By inverting the GSTCs, the effective nonlinear surface susceptibilities of the metasurfaces can be solved for, leading to a generalized retrieval method for nonlinear metasurfaces. The application of the homogenization procedure and the GSTCs are demonstrated by retrieving the nonlinear susceptibilities of a SiO2 nonlinear slab. As an example, we investigate a nonlinear metasurface which presents nonlinear magnetoelectric coupling in near infrared regime. The method is expected to apply to any patterned metasurface whose thickness is much smaller than the wavelengths of operation, with inclusions of arbitrary geometry

Feature-Based and String-Based Models for Predicting RNA-Protein Interaction

Directory of Open Access Journals (Sweden)

Donald Adjeroh

2018-03-01

Full Text Available In this work, we study two approaches for the problem of RNA-Protein Interaction (RPI. In the first approach, we use a feature-based technique by combining extracted features from both sequences and secondary structures. The feature-based approach enhanced the prediction accuracy as it included much more available information about the RNA-protein pairs. In the second approach, we apply search algorithms and data structures to extract effective string patterns for prediction of RPI, using both sequence information (protein and RNA sequences, and structure information (protein and RNA secondary structures. This led to different string-based models for predicting interacting RNA-protein pairs. We show results that demonstrate the effectiveness of the proposed approaches, including comparative results against leading state-of-the-art methods.

Recognition determinants for proteins and antibiotics within 23S rRNA

DEFF Research Database (Denmark)

Douthwaite, Stephen Roger; Voldborg, Bjørn Gunnar Rude; Hansen, Lykke Haastrup

1995-01-01

Ribosomal RNAs fold into phylogenetically conserved secondary and tertiary structures that determine their function in protein synthesis. We have investigated Escherichia coli 23S rRNA to identify structural elements that interact with antibiotic and protein ligands. Using a combination of molecu......Ribosomal RNAs fold into phylogenetically conserved secondary and tertiary structures that determine their function in protein synthesis. We have investigated Escherichia coli 23S rRNA to identify structural elements that interact with antibiotic and protein ligands. Using a combination......-proteins L10.(L12)4 and L11 and is inhibited by interaction with the antibiotic thiostrepton. The peptidyltransferase center within domain V is inhibited by macrolide, lincosamide, and streptogramin B antibiotics, which interact with the rRNA around nucleotide A2058. Drug resistance is conferred by mutations...

Contribution of long-range interactions to the secondary structure of an unfolded globin.

Science.gov (United States)

Fedyukina, Daria V; Rajagopalan, Senapathy; Sekhar, Ashok; Fulmer, Eric C; Eun, Ye-Jin; Cavagnero, Silvia

2010-09-08

This work explores the effect of long-range tertiary contacts on the distribution of residual secondary structure in the unfolded state of an alpha-helical protein. N-terminal fragments of increasing length, in conjunction with multidimensional nuclear magnetic resonance, were employed. A protein representative of the ubiquitous globin fold was chosen as the model system. We found that, while most of the detectable alpha-helical population in the unfolded ensemble does not depend on the presence of the C-terminal region (corresponding to the native G and H helices), specific N-to-C long-range contacts between the H and A-B-C regions enhance the helical secondary structure content of the N terminus (A-B-C regions). The simple approach introduced here, based on the evaluation of N-terminal polypeptide fragments of increasing length, is of general applicability to identify the influence of long-range interactions in unfolded proteins. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Device Applications of Nonlinear Dynamics

CERN Document Server

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.

Exact Solutions to Nonlinear Schroedinger Equation and Higher-Order Nonlinear Schroedinger Equation

International Nuclear Information System (INIS)

Ren Ji; Ruan Hangyu

2008-01-01

We study solutions of the nonlinear Schroedinger equation (NLSE) and higher-order nonlinear Schroedinger equation (HONLSE) with variable coefficients. By considering all the higher-order effect of HONLSE as a new dependent variable, the NLSE and HONLSE can be changed into one equation. Using the generalized Lie group reduction method (GLGRM), the abundant solutions of NLSE and HONLSE are obtained

Direct electrochemistry and electrocatalysis of heme proteins immobilised in carbon-coated nickel magnetic nanoparticle-chitosan-dimethylformamide composite films in room-temperature ionic liquids.

Science.gov (United States)

Wang, Ting; Wang, Lu; Tu, Jiaojiao; Xiong, Huayu; Wang, Shengfu

2013-12-01

The direct electrochemistry and electrocatalysis of heme proteins entrapped in carbon-coated nickel magnetic nanoparticle-chitosan-dimethylformamide (CNN-CS-DMF) composite films were investigated in the hydrophilic ionic liquid [bmim][BF4]. The surface morphologies of a representative set of films were characterised via scanning electron microscopy. The proteins immobilised in the composite films were shown to retain their native secondary structure using UV-vis spectroscopy. The electrochemical performance of the heme proteins-CNN-CS-DMF films was evaluated via cyclic voltammetry and chronoamperometry. A pair of stable and well-defined redox peaks was observed for the heme protein films at formal potentials of -0.151 V (HRP), -0.167 V (Hb), -0.155 V (Mb) and -0.193 V (Cyt c) in [bmim][BF4]. Moreover, several electrochemical parameters of the heme proteins were calculated by nonlinear regression analysis of the square-wave voltammetry. The addition of CNN significantly enhanced not only the electron transfer of the heme proteins but also their electrocatalytic activity toward the reduction of H2O2. Low apparent Michaelis-Menten constants were obtained for the heme protein-CNN-CS-DMF films, demonstrating that the biosensors have a high affinity for H2O2. In addition, the resulting electrodes displayed a low detection limit and improved sensitivity for detecting H2O2, which indicates that the biocomposite film can serve as a platform for constructing new non-aqueous biosensors for real detection. Copyright © 2013 Elsevier B.V. All rights reserved.

Modeling of a New Structure of Precision Air Conditioning System Using Secondary Condenser for Rh Regulation

Directory of Open Access Journals (Sweden)

Aries Subiantoro

2012-05-01

Full Text Available A dynamic mathematical model for a new structure of precision air conditioning (PAC has been developed. The proposed PAC uses an additional secondary condenser for relative humidity regulation compared to a basic refrigeration system. The work mechanism for this system and a vapour-compression cycle process of the system are illustrated using psychrometric chart and pressure-enthalpy diagram. A non-linear system model is derived based on the conservation of mass and energy balance principles and then linearized at steady state operating point for developing a 8th-order state space model suited for multivariable controller design. The quality of linearized model is analyzed in terms of transient response, controllability, observability, and interaction between input-output variables. The developed model is verified through simulation showing its ability for imitating the nonlinear behavior and the interaction of input-output variables.

JAC, 2-D Finite Element Method Program for Quasi Static Mechanics Problems by Nonlinear Conjugate Gradient (CG) Method

International Nuclear Information System (INIS)

Biffle, J.H.

1991-01-01

1 - Description of program or function: JAC is a two-dimensional finite element program for solving large deformation, temperature dependent, quasi-static mechanics problems with the nonlinear conjugate gradient (CG) technique. Either plane strain or axisymmetric geometry may be used with material descriptions which include temperature dependent elastic-plastic, temperature dependent secondary creep, and isothermal soil models. The nonlinear effects examined include material and geometric nonlinearities due to large rotations, large strains, and surface which slide relative to one another. JAC is vectorized to perform efficiently on the Cray1 computer. A restart capability is included. 2 - Method of solution: The nonlinear conjugate gradient method is employed in a two-dimensional plane strain or axisymmetric setting with various techniques for accelerating convergence. Sliding interface conditions are also implemented. A four-node Lagrangian uniform strain element is used with orthogonal hourglass viscosity to control the zero energy modes. Three sets of continuum equations are needed - kinematic statements, constitutive equations, and equations of equilibrium - to describe the deformed configuration of the body. 3 - Restrictions on the complexity of the problem - Maxima of: 10 load and solution control functions, 4 materials. The strain rate is assumed constant over a time interval. Current large rotation theory is applicable to a maximum shear strain of 1.0. JAC should be used with caution for large shear strains. Problem size is limited only by available memory

Nonlinear approaches in engineering applications 2

CERN Document Server

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

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

A Modified Lindstedt–Poincaré Method for a Strongly Nonlinear System with Quadratic and Cubic Nonlinearities

Directory of Open Access Journals (Sweden)

S.H. Chen

1996-01-01

Full Text Available A modified Lindstedt–Poincaré method is presented for extending the range of the validity of perturbation expansion to strongly nonlinear oscillations of a system with quadratic and cubic nonlinearities. Different parameter transformations are introduced to deal with equations with different nonlinear characteristics. All examples show that the efficiency and accuracy of the present method are very good.

Secondary Hypertension

Science.gov (United States)

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, ...

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.

Nonlinearly stacked low noise turbofan stator

Science.gov (United States)

Schuster, William B. (Inventor); Nolcheff, Nick A. (Inventor); Gunaraj, John A. (Inventor); Kontos, Karen B. (Inventor); Weir, Donald S. (Inventor)

2009-01-01

A nonlinearly stacked low noise turbofan stator vane having a characteristic curve that is characterized by a nonlinear sweep and a nonlinear lean is provided. The stator is in an axial fan or compressor turbomachinery stage that is comprised of a collection of vanes whose highly three-dimensional shape is selected to reduce rotor-stator and rotor-strut interaction noise while maintaining the aerodynamic and mechanical performance of the vane. The nonlinearly stacked low noise turbofan stator vane reduces noise associated with the fan stage of turbomachinery to improve environmental compatibility.

The nonlinear universe chaos, emergence, life

CERN Document Server

Scott, A C

2007-01-01

Written in Alwyn Scott’s inimitable style – lucid and accessible – The Nonlinear Universe surveys and explores the explosion of activity in nonlinear science that began in the 1970s and 1980s and continues today. The book explains the wide-ranging implications of nonlinear phenomena for future developments in many areas of modern science, including mathematics, physics, engineering, chemistry, biology, and neuroscience. Arguably as important as quantum theory, modern nonlinear science – and an appreciation of its implications – is essential for understanding scientific developments of the twenty-first century.

Nonlinear Photonics and Novel Optical Phenomena

CERN Document Server

Morandotti, Roberto

2012-01-01

Nonlinear Photonics and Novel Optical Phenomena contains contributed chapters from leading experts in nonlinear optics and photonics, and provides a comprehensive survey of fundamental concepts as well as hot topics in current research on nonlinear optical waves and related novel phenomena. The book covers self-accelerating airy beams, integrated photonics based on high index doped-silica glass, linear and nonlinear spatial beam dynamics in photonic lattices and waveguide arrays, polariton solitons and localized structures in semiconductor microcavities, terahertz waves, and other novel phenomena in different nanophotonic and optical systems.

Non-reciprocity in nonlinear elastodynamics

Science.gov (United States)

Blanchard, Antoine; Sapsis, Themistoklis P.; Vakakis, Alexander F.

2018-01-01

Reciprocity is a fundamental property of linear time-invariant (LTI) acoustic waveguides governed by self-adjoint operators with symmetric Green's functions. The break of reciprocity in LTI elastodynamics is only possible through the break of time reversal symmetry on the micro-level, and this can be achieved by imposing external biases, adding nonlinearities or allowing for time-varying system properties. We present a Volterra-series based asymptotic analysis for studying spatial non-reciprocity in a class of one-dimensional (1D), time-invariant elastic systems with weak stiffness nonlinearities. We show that nonlinearity is neither necessary nor sufficient for breaking reciprocity in this class of systems; rather, it depends on the boundary conditions, the symmetries of the governing linear and nonlinear operators, and the choice of the spatial points where the non-reciprocity criterion is tested. Extension of the analysis to higher dimensions and time-varying systems is straightforward from a mathematical point of view (but not in terms of new non-reciprocal physical phenomena), whereas the connection of non-reciprocity and time irreversibility can be studied as well. Finally, we show that suitably defined non-reciprocity measures enable optimization, and can provide physical understanding of the nonlinear effects in the dynamics, enabling one to establish regimes of "maximum nonlinearity." We highlight the theoretical developments by means of a numerical example.

Nonlinear and turbulent processes in physics. Volume 2. Nonlinear effects in various areas of science

Energy Technology Data Exchange (ETDEWEB)

Sagdeev, R Z

1984-01-01

The results of theoretical and experimental investigations of nonlinear and turbulent phenomena from a wide range of fields in physics are presented in reviews and reports. Topics examined include localized vortex formations in an ideal fluid, phase transitions in crystals, spatially nonuniform structures in condensed matter, solitons in molecular systems, the migration of quasi-particles in easily deformed crystals, bifurcations and dissipative structures in distributed kinetic systems, and structures in a nonlinear burning medium. Consideration is given to macroscopic motion generation in nonequilibrium media, the interaction of bulk and surface wave trains, near-threshold instabilities in hydrodynamics, solitons in nonlinear elastic rods with variable characteristics, the generation of solitons and vortices from chaos, and nonlinear electromagnetic-wave dissipation in an electron system.

Generalized solutions of nonlinear partial differential equations

CERN Document Server

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 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.)

[Job stress of nursing aides in Swiss nursing homes : Nonlinear canonical analysis].

Science.gov (United States)

Ziegler, A; Bernet, M; Metzenthin, P; Conca, A; Hahn, S

2016-08-01

Due to demographic changes, the demand for care in nursing homes for the elderly and infirmed is growing. At the same time nursing staff shortages are also increasing. Nursing aides are the primary care providers and comprise the largest staff group in Swiss nursing homes. They are exposed to various forms of job stress, which threaten job retention. The aim of this study was to discover which features of the work situation and which personal characteristics of the nursing aides were related to the workload. Data from nursing aides in Swiss nursing homes were investigated through a secondary analysis of a national quantitative cross-sectional study, using descriptive statistics and a nonlinear canonical correlation analysis. A total of 1054 nursing aides were included in the secondary analysis, 94.6 % of whom were women between the ages of 42 and 61 years. The job stress most frequently mentioned in the descriptive analysis, almost 60 % of the participants referred to it, was staff shortage. The nonlinear canonical correlation analysis revealed that many job strains are caused by social and organizational issues. In particular, a lack of support from supervisors was associated with staff not feeling appreciated. These job strains correlated with a high level of responsibility, the feeling of being unable to work independently and a feeling of being exploited. These strains were predominant in the nursing aides between 32 and 51 years old who had part time jobs but workloads of 80-90 %. Middle-aged nursing aides who worked to 80-90 % are particularly at risk to resign from the position prematurely. Measures need to be mainly implemented in the social and organizational areas. It can be assumed that a targeted individual support, recognition and promotion of nursing aides may decrease the level of job strain.

Nonlinear dynamics experiment in the Tevatron

International Nuclear Information System (INIS)

Merminga, N.; Edwards, D.; Finley, D.

1989-01-01

Results of the continuing analysis of the nonlinear dynamics experiment E778 are presented. Sixteen special sextupoles introduced nonlinearities in the Tevatron. 'Smear,' which is one of the parameters used to quantify the degree of nonlinearity, was extracted from the data and compared with calculation. Injection efficiency in the presence of nonlinearities was studied. Measurements of the dynamic aperture were performed. The final results in one degree of freedom of the smear, the injection efficiency and the dynamic aperture are presented. Particles captured on nonlinear resonance islands were directly observed and measurements were performed. The capture efficiency was extracted from the data and compared with prediction. The influence of tune modulation on the stability of these islands was investigated. Plans for future measurements are discussed. 4 refs., 6 figs

Structural alterations in rat liver proteins due to streptozotocin-induced diabetes and the recovery effect of selenium: Fourier transform infrared microspectroscopy and neural network study

Science.gov (United States)

Bozkurt, Ozlem; Haman Bayari, Sevgi; Severcan, Mete; Krafft, Christoph; Popp, Jürgen; Severcan, Feride

2012-07-01

The relation between protein structural alterations and tissue dysfunction is a major concern as protein fibrillation and/or aggregation due to structural alterations has been reported in many disease states. In the current study, Fourier transform infrared microspectroscopic imaging has been used to investigate diabetes-induced changes on protein secondary structure and macromolecular content in streptozotocin-induced diabetic rat liver. Protein secondary structural alterations were predicted using neural network approach utilizing the amide I region. Moreover, the role of selenium in the recovery of diabetes-induced alterations on macromolecular content and protein secondary structure was also studied. The results revealed that diabetes induced a decrease in lipid to protein and glycogen to protein ratios in diabetic livers. Significant alterations in protein secondary structure were observed with a decrease in α-helical and an increase in β-sheet content. Both doses of selenium restored diabetes-induced changes in lipid to protein and glycogen to protein ratios. However, low-dose selenium supplementation was not sufficient to recover the effects of diabetes on protein secondary structure, while a higher dose of selenium fully restored diabetes-induced alterations in protein structure.

Applications of nonlinear fiber optics

CERN Document Server

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

Secondary structure classification of amino-acid sequences using state-space modeling

OpenAIRE

Brunnert, Marcus; Krahnke, Tillmann; Urfer, Wolfgang

2001-01-01

The secondary structure classification of amino acid sequences can be carried out by a statistical analysis of sequence and structure data using state-space models. Aiming at this classification, a modified filter algorithm programmed in S is applied to data of three proteins. The application leads to correct classifications of two proteins even when using relatively simple estimation methods for the parameters of the state-space models. Furthermore, it has been shown that the assumed initial...

Myowater dynamics and protein secondary structural changes as affected by heating rate in three pork qualities: a combined FT-IR microspectroscopic and 1H NMR relaxometry study.

Science.gov (United States)

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.

Nonlinear chaos control and synchronization

NARCIS (Netherlands)

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

Non-linear corrections to the time-covariance function derived from a multi-state chemical master equation.

Science.gov (United States)

Scott, M

2012-08-01

The time-covariance function captures the dynamics of biochemical fluctuations and contains important information about the underlying kinetic rate parameters. Intrinsic fluctuations in biochemical reaction networks are typically modelled using a master equation formalism. In general, the equation cannot be solved exactly and approximation methods are required. For small fluctuations close to equilibrium, a linearisation of the dynamics provides a very good description of the relaxation of the time-covariance function. As the number of molecules in the system decrease, deviations from the linear theory appear. Carrying out a systematic perturbation expansion of the master equation to capture these effects results in formidable algebra; however, symbolic mathematics packages considerably expedite the computation. The authors demonstrate that non-linear effects can reveal features of the underlying dynamics, such as reaction stoichiometry, not available in linearised theory. Furthermore, in models that exhibit noise-induced oscillations, non-linear corrections result in a shift in the base frequency along with the appearance of a secondary harmonic.

Structures composing protein domains.

Science.gov (United States)

Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

2013-08-01

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Soliton concepts and protein structure

Science.gov (United States)

Krokhotin, Andrei; Niemi, Antti J.; Peng, Xubiao

2012-03-01

Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion from a relatively small number of components. Here we propose that the modular building blocks are made of the dark soliton solution of a generalized discrete nonlinear Schrödinger equation. We find that practically all protein loops can be obtained simply by scaling the size and by joining together a number of copies of the soliton, one after another. The soliton has only two loop-specific parameters, and we compute their statistical distribution in the Protein Data Bank (PDB). We explicitly construct a collection of 200 sets of parameters, each determining a soliton profile that describes a different short loop. The ensuing profiles cover practically all those proteins in PDB that have a resolution which is better than 2.0 Å, with a precision such that the average root-mean-square distance between the loop and its soliton is less than the experimental B-factor fluctuation distance. We also present two examples that describe how the loop library can be employed both to model and to analyze folded proteins.

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 laser-plasma interactions

Science.gov (United States)

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

Nonlinear Source Emulator

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...

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.)

A study of discrete nonlinear systems

International Nuclear Information System (INIS)

Dhillon, H.S.

2001-04-01

An investigation of various spatially discrete time-independent nonlinear models was undertaken. These models are generically applicable to many different physical systems including electron-phonon interactions in solids, magnetic multilayers, layered superconductors and classical lattice systems. To characterise the possible magnetic structures created on magnetic multilayers a model has been formulated and studied. The Euler-Lagrange equation for this model is a discrete version of the Sine-Gordon equation. Solutions of this equation are generated by applying the methods of Chaotic Dynamics - treating the space variable associated with the layer number as a discrete time variable. The states found indicate periodic, quasiperiodic and chaotic structures. Analytic solutions to the discrete nonlinear Schroedinger Equation (DNSE) with cubic nonlinearity are presented in the strong coupling limit. Using these as a starting point, a procedure is developed to determine the wave function and the energy eigenvalue for moderate coupling. The energy eigenvalues of the different structures of the wave function are found to be in excellent agreement with the exact strong coupling result. The solutions to the DNSE indicate commensurate and incommensurate spatial structures associated with different localisation patterns of the wave function. The states which arise may be fractal, periodic, quasiperiodic or chaotic. This work is then extended to solve a first order discrete nonlinear equation. The exact solutions for both the first and second order discrete nonlinear equations with cubic nonlinearity suggests that this method of studying discrete nonlinear equations may be applied to solve discrete equations with any order difference and cubic nonlinearity. (author)

Missense mutation Lys18Asn in dystrophin that triggers X-linked dilated cardiomyopathy decreases protein stability, increases protein unfolding, and perturbs protein structure, but does not affect protein function.

Directory of Open Access Journals (Sweden)

Surinder M Singh

Full Text Available Genetic mutations in a vital muscle protein dystrophin trigger X-linked dilated cardiomyopathy (XLDCM. However, disease mechanisms at the fundamental protein level are not understood. Such molecular knowledge is essential for developing therapies for XLDCM. Our main objective is to understand the effect of disease-causing mutations on the structure and function of dystrophin. This study is on a missense mutation K18N. The K18N mutation occurs in the N-terminal actin binding domain (N-ABD. We created and expressed the wild-type (WT N-ABD and its K18N mutant, and purified to homogeneity. Reversible folding experiments demonstrated that both mutant and WT did not aggregate upon refolding. Mutation did not affect the protein's overall secondary structure, as indicated by no changes in circular dichroism of the protein. However, the mutant is thermodynamically less stable than the WT (denaturant melts, and unfolds faster than the WT (stopped-flow kinetics. Despite having global secondary structure similar to that of the WT, mutant showed significant local structural changes at many amino acids when compared with the WT (heteronuclear NMR experiments. These structural changes indicate that the effect of mutation is propagated over long distances in the protein structure. Contrary to these structural and stability changes, the mutant had no significant effect on the actin-binding function as evident from co-sedimentation and depolymerization assays. These results summarize that the K18N mutation decreases thermodynamic stability, accelerates unfolding, perturbs protein structure, but does not affect the function. Therefore, K18N is a stability defect rather than a functional defect. Decrease in stability and increase in unfolding decrease the net population of dystrophin molecules available for function, which might trigger XLDCM. Consistently, XLDCM patients have decreased levels of dystrophin in cardiac muscle.

Nonlinear Dynamic Phenomena in Mechanics

CERN Document Server

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

Nonlinear dynamics of quadratically cubic systems

International Nuclear Information System (INIS)

Rudenko, O V

2013-01-01

We propose a modified form of the well-known nonlinear dynamic equations with quadratic relations used to model a cubic nonlinearity. We show that such quadratically cubic equations sometimes allow exact solutions and sometimes make the original problem easier to analyze qualitatively. Occasionally, exact solutions provide a useful tool for studying new phenomena. Examples considered include nonlinear ordinary differential equations and Hopf, Burgers, Korteweg–de Vries, and nonlinear Schrödinger partial differential equations. Some problems are solved exactly in the space–time and spectral representations. Unsolved problems potentially solvable by the proposed approach are listed. (methodological notes)

Nonlinear acceleration of transport criticality problems

International Nuclear Information System (INIS)

Park, H.; Knoll, D.A.; Newman, C.K.

2011-01-01

We present a nonlinear acceleration algorithm for the transport criticality problem. The algorithm combines the well-known nonlinear diffusion acceleration (NDA) with a recently developed, Newton-based, nonlinear criticality acceleration (NCA) algorithm. The algorithm first employs the NDA to reduce the system to scalar flux, then the NCA is applied to the resulting drift-diffusion system. We apply a nonlinear elimination technique to eliminate the eigenvalue from the Jacobian matrix. Numerical results show that the algorithm reduces the CPU time a factor of 400 in a very diffusive system, and a factor of 5 in a non-diffusive system. (author)

Cavity nonlinear optics with layered materials

Directory of Open Access Journals (Sweden)

Fryett Taylor

2017-12-01

Full Text Available Unprecedented material compatibility and ease of integration, in addition to the unique and diverse optoelectronic properties of layered materials, have generated significant interest in their utilization in nanophotonic devices. While initial nanophotonic experiments with layered materials primarily focused on light sources, modulators, and detectors, recent efforts have included nonlinear optical devices. In this paper, we review the current state of cavity-enhanced nonlinear optics with layered materials. Along with conventional nonlinear optics related to harmonic generation, we report on emerging directions of nonlinear optics, where layered materials can potentially play a significant role.

Secondary biogeneous radiation of human organism

International Nuclear Information System (INIS)

Kuzin, A.M.; Surkenova, G.N.

1999-01-01

When studying samples of three types of tissues of alive healthy human organism (hands, surface of breast, hair) it is shown that hair permanently emit secondary biogeneous radiation (SBR) which may registered with biological detectors. The hypothesis is suggested that natural background radiation permanently exciting biopolymers (proteins, nuclei acids) being present in alive organism in condensed state induces permanently present electromagnetic field of SBR which is vitally important for human organism. The field partly extends beyond the organism, where it is registered with sensitive biological detectors [ru

Homogeneous shear turbulence – bypass concept via interplay of linear transient growth and nonlinear transverse cascade

International Nuclear Information System (INIS)

Mamatsashvili, George; Dong, Siwei; Jiménez, Javier; Khujadze, George; Chagelishvili, George; Foysi, Holger

2016-01-01

We performed direct numerical simulations of homogeneous shear turbulence to study the mechanism of the self-sustenance of subcritical turbulence in spectrally stable (constant) shear flows. For this purpose, we analyzed the turbulence dynamics in Fourier/wavenumber/spectral space based on the simulation data for the domain aspect ratio 1 : 1 : 1. Specifically, we examined the interplay of linear transient growth of Fourier harmonics and nonlinear processes. The transient growth of harmonics is strongly anisotropic in spectral space. This, in turn, leads to anisotropy of nonlinear processes in spectral space and, as a result, the main nonlinear process appears to be not a direct/inverse, but rather a transverse/angular redistribution of harmonics in Fourier space referred to as the nonlinear transverse cascade. It is demonstrated that the turbulence is sustained by the interplay of the linear transient, or nonmodal growth and the transverse cascade. This course of events reliably exemplifies the wellknown bypass scenario of subcritical turbulence in spectrally stable shear flows. These processes mainly operate at large length scales, comparable to the box size. Consequently, the central, small wavenumber area of Fourier space (the size of which is determined below) is crucial in the self-sustenance and is labeled the vital area. Outside the vital area, the transient growth and the transverse cascade are of secondary importance - Fourier harmonics are transferred to dissipative scales by the nonlinear direct cascade. The number of harmonics actively participating in the self-sustaining process (i.e., the harmonics whose energies grow more than 10% of the maximum spectral energy at least once during evolution) is quite large - it is equal to 36 for the considered box aspect ratio - and obviously cannot be described by low-order models. (paper)

Investigations of the role of nonlinear couplings in structure formation and transport regulation in plasma turbulence

Science.gov (United States)

Holland, Christopher George

Studies of nonlinear couplings and dynamics in plasma turbulence are presented. Particular areas of focus are analytic studies of coherent structure formation in electron temperature gradient turbulence, measurement of nonlinear energy transfer in simulations of plasma turbulence, and bispectral analysis of experimental and computational data. The motivation for these works has been to develop and expand the existing theories of plasma transport, and verify the nonlinear predictions of those theories in simulation and experiment. In Chapter II, we study electromagnetic secondary instabilities of electron temperature gradient turbulence. The growth rate for zonal flow generation via modulational instability of electromagnetic ETG turbulence is calculated, as well as that for zonal (magnetic) field generation. In Chapter III, the stability and saturation of streamers in ETG turbulence is considered, and shown to depend sensitively upon geometry and the damping rates of the Kelvin-Helmholtz mode. Requirements for a credible theory of streamer transport are presented. In addition, a self-consistent model for interactions between ETG and ITG (ion temperature gradient) turbulence is presented. In Chapter IV, the nonlinear transfer of kinetic and internal energy is measured in simulations of plasma turbulence. The regulation of turbulence by radial decorrelation due to zonal flows and generation of zonal flows via the Reynolds stress are explicitly demonstrated, and shown to be symmetric facets of a single nonlinear process. Novel nonlinear saturation mechanisms for zonal flows are discussed. In Chapter V, measurements of fluctuation bicoherence in the edge of the DIII-D tokamak are presented. It is shown that the bicoherence increases transiently before a L-H transition, and decays to its initial value after the barrier has formed. The increase in bicoherence is localized to the region where the transport barrier forms, and shows strong coupling between well

Nonlinear dynamics aspects of particle accelerators. Proceedings

Energy Technology Data Exchange (ETDEWEB)

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).

Mathematical modeling and applications in nonlinear dynamics

CERN Document Server

Merdan, Hüseyin

2016-01-01

The book covers nonlinear physical problems and mathematical modeling, including molecular biology, genetics, neurosciences, artificial intelligence with classical problems in mechanics and astronomy and physics. The chapters present nonlinear mathematical modeling in life science and physics through nonlinear differential equations, nonlinear discrete equations and hybrid equations. Such modeling can be effectively applied to the wide spectrum of nonlinear physical problems, including the KAM (Kolmogorov-Arnold-Moser (KAM)) theory, singular differential equations, impulsive dichotomous linear systems, analytical bifurcation trees of periodic motions, and almost or pseudo- almost periodic solutions in nonlinear dynamical systems. Provides methods for mathematical models with switching, thresholds, and impulses, each of particular importance for discontinuous processes Includes qualitative analysis of behaviors on Tumor-Immune Systems and methods of analysis for DNA, neural networks and epidemiology Introduces...

Design of a nonlinear torsional vibration absorber