Wu, Sangwook
2016-04-01
The three transmembrane and the four transmembrane helix models are suggested for human vitamin K epoxide reductase (VKOR). In this study, we investigate the stability of the human three transmembrane/four transmembrane VKOR models by employing a coarse-grained normal mode analysis and molecular dynamics simulation. Based on the analysis of the mobility of each transmembrane domain, we suggest that the three transmembrane human VKOR model is more stable than the four transmembrane human VKOR model.
Modeling of Transmembrane Potential in Realistic Multicellular Structures before Electroporation.
Murovec, Tomo; Sweeney, Daniel C; Latouche, Eduardo; Davalos, Rafael V; Brosseau, Christian
2016-11-15
Many approaches for studying the transmembrane potential (TMP) induced during the treatment of biological cells with pulsed electric fields have been reported. From the simple analytical models to more complex numerical models requiring significant computational resources, a gamut of methods have been used to recapitulate multicellular environments in silico. Cells have been modeled as simple shapes in two dimensions as well as more complex geometries attempting to replicate realistic cell shapes. In this study, we describe a method for extracting realistic cell morphologies from fluorescence microscopy images to generate the piecewise continuous mesh used to develop a finite element model in two dimensions. The preelectroporation TMP induced in tightly packed cells is analyzed for two sets of pulse parameters inspired by clinical irreversible electroporation treatments. We show that high-frequency bipolar pulse trains are better, and more homogeneously raise the TMP of tightly packed cells to a simulated electroporation threshold than conventional irreversible electroporation pulse trains, at the expense of larger applied potentials. Our results demonstrate the viability of our method and emphasize the importance of considering multicellular effects in the numerical models used for studying the response of biological tissues exposed to electric fields. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Modelling of a transmembrane evaporation module for desalination of seawater
Guijt, Caroliene M.; Rácz, Imre G.; Heuven, van Jan Willem; Reith, Tom; Haan, de André B.
1999-01-01
Transmembrane evaporation (often called membrane distillation) carried out in a countercurrent flow module, in which incoming cold seawater is heated by the condensing product water flow, is a promising technology for low-cost seawater desalination. This paper presents a model for preliminary design
A hidden Markov model for prediction transmembrane helices in proteinsequences
DEFF Research Database (Denmark)
Sonnhammer, Erik L.L.; von Heijne, Gunnar; Krogh, Anders Stærmose
1998-01-01
and constraints involved. Models were estimated both by maximum likelihood and a discriminative method, and a method for reassignment of the membrane helix boundaries were developed. In a cross validated test on single sequences, our transmembrane HMM, TMHMM, correctly predicts the entire topology for 77...
Transmembrane Protein 147 (TMEM147) Is a Novel Component of the Nicalin-NOMO Protein Complex*
Dettmer, Ulf; Kuhn, Peer-Hendrik; Abou-Ajram, Claudia; Lichtenthaler, Stefan F.; Krüger, Marcus; Kremmer, Elisabeth; Haass, Christian; Haffner, Christof
2010-01-01
Nicastrin and its relative Nicalin (Nicastrin-like protein) are both members of larger protein complexes, namely γ-secretase and the Nicalin-NOMO (Nodal modulator) complex. The γ-secretase complex, which contains Presenilin, APH-1, and PEN-2 in addition to Nicastrin, catalyzes the proteolytic cleavage of the transmembrane domain of various proteins including the β-amyloid precursor protein and Notch. Nicalin and its binding partner NOMO form a complex that was shown to modulate Nodal signalin...
Development of a Proteoliposome Model to Probe Transmembrane Electron-Transfer Reactions
Energy Technology Data Exchange (ETDEWEB)
White, Gaye F. [Univ. of East Anglia, Norwich (United Kingdom); Shi, Zhi [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Shi, Liang [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Dohnalkova, Alice [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Fredrickson, Jim K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Zachara, John M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Butt, Julea N. [Univ. of East Anglia, Norwich (United Kingdom); Richardson, David J. [Univ. of East Anglia, Norwich (United Kingdom); Clarke, Thomas [Univ. of East Anglia, Norwich (United Kingdom)
2012-12-01
The mineral respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decaheme cytochromes brought together inside a transmembrane porin to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system has been developed that contains methyl viologen (MV) as an internalised electron acceptor and valinomycin (V) as a membrane associated cation exchanger. These proteoliposomes can be used as a model system to investigate MtrCAB function.
Hidden markov model for the prediction of transmembrane proteins using MATLAB.
Chaturvedi, Navaneet; Shanker, Sudhanshu; Singh, Vinay Kumar; Sinha, Dhiraj; Pandey, Paras Nath
2011-01-01
Since membranous proteins play a key role in drug targeting therefore transmembrane proteins prediction is active and challenging area of biological sciences. Location based prediction of transmembrane proteins are significant for functional annotation of protein sequences. Hidden markov model based method was widely applied for transmembrane topology prediction. Here we have presented a revised and a better understanding model than an existing one for transmembrane protein prediction. Scripting on MATLAB was built and compiled for parameter estimation of model and applied this model on amino acid sequence to know the transmembrane and its adjacent locations. Estimated model of transmembrane topology was based on TMHMM model architecture. Only 7 super states are defined in the given dataset, which were converted to 96 states on the basis of their length in sequence. Accuracy of the prediction of model was observed about 74 %, is a good enough in the area of transmembrane topology prediction. Therefore we have concluded the hidden markov model plays crucial role in transmembrane helices prediction on MATLAB platform and it could also be useful for drug discovery strategy. The database is available for free at bioinfonavneet@gmail.comvinaysingh@bhu.ac.in.
The transmembrane nucleoporin NDC1 is required for targeting of ALADIN to nuclear pore complexes
Energy Technology Data Exchange (ETDEWEB)
Yamazumi, Yusuke; Kamiya, Atsushi; Nishida, Ayumu; Nishihara, Ayako [Laboratory of Molecular and Genetic Information, Institute for Molecular and Cellular Bioscience, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Iemura, Shun-ichiro; Natsume, Tohru [Biological Information Research Center (AIST), Japan Biological Information Research Center (JBIC), Aomi 2-41-6, Koutou-ku, Tokyo 135-0064 (Japan); Akiyama, Tetsu, E-mail: akiyama@iam.u-tokyo.ac.jp [Laboratory of Molecular and Genetic Information, Institute for Molecular and Cellular Bioscience, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan)
2009-11-06
NDC1 is a transmembrane nucleoporin that is required for NPC assembly and nucleocytoplasmic transport. We show here that NDC1 directly interacts with the nucleoporin ALADIN, mutations of which are responsible for triple-A syndrome, and that this interaction is required for targeting of ALADIN to nuclear pore complexes (NPCs). Furthermore, we show that NDC1 is required for selective nuclear import. Our findings suggest that NDC1-mediated localization of ALADIN to NPCs is essential for selective nuclear protein import, and that abrogation of the interaction between ALADIN and NDC1 may be important for the development of triple-A syndrome.
Transmembrane Protein 147 (TMEM147) Is a Novel Component of the Nicalin-NOMO Protein Complex*
Dettmer, Ulf; Kuhn, Peer-Hendrik; Abou-Ajram, Claudia; Lichtenthaler, Stefan F.; Krüger, Marcus; Kremmer, Elisabeth; Haass, Christian; Haffner, Christof
2010-01-01
Nicastrin and its relative Nicalin (Nicastrin-like protein) are both members of larger protein complexes, namely γ-secretase and the Nicalin-NOMO (Nodal modulator) complex. The γ-secretase complex, which contains Presenilin, APH-1, and PEN-2 in addition to Nicastrin, catalyzes the proteolytic cleavage of the transmembrane domain of various proteins including the β-amyloid precursor protein and Notch. Nicalin and its binding partner NOMO form a complex that was shown to modulate Nodal signaling in developing zebrafish embryos. Because its experimentally determined native size (200–220 kDa) could not be satisfyingly explained by the molecular masses of Nicalin (60 kDa) and NOMO (130 kDa), we searched in affinity-purified complex preparations for additional components in the low molecular mass range. A ∼22-kDa protein was isolated and identified by mass spectrometry as transmembrane protein 147 (TMEM147), a novel, highly conserved membrane protein with a putative topology similar to APH-1. Like Nicalin and NOMO, it localizes to the endoplasmic reticulum and is expressed during early zebrafish development. Overexpression and knockdown experiments in cultured cells demonstrate a close relationship between the three proteins and suggest that they are components of the same complex. We present evidence that, similar to γ-secretase, its assembly is hierarchical starting with the formation of a Nicalin-NOMO intermediate. Nicalin appears to represent the limiting factor regulating the assembly rate by stabilizing the other two components. We conclude that TMEM147 is a novel core component of the Nicalin-NOMO complex, further emphasizing its similarity with γ-secretase. PMID:20538592
Transmembrane protein 147 (TMEM147) is a novel component of the Nicalin-NOMO protein complex.
Dettmer, Ulf; Kuhn, Peer-Hendrik; Abou-Ajram, Claudia; Lichtenthaler, Stefan F; Krüger, Marcus; Kremmer, Elisabeth; Haass, Christian; Haffner, Christof
2010-08-20
Nicastrin and its relative Nicalin (Nicastrin-like protein) are both members of larger protein complexes, namely gamma-secretase and the Nicalin-NOMO (Nodal modulator) complex. The gamma-secretase complex, which contains Presenilin, APH-1, and PEN-2 in addition to Nicastrin, catalyzes the proteolytic cleavage of the transmembrane domain of various proteins including the beta-amyloid precursor protein and Notch. Nicalin and its binding partner NOMO form a complex that was shown to modulate Nodal signaling in developing zebrafish embryos. Because its experimentally determined native size (200-220 kDa) could not be satisfyingly explained by the molecular masses of Nicalin (60 kDa) and NOMO (130 kDa), we searched in affinity-purified complex preparations for additional components in the low molecular mass range. A approximately 22-kDa protein was isolated and identified by mass spectrometry as transmembrane protein 147 (TMEM147), a novel, highly conserved membrane protein with a putative topology similar to APH-1. Like Nicalin and NOMO, it localizes to the endoplasmic reticulum and is expressed during early zebrafish development. Overexpression and knockdown experiments in cultured cells demonstrate a close relationship between the three proteins and suggest that they are components of the same complex. We present evidence that, similar to gamma-secretase, its assembly is hierarchical starting with the formation of a Nicalin-NOMO intermediate. Nicalin appears to represent the limiting factor regulating the assembly rate by stabilizing the other two components. We conclude that TMEM147 is a novel core component of the Nicalin-NOMO complex, further emphasizing its similarity with gamma-secretase.
Crystal structure of AcrB in complex with a single transmembrane subunit reveals another twist.
Törnroth-Horsefield, Susanna; Gourdon, Pontus; Horsefield, Rob; Brive, Lars; Yamamoto, Natsuko; Mori, Hirotada; Snijder, Arjan; Neutze, Richard
2007-12-01
Bacterial drug resistance is a serious concern for human health. Multidrug efflux pumps export a broad variety of substrates out of the cell and thereby convey resistance to the host. In Escherichia coli, the AcrB:AcrA:TolC efflux complex forms a principal transporter for which structures of the individual component proteins have been determined in isolation. Here, we present the X-ray structure of AcrB in complex with a single transmembrane protein, assigned by mass spectrometry as YajC. A specific rotation of the periplasmic porter domain of AcrB is also revealed, consistent with the hypothesized "twist-to-open" mechanism for TolC activation. Growth experiments with yajc-deleted E. coli reveal a modest increase in the organism's susceptibility to beta-lactam antibiotics, but this effect could not conclusively be attributed to the loss of interactions between YajC and AcrB.
Modeling the Q-cycle mechanism of transmembrane energy conversion
Smirnov, Anatoly Yu
2011-01-01
The Q-cycle mechanism plays an important role in the conversion of the redox energy into the energy of the proton electrochemical gradient across the biomembrane. The bifurcated electron transfer reaction, which is built into this mechanism, recycles one electron, thus, allowing to translocate two protons per one electron moving to the high-potential redox chain. We study a kinetic model of the Q-cycle mechanism in an artificial system which mimics the bf complex of plants and cyanobacteria in the regime of ferredoxin-dependent cyclic electron flow. Using methods of condensed matter physics, we derive a set of master equations and describe a time sequence of electron and proton transfer reactions in the complex. We find energetic conditions when the bifurcation of the electron pathways at the positive side of the membrane occurs naturally, without any additional gates. For reasonable parameter values, we show that this system is able to translocate more than 1.8 protons, on average, per one electron, with a t...
A quantitative model for using acridine orange as a transmembrane pH gradient probe.
Clerc, S; Barenholz, Y
1998-05-15
Monitoring the acidification of the internal space of membrane vesicles by proton pumps can be achieved easily with optical probes. Transmembrane pH gradients cause a blue-shift in the absorbance spectrum and the quenching of the fluorescence of the cationic dye acridine orange. It has been postulated that these changes are caused by accumulation and aggregation of the dye inside the vesicles. We tested this hypothesis using liposomes with transmembrane concentration gradients of ammonium sulfate as model system. Fluorescence intensity of acridine orange solutions incubated with liposomes was affected by magnitude of the gradient, volume trapped by vesicles, and temperature. These experimental data were compared to a theoretical model describing the accumulation of acridine orange monomers in the vesicles according to the inside-to-outside ratio of proton concentrations, and the intravesicular formation of sandwich-like piles of acridine orange cations. This theoretical model predicted quantitatively the relationship between the transmembrane pH gradients and spectral changes of acridine orange. Therefore, adequate characterization of aggregation of dye in the lumen of biological vesicles provides the theoretical basis for using acridine orange as an optical probe to quantify transmembrane pH gradients.
Directory of Open Access Journals (Sweden)
Zhao Xueqiang
2009-10-01
Full Text Available Abstract Background In eukaryotic cells co- and post-translational protein translocation is mediated by the trimeric Sec61 complex. Currently, the role of the Sec61 complex β-subunit in protein translocation is poorly understood. We have shown previously that in Saccharomyces cerevisiae the trans-membrane domain alone is sufficient for the function of the β-subunit Sbh1p in co-translational protein translocation. In addition, Sbh1p co-purifies not only with the protein translocation channel subunits Sec61p and Sss1p, but also with the reticulon family protein Rtn1p. Results We used random mutagenesis to generate novel Sbh1p mutants in order to functionally map the Sbh1p trans-membrane domain. These mutants were analyzed for their interactions with Sec61p and how they support co-translational protein translocation. The distribution of mutations identifies one side of the Sbh1p trans-membrane domain α-helix that is involved in interactions with Sec61p and that is important for Sbh1p function in protein translocation. At the same time, these mutations do not affect Sbh1p interaction with Rtn1p. Furthermore we show that Sbh1p is found in protein complexes containing not only Rtn1p, but also the two other reticulon-like proteins Rtn2p and Yop1p. Conclusion Our results identify functionally important amino acids in the Sbh1p trans-membrane domain. In addition, our results provide additional support for the involvement of Sec61β in processes unlinked to protein translocation.
Quiroga, Rodrigo; Trenchi, Alejandra; González Montoro, Ayelén; Valdez Taubas, Javier; Maccioni, Hugo J F
2013-12-01
It is still unclear why some proteins that travel along the secretory pathway are retained in the Golgi complex whereas others make their way to the plasma membrane. Recent bioinformatic analyses on a large number of single-spanning membrane proteins support the hypothesis that specific features of the transmembrane domain (TMD) are relevant to the sorting of these proteins to particular organelles. Here we experimentally test this hypothesis for Golgi and plasma membrane proteins. Using the Golgi SNARE protein Sft1 and the plasma membrane SNARE protein Sso1 from Saccharomyces cerevisiae as model proteins, we modified the length of their TMDs and the volume of their exoplasmic hemi-TMD, and determined their subcellular localization both in yeast and mammalian cells. We found that short TMDs with high-volume exoplasmic hemi-TMDs confer Golgi membrane residence, whereas TMDs with low-volume exoplasmic hemi-TMDs, either short or long, confer plasma membrane residence to these proteins. Results indicate that the shape of the exoplasmic hemi-TMD, in addition to the length of the entire TMD, determine retention in the Golgi or exit to the plasma membrane of Type II membrane proteins.
Cystic Fibrosis Transmembrane Conductance Regulator (CFTR): CLOSED AND OPEN STATE CHANNEL MODELS.
Corradi, Valentina; Vergani, Paola; Tieleman, D Peter
2015-09-18
The cystic fibrosis transmembrane conductance regulator (CFTR) is a member of the ATP-binding cassette (ABC) transporter superfamily. CFTR controls the flow of anions through the apical membrane of epithelia. Dysfunctional CFTR causes the common lethal genetic disease cystic fibrosis. Transitions between open and closed states of CFTR are regulated by ATP binding and hydrolysis on the cytosolic nucleotide binding domains, which are coupled with the transmembrane (TM) domains forming the pathway for anion permeation. Lack of structural data hampers a global understanding of CFTR and thus the development of "rational" approaches directly targeting defective CFTR. In this work, we explored possible conformational states of the CFTR gating cycle by means of homology modeling. As templates, we used structures of homologous ABC transporters, namely TM(287-288), ABC-B10, McjD, and Sav1866. In the light of published experimental results, structural analysis of the transmembrane cavity suggests that the TM(287-288)-based CFTR model could correspond to a commonly occupied closed state, whereas the McjD-based model could represent an open state. The models capture the important role played by Phe-337 as a filter/gating residue and provide structural information on the conformational transition from closed to open channel.
Romano, Fabian B; Rossi, Kyle C; Savva, Christos G; Holzenburg, Andreas; Clerico, Eugenia M; Heuck, Alejandro P
2011-08-23
Translocation of bacterial toxins or effectors into host cells using the type III secretion (T3S) system is a conserved mechanism shared by many Gram-negative pathogens. Pseudomonas aeruginosa injects different proteins across the plasma membrane of target cells, altering the normal metabolism of the host. Protein translocation presumably occurs through a proteinaceous transmembrane pore formed by two T3S secreted protein translocators, PopB and PopD. Unfolded translocators are secreted through the T3S needle prior to insertion into the target membrane. Purified PopB and PopD form pores in model membranes. However, their tendency to form heterogeneous aggregates in solution had hampered the analysis of how these proteins undergo the transition from a denatured state to a membrane-inserted state. Translocators were purified as stable complexes with the cognate chaperone PcrH and isolated from the chaperone using 6 M urea. We report here the assembly of stable transmembrane pores by dilution of urea-denatured translocators in the presence of membranes. PopB and PopD spontaneously bound liposomes containing anionic phospholipids and cholesterol in a pH-dependent manner as observed by two independent assays, time-resolved Förster resonance energy transfer and sucrose-step gradient ultracentrifugation. Using Bodipy-labeled proteins, we found that PopB interacts with PopD on the membrane surface as determined by excitation energy migration and fluorescence quenching. Stable transmembrane pores are more efficiently assembled at pH <5.0, suggesting that acidic residues might be involved in the initial membrane binding and/or insertion. Altogether, the experimental setup described here represents an efficient method for the reconstitution and analysis of membrane-inserted translocators.
Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach
Indian Academy of Sciences (India)
S Ramakrishna; Siladitya Padhi; U Deva Priyakumar
2015-12-01
3a is an accessory protein from SARS coronavirus that is known to play a significant role in the proliferation of the virus by forming tetrameric ion channels. Although the monomeric units are known to consist of three transmembrane (TM) domains, there are no solved structures available for the complete monomer. The present study proposes a structural model for the transmembrane region of the monomer by employing our previously tested approach, which predicts potential orientations of TM -helices by minimizing the unfavorable contact surfaces between the different TM domains. The best model structure comprising all three -helices has been subjected to MD simulations to examine its quality. The TM bundle was found to form a compact and stable structure with significant intermolecular interactions. The structural features of the proposed model of 3a account for observations from previous experimental investigations on the activity of the protein. Further analysis indicates that residues from the TM2 and TM3 domains are likely to line the pore of the ion channel, which is in good agreement with a recent experimental study. In the absence of an experimental structure for the protein, the proposed structure can serve as a useful model for inferring structure-function relationships about the protein.
Functional and Modeling Studies of the Transmembrane Region of the TRPM8 Channel.
Bidaux, Gabriel; Sgobba, Miriam; Lemonnier, Loic; Borowiec, Anne-Sophie; Noyer, Lucile; Jovanovic, Srdan; Zholos, Alexander V; Haider, Shozeb
2015-11-03
Members of the transient receptor potential (TRP) ion channel family act as polymodal cellular sensors, which aid in regulating Ca(2+) homeostasis. Within the TRP family, TRPM8 is the cold receptor that forms a nonselective homotetrameric cation channel. In the absence of TRPM8 crystal structure, little is known about the relationship between structure and function. Inferences of TRPM8 structure have come from mutagenesis experiments coupled to electrophysiology, mainly regarding the fourth transmembrane helix (S4), which constitutes a moderate voltage-sensing domain, and about cold sensor and phosphatidylinositol 4,5-bisphosphate binding sites, which are both located in the C-terminus of TRPM8. In this study, we use a combination of molecular modeling and experimental techniques to examine the structure of the TRPM8 transmembrane and pore helix region including the conducting conformation of the selectivity filter. The model is consistent with a large amount of functional data and was further tested by mutagenesis. We present structural insight into the role of residues involved in intra- and intersubunit interactions and their link with the channel activity, sensitivity to icilin, menthol and cold, and impact on channel oligomerization.
A model of a transmembrane drug-efflux pump from Gram-negative bacteria.
Fernandez-Recio, Juan; Walas, Fabien; Federici, Luca; Venkatesh Pratap, J; Bavro, Vassiliy N; Miguel, Ricardo Nunez; Mizuguchi, Kenji; Luisi, Ben
2004-12-03
In Gram-negative bacteria, drug resistance is due in part to the activity of transmembrane efflux-pumps, which are composed of three types of proteins. A representative pump from Escherichia coli is an assembly of the trimeric outer-membrane protein TolC, which is an allosteric channel, the trimeric inner-membrane proton-antiporter AcrB, and the periplasmic protein, AcrA. The pump displaces drugs vectorially from the bacterium using proton electrochemical force. Crystal structures are available for TolC and AcrB from E. coli, and for the AcrA homologue MexA from Pseudomonas aeruginosa. Based on homology modelling and molecular docking, we show how AcrA, AcrB and TolC might assemble to form a tripartite pump, and how allostery may occur during transport.
Role of the import motor in insertion of transmembrane segments by the mitochondrial TIM23 complex.
Popov-Čeleketić, Dušan; Waegemann, Karin; Mapa, Koyeli; Neupert, Walter; Mokranjac, Dejana
2011-06-01
The TIM23 complex mediates translocation of proteins across, and their lateral insertion into, the mitochondrial inner membrane. Translocation of proteins requires both the membrane-embedded core of the complex and its ATP-dependent import motor. Insertion of some proteins, however, occurs in the absence of ATP, questioning the need for the import motor during lateral insertion. We show here that the import motor associates with laterally inserted proteins even when its ATPase activity is not required. Furthermore, our results suggest a role for the import motor in lateral insertion. Thus, the import motor is involved in ATP-dependent translocation and ATP-independent lateral insertion.
Mohammadiarani, Hossein; Vashisth, Harish
2016-01-01
The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane-solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane-solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor.
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Christine Dorothee Schmeitz
2013-09-01
Full Text Available Fate decision processes of T lymphocytes are crucial for health and disease. Whether a T lymphocyte is activated, divides, gets anergic or initiates apoptosis depends on extracellular triggers and intracellular signalling. Free cytosolic calcium dynamics plays an important role in this context. The relative contributions of store-derived calcium entry and calcium entry from extracellular space to T lymphocyte activation are still a matter of debate. Here we develop a quantitative mathematical model of T lymphocyte calcium dynamics in order to establish a tool which allows to disentangle cause-effect relationships between ion fluxes and observed calcium time courses. The model is based on single transmembrane protein characteristics which have been determined in independent experiments. This reduces the number of unknown parameters in the model to a minimum and ensures the predictive power of the model. Simulation results are subsequently used for an analysis of whole cell calcium dynamics measured under various experimental conditions. The model accounts for a variety of these conditions, which supports the suitability of the modelling approach. The simulation results suggest a model in which calcium dynamics dominantly relies on the opening of channels in calcium stores while calcium entry through calcium-release activated channels (CRAC is more associated with the maintenance of the T lymphocyte calcium levels and prevents the cell from calcium depletion. Our findings indicate that CRAC guarantees a long-term stable calcium level which is required for cell survival and sustained calcium enhancement.
Transmembrane Signaling Proteoglycans
DEFF Research Database (Denmark)
Couchman, John R
2010-01-01
Virtually all metazoan cells contain at least one and usually several types of transmembrane proteoglycans. These are varied in protein structure and type of polysaccharide, but the total number of vertebrate genes encoding transmembrane proteoglycan core proteins is less than 10. Some core...... proteins, including those of the syndecans, always possess covalently coupled glycosaminoglycans; others do not. Syndecan has a long evolutionary history, as it is present in invertebrates, but many other transmembrane proteoglycans are vertebrate inventions. The variety of proteins......, and linkage to PDZ protein networks. Many transmembrane proteoglycans associate on the cell surface with metzincin proteases and can be shed by them. Work with model systems in vivo and in vitro reveal roles in growth, adhesion, migration, and metabolism. Furthermore, a wide range of phenotypes for the core...
Multiscale modeling and computation of nano-electronic transistors and transmembrane proton channels
Chen, Duan
The miniaturization of nano-scale electronic transistors, such as metal oxide semiconductor field effect transistors (MOSFETs), has given rise to a pressing demand in the new theoretical understanding and practical tactic for dealing with quantum mechanical effects in integrated circuits. In biology, proton dynamics and transport across membrane proteins are of paramount importance to the normal function of living cells. Similar physical characteristics are behind the two subjects, and model simulations share common mathematical interests/challenges. In this thesis work, multiscale and multiphysical models are proposed to study the mechanisms of nanotransistors and proton transport in transmembrane at the atomic level. For nano-electronic transistors, we introduce a unified two-scale energy functional to describe the electrons and the continuum electrostatic potential. This framework enables us to put microscopic and macroscopic descriptions on an equal footing at nano-scale. Additionally, this model includes layered structures and random doping effect of nano-transistors. For transmembrane proton channels, we describe proton dynamics quantum mechanically via a density functional approach while implicitly treat numerous solvent molecules as a dielectric continuum. The densities of all other ions in the solvent are assumed to obey the Boltzmann distribution. The impact of protein molecular structure and its charge polarization on the proton transport is considered in atomic details. We formulate a total free energy functional to include kinetic and potential energies of protons, as well as electrostatic energy of all other ions on an equal footing. For both nano-transistors and proton channels systems, the variational principle is employed to derive nonlinear governing equations. The Poisson-Kohn-Sham equations are derived for nano-transistors while the generalized Poisson-Boltzmann equation and Kohn-Sham equation are obtained for proton channels. Related numerical
DEFF Research Database (Denmark)
Elling, Christian E; Frimurer, Thomas M; Gerlach, Lars-Ole;
2006-01-01
Much evidence indicates that, during activation of seven-transmembrane (7TM) receptors, the intracellular segments of the transmembrane helices (TMs) move apart with large amplitude, rigid body movements of especially TM-VI and TM-VII. In this study, AspIII:08 (Asp113), the anchor point for monoa...... that the pivots for these vertical seesaw movements are the highly conserved proline bends of the involved helices....
Directory of Open Access Journals (Sweden)
Luka eDrinovec
2012-08-01
Full Text Available The idea that seven transmembrane receptors (7TMRs; also designated G-protein coupled receptors (GPCRs might form dimers or higher order oligomeric complexes was formulated more than 20 years ago and has been intensively studied since then. In the last decade, bioluminescence resonance energy transfer (BRET has been one of the most frequently used biophysical methods for studying 7TMRs oligomerization. This technique enables monitoring physical interactions between protein partners in living cells fused to donor and acceptor moieties. It relies on non-radiative transfer of energy between donor and acceptor, depending on their intermolecular distance (1–10 nm and relative orientation. Results derived from BRET-based techniques are very persuasive; however, they need appropriate controls and critical interpretation. To overcome concerns about the specificity of BRET-derived results, a set of experiments has been proposed, including negative control with a non-interacting receptor or protein, BRET dilution, saturation and competition assays. This article presents the theoretical background behind BRET assays, then outlines mathematical models for quantitative interpretation of BRET saturation and competition assay results, gives examples of their utilization and discusses the possibilities of quantitative analysis of data generated with other RET-based techniques.
Zheng, Yu; Gao, Yang; Chen, Ruijuan; Wang, Huiquan; Dong, Lei; Dou, Junrong
2016-10-01
Time-varying electromagnetic fields (EMF) can induce some physiological effects in neuronal tissues, which have been explored in many applications such as transcranial magnetic stimulation. Although transmembrane potentials and induced currents have already been the subjects of many theoretical studies, most previous works about this topic are mainly completed by utilizing Maxwell's equations, often by solving a Laplace equation. In previous studies, cells were often considered to be three-compartment models with different electroconductivities in different regions (three compartments are often intracellular regions, membrane, and extracellular regions). However, models like that did not take dynamic ion channels into consideration. Therefore, one cannot obtain concrete ionic current changes such as potassium current change or sodium current change by these models. The aim of the present work is to present a new and more detailed model for calculating transmembrane potentials and ionic currents induced by time-varying EMF. Equations used in the present paper originate from Nernst-Plank equations, which are ionic current-related equations. The main work is to calculate ionic current changes induced by EMF exposure, and then transmembrane potential changes are calculated with Hodgkin-Huxley model. Bioelectromagnetics. 37:481-492, 2016. © 2016 Wiley Periodicals, Inc.
Yeast as a model system for mammalian seven-transmembrane segment receptors
Energy Technology Data Exchange (ETDEWEB)
Jeansonne, N.E. [East Carolina Univ. Medical School, Greenville, NC (United States)
1994-05-01
Investigators have used the budding yeast Saccharomyces cerevisiae as a model system in which to study the {beta}-adrenergic receptor, the T-cell receptor pathway, initiation of mammalian DNA replication, initiation of mammalian transcription, secretion, the CDC2 kinase system, cell cycle control, and aging, as well as the function of oncogenes. This list continues to growth with the discovery of an immunoglobulin heavy-chain binding homologue in yeast, an Rb binding protein homologue, and a possible yeast arrestin. Yeast is relatively easy to maintain, to grow, and to genetically manipulate. A single gene can be overexpressed, selectively mutated or deleted from its chromosomal location. In this way, the in vivo function of a gene can be studied. It has become reasonable to consider yeast as a model system for studying the seven transmembrane segments (7-TMS) receptor family. Currently, subtypes of the {beta}-adrenergic receptor are being studied in yeast. The receptor and its G{sub {alpha}}-G-protein, trigger the mating pheromone receptor pathway. This provides a powerful assay for determining receptor function. Studies expressing the muscarinic cholinergic receptor in yeast are underway. The yeast pheromone receptor belongs to this receptor family, sharing sequences and secondary structure homology. An effective strategy has been to identify a yeast pathway or process which is homologous to a mammalian system. The pathway is delineated in yeast, identifying other genetic components. Then yeast genes are used to screen for human homologues of these components. The putative human homologues are then expressed in yeast and in mammalian cells to determine function. When this type of {open_quotes}mixing and matching{close_quotes} works, yeast genetics can be a powerful tool. 115 refs.
Magzoub, Mazin; Pramanik, Aladdin; Gräslund, Astrid
2005-11-15
Cell-penetrating peptides (CPPs) are able to mediate the efficient cellular uptake of a wide range of cargoes. Internalization of a number of CPPs requires uptake by endocytosis, initiated by binding to anionic cell surface heparan sulfate (HS), followed by escape from endosomes. To elucidate the endosomal escape mechanism, we have modeled the process for two CPPs: penetratin (pAntp) and the N-terminal signal peptide of the unprocessed bovine prion protein (bPrPp). Large unilamellar phospholipid vesicles (LUVs) were produced encapsulating either peptide, and an ionophore, nigericin, was used to create a transmembrane pH gradient (DeltapH(mem), inside acidic) similar to the one arising in endosomes in vivo. In the absence of DeltapH(mem), no pAntp escape from the LUVs is observed, while a fraction of bPrPp escapes. In the presence of DeltapH(mem), a significant amount of pAntp escapes and an even higher degree of bPrPp escape takes place. These results, together with the differences in kinetics of escape, indicate different escape mechanisms for the two peptides. A minimum threshold peptide concentration exists for the escape of both peptides. Coupling of the peptides to a cargo reduces the fraction escaping, while complexation with HS significantly hinders the escape. Fluorescence correlation spectroscopy results show that during the escape process the LUVs are intact. Taken together, these results suggest a model for endosomal escape of CPPs: DeltapH(mem)-mediated mechanism, following dissociation from HS of the peptides, above a minimum threshold peptide concentration, in a process that does not involve lysis of the vesicles.
Baticados, Waren N; Inoue, Noboru; Sugimoto, Chihiro; Nagasawa, Hideyuki; Baticados, Abigail M
2011-01-01
The partial nucleotide sequence of putative Trypanosoma brucei rhodesiense oligosaccharyl transferase gene was previously reported. Here, we describe the determination of its full-length nucleotide sequence by Inverse PCR (IPCR), subsequent biological sequence analysis and transmembrane topology modelling. The full-length DNA sequence has an Open Reading Frame (ORF) of 2406 bp and encodes a polypeptide of 801 amino acid residues. Protein and DNA sequence analyses revealed that homologues within the genome of other kinetoplastid and various origins exist. Protein topology analysis predicted that Trypanosoma brucei rhodesiense putative oligosaccharyl transferase clone II (TbOST II) is a transmembrane protein with transmembrane helices in probably an N(cytosol)-C(cytosol) orientation. Data from the GenBank database assembly and sequence analyses in general clearly state that TbOST II is the STT3 subunit of OST in T.b. rhodesiense that necessitates further characterisation and functional studies with RNAi. TbOST II sequence had been deposited in the GenBank (accession number GU245937).
Directory of Open Access Journals (Sweden)
Oleg Svatos
2013-01-01
Full Text Available In this paper we analyze complexity of time limits we can find especially in regulated processes of public administration. First we review the most popular process modeling languages. There is defined an example scenario based on the current Czech legislature which is then captured in discussed process modeling languages. Analysis shows that the contemporary process modeling languages support capturing of the time limit only partially. This causes troubles to analysts and unnecessary complexity of the models. Upon unsatisfying results of the contemporary process modeling languages we analyze the complexity of the time limits in greater detail and outline lifecycles of a time limit using the multiple dynamic generalizations pattern. As an alternative to the popular process modeling languages there is presented PSD process modeling language, which supports the defined lifecycles of a time limit natively and therefore allows keeping the models simple and easy to understand.
Energy Technology Data Exchange (ETDEWEB)
Brown, T.W.
2010-11-15
The same complex matrix model calculates both tachyon scattering for the c=1 non-critical string at the self-dual radius and certain correlation functions of half-BPS operators in N=4 super- Yang-Mills. It is dual to another complex matrix model where the couplings of the first model are encoded in the Kontsevich-like variables of the second. The duality between the theories is mirrored by the duality of their Feynman diagrams. Analogously to the Hermitian Kontsevich- Penner model, the correlation functions of the second model can be written as sums over discrete points in subspaces of the moduli space of punctured Riemann surfaces. (orig.)
Molecular modeling of transmembrane delivery of paclitaxel by shock waves with nanobubbles
Lu, Xue-mei; Yuan, Bing; Zhang, Xian-ren; Yang, Kai; Ma, Yu-qiang
2017-01-01
The development of advanced delivery strategies for anticancer drugs that can permeate through cellular membranes is urgently required for biomedical applications. In this work, we investigated the dynamic transmembrane behavior of paclitaxel (PTX), a powerful anticancer drug, under the combined impact of shock waves and nanobubbles, by using atomistic molecular dynamics simulations. Our simulations show that the PTX molecule experiences complicated motion modes during the action process with the membrane, as a consequence of its interplay with the lipid bilayer and water, under the joint effect of the shock wave and nanobubble. Moreover, it was found that the transmembrane movement of PTX is closely associated with the conformation changes of PTX, as well as the structural changes of the membrane (e.g., compression and poration in membrane). The nanobubble collapse induced by the shock wave, the proper PTX location with respect to the nanobubble, and a suitable nanobubble size and shock impulse are all necessary for the delivery of PTX into the cell. This work provides a molecular understanding of the interaction mechanism between drug molecules and cell membranes under the influence of shock waves and nanobubbles, and paves the way for exploiting targeted drug delivery systems that combine nanobubbles and ultrasound.
Debating complexity in modeling
Hunt, Randall J.; Zheng, Chunmiao
1999-01-01
Complexity in modeling would seem to be an issue of universal importance throughout the geosciences, perhaps throughout all science, if the debate last year among groundwater modelers is any indication. During the discussion the following questions and observations made up the heart of the debate.
Moon, Changsuk; Zhang, Weiqiang; Ren, Aixia; Arora, Kavisha; Sinha, Chandrima; Yarlagadda, Sunitha; Woodrooffe, Koryse; Schuetz, John D; Valasani, Koteswara Rao; de Jonge, Hugo R; Shanmukhappa, Shiva Kumar; Shata, Mohamed Tarek M; Buddington, Randal K; Parthasarathi, Kaushik; Naren, Anjaparavanda P
2015-05-01
Diarrhea is one of the most common adverse side effects observed in ∼7% of individuals consuming Food and Drug Administration (FDA)-approved drugs. The mechanism of how these drugs alter fluid secretion in the gut and induce diarrhea is not clearly understood. Several drugs are either substrates or inhibitors of multidrug resistance protein 4 (MRP4), such as the anti-colon cancer drug irinotecan and an anti-retroviral used to treat HIV infection, 3'-azido-3'-deoxythymidine (AZT). These drugs activate cystic fibrosis transmembrane conductance regulator (CFTR)-mediated fluid secretion by inhibiting MRP4-mediated cAMP efflux. Binding of drugs to MRP4 augments the formation of MRP4-CFTR-containing macromolecular complexes that is mediated via scaffolding protein PDZK1. Importantly, HIV patients on AZT treatment demonstrate augmented MRP4-CFTR complex formation in the colon, which defines a novel paradigm of drug-induced diarrhea.
Boccara, Nino
2010-01-01
Modeling Complex Systems, 2nd Edition, explores the process of modeling complex systems, providing examples from such diverse fields as ecology, epidemiology, sociology, seismology, and economics. It illustrates how models of complex systems are built and provides indispensable mathematical tools for studying their dynamics. This vital introductory text is useful for advanced undergraduate students in various scientific disciplines, and serves as an important reference book for graduate students and young researchers. This enhanced second edition includes: . -recent research results and bibliographic references -extra footnotes which provide biographical information on cited scientists who have made significant contributions to the field -new and improved worked-out examples to aid a student’s comprehension of the content -exercises to challenge the reader and complement the material Nino Boccara is also the author of Essentials of Mathematica: With Applications to Mathematics and Physics (Springer, 2007).
Modeling complexes of modeled proteins.
Anishchenko, Ivan; Kundrotas, Petras J; Vakser, Ilya A
2017-03-01
Structural characterization of proteins is essential for understanding life processes at the molecular level. However, only a fraction of known proteins have experimentally determined structures. This fraction is even smaller for protein-protein complexes. Thus, structural modeling of protein-protein interactions (docking) primarily has to rely on modeled structures of the individual proteins, which typically are less accurate than the experimentally determined ones. Such "double" modeling is the Grand Challenge of structural reconstruction of the interactome. Yet it remains so far largely untested in a systematic way. We present a comprehensive validation of template-based and free docking on a set of 165 complexes, where each protein model has six levels of structural accuracy, from 1 to 6 Å C(α) RMSD. Many template-based docking predictions fall into acceptable quality category, according to the CAPRI criteria, even for highly inaccurate proteins (5-6 Å RMSD), although the number of such models (and, consequently, the docking success rate) drops significantly for models with RMSD > 4 Å. The results show that the existing docking methodologies can be successfully applied to protein models with a broad range of structural accuracy, and the template-based docking is much less sensitive to inaccuracies of protein models than the free docking. Proteins 2017; 85:470-478. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Zhao, Gang; Takamatsu, Hiroshi; He, Xiaoming
2014-04-14
A new model was developed to predict transmembrane water transport and diffusion-limited ice formation in cells during freezing without the ideal-solution assumption that has been used in previous models. The model was applied to predict cell dehydration and intracellular ice formation (IIF) during cryopreservation of mouse oocytes and bovine carotid artery endothelial cells in aqueous sodium chloride (NaCl) solution with glycerol as the cryoprotectant or cryoprotective agent. A comparison of the predictions between the present model and the previously reported models indicated that the ideal-solution assumption results in under-prediction of the amount of intracellular ice at slow cooling rates (<50 K/min). In addition, the lower critical cooling rates for IIF that is lethal to cells predicted by the present model were much lower than those estimated with the ideal-solution assumption. This study represents the first investigation on how accounting for solution nonideality in modeling water transport across the cell membrane could affect the prediction of diffusion-limited ice formation in biological cells during freezing. Future studies are warranted to look at other assumptions alongside nonideality to further develop the model as a useful tool for optimizing the protocol of cell cryopreservation for practical applications.
Tilleman, Lesley; Germani, Francesca; De Henau, Sasha; Helbo, Signe; Desmet, Filip; Berghmans, Herald; Van Doorslaer, Sabine; Hoogewijs, David; Schoofs, Liliane; Braeckman, Bart P; Moens, Luc; Fago, Angela; Dewilde, Sylvia
2015-04-17
We report the structural and biochemical characterization of GLB-33, a putative neuropeptide receptor that is exclusively expressed in the nervous system of the nematode Caenorhabditis elegans. This unique chimeric protein is composed of a 7-transmembrane domain (7TM), GLB-33 7TM, typical of a G-protein-coupled receptor, and of a globin domain (GD), GLB-33 GD. Comprehensive sequence similarity searches in the genome of the parasitic nematode, Ascaris suum, revealed a chimeric protein that is similar to a Phe-Met-Arg-Phe-amide neuropeptide receptor. The three-dimensional structures of the separate domains of both species and of the full-length proteins were modeled. The 7TM domains of both proteins appeared very similar, but the globin domain of the A. suum receptor surprisingly seemed to lack several helices, suggesting a novel truncated globin fold. The globin domain of C. elegans GLB-33, however, was very similar to a genuine myoglobin-type molecule. Spectroscopic analysis of the recombinant GLB-33 GD showed that the heme is pentacoordinate when ferrous and in the hydroxide-ligated form when ferric, even at neutral pH. Flash-photolysis experiments showed overall fast biphasic CO rebinding kinetics. In its ferrous deoxy form, GLB-33 GD is capable of reversibly binding O2 with a very high affinity and of reducing nitrite to nitric oxide faster than other globins. Collectively, these properties suggest that the globin domain of GLB-33 may serve as a highly sensitive oxygen sensor and/or as a nitrite reductase. Both properties are potentially able to modulate the neuropeptide sensitivity of the neuronal transmembrane receptor. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
Sporadic meteoroid complex: Modeling
Andreev, V.
2014-07-01
The distribution of the sporadic meteoroids flux density over the celestial sphere is the common form of representation of the meteoroids distribution in the vicinity of the Earth's orbit. The determination of the flux density of sporadic meteor bodies is Q(V,e,f) = Q_0 P_e(V) P(e,f) where V is the meteoroid velocity, e,f are the radiant coordinates, Q_0 is the meteoroid flux over whole celestial sphere, P_e(V) is the conditional velocity distributions and P(e,f) is the radiant distribution over the celestial sphere. The sporadic meteoroid complex model is analytical and based on heliocentric velocities and radiant distributions. The multi-mode character of the heliocentric velocity and radiant distributions follows from the analysis of meteor observational data. This fact points to a complicated structure of the sporadic meteoroid complex. It is the consequence of the plurality of the parent bodies and the origin mechanisms of the meteoroids. The meteoroid complex was divided into four groups for that reason and with a goal of more accurate modelling of velocities and radiant distributions. As the classifying parameter to determine the meteoroid membership in any group, we adopt the Tisserand invariant relative to Jupiter T_J = 1/a + 2 A_J^{-3/2} √{a (1 - e^2)} cos i and the meteoroid orbit inclination i. Two meteoroid groups relate to long-period and short-period comets. One meteoroid group is related to asteroids. The relationship to the last, fourth group is a problematic one. Then, we construct models of radiant and velocity distributions for each group. The analytical model for the whole sporadic meteoroid complex is the sum of the ones for each group.
Predictive Surface Complexation Modeling
Energy Technology Data Exchange (ETDEWEB)
Sverjensky, Dimitri A. [Johns Hopkins Univ., Baltimore, MD (United States). Dept. of Earth and Planetary Sciences
2016-11-29
Surface complexation plays an important role in the equilibria and kinetics of processes controlling the compositions of soilwaters and groundwaters, the fate of contaminants in groundwaters, and the subsurface storage of CO_{2} and nuclear waste. Over the last several decades, many dozens of individual experimental studies have addressed aspects of surface complexation that have contributed to an increased understanding of its role in natural systems. However, there has been no previous attempt to develop a model of surface complexation that can be used to link all the experimental studies in order to place them on a predictive basis. Overall, my research has successfully integrated the results of the work of many experimentalists published over several decades. For the first time in studies of the geochemistry of the mineral-water interface, a practical predictive capability for modeling has become available. The predictive correlations developed in my research now enable extrapolations of experimental studies to provide estimates of surface chemistry for systems not yet studied experimentally and for natural and anthropogenically perturbed systems.
Directory of Open Access Journals (Sweden)
Debra J. Knisley
2013-01-01
Full Text Available Cystic fibrosis is one of the most common inherited diseases and is caused by a mutation in a membrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR. This protein serves as a chloride channel and regulates the viscosity of mucus lining the ducts of a number of organs. Although much has been learned about the consequences of mutations on the energy landscape and the resulting disrupted folding pathway of CFTR, a level of understanding needed to correct the misfolding has not been achieved. The most common mutations of CFTR are located in one of two nucleotide binding domains, namely, the nucleotide binding domain 1 (NBD1. We model NBD1 using a nested graph model. The vertices in the lowest layer each represent an atom in the structure of an amino acid residue, while the vertices in the mid layer each represent the residue. The vertices in the top layer each represent a subdomain of the nucleotide binding domain. We use this model to quantify the effects of a single point mutation on the protein domain. We compare the wildtype structure with eight of the most common mutations. The graph-theoretic model provides insight into how a single point mutation can have such profound structural consequences.
Polystochastic Models for Complexity
Iordache, Octavian
2010-01-01
This book is devoted to complexity understanding and management, considered as the main source of efficiency and prosperity for the next decades. Divided into six chapters, the book begins with a presentation of basic concepts as complexity, emergence and closure. The second chapter looks to methods and introduces polystochastic models, the wave equation, possibilities and entropy. The third chapter focusing on physical and chemical systems analyzes flow-sheet synthesis, cyclic operations of separation, drug delivery systems and entropy production. Biomimetic systems represent the main objective of the fourth chapter. Case studies refer to bio-inspired calculation methods, to the role of artificial genetic codes, neural networks and neural codes for evolutionary calculus and for evolvable circuits as biomimetic devices. The fifth chapter, taking its inspiration from systems sciences and cognitive sciences looks to engineering design, case base reasoning methods, failure analysis, and multi-agent manufacturing...
Modelling Complexity in Musical Rhythm
Liou, Cheng-Yuan; Wu, Tai-Hei; Lee, Chia-Ying
2007-01-01
This paper constructs a tree structure for the music rhythm using the L-system. It models the structure as an automata and derives its complexity. It also solves the complexity for the L-system. This complexity can resolve the similarity between trees. This complexity serves as a measure of psychological complexity for rhythms. It resolves the music complexity of various compositions including the Mozart effect K488. Keyword: music perception, psychological complexity, rhythm, L-system, autom...
Directory of Open Access Journals (Sweden)
Angel G Valdivieso
Full Text Available Cystic fibrosis (CF is a frequent and lethal autosomal recessive disease. It results from different possible mutations in the CFTR gene, which encodes the CFTR chloride channel. We have previously studied the differential expression of genes in CF and CF corrected cell lines, and found a reduced expression of MTND4 in CF cells. MTND4 is a mitochondrial gene encoding the MTND4 subunit of the mitochondrial Complex I (mCx-I. Since this subunit is essential for the assembly and activity of mCx-I, we have now studied whether the activity of this complex was also affected in CF cells. By using Blue Native-PAGE, the in-gel activity (IGA of the mCx-I was found reduced in CFDE and IB3-1 cells (CF cell lines compared with CFDE/6RepCFTR and S9 cells, respectively (CFDE and IB3-1 cells ectopically expressing wild-type CFTR. Moreover, colon carcinoma T84 and Caco-2 cells, which express wt-CFTR, either treated with CFTR inhibitors (glibenclamide, CFTR(inh-172 or GlyH101 or transfected with a CFTR-specific shRNAi, showed a significant reduction on the IGA of mCx-I. The reduction of the mCx-I activity caused by CFTR inhibition under physiological or pathological conditions may have a profound impact on mitochondrial functions of CF and non-CF cells.
Gimsa, J; Wachner, D
1998-08-01
Dielectric properties of suspended cells are explored by analysis of the frequency-dependent response to electric fields. Impedance (IMP) registers the electric response, and kinetic phenomena like orientation, translation, deformation, or rotation can also be analyzed. All responses can generally be described by a unified theory. This is demonstrated by an RC model for the structural polarizations of biological cells, allowing intuitive comparison of the IMP, dielectrophoresis (DP), and electrorotation (ER) methods. For derivations, cells of prismatic geometry embedded in elementary cubes formed by the external solution were assumed. All geometrical constituents of the model were described by parallel circuits of a capacitor and a resistor. The IMP of the suspension is given by a meshwork of elementary cubes. Each elementary cube was modeled by two branches describing the current flow through and around the cell. To model DP and ER, the external branch was subdivided to obtain a reference potential. Real and imaginary parts of the potential difference of the cell surface and the reference reflect the frequency behavior of DP and ER. The scheme resembles an unbalanced Wheatstone bridge, in which IMP measures the current-voltage behavior of the feed signal and DP and ER are the measuring signal. Model predictions were consistent with IMP, DP, and ER experiments on human red cells, as well as with the frequency dependence of field-induced hemolysis. The influential radius concept is proposed, which allows easy derivation of simplified equations for the characteristic properties of a spherical single-shell model on the basis of the RC model.
Complexity regularized hydrological model selection
Pande, S.; Arkesteijn, L.; Bastidas, L.A.
2014-01-01
This paper uses a recently proposed measure of hydrological model complexity in a model selection exercise. It demonstrates that a robust hydrological model is selected by penalizing model complexity while maximizing a model performance measure. This especially holds when limited data is available.
Complexity regularized hydrological model selection
Pande, S.; Arkesteijn, L.; Bastidas, L.A.
2014-01-01
This paper uses a recently proposed measure of hydrological model complexity in a model selection exercise. It demonstrates that a robust hydrological model is selected by penalizing model complexity while maximizing a model performance measure. This especially holds when limited data is available.
Directory of Open Access Journals (Sweden)
Ken-ichi Sato
2014-12-01
Full Text Available Fertilization is a cell biological phenomenon of crucial importance for the birth of new life in a variety of multicellular and sexual reproduction species such as algae, animal and plants. Fertilization involves a sequence of events, in which the female gamete “egg” and the male gamete “spermatozoon (sperm” develop, acquire their functions, meet and fuse with each other, to initiate embryonic and zygotic development. Here, it will be briefly reviewed how oocyte cytoplasmic components are orchestrated to undergo hormone-induced oocyte maturation and sperm-induced activation of development. I then review how sperm-egg membrane interaction/fusion and activation of development in the fertilized egg are accomplished and regulated through egg coat- or egg plasma membrane-associated components, highlighting recent findings and future directions in the studies using Xenopus laevis as a model experimental animal.
Modeling the endosomal escape of cell-penetrating peptides using a transmembrane pH gradient.
Madani, Fatemeh; Abdo, Rania; Lindberg, Staffan; Hirose, Hisaaki; Futaki, Shiroh; Langel, Ulo; Gräslund, Astrid
2013-04-01
Cell-penetrating peptides (CPPs) can internalize into cells with covalently or non-covalently bound biologically active cargo molecules, which by themselves are not able to pass the cell membrane. Direct penetration and endocytosis are two main pathways suggested for the cellular uptake of CPPs. Cargo molecules which have entered the cell via an endocytotic pathway must be released from the endosome before degradation by enzymatic processes and endosomal acidification. Endosomal entrapment seems to be a major limitation in delivery of these molecules into the cytoplasm. Bacteriorhodopsin (BR) asymmetrically introduced into large unilamellar vesicles (LUVs) was used to induce a pH gradient across the lipid bilayer. By measuring pH outside the LUVs, we observed light-induced proton pumping mediated by BR from the outside to the inside of the LUVs, creating an acidic pH inside the LUVs, similar to the late endosomes in vivo. Here we studied the background mechanism(s) of endosomal escape. 20% negatively charged LUVs were used as model endosomes with incorporated BR into the membrane and fluorescein-labeled CPPs entrapped inside the LUVs, together with a fluorescence quencher. The translocation of different CPPs in the presence of a pH gradient across the membrane was studied. The results show that the light-induced pH gradient induced by BR facilitates vesicle membrane translocation, particularly for the intermediately hydrophobic CPPs, and much less for hydrophilic CPPs. The presence of chloroquine inside the LUVs or addition of pyrenebutyrate outside the LUVs destabilizes the vesicle membrane, resulting in significant changes of the pH gradient across the membrane.
Directory of Open Access Journals (Sweden)
Liqun Zhang
Full Text Available Single-pass transmembrane (TM receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and -B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, -A3, -A4, -C1 and -D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 - trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The
Akdim, Mohamed Reda
2003-09-01
Nowadays plasmas are used for various applications such as the fabrication of silicon solar cells, integrated circuits, coatings and dental cleaning. In the case of a processing plasma, e.g. for the fabrication of amorphous silicon solar cells, a mixture of silane and hydrogen gas is injected in a reactor. These gases are decomposed by making a plasma. A plasma with a low degree of ionization (typically 10_5) is usually made in a reactor containing two electrodes driven by a radio-frequency (RF) power source in the megahertz range. Under the right circumstances the radicals, neutrals and ions can react further to produce nanometer sized dust particles. The particles can stick to the surface and thereby contribute to a higher deposition rate. Another possibility is that the nanometer sized particles coagulate and form larger micron sized particles. These particles obtain a high negative charge, due to their large radius and are usually trapped in a radiofrequency plasma. The electric field present in the discharge sheaths causes the entrapment. Such plasmas are called dusty or complex plasmas. In this thesis numerical models are presented which describe dusty plasmas in reactive and nonreactive plasmas. We started first with the development of a simple one-dimensional silane fluid model where a dusty radio-frequency silane/hydrogen discharge is simulated. In the model, discharge quantities like the fluxes, densities and electric field are calculated self-consistently. A radius and an initial density profile for the spherical dust particles are given and the charge and the density of the dust are calculated with an iterative method. During the transport of the dust, its charge is kept constant in time. The dust influences the electric field distribution through its charge and the density of the plasma through recombination of positive ions and electrons at its surface. In the model this process gives an extra production of silane radicals, since the growth of dust is
Appropriate complexity landscape modeling
Larsen, Laurel G.; Eppinga, Maarten B.|info:eu-repo/dai/nl/304834971; Passalacqua, Paola; Getz, Wayne M.; Rose, Kenneth A.; Liang, Man
2016-01-01
Advances in computing technology, new and ongoing restoration initiatives, concerns about climate change's effects, and the increasing interdisciplinarity of research have encouraged the development of landscape-scale mechanistic models of coupled ecological-geophysical systems. However, communicati
Amaral, Flávio A; Bastos, Leandro F S; Oliveira, Thiago H C; Dias, Ana C F; Oliveira, Vívian L S; Tavares, Lívia D; Costa, Vivian V; Galvão, Izabela; Soriani, Frederico M; Szymkowski, David E; Ryffel, Bernhard; Souza, Danielle G; Teixeira, Mauro M
2016-01-01
Gout manifests as recurrent episodes of acute joint inflammation and pain due to the deposition of monosodium urate (MSU) crystals within the affected tissue in a process dependent on NLRP3 inflammasome activation. The synthesis, activation, and release of IL-1β are crucial for MSU-induced inflammation. The current study evaluated the mechanism by which TNF-α contributed to MSU-induced inflammation. Male C57BL/6J or transgenic mice were used in this study and inflammation was induced by the injection of MSU crystals into the joint. TNF-α was markedly increased in the joint after the injection of MSU. There was inhibition in the infiltration of neutrophils, production of CXCL1 and IL-1β, and decreased hypernociception in mice deficient for TNF-α or its receptors. Pharmacological blockade of TNF-α with Etanercept or pentoxyfylline produced similar results. Mechanistically, TNF-α blockade resulted in lower amounts of IL-1β protein and pro-IL-1β mRNA transcripts in joints. Gene-modified mice that express only transmembrane TNF-α had an inflammatory response similar to that of WT mice and blockade of soluble TNF-α (XPro™1595) did not decrease MSU-induced inflammation. In conclusion, TNF-α drives expression of pro-IL-1β mRNA and IL-1β protein in experimental gout and that its transmembrane form is sufficient to trigger MSU-induced inflammation in mice.
Prediction models in complex terrain
DEFF Research Database (Denmark)
Marti, I.; Nielsen, Torben Skov; Madsen, Henrik
2001-01-01
The objective of the work is to investigatethe performance of HIRLAM in complex terrain when used as input to energy production forecasting models, and to develop a statistical model to adapt HIRLAM prediction to the wind farm. The features of the terrain, specially the topography, influence...
Pluralistic Modeling of Complex Systems
Helbing, Dirk
2010-01-01
The modeling of complex systems such as ecological or socio-economic systems can be very challenging. Although various modeling approaches exist, they are generally not compatible and mutually consistent, and empirical data often do not allow one to decide what model is the right one, the best one, or most appropriate one. Moreover, as the recent financial and economic crisis shows, relying on a single, idealized model can be very costly. This contribution tries to shed new light on problems that arise when complex systems are modeled. While the arguments can be transferred to many different systems, the related scientific challenges are illustrated for social, economic, and traffic systems. The contribution discusses issues that are sometimes overlooked and tries to overcome some frequent misunderstandings and controversies of the past. At the same time, it is highlighted how some long-standing scientific puzzles may be solved by considering non-linear models of heterogeneous agents with spatio-temporal inte...
Dutt, Meenakshi; Kuksenok, Olga; Nayhouse, Michael J; Little, Steven R; Balazs, Anna C
2011-06-28
Via dissipative particle dynamics (DPD), we simulate the self-assembly of end-functionalized, amphiphilic nanotubes and lipids in a hydrophilic solvent. Each nanotube encompasses a hydrophobic stalk and two hydrophilic ends, which are functionalized with end-tethered chains. With a relatively low number of the nanotubes in solution, the components self-assemble into stable lipid-nanotube vesicles. As the number of nanotubes is increased, the system exhibits a vesicle-to-bicelle transition, resulting in stable hybrid bicelle. Moreover, our results reveal that the nanotubes cluster into distinct tripod-like structures within the vesicles and aggregate into a ring-like assembly within the bicelles. For both the vesicles and bicelles, the nanotubes assume trans-membrane orientations, with the tethered hairs extending into the surrounding solution or the encapsulated fluid. Thus, the hairs provide a means of regulating the transport of species through the self-assembled structures. Our findings provide guidelines for creating nanotube clusters with distinctive morphologies that might be difficult to achieve through more conventional means. The results also yield design rules for creating synthetic cell-like objects or microreactors that can exhibit biomimetic functionality.
Computational models of complex systems
Dabbaghian, Vahid
2014-01-01
Computational and mathematical models provide us with the opportunities to investigate the complexities of real world problems. They allow us to apply our best analytical methods to define problems in a clearly mathematical manner and exhaustively test our solutions before committing expensive resources. This is made possible by assuming parameter(s) in a bounded environment, allowing for controllable experimentation, not always possible in live scenarios. For example, simulation of computational models allows the testing of theories in a manner that is both fundamentally deductive and experimental in nature. The main ingredients for such research ideas come from multiple disciplines and the importance of interdisciplinary research is well recognized by the scientific community. This book provides a window to the novel endeavours of the research communities to present their works by highlighting the value of computational modelling as a research tool when investigating complex systems. We hope that the reader...
Prediction models in complex terrain
DEFF Research Database (Denmark)
Marti, I.; Nielsen, Torben Skov; Madsen, Henrik
2001-01-01
are calculated using on-line measurements of power production as well as HIRLAM predictions as input thus taking advantage of the auto-correlation, which is present in the power production for shorter pediction horizons. Statistical models are used to discribe the relationship between observed energy production......The objective of the work is to investigatethe performance of HIRLAM in complex terrain when used as input to energy production forecasting models, and to develop a statistical model to adapt HIRLAM prediction to the wind farm. The features of the terrain, specially the topography, influence...... and HIRLAM predictions. The statistical models belong to the class of conditional parametric models. The models are estimated using local polynomial regression, but the estimation method is here extended to be adaptive in order to allow for slow changes in the system e.g. caused by the annual variations...
Complex Networks in Psychological Models
Wedemann, R. S.; Carvalho, L. S. A. V. D.; Donangelo, R.
We develop schematic, self-organizing, neural-network models to describe mechanisms associated with mental processes, by a neurocomputational substrate. These models are examples of real world complex networks with interesting general topological structures. Considering dopaminergic signal-to-noise neuronal modulation in the central nervous system, we propose neural network models to explain development of cortical map structure and dynamics of memory access, and unify different mental processes into a single neurocomputational substrate. Based on our neural network models, neurotic behavior may be understood as an associative memory process in the brain, and the linguistic, symbolic associative process involved in psychoanalytic working-through can be mapped onto a corresponding process of reconfiguration of the neural network. The models are illustrated through computer simulations, where we varied dopaminergic modulation and observed the self-organizing emergent patterns at the resulting semantic map, interpreting them as different manifestations of mental functioning, from psychotic through to normal and neurotic behavior, and creativity.
Nonparametric Bayesian Modeling of Complex Networks
DEFF Research Database (Denmark)
Schmidt, Mikkel Nørgaard; Mørup, Morten
2013-01-01
Modeling structure in complex networks using Bayesian nonparametrics makes it possible to specify flexible model structures and infer the adequate model complexity from the observed data. This article provides a gentle introduction to nonparametric Bayesian modeling of complex networks: Using...... for complex networks can be derived and point out relevant literature....
Complex fluids modeling and algorithms
Saramito, Pierre
2016-01-01
This book presents a comprehensive overview of the modeling of complex fluids, including many common substances, such as toothpaste, hair gel, mayonnaise, liquid foam, cement and blood, which cannot be described by Navier-Stokes equations. It also offers an up-to-date mathematical and numerical analysis of the corresponding equations, as well as several practical numerical algorithms and software solutions for the approximation of the solutions. It discusses industrial (molten plastics, forming process), geophysical (mud flows, volcanic lava, glaciers and snow avalanches), and biological (blood flows, tissues) modeling applications. This book is a valuable resource for undergraduate students and researchers in applied mathematics, mechanical engineering and physics.
Hybrid models for complex fluids
Tronci, Cesare
2010-01-01
This paper formulates a new approach to complex fluid dynamics, which accounts for microscopic statistical effects in the micromotion. While the ordinary fluid variables (mass density and momentum) undergo usual dynamics, the order parameter field is replaced by a statistical distribution on the order parameter space. This distribution depends also on the point in physical space and its dynamics retains the usual fluid transport features while containing the statistical information on the order parameter space. This approach is based on a hybrid moment closure for Yang-Mills Vlasov plasmas, which replaces the usual cold-plasma assumption. After presenting the basic properties of the hybrid closure, such as momentum map features, singular solutions and Casimir invariants, the effect of Yang-Mills fields is considered and a direct application to ferromagnetic fluids is presented. Hybrid models are also formulated for complex fluids with symmetry breaking. For the special case of liquid crystals, a hybrid formul...
The Origins of Transmembrane Ion Channels
Pohorille, Andrew; Wilson, Michael A.
2012-01-01
Even though membrane proteins that mediate transport of ions and small molecules across cell walls are among the largest and least understood biopolymers in contemporary cells, it is still possible to shed light on their origins and early evolution. The central observation is that transmembrane portions of most ion channels are simply bundles of -helices. By combining results of experimental and computer simulation studies on synthetic models and natural channels, mostly of non-genomic origin, we show that the emergence of -helical channels was protobiologically plausible, and did not require highly specific amino acid sequences. Despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. Specifically, we explain how the antiamoebin channels, which are made of identical helices, 16 amino acids in length, achieve efficiency comparable to that of highly evolved channels. We further show that antiamoebin channels are extremely flexible, compared to modern, genetically coded channels. On the basis of our results, we propose that channels evolved further towards high structural complexity because they needed to acquire stable rigid structures and mechanisms for precise regulation rather than improve efficiency. In general, even though architectures of membrane proteins are not nearly as diverse as those of water-soluble proteins, they are sufficiently flexible to adapt readily to the functional demands arising during evolution.
Complexity Metrics for Spreadsheet Models
Bregar, Andrej
2008-01-01
Several complexity metrics are described which are related to logic structure, data structure and size of spreadsheet models. They primarily concentrate on the dispersion of cell references and cell paths. Most metrics are newly defined, while some are adapted from traditional software engineering. Their purpose is the identification of cells which are liable to errors. In addition, they can be used to estimate the values of dependent process metrics, such as the development duration and effort, and especially to adjust the cell error rate in accordance with the contents of each individual cell, in order to accurately asses the reliability of a model. Finally, two conceptual constructs - the reference branching condition cell and the condition block - are discussed, aiming at improving the reliability, modifiability, auditability and comprehensibility of logical tests.
DEFF Research Database (Denmark)
He, Li; Steinocher, Helena; Shelar, Ashish
2017-01-01
Transmembrane domains (TMDs) engage in protein-protein interactions that regulate many cellular processes, but the rules governing the specificity of these interactions are poorly understood. To discover these principles, we analyzed 26-residue model transmembrane proteins consisting exclusively ...
Molecular Insights into the Transmembrane Domain of the Thyrotropin Receptor.
Directory of Open Access Journals (Sweden)
Vanessa Chantreau
Full Text Available The thyrotropin receptor (TSHR is a G protein-coupled receptor (GPCR that is member of the leucine-rich repeat subfamily (LGR. In the absence of crystal structure, the success of rational design of ligands targeting the receptor internal cavity depends on the quality of the TSHR models built. In this subfamily, transmembrane helices (TM 2 and 5 are characterized by the absence of proline compared to most receptors, raising the question of the structural conformation of these helices. To gain insight into the structural properties of these helices, we carried out bioinformatics and experimental studies. Evolutionary analysis of the LGR family revealed a deletion in TM5 but provided no information on TM2. Wild type residues at positions 2.58, 2.59 or 2.60 in TM2 and/or at position 5.50 in TM5 were substituted to proline. Depending on the position of the proline substitution, different effects were observed on membrane expression, glycosylation, constitutive cAMP activity and responses to thyrotropin. Only proline substitution at position 2.59 maintained complex glycosylation and high membrane expression, supporting occurrence of a bulged TM2. The TSHR transmembrane domain was modeled by homology with the orexin 2 receptor, using a protocol that forced the deletion of one residue in the TM5 bulge of the template. The stability of the model was assessed by molecular dynamics simulations. TM5 straightened during the equilibration phase and was stable for the remainder of the simulations. Our data support a structural model of the TSHR transmembrane domain with a bulged TM2 and a straight TM5 that is specific of glycoprotein hormone receptors.
Hydrophobic pulses predict transmembrane helix irregularities and channel transmembrane units
Directory of Open Access Journals (Sweden)
Claustres Mireille
2011-05-01
Full Text Available Abstract Background Few high-resolution structures of integral membranes proteins are available, as crystallization of such proteins needs yet to overcome too many technical limitations. Nevertheless, prediction of their transmembrane (TM structure by bioinformatics tools provides interesting insights on the topology of these proteins. Methods We describe here how to extract new information from the analysis of hydrophobicity variations or hydrophobic pulses (HPulses in the sequence of integral membrane proteins using the Hydrophobic Pulse Predictor, a new tool we developed for this purpose. To analyze the primary sequence of 70 integral membrane proteins we defined two levels of analysis: G1-HPulses for sliding windows of n = 2 to 6 and G2-HPulses for sliding windows of n = 12 to 16. Results The G2-HPulse analysis of 541 transmembrane helices allowed the definition of the new concept of transmembrane unit (TMU that groups together transmembrane helices and segments with potential adjacent structures. In addition, the G1-HPulse analysis identified helix irregularities that corresponded to kinks, partial helices or unannotated structural events. These irregularities could represent key dynamic elements that are alternatively activated depending on the channel status as illustrated by the crystal structures of the lactose permease in different conformations. Conclusions Our results open a new way in the understanding of transmembrane secondary structures: hydrophobicity through hydrophobic pulses strongly impacts on such embedded structures and is not confined to define the transmembrane status of amino acids.
Mechanisms for quality control of misfolded transmembrane proteins
Houck, Scott A.; Cyr, Douglas M.
2011-01-01
To prevent the accumulation of misfolded and aggregated proteins, the cell has developed a complex network of cellular quality control (QC) systems to recognize misfolded proteins and facilitate their refolding or degradation. The cell faces numerous obstacles when performing quality control on transmembrane proteins. Transmembrane proteins have domains on both sides of a membrane and QC systems in distinct compartments must coordinate to monitor the folding status of the protein. Additionall...
Biophysical Aspects of Transmembrane Signaling
Damjanovich, Sandor
2005-01-01
Transmembrane signaling is one of the most significant cell biological events in the life and death of cells in general and lymphocytes in particular. Until recently biochemists and biophysicists were not accustomed to thinking of these processes from the side of a high number of complex biochemical events and an equally high number of physical changes at molecular and cellular levels at the same time. Both types of researchers were convinced that their findings are the most decisive, having higher importance than the findings of the other scientist population. Both casts were wrong. Life, even at cellular level, has a number of interacting physical and biochemical mechanisms, which finally build up the creation of an "excited" cell that will respond to particular signals from the outer or inner world. This book handles both aspects of the signalling events, and in some cases tries to unify our concepts and help understand the signals that govern the life and death of our cells. Not only the understanding, bu...
Teacher Modeling Using Complex Informational Texts
Fisher, Douglas; Frey, Nancy
2015-01-01
Modeling in complex texts requires that teachers analyze the text for factors of qualitative complexity and then design lessons that introduce students to that complexity. In addition, teachers can model the disciplinary nature of content area texts as well as word solving and comprehension strategies. Included is a planning guide for think aloud.
Structural basis of transmembrane domain interactions in integrin signaling.
Ulmer, Tobias S
2010-01-01
Cell surface receptors of the integrin family are pivotal to cell adhesion and migration. The activation state of heterodimeric alphabeta integrins is correlated to the association state of the single-pass alpha and beta transmembrane domains. The association of integrin alphaIIbbeta3 transmembrane domains, resulting in an inactive receptor, is characterized by the asymmetric arrangement of a straight (alphaIIb) and tilted (beta3) helix relative to the membrane in congruence to the dissociated structures. This allows for a continuous association interface centered on helix-helix glycine-packing and an unusual alphaIIb(GFF) structural motif that packs the conserved Phe-Phe residues against the beta3 transmembrane helix, enabling alphaIIb(D723)beta3(R995) electrostatic interactions. The transmembrane complex is further stabilized by the inactive ectodomain, thereby coupling its association state to the ectodomain conformation. In combination with recently determined structures of an inactive integrin ectodomain and an activating talin/beta complex that overlap with the alphabeta transmembrane complex, a comprehensive picture of integrin bi-directional transmembrane signaling has emerged.
Unden, G; Wörner, S; Monzel, C
2016-01-01
Many membrane-bound sensor kinases require accessory proteins for function. The review describes functional control of membrane-bound sensors by transporters. The C4-dicarboxylate sensor kinase DcuS requires the aerobic or anaerobic C4-dicarboxylate transporters DctA or DcuB, respectively, for function and forms DctA/DcuS or DcuB/DcuS sensor complexes. Free DcuS is in the permanent (ligand independent) ON state. The DctA/DcuS and DcuB/DcuS complexes, on the other hand, control expression in response to C4-dicarboxylates. In DctA/DcuS, helix 8b of DctA and the PASC domain of DcuS are involved in interaction. The stimulus is perceived by the extracytoplasmic sensor domain (PASP) of DcuS. The signal is transmitted across the membrane by a piston-type movement of TM2 of DcuS which appears to be pulled (by analogy to the homologous citrate sensor CitA) by compaction of PASP after C4-dicarboxylate binding. In the cytoplasm, the signal is perceived by the PASC domain of DcuS. PASC inhibits together with DctA the kinase domain of DcuS which is released after C4-dicarboxylate binding. DcuS exhibits two modes for regulating expression of target genes. At higher C4-dicarboxylate levels, DcuS is part of the DctA/DcuS complex and in the C4-dicarboxylate-responsive form which stimulates expression of target genes in response to the concentration of the C4-dicarboxylates (catabolic use of C4-dicarboxylates, mode I regulation). At limiting C4-dicarboxylate concentrations (≤0.05mM), expression of DctA drops and free DcuS appears. Free DcuS is in the permanent ON state (mode II regulation) and stimulates low level (C4-dicarboxylate independent) DctA synthesis for DctA/DcuS complex formation and anabolic C4-dicarboxylate uptake.
Lupardus, Patrick J.; Skiniotis, Georgios; Rice, Amanda J.; Thomas, Christoph; Fischer, Suzanne; Walz, Thomas; Garcia, K. Christopher
2011-01-01
Summary The shared cytokine receptor gp130 signals as a homodimer or heterodimer through activation of Janus kinases (Jaks) associated with the receptor intracellular domains. Here we reconstitute, in parts and whole, the full-length gp130 homodimer in complex with the cytokine interleukin-6 (IL-6), its alpha receptor (IL-6Rα) and Jak1, for electron microscopy imaging. We find that the full-length gp130 homodimer complex has intimate interactions between the trans- and juxtamembrane segments of the two receptors, appearing to rigidify the connection between the extra- and intracellular regions. 2D averages and 3D reconstructions of full-length Jak1 reveal a three-lobed structure comprised of FERM-SH2, pseudokinase and kinase modules possessing extensive inter-segmental flexibility that likely facilitates allosteric activation. Single-particle imaging of the gp130/IL-6/IL-6Rα/Jak1 holocomplex shows Jak1 associated with the membrane proximal intracellular regions of gp130, abutting the would-be inner leaflet of the cell membrane. Jak1 association with gp130 is enhanced by the presence of a membrane environment. PMID:21220115
Capturing Complexity through Maturity Modelling
Underwood, Jean; Dillon, Gayle
2004-01-01
The impact of information and communication technologies (ICT) on the process and products of education is difficult to assess for a number of reasons. In brief, education is a complex system of interrelationships, of checks and balances. This context is not a neutral backdrop on which teaching and learning are played out. Rather, it may help, or…
Lin, Ying-Ju; Wu, Suh-Chin
2005-07-01
The formation of the flavivirus prM-E complex is an important step for the biogenesis of immature virions, which is followed by a subsequent cleavage of prM to M protein through cellular protease to result in the production and release of mature virions. In this study, the intracellular formation of the prM-E complex of Japanese encephalitis virus was investigated by baculovirus coexpression of prM and E in trans in Sf9 insect cells as analyzed by anti-E antibody immunoprecipitation and sucrose gradient sedimentation analysis. A series of carboxyl-terminally truncated prM mutant baculoviruses was constructed to demonstrate that the truncations of the transmembrane (TM) region resulted in a reduction of the formation of the stable prM-E complex by approximately 40% for the TM1 (at residues 130 to 147 [prM130-147]) truncation and 20% for TM2 (at prM153-167) truncation. Alanine-scanning site-directed mutagenesis on the prM99-103 region indicated that the His99 residue was the critical prM binding element for stable prM-E heterodimeric complex formation. The single amino acid mutation at the His99 residue of prM abolishing the prM-E interaction was not due to reduced expression or different subcellular location of the mutant prM protein involved in prM-E interactions as characterized by pulse-chase labeling and confocal scanning microscopic analysis. Recombinant subviral particles were detected in the Sf9 cell culture supernatants by baculovirus coexpression of prM and E proteins but not with the prM H99A mutant. Sequence alignment analysis was further conducted with different groups of flaviviruses to show that the prM H99 residues are generally conserved. Our findings are the first report to characterize the minimum binding elements of the prM protein that are involved in prM-E interactions of flaviviruses. This information, concerning a molecular framework for the prM protein, is considered to elucidate the structure/function relationship of the prM-E complex
Osteosarcoma models : understanding complex disease
Mohseny, Alexander Behzad
2012-01-01
A mesenchymal stem cell (MSC) based osteosarcoma model was established. The model provided evidence for a MSC origin of osteosarcoma. Normal MSCs transformed spontaneously to osteosarcoma-like cells which was always accompanied by genomic instability and loss of the Cdkn2a locus. Accordingly loss of
Osteosarcoma models : understanding complex disease
Mohseny, Alexander Behzad
2012-01-01
A mesenchymal stem cell (MSC) based osteosarcoma model was established. The model provided evidence for a MSC origin of osteosarcoma. Normal MSCs transformed spontaneously to osteosarcoma-like cells which was always accompanied by genomic instability and loss of the Cdkn2a locus. Accordingly loss of
Kitjaruwankul, Sunan; Khrutto, Channarong; Sompornpisut, Pornthep; Farmer, B. L.; Pandey, R. B.
2016-10-01
Structure of CorA protein and its inner (i.corA) and outer (o.corA) transmembrane (TM) components are investigated as a function of temperature by a coarse-grained Monte Carlo simulation. Thermal response of i.corA is found to differ considerably from that of the outer component, o.corA. Analysis of the radius of gyration reveals that the inner TM component undergoes a continuous transition from a globular conformation to a random coil structure on raising the temperature. In contrast, the outer transmembrane component exhibits an abrupt (nearly discontinuous) thermal response in a narrow range of temperature. Scaling of the structure factor shows a globular structure of i.corA at a low temperature with an effective dimension D ˜ 3 and a random coil at a high temperature with D ˜ 2. The residue distribution in o.corA is slightly sparser than that of i.corA in a narrow thermos-responsive regime. The difference in thermos-response characteristics of these components (i.corA and o.corA) may reflect their unique transmembrane functions.
Molecular simulation and modeling of complex I.
Hummer, Gerhard; Wikström, Mårten
2016-07-01
Molecular modeling and molecular dynamics simulations play an important role in the functional characterization of complex I. With its large size and complicated function, linking quinone reduction to proton pumping across a membrane, complex I poses unique modeling challenges. Nonetheless, simulations have already helped in the identification of possible proton transfer pathways. Simulations have also shed light on the coupling between electron and proton transfer, thus pointing the way in the search for the mechanistic principles underlying the proton pump. In addition to reviewing what has already been achieved in complex I modeling, we aim here to identify pressing issues and to provide guidance for future research to harness the power of modeling in the functional characterization of complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt. Copyright © 2016 Elsevier B.V. All rights reserved.
Complex networks analysis in socioeconomic models
Varela, Luis M; Ausloos, Marcel; Carrete, Jesus
2014-01-01
This chapter aims at reviewing complex networks models and methods that were either developed for or applied to socioeconomic issues, and pertinent to the theme of New Economic Geography. After an introduction to the foundations of the field of complex networks, the present summary adds insights on the statistical mechanical approach, and on the most relevant computational aspects for the treatment of these systems. As the most frequently used model for interacting agent-based systems, a brief description of the statistical mechanics of the classical Ising model on regular lattices, together with recent extensions of the same model on small-world Watts-Strogatz and scale-free Albert-Barabasi complex networks is included. Other sections of the chapter are devoted to applications of complex networks to economics, finance, spreading of innovations, and regional trade and developments. The chapter also reviews results involving applications of complex networks to other relevant socioeconomic issues, including res...
Models of organometallic complexes for optoelectronic applications
Jacko, A C; Powell, B J
2010-01-01
Organometallic complexes have potential applications as the optically active components of organic light emitting diodes (OLEDs) and organic photovoltaics (OPV). Development of more effective complexes may be aided by understanding their excited state properties. Here we discuss two key theoretical approaches to investigate these complexes: first principles atomistic models and effective Hamiltonian models. We review applications of these methods, such as, determining the nature of the emitting state, predicting the fraction of injected charges that form triplet excitations, and explaining the sensitivity of device performance to small changes in the molecular structure of the organometallic complexes.
Modelling the structure of complex networks
DEFF Research Database (Denmark)
Herlau, Tue
networks has been independently studied as mathematical objects in their own right. As such, there has been both an increased demand for statistical methods for complex networks as well as a quickly growing mathematical literature on the subject. In this dissertation we explore aspects of modelling complex....... The next chapters will treat some of the various symmetries, representer theorems and probabilistic structures often deployed in the modelling complex networks, the construction of sampling methods and various network models. The introductory chapters will serve to provide context for the included written...
Scaffolding in Complex Modelling Situations
Stender, Peter; Kaiser, Gabriele
2015-01-01
The implementation of teacher-independent realistic modelling processes is an ambitious educational activity with many unsolved problems so far. Amongst others, there hardly exists any empirical knowledge about efficient ways of possible teacher support with students' activities, which should be mainly independent from the teacher. The research…
Mixture model analysis of complex samples
Wedel, M; ter Hofstede, F; Steenkamp, JBEM
1998-01-01
We investigate the effects of a complex sampling design on the estimation of mixture models. An approximate or pseudo likelihood approach is proposed to obtain consistent estimates of class-specific parameters when the sample arises from such a complex design. The effects of ignoring the sample desi
Atlases: Complex models of geospace
Directory of Open Access Journals (Sweden)
Ikonović Vesna
2005-01-01
Full Text Available Atlas is modeled contexture contents of treated thematic of space on optimal map union. Atlases are higher form of cartography. Atlases content composition of maps which are different by projection, scale, format methods, contents, usage and so. Atlases can be classified by multi criteria. Modern classification of atlases by technology of making would be on: 1. classical or traditional (printed on paper and 2. electronic (made on electronic media - computer or computer station. Electronic atlases divided in three large groups: view-only electronic atlases, 2. interactive electronic atlases and 3. analytical electronic atlases.
Numerical models of complex diapirs
Podladchikov, Yu.; Talbot, C.; Poliakov, A. N. B.
1993-12-01
Numerically modelled diapirs that rise into overburdens with viscous rheology produce a large variety of shapes. This work uses the finite-element method to study the development of diapirs that rise towards a surface on which a diapir-induced topography creeps flat or disperses ("erodes") at different rates. Slow erosion leads to diapirs with "mushroom" shapes, moderate erosion rate to "wine glass" diapirs and fast erosion to "beer glass"- and "column"-shaped diapirs. The introduction of a low-viscosity layer at the top of the overburden causes diapirs to develop into structures resembling a "Napoleon hat". These spread lateral sheets.
Thermodynamic modeling of complex systems
DEFF Research Database (Denmark)
Liang, Xiaodong
Offshore reservoirs represent one of the major growth areas of the oil and gas industry, and environmental safety is one of the biggest challenges for the offshore exploration and production. The oil accidents in the Gulf of Mexico in 1979 and 2010 were two of the biggest disasters in history...... after an oil spill. Engineering thermodynamics could be applied in the state-of-the-art sonar products through advanced artificial technology, if the speed of sound, solubility and density of oil-seawater systems could be satisfactorily modelled. The addition of methanol or glycols into unprocessed well...
Modeling complex work systems - method meets reality
Veer, van der, C.G.; Hoeve, Machteld; Lenting, Bert F.
1996-01-01
Modeling an existing task situation is often a first phase in the (re)design of information systems. For complex systems design, this model should consider both the people and the organization involved, the work, and situational aspects. Groupware Task Analysis (GTA) as part of a method for the design of complex systems, has been applied in a situation of redesign of a Dutch public administration system. The most feasible method to collect information in this case was ethnography, the resulti...
Fatigue modeling of materials with complex microstructures
DEFF Research Database (Denmark)
Qing, Hai; Mishnaevsky, Leon
2011-01-01
A new approach and method of the analysis of microstructure-lifetime relationships of materials with complex structures is presented. The micromechanical multiscale computational analysis of damage evolution in materials with complex hierarchical microstructures is combined with the phenomenologi......A new approach and method of the analysis of microstructure-lifetime relationships of materials with complex structures is presented. The micromechanical multiscale computational analysis of damage evolution in materials with complex hierarchical microstructures is combined...... with the phenomenological model of fatigue damage growth. As a result, the fatigue lifetime of materials with complex structures can be determined as a function of the parameters of their structures. As an example, the fatigue lifetimes of wood modeled as a cellular material with multilayered, fiber reinforced walls were...
Preferential urn model and nongrowing complex networks.
Ohkubo, Jun; Yasuda, Muneki; Tanaka, Kazuyuki
2005-12-01
A preferential urn model, which is based on the concept "the rich get richer," is proposed. From a relationship between a nongrowing model for complex networks and the preferential urn model in regard to degree distributions, it is revealed that a fitness parameter in the nongrowing model is interpreted as an inverse local temperature in the preferential urn model. Furthermore, it is clarified that the preferential urn model with randomness generates a fat-tailed occupation distribution; the concept of the local temperature enables us to understand the fat-tailed occupation distribution intuitively. Since the preferential urn model is a simple stochastic model, it can be applied to research on not only the nongrowing complex networks, but also many other fields such as econophysics and social sciences.
The Kuramoto model in complex networks
Rodrigues, Francisco A; Ji, Peng; Kurths, Jürgen
2016-01-01
Synchronization of an ensemble of oscillators is an emergent phenomenon present in several complex systems, ranging from social and physical to biological and technological systems. The most successful approach to describe how coherent behavior emerges in these complex systems is given by the paradigmatic Kuramoto model. This model has been traditionally studied in complete graphs. However, besides being intrinsically dynamical, complex systems present very heterogeneous structure, which can be represented as complex networks. This report is dedicated to review main contributions in the field of synchronization in networks of Kuramoto oscillators. In particular, we provide an overview of the impact of network patterns on the local and global dynamics of coupled phase oscillators. We cover many relevant topics, which encompass a description of the most used analytical approaches and the analysis of several numerical results. Furthermore, we discuss recent developments on variations of the Kuramoto model in net...
Modelling Canopy Flows over Complex Terrain
Grant, Eleanor R.; Ross, Andrew N.; Gardiner, Barry A.
2016-06-01
Recent studies of flow over forested hills have been motivated by a number of important applications including understanding CO_2 and other gaseous fluxes over forests in complex terrain, predicting wind damage to trees, and modelling wind energy potential at forested sites. Current modelling studies have focussed almost exclusively on highly idealized, and usually fully forested, hills. Here, we present model results for a site on the Isle of Arran, Scotland with complex terrain and heterogeneous forest canopy. The model uses an explicit representation of the canopy and a 1.5-order turbulence closure for flow within and above the canopy. The validity of the closure scheme is assessed using turbulence data from a field experiment before comparing predictions of the full model with field observations. For near-neutral stability, the results compare well with the observations, showing that such a relatively simple canopy model can accurately reproduce the flow patterns observed over complex terrain and realistic, variable forest cover, while at the same time remaining computationally feasible for real case studies. The model allows closer examination of the flow separation observed over complex forested terrain. Comparisons with model simulations using a roughness length parametrization show significant differences, particularly with respect to flow separation, highlighting the need to explicitly model the forest canopy if detailed predictions of near-surface flow around forests are required.
Complex system modelling for veterinary epidemiology.
Lanzas, Cristina; Chen, Shi
2015-02-01
The use of mathematical models has a long tradition in infectious disease epidemiology. The nonlinear dynamics and complexity of pathogen transmission pose challenges in understanding its key determinants, in identifying critical points, and designing effective mitigation strategies. Mathematical modelling provides tools to explicitly represent the variability, interconnectedness, and complexity of systems, and has contributed to numerous insights and theoretical advances in disease transmission, as well as to changes in public policy, health practice, and management. In recent years, our modelling toolbox has considerably expanded due to the advancements in computing power and the need to model novel data generated by technologies such as proximity loggers and global positioning systems. In this review, we discuss the principles, advantages, and challenges associated with the most recent modelling approaches used in systems science, the interdisciplinary study of complex systems, including agent-based, network and compartmental modelling. Agent-based modelling is a powerful simulation technique that considers the individual behaviours of system components by defining a set of rules that govern how individuals ("agents") within given populations interact with one another and the environment. Agent-based models have become a recent popular choice in epidemiology to model hierarchical systems and address complex spatio-temporal dynamics because of their ability to integrate multiple scales and datasets.
Modelling Canopy Flows over Complex Terrain
Grant, Eleanor R.; Ross, Andrew N.; Gardiner, Barry A.
2016-12-01
Recent studies of flow over forested hills have been motivated by a number of important applications including understanding CO_2 and other gaseous fluxes over forests in complex terrain, predicting wind damage to trees, and modelling wind energy potential at forested sites. Current modelling studies have focussed almost exclusively on highly idealized, and usually fully forested, hills. Here, we present model results for a site on the Isle of Arran, Scotland with complex terrain and heterogeneous forest canopy. The model uses an explicit representation of the canopy and a 1.5-order turbulence closure for flow within and above the canopy. The validity of the closure scheme is assessed using turbulence data from a field experiment before comparing predictions of the full model with field observations. For near-neutral stability, the results compare well with the observations, showing that such a relatively simple canopy model can accurately reproduce the flow patterns observed over complex terrain and realistic, variable forest cover, while at the same time remaining computationally feasible for real case studies. The model allows closer examination of the flow separation observed over complex forested terrain. Comparisons with model simulations using a roughness length parametrization show significant differences, particularly with respect to flow separation, highlighting the need to explicitly model the forest canopy if detailed predictions of near-surface flow around forests are required.
From Complex to Simple: Interdisciplinary Stochastic Models
Mazilu, D. A.; Zamora, G.; Mazilu, I.
2012-01-01
We present two simple, one-dimensional, stochastic models that lead to a qualitative understanding of very complex systems from biology, nanoscience and social sciences. The first model explains the complicated dynamics of microtubules, stochastic cellular highways. Using the theory of random walks in one dimension, we find analytical expressions…
Modeling complex work systems - method meets reality
van der Veer, Gerrit C.; Hoeve, Machteld; Lenting, Bert
1996-01-01
Modeling an existing task situation is often a first phase in the (re)design of information systems. For complex systems design, this model should consider both the people and the organization involved, the work, and situational aspects. Groupware Task Analysis (GTA) as part of a method for the
Modeling complex work systems - method meets reality
Veer, van der Gerrit C.; Hoeve, Machteld; Lenting, Bert F.
1996-01-01
Modeling an existing task situation is often a first phase in the (re)design of information systems. For complex systems design, this model should consider both the people and the organization involved, the work, and situational aspects. Groupware Task Analysis (GTA) as part of a method for the desi
A differential model of the complex cell.
Hansard, Miles; Horaud, Radu
2011-09-01
The receptive fields of simple cells in the visual cortex can be understood as linear filters. These filters can be modeled by Gabor functions or gaussian derivatives. Gabor functions can also be combined in an energy model of the complex cell response. This letter proposes an alternative model of the complex cell, based on gaussian derivatives. It is most important to account for the insensitivity of the complex response to small shifts of the image. The new model uses a linear combination of the first few derivative filters, at a single position, to approximate the first derivative filter, at a series of adjacent positions. The maximum response, over all positions, gives a signal that is insensitive to small shifts of the image. This model, unlike previous approaches, is based on the scale space theory of visual processing. In particular, the complex cell is built from filters that respond to the 2D differential structure of the image. The computational aspects of the new model are studied in one and two dimensions, using the steerability of the gaussian derivatives. The response of the model to basic images, such as edges and gratings, is derived formally. The response to natural images is also evaluated, using statistical measures of shift insensitivity. The neural implementation and predictions of the model are discussed.
Complex-temperature singularities of Ising models
Shrock, R E
1995-01-01
We report new results on complex-temperature properties of Ising models. These include studies of the s=1/2 model on triangular, honeycomb, kagom\\'e, 3 \\cdot 12^2, and 4 \\cdot 8^2 lattices. We elucidate the complex--T phase diagrams of the higher-spin 2D Ising models, using calculations of partition function zeros. Finally, we investigate the 2D Ising model in an external magnetic field, mapping the complex--T phase diagram and exploring various singularities therein. For the case \\beta H=i\\pi/2, we give exact results on the phase diagram and obtain susceptibility exponents \\gamma' at various singularities from low-temperature series analyses.
Updating the debate on model complexity
Simmons, Craig T.; Hunt, Randall J.
2012-01-01
As scientists who are trying to understand a complex natural world that cannot be fully characterized in the field, how can we best inform the society in which we live? This founding context was addressed in a special session, “Complexity in Modeling: How Much is Too Much?” convened at the 2011 Geological Society of America Annual Meeting. The session had a variety of thought-provoking presentations—ranging from philosophy to cost-benefit analyses—and provided some areas of broad agreement that were not evident in discussions of the topic in 1998 (Hunt and Zheng, 1999). The session began with a short introduction during which model complexity was framed borrowing from an economic concept, the Law of Diminishing Returns, and an example of enjoyment derived by eating ice cream. Initially, there is increasing satisfaction gained from eating more ice cream, to a point where the gain in satisfaction starts to decrease, ending at a point when the eater sees no value in eating more ice cream. A traditional view of model complexity is similar—understanding gained from modeling can actually decrease if models become unnecessarily complex. However, oversimplified models—those that omit important aspects of the problem needed to make a good prediction—can also limit and confound our understanding. Thus, the goal of all modeling is to find the “sweet spot” of model sophistication—regardless of whether complexity was added sequentially to an overly simple model or collapsed from an initial highly parameterized framework that uses mathematics and statistics to attain an optimum (e.g., Hunt et al., 2007). Thus, holistic parsimony is attained, incorporating “as simple as possible,” as well as the equally important corollary “but no simpler.”
Balancing model complexity and measurements in hydrology
Van De Giesen, N.; Schoups, G.; Weijs, S. V.
2012-12-01
The Data Processing Inequality implies that hydrological modeling can only reduce, and never increase, the amount of information available in the original data used to formulate and calibrate hydrological models: I(X;Z(Y)) ≤ I(X;Y). Still, hydrologists around the world seem quite content building models for "their" watersheds to move our discipline forward. Hydrological models tend to have a hybrid character with respect to underlying physics. Most models make use of some well established physical principles, such as mass and energy balances. One could argue that such principles are based on many observations, and therefore add data. These physical principles, however, are applied to hydrological models that often contain concepts that have no direct counterpart in the observable physical universe, such as "buckets" or "reservoirs" that fill up and empty out over time. These not-so-physical concepts are more like the Artificial Neural Networks and Support Vector Machines of the Artificial Intelligence (AI) community. Within AI, one quickly came to the realization that by increasing model complexity, one could basically fit any dataset but that complexity should be controlled in order to be able to predict unseen events. The more data are available to train or calibrate the model, the more complex it can be. Many complexity control approaches exist in AI, with Solomonoff inductive inference being one of the first formal approaches, the Akaike Information Criterion the most popular, and Statistical Learning Theory arguably being the most comprehensive practical approach. In hydrology, complexity control has hardly been used so far. There are a number of reasons for that lack of interest, the more valid ones of which will be presented during the presentation. For starters, there are no readily available complexity measures for our models. Second, some unrealistic simplifications of the underlying complex physics tend to have a smoothing effect on possible model
Complexity, Modeling, and Natural Resource Management
Directory of Open Access Journals (Sweden)
Paul Cilliers
2013-09-01
Full Text Available This paper contends that natural resource management (NRM issues are, by their very nature, complex and that both scientists and managers in this broad field will benefit from a theoretical understanding of complex systems. It starts off by presenting the core features of a view of complexity that not only deals with the limits to our understanding, but also points toward a responsible and motivating position. Everything we do involves explicit or implicit modeling, and as we can never have comprehensive access to any complex system, we need to be aware both of what we leave out as we model and of the implications of the choice of our modeling framework. One vantage point is never sufficient, as complexity necessarily implies that multiple (independent conceptualizations are needed to engage the system adequately. We use two South African cases as examples of complex systems - restricting the case narratives mainly to the biophysical domain associated with NRM issues - that make the point that even the behavior of the biophysical subsystems themselves are already complex. From the insights into complex systems discussed in the first part of the paper and the lessons emerging from the way these cases have been dealt with in reality, we extract five interrelated generic principles for practicing science and management in complex NRM environments. These principles are then further elucidated using four further South African case studies - organized as two contrasting pairs - and now focusing on the more difficult organizational and social side, comparing the human organizational endeavors in managing such systems.
Trends in modeling Biomedical Complex Systems
Directory of Open Access Journals (Sweden)
Remondini Daniel
2009-10-01
Full Text Available Abstract In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments, informatics tools and technologies suitable for biological and biomedical research, which are becoming increasingly multidisciplinary, multidimensional and information-driven. The most important concepts on mathematical modeling methodologies and statistical inference, bioinformatics and standards tools to investigate complex biomedical systems are discussed and the prominent literature useful to both the practitioner and the theoretician are presented.
Characteristic Polynomials of Complex Random Matrix Models
Akemann, G
2003-01-01
We calculate the expectation value of an arbitrary product of characteristic polynomials of complex random matrices and their hermitian conjugates. Using the technique of orthogonal polynomials in the complex plane our result can be written in terms of a determinant containing these polynomials and their kernel. It generalizes the known expression for hermitian matrices and it also provides a generalization of the Christoffel formula to the complex plane. The derivation we present holds for complex matrix models with a general weight function at finite-N, where N is the size of the matrix. We give some explicit examples at finite-N for specific weight functions. The characteristic polynomials in the large-N limit at weak and strong non-hermiticity follow easily and they are universal in the weak limit. We also comment on the issue of the BMN large-N limit.
Transmembrane protein sorting driven by membrane curvature
Strahl, H.; Ronneau, S.; González, B. Solana; Klutsch, D.; Schaffner-Barbero, C.; Hamoen, L. W.
2015-11-01
The intricate structure of prokaryotic and eukaryotic cells depends on the ability to target proteins to specific cellular locations. In most cases, we have a poor understanding of the underlying mechanisms. A typical example is the assembly of bacterial chemoreceptors at cell poles. Here we show that the classical chemoreceptor TlpA of Bacillus subtilis does not localize according to the consensus stochastic nucleation mechanism but accumulates at strongly curved membrane areas generated during cell division. This preference was confirmed by accumulation at non-septal curved membranes. Localization appears to be an intrinsic property of the protein complex and does not rely on chemoreceptor clustering, as was previously shown for Escherichia coli. By constructing specific amino-acid substitutions, we demonstrate that the preference for strongly curved membranes arises from the curved shape of chemoreceptor trimer of dimers. These findings demonstrate that the intrinsic shape of transmembrane proteins can determine their cellular localization.
Complex Behaviors of a Simple Traffic Model
Institute of Scientific and Technical Information of China (English)
GAO Xing-Ru
2006-01-01
In this paper, we propose a modified traffic model in which a single car moves through a sequence of traffic lights controlled by a step function instead of a sine function. In contrast to the previous work [Phys. Rev. E 70 (2004)016107], we have investigated in detail the dependence of the behavior on four parameters, ω, α, η, and a1, and given three kinds of bifurcation diagrams, which show three kinds of complex behaviors. We have found that in this model there are chaotic and complex periodic motions, as well as special singularities. We have also analyzed the characteristic of the complex period motion and the essential feature of the singularity.
Complex Systems and Self-organization Modelling
Bertelle, Cyrille; Kadri-Dahmani, Hakima
2009-01-01
The concern of this book is the use of emergent computing and self-organization modelling within various applications of complex systems. The authors focus their attention both on the innovative concepts and implementations in order to model self-organizations, but also on the relevant applicative domains in which they can be used efficiently. This book is the outcome of a workshop meeting within ESM 2006 (Eurosis), held in Toulouse, France in October 2006.
A cognitive model for software architecture complexity
Bouwers, E.; Lilienthal, C.; Visser, J.; Van Deursen, A.
2010-01-01
Evaluating the complexity of the architecture of a softwaresystem is a difficult task. Many aspects have to be considered to come to a balanced assessment. Several architecture evaluation methods have been proposed, but very few define a quality model to be used during the evaluation process. In add
The Kuramoto model in complex networks
Rodrigues, Francisco A.; Peron, Thomas K. DM.; Ji, Peng; Kurths, Jürgen
2016-01-01
Synchronization of an ensemble of oscillators is an emergent phenomenon present in several complex systems, ranging from social and physical to biological and technological systems. The most successful approach to describe how coherent behavior emerges in these complex systems is given by the paradigmatic Kuramoto model. This model has been traditionally studied in complete graphs. However, besides being intrinsically dynamical, complex systems present very heterogeneous structure, which can be represented as complex networks. This report is dedicated to review main contributions in the field of synchronization in networks of Kuramoto oscillators. In particular, we provide an overview of the impact of network patterns on the local and global dynamics of coupled phase oscillators. We cover many relevant topics, which encompass a description of the most used analytical approaches and the analysis of several numerical results. Furthermore, we discuss recent developments on variations of the Kuramoto model in networks, including the presence of noise and inertia. The rich potential for applications is discussed for special fields in engineering, neuroscience, physics and Earth science. Finally, we conclude by discussing problems that remain open after the last decade of intensive research on the Kuramoto model and point out some promising directions for future research.
Modelling biological complexity: a physical scientist's perspective.
Coveney, Peter V; Fowler, Philip W
2005-09-22
We discuss the modern approaches of complexity and self-organization to understanding dynamical systems and how these concepts can inform current interest in systems biology. From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application of the study of complexity. We briefly describe how the dynamics of the heart and circadian rhythms, canonical examples of systems biology, are modelled by sets of nonlinear coupled differential equations, which have to be solved numerically. A major difficulty with this approach is that all the parameters within these equations are not usually known. Coupled models that include biomolecular detail could help solve this problem. Coupling models across large ranges of length- and time-scales is central to describing complex systems and therefore to biology. Such coupling may be performed in at least two different ways, which we refer to as hierarchical and hybrid multiscale modelling. While limited progress has been made in the former case, the latter is only beginning to be addressed systematically. These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length- and time-scales, a key aim of systems biology. Multiscale models couple behaviour at the molecular biological level to that at the cellular level, thereby providing a route for calculating many unknown parameters as well as investigating the effects at, for example, the cellular level, of small changes at the biomolecular level, such as a genetic mutation or the presence of a drug. The modelling and simulation of biomolecular systems is itself very computationally intensive; we describe a recently developed hybrid continuum-molecular model, HybridMD, and its associated molecular insertion algorithm, which point the way towards the
Delineating Parameter Unidentifiabilities in Complex Models
Raman, Dhruva V; Papachristodoulou, Antonis
2016-01-01
Scientists use mathematical modelling to understand and predict the properties of complex physical systems. In highly parameterised models there often exist relationships between parameters over which model predictions are identical, or nearly so. These are known as structural or practical unidentifiabilities, respectively. They are hard to diagnose and make reliable parameter estimation from data impossible. They furthermore imply the existence of an underlying model simplification. We describe a scalable method for detecting unidentifiabilities, and the functional relations defining them, for generic models. This allows for model simplification, and appreciation of which parameters (or functions thereof) cannot be estimated from data. Our algorithm can identify features such as redundant mechanisms and fast timescale subsystems, as well as the regimes in which such approximations are valid. We base our algorithm on a novel quantification of regional parametric sensitivity: multiscale sloppiness. Traditional...
Computing the complexity for Schelling segregation models
Gerhold, Stefan; Glebsky, Lev; Schneider, Carsten; Weiss, Howard; Zimmermann, Burkhard
2008-12-01
The Schelling segregation models are "agent based" population models, where individual members of the population (agents) interact directly with other agents and move in space and time. In this note we study one-dimensional Schelling population models as finite dynamical systems. We define a natural notion of entropy which measures the complexity of the family of these dynamical systems. The entropy counts the asymptotic growth rate of the number of limit states. We find formulas and deduce precise asymptotics for the number of limit states, which enable us to explicitly compute the entropy.
A Practical Philosophy of Complex Climate Modelling
Schmidt, Gavin A.; Sherwood, Steven
2014-01-01
We give an overview of the practice of developing and using complex climate models, as seen from experiences in a major climate modelling center and through participation in the Coupled Model Intercomparison Project (CMIP).We discuss the construction and calibration of models; their evaluation, especially through use of out-of-sample tests; and their exploitation in multi-model ensembles to identify biases and make predictions. We stress that adequacy or utility of climate models is best assessed via their skill against more naive predictions. The framework we use for making inferences about reality using simulations is naturally Bayesian (in an informal sense), and has many points of contact with more familiar examples of scientific epistemology. While the use of complex simulations in science is a development that changes much in how science is done in practice, we argue that the concepts being applied fit very much into traditional practices of the scientific method, albeit those more often associated with laboratory work.
A Practical Philosophy of Complex Climate Modelling
Schmidt, Gavin A.; Sherwood, Steven
2014-01-01
We give an overview of the practice of developing and using complex climate models, as seen from experiences in a major climate modelling center and through participation in the Coupled Model Intercomparison Project (CMIP).We discuss the construction and calibration of models; their evaluation, especially through use of out-of-sample tests; and their exploitation in multi-model ensembles to identify biases and make predictions. We stress that adequacy or utility of climate models is best assessed via their skill against more naive predictions. The framework we use for making inferences about reality using simulations is naturally Bayesian (in an informal sense), and has many points of contact with more familiar examples of scientific epistemology. While the use of complex simulations in science is a development that changes much in how science is done in practice, we argue that the concepts being applied fit very much into traditional practices of the scientific method, albeit those more often associated with laboratory work.
Intrinsic Uncertainties in Modeling Complex Systems.
Energy Technology Data Exchange (ETDEWEB)
Cooper, Curtis S; Bramson, Aaron L.; Ames, Arlo L.
2014-09-01
Models are built to understand and predict the behaviors of both natural and artificial systems. Because it is always necessary to abstract away aspects of any non-trivial system being modeled, we know models can potentially leave out important, even critical elements. This reality of the modeling enterprise forces us to consider the prospective impacts of those effects completely left out of a model - either intentionally or unconsidered. Insensitivity to new structure is an indication of diminishing returns. In this work, we represent a hypothetical unknown effect on a validated model as a finite perturba- tion whose amplitude is constrained within a control region. We find robustly that without further constraints, no meaningful bounds can be placed on the amplitude of a perturbation outside of the control region. Thus, forecasting into unsampled regions is a very risky proposition. We also present inherent difficulties with proper time discretization of models and representing in- herently discrete quantities. We point out potentially worrisome uncertainties, arising from math- ematical formulation alone, which modelers can inadvertently introduce into models of complex systems. Acknowledgements This work has been funded under early-career LDRD project #170979, entitled "Quantify- ing Confidence in Complex Systems Models Having Structural Uncertainties", which ran from 04/2013 to 09/2014. We wish to express our gratitude to the many researchers at Sandia who con- tributed ideas to this work, as well as feedback on the manuscript. In particular, we would like to mention George Barr, Alexander Outkin, Walt Beyeler, Eric Vugrin, and Laura Swiler for provid- ing invaluable advice and guidance through the course of the project. We would also like to thank Steven Kleban, Amanda Gonzales, Trevor Manzanares, and Sarah Burwell for their assistance in managing project tasks and resources.
Modeling auditory evoked potentials to complex stimuli
DEFF Research Database (Denmark)
Rønne, Filip Munch
The auditory evoked potential (AEP) is an electrical signal that can be recorded from electrodes attached to the scalp of a human subject when a sound is presented. The signal is considered to reflect neural activity in response to the acoustic stimulation and is a well established clinical...... clinically and in research towards using realistic and complex stimuli, such as speech, to electrophysiologically assess the human hearing. However, to interpret the AEP generation to complex sounds, the potential patterns in response to simple stimuli needs to be understood. Therefore, the model was used...... to simulate auditory brainstem responses (ABRs) evoked by classic stimuli like clicks, tone bursts and chirps. The ABRs to these simple stimuli were compared to literature data and the model was shown to predict the frequency dependence of tone-burst ABR wave-V latency and the level-dependence of ABR wave...
Complex Evaluation Model of Corporate Energy Management
Ágnes Kádár Horváth
2014-01-01
With the ever increasing energy problems at the doorstep alongside with political, economic, social and environmental challenges, conscious energy management has become of increasing importance in corporate resource management. Rising energy costs, stricter environmental and climate regulations as well as considerable changes in the energy market require companies to rationalise their energy consumption and cut energy costs. This study presents a complex evaluation model of corporate energy m...
FRAM Modelling Complex Socio-technical Systems
Hollnagel, Erik
2012-01-01
There has not yet been a comprehensive method that goes behind 'human error' and beyond the failure concept, and various complicated accidents have accentuated the need for it. The Functional Resonance Analysis Method (FRAM) fulfils that need. This book presents a detailed and tested method that can be used to model how complex and dynamic socio-technical systems work, and understand both why things sometimes go wrong but also why they normally succeed.
Noncommutative complex Grosse-Wulkenhaar model
Hounkonnou, Mahouton Norbert
2012-01-01
This paper stands for an application of the noncommutative (NC) Noether theorem, given in our previous work [AIP Proc 956 (2007) 55-60], for the NC complex Grosse-Wulkenhaar model. It provides with an extension of a recent work [Physics Letters B 653 (2007) 343-345]. The local conservation of energy-momentum tensors (EMTs) is recovered using improvement procedures based on Moyal algebraic techniques. Broken dilatation symmetry is discussed. NC gauge currents are also explicitly computed.
Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling.
Bischofberger, Mirko; Iacovache, Ioan; Boss, Daniel; Naef, Felix; van der Goot, F Gisou; Molina, Nacho
2016-04-12
Many biological processes depend on the sequential assembly of protein complexes. However, studying the kinetics of such processes by direct methods is often not feasible. As an important class of such protein complexes, pore-forming toxins start their journey as soluble monomeric proteins, and oligomerize into transmembrane complexes to eventually form pores in the target cell membrane. Here, we monitored pore formation kinetics for the well-characterized bacterial pore-forming toxin aerolysin in single cells in real time to determine the lag times leading to the formation of the first functional pores per cell. Probabilistic modeling of these lag times revealed that one slow and seven equally fast rate-limiting reactions best explain the overall pore formation kinetics. The model predicted that monomer activation is the rate-limiting step for the entire pore formation process. We hypothesized that this could be through release of a propeptide and indeed found that peptide removal abolished these steps. This study illustrates how stochasticity in the kinetics of a complex process can be exploited to identify rate-limiting mechanisms underlying multistep biomolecular assembly pathways.
The noisy voter model on complex networks
Carro, Adrián; Miguel, Maxi San
2016-01-01
We propose a new analytical method to study stochastic, binary-state models on complex networks. Moving beyond the usual mean-field theories, this alternative approach is based on the introduction of an uncorrelated network approximation, allowing to deal with the network structure as parametric heterogeneity. As an illustration, we study the noisy voter model, a modification of the original voter model including random changes of state. The proposed method is able to unfold the dependence of the model not only on the mean degree (the mean-field prediction) but also on more complex averages over the degree distribution. In particular, we find that the degree heterogeneity ---variance of the underlying degree distribution--- has a strong influence on the location of the critical point of a noise-induced, finite-size transition occurring in the model, on the local ordering of the system, and on the functional form of its temporal correlations. Finally, we show how this latter point opens the possibility of infe...
Directory of Open Access Journals (Sweden)
Chetan Poojari
Full Text Available Interactions of the amyloid β-protein (Aβ with neuronal cell membranes, leading to the disruption of membrane integrity, are considered to play a key role in the development of Alzheimer's disease. Natural mutations in Aβ42, such as the Arctic mutation (E22G have been shown to increase Aβ42 aggregation and neurotoxicity, leading to the early-onset of Alzheimer's disease. A correlation between the propensity of Aβ42 to form protofibrils and its effect on neuronal dysfunction and degeneration has been established. Using rational mutagenesis of the Aβ42 peptide it was further revealed that the aggregation of different Aβ42 mutants in lipid membranes results in a variety of polymorphic aggregates in a mutation dependent manner. The mutant peptides also have a variable ability to disrupt bilayer integrity. To further test the connection between Aβ42 mutation and peptide-membrane interactions, we perform molecular dynamics simulations of membrane-inserted Aβ42 variants (wild-type and E22G, D23G, E22G/D23G, K16M/K28M and K16M/E22G/D23G/K28M mutants as β-sheet monomers and tetramers. The effects of charged residues on transmembrane Aβ42 stability and membrane integrity are analyzed at atomistic level. We observe an increased stability for the E22G Aβ42 peptide and a decreased stability for D23G compared to wild-type Aβ42, while D23G has the largest membrane-disruptive effect. These results support the experimental observation that the altered toxicity arising from mutations in Aβ is not only a result of the altered aggregation propensity, but also originates from modified Aβ interactions with neuronal membranes.
Directory of Open Access Journals (Sweden)
Sergi Vaquer
2014-08-01
Full Text Available Abstract Microgravity has been shown to influence the expression of ABC (ATP-Binding Cassette transporters in bacteria, fungi and mammals, but also to modify the activity of certain cellular components with structural and functional similarities to ABC transporters. Changes in activity of ABC transporters could lead to important metabolic disorders and undesired pharmacological effects during spaceflights. However, no current means exist to study the functionality of these transporters in microgravity. To this end, a Vesicular Transport Assay® (Solvo Biotechnology, Hungary was adapted to evaluate multi-drug resistance-associated protein 2 (MRP2 trans-membrane estradiol-17-β-glucuronide (E17βG transport activity, when activated by adenosine-tri-phosphate (ATP during parabolic flights. Simple diffusion, ATP-independent transport and benzbromarone inhibition were also evaluated. A high accuracy engineering system was designed to perform, monitor and synchronize all procedures. Samples were analysed using a validated high sensitivity drug detection protocol. Experiments were performed in microgravity during parabolic flights, and compared to 1g on ground results using identical equipment and procedures in all cases. Our results revealed that sufficient equipment accuracy and analytical sensitivity were reached to detect transport activity in both gravitational conditions. Additionally, transport activity levels of on ground samples were within commercial transport standards, proving the validity of the methods and equipment used. MRP2 net transport activity was significantly reduced in microgravity, so was signal detected in simple diffusion samples. Ultra-structural changes induced by gravitational stress upon vesicle membranes or transporters could explain the current results, although alternative explanations are possible. Further research is needed to provide a conclusive answer in this regard. Nevertheless, the present validated technology
Describing Ecosystem Complexity through Integrated Catchment Modeling
Shope, C. L.; Tenhunen, J. D.; Peiffer, S.
2011-12-01
Land use and climate change have been implicated in reduced ecosystem services (ie: high quality water yield, biodiversity, and agricultural yield. The prediction of ecosystem services expected under future land use decisions and changing climate conditions has become increasingly important. Complex policy and management decisions require the integration of physical, economic, and social data over several scales to assess effects on water resources and ecology. Field-based meteorology, hydrology, soil physics, plant production, solute and sediment transport, economic, and social behavior data were measured in a South Korean catchment. A variety of models are being used to simulate plot and field scale experiments within the catchment. Results from each of the local-scale models provide identification of sensitive, local-scale parameters which are then used as inputs into a large-scale watershed model. We used the spatially distributed SWAT model to synthesize the experimental field data throughout the catchment. The approach of our study was that the range in local-scale model parameter results can be used to define the sensitivity and uncertainty in the large-scale watershed model. Further, this example shows how research can be structured for scientific results describing complex ecosystems and landscapes where cross-disciplinary linkages benefit the end result. The field-based and modeling framework described is being used to develop scenarios to examine spatial and temporal changes in land use practices and climatic effects on water quantity, water quality, and sediment transport. Development of accurate modeling scenarios requires understanding the social relationship between individual and policy driven land management practices and the value of sustainable resources to all shareholders.
Complex Constructivism: A Theoretical Model of Complexity and Cognition
Doolittle, Peter E.
2014-01-01
Education has long been driven by its metaphors for teaching and learning. These metaphors have influenced both educational research and educational practice. Complexity and constructivism are two theories that provide functional and robust metaphors. Complexity provides a metaphor for the structure of myriad phenomena, while constructivism…
Pennisi, Cristian Pablo; Greenbaum, Elias; Yoshida, Ken
2010-01-01
Photosystem I (PSI) complexes can support a light-driven electrochemical gradient for protons, which is the driving force for energy-conserving reactions across biological membranes. In this work, a computational model that enables a quantitative description of the light-induced proton gradients across the membrane of PSI proteoliposomes is presented. Using a set of electrodiffusion equations, a compartmental model of a vesicle suspended in aqueous medium was studied. The light-mediated proton movement was modeled as a single proton pumping step with backpressure of the electric potential. The model fits determinations of pH obtained from PSI proteoliposomes illuminated in the presence of mediators of cyclic electron transport. The model also allows analysis of the proton gradients in relation to the transmembrane ion fluxes and electric potential. Sensitivity analysis enabled a determination of the parameters that have greater influence on steady-state levels and onset/decay rates of transmembrane pH and electric potential. This model could be used as a tool for optimizing PSI proteoliposomes for photo-electrochemical applications.
Energy Technology Data Exchange (ETDEWEB)
Pennisi, Cristian P. [Aalborg University, Aalborg, Denmark; Greenbaum, Elias [ORNL; Yoshida, Ken [Aalborg University, Aalborg, Denmark
2010-01-01
Photosystem I (PSI) complexes can support a light-driven electrochemical gradient for protons, which is the driving force for energy-conserving reactions across biological membranes. In this work, a computational model that enables a quantitative description of the light-induced proton gradients across the membrane of PSI proteoliposomes is presented. Using a set of electrodiffusion equations, a compartmental model of a vesicle suspended in aqueous medium was studied. The light-mediated proton movement was modeled as a single proton pumping step with backpressure of the electric potential. The model fits determinations of pH obtained from PSI proteoliposomes illuminated in the presence of mediators of cyclic electron transport. The model also allows analysis of the proton gradients in relation to the transmembrane ion fluxes and electric potential. Sensitivity analysis enabled a determination of the parameters that have greater influence on steady-state levels and onset/decay rates of transmembrane pH and electric potential. This model could be used as a tool for optimizing PSI proteoliposomes for photo-electrochemical applications.
Henricson, Anna; Käll, Lukas; Sonnhammer, Erik L L
2005-06-01
The transmembrane topology of presenilins is still the subject of debate despite many experimental topology studies using antibodies or gene fusions. The results from these studies are partly contradictory and consequently several topology models have been proposed. Studies of presenilin-interacting proteins have produced further contradiction, primarily regarding the location of the C-terminus. It is thus impossible to produce a topology model that agrees with all published data on presenilin. We have analyzed the presenilin topology through computational sequence analysis of the presenilin family and the homologous presenilin-like protein family. Members of these families are intramembrane-cleaving aspartyl proteases. Although the overall sequence homology between the two families is low, they share the conserved putative active site residues and the conserved 'PAL' motif. Therefore, the topology model for the presenilin-like proteins can give some clues about the presenilin topology. Here we propose a novel nine-transmembrane topology with the C-terminus in the extracytosolic space. This model has strong support from published data on gamma-secretase function and presenilin topology. Contrary to most presenilin topology models, we show that hydrophobic region X is probably a transmembrane segment. Consequently, the C-terminus would be located in the extracytosolic space. However, the last C-terminal amino acids are relatively hydrophobic and in conjunction with existing experimental data we cannot exclude the possibility that the extreme C-terminus could be buried within the gamma-secretase complex. This might explain the difficulties in obtaining consistent experimental evidence regarding the location of the C-terminal region of presenilin.
Wind and diffusion modeling for complex terrain
Energy Technology Data Exchange (ETDEWEB)
Cox, R.M.; Sontowski, J.; Fry, R.N. Jr. [and others
1996-12-31
Atmospheric transport and dispersion over complex terrain were investigated. Meteorological and sulfur hexafluoride (SF{sub 6}) concentration data were collected and used to evaluate the performance of a transport and diffusion model coupled with a mass consistency wind field model. Meteorological data were collected throughout April 1995. Both meteorological and concentration data were measured in December 1995. The data included 11 to 15 surface stations, 1 to 3 upper air stations, and 1 mobile profiler. A range of conditions was encountered, including inversion and post-inversion breakup, light to strong winds, and a broad distribution of wind directions. The models used included the SCIPUFF (Second-order Closure Integrated Puff) transport and diffusion model and the MINERVE mass consistency wind model. Evaluation of the models was focused primarily on their effectiveness as a short term (one to four hours) predictive tool. These studies showed how they can be used to help direct emergency response following a hazardous material release. For purposes of the experiments, the models were used to direct the deployment of mobile sensors intended to intercept and measure tracer clouds.
Structured analysis and modeling of complex systems
Strome, David R.; Dalrymple, Mathieu A.
1992-01-01
The Aircrew Evaluation Sustained Operations Performance (AESOP) facility at Brooks AFB, Texas, combines the realism of an operational environment with the control of a research laboratory. In recent studies we collected extensive data from the Airborne Warning and Control Systems (AWACS) Weapons Directors subjected to high and low workload Defensive Counter Air Scenarios. A critical and complex task in this environment involves committing a friendly fighter against a hostile fighter. Structured Analysis and Design techniques and computer modeling systems were applied to this task as tools for analyzing subject performance and workload. This technology is being transferred to the Man-Systems Division of NASA Johnson Space Center for application to complex mission related tasks, such as manipulating the Shuttle grappler arm.
Superelement Verification in Complex Structural Models
Directory of Open Access Journals (Sweden)
B. Dupont
2008-01-01
Full Text Available The objective of this article is to propose decision indicators to guide the analyst in the optimal definition of an ensemble of superelements in a complex structural assembly. These indicators are constructed based on comparisons between the unreduced physical model and the approximate solution provided by a nominally reduced superelement model. First, the low contribution substructure slave modes are filtered. Then, the minimum dynamical residual expansion is used to localize the superelements which are the most responsible for the response prediction errors. Moreover, it is shown that static residual vectors, which are a natural result of these calculations, can be included to represent the contribution of important truncated slave modes and consequently correct the deficient superelements. The proposed methodology is illustrated on a subassembly of an aeroengine model.
Modeling the human prothrombinase complex components
Orban, Tivadar
Thrombin generation is the culminating stage of the blood coagulation process. Thrombin is obtained from prothrombin (the substrate) in a reaction catalyzed by the prothrombinase complex (the enzyme). The prothrombinase complex is composed of factor Xa (the enzyme), factor Va (the cofactor) associated in the presence of calcium ions on a negatively charged cell membrane. Factor Xa, alone, can activate prothrombin to thrombin; however, the rate of conversion is not physiologically relevant for survival. Incorporation of factor Va into prothrombinase accelerates the rate of prothrombinase activity by 300,000-fold, and provides the physiological pathway of thrombin generation. The long-term goal of the current proposal is to provide the necessary support for the advancing of studies to design potential drug candidates that may be used to avoid development of deep venous thrombosis in high-risk patients. The short-term goals of the present proposal are to (1) to propose a model of a mixed asymmetric phospholipid bilayer, (2) expand the incomplete model of human coagulation factor Va and study its interaction with the phospholipid bilayer, (3) to create a homology model of prothrombin (4) to study the dynamics of interaction between prothrombin and the phospholipid bilayer.
Chaos from simple models to complex systems
Cencini, Massimo; Vulpiani, Angelo
2010-01-01
Chaos: from simple models to complex systems aims to guide science and engineering students through chaos and nonlinear dynamics from classical examples to the most recent fields of research. The first part, intended for undergraduate and graduate students, is a gentle and self-contained introduction to the concepts and main tools for the characterization of deterministic chaotic systems, with emphasis to statistical approaches. The second part can be used as a reference by researchers as it focuses on more advanced topics including the characterization of chaos with tools of information theor
Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems
Directory of Open Access Journals (Sweden)
Peter Spijker
2010-06-01
Full Text Available Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.
On Complexity of the Quantum Ising Model
Bravyi, Sergey; Hastings, Matthew
2017-01-01
We study complexity of several problems related to the Transverse field Ising Model (TIM). First, we consider the problem of estimating the ground state energy known as the Local Hamiltonian Problem (LHP). It is shown that the LHP for TIM on degree-3 graphs is equivalent modulo polynomial reductions to the LHP for general k-local `stoquastic' Hamiltonians with any constant {k ≥ 2}. This result implies that estimating the ground state energy of TIM on degree-3 graphs is a complete problem for the complexity class {StoqMA} —an extension of the classical class {MA}. As a corollary, we complete the complexity classification of 2-local Hamiltonians with a fixed set of interactions proposed recently by Cubitt and Montanaro. Secondly, we study quantum annealing algorithms for finding ground states of classical spin Hamiltonians associated with hard optimization problems. We prove that the quantum annealing with TIM Hamiltonians is equivalent modulo polynomial reductions to the quantum annealing with a certain subclass of k-local stoquastic Hamiltonians. This subclass includes all Hamiltonians representable as a sum of a k-local diagonal Hamiltonian and a 2-local stoquastic Hamiltonian.
Wind and Diffusion Modeling for Complex Terrain.
Cox, Robert M.; Sontowski, John; Fry, Richard N., Jr.; Dougherty, Catherine M.; Smith, Thomas J.
1998-10-01
Atmospheric transport and dispersion over complex terrain were investigated. Meteorological and sulfur hexafluoride (SF6) concentration data were collected and used to evaluate the performance of a transport and diffusion model coupled with a mass consistency wind field model. Meteorological data were collected throughout April 1995. Both meteorological and plume location and concentration data were measured in December 1995. The meteorological data included measurements taken at 11-15 surface stations, one to three upper-air stations, and one mobile profiler. A range of conditions was encountered, including inversion and postinversion breakup, light to strong winds, and a broad distribution of wind directions.The models used were the MINERVE mass consistency wind model and the SCIPUFF (Second-Order Closure Integrated Puff) transport and diffusion model. These models were expected to provide and use high-resolution three-dimensional wind fields. An objective of the experiment was to determine if these models could provide emergency personnel with high-resolution hazardous plume information for quick response operations.Evaluation of the models focused primarily on their effectiveness as a short-term (1-4 h) predictive tool. These studies showed how they could be used to help direct emergency response following a hazardous material release. For purposes of the experiments, the models were used to direct the deployment of mobile sensors intended to intercept and measure tracer clouds.The April test was conducted to evaluate the performance of the MINERVE wind field generation model. It was evaluated during the early morning radiation inversion, inversion dissipation, and afternoon mixed atmosphere. The average deviations in wind speed and wind direction as compared to observations were within 0.4 m s1 and less than 10° for up to 2 h after data time. These deviations increased as time from data time increased. It was also found that deviations were greatest during
Extension of association models to complex chemicals
DEFF Research Database (Denmark)
Avlund, Ane Søgaard
Summary of “Extension of association models to complex chemicals”. Ph.D. thesis by Ane Søgaard Avlund The subject of this thesis is application of SAFT type equations of state (EoS). Accurate and predictive thermodynamic models are important in many industries including the petroleum industry....... The SAFT EoS was developed 20 years ago, and a large number of papers on the subject has been published since, but many issues still remain unsolved. These issues are both theoretical and practical. The SAFT theory does not account for intramolecular association, it can only treat flexible chains, and does...... not account for steric self-hindrance for tree-like structures. An important practical problem is how to obtain optimal and consistent parameters. Moreover, multifunctional associating molecules represent a special challenge. In this work two equations of state using the SAFT theory for association are used...
Precalibrating an intermediate complexity climate model
Energy Technology Data Exchange (ETDEWEB)
Edwards, Neil R. [The Open University, Earth and Environmental Sciences, Milton Keynes (United Kingdom); Cameron, David [Centre for Ecology and Hydrology, Edinburgh (United Kingdom); Rougier, Jonathan [University of Bristol, Department of Mathematics, Bristol (United Kingdom)
2011-10-15
Credible climate predictions require a rational quantification of uncertainty, but full Bayesian calibration requires detailed estimates of prior probability distributions and covariances, which are difficult to obtain in practice. We describe a simplified procedure, termed precalibration, which provides an approximate quantification of uncertainty in climate prediction, and requires only that uncontroversially implausible values of certain inputs and outputs are identified. The method is applied to intermediate-complexity model simulations of the Atlantic meridional overturning circulation (AMOC) and confirms the existence of a cliff-edge catastrophe in freshwater-forcing input space. When uncertainty in 14 further parameters is taken into account, an implausible, AMOC-off, region remains as a robust feature of the model dynamics, but its location is found to depend strongly on values of the other parameters. (orig.)
Delineating parameter unidentifiabilities in complex models
Raman, Dhruva V.; Anderson, James; Papachristodoulou, Antonis
2017-03-01
Scientists use mathematical modeling as a tool for understanding and predicting the properties of complex physical systems. In highly parametrized models there often exist relationships between parameters over which model predictions are identical, or nearly identical. These are known as structural or practical unidentifiabilities, respectively. They are hard to diagnose and make reliable parameter estimation from data impossible. They furthermore imply the existence of an underlying model simplification. We describe a scalable method for detecting unidentifiabilities, as well as the functional relations defining them, for generic models. This allows for model simplification, and appreciation of which parameters (or functions thereof) cannot be estimated from data. Our algorithm can identify features such as redundant mechanisms and fast time-scale subsystems, as well as the regimes in parameter space over which such approximations are valid. We base our algorithm on a quantification of regional parametric sensitivity that we call `multiscale sloppiness'. Traditionally, the link between parametric sensitivity and the conditioning of the parameter estimation problem is made locally, through the Fisher information matrix. This is valid in the regime of infinitesimal measurement uncertainty. We demonstrate the duality between multiscale sloppiness and the geometry of confidence regions surrounding parameter estimates made where measurement uncertainty is non-negligible. Further theoretical relationships are provided linking multiscale sloppiness to the likelihood-ratio test. From this, we show that a local sensitivity analysis (as typically done) is insufficient for determining the reliability of parameter estimation, even with simple (non)linear systems. Our algorithm can provide a tractable alternative. We finally apply our methods to a large-scale, benchmark systems biology model of necrosis factor (NF)-κ B , uncovering unidentifiabilities.
Using Perspective to Model Complex Processes
Energy Technology Data Exchange (ETDEWEB)
Kelsey, R.L.; Bisset, K.R.
1999-04-04
The notion of perspective, when supported in an object-based knowledge representation, can facilitate better abstractions of reality for modeling and simulation. The object modeling of complex physical and chemical processes is made more difficult in part due to the poor abstractions of state and phase changes available in these models. The notion of perspective can be used to create different views to represent the different states of matter in a process. These techniques can lead to a more understandable model. Additionally, the ability to record the progress of a process from start to finish is problematic. It is desirable to have a historic record of the entire process, not just the end result of the process. A historic record should facilitate backtracking and re-start of a process at different points in time. The same representation structures and techniques can be used to create a sequence of process markers to represent a historic record. By using perspective, the sequence of markers can have multiple and varying views tailored for a particular user's context of interest.
On hydrological model complexity, its geometrical interpretations and prediction uncertainty
Arkesteijn, E.C.M.M.; Pande, S.
2013-01-01
Knowledge of hydrological model complexity can aid selection of an optimal prediction model out of a set of available models. Optimal model selection is formalized as selection of the least complex model out of a subset of models that have lower empirical risk. This may be considered equivalent to
Ants (Formicidae): models for social complexity.
Smith, Chris R; Dolezal, Adam; Eliyahu, Dorit; Holbrook, C Tate; Gadau, Jürgen
2009-07-01
The family Formicidae (ants) is composed of more than 12,000 described species that vary greatly in size, morphology, behavior, life history, ecology, and social organization. Ants occur in most terrestrial habitats and are the dominant animals in many of them. They have been used as models to address fundamental questions in ecology, evolution, behavior, and development. The literature on ants is extensive, and the natural history of many species is known in detail. Phylogenetic relationships for the family, as well as within many subfamilies, are known, enabling comparative studies. Their ease of sampling and ecological variation makes them attractive for studying populations and questions relating to communities. Their sociality and variation in social organization have contributed greatly to an understanding of complex systems, division of labor, and chemical communication. Ants occur in colonies composed of tens to millions of individuals that vary greatly in morphology, physiology, and behavior; this variation has been used to address proximate and ultimate mechanisms generating phenotypic plasticity. Relatedness asymmetries within colonies have been fundamental to the formulation and empirical testing of kin and group selection theories. Genomic resources have been developed for some species, and a whole-genome sequence for several species is likely to follow in the near future; comparative genomics in ants should provide new insights into the evolution of complexity and sociogenomics. Future studies using ants should help establish a more comprehensive understanding of social life, from molecules to colonies.
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)
Rosenberg, Mark F.; O'Ryan, Liam P.; Hughes, Guy; Zhao, Zhefeng; Aleksandrov, Luba A.; Riordan, John R.; Ford, Robert C.
2011-01-01
Cystic fibrosis affects about 1 in 2500 live births and involves loss of transmembrane chloride flux due to a lack of a membrane protein channel termed the cystic fibrosis transmembrane conductance regulator (CFTR). We have studied CFTR structure by electron crystallography. The data were compared with existing structures of other ATP-binding cassette transporters. The protein was crystallized in the outward facing state and resembled the well characterized Sav1866 transporter. We identified ...
Analytical models for complex swirling flows
Borissov, A.; Hussain, V.
1996-11-01
We develops a new class of analytical solutions of the Navier-Stokes equations for swirling flows, and suggests ways to predict and control such flows occurring in various technological applications. We view momentum accumulation on the axis as a key feature of swirling flows and consider vortex-sink flows on curved axisymmetric surfaces with an axial flow. We show that these solutions model swirling flows in a cylindrical can, whirlpools, tornadoes, and cosmic swirling jets. The singularity of these solutions on the flow axis is removed by matching them with near-axis Schlichting and Long's swirling jets. The matched solutions model flows with very complex patterns, consisting of up to seven separation regions with recirculatory 'bubbles' and vortex rings. We apply the matched solutions for computing flows in the Ranque-Hilsch tube, in the meniscus of electrosprays, in vortex breakdown, and in an industrial vortex burner. The simple analytical solutions allow a clear understanding of how different control parameters affect the flow and guide selection of optimal parameter values for desired flow features. These solutions permit extension to other problems (such as heat transfer and chemical reaction) and have the potential of being significantly useful for further detailed investigation by direct or large-eddy numerical simulations as well as laboratory experimentation.
Discrete Element Modeling of Complex Granular Flows
Movshovitz, N.; Asphaug, E. I.
2010-12-01
Granular materials occur almost everywhere in nature, and are actively studied in many fields of research, from food industry to planetary science. One approach to the study of granular media, the continuum approach, attempts to find a constitutive law that determines the material's flow, or strain, under applied stress. The main difficulty with this approach is that granular systems exhibit different behavior under different conditions, behaving at times as an elastic solid (e.g. pile of sand), at times as a viscous fluid (e.g. when poured), or even as a gas (e.g. when shaken). Even if all these physics are accounted for, numerical implementation is made difficult by the wide and often discontinuous ranges in continuum density and sound speed. A different approach is Discrete Element Modeling (DEM). Here the goal is to directly model every grain in the system as a rigid body subject to various body and surface forces. The advantage of this method is that it treats all of the above regimes in the same way, and can easily deal with a system moving back and forth between regimes. But as a granular system typically contains a multitude of individual grains, the direct integration of the system can be very computationally expensive. For this reason most DEM codes are limited to spherical grains of uniform size. However, spherical grains often cannot replicate the behavior of real world granular systems. A simple pile of spherical grains, for example, relies on static friction alone to keep its shape, while in reality a pile of irregular grains can maintain a much steeper angle by interlocking force chains. In the present study we employ a commercial DEM, nVidia's PhysX Engine, originally designed for the game and animation industry, to simulate complex granular flows with irregular, non-spherical grains. This engine runs as a multi threaded process and can be GPU accelerated. We demonstrate the code's ability to physically model granular materials in the three regimes
Prediction of transmembrane helix orientation in polytopic membrane proteins
Directory of Open Access Journals (Sweden)
Liang Jie
2006-06-01
Full Text Available Abstract Background Membrane proteins compose up to 30% of coding sequences within genomes. However, their structure determination is lagging behind compared with soluble proteins due to the experimental difficulties. Therefore, it is important to develop reliable computational methods to predict structures of membrane proteins. Results We present a method for prediction of the TM helix orientation, which is an essential step in ab initio modeling of membrane proteins. Our method is based on a canonical model of the heptad repeat originally developed for coiled coils. We identify the helical surface patches that interface with lipid molecules at an accuracy of about 88% from the sequence information alone, using an empirical scoring function LIPS (LIPid-facing Surface, which combines lipophilicity and conservation of residues in the helix. We test and discuss results of prediction of helix-lipid interfaces on 162 transmembrane helices from 18 polytopic membrane proteins and present predicted orientations of TM helices in TRPV1 channel. We also apply our method to two structures of homologous cytochrome b6f complexes and find discrepancy in the assignment of TM helices from subunits PetG, PetN and PetL. The results of LIPS calculations and analysis of packing and H-bonding interactions support the helix assignment found in the cytochrome b6f structure from green alga but not the assignment of TM helices in the cyanobacterium b6f structure. Conclusion LIPS calculations can be used for the prediction of helix orientation in ab initio modeling of polytopic membrane proteins. We also show with the example of two cytochrome b6f structures that our method can identify questionable helix assignments in membrane proteins. The LIPS server is available online at http://gila.bioengr.uic.edu/lab/larisa/lips.html.
Complex Modeling - SAHG | LSDB Archive [Life Science Database Archive metadata
Lifescience Database Archive (English)
Full Text Available List Contact us SAHG Complex Modeling Data detail Data name Complex Modeling DOI 10.18908/lsdba.nbdc01193-00...3 Description of data contents Protein-protein copmlex modeling predition Data file File name: sahg_complex....zip File URL: ftp://ftp.biosciencedbc.jp/archive/sahg/LATEST/sahg_complex.zip File size: 147 KB Simple searc...h URL http://togodb.biosciencedbc.jp/togodb/view/sahg_complex#en Data acquisition... method If a target sequence was related to a given subunit of a template complex in PQS database with >=80%
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server
DEFF Research Database (Denmark)
Käll, Lukas; Krogh, Anders; Sonnhammer, Erik L L
2007-01-01
predicted transmembrane topologies overlap. This impairs predictions of 5-10% of the proteome, hence this is an important issue in protein annotation. To address this problem, we previously designed a hidden Markov model, Phobius, that combines transmembrane topology and signal peptide predictions....... The method makes an optimal choice between transmembrane segments and signal peptides, and also allows constrained and homology-enriched predictions. We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius. Udgivelsesdato: 2007-Jul...
Modeling competitive substitution in a polyelectrolyte complex
Energy Technology Data Exchange (ETDEWEB)
Peng, B.; Muthukumar, M., E-mail: muthu@polysci.umass.edu [Department of Polymer Science and Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003 (United States)
2015-12-28
We have simulated the invasion of a polyelectrolyte complex made of a polycation chain and a polyanion chain, by another longer polyanion chain, using the coarse-grained united atom model for the chains and the Langevin dynamics methodology. Our simulations reveal many intricate details of the substitution reaction in terms of conformational changes of the chains and competition between the invading chain and the chain being displaced for the common complementary chain. We show that the invading chain is required to be sufficiently longer than the chain being displaced for effecting the substitution. Yet, having the invading chain to be longer than a certain threshold value does not reduce the substitution time much further. While most of the simulations were carried out in salt-free conditions, we show that presence of salt facilitates the substitution reaction and reduces the substitution time. Analysis of our data shows that the dominant driving force for the substitution process involving polyelectrolytes lies in the release of counterions during the substitution.
Complex networks repair strategies: Dynamic models
Fu, Chaoqi; Wang, Ying; Gao, Yangjun; Wang, Xiaoyang
2017-09-01
Network repair strategies are tactical methods that restore the efficiency of damaged networks; however, unreasonable repair strategies not only waste resources, they are also ineffective for network recovery. Most extant research on network repair focuses on static networks, but results and findings on static networks cannot be applied to evolutionary dynamic networks because, in dynamic models, complex network repair has completely different characteristics. For instance, repaired nodes face more severe challenges, and require strategic repair methods in order to have a significant effect. In this study, we propose the Shell Repair Strategy (SRS) to minimize the risk of secondary node failures due to the cascading effect. Our proposed method includes the identification of a set of vital nodes that have a significant impact on network repair and defense. Our identification of these vital nodes reduces the number of switching nodes that face the risk of secondary failures during the dynamic repair process. This is positively correlated with the size of the average degree and enhances network invulnerability.
Rigidity of transmembrane proteins determines their cluster shape
Jafarinia, Hamidreza; Jalali, Mir Abbas
2015-01-01
Protein aggregation in cell membrane is vital for majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\\alpha$-helices and $\\beta$-sheets have different structural rigidity. We use molecular dynamics simulation of a coarse-grained model of protein-embedded lipid membranes to investigate the mechanisms of protein clustering. For a variety of protein concentrations, our simulations in thermal equilibrium conditions reveal that the structural rigidity of transmembrane domains dramatically affects interactions and changes the shape of the cluster. We have observed stable large aggregates even in the absence of hydrophobic mismatch which has been previously proposed as the mechanism of protein aggregation. According to our results, semi-flexible proteins aggregate to form two-dimensional clusters while rigid proteins, by contrast, form one-dimensional string-like structures. By assuming two probable scenarios for the formation of a two-dimensional tr...
Modeling Complex Chemical Systems: Problems and Solutions
van Dijk, Jan
2016-09-01
Non-equilibrium plasmas in complex gas mixtures are at the heart of numerous contemporary technologies. They typically contain dozens to hundreds of species, involved in hundreds to thousands of reactions. Chemists and physicists have always been interested in what are now called chemical reduction techniques (CRT's). The idea of such CRT's is that they reduce the number of species that need to be considered explicitly without compromising the validity of the model. This is usually achieved on the basis of an analysis of the reaction time scales of the system under study, which identifies species that are in partial equilibrium after a given time span. The first such CRT that has been widely used in plasma physics was developed in the 1960's and resulted in the concept of effective ionization and recombination rates. It was later generalized to systems in which multiple levels are effected by transport. In recent years there has been a renewed interest in tools for chemical reduction and reaction pathway analysis. An example of the latter is the PumpKin tool. Another trend is that techniques that have previously been developed in other fields of science are adapted as to be able to handle the plasma state of matter. Examples are the Intrinsic Low Dimension Manifold (ILDM) method and its derivatives, which originate from combustion engineering, and the general-purpose Principle Component Analysis (PCA) technique. In this contribution we will provide an overview of the most common reduction techniques, then critically assess the pros and cons of the methods that have gained most popularity in recent years. Examples will be provided for plasmas in argon and carbon dioxide.
Clinical complexity in medicine: A measurement model of task and patient complexity
Islam, R.; Weir, C.; Fiol, G. Del
2016-01-01
Summary Background Complexity in medicine needs to be reduced to simple components in a way that is comprehensible to researchers and clinicians. Few studies in the current literature propose a measurement model that addresses both task and patient complexity in medicine. Objective The objective of this paper is to develop an integrated approach to understand and measure clinical complexity by incorporating both task and patient complexity components focusing on infectious disease domain. The measurement model was adapted and modified to healthcare domain. Methods Three clinical Infectious Disease teams were observed, audio-recorded and transcribed. Each team included an Infectious Diseases expert, one Infectious Diseases fellow, one physician assistant and one pharmacy resident fellow. The transcripts were parsed and the authors independently coded complexity attributes. This baseline measurement model of clinical complexity was modified in an initial set of coding process and further validated in a consensus-based iterative process that included several meetings and email discussions by three clinical experts from diverse backgrounds from the Department of Biomedical Informatics at the University of Utah. Inter-rater reliability was calculated using Cohen’s kappa. Results The proposed clinical complexity model consists of two separate components. The first is a clinical task complexity model with 13 clinical complexity-contributing factors and 7 dimensions. The second is the patient complexity model with 11 complexity-contributing factors and 5 dimensions. Conclusion The measurement model for complexity encompassing both task and patient complexity will be a valuable resource for future researchers and industry to measure and understand complexity in healthcare. PMID:26404626
Transmembrane Inhibitor of RICTOR/mTORC2 in Hematopoietic Progenitors
Directory of Open Access Journals (Sweden)
Dongjun Lee
2014-11-01
Full Text Available Central to cellular proliferative, survival, and metabolic responses is the serine/threonine kinase mTOR, which is activated in many human cancers. mTOR is present in distinct complexes that are either modulated by AKT (mTORC1 or are upstream and regulatory of it (mTORC2. Governance of mTORC2 activity is poorly understood. Here, we report a transmembrane molecule in hematopoietic progenitor cells that physically interacts with and inhibits RICTOR, an essential component of mTORC2. Upstream of mTORC2 (UT2 negatively regulates mTORC2 enzymatic activity, reducing AKTS473, PKCα, and NDRG1 phosphorylation and increasing FOXO transcriptional activity in an mTORC2-dependent manner. Modulating UT2 levels altered animal survival in a T cell acute lymphoid leukemia (T-ALL model that is known to be mTORC2 sensitive. These studies identify an inhibitory component upstream of mTORC2 in hematopoietic cells that can reduce mortality from NOTCH-induced T-ALL. A transmembrane inhibitor of mTORC2 may provide an attractive target to affect this critical cell regulatory pathway.
Chyau, Charng-Cherng; Ker, Yaw-Bee; Chang, Chi-Huang; Huang, Shiau-Huei; Wang, Hui-Er; Peng, Chiung-Chi; Peng, Robert Y.
2014-01-01
Schisandra chinensis (Turz Baill) (S. chinensis) (SC) fruit is a hepatoprotective herb containing many lignans and a large amount of polysaccharides. A novel polysaccharide (called SC-2) was isolated from SC of MW 841 kDa, which exhibited a protein-to-polysaccharide ratio of 0.4089, and showed a characteristic FTIR spectrum of a peptidoglycan. Powder X-ray diffraction revealed microcrystalline structures within SC-2. SC-2 contained 10 monosaccharides and 15 amino acids (essential amino acids of 78.12%w/w). In a HepG2 cell model, SC-2 was shown by MTT and TUNEL assay to be completely non-cytotoxic. A kinetic analysis and fluorescence-labeling technique revealed no intracellular disposition of SC-2. Combined treatment of lignans with SC-2 enhanced the intracellular transport of schisandrin B and deoxyschisandrin but decreased that of gomisin C, resulting in alteration of cell-killing bioactivity. The Second Law of Thermodynamics allows this type of unidirectional transport. Conclusively, SC-2 alters the transport and cell killing capability by a “Catcher-Pitcher Unidirectional Transport Mechanism”. PMID:24475039
Directory of Open Access Journals (Sweden)
Charng-Cherng Chyau
Full Text Available Schisandra chinensis (Turz Baill (S. chinensis (SC fruit is a hepatoprotective herb containing many lignans and a large amount of polysaccharides. A novel polysaccharide (called SC-2 was isolated from SC of MW 841 kDa, which exhibited a protein-to-polysaccharide ratio of 0.4089, and showed a characteristic FTIR spectrum of a peptidoglycan. Powder X-ray diffraction revealed microcrystalline structures within SC-2. SC-2 contained 10 monosaccharides and 15 amino acids (essential amino acids of 78.12%w/w. In a HepG2 cell model, SC-2 was shown by MTT and TUNEL assay to be completely non-cytotoxic. A kinetic analysis and fluorescence-labeling technique revealed no intracellular disposition of SC-2. Combined treatment of lignans with SC-2 enhanced the intracellular transport of schisandrin B and deoxyschisandrin but decreased that of gomisin C, resulting in alteration of cell-killing bioactivity. The Second Law of Thermodynamics allows this type of unidirectional transport. Conclusively, SC-2 alters the transport and cell killing capability by a "Catcher-Pitcher Unidirectional Transport Mechanism".
Berry, Edward A; Walker, F Ann
2008-05-01
Early investigation of the electron paramagnetic resonance spectra of bis-histidine-coordinated membrane-bound ferriheme proteins led to the description of a spectral signal that had only one resolved feature. These became known as "highly anisotropic low-spin" or "large g(max)" ferriheme centers. Extensive work with small-molecule model heme complexes showed that this spectroscopic signature occurs in bis-imidazole ferrihemes in which the planes of the imidazole ligands are nearly perpendicular, deltaphi = 57-90 degrees. In the last decade protein crystallographic studies have revealed the atomic structures of a number of examples of bis-histidine heme proteins. A frequent characteristic of these large g(max) ferrihemes in membrane-bound proteins is the occurrence of the heme within a four-helix bundle with a left-handed twist. The histidine ligands occur at the same level on two diametrically opposed helices of the bundle. These ligands have the same side-chain conformation and ligate heme iron on the bundle axis, resulting in a quasi-twofold symmetric structure. The two non-ligand-bearing helices also obey this symmetry, and have a conserved small residue, usually glycine, where the edge of the heme ring makes contact with the helix backbones. In many cases this small residue is preceded by a threonine or serine residue whose side-chain hydroxyl oxygen acts as a hydrogen-bond acceptor from the N(delta1) atom of the heme-ligating histidine. The deltaphi angle is thus determined by the common histidine side-chain conformation and the crossing angle of the ligand-bearing helices, in some cases constrained by hydrogen bonds to the serine/threonine residues on the non-ligand-bearing helices.
Mixed Effects Models for Complex Data
Wu, Lang
2009-01-01
Presenting effective approaches to address missing data, measurement errors, censoring, and outliers in longitudinal data, this book covers linear, nonlinear, generalized linear, nonparametric, and semiparametric mixed effects models. It links each mixed effects model with the corresponding class of regression model for cross-sectional data and discusses computational strategies for likelihood estimations of mixed effects models. The author briefly describes generalized estimating equations methods and Bayesian mixed effects models and explains how to implement standard models using R and S-Pl
A Measure of Learning Model Complexity by VC Dimension
Institute of Scientific and Technical Information of China (English)
WANG Wen-jian; ZHANG Li-xia; XU Zong-ben
2002-01-01
When developing models there is always a trade-off between model complexity and model fit. In this paper, a measure of learning model complexity based on VC dimension is presented, and some relevant mathematical theory surrounding the derivation and use of this metric is summarized. The measure allows modelers to control the amount of error that is returned from a modeling system and to state upper bounds on the amount of error that the modeling system will return on all future, as yet unseen and uncollected data sets. It is possible for modelers to use the VC theory to determine which type of model more accurately represents a system.
Multi-perspective modelling of complex phenomena
Seck, M.D.; Honig, H.J.
2012-01-01
This conceptual paper discusses the limitations of a single-perspective hierarchical approach to modelling and proposes multi-perspective modelling as a way to overcome them. As it turns out, multi-perspective modelling is primarily a new methodology, using existing modelling techniques but
Lin, Ying-Ju; Wu, Suh-Chin
2005-01-01
The formation of the flavivirus prM-E complex is an important step for the biogenesis of immature virions, which is followed by a subsequent cleavage of prM to M protein through cellular protease to result in the production and release of mature virions. In this study, the intracellular formation of the prM-E complex of Japanese encephalitis virus was investigated by baculovirus coexpression of prM and E in trans in Sf9 insect cells as analyzed by anti-E antibody immunoprecipitation and sucro...
Complex systems modeling by cellular automata
Kroc, J.; Sloot, P.M.A.; Rabuñal Dopico, J.R.; Dorado de la Calle, J.; Pazos Sierra, A.
2009-01-01
In recent years, the notion of complex systems proved to be a very useful concept to define, describe, and study various natural phenomena observed in a vast number of scientific disciplines. Examples of scientific disciplines that highly benefit from this concept range from physics, mathematics, an
The utility of Earth system Models of Intermediate Complexity
Weber, S.L.
2010-01-01
Intermediate-complexity models are models which describe the dynamics of the atmosphere and/or ocean in less detail than conventional General Circulation Models (GCMs). At the same time, they go beyond the approach taken by atmospheric Energy Balance Models (EBMs) or ocean box models by
Advances in dynamic network modeling in complex transportation systems
Ukkusuri, Satish V
2013-01-01
This book focuses on the latest in dynamic network modeling, including route guidance and traffic control in transportation systems and other complex infrastructure networks. Covers dynamic traffic assignment, flow modeling, mobile sensor deployment and more.
The Cognitive Complexity in Modelling the Group Decision Process
Directory of Open Access Journals (Sweden)
Barna Iantovics
2010-06-01
Full Text Available The paper investigates for some basic contextual factors (such
us the problem complexity, the users' creativity and the problem space complexity the cognitive complexity associated with modelling the group decision processes (GDP in e-meetings. The analysis is done by conducting a socio-simulation experiment for an envisioned collaborative software tool that acts as a stigmergic environment for modelling the GDP. The simulation results revels some interesting design guidelines for engineering some contextual functionalities that minimize the cognitive complexity associated with modelling the GDP.
Modelling Complex Inlet Geometries in CFD
DEFF Research Database (Denmark)
Skovgaard, M.; Nielsen, Peter V.
Modem inlet devices applied in the field of ventilation of rooms are getting more complex in terms of geometry in order to fulfil the occupants' demand for thermal comfort in the room and in order to decrease the energy consumption. This expresses the need for a more precise calculation of the fl...... and tested. The method is based upon threedimensional - and radial wall jet theory and upon diffuser specific experimental data....
Modeling Electronic Properties of Complex Oxides
Krishnaswamy, Karthik
Complex oxides are a class of materials that have recently emerged as potential candidates for electronic applications owing to their interesting electronic properties. The goal of this dissertation is to develop a fundamental understanding of these electronic properties using a combination of first-principles approaches based on density functional theory (DFT), and Schr odinger-Poisson (SP) simulation (Abstract shortened by ProQuest.
Goncharuk, M V; Shul'ga, A A; Ermoliuk, Ia S; Tkach, E N; Goncharuk, S A; Pustovalova, Iu E; Mineev, K S; Bocharov, É V; Maslennikov, I V; Arsen'ev, A S; Kirpichnikov, M P
2011-01-01
A family of epidermal growth factor receptors, ErbB, represents an important class of receptor tyrosine kinases, playing a leading role in cellular growth, development and differentiation. Transmembrane domains of these receptors transduce biochemical signals across plasma membrane via lateral homo- and heterodimerization. Relatively small size of complexes of ErbB transmembrane domains with detergents or lipids allows one to study their detailed spatial structure using three-dimensional heteronuclear high-resolution NMR spectroscopy. Here, we describe the effective expression system and purification procedure for preparative-scale production of transmembrane peptides from four representatives of ErbB family, ErbB1, ErbB2, ErbB3, ErbB4, for structural studies. The recombinant peptides were produced in Escherichia coli BL21(DE3)pLysS as C-terminal extensions of thioredoxin A. The fusion protein cleavage was accomplished with the light subunit of human enterokinase. Several (10-30) milligrams of purified isotope-labeled transmembrane peptides were isolated with the use of a simple and convenient procedure, which consists of consecutive steps of immobilized metal affinity chromatography and cation-exchange chromatography. The purified peptides were reconstituted in lipid/detergent environment (micelles or bicelles) and characterized using dynamic light scattering, CD and NMR spectroscopy. The data obtained indicate that the purified ErbB transmembrane peptides are suitable for structural and dynamic studies of their homo- and heterodimer complexes using high resolution NMR spectroscopy.
Linking Complexity and Sustainability Theories: Implications for Modeling Sustainability Transitions
Directory of Open Access Journals (Sweden)
Camaren Peter
2014-03-01
Full Text Available In this paper, we deploy a complexity theory as the foundation for integration of different theoretical approaches to sustainability and develop a rationale for a complexity-based framework for modeling transitions to sustainability. We propose a framework based on a comparison of complex systems’ properties that characterize the different theories that deal with transitions to sustainability. We argue that adopting a complexity theory based approach for modeling transitions requires going beyond deterministic frameworks; by adopting a probabilistic, integrative, inclusive and adaptive approach that can support transitions. We also illustrate how this complexity-based modeling framework can be implemented; i.e., how it can be used to select modeling techniques that address particular properties of complex systems that we need to understand in order to model transitions to sustainability. In doing so, we establish a complexity-based approach towards modeling sustainability transitions that caters for the broad range of complex systems’ properties that are required to model transitions to sustainability.
Complex Systems and Human Performance Modeling
2013-12-01
constitute a cognitive architecture or decomposing the work flows and resource constraints that characterize human-system interactions, the modeler...also explored the generation of so-called “ fractal ” series from simple task network models where task times are the calculated by way of a moving
Information, complexity and efficiency: The automobile model
Energy Technology Data Exchange (ETDEWEB)
Allenby, B. [Lucent Technologies (United States)]|[Lawrence Livermore National Lab., CA (United States)
1996-08-08
The new, rapidly evolving field of industrial ecology - the objective, multidisciplinary study of industrial and economic systems and their linkages with fundamental natural systems - provides strong ground for believing that a more environmentally and economically efficient economy will be more information intensive and complex. Information and intellectual capital will be substituted for the more traditional inputs of materials and energy in producing a desirable, yet sustainable, quality of life. While at this point this remains a strong hypothesis, the evolution of the automobile industry can be used to illustrate how such substitution may, in fact, already be occurring in an environmentally and economically critical sector.
Lau, Tong-Lay; Partridge, Anthony W; Ginsberg, Mark H; Ulmer, Tobias S
2008-04-01
Integrin adhesion receptors transduce bidirectional signals across the plasma membrane, with the integrin transmembrane domains acting as conduits in this process. Here, we report the first high-resolution structure of an integrin transmembrane domain. To assess the influence of the membrane model system, structure determinations of the beta3 integrin transmembrane segment and flanking sequences were carried out in both phospholipid bicelles and detergent micelles. In bicelles, a 30-residue linear alpha-helix, encompassing residues I693-H772, is adopted, of which I693-I721 appear embedded in the hydrophobic bicelle core. This relatively long transmembrane helix implies a pronounced helix tilt within a typical lipid bilayer, which facilitates the snorkeling of K716's charged side chain out of the lipid core while simultaneously immersing hydrophobic L717-I721 in the membrane. A shortening of bicelle lipid hydrocarbon tails does not lead to the transfer of L717-I721 into the aqueous phase, suggesting that the reported embedding represents the preferred beta3 state. The nature of the lipid headgroup affected only the intracellular part of the transmembrane helix, indicating that an asymmetric lipid distribution is not required for studying the beta3 transmembrane segment. In the micelle, residues L717-I721 are also embedded but deviate from linear alpha-helical conformation in contrast to I693-K716, which closely resemble the bicelle structure.
Cellular Potts modeling of complex multicellular behaviors in tissue morphogenesis
T. Hirashima (Tsuyoshi); E.G. Rens (Lisanne); R.M.H. Merks (Roeland)
2017-01-01
textabstractMathematical modeling is an essential approach for the understanding of complex multicellular behaviors in tissue morphogenesis. Here, we review the cellular Potts model (CPM; also known as the Glazier-Graner-Hogeweg model), an effective computational modeling framework. We discuss its
Mathematical modeling of complex noise barriers
Energy Technology Data Exchange (ETDEWEB)
Hayek, S.I.
1982-01-01
Mathematical modeling of the noise reduction efficiency of highway noise barriers depends on the shape and absorptivity of the barrier, the influence of the impedance of the ground under the receiver, the atmospheric conditions as well as traffic details. The mathematical model for a barrier's noise reduction requires the knowledge of point-to-point acoustic diffraction models. In many instances, the shape of the barrier is simple; such as thin wall (edge), sharp wedge, and cylindrically topped berms. However, new designs of more efficient barriers have been investigated recently.
Complex spectrum of spin models for finite-density QCD
Nishimura, Hiromichi; Pangeni, Kamal
2016-01-01
We consider the spectrum of transfer matrix eigenvalues associated with Polyakov loops in lattice QCD at strong coupling. The transfer matrix at finite density is non-Hermitian, and its eigenvalues become complex as a manifestation of the sign problem. We show that the symmetry under charge conjugation and complex conjugation ensures that the eigenvalues are either real or part of a complex conjugate pair, and the complex pairs lead to damped oscillatory behavior in Polyakov loop correlation functions, which also appeared in our previous phenomenological models using complex saddle points. We argue that this effect should be observable in lattice simulations of QCD at finite density.
Modeling Power Systems as Complex Adaptive Systems
Energy Technology Data Exchange (ETDEWEB)
Chassin, David P.; Malard, Joel M.; Posse, Christian; Gangopadhyaya, Asim; Lu, Ning; Katipamula, Srinivas; Mallow, J V.
2004-12-30
Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today's most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This report explores the state-of-the-art physical analogs for understanding the behavior of some econophysical systems and deriving stable and robust control strategies for using them. We review and discuss applications of some analytic methods based on a thermodynamic metaphor, according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood. We apply these methods to the question of how power markets can be expected to behave under a variety of conditions.
Smart modeling and simulation for complex systems practice and theory
Ren, Fenghui; Zhang, Minjie; Ito, Takayuki; Tang, Xijin
2015-01-01
This book aims to provide a description of these new Artificial Intelligence technologies and approaches to the modeling and simulation of complex systems, as well as an overview of the latest scientific efforts in this field such as the platforms and/or the software tools for smart modeling and simulating complex systems. These tasks are difficult to accomplish using traditional computational approaches due to the complex relationships of components and distributed features of resources, as well as the dynamic work environments. In order to effectively model the complex systems, intelligent technologies such as multi-agent systems and smart grids are employed to model and simulate the complex systems in the areas of ecosystem, social and economic organization, web-based grid service, transportation systems, power systems and evacuation systems.
Stability of Rotor Systems: A Complex Modelling Approach
DEFF Research Database (Denmark)
Kliem, Wolfhard; Pommer, Christian; Stoustrup, Jakob
1996-01-01
A large class of rotor systems can be modelled by a complex matrix differential equation of secondorder. The angular velocity of the rotor plays the role of a parameter. We apply the Lyapunov matrix equation in a complex setting and prove two new stability results which are compared with the resu......A large class of rotor systems can be modelled by a complex matrix differential equation of secondorder. The angular velocity of the rotor plays the role of a parameter. We apply the Lyapunov matrix equation in a complex setting and prove two new stability results which are compared...
Mathematical modeling and optimization of complex structures
Repin, Sergey; Tuovinen, Tero
2016-01-01
This volume contains selected papers in three closely related areas: mathematical modeling in mechanics, numerical analysis, and optimization methods. The papers are based upon talks presented on the International Conference for Mathematical Modeling and Optimization in Mechanics, held in Jyväskylä, Finland, March 6-7, 2014 dedicated to Prof. N. Banichuk on the occasion of his 70th birthday. The articles are written by well-known scientists working in computational mechanics and in optimization of complicated technical models. Also, the volume contains papers discussing the historical development, the state of the art, new ideas, and open problems arising in modern continuum mechanics and applied optimization problems. Several papers are concerned with mathematical problems in numerical analysis, which are also closely related to important mechanical models. The main topics treated include: * Computer simulation methods in mechanics, physics, and biology; * Variational problems and methods; minimiz...
Investigating complex networks with inverse models
Wens, Vincent
2014-01-01
Recent advances in neuroscience have motivated the study of network organization in spatially distributed dynamical systems from indirect measurements. However, the associated connectivity estimation, when combined with inverse modeling, is strongly affected by spatial leakage. We formulate this problem in a general framework and develop a new approach to model spatial leakage and limit its effects. It is analytically compared to existing regression-based methods used in electrophysiology, which are shown to yield biased estimates of amplitude and phase couplings.
A complex autoregressive model and application to monthly temperature forecasts
Directory of Open Access Journals (Sweden)
X. Gu
2005-11-01
Full Text Available A complex autoregressive model was established based on the mathematic derivation of the least squares for the complex number domain which is referred to as the complex least squares. The model is different from the conventional way that the real number and the imaginary number are separately calculated. An application of this new model shows a better forecast than forecasts from other conventional statistical models, in predicting monthly temperature anomalies in July at 160 meteorological stations in mainland China. The conventional statistical models include an autoregressive model, where the real number and the imaginary number are separately disposed, an autoregressive model in the real number domain, and a persistence-forecast model.
Understanding complex urban systems integrating multidisciplinary data in urban models
Gebetsroither-Geringer, Ernst; Atun, Funda; Werner, Liss
2016-01-01
This book is devoted to the modeling and understanding of complex urban systems. This second volume of Understanding Complex Urban Systems focuses on the challenges of the modeling tools, concerning, e.g., the quality and quantity of data and the selection of an appropriate modeling approach. It is meant to support urban decision-makers—including municipal politicians, spatial planners, and citizen groups—in choosing an appropriate modeling approach for their particular modeling requirements. The contributors to this volume are from different disciplines, but all share the same goal: optimizing the representation of complex urban systems. They present and discuss a variety of approaches for dealing with data-availability problems and finding appropriate modeling approaches—and not only in terms of computer modeling. The selection of articles featured in this volume reflect a broad variety of new and established modeling approaches such as: - An argument for using Big Data methods in conjunction with Age...
Modeling complex systems in the geosciences
Balcerak, Ernie
2013-03-01
Many geophysical phenomena can be described as complex systems, involving phenomena such as extreme or "wild" events that often do not follow the Gaussian distribution that would be expected if the events were simply random and uncorrelated. For instance, some geophysical phenomena like earthquakes show a much higher occurrence of relatively large values than would a Gaussian distribution and so are examples of the "Noah effect" (named by Benoit Mandelbrot for the exceptionally heavy rain in the biblical flood). Other geophysical phenomena are examples of the "Joseph effect," in which a state is especially persistent, such as a spell of multiple consecutive hot days (heat waves) or several dry summers in a row. The Joseph effect was named after the biblical story in which Joseph's dream of seven fat cows and seven thin ones predicted 7 years of plenty followed by 7 years of drought.
Transmembrane anion transport and cytotoxicity of synthetic tambjamine analogs.
Hernando, Elsa; Soto-Cerrato, Vanessa; Cortés-Arroyo, Susana; Pérez-Tomás, Ricardo; Quesada, Roberto
2014-03-21
Ten synthetic analogs of the marine alkaloids tambjamines, bearing aromatic enamine moieties, have been synthesized. These compounds proved to be highly efficient transmembrane anion transporters in model liposomes. Changes in the electronic nature of the substituents of the aromatic enamine or the alkoxy group of the central pyrrole group did not affect this anionophore activity. The in vitro activity of these compounds has also been studied. They trigger apoptosis in several cancer cell lines with IC50 values in the low micromolar range as well as modify the intracellular pH, inducing the basification of acidic organelles.
Esque, Jérémy; Urbain, Aurélie; Etchebest, Catherine; de Brevern, Alexandre G
2015-11-01
Transmembrane proteins (TMPs) are major drug targets, but the knowledge of their precise topology structure remains highly limited compared with globular proteins. In spite of the difficulties in obtaining their structures, an important effort has been made these last years to increase their number from an experimental and computational point of view. In view of this emerging challenge, the development of computational methods to extract knowledge from these data is crucial for the better understanding of their functions and in improving the quality of structural models. Here, we revisit an efficient unsupervised learning procedure, called Hybrid Protein Model (HPM), which is applied to the analysis of transmembrane proteins belonging to the all-α structural class. HPM method is an original classification procedure that efficiently combines sequence and structure learning. The procedure was initially applied to the analysis of globular proteins. In the present case, HPM classifies a set of overlapping protein fragments, extracted from a non-redundant databank of TMP 3D structure. After fine-tuning of the learning parameters, the optimal classification results in 65 clusters. They represent at best similar relationships between sequence and local structure properties of TMPs. Interestingly, HPM distinguishes among the resulting clusters two helical regions with distinct hydrophobic patterns. This underlines the complexity of the topology of these proteins. The HPM classification enlightens unusual relationship between amino acids in TMP fragments, which can be useful to elaborate new amino acids substitution matrices. Finally, two challenging applications are described: the first one aims at annotating protein functions (channel or not), the second one intends to assess the quality of the structures (X-ray or models) via a new scoring function deduced from the HPM classification.
NMR-based approach to measure the free energy of transmembrane helix-helix interactions.
Mineev, Konstantin S; Lesovoy, Dmitry M; Usmanova, Dinara R; Goncharuk, Sergey A; Shulepko, Mikhail A; Lyukmanova, Ekaterina N; Kirpichnikov, Mikhail P; Bocharov, Eduard V; Arseniev, Alexander S
2014-01-01
Knowledge of the energetic parameters of transmembrane helix-helix interactions is necessary for the establishment of a structure-energy relationship for α-helical membrane domains. A number of techniques have been developed to measure the free energies of dimerization and oligomerization of transmembrane α-helices, and all of these have their advantages and drawbacks. In this study we propose a methodology to determine the magnitudes of the free energy of interactions between transmembrane helices in detergent micelles. The suggested approach employs solution nuclear magnetic resonance (NMR) spectroscopy to determine the population of the oligomeric states of the transmembrane domains and introduces a new formalism to describe the oligomerization equilibrium, which is based on the assumption that both the dimerization of the transmembrane domains and the dissociation of the dimer can occur only upon the collision of detergent micelles. The technique has three major advantages compared with other existing approaches: it may be used to analyze both weak and relatively strong dimerization/oligomerization processes, it works well for the analysis of complex equilibria, e.g. when monomer, dimer and high-order oligomer populations are simultaneously present in the solution, and it can simultaneously yield both structural and energetic characteristics of the helix-helix interaction under study. The proposed methodology was applied to investigate the oligomerization process of transmembrane domains of fibroblast growth factor receptor 3 (FGFR3) and vascular endothelium growth factor receptor 2 (VEGFR2), and allowed the measurement of the free energy of dimerization of both of these objects. In addition the proposed method was able to describe the multi-state oligomerization process of the VEGFR2 transmembrane domain.
Modelling Complex Relevance Spaces with Copulas
C. Eickhoff (Carsten); A.P. de Vries (Arjen)
2014-01-01
htmlabstractModern relevance models consider a wide range of criteria in order to identify those documents that are expected to satisfy the user's information need. With growing dimensionality of the underlying relevance spaces the need for sophisticated score combination and estimation schemes
The sigma model on complex projective superspaces
Energy Technology Data Exchange (ETDEWEB)
Candu, Constantin; Mitev, Vladimir; Schomerus, Volker [DESY, Hamburg (Germany). Theory Group; Quella, Thomas [Amsterdam Univ. (Netherlands). Inst. for Theoretical Physics; Saleur, Hubert [CEA Saclay, 91 - Gif-sur-Yvette (France). Inst. de Physique Theorique; USC, Los Angeles, CA (United States). Physics Dept.
2009-08-15
The sigma model on projective superspaces CP{sup S-1} {sup vertical} {sup stroke} {sup S} gives rise to a continuous family of interacting 2D conformal field theories which are parametrized by the curvature radius R and the theta angle {theta}. Our main goal is to determine the spectrum of the model, non-perturbatively as a function of both parameters. We succeed to do so for all open boundary conditions preserving the full global symmetry of the model. In string theory parlor, these correspond to volume filling branes that are equipped with a monopole line bundle and connection. The paper consists of two parts. In the first part, we approach the problem within the continuum formulation. Combining combinatorial arguments with perturbative studies and some simple free field calculations, we determine a closed formula for the partition function of the theory. This is then tested numerically in the second part. There we propose a spin chain regularization of the CP{sup S-1} {sup vertical} {sup stroke} {sup S} model with open boundary conditions and use it to determine the spectrum at the conformal fixed point. The numerical results are in remarkable agreement with the continuum analysis. (orig.)
Non-commutative Complex Projective Spaces and the Standard Model
Dolan, Brian P
2003-01-01
The standard model fermion spectrum, including a right handed neutrino, can be obtained as a zero-mode of the Dirac operator on a space which is the product of complex projective spaces of complex dimension two and three. The construction requires the introduction of topologically non-trivial background gauge fields. By borrowing from ideas in Connes' non-commutative geometry and making the complex spaces `fuzzy' a matrix approximation to the fuzzy space allows for three generations to emerge...
Localized lipid packing of transmembrane domains impedes integrin clustering.
Directory of Open Access Journals (Sweden)
Mehrdad Mehrbod
Full Text Available Integrin clustering plays a pivotal role in a host of cell functions. Hetero-dimeric integrin adhesion receptors regulate cell migration, survival, and differentiation by communicating signals bidirectionally across the plasma membrane. Thus far, crystallographic structures of integrin components are solved only separately, and for some integrin types. Also, the sequence of interactions that leads to signal transduction remains ambiguous. Particularly, it remains controversial whether the homo-dimerization of integrin transmembrane domains occurs following the integrin activation (i.e. when integrin ectodomain is stretched out or if it regulates integrin clustering. This study employs molecular dynamics modeling approaches to address these questions in molecular details and sheds light on the crucial effect of the plasma membrane. Conducting a normal mode analysis of the intact αllbβ3 integrin, it is demonstrated that the ectodomain and transmembrane-cytoplasmic domains are connected via a membrane-proximal hinge region, thus merely transmembrane-cytoplasmic domains are modeled. By measuring the free energy change and force required to form integrin homo-oligomers, this study suggests that the β-subunit homo-oligomerization potentially regulates integrin clustering, as opposed to α-subunit, which appears to be a poor regulator for the clustering process. If α-subunits are to regulate the clustering they should overcome a high-energy barrier formed by a stable lipid pack around them. Finally, an outside-in activation-clustering scenario is speculated, explaining how further loading the already-active integrin affects its homo-oligomerization so that focal adhesions grow in size.
The cystic fibrosis transmembrane recruiter the alter ego of CFTR as a multi-kinase anchor.
Mehta, Anil
2007-11-01
This review focuses on a newly discovered interaction between protein kinases involved in cellular energetics, a process that may be disturbed in cystic fibrosis for unknown reasons. I propose a new model where kinase-mediated cellular transmission of energy provides mechanistic insight to a latent role of the cystic fibrosis transmembrane conductance regulator (CFTR). I suggest that CFTR acts as a multi-kinase recruiter to the apical epithelial membrane. My group finds that, in the cytosol, two protein kinases involved in cell energy homeostasis, nucleoside diphosphate kinase (NDPK) and AMP-activated kinase (AMPK), bind one another. Preliminary data suggest that both can also bind CFTR (function unclear). The disrupted role of this CFTR-kinase complex as 'membrane transmitter to the cell' is proposed as an alternative paradigm to the conventional ion transport mediated and CFTR/chloride-centric view of cystic fibrosis pathogenesis. Chloride remains important, but instead, chloride-induced control of the phosphohistidine content of one kinase component (NDPK, via a multi-kinase complex that also includes a third kinase, CK2; formerly casein kinase 2). I suggest that this complex provides the necessary near-equilibrium conditions needed for efficient transmission of phosphate energy to proteins controlling cellular energetics. Crucially, a new role for CFTR as a kinase controller is proposed with ionic concentration acting as a signal. The model posits a regulatory control relay for energy sensing involving a cascade of protein kinases bound to CFTR.
A musculoskeletal model of the elbow joint complex
Gonzalez, Roger V.; Barr, Ronald E.; Abraham, Lawrence D.
1993-01-01
This paper describes a musculoskeletal model that represents human elbow flexion-extension and forearm pronation-supination. Musculotendon parameters and the skeletal geometry were determined for the musculoskeletal model in the analysis of ballistic elbow joint complex movements. The key objective was to develop a computational model, guided by optimal control, to investigate the relationship among patterns of muscle excitation, individual muscle forces, and movement kinematics. The model was verified using experimental kinematic, torque, and electromyographic data from volunteer subjects performing both isometric and ballistic elbow joint complex movements. In general, the model predicted kinematic and muscle excitation patterns similar to what was experimentally measured.
Cellular Potts modeling of complex multicellular behaviors in tissue morphogenesis.
Hirashima, Tsuyoshi; Rens, Elisabeth G; Merks, Roeland M H
2017-06-01
Mathematical modeling is an essential approach for the understanding of complex multicellular behaviors in tissue morphogenesis. Here, we review the cellular Potts model (CPM; also known as the Glazier-Graner-Hogeweg model), an effective computational modeling framework. We discuss its usability for modeling complex developmental phenomena by examining four fundamental examples of tissue morphogenesis: (i) cell sorting, (ii) cyst formation, (iii) tube morphogenesis in kidney development, and (iv) blood vessel formation. The review provides an introduction for biologists for starting simulation analysis using the CPM framework. © 2017 Japanese Society of Developmental Biologists.
Model Reduction for Complex Hyperbolic Networks
Himpe, Christian; Ohlberger, Mario
2013-01-01
We recently introduced the joint gramian for combined state and parameter reduction [C. Himpe and M. Ohlberger. Cross-Gramian Based Combined State and Parameter Reduction for Large-Scale Control Systems. arXiv:1302.0634, 2013], which is applied in this work to reduce a parametrized linear time-varying control system modeling a hyperbolic network. The reduction encompasses the dimension of nodes and parameters of the underlying control system. Networks with a hyperbolic structure have many app...
Efficient Electromagnetic Modelling of Complex Structures
Tobon Vasquez, Jorge Alberto
2014-01-01
Part 1. Space vehicles re-entering earth's atmosphere produce a shock wave which in turns results in a bow of plasma around the vehicle body. This plasma signicantly affects all radio links between the vehicle and ground, since the electron plasma frequency reaches beyond several GHz. In this work, a model of the propagation in plasma issue is developed. The radiofrequency propagation from/to antennae installed aboard the vehicle to the ground stations (or Data Relay Satellites) can be predic...
Modeling of Complex Mixtures: JP-8 Toxicokinetics
2008-10-01
diffusion, including metabolic loss via the cytochrome P-450 system, described by non-linear Michaelis - Menten kinetics as shown in the following...point. Inhalation and iv were the dose routes for the rat study. The modelers used saturable ( Michaelis - Menten ) kinetics as well as a second... Michaelis - Menten liver metabolic constants for n-decane have been measured (Km = 1.5 mg/L and Vmax = 0.4 mg/hour) using rat liver slices in a vial
The Transmembrane Adaptor Protein SIT Inhibits TCR-Mediated Signaling
Arndt, Börge; Krieger, Tina; Kalinski, Thomas; Thielitz, Anja; Reinhold, Dirk; Roessner, Albert; Schraven, Burkhart; Simeoni, Luca
2011-01-01
Transmembrane adaptor proteins (TRAPs) organize signaling complexes at the plasma membrane, and thus function as critical linkers and integrators of signaling cascades downstream of antigen receptors. We have previously shown that the transmembrane adaptor protein SIT regulates the threshold for thymocyte selection. Moreover, T cells from SIT-deficient mice are hyperresponsive to CD3 stimulation and undergo enhanced lymphopenia-induced homeostatic proliferation, thus indicating that SIT inhibits TCR-mediated signaling. Here, we have further addressed how SIT regulates signaling cascades in T cells. We demonstrate that the loss of SIT enhances TCR-mediated Akt activation and increased phosphorylation/inactivation of Foxo1, a transcription factor of the Forkhead family that inhibits cell cycle progression and regulates T-cell homeostasis. We have also shown that CD4+ T cells from SIT-deficient mice display increased CD69 and CD40L expression indicating an altered activation status. Additional biochemical analyses further revealed that suppression of SIT expression by RNAi in human T cells resulted in an enhanced proximal TCR signaling. In summary, the data identify SIT as an important modulator of TCR-mediated signaling that regulates T-cell activation, homeostasis and tolerance. PMID:21957439
Toward Modeling the Intrinsic Complexity of Test Problems
Shoufan, Abdulhadi
2017-01-01
The concept of intrinsic complexity explains why different problems of the same type, tackled by the same problem solver, can require different times to solve and yield solutions of different quality. This paper proposes a general four-step approach that can be used to establish a model for the intrinsic complexity of a problem class in terms of…
Fluid flow modeling in complex areas*, **
Directory of Open Access Journals (Sweden)
Poullet Pascal
2012-04-01
Full Text Available We show first results of 3D simulation of sea currents in a realistic context. We use the full Navier–Stokes equations for incompressible viscous fluid. The problem is solved using a second order incremental projection method associated with the finite volume of the staggered (MAC scheme for the spatial discretization. After validation on classical cases, it is used in a numerical simulation of the Pointe à Pitre harbour area. The use of the fictious domain method permits us to take into account the complexity of bathymetric data and allows us to work with regular meshes and thus preserves the efficiency essential for a 3D code. Dans cette étude, nous présentons les premiers résultats de simulation d’un écoulement d’un fluide incompressible visqueux dans un contexte environnemental réel. L’approche utilisée utilise une méthode de domaines fictifs pour une prise en compte d’un domaine physique tridimensionnel très irrégulier. Le schéma numérique combine un schéma de projection incrémentale et des volumes finis utilisant des volumes de contrôle adaptés à un maillage décalé. Les tests de validation sont menés pour les cas tests de la cavité double entraînée ainsi que l’écoulement dans un canal avec un obstacle placé de manière asymmétrique.
Fossati, Matteo; Goud, Bruno; Borgese, Nica; Manneville, Jean-Baptiste
2014-01-01
Sorting of membrane proteins within the secretory pathway of eukaryotic cells is a complex process involving discrete sorting signals as well as physico-chemical properties of the transmembrane domain (TMD). Previous work demonstrated that tail-anchored (TA) protein sorting at the interface between the Endoplasmic Reticulum (ER) and the Golgi complex is exquisitely dependent on the length and hydrophobicity of the transmembrane domain, and suggested that an imbalance between TMD length and bilayer thickness (hydrophobic mismatch) could drive long TMD-containing proteins into curved membrane domains, including ER exit sites, with consequent export of the mismatched protein out of the ER. Here, we tested a possible role of curvature in TMD-dependent sorting in a model system consisting of Giant Unilamellar Vesicles (GUVs) from which narrow membrane tubes were pulled by micromanipulation. Fluorescent TA proteins differing in TMD length were incorporated into GUVs of uniform lipid composition or made of total ER lipids, and TMD-dependent sorting and diffusion, as well as the bending rigidity of bilayers made of microsomal lipids, were investigated. Long and short TMD-containing constructs were inserted with similar orientation, diffused equally rapidly in GUVs and in tubes pulled from GUVs, and no difference in their final distribution between planar and curved regions was detected. These results indicate that curvature alone is not sufficient to drive TMD-dependent sorting at the ER-Golgi interface, and set the basis for the investigation of the additional factors that must be required. PMID:25210649
Coping with Complexity Model Reduction and Data Analysis
Gorban, Alexander N
2011-01-01
This volume contains the extended version of selected talks given at the international research workshop 'Coping with Complexity: Model Reduction and Data Analysis', Ambleside, UK, August 31 - September 4, 2009. This book is deliberately broad in scope and aims at promoting new ideas and methodological perspectives. The topics of the chapters range from theoretical analysis of complex and multiscale mathematical models to applications in e.g., fluid dynamics and chemical kinetics.
Supply Chain as Complex Adaptive System and Its Modeling
Institute of Scientific and Technical Information of China (English)
MingmingWang
2004-01-01
Supply chain is a complex, hierarchical, integrated, open and dynamic network.Every node in the network is an independent business unit that unites other organizations to develop its value, the competition and cooperation between these units are basic impetus of the development and evolution of the supply chain system. The characteristics of supply chain as a complex adaptive system and its modeling are discussed in this paper, and use an example demonstrating the feasibility of CAS modeling in supply chain management study.
Reduction of the complexity of product modelling by modularisation
DEFF Research Database (Denmark)
Andreasen, Mogens Myrup
1998-01-01
The complexity in handling product aspects in design and production may be reduced by using approaches, which are applied in the field of modular engineering. This unit-oriented "spelling" of products, leading to product models with encapsulation, is introduced.......The complexity in handling product aspects in design and production may be reduced by using approaches, which are applied in the field of modular engineering. This unit-oriented "spelling" of products, leading to product models with encapsulation, is introduced....
Reduction of the complexity of product modelling by modularisation
DEFF Research Database (Denmark)
Andreasen, Mogens Myrup
1998-01-01
The complexity in handling product aspects in design and production may be reduced by using approaches, which are applied in the field of modular engineering. This unit-oriented "spelling" of products, leading to product models with encapsulation, is introduced.......The complexity in handling product aspects in design and production may be reduced by using approaches, which are applied in the field of modular engineering. This unit-oriented "spelling" of products, leading to product models with encapsulation, is introduced....
Model Analysis of Complex Systems Behavior using MADS
Vesselinov, V. V.; O'Malley, D.
2016-12-01
Evaluation of robustness (reliability) of model predictions is challenging for models representing complex system behavior. Frequently in science and engineering applications related to complex systems, several alternative physics models may describe the available data equally well and are physically reasonable based on the available conceptual understanding. However, these alternative models could give very different predictions about the future states of the analyzed system. Furthermore, in the case of complex systems, we often must do modeling with an incomplete understanding of the underlying physical processes and model parameters. The analyses of model predictions representing complex system behavior are particularly challenging when we are quantifying uncertainties of rare events in the model prediction space that can have major consequences (also called "black swans"). These types of analyses are also computationally challenging. Here, we demonstrate the application of a general high-performance computational tool for Model Analysis & Decision Support (MADS; http://mads.lanl.gov) which can be applied to perform analyses using any external physics or systems model. The coupling between MADS and the external model can be performed using different methods. MADS is implemented in Julia, a high-level, high-performance dynamic programming language for technical computing (http://mads.lanl.gov/, https://github.com/madsjulia/Mads.jl, http://mads.readthedocs.org). MADS has been applied to perform analyses for environmental-management and water-energy-food nexus problems. To demonstrate MADS capabilities and functionalities, we analyze a series of synthetic problems consistent with actual real-world problems.
Applications of Nonlinear Dynamics Model and Design of Complex Systems
In, Visarath; Palacios, Antonio
2009-01-01
This edited book is aimed at interdisciplinary, device-oriented, applications of nonlinear science theory and methods in complex systems. In particular, applications directed to nonlinear phenomena with space and time characteristics. Examples include: complex networks of magnetic sensor systems, coupled nano-mechanical oscillators, nano-detectors, microscale devices, stochastic resonance in multi-dimensional chaotic systems, biosensors, and stochastic signal quantization. "applications of nonlinear dynamics: model and design of complex systems" brings together the work of scientists and engineers that are applying ideas and methods from nonlinear dynamics to design and fabricate complex systems.
Rational Characterization Complex Geology Model——Macro Velocity Model
Institute of Scientific and Technical Information of China (English)
SongWei
2004-01-01
The accuracy of migration velocity construction is always a key problem of the image quality of pre-stack depth migration. The velocity model construction process is a process from an unknown to unknown iteration procedure and involves three important steps -- model building, migration and model modification. It is necessary to rationally describe the velocity model, according to the complexity of the problem. Taking the Marmousi model as a study object, We established some standards for a rational description of the velocity model on the basis of different velocity space scales, analysis varieties of travel time, and image quality. It is considered that for any given seismic data gathered in the migration velocity model the space wavelength of velocity, which should be expressed in variation of space wavelength of various frequency contents, appears in the seismic data. Some space wavelengths, which are necessary for a description of the model velocity field, are also varying with the layer complexity. For a simple layer velocity structure it is sufficient to apply a simple velocity model (the space wavelength is large enough), whereas, for a complicated layer velocity structure it is necessary to take a velocity model of a more precise scale. In fact, when we establish a velocity model, it is difficult to describe the velocity model at a full space scale, so it is important to limit the space scale of the velocity model according to the complexity of a layer structure and establish a rational macro velocity model.
Unified Modeling of Complex Real-Time Control Systems
Hai, He; Chi-Lan, Cai
2011-01-01
Complex real-time control system is a software dense and algorithms dense system, which needs modern software engineering techniques to design. UML is an object-oriented industrial standard modeling language, used more and more in real-time domain. This paper first analyses the advantages and problems of using UML for real-time control systems design. Then, it proposes an extension of UML-RT to support time-continuous subsystems modeling. So we can unify modeling of complex real-time control systems on UML-RT platform, from requirement analysis, model design, simulation, until generation code.
Understanding complex urban systems multidisciplinary approaches to modeling
Gurr, Jens; Schmidt, J
2014-01-01
Understanding Complex Urban Systems takes as its point of departure the insight that the challenges of global urbanization and the complexity of urban systems cannot be understood – let alone ‘managed’ – by sectoral and disciplinary approaches alone. But while there has recently been significant progress in broadening and refining the methodologies for the quantitative modeling of complex urban systems, in deepening the theoretical understanding of cities as complex systems, or in illuminating the implications for urban planning, there is still a lack of well-founded conceptual thinking on the methodological foundations and the strategies of modeling urban complexity across the disciplines. Bringing together experts from the fields of urban and spatial planning, ecology, urban geography, real estate analysis, organizational cybernetics, stochastic optimization, and literary studies, as well as specialists in various systems approaches and in transdisciplinary methodologies of urban analysis, the volum...
Size and complexity in model financial systems.
Arinaminpathy, Nimalan; Kapadia, Sujit; May, Robert M
2012-11-06
The global financial crisis has precipitated an increasing appreciation of the need for a systemic perspective toward financial stability. For example: What role do large banks play in systemic risk? How should capital adequacy standards recognize this role? How is stability shaped by concentration and diversification in the financial system? We explore these questions using a deliberately simplified, dynamic model of a banking system that combines three different channels for direct transmission of contagion from one bank to another: liquidity hoarding, asset price contagion, and the propagation of defaults via counterparty credit risk. Importantly, we also introduce a mechanism for capturing how swings in "confidence" in the system may contribute to instability. Our results highlight that the importance of relatively large, well-connected banks in system stability scales more than proportionately with their size: the impact of their collapse arises not only from their connectivity, but also from their effect on confidence in the system. Imposing tougher capital requirements on larger banks than smaller ones can thus enhance the resilience of the system. Moreover, these effects are more pronounced in more concentrated systems, and continue to apply, even when allowing for potential diversification benefits that may be realized by larger banks. We discuss some tentative implications for policy, as well as conceptual analogies in ecosystem stability and in the control of infectious diseases.
Size and complexity in model financial systems
Arinaminpathy, Nimalan; Kapadia, Sujit; May, Robert M.
2012-01-01
The global financial crisis has precipitated an increasing appreciation of the need for a systemic perspective toward financial stability. For example: What role do large banks play in systemic risk? How should capital adequacy standards recognize this role? How is stability shaped by concentration and diversification in the financial system? We explore these questions using a deliberately simplified, dynamic model of a banking system that combines three different channels for direct transmission of contagion from one bank to another: liquidity hoarding, asset price contagion, and the propagation of defaults via counterparty credit risk. Importantly, we also introduce a mechanism for capturing how swings in “confidence” in the system may contribute to instability. Our results highlight that the importance of relatively large, well-connected banks in system stability scales more than proportionately with their size: the impact of their collapse arises not only from their connectivity, but also from their effect on confidence in the system. Imposing tougher capital requirements on larger banks than smaller ones can thus enhance the resilience of the system. Moreover, these effects are more pronounced in more concentrated systems, and continue to apply, even when allowing for potential diversification benefits that may be realized by larger banks. We discuss some tentative implications for policy, as well as conceptual analogies in ecosystem stability and in the control of infectious diseases. PMID:23091020
A marketing mix model for a complex and turbulent environment
Directory of Open Access Journals (Sweden)
R. B. Mason
2007-12-01
Full Text Available Purpose: This paper is based on the proposition that the choice of marketing tactics is determined, or at least significantly influenced, by the nature of the companys external environment. It aims to illustrate the type of marketing mix tactics that are suggested for a complex and turbulent environment when marketing and the environment are viewed through a chaos and complexity theory lens. Design/Methodology/Approach: Since chaos and complexity theories are proposed as a good means of understanding the dynamics of complex and turbulent markets, a comprehensive review and analysis of literature on the marketing mix and marketing tactics from a chaos and complexity viewpoint was conducted. From this literature review, a marketing mix model was conceptualised.Findings: A marketing mix model considered appropriate for success in complex and turbulent environments was developed. In such environments, the literature suggests destabilising marketing activities are more effective, whereas stabilising type activities are more effective in simple, stable environments. Therefore the model proposes predominantly destabilising type tactics as appropriate for a complex and turbulent environment such as is currently being experienced in South Africa. Implications: This paper is of benefit to marketers by emphasising a new way to consider the future marketing activities of their companies. How this model can assist marketers and suggestions for research to develop and apply this model are provided. It is hoped that the model suggested will form the basis of empirical research to test its applicability in the turbulent South African environment. Originality/Value: Since businesses and markets are complex adaptive systems, using complexity theory to understand how to cope in complex, turbulent environments is necessary, but has not been widely researched. In fact, most chaos and complexity theory work in marketing has concentrated on marketing strategy, with
HIGH AND LOW RESOLUTION TEXTURED MODELS OF COMPLEX ARCHITECTURAL SURFACES
Directory of Open Access Journals (Sweden)
E. K. Stathopoulou
2012-09-01
Full Text Available During the recent years it has become obvious that 3D technology, applied mainly with the use of terrestrial laser scanners (TLS is the most suitable technique for the complete geometric documentation of complex objects, whether they are monuments or architectural constructions in general. However, it is rather a challenging task to convert an acquired point cloud into a realistic 3D polygonal model that can simultaneously satisfy high resolution modeling and visualization demands. The aim of the visualization of a simple or complex object is to create a 3D model that best describes the reality within the computer environment. This paper is dedicated especially in the visualization of a complex object's 3D model, through high, as well as low resolution textured models. The object of interest for this study was the Almoina (Romanesque Door of the Cathedral of Valencia in Spain.
Backward Causation in Complex Action Model --- Superdeterminism and Transactional Interpretations
Nielsen, Holger B
2010-01-01
It is shown that the transactional interpretation of quantum mechanics being referred back to Feynman-Wheeler's time reversal symmetric radiation theory has reminiscences to our complex action model. In this complex action model the initial conditions are in principle even calculable. Thus it philosophically points towards superdeterminism, but really the Bell theorem problem is solved in our model of complex action by removing the significance of signals running slower than by light velocity. Our model as earlier published predicts that LHC should have some failure before reaching to have produced as many Higgs-particles as would have been produced the SSC accelerator. In the present article, we point out that a cardgame involving whether to restrict LHC-running as we have proposed to test our model will under all circumstances be a success.
High and Low Resolution Textured Models of Complex Architectural Surfaces
Stathopoulou, E. K.; Valanis, A.; Lerma, J. L.; Georgopoulos, A.
2011-09-01
During the recent years it has become obvious that 3D technology, applied mainly with the use of terrestrial laser scanners (TLS) is the most suitable technique for the complete geometric documentation of complex objects, whether they are monuments or architectural constructions in general. However, it is rather a challenging task to convert an acquired point cloud into a realistic 3D polygonal model that can simultaneously satisfy high resolution modeling and visualization demands. The aim of the visualization of a simple or complex object is to create a 3D model that best describes the reality within the computer environment. This paper is dedicated especially in the visualization of a complex object's 3D model, through high, as well as low resolution textured models. The object of interest for this study was the Almoina (Romanesque) Door of the Cathedral of Valencia in Spain.
Complexity vs. Simplicity: Tradeoffs in Integrated Water Resources Models
Gonda, J.; Elshorbagy, A. A.; Wheater, H. S.; Razavi, S.
2014-12-01
Integrated Water Resources Management is an interdisciplinary approach to managing water. Integration often involves linking hydrologic processes with socio-economic development. When implemented through a simulation or optimization model, complexities arise. This complexity is due to the large data requirements, making it difficult to implement by the end users. Not only is computational efficiency at stake, but it becomes cumbersome to future model users. To overcome this issue the model may be simplified through emulation, at the expense of information loss. Herein lies a tradeoff: Complexity involved in an accurate, detailed model versus the transparency and saliency of a simplified model. This presentation examines the role of model emulation towards simplifying a water allocation model. The case study is located in Southern Alberta, Canada. Water here is allocated between agricultural, municipal, environmental and energy sectors. Currently, water allocation is modeled through a detailed optimization model, WRMM. Although WRMM can allocate water on a priority basis, it lacks the simplicity needed by the end user. The proposed System Dynamics-based model, SWAMP 2.0, emulates this optimization model, utilizing two scales of complexity. A regional scale spatially aggregates individual components, reducing the complexity of the original model. A local scale retains the original detail, and is contained within the regional scale. This two tiered emulation presents relevant spatial scales to water managers, who may not be interested in all the details of WRMM. By evaluating the accuracy of SWAMP 2.0 against the original allocation model, the tradeoff of accuracy for simplicity can be further realized.
BlenX-based compositional modeling of complex reaction mechanisms
Zámborszky, Judit; 10.4204/EPTCS.19.6
2010-01-01
Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model buildin...
Generalized complex geometry, generalized branes and the Hitchin sigma model
Energy Technology Data Exchange (ETDEWEB)
Zucchini, Roberto E-mail: zucchinir@bo.infn.it
2005-03-01
Hitchin's generalized complex geometry has been shown to be relevant in compactifications of superstring theory with fluxes and is expected to lead to a deeper understanding of mirror symmetry. Gualtieri's notion of generalized complex submanifold seems to be a natural candidate for the description of branes in this context. Recently, we introduced a Batalin-Vilkovisky field theoretic realization of generalized complex geometry, the Hitchin sigma model, extending the well known Poisson sigma model. In this paper, exploiting Gualtieri's formalism, we incorporate branes into the model. A detailed study of the boundary conditions obeyed by the world sheet fields is provided. Finally, it is found that, when branes are present, the classical Batalin-Vilkovisky cohomology contains an extra sector that is related non trivially to a novel cohomology associated with the branes as generalized complex submanifolds. (author)
Generalized complex geometry, generalized branes and the Hitchin sigma model
Zucchini, R
2005-01-01
Hitchin's generalized complex geometry has been shown to be relevant in compactifications of superstring theory with fluxes and is expected to lead to a deeper understanding of mirror symmetry. Gualtieri's notion of generalized complex submanifold seems to be a natural candidate for the description of branes in this context. Recently, we introduced a field theoretic realization of generalized complex geometry, the Hitchin sigma model, extending the well known Poisson sigma model. In this paper, exploiting Gualtieri's formalism, we incorporate branes into the model. A detailed study of the boundary conditions obeyed by the world sheet fields is provided. Finally, it is found that, when branes are present, the classical Batalin--Vilkovisky cohomology contains an extra sector that is related non trivially to a novel cohomology associated with the branes as generalized complex submanifolds.
Finite element analysis to model complex mitral valve repair.
Labrosse, Michel; Mesana, Thierry; Baxter, Ian; Chan, Vincent
2016-01-01
Although finite element analysis has been used to model simple mitral repair, it has not been used to model complex repair. A virtual mitral valve model was successful in simulating normal and abnormal valve function. Models were then developed to simulate an edge-to-edge repair and repair employing quadrangular resection. Stress contour plots demonstrated increased stresses along the mitral annulus, corresponding to the annuloplasty. The role of finite element analysis in guiding clinical practice remains undetermined.
Large-Conductance Transmembrane Porin Made from DNA Origami.
Göpfrich, Kerstin; Li, Chen-Yu; Ricci, Maria; Bhamidimarri, Satya Prathyusha; Yoo, Jejoong; Gyenes, Bertalan; Ohmann, Alexander; Winterhalter, Mathias; Aksimentiev, Aleksei; Keyser, Ulrich F
2016-09-27
DNA nanotechnology allows for the creation of three-dimensional structures at nanometer scale. Here, we use DNA to build the largest synthetic pore in a lipid membrane to date, approaching the dimensions of the nuclear pore complex and increasing the pore-area and the conductance 10-fold compared to previous man-made channels. In our design, 19 cholesterol tags anchor a megadalton funnel-shaped DNA origami porin in a lipid bilayer membrane. Confocal imaging and ionic current recordings reveal spontaneous insertion of the DNA porin into the lipid membrane, creating a transmembrane pore of tens of nanosiemens conductance. All-atom molecular dynamics simulations characterize the conductance mechanism at the atomic level and independently confirm the DNA porins' large ionic conductance.
Hkat, a novel nutritionally regulated transmembrane protein in adipose tissues.
Zhang, Ren
2012-01-01
White adipose tissue is an active endocrine organ regulating many aspects of whole body physiology and pathology. Adipogenesis, a process in which premature cells differentiate into adipocytes, is a complex process that includes orchestrated changes in gene expression and cell morphology in response to various nutritional and hormonal stimuli. To profile transcriptome changes in response to nutritional stimulation, we performed RNA-seq on fat in mice treated with either a high-fat diet or fasting. We identified a novel nutritionally regulated gene, Gm12824, named Hkat (heart, kidney, adipose-enriched transmembrane protein). We show that both fasting and obesity dramatically reduce Hkat in white adipose tissue, and that fasting reduces while obesity increases its expression in brown fat. Hkat is localized to the plasma membrane and induced during adipogenesis. Therefore, Hkat is a novel nutritionally regulated gene that is potentially involved in metabolism.
Routine Discovery of Complex Genetic Models using Genetic Algorithms.
Moore, Jason H; Hahn, Lance W; Ritchie, Marylyn D; Thornton, Tricia A; White, Bill C
2004-02-01
Simulation studies are useful in various disciplines for a number of reasons including the development and evaluation of new computational and statistical methods. This is particularly true in human genetics and genetic epidemiology where new analytical methods are needed for the detection and characterization of disease susceptibility genes whose effects are complex, nonlinear, and partially or solely dependent on the effects of other genes (i.e. epistasis or gene-gene interaction). Despite this need, the development of complex genetic models that can be used to simulate data is not always intuitive. In fact, only a few such models have been published. We have previously developed a genetic algorithm approach to discovering complex genetic models in which two single nucleotide polymorphisms (SNPs) influence disease risk solely through nonlinear interactions. In this paper, we extend this approach for the discovery of high-order epistasis models involving three to five SNPs. We demonstrate that the genetic algorithm is capable of routinely discovering interesting high-order epistasis models in which each SNP influences risk of disease only through interactions with the other SNPs in the model. This study opens the door for routine simulation of complex gene-gene interactions among SNPs for the development and evaluation of new statistical and computational approaches for identifying common, complex multifactorial disease susceptibility genes.
Geometric modeling of subcellular structures, organelles, and multiprotein complexes
Feng, Xin; Xia, Kelin; Tong, Yiying; Wei, Guo-Wei
2013-01-01
SUMMARY Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multi-protein complexes have emerged as a leading interest in structural biology. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics. This paper introduces a suite of computational tools for volumetric data processing, information extraction, surface mesh rendering, geometric measurement, and curvature estimation of biomolecular complexes. Particular emphasis is given to the modeling of cryo-electron microscopy data. Lagrangian-triangle meshes are employed for the surface presentation. On the basis of this representation, algorithms are developed for surface area and surface-enclosed volume calculation, and curvature estimation. Methods for volumetric meshing have also been presented. Because the technological development in computer science and mathematics has led to multiple choices at each stage of the geometric modeling, we discuss the rationales in the design and selection of various algorithms. Analytical models are designed to test the computational accuracy and convergence of proposed algorithms. Finally, we select a set of six cryo-electron microscopy data representing typical subcellular complexes to demonstrate the efficacy of the proposed algorithms in handling biomolecular surfaces and explore their capability of geometric characterization of binding targets. This paper offers a comprehensive protocol for the geometric modeling of subcellular structures, organelles, and multiprotein complexes. PMID:23212797
Between complexity of modelling and modelling of complexity: An essay on econophysics
Schinckus, C.
2013-09-01
Econophysics is an emerging field dealing with complex systems and emergent properties. A deeper analysis of themes studied by econophysicists shows that research conducted in this field can be decomposed into two different computational approaches: “statistical econophysics” and “agent-based econophysics”. This methodological scission complicates the definition of the complexity used in econophysics. Therefore, this article aims to clarify what kind of emergences and complexities we can find in econophysics in order to better understand, on one hand, the current scientific modes of reasoning this new field provides; and on the other hand, the future methodological evolution of the field.
Stochastic simulation of HIV population dynamics through complex network modelling
Sloot, P.M.A.; Ivanov, S.V.; Boukhanovsky, A.V.; van de Vijver, D.A.M.C.; Boucher, C.A.B.
2008-01-01
We propose a new way to model HIV infection spreading through the use of dynamic complex networks. The heterogeneous population of HIV exposure groups is described through a unique network degree probability distribution. The time evolution of the network nodes is modelled by a Markov process and
Stochastic simulation of HIV population dynamics through complex network modelling
Sloot, P. M. A.; Ivanov, S. V.; Boukhanovsky, A. V.; van de Vijver, D. A. M. C.; Boucher, C. A. B.
We propose a new way to model HIV infection spreading through the use of dynamic complex networks. The heterogeneous population of HIV exposure groups is described through a unique network degree probability distribution. The time evolution of the network nodes is modelled by a Markov process and
Energy Technology Data Exchange (ETDEWEB)
Brayman, A.A.; Miller, M.W.; Brulfert, A.
1986-08-01
The region of elongation in Cucumis sativus and Cucurbita maxima roots was marked at increasing distances from the apex to provide an analog of increasing cell size. These roots were exposed/sham-exposed to 60 Hz electric fields and the growth rates of the root segments measured. The growth rate effect magnitude varied with increasing distance from the root tip at constant field strength, and with increasing applied field strength. These results provide strong, qualitative support for the postulate that ELF transmembrane potential induction is involved in the stimulation of ELF electric field effects in the plant root model system.
Stability analysis of the inverse transmembrane potential problem in electrocardiography
Burger, Martin; Mardal, Kent-André; Nielsen, Bjørn Fredrik
2010-10-01
In this paper we study some mathematical properties of an inverse problem arising in connection with electrocardiograms (ECGs). More specifically, we analyze the possibility for recovering the transmembrane potential in the heart from ECG recordings, a challenge currently investigated by a growing number of groups. Our approach is based on the bidomain model for the electrical activity in the myocardium, and leads to a parameter identification problem for elliptic partial differential equations (PDEs). It turns out that this challenge can be split into two subproblems: the task of recovering the potential at the heart surface from body surface recordings; the problem of computing the transmembrane potential inside the heart from the potential determined at the heart surface. Problem (1), which can be formulated as the Cauchy problem for an elliptic PDE, has been extensively studied and is well known to be severely ill-posed. The main purpose of this paper is to prove that problem (2) is stable and well posed if a suitable prior is available. Moreover, our theoretical findings are illuminated by a series of numerical experiments. Finally, we discuss some aspects of uniqueness related to the anisotropy in the heart.
Role of α and β Transmembrane Domains in Integrin Clustering
Directory of Open Access Journals (Sweden)
Amir Shamloo
2015-11-01
Full Text Available Integrins are transmembrane proteins playing a crucial role in the mechanical signal transduction from the outside to the inside of a cell, and vice versa. Nevertheless, this signal transduction could not be implemented by a single protein. Rather, in order for integrins to be able to participate in signal transduction, they need to be activated and produce clusters first. As integrins consist of α- and β-subunits that are separate in the active state, studying both subunits separately is of a great importance, for, in the active state, the distance between α- and β-subunits is long enough that they do not influence one another significantly. Thus, this study aims to investigate the tendency of transmembrane domains of integrins to form homodimers. We used both Steered and MARTINI Coarse-grained molecular dynamics method to perform our simulations, mainly because of a better resolution and computational feasibility that each of these methods could provide to us. Using the Steered molecular dynamics method for α- and β-subunits, we found that the localized lipid packing prevented them from clustering. Nonetheless, the lipid packing phenomenon was found to be an artifact after investigating this process using a coarse grained (CG model. Exploiting the coarse-grained molecular dynamics simulations, we found that α- and β-subunits tend to form a stable homo-dimer.
Complexation and molecular modeling studies of europium(III)-gallic acid-amino acid complexes.
Taha, Mohamed; Khan, Imran; Coutinho, João A P
2016-04-01
With many metal-based drugs extensively used today in the treatment of cancer, attention has focused on the development of new coordination compounds with antitumor activity with europium(III) complexes recently introduced as novel anticancer drugs. The aim of this work is to design new Eu(III) complexes with gallic acid, an antioxida'nt phenolic compound. Gallic acid was chosen because it shows anticancer activity without harming health cells. As antioxidant, it helps to protect human cells against oxidative damage that implicated in DNA damage, cancer, and accelerated cell aging. In this work, the formation of binary and ternary complexes of Eu(III) with gallic acid, primary ligand, and amino acids alanine, leucine, isoleucine, and tryptophan was studied by glass electrode potentiometry in aqueous solution containing 0.1M NaNO3 at (298.2 ± 0.1) K. Their overall stability constants were evaluated and the concentration distributions of the complex species in solution were calculated. The protonation constants of gallic acid and amino acids were also determined at our experimental conditions and compared with those predicted by using conductor-like screening model for realistic solvation (COSMO-RS) model. The geometries of Eu(III)-gallic acid complexes were characterized by the density functional theory (DFT). The spectroscopic UV-visible and photoluminescence measurements are carried out to confirm the formation of Eu(III)-gallic acid complexes in aqueous solutions.
Bim Automation: Advanced Modeling Generative Process for Complex Structures
Banfi, F.; Fai, S.; Brumana, R.
2017-08-01
The new paradigm of the complexity of modern and historic structures, which are characterised by complex forms, morphological and typological variables, is one of the greatest challenges for building information modelling (BIM). Generation of complex parametric models needs new scientific knowledge concerning new digital technologies. These elements are helpful to store a vast quantity of information during the life cycle of buildings (LCB). The latest developments of parametric applications do not provide advanced tools, resulting in time-consuming work for the generation of models. This paper presents a method capable of processing and creating complex parametric Building Information Models (BIM) with Non-Uniform to NURBS) with multiple levels of details (Mixed and ReverseLoD) based on accurate 3D photogrammetric and laser scanning surveys. Complex 3D elements are converted into parametric BIM software and finite element applications (BIM to FEA) using specific exchange formats and new modelling tools. The proposed approach has been applied to different case studies: the BIM of modern structure for the courtyard of West Block on Parliament Hill in Ottawa (Ontario) and the BIM of Masegra Castel in Sondrio (Italy), encouraging the dissemination and interaction of scientific results without losing information during the generative process.
Experimental porcine model of complex fistula-in-ano
A Ba-Bai-Ke-Re, Ma-Mu-Ti-Jiang; Chen, Hui; Liu, Xue; Wang, Yun-Hai
2017-01-01
AIM To establish and evaluate an experimental porcine model of fistula-in-ano. METHODS Twelve healthy pigs were randomly divided into two groups. Under general anesthesia, the experimental group underwent rubber band ligation surgery, and the control group underwent an artificial damage technique. Clinical magnetic resonance imaging (MRI) and histopathological evaluation were performed on the 38th d and 48th d after surgery in both groups, respectively. RESULTS There were no significant differences between the experimental group and the control group in general characteristics such as body weight, gender, and the number of fistula (P > 0.05). In the experimental group, 15 fistulas were confirmed clinically, 13 complex fistulas were confirmed by MRI, and 11 complex fistulas were confirmed by histopathology. The success rate in the porcine complex fistula model establishment was 83.33%. Among the 18 fistulas in the control group, 5 fistulas were confirmed clinically, 4 complex fistulas were confirmed by MRI, and 3 fistulas were confirmed by histopathology. The success rate in the porcine fistula model establishment was 27.78%. Thus, the success rate of the rubber band ligation group was significantly higher than the control group (P fistula-in-ano models. Large animal models of complex anal fistulas can be used for the diagnosis and treatment of anal fistulas. PMID:28348488
Pedigree models for complex human traits involving the mitochrondrial genome
Energy Technology Data Exchange (ETDEWEB)
Schork, N.J.; Guo, S.W. (Univ. of Michigan, Ann Arbor, MI (United States))
1993-12-01
Recent biochemical and molecular-genetic discoveries concerning variations in human mtDNA have suggested a role for mtDNA mutations in a number of human traits and disorders. Although the importance of these discoveries cannot be emphasized enough, the complex natures of mitochondrial biogenesis, mutant mtDNA phenotype expression, and the maternal inheritance pattern exhibited by mtDNA transmission make it difficult to develop models that can be used routinely in pedigree analyses to quantify and test hypotheses about the role of mtDNA in the expression of a trait. In the present paper, the authors describe complexities inherent in mitochondrial biogenesis and genetic transmission and show how these complexities can be incorporated into appropriate mathematical models. The authors offer a variety of likelihood-based models which account for the complexities discussed. The derivation of the models is meant to stimulate the construction of statistical tests for putative mtDNA contribution to a trait. Results of simulation studies which make use of the proposed models are described. The results of the simulation studies suggest that, although pedigree models of mtDNA effects can be reliable, success in mapping chromosomal determinants of a trait does not preclude the possibility that mtDNA determinants exist for the trait as well. Shortcomings inherent in the proposed models are described in an effort to expose areas in need of additional research. 58 refs., 5 figs., 2 tabs.
Integrated modeling and 3D visualization for mine complex fields
Institute of Scientific and Technical Information of China (English)
LI Zhong-xue; SUN En-ji; LI Cui-ping; MA Bin
2007-01-01
Proposed a novel approach to the problem of mine complex fields in a perspective of digital modeling and visual representation, and it aimed at developing a theoretical framework for mine complex fields with the factors and their relationships delineated in a unified manner and at building a prototype for an integrated system of methods, models,and techniques with mine complex fields modeled digitally and represented visually. Specifically, the paper addressed the issues of data mining and knowledge discovery techniques as used in the processing of geological and ore deposit samples, digital modeling techniques as used in the description of mine complex fields, 3D visual simulation techniques as used in the representation of ore bodies and underground excavations, seamless interfacing techniques with other systems such as CAD and web GIS as used in the restructuring of 2D data into 3D models and mapping of 3D models onto 2D graphics, and implementation techniques as used in the case of building a web based prototype system for the integrated modeling and visualization of underground mines.
Emulator-assisted data assimilation in complex models
Margvelashvili, Nugzar Yu; Herzfeld, Mike; Rizwi, Farhan; Mongin, Mathieu; Baird, Mark E.; Jones, Emlyn; Schaffelke, Britta; King, Edward; Schroeder, Thomas
2016-09-01
Emulators are surrogates of complex models that run orders of magnitude faster than the original model. The utility of emulators for the data assimilation into ocean models is still not well understood. High complexity of ocean models translates into high uncertainty of the corresponding emulators which may undermine the quality of the assimilation schemes based on such emulators. Numerical experiments with a chaotic Lorenz-95 model are conducted to illustrate this point and suggest a strategy to alleviate this problem through the localization of the emulation and data assimilation procedures. Insights gained through these experiments are used to design and implement data assimilation scenario for a 3D fine-resolution sediment transport model of the Great Barrier Reef (GBR), Australia.
Systems Engineering Metrics: Organizational Complexity and Product Quality Modeling
Mog, Robert A.
1997-01-01
Innovative organizational complexity and product quality models applicable to performance metrics for NASA-MSFC's Systems Analysis and Integration Laboratory (SAIL) missions and objectives are presented. An intensive research effort focuses on the synergistic combination of stochastic process modeling, nodal and spatial decomposition techniques, organizational and computational complexity, systems science and metrics, chaos, and proprietary statistical tools for accelerated risk assessment. This is followed by the development of a preliminary model, which is uniquely applicable and robust for quantitative purposes. Exercise of the preliminary model using a generic system hierarchy and the AXAF-I architectural hierarchy is provided. The Kendall test for positive dependence provides an initial verification and validation of the model. Finally, the research and development of the innovation is revisited, prior to peer review. This research and development effort results in near-term, measurable SAIL organizational and product quality methodologies, enhanced organizational risk assessment and evolutionary modeling results, and 91 improved statistical quantification of SAIL productivity interests.
Minimal model for complex dynamics in cellular processes.
Suguna, C; Chowdhury, K K; Sinha, S
1999-11-01
Cellular functions are controlled and coordinated by the complex circuitry of biochemical pathways regulated by genetic and metabolic feedback processes. This paper aims to show, with the help of a minimal model of a regulated biochemical pathway, that the common nonlinearities and control structures present in biomolecular interactions are capable of eliciting a variety of functional dynamics, such as homeostasis, periodic, complex, and chaotic oscillations, including transients, that are observed in various cellular processes.
Calcium-Amidoborane-Ammine Complexes : Thermal Decomposition of Model Systems
Harder, Sjoerd; Spielmann, Jan; Tobey, Briac
2012-01-01
Hydrocarbon-soluble model systems for the calcium-amidoborane-ammine complex Ca(NH2BH3)2.(NH3)2 were prepared and structurally characterized. The following complexes were obtained by the reaction of RNH2BH3 (R=H, Me, iPr, DIPP; DIPP=2,6-diisopropylphenyl) with Ca(DIPP-nacnac)(NH2).(NH3)2 (DIPP-nacna
Calcium-Amidoborane-Ammine Complexes : Thermal Decomposition of Model Systems
Harder, Sjoerd; Spielmann, Jan; Tobey, Briac
2012-01-01
Hydrocarbon-soluble model systems for the calcium-amidoborane-ammine complex Ca(NH2BH3)2.(NH3)2 were prepared and structurally characterized. The following complexes were obtained by the reaction of RNH2BH3 (R=H, Me, iPr, DIPP; DIPP=2,6-diisopropylphenyl) with Ca(DIPP-nacnac)(NH2).(NH3)2 (DIPP-nacna
A Knowledge base model for complex forging die machining
Mawussi, Kwamiwi; Tapie, Laurent
2011-01-01
International audience; Recent evolutions on forging process induce more complex shape on forging die. These evolutions, combined with High Speed Machining (HSM) process of forging die lead to important increase in time for machining preparation. In this context, an original approach for generating machining process based on machining knowledge is proposed in this paper. The core of this approach is to decompose a CAD model of complex forging die in geometric features. Technological data and ...
Tsaousis, Georgios N; Bagos, Pantelis G; Hamodrakas, Stavros J
2014-02-01
During the last two decades a large number of computational methods have been developed for predicting transmembrane protein topology. Current predictors rely on topogenic signals in the protein sequence, such as the distribution of positively charged residues in extra-membrane loops and the existence of N-terminal signals. However, phosphorylation and glycosylation are post-translational modifications (PTMs) that occur in a compartment-specific manner and therefore the presence of a phosphorylation or glycosylation site in a transmembrane protein provides topological information. We examine the combination of phosphorylation and glycosylation site prediction with transmembrane protein topology prediction. We report the development of a Hidden Markov Model based method, capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites along the protein sequence. Our method integrates a novel feature in transmembrane protein topology prediction, which results in improved performance for topology prediction and reliable prediction of phosphorylation and glycosylation sites. The method is freely available at http://bioinformatics.biol.uoa.gr/HMMpTM.
Błachnio, Karina
2010-01-01
Detergents commonly used for solubilization of membrane proteins may be ionic or non-ionic. Exposing membrane proteins to detergents, however, can adversely affect their native structure, which can be a major hindrance for functional studies. This is especially true for proteins with multiple transmembrane domains. The ProteoExtract Transmembrane Protein Extraction Kit (TM-PEK), offered by Merck, provides a detergent-free novel reagents to enable the mild and efficient extraction of proteins containing seven transmembrane domains, such as GPCRs (G-Protein Coupled Receptors) e.g.: Frizzled-4 and CELSR-3, from mammalian cells. The fraction enriched in transmembrane proteins using TM-PEK is directly compatible with enzyme assays, non-denaturing gel electrophoresis, 1- and 2-D SDS-PAGE, MS analysis, Western blotting, immunoprecipitation and ELISA. Unlike many alternatives, TM-PEK extraction procedure does not require sonication, extended rigorous vortexing, ultracentrifugation, or incubation of samples at elevated temperatures--thus minimizing the risk of post-extraction degradation or modifications.
Complex groundwater flow systems as traveling agent models
López-Corona, Oliver; Escolero, Oscar; González, Tomás; Morales-Casique, Eric
2014-01-01
Analyzing field data from pumping tests, we show that as with many other natural phenomena, groundwater flow exhibits a complex dynamics described by 1/f power spectrum. This result is theoretically studied within an agent perspective. Using a traveling agent model, we prove that this statistical behavior emerges when the medium is complex. Some heuristic reasoning is provided to justify both spatial and dynamic complexity, as the result of the superposition of an infinite number of stochastic processes. Even more, we show that this implies that non-Kolmogorovian probability is needed for its study, and provide a set of new partial differential equations for groundwater flow.
How much physical complexity is needed to model flood inundation?
Neal, J.; Bates, P; Villanueva, I; Wright, N.; Willis, T; Fewtrell, T
2011-01-01
Two-dimensional flood inundation models are widely used tools for flood hazard mapping and an essential component of statutory flood risk management guidelines in many countries. Yet, we still do not know how much physical complexity a flood inundation model needs for a given problem. Here, three two-dimensional explicit hydraulic models, which can be broadly defined as simulating diffusive, inertial or shallow water waves, have been benchmarked using test cases from a recent Environment Agen...
A dynamic epidemic control model on uncorrelated complex networks
Institute of Scientific and Technical Information of China (English)
Pei Wei-Dong; Chen Zeng-Qiang; Yuan Zhu-Zhi
2008-01-01
In this paper,a dynamic epidemic control model on the uncorrelated complex networks is proposed.By means of theoretical analysis,we found that the new model has a similar epidemic threshold as that of the susceptible-infectedrecovered (SIR) model on the above networks,but it can reduce the prevalence of the infected individuals remarkably.This result may help us understand epidemic spreading phenomena on real networks and design appropriate strategies to control infections.
Evolution of vertebrate interferon inducible transmembrane proteins
Directory of Open Access Journals (Sweden)
Hickford Danielle
2012-04-01
Full Text Available Abstract Background Interferon inducible transmembrane proteins (IFITMs have diverse roles, including the control of cell proliferation, promotion of homotypic cell adhesion, protection against viral infection, promotion of bone matrix maturation and mineralisation, and mediating germ cell development. Most IFITMs have been well characterised in human and mouse but little published data exists for other animals. This study characterised IFITMs in two distantly related marsupial species, the Australian tammar wallaby and the South American grey short-tailed opossum, and analysed the phylogeny of the IFITM family in vertebrates. Results Five IFITM paralogues were identified in both the tammar and opossum. As in eutherians, most marsupial IFITM genes exist within a cluster, contain two exons and encode proteins with two transmembrane domains. Only two IFITM genes, IFITM5 and IFITM10, have orthologues in both marsupials and eutherians. IFITM5 arose in bony fish and IFITM10 in tetrapods. The bone-specific expression of IFITM5 appears to be restricted to therian mammals, suggesting that its specialised role in bone production is a recent adaptation specific to mammals. IFITM10 is the most highly conserved IFITM, sharing at least 85% amino acid identity between birds, reptiles and mammals and suggesting an important role for this presently uncharacterised protein. Conclusions Like eutherians, marsupials also have multiple IFITM genes that exist in a gene cluster. The differing expression patterns for many of the paralogues, together with poor sequence conservation between species, suggests that IFITM genes have acquired many different roles during vertebrate evolution.
A Complex Systems Model Approach to Quantified Mineral Resource Appraisal
Gettings, M.E.; Bultman, M.W.; Fisher, F.S.
2004-01-01
For federal and state land management agencies, mineral resource appraisal has evolved from value-based to outcome-based procedures wherein the consequences of resource development are compared with those of other management options. Complex systems modeling is proposed as a general framework in which to build models that can evaluate outcomes. Three frequently used methods of mineral resource appraisal (subjective probabilistic estimates, weights of evidence modeling, and fuzzy logic modeling) are discussed to obtain insight into methods of incorporating complexity into mineral resource appraisal models. Fuzzy logic and weights of evidence are most easily utilized in complex systems models. A fundamental product of new appraisals is the production of reusable, accessible databases and methodologies so that appraisals can easily be repeated with new or refined data. The data are representations of complex systems and must be so regarded if all of their information content is to be utilized. The proposed generalized model framework is applicable to mineral assessment and other geoscience problems. We begin with a (fuzzy) cognitive map using (+1,0,-1) values for the links and evaluate the map for various scenarios to obtain a ranking of the importance of various links. Fieldwork and modeling studies identify important links and help identify unanticipated links. Next, the links are given membership functions in accordance with the data. Finally, processes are associated with the links; ideally, the controlling physical and chemical events and equations are found for each link. After calibration and testing, this complex systems model is used for predictions under various scenarios.
A compact model for the complex plant circadian clock
Directory of Open Access Journals (Sweden)
Didier eGonze
2016-02-01
Full Text Available The circadian clock is an endogenous timekeeper that allows organisms to anticipate and adapt to the daily variations of their environment. The plant clock is an intricate network of interlocked feedback loops, in which transcription factors regulate each other to generate oscillations with expression peaks at specific times of the day. Over the last decade, mathematical modeling approaches have been used to understand the inner workings of the clock in the model plant Arabidopsis thaliana. Those efforts have produced a number of models of ever increasing complexity. Here, we present an alternative model that combines a low number of equations and parameters, similar to the very earliest models, with the complex network structure found in more recent ones. This simple model describes the temporal evolution of the abundance of eight clock genes and captures key features of the clock on a qualitative level, namely the entrained and free-running behaviors of the wild type clock, as well as the defects found in knockout mutants (such as altered free-running periods, lack of entrainment, or changes in the expression of other clock genes. Additionally, our model produces complex responses to various light cues, such as extreme photoperiods and non-24h environmental cycles, and can describe the control of hypocotyl growth by the clock. Our model constitutes a useful tool to probe dynamical properties of the clock as well as model more clock-dependent processes.
Nostradamus 2014 prediction, modeling and analysis of complex systems
Suganthan, Ponnuthurai; Chen, Guanrong; Snasel, Vaclav; Abraham, Ajith; Rössler, Otto
2014-01-01
The prediction of behavior of complex systems, analysis and modeling of its structure is a vitally important problem in engineering, economy and generally in science today. Examples of such systems can be seen in the world around us (including our bodies) and of course in almost every scientific discipline including such “exotic” domains as the earth’s atmosphere, turbulent fluids, economics (exchange rate and stock markets), population growth, physics (control of plasma), information flow in social networks and its dynamics, chemistry and complex networks. To understand such complex dynamics, which often exhibit strange behavior, and to use it in research or industrial applications, it is paramount to create its models. For this purpose there exists a rich spectrum of methods, from classical such as ARMA models or Box Jenkins method to modern ones like evolutionary computation, neural networks, fuzzy logic, geometry, deterministic chaos amongst others. This proceedings book is a collection of accepted ...
Support vector regression model for complex target RCS predicting
Institute of Scientific and Technical Information of China (English)
Wang Gu; Chen Weishi; Miao Jungang
2009-01-01
The electromagnetic scattering computation has developed rapidly for many years; some computing problems for complex and coated targets cannot be solved by using the existing theory and computing models. A computing model based on data is established for making up the insufficiency of theoretic models. Based on the "support vector regression method", which is formulated on the principle of minimizing a structural risk, a data model to predicate the unknown radar cross section of some appointed targets is given. Comparison between the actual data and the results of this predicting model based on support vector regression method proved that the support vector regression method is workable and with a comparative precision.
Energy Technology Data Exchange (ETDEWEB)
Goldsby, Michael E.; Mayo, Jackson R.; Bhattacharyya, Arnab (Massachusetts Institute of Technology, Cambridge, MA); Armstrong, Robert C.; Vanderveen, Keith
2008-09-01
The goal of this research was to examine foundational methods, both computational and theoretical, that can improve the veracity of entity-based complex system models and increase confidence in their predictions for emergent behavior. The strategy was to seek insight and guidance from simplified yet realistic models, such as cellular automata and Boolean networks, whose properties can be generalized to production entity-based simulations. We have explored the usefulness of renormalization-group methods for finding reduced models of such idealized complex systems. We have prototyped representative models that are both tractable and relevant to Sandia mission applications, and quantified the effect of computational renormalization on the predictive accuracy of these models, finding good predictivity from renormalized versions of cellular automata and Boolean networks. Furthermore, we have theoretically analyzed the robustness properties of certain Boolean networks, relevant for characterizing organic behavior, and obtained precise mathematical constraints on systems that are robust to failures. In combination, our results provide important guidance for more rigorous construction of entity-based models, which currently are often devised in an ad-hoc manner. Our results can also help in designing complex systems with the goal of predictable behavior, e.g., for cybersecurity.
Manifold boundaries give "gray-box" approximations of complex models
Transtrum, Mark K
2016-01-01
We discuss a method of parameter reduction in complex models known as the Manifold Boundary Approximation Method (MBAM). This approach, based on a geometric interpretation of statistics, maps the model reduction problem to a geometric approximation problem. It operates iteratively, removing one parameter at a time, by approximating a high-dimension, but thin manifold by its boundary. Although the method makes no explicit assumption about the functional form of the model, it does require that the model manifold exhibit a hierarchy of boundaries, i.e., faces, edges, corners, hyper-corners, etc. We empirically show that a variety of model classes have this curious feature, making them amenable to MBAM. These model classes include models composed of elementary functions (e.g., rational functions, exponentials, and partition functions), a variety of dynamical system (e.g., chemical and biochemical kinetics, Linear Time Invariant (LTI) systems, and compartment models), network models (e.g., Bayesian networks, Marko...
Infinite multiple membership relational modeling for complex networks
DEFF Research Database (Denmark)
Mørup, Morten; Schmidt, Mikkel Nørgaard; Hansen, Lars Kai
2011-01-01
Learning latent structure in complex networks has become an important problem fueled by many types of networked data originating from practically all fields of science. In this paper, we propose a new non-parametric Bayesian multiple-membership latent feature model for networks. Contrary to exist......Learning latent structure in complex networks has become an important problem fueled by many types of networked data originating from practically all fields of science. In this paper, we propose a new non-parametric Bayesian multiple-membership latent feature model for networks. Contrary...... to existing multiplemembership models that scale quadratically in the number of vertices the proposed model scales linearly in the number of links admitting multiple-membership analysis in large scale networks. We demonstrate a connection between the single membership relational model and multiple membership...
Hierarchical Model for the Evolution of Cloud Complexes
Sánchez, N; Sanchez, Nestor; Parravano, Antonio
1999-01-01
The structure of cloud complexes appears to be well described by a "tree structure" representation when the image is partitioned into "clouds". In this representation, the parent-child relationships are assigned according to containment. Based on this picture, a hierarchical model for the evolution of Cloud Complexes, including star formation, is constructed, that follows the mass evolution of each sub-structure by computing its mass exchange (evaporation or condensation) with its parent and children, which depends on the radiation density at the interphase. For the set of parameters used as a reference model, the system produces IMFs with a maximum at too high mass (~2 M_sun) and the characteristic times for evolution seem too long. We show that these properties can be improved by adjusting model parameters. However, the emphasis here is to illustrate some general properties of this nonlinear model for the star formation process. Notwithstanding the simplifications involved, the model reveals an essential fe...
Complex human activities recognition using interval temporal syntactic model
Institute of Scientific and Technical Information of China (English)
夏利民; 韩芬; 王军
2016-01-01
A novel method based on interval temporal syntactic model was proposed to recognize human activities in video flow. The method is composed of two parts: feature extract and activities recognition. Trajectory shape descriptor, speeded up robust features (SURF) and histograms of optical flow (HOF) were proposed to represent human activities, which provide more exhaustive information to describe human activities on shape, structure and motion. In the process of recognition, a probabilistic latent semantic analysis model (PLSA) was used to recognize sample activities at the first step. Then, an interval temporal syntactic model, which combines the syntactic model with the interval algebra to model the temporal dependencies of activities explicitly, was introduced to recognize the complex activities with a time relationship. Experiments results show the effectiveness of the proposed method in comparison with other state-of-the-art methods on the public databases for the recognition of complex activities.
Turing instability in reaction-diffusion models on complex networks
Ide, Yusuke; Izuhara, Hirofumi; Machida, Takuya
2016-09-01
In this paper, the Turing instability in reaction-diffusion models defined on complex networks is studied. Here, we focus on three types of models which generate complex networks, i.e. the Erdős-Rényi, the Watts-Strogatz, and the threshold network models. From analysis of the Laplacian matrices of graphs generated by these models, we numerically reveal that stable and unstable regions of a homogeneous steady state on the parameter space of two diffusion coefficients completely differ, depending on the network architecture. In addition, we theoretically discuss the stable and unstable regions in the cases of regular enhanced ring lattices which include regular circles, and networks generated by the threshold network model when the number of vertices is large enough.
Modelling nutrient reduction targets - model structure complexity vs. data availability
Capell, Rene; Lausten Hansen, Anne; Donnelly, Chantal; Refsgaard, Jens Christian; Arheimer, Berit
2015-04-01
In most parts of Europe, macronutrient concentrations and loads in surface water are currently affected by human land use and land management choices. Moreover, current macronutrient concentration and load levels often violate European Water Framework Directive (WFD) targets and effective measures to reduce these levels are sought after by water managers. Identifying such effective measures in specific target catchments should consider the four key processes release, transport, retention, and removal, and thus physical catchment characteristics as e.g. soils and geomorphology, but also management data such as crop distribution and fertilizer application regimes. The BONUS funded research project Soils2Sea evaluates new, differentiated regulation strategies to cost-efficiently reduce nutrient loads to the Baltic Sea based on new knowledge of nutrient transport and retention processes between soils and the coast. Within the Soils2Sea framework, we here examine the capability of two integrated hydrological and nutrient transfer models, HYPE and Mike SHE, to model runoff and nitrate flux responses in the 100 km2 Norsminde catchment, Denmark, comparing different model structures and data bases. We focus on comparing modelled nitrate reductions within and below the root zone, and evaluate model performances as function of available model structures (process representation within the model) and available data bases (temporal forcing data and spatial information). This model evaluation is performed to aid in the development of model tools which will be used to estimate the effect of new nutrient reduction measures on the catchment to regional scale, where available data - both climate forcing and land management - typically are increasingly limited with the targeted spatial scale and may act as a bottleneck for process conceptualizations and thus the value of a model as tool to provide decision support for differentiated regulation strategies.
The Complexity of Model Checking Higher-Order Fixpoint Logic
DEFF Research Database (Denmark)
Axelsson, Roland; Lange, Martin; Somla, Rafal
2007-01-01
of solving rather large parity games of small index. As a consequence of this we obtain an ExpTime upper bound on the expression complexity of each HFLk,m. The lower bound is established by a reduction from the word problem for alternating (k-1)-fold exponential space bounded Turing Machines. As a corollary...... provides complexity results for its model checking problem. In particular we consider its fragments HFLk,m which are formed using types of bounded order k and arity m only. We establish k-ExpTime-completeness for model checking each HFLk,m fragment. For the upper bound we reduce the problem to the problem...
Chaos and complexity in a simple model of production dynamics
Directory of Open Access Journals (Sweden)
I. Katzorke
2000-01-01
Full Text Available We consider complex dynamical behavior in a simple model of production dynamics, based on the Wiendahl’s funnel approach. In the case of continuous order flow a model of three parallel funnels reduces to the one-dimensional Bernoulli-type map, and demonstrates strong chaotic properties. The optimization of production costs is possible with the OGY method of chaos control. The dynamics changes drastically in the case of discrete order flow. We discuss different dynamical behaviors, the complexity and the stability of this discrete system.
Transmembrane and secreted MUC1 probes show trafficking-dependent changes in O-glycan core profiles.
Engelmann, Katja; Kinlough, Carol L; Müller, Stefan; Razawi, Hani; Baldus, Stephan E; Hughey, Rebecca P; Hanisch, Franz-Georg
2005-11-01
The human mucin MUC1 is expressed both as a transmembrane heterodimeric protein complex that recycles via the trans-Golgi network (TGN) and as a secreted isoform. To determine whether differences in cellular trafficking might influence the O-glycosylation profiles on these isoforms, we developed a model system consisting of membrane-bound and secretory-recombinant glycosylation probes. Secretory MUC1-S contains only a truncated repeat domain, whereas in MUC1-M constructs this domain is attached to the native transmembrane and cytoplasmic domains of MUC1 either directly (M0) or via an intermitting nonfunctional (M1) or functional sperm protein-enterokinase-agrin (SEA) module (M2); the SEA module contains a putative proteolytic cleavage site and is associated with proteins receiving extensive O-glycosylation. We showed that MUC1-M2 simulates endogenous MUC1 by recycling from the cell surface of Chinese hamster ovary (CHO) mutant ldlD14 cells through intracellular compartments where its glycosylation continues. The profiles of O-linked glycans on MUC1-S secreted by epithelial EBNA-293 and MCF-7 breast cancer cells revealed patterns dominated by core 2-based oligosaccharides. In contrast, the respective membrane-shed probes expressed in the same cells showed a complete shift to patterns dominated by sialyl core 1. In conclusion, glycan core profiles reflected the subcellular trafficking pathways of the secretory or membranous probes and the modifying activities of the resident glycosyltransferases.
Reduced Complexity Channel Models for IMT-Advanced Evaluation
Directory of Open Access Journals (Sweden)
Yu Zhang
2009-01-01
Full Text Available Accuracy and complexity are two crucial aspects of the applicability of a channel model for wideband multiple input multiple output (MIMO systems. For small number of antenna element pairs, correlation-based models have lower computational complexity while the geometry-based stochastic models (GBSMs can provide more accurate modeling of real radio propagation. This paper investigates several potential simplifications of the GBSM to reduce the complexity with minimal impact on accuracy. In addition, we develop a set of broadband metrics which enable a thorough investigation of the differences between the GBSMs and the simplified models. The impact of various random variables which are employed by the original GBSM on the system level simulation are also studied. Both simulation results and a measurement campaign show that complexity can be reduced significantly with a negligible loss of accuracy in the proposed metrics. As an example, in the presented scenarios, the computational time can be reduced by up to 57% while keeping the relative deviation of 5% outage capacity within 5%.
(Relatively) Simple Models of Flow in Complex Terrain
Taylor, Peter; Weng, Wensong; Salmon, Jim
2013-04-01
The term, "complex terrain" includes both topography and variations in surface roughness and thermal properties. The scales that are affected can differ and there are some advantages to modeling them separately. In studies of flow in complex terrain we have developed 2 D and 3 D models of atmospheric PBL boundary layer flow over roughness changes, appropriate for longer fetches than most existing models. These "internal boundary layers" are especially important for understanding and predicting wind speed variations with distance from shorelines, an important factor for wind farms around, and potentially in, the Great Lakes. The models can also form a base for studying the wakes behind woodlots and wind turbines. Some sample calculations of wind speed evolution over water and the reduced wind speeds behind an isolated woodlot, represented simply in terms of an increase in surface roughness, will be presented. Note that these models can also include thermal effects and non-neutral stratification. We can use the model to deal with 3-D roughness variations and will describe applications to both on-shore and off-shore situations around the Great Lakes. In particular we will show typical results for hub height winds and indicate the length of over-water fetch needed to get the full benefit of siting turbines over water. The linear Mixed Spectral Finite-Difference (MSFD) and non-linear (NLMSFD) models for surface boundary-layer flow over complex terrain have been extended to planetary boundary-layer flow over topography This allows for their use for larger scale regions and increased heights. The models have been applied to successfully simulate the Askervein hill experimental case and we will show examples of applications to more complex terrain, typical of some Canadian wind farms. Output from the model can be used as an alternative to MS-Micro, WAsP or other CFD calculations of topographic impacts for input to wind farm design software.
Surface complexation modeling of inositol hexaphosphate sorption onto gibbsite.
Ruyter-Hooley, Maika; Larsson, Anna-Carin; Johnson, Bruce B; Antzutkin, Oleg N; Angove, Michael J
2015-02-15
The sorption of Inositol hexaphosphate (IP6) onto gibbsite was investigated using a combination of adsorption experiments, (31)P solid-state MAS NMR spectroscopy, and surface complexation modeling. Adsorption experiments conducted at four temperatures showed that IP6 sorption decreased with increasing pH. At pH 6, IP6 sorption increased with increasing temperature, while at pH 10 sorption decreased as the temperature was raised. (31)P MAS NMR measurements at pH 3, 6, 9 and 11 produced spectra with broad resonance lines that could be de-convoluted with up to five resonances (+5, 0, -6, -13 and -21ppm). The chemical shifts suggest the sorption process involves a combination of both outer- and inner-sphere complexation and surface precipitation. Relative intensities of the observed resonances indicate that outer-sphere complexation is important in the sorption process at higher pH, while inner-sphere complexation and surface precipitation are dominant at lower pH. Using the adsorption and (31)P MAS NMR data, IP6 sorption to gibbsite was modeled with an extended constant capacitance model (ECCM). The adsorption reactions that best described the sorption of IP6 to gibbsite included two inner-sphere surface complexes and one outer-sphere complex: ≡AlOH + IP₆¹²⁻ + 5H⁺ ↔ ≡Al(IP₆H₄)⁷⁻ + H₂O, ≡3AlOH + IP₆¹²⁻ + 6H⁺ ↔ ≡Al₃(IP₆H₃)⁶⁻ + 3H₂O, ≡2AlOH + IP₆¹²⁻ + 4H⁺ ↔ (≡AlOH₂)₂²⁺(IP₆H₂)¹⁰⁻. The inner-sphere complex involving three surface sites may be considered to be equivalent to a surface precipitate. Thermodynamic parameters were obtained from equilibrium constants derived from surface complexation modeling. Enthalpies for the formation of inner-sphere surface complexes were endothermic, while the enthalpy for the outer-sphere complex was exothermic. The entropies for the proposed sorption reactions were large and positive suggesting that changes in solvation of species play a major role in driving
Predictive modelling of complex agronomic and biological systems.
Keurentjes, Joost J B; Molenaar, Jaap; Zwaan, Bas J
2013-09-01
Biological systems are tremendously complex in their functioning and regulation. Studying the multifaceted behaviour and describing the performance of such complexity has challenged the scientific community for years. The reduction of real-world intricacy into simple descriptive models has therefore convinced many researchers of the usefulness of introducing mathematics into biological sciences. Predictive modelling takes such an approach another step further in that it takes advantage of existing knowledge to project the performance of a system in alternating scenarios. The ever growing amounts of available data generated by assessing biological systems at increasingly higher detail provide unique opportunities for future modelling and experiment design. Here we aim to provide an overview of the progress made in modelling over time and the currently prevalent approaches for iterative modelling cycles in modern biology. We will further argue for the importance of versatility in modelling approaches, including parameter estimation, model reduction and network reconstruction. Finally, we will discuss the difficulties in overcoming the mathematical interpretation of in vivo complexity and address some of the future challenges lying ahead. © 2013 John Wiley & Sons Ltd.
Complexity, accuracy and practical applicability of different biogeochemical model versions
Los, F. J.; Blaas, M.
2010-04-01
The construction of validated biogeochemical model applications as prognostic tools for the marine environment involves a large number of choices particularly with respect to the level of details of the .physical, chemical and biological aspects. Generally speaking, enhanced complexity might enhance veracity, accuracy and credibility. However, very complex models are not necessarily effective or efficient forecast tools. In this paper, models of varying degrees of complexity are evaluated with respect to their forecast skills. In total 11 biogeochemical model variants have been considered based on four different horizontal grids. The applications vary in spatial resolution, in vertical resolution (2DH versus 3D), in nature of transport, in turbidity and in the number of phytoplankton species. Included models range from 15 year old applications with relatively simple physics up to present state of the art 3D models. With all applications the same year, 2003, has been simulated. During the model intercomparison it has been noticed that the 'OSPAR' Goodness of Fit cost function (Villars and de Vries, 1998) leads to insufficient discrimination of different models. This results in models obtaining similar scores although closer inspection of the results reveals large differences. In this paper therefore, we have adopted the target diagram by Jolliff et al. (2008) which provides a concise and more contrasting picture of model skill on the entire model domain and for the entire period of the simulations. Correctness in prediction of the mean and the variability are separated and thus enhance insight in model functioning. Using the target diagrams it is demonstrated that recent models are more consistent and have smaller biases. Graphical inspection of time series confirms this, as the level of variability appears more realistic, also given the multi-annual background statistics of the observations. Nevertheless, whether the improvements are all genuine for the particular
Infinite Multiple Membership Relational Modeling for Complex Networks
DEFF Research Database (Denmark)
Mørup, Morten; Schmidt, Mikkel Nørgaard; Hansen, Lars Kai
Learning latent structure in complex networks has become an important problem fueled by many types of networked data originating from practically all fields of science. In this paper, we propose a new non-parametric Bayesian multiplemembership latent feature model for networks. Contrary to existing...... multiplemembership models that scale quadratically in the number of vertices the proposedmodel scales linearly in the number of links admittingmultiple-membership analysis in large scale networks. We demonstrate a connection between the single membership relational model and multiple membership models and show...
Stålne, Kristian; Kjellström, Sofia; Utriainen, Jukka
2016-01-01
An important aspect of higher education is to educate students who can manage complex relationships and solve complex problems. Teachers need to be able to evaluate course content with regard to complexity, as well as evaluate students' ability to assimilate complex content and express it in the form of a learning outcome. One model for evaluating…
Modeling data irregularities and structural complexities in data envelopment analysis
Zhu, Joe
2007-01-01
In a relatively short period of time, Data Envelopment Analysis (DEA) has grown into a powerful quantitative, analytical tool for measuring and evaluating performance. It has been successfully applied to a whole variety of problems in many different contexts worldwide. This book deals with the micro aspects of handling and modeling data issues in modeling DEA problems. DEA's use has grown with its capability of dealing with complex "service industry" and the "public service domain" types of problems that require modeling of both qualitative and quantitative data. This handbook treatment deals with specific data problems including: imprecise or inaccurate data; missing data; qualitative data; outliers; undesirable outputs; quality data; statistical analysis; software and other data aspects of modeling complex DEA problems. In addition, the book will demonstrate how to visualize DEA results when the data is more than 3-dimensional, and how to identify efficiency units quickly and accurately.
Computer models of complex multiloop branched pipeline systems
Kudinov, I. V.; Kolesnikov, S. V.; Eremin, A. V.; Branfileva, A. N.
2013-11-01
This paper describes the principal theoretical concepts of the method used for constructing computer models of complex multiloop branched pipeline networks, and this method is based on the theory of graphs and two Kirchhoff's laws applied to electrical circuits. The models make it possible to calculate velocities, flow rates, and pressures of a fluid medium in any section of pipeline networks, when the latter are considered as single hydraulic systems. On the basis of multivariant calculations the reasons for existing problems can be identified, the least costly methods of their elimination can be proposed, and recommendations for planning the modernization of pipeline systems and construction of their new sections can be made. The results obtained can be applied to complex pipeline systems intended for various purposes (water pipelines, petroleum pipelines, etc.). The operability of the model has been verified on an example of designing a unified computer model of the heat network for centralized heat supply of the city of Samara.
Complex Network Structure of Flocks in the Standard Vicsek Model
Baglietto, Gabriel; Albano, Ezequiel V.; Candia, Julián
2013-10-01
In flocking models, the collective motion of self-driven individuals leads to the formation of complex spatiotemporal patterns. The Standard Vicsek Model (SVM) considers individuals that tend to adopt the direction of movement of their neighbors under the influence of noise. By performing an extensive complex network characterization of the structure of SVM flocks, we show that flocks are highly clustered, assortative, and non-hierarchical networks with short-tailed degree distributions. Moreover, we also find that the SVM dynamics leads to the formation of complex structures with an effective dimension higher than that of the space where the actual displacements take place. Furthermore, we show that these structures are capable of sustaining mean-field-like orientationally ordered states when the displacements are suppressed, thus suggesting a linkage between the onset of order and the enhanced dimensionality of SVM flocks.
Free particles from Brauer algebras in complex matrix models
Kimura, Yusuke; Turton, David
2009-01-01
The gauge invariant degrees of freedom of matrix models based on an N x N complex matrix, with U(N) gauge symmetry, contain hidden free particle structures. These are exhibited using triangular matrix variables via the Schur decomposition. The Brauer algebra basis for complex matrix models developed earlier is useful in projecting to a sector which matches the state counting of N free fermions on a circle. The Brauer algebra projection is characterized by the vanishing of a scale invariant laplacian constructed from the complex matrix. The special case of N=2 is studied in detail: the ring of gauge invariant functions as well as a ring of scale and gauge invariant differential operators are characterized completely. The orthonormal basis of wavefunctions in this special case is completely characterized by a set of five commuting Hamiltonians, which display free particle structures. Applications to the reduced matrix quantum mechanics coming from radial quantization in N=4 SYM are described. We propose that th...
Modelling, Estimation and Control of Networked Complex Systems
Chiuso, Alessandro; Frasca, Mattia; Rizzo, Alessandro; Schenato, Luca; Zampieri, Sandro
2009-01-01
The paradigm of complexity is pervading both science and engineering, leading to the emergence of novel approaches oriented at the development of a systemic view of the phenomena under study; the definition of powerful tools for modelling, estimation, and control; and the cross-fertilization of different disciplines and approaches. This book is devoted to networked systems which are one of the most promising paradigms of complexity. It is demonstrated that complex, dynamical networks are powerful tools to model, estimate, and control many interesting phenomena, like agent coordination, synchronization, social and economics events, networks of critical infrastructures, resources allocation, information processing, or control over communication networks. Moreover, it is shown how the recent technological advances in wireless communication and decreasing in cost and size of electronic devices are promoting the appearance of large inexpensive interconnected systems, each with computational, sensing and mobile cap...
ABOUT COMPLEX APPROACH TO MODELLING OF TECHNOLOGICAL MACHINES FUNCTIONING
Directory of Open Access Journals (Sweden)
A. A. Honcharov
2015-01-01
Full Text Available Problems arise in the process of designing, production and investigation of a complicated technological machine. These problems concern not only properties of some types of equipment but they have respect to regularities of control object functioning as a whole. A technological machine is thought of as such technological complex where it is possible to lay emphasis on a control system (or controlling device and a controlled object. The paper analyzes a number of existing approaches to construction of models for controlling devices and their functioning. A complex model for a technological machine operation has been proposed in the paper; in other words it means functioning of a controlling device and a controlled object of the technological machine. In this case models of the controlling device and the controlled object of the technological machine can be represented as aggregate combination (elements of these models. The paper describes a conception on realization of a complex model for a technological machine as a model for interaction of units (elements in the controlling device and the controlled object. When a control activation is given to the controlling device of the technological machine its modelling is executed at an algorithmic or logic level and the obtained output signals are interpreted as events and information about them is transferred to executive mechanisms.The proposed scheme of aggregate integration considers element models as object classes and the integration scheme is presented as a combination of object property values (combination of a great many input and output contacts and combination of object interactions (in the form of an integration operator. Spawn of parent object descendants of the technological machine model and creation of their copies in various project parts is one of the most important means of the distributed technological machine modelling that makes it possible to develop complicated models of
Petri net model for analysis of concurrently processed complex algorithms
Stoughton, John W.; Mielke, Roland R.
1986-01-01
This paper presents a Petri-net model suitable for analyzing the concurrent processing of computationally complex algorithms. The decomposed operations are to be processed in a multiple processor, data driven architecture. Of particular interest is the application of the model to both the description of the data/control flow of a particular algorithm, and to the general specification of the data driven architecture. A candidate architecture is also presented.
Energy Technology Data Exchange (ETDEWEB)
Brayman, A.A.; Miller, M.W.
1986-08-01
Seminal roots of Cucumis sativus and Cucurbita maxima were exposed to 60 Hz electric fields of 100-500 V . m/sup -1/ in a conducting aqueous inorganic growth medium. Root growth rates were measured to produce a dose-response relationship for each species. The species were selected for study because of their familial relationship, reported sensitivity to 60 Hz, 360 V . m/sup -1/ electric fields, and differing average root cell sizes. The latter characteristic influences the magnitude of ELF membrane potentials induced by constant-strength applied electric fields, but does not affect the magnitude of the electric field strength tangent to the cell surface. The difference in average root cell size between C. sativus (smaller cells) and C. maxima (larger cells) was used to evaluate two alternate hypotheses that the observed effect on root growth is stimulated by the electric field tangent to the cell surface, or a field-induced perturbation in the normal transmembrane potential of the cells. The results of the dose-response relationship studies are qualitatively consistent with the hypothesis that the effect is elicited by induced transmembrane potentials. The smaller-celled roots showed a substantially higher response threshold (C. sativus; E/sub 0/sup(TH) approx.= 330 V . m/sup -1/) than did the larger-celled species (C. maxima; E/sub 0/sup(TH) approx.= 200 V . m/sup -1/). At field strengths above the response thresholds in both species, the growth rate of C. sativus roots was less affected than that of C. maxima roots exposed to the same field strength.
Virus-Encoded 7 Transmembrane Receptors
DEFF Research Database (Denmark)
Mølleskov-Jensen, Ann-Sofie; Oliveira, MarthaTrindade; Farrell, Helen Elizabeth
2015-01-01
Herpesviruses are an ancient group which have exploited gene capture of multiple cellular modulators of the immune response. Viral homologues of 7 transmembrane receptors (v7TMRs) are a consistent feature of beta- and gammaherpesviruses; the majority of the v7TMRs are homologous to cellular...... chemokine receptors (CKRs). Conserved families of v7TMRs distinguish between beta- versus gammaherpesviruses; furthermore, significant divisions within these subfamilies, such as between genera of the gammaherpesviruses or between the primate and rodent cytomegaloviruses, coincide with specific v7TMR gene...... families. Divergence of functional properties between the viral 7TMR and their cellular counterparts is likely, therefore, to reflect adaptation supporting various aspects of the viral lifecycle with concomitant effects upon viral pathogenesis. Consistent with their long evolutionary history, the v7TMRs...
Interactive Visualizations of Complex Seismic Data and Models
Chai, C.; Ammon, C. J.; Maceira, M.; Herrmann, R. B.
2016-12-01
The volume and complexity of seismic data and models have increased dramatically thanks to dense seismic station deployments and advances in data modeling and processing. Seismic observations such as receiver functions and surface-wave dispersion are multidimensional: latitude, longitude, time, amplitude and latitude, longitude, period, and velocity. Three-dimensional seismic velocity models are characterized with three spatial dimensions and one additional dimension for the speed. In these circumstances, exploring the data and models and assessing the data fits is a challenge. A few professional packages are available to visualize these complex data and models. However, most of these packages rely on expensive commercial software or require a substantial time investment to master, and even when that effort is complete, communicating the results to others remains a problem. A traditional approach during the model interpretation stage is to examine data fits and model features using a large number of static displays. Publications include a few key slices or cross-sections of these high-dimensional data, but this prevents others from directly exploring the model and corresponding data fits. In this presentation, we share interactive visualization examples of complex seismic data and models that are based on open-source tools and are easy to implement. Model and data are linked in an intuitive and informative web-browser based display that can be used to explore the model and the features in the data that influence various aspects of the model. We encode the model and data into HTML files and present high-dimensional information using two approaches. The first uses a Python package to pack both data and interactive plots in a single file. The second approach uses JavaScript, CSS, and HTML to build a dynamic webpage for seismic data visualization. The tools have proven useful and led to deeper insight into 3D seismic models and the data that were used to construct them
Modelling and simulating in-stent restenosis with complex automata
Hoekstra, A.G.; Lawford, P.; Hose, R.
2010-01-01
In-stent restenosis, the maladaptive response of a blood vessel to injury caused by the deployment of a stent, is a multiscale system involving a large number of biological and physical processes. We describe a Complex Automata Model for in-stent restenosis, coupling bulk flow, drug diffusion, and s
Modelling of Voids in Complex Radio Frequency Plasmas
W. J. Goedheer,; Land, V.; Venema, J.
2009-01-01
In this paper hydrodynamic and kinetic approaches to model low pressure capacitively coupled complex radio-frequency discharges are discussed and applied to discharges under microgravity. Experiments in the PKE-Nefedov reactor on board the International Space Station, as well as discharges in which
Modelling storm impact on complex coastlines: Westkapelle, The Netherlands
Van Santen, R.B.; Steetzel, H.J.; Van Thiel de Vries, J.S.M.; Van Dongeren, A.
2012-01-01
Regular dune safety assessments in the Netherlands are presently based on a 1D model approach, which is insufficiently applicable for more complex coastal areas with structures, tidal channels or spatially strong varying bathymetry. These situations require more advanced methods to assess the safety
Modelling storm impact on complex coastlines: Westkapelle, The Netherlands
Van Santen, R.B.; Steetzel, H.J.; Van Thiel de Vries, J.S.M.; Van Dongeren, A.
2012-01-01
Regular dune safety assessments in the Netherlands are presently based on a 1D model approach, which is insufficiently applicable for more complex coastal areas with structures, tidal channels or spatially strong varying bathymetry. These situations require more advanced methods to assess the safety
Performance of Random Effects Model Estimators under Complex Sampling Designs
Jia, Yue; Stokes, Lynne; Harris, Ian; Wang, Yan
2011-01-01
In this article, we consider estimation of parameters of random effects models from samples collected via complex multistage designs. Incorporation of sampling weights is one way to reduce estimation bias due to unequal probabilities of selection. Several weighting methods have been proposed in the literature for estimating the parameters of…
Modelling and simulating in-stent restenosis with complex automata
Hoekstra, A.G.; Lawford, P.; Hose, R.
2010-01-01
In-stent restenosis, the maladaptive response of a blood vessel to injury caused by the deployment of a stent, is a multiscale system involving a large number of biological and physical processes. We describe a Complex Automata Model for in-stent restenosis, coupling bulk flow, drug diffusion, and s
Copper complexes as biomimetic models of catechol oxidase : mechanistic studies
Koval, Iryna A.
2006-01-01
The research described in this thesis deals with the synthesis of copper(II) complexes with phenol-based or macrocyclic ligands, which can be regarded as model compounds of the active site of catechol oxidase, and with the mechanism of the catalytic oxidation of catechol mediated by these compounds.
Satlc model lesson for teaching and learning complex ...
African Journals Online (AJOL)
Satlc model lesson for teaching and learning complex environmental issues related to the ... In the absence of necessary input of biological sciences, mathematics, ... Recently concept based teaching methodology; namely systemic approach to ... By Country · List All Titles · Open Access Titles This Journal is Open Access.
Model-based safety architecture framework for complex systems
Schuitemaker, K.; Rajabalinejad, M.; Braakhuis, J.G.; Podofilini, Luca; Sudret, Bruno; Stojadinovic, Bozidar; Zio, Enrico; Kröger, Wolfgang
2015-01-01
The shift to transparency and rising need of the general public for safety, together with the increasing complexity and interdisciplinarity of modern safety-critical Systems of Systems (SoS) have resulted in a Model-Based Safety Architecture Framework (MBSAF) for capturing and sharing architectural
Surface complexation modeling of americium sorption onto volcanic tuff.
Ding, M; Kelkar, S; Meijer, A
2014-10-01
Results of a surface complexation model (SCM) for americium sorption on volcanic rocks (devitrified and zeolitic tuff) are presented. The model was developed using PHREEQC and based on laboratory data for americium sorption on quartz. Available data for sorption of americium on quartz as a function of pH in dilute groundwater can be modeled with two surface reactions involving an americium sulfate and an americium carbonate complex. It was assumed in applying the model to volcanic rocks from Yucca Mountain, that the surface properties of volcanic rocks can be represented by a quartz surface. Using groundwaters compositionally representative of Yucca Mountain, americium sorption distribution coefficient (Kd, L/Kg) values were calculated as function of pH. These Kd values are close to the experimentally determined Kd values for americium sorption on volcanic rocks, decreasing with increasing pH in the pH range from 7 to 9. The surface complexation constants, derived in this study, allow prediction of sorption of americium in a natural complex system, taking into account the inherent uncertainty associated with geochemical conditions that occur along transport pathways.
Molecular mechanisms for generating transmembrane proton gradients.
Gunner, M R; Amin, Muhamed; Zhu, Xuyu; Lu, Jianxun
2013-01-01
Membrane proteins use the energy of light or high energy substrates to build a transmembrane proton gradient through a series of reactions leading to proton release into the lower pH compartment (P-side) and proton uptake from the higher pH compartment (N-side). This review considers how the proton affinity of the substrates, cofactors and amino acids are modified in four proteins to drive proton transfers. Bacterial reaction centers (RCs) and photosystem II (PSII) carry out redox chemistry with the species to be oxidized on the P-side while reduction occurs on the N-side of the membrane. Terminal redox cofactors are used which have pKas that are strongly dependent on their redox state, so that protons are lost on oxidation and gained on reduction. Bacteriorhodopsin is a true proton pump. Light activation triggers trans to cis isomerization of a bound retinal. Strong electrostatic interactions within clusters of amino acids are modified by the conformational changes initiated by retinal motion leading to changes in proton affinity, driving transmembrane proton transfer. Cytochrome c oxidase (CcO) catalyzes the reduction of O2 to water. The protons needed for chemistry are bound from the N-side. The reduction chemistry also drives proton pumping from N- to P-side. Overall, in CcO the uptake of 4 electrons to reduce O2 transports 8 charges across the membrane, with each reduction fully coupled to removal of two protons from the N-side, the delivery of one for chemistry and transport of the other to the P-side.
Specificity of transmembrane protein palmitoylation in yeast.
Directory of Open Access Journals (Sweden)
Ayelén González Montoro
Full Text Available Many proteins are modified after their synthesis, by the addition of a lipid molecule to one or more cysteine residues, through a thioester bond. This modification is called S-acylation, and more commonly palmitoylation. This reaction is carried out by a family of enzymes, called palmitoyltransferases (PATs, characterized by the presence of a conserved 50- aminoacids domain called "Asp-His-His-Cys- Cysteine Rich Domain" (DHHC-CRD. There are 7 members of this family in the yeast Saccharomyces cerevisiae, and each of these proteins is thought to be responsible for the palmitoylation of a subset of substrates. Substrate specificity of PATs, however, is not yet fully understood. Several yeast PATs seem to have overlapping specificity, and it has been proposed that the machinery responsible for palmitoylating peripheral membrane proteins in mammalian cells, lacks specificity altogether.Here we investigate the specificity of transmembrane protein palmitoylation in S. cerevisiae, which is carried out predominantly by two PATs, Swf1 and Pfa4. We show that palmitoylation of transmembrane substrates requires dedicated PATs, since other yeast PATs are mostly unable to perform Swf1 or Pfa4 functions, even when overexpressed. Furthermore, we find that Swf1 is highly specific for its substrates, as it is unable to substitute for other PATs. To identify where Swf1 specificity lies, we carried out a bioinformatics survey to identify amino acids responsible for the determination of specificity or Specificity Determination Positions (SDPs and showed experimentally, that mutation of the two best SDP candidates, A145 and K148, results in complete and partial loss of function, respectively. These residues are located within the conserved catalytic DHHC domain suggesting that it could also be involved in the determination of specificity. Finally, we show that modifying the position of the cysteines in Tlg1, a Swf1 substrate, results in lack of palmitoylation, as
A perspective on modeling and simulation of complex dynamical systems
Åström, K. J.
2011-09-01
There has been an amazing development of modeling and simulation from its beginning in the 1920s, when the technology was available only at a handful of University groups who had access to a mechanical differential analyzer. Today, tools for modeling and simulation are available for every student and engineer. This paper gives a perspective on the development with particular emphasis on technology and paradigm shifts. Modeling is increasingly important for design and operation of complex natural and man-made systems. Because of the increased use of model based control such as Kalman filters and model predictive control, models are also appearing as components of feedback systems. Modeling and simulation are multidisciplinary, it is used in a wide variety of fields and their development have been strongly influenced by mathematics, numerics, computer science and computer technology.
Bayesian Case-deletion Model Complexity and Information Criterion.
Zhu, Hongtu; Ibrahim, Joseph G; Chen, Qingxia
2014-10-01
We establish a connection between Bayesian case influence measures for assessing the influence of individual observations and Bayesian predictive methods for evaluating the predictive performance of a model and comparing different models fitted to the same dataset. Based on such a connection, we formally propose a new set of Bayesian case-deletion model complexity (BCMC) measures for quantifying the effective number of parameters in a given statistical model. Its properties in linear models are explored. Adding some functions of BCMC to a conditional deviance function leads to a Bayesian case-deletion information criterion (BCIC) for comparing models. We systematically investigate some properties of BCIC and its connection with other information criteria, such as the Deviance Information Criterion (DIC). We illustrate the proposed methodology on linear mixed models with simulations and a real data example.
Directory of Open Access Journals (Sweden)
Henry de-Graft Acquah
2013-01-01
Full Text Available Information Criteria provides an attractive basis for selecting the best model from a set of competing asymmetric price transmission models or theories. However, little is understood about the sensitivity of the model selection methods to model complexity. This study therefore fits competing asymmetric price transmission models that differ in complexity to simulated data and evaluates the ability of the model selection methods to recover the true model. The results of Monte Carlo experimentation suggest that in general BIC, CAIC and DIC were superior to AIC when the true data generating process was the standard error correction model, whereas AIC was more successful when the true model was the complex error correction model. It is also shown that the model selection methods performed better in large samples for a complex asymmetric data generating process than with a standard asymmetric data generating process. Except for complex models, AIC's performance did not make substantial gains in recovery rates as sample size increased. The research findings demonstrate the influence of model complexity in asymmetric price transmission model comparison and selection.
Complexity vs. simplicity: groundwater model ranking using information criteria.
Engelhardt, I; De Aguinaga, J G; Mikat, H; Schüth, C; Liedl, R
2014-01-01
A groundwater model characterized by a lack of field data about hydraulic model parameters and boundary conditions combined with many observation data sets for calibration purpose was investigated concerning model uncertainty. Seven different conceptual models with a stepwise increase from 0 to 30 adjustable parameters were calibrated using PEST. Residuals, sensitivities, the Akaike information criterion (AIC and AICc), Bayesian information criterion (BIC), and Kashyap's information criterion (KIC) were calculated for a set of seven inverse calibrated models with increasing complexity. Finally, the likelihood of each model was computed. Comparing only residuals of the different conceptual models leads to an overparameterization and certainty loss in the conceptual model approach. The model employing only uncalibrated hydraulic parameters, estimated from sedimentological information, obtained the worst AIC, BIC, and KIC values. Using only sedimentological data to derive hydraulic parameters introduces a systematic error into the simulation results and cannot be recommended for generating a valuable model. For numerical investigations with high numbers of calibration data the BIC and KIC select as optimal a simpler model than the AIC. The model with 15 adjusted parameters was evaluated by AIC as the best option and obtained a likelihood of 98%. The AIC disregards the potential model structure error and the selection of the KIC is, therefore, more appropriate. Sensitivities to piezometric heads were highest for the model with only five adjustable parameters and sensitivity coefficients were directly influenced by the changes in extracted groundwater volumes.
ATPase activity of the cystic fibrosis transmembrane conductance regulator.
Li, C; Ramjeesingh, M; Wang, W; Garami, E; Hewryk, M; Lee, D; Rommens, J M; Galley, K; Bear, C E
1996-11-08
The gene mutated in cystic fibrosis codes for the cystic fibrosis transmembrane conductance regulator (CFTR), a cyclic AMP-activated chloride channel thought to be critical for salt and water transport by epithelial cells. Plausible models exist to describe a role for ATP hydrolysis in CFTR channel activity; however, biochemical evidence that CFTR possesses intrinsic ATPase activity is lacking. In this study, we report the first measurements of the rate of ATP hydrolysis by purified, reconstituted CFTR. The mutation CFTRG551D resides within a motif conserved in many nucleotidases and is known to cause severe human disease. Following reconstitution the mutant protein exhibited both defective ATP hydrolysis and channel gating, providing direct evidence that CFTR utilizes ATP to gate its channel activity.
Sulis, William H
2017-10-01
Walter Freeman III pioneered the application of nonlinear dynamical systems theories and methodologies in his work on mesoscopic brain dynamics.Sadly, mainstream psychology and psychiatry still cling to linear correlation based data analysis techniques, which threaten to subvert the process of experimentation and theory building. In order to progress, it is necessary to develop tools capable of managing the stochastic complexity of complex biopsychosocial systems, which includes multilevel feedback relationships, nonlinear interactions, chaotic dynamics and adaptability. In addition, however, these systems exhibit intrinsic randomness, non-Gaussian probability distributions, non-stationarity, contextuality, and non-Kolmogorov probabilities, as well as the absence of mean and/or variance and conditional probabilities. These properties and their implications for statistical analysis are discussed. An alternative approach, the Process Algebra approach, is described. It is a generative model, capable of generating non-Kolmogorov probabilities. It has proven useful in addressing fundamental problems in quantum mechanics and in the modeling of developing psychosocial systems.
Lemmin, Thomas; Soto, Cinque S; Clinthorne, Graham; DeGrado, William F; Dal Peraro, Matteo
2013-01-01
The PhoQP two-component system is a signaling complex essential for bacterial virulence and cationic antimicrobial peptide resistance. PhoQ is the histidine kinase chemoreceptor of this tandem machine and assembles in a homodimer conformation spanning the bacterial inner membrane. Currently, a full understanding of the PhoQ signal transduction is hindered by the lack of a complete atomistic structure. In this study, an atomistic model of the key transmembrane (TM) domain is assembled by using molecular simulations, guided by experimental cross-linking data. The formation of a polar pocket involving Asn202 in the lumen of the tetrameric TM bundle is crucial for the assembly and solvation of the domain. Moreover, a concerted displacement of the TM helices at the periplasmic side is found to modulate a rotation at the cytoplasmic end, supporting the transduction of the chemical signal through a combination of scissoring and rotational movement of the TM helices.
Directory of Open Access Journals (Sweden)
Thomas Lemmin
Full Text Available The PhoQP two-component system is a signaling complex essential for bacterial virulence and cationic antimicrobial peptide resistance. PhoQ is the histidine kinase chemoreceptor of this tandem machine and assembles in a homodimer conformation spanning the bacterial inner membrane. Currently, a full understanding of the PhoQ signal transduction is hindered by the lack of a complete atomistic structure. In this study, an atomistic model of the key transmembrane (TM domain is assembled by using molecular simulations, guided by experimental cross-linking data. The formation of a polar pocket involving Asn202 in the lumen of the tetrameric TM bundle is crucial for the assembly and solvation of the domain. Moreover, a concerted displacement of the TM helices at the periplasmic side is found to modulate a rotation at the cytoplasmic end, supporting the transduction of the chemical signal through a combination of scissoring and rotational movement of the TM helices.
Probabilistic Analysis Techniques Applied to Complex Spacecraft Power System Modeling
Hojnicki, Jeffrey S.; Rusick, Jeffrey J.
2005-01-01
Electric power system performance predictions are critical to spacecraft, such as the International Space Station (ISS), to ensure that sufficient power is available to support all the spacecraft s power needs. In the case of the ISS power system, analyses to date have been deterministic, meaning that each analysis produces a single-valued result for power capability because of the complexity and large size of the model. As a result, the deterministic ISS analyses did not account for the sensitivity of the power capability to uncertainties in model input variables. Over the last 10 years, the NASA Glenn Research Center has developed advanced, computationally fast, probabilistic analysis techniques and successfully applied them to large (thousands of nodes) complex structural analysis models. These same techniques were recently applied to large, complex ISS power system models. This new application enables probabilistic power analyses that account for input uncertainties and produce results that include variations caused by these uncertainties. Specifically, N&R Engineering, under contract to NASA, integrated these advanced probabilistic techniques with Glenn s internationally recognized ISS power system model, System Power Analysis for Capability Evaluation (SPACE).
Synchronization criteria based on a general complex dynamical network model
Institute of Scientific and Technical Information of China (English)
ZHANG Jian-lin; WANG Chang-jian; XU Cong-fu
2008-01-01
Many complex dynamical networks display synchronization phenomena. We introduce a general complex dynamical network model. The model is equivalent to a simple vector model of adopting the Kronecker product. Some synchronization criteria, including time-variant networks and time-varying networks, are deduced based on Lyapunov's stability theory, and they are proven on the condition of obtaining a certain synchronous solution of an isolated cell. In particular, the inner-coupling matrix directly determines the synchronization of the time-invariant network; while for a time-varying periodic dynamical network, the asymptotic stability of a synchronous solution is determined by a constant matrix which is related to the fundamental solution matrices of the linearization system. Finally, illustrative examples are given to validate the results.
Equivalence of Matrix Models for Complex QCD Dirac Spectra
Akemann, G
2003-01-01
Two different matrix models for QCD with a non-vanishing quark chemical potential are shown to be equivalent by mapping the corresponding partition functions. The equivalence holds in the phase with broken chiral symmetry. It is exact in the limit of weak non-Hermiticity, where the chemical potential squared is rescaled with the volume. At strong non-Hermiticity it holds only for small chemical potential. The first model proposed by Stephanov is directly related to QCD and allows to analyze the QCD phase diagram. In the second model suggested by the author all microscopic spectral correlation functions of complex Dirac operators can be calculated in the broken phase. We briefly compare those predictions to complex Dirac eigenvalues from quenched QCD lattice simulations.
Bloch-Redfield equations for modeling light-harvesting complexes
Jeske, Jan; Plenio, Martin B; Huelga, Susana F; Cole, Jared H
2014-01-01
We challenge the commonly held view that Bloch-Redfield equations are a less powerful tool than phenomenological Lindblad equations for modeling exciton transport in photosynthetic complexes. This view predominantly originates from the misuse of the secular approximation. We provide a detailed description of how to model both coherent oscillations and several types of noise, giving explicit examples. All issues with non-positivity are overcome by a consistent straightforward physical noise model. Herein also lies the strength of the Bloch-Redfield approach because it facilitates the analysis of noise-effects by linking them back to physical parameters of the noise environment. This includes temporal and spatial correlations and the strength and type of interaction between the noise and the system of interest. Finally we analyze a prototypical dimer system as well as a 7-site Fenna-Matthews-Olson (FMO) complex in regards to spatial correlation length of the noise, noise strength, temperature and their connecti...
Reduced Complexity Volterra Models for Nonlinear System Identification
Directory of Open Access Journals (Sweden)
Hacıoğlu Rıfat
2001-01-01
Full Text Available A broad class of nonlinear systems and filters can be modeled by the Volterra series representation. However, its practical use in nonlinear system identification is sometimes limited due to the large number of parameters associated with the Volterra filter′s structure. The parametric complexity also complicates design procedures based upon such a model. This limitation for system identification is addressed in this paper using a Fixed Pole Expansion Technique (FPET within the Volterra model structure. The FPET approach employs orthonormal basis functions derived from fixed (real or complex pole locations to expand the Volterra kernels and reduce the number of estimated parameters. That the performance of FPET can considerably reduce the number of estimated parameters is demonstrated by a digital satellite channel example in which we use the proposed method to identify the channel dynamics. Furthermore, a gradient-descent procedure that adaptively selects the pole locations in the FPET structure is developed in the paper.
Climate predictions: the chaos and complexity in climate models
Mihailović, Dragutin T; Arsenić, Ilija
2013-01-01
Some issues which are relevant for the recent state in climate modeling have been considered. A detailed overview of literature related to this subject is given. The concept in modeling of climate, as a complex system, seen through Godel's Theorem and Rosen's definition of complexity and predictability is discussed. It is pointed out to occurrence of chaos in computing the environmental interface temperature from the energy balance equation given in a difference form. A coupled system of equations, often used in climate models is analyzed. It is shown that the Lyapunov exponent mostly has positive values allowing presence of chaos in this systems. The horizontal energy exchange between environmental interfaces, which is described by the dynamics of driven coupled oscillators, is analyzed. Their behavior and synchronization, when a perturbation is introduced in the system, as a function of the coupling parameters, the logistic parameter and the parameter of exchange, was studied calculating the Lyapunov expone...
Seismic modeling in complex media; Modelagem sismica em meios complexos
Energy Technology Data Exchange (ETDEWEB)
Martins, Eldues Oliveira [Universidade Federal, Rio de Janeiro, RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia. Lab. de Metodos Computacionais em Engenharia (LAMCE)]. E-mail: eldues@lamce.ufrj.br; Soares Filho, Djalma M. [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas]. E-mail: djalma@cenpes.petrobras.com.br
2003-07-01
This work was divided in two phases: first we perform simulations in a realistic onshore model that has the presence of a thick shale layer (approx 1 km) above of a gas deposit, faults plane, vertical interfaces and relief of irregular topography. We esteem the wave-field complexity in a model with typical geology sub-Andean. In this case we applied TIV scheme. Second we simulate an offshore model that presents interfaces with high seismic impedance due to the presence of salt domes. In both simulations we compare seismograms obtained using isotropic and anisotropic layers. These comparisons show as the use of traditional tools (i.e., acoustic and isotropic) can be negligent in highly complex areas. (author)
BlenX-based compositional modeling of complex reaction mechanisms
Directory of Open Access Journals (Sweden)
Judit Zámborszky
2010-02-01
Full Text Available Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of BlenX compositionality.
Entropy, complexity, and Markov diagrams for random walk cancer models
Newton, Paul K.; Mason, Jeremy; Hurt, Brian; Bethel, Kelly; Bazhenova, Lyudmila; Nieva, Jorge; Kuhn, Peter
2014-12-01
The notion of entropy is used to compare the complexity associated with 12 common cancers based on metastatic tumor distribution autopsy data. We characterize power-law distributions, entropy, and Kullback-Liebler divergence associated with each primary cancer as compared with data for all cancer types aggregated. We then correlate entropy values with other measures of complexity associated with Markov chain dynamical systems models of progression. The Markov transition matrix associated with each cancer is associated with a directed graph model where nodes are anatomical locations where a metastatic tumor could develop, and edge weightings are transition probabilities of progression from site to site. The steady-state distribution corresponds to the autopsy data distribution. Entropy correlates well with the overall complexity of the reduced directed graph structure for each cancer and with a measure of systemic interconnectedness of the graph, called graph conductance. The models suggest that grouping cancers according to their entropy values, with skin, breast, kidney, and lung cancers being prototypical high entropy cancers, stomach, uterine, pancreatic and ovarian being mid-level entropy cancers, and colorectal, cervical, bladder, and prostate cancers being prototypical low entropy cancers, provides a potentially useful framework for viewing metastatic cancer in terms of predictability, complexity, and metastatic potential.
Entropy, complexity, and Markov diagrams for random walk cancer models.
Newton, Paul K; Mason, Jeremy; Hurt, Brian; Bethel, Kelly; Bazhenova, Lyudmila; Nieva, Jorge; Kuhn, Peter
2014-12-19
The notion of entropy is used to compare the complexity associated with 12 common cancers based on metastatic tumor distribution autopsy data. We characterize power-law distributions, entropy, and Kullback-Liebler divergence associated with each primary cancer as compared with data for all cancer types aggregated. We then correlate entropy values with other measures of complexity associated with Markov chain dynamical systems models of progression. The Markov transition matrix associated with each cancer is associated with a directed graph model where nodes are anatomical locations where a metastatic tumor could develop, and edge weightings are transition probabilities of progression from site to site. The steady-state distribution corresponds to the autopsy data distribution. Entropy correlates well with the overall complexity of the reduced directed graph structure for each cancer and with a measure of systemic interconnectedness of the graph, called graph conductance. The models suggest that grouping cancers according to their entropy values, with skin, breast, kidney, and lung cancers being prototypical high entropy cancers, stomach, uterine, pancreatic and ovarian being mid-level entropy cancers, and colorectal, cervical, bladder, and prostate cancers being prototypical low entropy cancers, provides a potentially useful framework for viewing metastatic cancer in terms of predictability, complexity, and metastatic potential.
Recombinant expression in E. coli of human FGFR2 with its transmembrane and extracellular domains
Directory of Open Access Journals (Sweden)
Adam Bajinting
2017-06-01
Full Text Available Fibroblast growth factor receptors (FGFRs are a family of receptor tyrosine kinases containing three domains: an extracellular receptor domain, a single transmembrane helix, and an intracellular tyrosine kinase domain. FGFRs are activated by fibroblast growth factors (FGFs as part of complex signal transduction cascades regulating angiogenesis, skeletal formation, cell differentiation, proliferation, cell survival, and cancer. We have developed the first recombinant expression system in E. coli to produce a construct of human FGFR2 containing its transmembrane and extracellular receptor domains. We demonstrate that the expressed construct is functional in binding heparin and dimerizing. Size exclusion chromatography demonstrates that the purified FGFR2 does not form a complex with FGF1 or adopts an inactive dimer conformation. Progress towards the successful recombinant production of intact FGFRs will facilitate further biochemical experiments and structure determination that will provide insight into how extracellular FGF binding activates intracellular kinase activity.
Complex humanitarian emergencies: A review of epidemiological and response models
Directory of Open Access Journals (Sweden)
Burkle Frederick
2006-01-01
Full Text Available Complex emergencies (CEs have been the most common human-generated disaster of the past two decades. These internal conflicts and associated acts of genocide have been poorly understood and poorly managed. This article provides an epidemiological background and understanding of developing and developed countries, and chronic or smoldering countries′ CEs, and explains in detail the prevailing models of response seen by the international community. Even though CEs are declining in number, they have become more complex and dangerous. The UN Charter reform is expected to address internal conflicts and genocide but may not provide a more effective and efficient means to respond.
Complex reaction noise in a molecular quasispecies model
Hochberg, David; Zorzano, María-Paz; Morán, Federico
2006-05-01
We have derived exact Langevin equations for a model of quasispecies dynamics. The inherent multiplicative reaction noise is complex and its statistical properties are specified completely. The numerical simulation of the complex Langevin equations is carried out using the Cholesky decomposition for the noise covariance matrix. This internal noise, which is due to diffusion-limited reactions, produces unavoidable spatio-temporal density fluctuations about the mean field value. In two dimensions, this noise strictly vanishes only in the perfectly mixed limit, a situation difficult to attain in practice.
Modeling of Carbohydrate Binding Modules Complexed to Cellulose
Energy Technology Data Exchange (ETDEWEB)
Nimlos, M. R.; Beckham, G. T.; Bu, L.; Himmel, M. E.; Crowley, M. F.; Bomble, Y. J.
2012-01-01
Modeling results are presented for the interaction of two carbohydrate binding modules (CBMs) with cellulose. The family 1 CBM from Trichoderma reesei's Cel7A cellulase was modeled using molecular dynamics to confirm that this protein selectively binds to the hydrophobic (100) surface of cellulose fibrils and to determine the energetics and mechanisms for locating this surface. Modeling was also conducted of binding of the family 4 CBM from the CbhA complex from Clostridium thermocellum. There is a cleft in this protein, which may accommodate a cellulose chain that is detached from crystalline cellulose. This possibility is explored using molecular dynamics.
A Generalized Preferential Attachment Model for Complex Systems
Yamasaki, K; Fu, D; Buldyrev, S V; Pammolli, F; Riccaboni, M; Stanley, H E; Yamasaki, Kazuko; Matia, Kaushik; Fu, Dongfeng; Buldyrev, Sergey V.; Pammolli, Fabio; Riccaboni, Massimo
2005-01-01
Complex systems can be characterized by classes of equivalency of their elements defined according to system specific rules. We propose a generalized preferential attachment model to describe the class size distribution. The model postulates preferential growth of the existing classes and the steady influx of new classes. We investigate how the distribution depends on the initial conditions and changes from a pure exponential form for zero influx of new classes to a power law with an exponential cutoff form when the influx of new classes is substantial. We apply the model to study the growth dynamics of pharmaceutical industry.
Multiscale modeling of complex materials phenomenological, theoretical and computational aspects
Trovalusci, Patrizia
2014-01-01
The papers in this volume deal with materials science, theoretical mechanics and experimental and computational techniques at multiple scales, providing a sound base and a framework for many applications which are hitherto treated in a phenomenological sense. The basic principles are formulated of multiscale modeling strategies towards modern complex multiphase materials subjected to various types of mechanical, thermal loadings and environmental effects. The focus is on problems where mechanics is highly coupled with other concurrent physical phenomena. Attention is also focused on the historical origins of multiscale modeling and foundations of continuum mechanics currently adopted to model non-classical continua with substructure, for which internal length scales play a crucial role.
Complex Dynamics of Discrete SEIS Models with Simple Demography
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Hui Cao
2011-01-01
Full Text Available We investigate bifurcations and dynamical behaviors of discrete SEIS models with exogenous reinfections and a variety of treatment strategies. Bifurcations identified from the models include period doubling, backward, forward-backward, and multiple backward bifurcations. Multiple attractors, such as bistability and tristability, are observed. We also estimate the ultimate boundary of the infected regardless of initial status. Our rigorously mathematical analysis together with numerical simulations show that epidemiological factors alone can generate complex dynamics, though demographic factors only support simple equilibrium dynamics. Our model analysis supports and urges to treat a fixed percentage of exposed individuals.
Modeling and Algorithmic Approaches to Constitutively-Complex, Microstructured Fluids
Energy Technology Data Exchange (ETDEWEB)
Miller, Gregory H. [Univ. of California, Davis, CA (United States); Forest, Gregory [Univ. of California, Davis, CA (United States)
2014-05-01
We present a new multiscale model for complex fluids based on three scales: microscopic, kinetic, and continuum. We choose the microscopic level as Kramers' bead-rod model for polymers, which we describe as a system of stochastic differential equations with an implicit constraint formulation. The associated Fokker-Planck equation is then derived, and adiabatic elimination removes the fast momentum coordinates. Approached in this way, the kinetic level reduces to a dispersive drift equation. The continuum level is modeled with a finite volume Godunov-projection algorithm. We demonstrate computation of viscoelastic stress divergence using this multiscale approach.
Hill, Renee J; Chopra, Pradeep; Richardi, Toni
2012-01-01
Explaining the etiology of Complex Regional Pain Syndrome (CRPS) from the psychogenic model is exceedingly unsophisticated, because neurocognitive deficits, neuroanatomical abnormalities, and distortions in cognitive mapping are features of CRPS pathology. More importantly, many people who have developed CRPS have no history of mental illness. The psychogenic model offers comfort to physicians and mental health practitioners (MHPs) who have difficulty understanding pain maintained by newly uncovered neuro inflammatory processes. With increased education about CRPS through a biopsychosocial perspective, both physicians and MHPs can better diagnose, treat, and manage CRPS symptomatology.
Hill, Renee J.; Chopra, Pradeep; Richardi, Toni
2012-01-01
Abstract Explaining the etiology of Complex Regional Pain Syndrome (CRPS) from the psychogenic model is exceedingly unsophisticated, because neurocognitive deficits, neuroanatomical abnormalities, and distortions in cognitive mapping are features of CRPS pathology. More importantly, many people who have developed CRPS have no history of mental illness. The psychogenic model offers comfort to physicians and mental health practitioners (MHPs) who have difficulty understanding pain maintained by newly uncovered neuro inflammatory processes. With increased education about CRPS through a biopsychosocial perspective, both physicians and MHPs can better diagnose, treat, and manage CRPS symptomatology. PMID:24223338
Building Better Ecological Machines: Complexity Theory and Alternative Economic Models
Directory of Open Access Journals (Sweden)
Jess Bier
2016-12-01
Full Text Available Computer models of the economy are regularly used to predict economic phenomena and set financial policy. However, the conventional macroeconomic models are currently being reimagined after they failed to foresee the current economic crisis, the outlines of which began to be understood only in 2007-2008. In this article we analyze the most prominent of this reimagining: Agent-Based models (ABMs. ABMs are an influential alternative to standard economic models, and they are one focus of complexity theory, a discipline that is a more open successor to the conventional chaos and fractal modeling of the 1990s. The modelers who create ABMs claim that their models depict markets as ecologies, and that they are more responsive than conventional models that depict markets as machines. We challenge this presentation, arguing instead that recent modeling efforts amount to the creation of models as ecological machines. Our paper aims to contribute to an understanding of the organizing metaphors of macroeconomic models, which we argue is relevant conceptually and politically, e.g., when models are used for regulatory purposes.
Modelling and simulation of gas explosions in complex geometries
Energy Technology Data Exchange (ETDEWEB)
Saeter, Olav
1998-12-31
This thesis presents a three-dimensional Computational Fluid Dynamics (CFD) code (EXSIM94) for modelling and simulation of gas explosions in complex geometries. It gives the theory and validates the following sub-models : (1) the flow resistance and turbulence generation model for densely packed regions, (2) the flow resistance and turbulence generation model for single objects, and (3) the quasi-laminar combustion model. It is found that a simple model for flow resistance and turbulence generation in densely packed beds is able to reproduce the medium and large scale MERGE explosion experiments of the Commission of European Communities (CEC) within a band of factor 2. The model for a single representation is found to predict explosion pressure in better agreement with the experiments with a modified k-{epsilon} model. This modification also gives a slightly improved grid independence for realistic gas explosion approaches. One laminar model is found unsuitable for gas explosion modelling because of strong grid dependence. Another laminar model is found to be relatively grid independent and to work well in harmony with the turbulent combustion model. The code is validated against 40 realistic gas explosion experiments. It is relatively grid independent in predicting explosion pressure in different offshore geometries. It can predict the influence of ignition point location, vent arrangements, different geometries, scaling effects and gas reactivity. The validation study concludes with statistical and uncertainty analyses of the code performance. 98 refs., 96 figs, 12 tabs.
Bridging Mechanistic and Phenomenological Models of Complex Biological Systems
Transtrum, Mark K.; Qiu, Peng
2016-01-01
The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM) as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior. PMID:27187545
Complex Modelling of Open System Design for Sustainable Architecture
Gu, Yan; Frazer, John
This paper argues a model of complex system design for sustainable architecture within a framework of entropy evolution. The spectrum of sustainable architecture consists of the efficient use of energy and material resource in life-cycle of buildings, the active involvement of the occupants in micro-climate control within buildings, and the natural environmental context. The interactions of the parameters compose a complex system of sustainable architectural design, of which the conventional linear and fragmented design technologies are insufficient to indicate holistic and ongoing environmental performance. The complexity theory of dissipative structure states a microscopic formulation of open system evolution, which provides a system design framework for the evolution of building environmental performance towards an optimization of sustainability in architecture.
Theory and model of water resources complex adaptive allocation system
Institute of Scientific and Technical Information of China (English)
ZHAOJianshi; WANGZhongjing; WENGWenbin
2003-01-01
Complex adaptive system theory is a new and important embranchment of system science,which provides a new thought to research water resources allocation system.Based on the analysis of complexity and complex adaptive mechanism of water resources allocation system,a fire-new analysis model is presented in this paper.With the description of Dynamical mechanism of system,behavior characters of agents and the evalustion method of system status,an integrity research system is built to analyse the evolvement rule of water resources allocation system.And a brief research for the impact of water resources allocation in beneficial regions of the Water Transfer from south to North China Project is conducted.
a Model Study of Complex Behavior in the Belousov - Reaction.
Lindberg, David Mark
1988-12-01
We have studied the complex oscillatory behavior in a model of the Belousov-Zhabotinskii (BZ) reaction in a continuously-fed stirred tank reactor (CSTR). The model consisted of a set of nonlinear ordinary differential equations derived from a reduced mechanism of the chemical system. These equations were integrated numerically on a computer, which yielded the concentrations of the constituent chemicals as functions of time. In addition, solutions were tracked as functions of a single parameter, the stability of the solutions was determined, and bifurcations of the solutions were located and studied. The intent of this study was to use this BZ model to explore further a region of complex oscillatory behavior found in experimental investigations, the most thorough of which revealed an alternating periodic-chaotic (P-C) sequence of states. A P-C sequence was discovered in the model which showed the same qualitative features as the experimental sequence. In order to better understand the P-C sequence, a detailed study was conducted in the vicinity of the P-C sequence, with two experimentally accessible parameters as control variables. This study mapped out the bifurcation sets, and included examination of the dynamics of the stable periodic, unstable periodic, and chaotic oscillatory motion. Observations made from the model results revealed a rough symmetry which suggests a new way of looking at the P-C sequence. Other nonlinear phenomena uncovered in the model were boundary and interior crises, several codimension-two bifurcations, and similarities in the shapes of areas of stability for periodic orbits in two-parameter space. Each earlier model study of this complex region involved only a limited one-parameter scan and had limited success in producing agreement with experiments. In contrast, for those regions of complex behavior that have been studied experimentally, the observations agree qualitatively with our model results. Several new predictions of the model
Mechanistic modeling confronts the complexity of molecular cell biology.
Phair, Robert D
2014-11-05
Mechanistic modeling has the potential to transform how cell biologists contend with the inescapable complexity of modern biology. I am a physiologist-electrical engineer-systems biologist who has been working at the level of cell biology for the past 24 years. This perspective aims 1) to convey why we build models, 2) to enumerate the major approaches to modeling and their philosophical differences, 3) to address some recurrent concerns raised by experimentalists, and then 4) to imagine a future in which teams of experimentalists and modelers build-and subject to exhaustive experimental tests-models covering the entire spectrum from molecular cell biology to human pathophysiology. There is, in my view, no technical obstacle to this future, but it will require some plasticity in the biological research mind-set.
The semiotics of control and modeling relations in complex systems.
Joslyn, C
2001-01-01
We provide a conceptual analysis of ideas and principles from the systems theory discourse which underlie Pattee's semantic or semiotic closure, which is itself foundational for a school of theoretical biology derived from systems theory and cybernetics, and is now being related to biological semiotics and explicated in the relational biological school of Rashevsky and Rosen. Atomic control systems and models are described as the canonical forms of semiotic organization, sharing measurement relations, but differing topologically in that control systems are circularly and models linearly related to their environments. Computation in control systems is introduced, motivating hierarchical decomposition, hybrid modeling and control systems, and anticipatory or model-based control. The semiotic relations in complex control systems are described in terms of relational constraints, and rules and laws are distinguished as contingent and necessary functional entailments, respectively. Finally, selection as a meta-level of constraint is introduced as the necessary condition for semantic relations in control systems and models.
Predicting the future completing models of observed complex systems
Abarbanel, Henry
2013-01-01
Predicting the Future: Completing Models of Observed Complex Systems provides a general framework for the discussion of model building and validation across a broad spectrum of disciplines. This is accomplished through the development of an exact path integral for use in transferring information from observations to a model of the observed system. Through many illustrative examples drawn from models in neuroscience, fluid dynamics, geosciences, and nonlinear electrical circuits, the concepts are exemplified in detail. Practical numerical methods for approximate evaluations of the path integral are explored, and their use in designing experiments and determining a model's consistency with observations is investigated. Using highly instructive examples, the problems of data assimilation and the means to treat them are clearly illustrated. This book will be useful for students and practitioners of physics, neuroscience, regulatory networks, meteorology and climate science, network dynamics, fluid dynamics, and o...
Computational and analytical modeling of cationic lipid-DNA complexes.
Farago, Oded; Grønbech-Jensen, Niels
2007-05-01
We present a theoretical study of the physical properties of cationic lipid-DNA (CL-DNA) complexes--a promising synthetically based nonviral carrier of DNA for gene therapy. The study is based on a coarse-grained molecular model, which is used in Monte Carlo simulations of mesoscopically large systems over timescales long enough to address experimental reality. In the present work, we focus on the statistical-mechanical behavior of lamellar complexes, which in Monte Carlo simulations self-assemble spontaneously from a disordered random initial state. We measure the DNA-interaxial spacing, d(DNA), and the local cationic area charge density, sigma(M), for a wide range of values of the parameter (c) representing the fraction of cationic lipids. For weakly charged complexes (low values of (c)), we find that d(DNA) has a linear dependence on (c)(-1), which is in excellent agreement with x-ray diffraction experimental data. We also observe, in qualitative agreement with previous Poisson-Boltzmann calculations of the system, large fluctuations in the local area charge density with a pronounced minimum of sigma(M) halfway between adjacent DNA molecules. For highly-charged complexes (large (c)), we find moderate charge density fluctuations and observe deviations from linear dependence of d(DNA) on (c)(-1). This last result, together with other findings such as the decrease in the effective stretching modulus of the complex and the increased rate at which pores are formed in the complex membranes, are indicative of the gradual loss of mechanical stability of the complex, which occurs when (c) becomes large. We suggest that this may be the origin of the recently observed enhanced transfection efficiency of lamellar CL-DNA complexes at high charge densities, because the completion of the transfection process requires the disassembly of the complex and the release of the DNA into the cytoplasm. Some of the structural properties of the system are also predicted by a continuum
Reduced Complexity Modeling (RCM): toward more use of less
Paola, Chris; Voller, Vaughan
2014-05-01
Although not exact, there is a general correspondence between reductionism and detailed, high-fidelity models, while 'synthesism' is often associated with reduced-complexity modeling. There is no question that high-fidelity reduction- based computational models are extremely useful in simulating the behaviour of complex natural systems. In skilled hands they are also a source of insight and understanding. We focus here on the case for the other side (reduced-complexity models), not because we think they are 'better' but because their value is more subtle, and their natural constituency less clear. What kinds of problems and systems lend themselves to the reduced-complexity approach? RCM is predicated on the idea that the mechanism of the system or phenomenon in question is, for whatever reason, insensitive to the full details of the underlying physics. There are multiple ways in which this can happen. B.T. Werner argued for the importance of process hierarchies in which processes at larger scales depend on only a small subset of everything going on at smaller scales. Clear scale breaks would seem like a way to test systems for this property but to our knowledge has not been used in this way. We argue that scale-independent physics, as for example exhibited by natural fractals, is another. We also note that the same basic criterion - independence of the process in question from details of the underlying physics - underpins 'unreasonably effective' laboratory experiments. There is thus a link between suitability for experimentation at reduced scale and suitability for RCM. Examples from RCM approaches to erosional landscapes, braided rivers, and deltas illustrate these ideas, and suggest that they are insufficient. There is something of a 'wild west' nature to RCM that puts some researchers off by suggesting a departure from traditional methods that have served science well for centuries. We offer two thoughts: first, that in the end the measure of a model is its
Modelling of Rare Earth Elements Complexation With Humic Acid
Pourret, O.; Davranche, M.; Gruau, G.; Dia, A.
2006-12-01
The binding of rare earth elements (REE) to humic acid (HA) was studied by combining Ultrafiltration and ICP- MS techniques. REE-HA complexation experiments were performed at various pH conditions (ranging from 2 to 10.5) using a standard batch equilibration method. Results show that the amount of REE bound to HA strongly increase with increasing pH. Moreover, a Middle REE (MREE) downward concavity is evidenced by REE distribution patterns at acidic pH. Modelling of the experimental data using Humic Ion Binding Model VI provided a set of log KMA values (i.e. the REE-HA complexation constants specific to Model VI) for the entire REE series. The log KMA pattern obtained displays a MREE downward concavity. Log KMA values range from 2.42 to 2.79. These binding constants are in good agreement with the few existing datasets quantifying the binding of REE with humic substances except a recently published study which evidence a lanthanide contraction effect (i.e. continuous increase of the constant from La to Lu). The MREE downward concavity displayed by REE-HA complexation pattern determined in this study compares well with results from REE-fulvic acid (FA) and REE-acetic acid complexation studies. This similarity in the REE complexation pattern shapes suggests that carboxylic groups are the main binding sites of REE in HA. This conclusion is further supported by a detailed review of published studies for natural, organic-rich, river- and ground-waters which show no evidence of a lanthanide contraction effect in REE pattern shape. Finally, application of Model VI using the new, experimentally determined log KMA values to World Average River Water confirms earlier suggestions that REE occur predominantly as organic complexes (> 60 %) in the pH range between 5-5.5 and 7-8.5 (i.e. in circumneutral pH waters). The only significant difference as compared to earlier model predictions made using estimated log KMA values is that the experimentally determined log KMA values
A Knowledge base model for complex forging die machining
Mawussi, Kwamiwi; 10.1016/j.cie.2011.02.016
2011-01-01
Recent evolutions on forging process induce more complex shape on forging die. These evolutions, combined with High Speed Machining (HSM) process of forging die lead to important increase in time for machining preparation. In this context, an original approach for generating machining process based on machining knowledge is proposed in this paper. The core of this approach is to decompose a CAD model of complex forging die in geometric features. Technological data and topological relations are aggregated to a geometric feature in order to create machining features. Technological data, such as material, surface roughness and form tolerance are defined during forging process and dies design. These data are used to choose cutting tools and machining strategies. Topological relations define relative positions between the surfaces of the die CAD model. After machining features identification cutting tools and machining strategies currently used in HSM of forging die, are associated to them in order to generate mac...
Information Society: Modeling A Complex System With Scarce Data
Olivera, Noemi L; Ausloos, Marcel
2012-01-01
Considering electronic implications in the Information Society (IS) as a complex system, complexity science tools are used to describe the processes that are seen to be taking place. The sometimes troublesome relationship between the information and communication new technologies and e-society gives rise to different problems, some of them being unexpected. Probably, the Digital Divide (DD) and the Internet Governance (IG) are among the most conflictive ones of internationally based e-Affairs. Admitting that solutions should be found for these problems, certain international policies are required. In this context, data gathering and subsequent analysis, as well as the construction of adequate physical models are extremely important in order to imagine different future scenarios and suggest some subsequent control. In the main text, mathematical modelization helps for visualizing how policies could e.g. influence the individual and collective behavior in an empirical social agent system. In order to show how t...
Complexity and agent-based modelling in urban research
DEFF Research Database (Denmark)
Fertner, Christian
Urbanisation processes are results of a broad variety of actors or actor groups and their behaviour and decisions based on different experiences, knowledge, resources, values etc. The decisions done are often on a micro/individual level but resulting in macro/collective behaviour. In urban research...... influence on the bigger system. Traditional scientific methods or theories often tried to simplify, not accounting complex relations of actors and decision-making. The introduction of computers in simulation made new approaches in modelling, as for example agent-based modelling (ABM), possible, dealing...... of complexity for a majority of science, there exists a huge number of scientific articles, books, tutorials etc. to these topics which doesn’t make it easy for a novice in the field to find the right literature. The literature used gives an optimistic outlook for the future of this methodology, although ABM...
Engineering complex topological memories from simple Abelian models
Wootton, James R.; Lahtinen, Ville; Doucot, Benoit; Pachos, Jiannis K.
2011-09-01
In three spatial dimensions, particles are limited to either bosonic or fermionic statistics. Two-dimensional systems, on the other hand, can support anyonic quasiparticles exhibiting richer statistical behaviors. An exciting proposal for quantum computation is to employ anyonic statistics to manipulate information. Since such statistical evolutions depend only on topological characteristics, the resulting computation is intrinsically resilient to errors. The so-called non-Abelian anyons are most promising for quantum computation, but their physical realization may prove to be complex. Abelian anyons, however, are easier to understand theoretically and realize experimentally. Here we show that complex topological memories inspired by non-Abelian anyons can be engineered in Abelian models. We explicitly demonstrate the control procedures for the encoding and manipulation of quantum information in specific lattice models that can be implemented in the laboratory. This bridges the gap between requirements for anyonic quantum computation and the potential of state-of-the-art technology.
Modeling and Analysis of Complex Equipment Maintenance Dynamics
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
An equipment maintenance system is naturally a complex dynamical system. The effective maintenance management must be based on the knowledge of the system's intrinsic dynamics. And the structure of the maintenance system determines its behavior. This paper analyzes the basic structures and elements of a maintenance system for complex multi-components equipment. The maintenance system is considered as a dynamic system whose behavior is influenced by its structure's feedback and interaction, and the system's available resources. Building the dynamical model with Simulink, we show some results about the maintenance system's nonlinear dynamics, which are never given by stochastic process methods. The model can be used for understanding and determining maintenance system behavior, towards which operational adjustments of maintenance infrastructure, precise prediction of maintenance requirements and timely supply of maintenance resources can be made in a more informed way.
A corticothalamic circuit model for sound identification in complex scenes.
Directory of Open Access Journals (Sweden)
Gonzalo H Otazu
Full Text Available The identification of the sound sources present in the environment is essential for the survival of many animals. However, these sounds are not presented in isolation, as natural scenes consist of a superposition of sounds originating from multiple sources. The identification of a source under these circumstances is a complex computational problem that is readily solved by most animals. We present a model of the thalamocortical circuit that performs level-invariant recognition of auditory objects in complex auditory scenes. The circuit identifies the objects present from a large dictionary of possible elements and operates reliably for real sound signals with multiple concurrently active sources. The key model assumption is that the activities of some cortical neurons encode the difference between the observed signal and an internal estimate. Reanalysis of awake auditory cortex recordings revealed neurons with patterns of activity corresponding to such an error signal.
A computational framework for modeling targets as complex adaptive systems
Santos, Eugene; Santos, Eunice E.; Korah, John; Murugappan, Vairavan; Subramanian, Suresh
2017-05-01
Modeling large military targets is a challenge as they can be complex systems encompassing myriad combinations of human, technological, and social elements that interact, leading to complex behaviors. Moreover, such targets have multiple components and structures, extending across multiple spatial and temporal scales, and are in a state of change, either in response to events in the environment or changes within the system. Complex adaptive system (CAS) theory can help in capturing the dynamism, interactions, and more importantly various emergent behaviors, displayed by the targets. However, a key stumbling block is incorporating information from various intelligence, surveillance and reconnaissance (ISR) sources, while dealing with the inherent uncertainty, incompleteness and time criticality of real world information. To overcome these challenges, we present a probabilistic reasoning network based framework called complex adaptive Bayesian Knowledge Base (caBKB). caBKB is a rigorous, overarching and axiomatic framework that models two key processes, namely information aggregation and information composition. While information aggregation deals with the union, merger and concatenation of information and takes into account issues such as source reliability and information inconsistencies, information composition focuses on combining information components where such components may have well defined operations. Since caBKBs can explicitly model the relationships between information pieces at various scales, it provides unique capabilities such as the ability to de-aggregate and de-compose information for detailed analysis. Using a scenario from the Network Centric Operations (NCO) domain, we will describe how our framework can be used for modeling targets with a focus on methodologies for quantifying NCO performance metrics.
Fundamentals of complex networks models, structures and dynamics
Chen, Guanrong; Li, Xiang
2014-01-01
Complex networks such as the Internet, WWW, transportationnetworks, power grids, biological neural networks, and scientificcooperation networks of all kinds provide challenges for futuretechnological development. In particular, advanced societies havebecome dependent on large infrastructural networks to an extentbeyond our capability to plan (modeling) and to operate (control).The recent spate of collapses in power grids and ongoing virusattacks on the Internet illustrate the need for knowledge aboutmodeling, analysis of behaviors, optimized planning and performancecontrol in such networks. F
COMPUTER DATA ANALYSIS AND MODELING: COMPLEX STOCHASTIC DATA AND SYSTEMS
2010-01-01
This collection of papers includes proceedings of the Ninth International Conference “Computer Data Analysis and Modeling: Complex Stochastic Data and Systems” organized by the Belarusian State University and held in September 2010 in Minsk. The papers are devoted to the topical problems: robust and nonparametric data analysis; statistical analysis of time series and forecasting; multivariate data analysis; design of experiments; statistical signal and image processing...
Modeling Complex Nesting Structures in International Business Research
DEFF Research Database (Denmark)
Nielsen, Bo Bernhard; Nielsen, Sabina
2013-01-01
International business (IB) phenomena often involve complex relationships between factors at different levels. Multinational corporations (MNCs) are influenced both by different country and industry environments which may have independent as well as interactive effects on MNC performance. While...... of analysis may yield novel insights to IB research. The results have implications for IB research in its pursuit of an integrative approach to understanding the multilevel determinants of firm internationalization and performance. The paper further illustrates the importance of adequately modeling crossed...
EVALUATING EMERGENCY RESPONSE MODELS OF RADIOLOGICAL DISPERSION IN COMPLEX TERRAIN
Dyer, L.L.; Pascoe, J.H.
2008-01-01
Abstract: Operational airborne releases of trace quantities of the radioactive noble gas Ar-41 from the HIFAR Nuclear Research Reactor located in Sydney, Australia are valuable for evaluating emergency response models incorporating radiological dispersion. The Australian Nuclear Science and Technology Organisation (ANSTO), where the reactor is located, has a network of meteorological stations and GR-150 environmental gamma dose detectors placed in complex terrain within a 5km radius ...
Modeling Reduced Human Performance as a Complex Adaptive System
2003-09-01
fittingly, the latest research paper describes these types of components as LEGOs (listener event graph objects). “The name is also a metaphor for how...Buss, A. H. and P. J. Sanchez (2002). Building Complex Models With LEGOs (Listener Event Graph Objects). Winter Simulation Conference. Buss, D. (1999...Kaarlela, C. (1997). New Gene Therapy Technique Could Eliminate Insulin Injections for many Diabetics, Jeffrey Norris and Jennifer O’Brien (415) 476-481
MULTILEVEL RECURRENT MODEL FOR HIERARCHICAL CONTROL OF COMPLEX REGIONAL SECURITY
Directory of Open Access Journals (Sweden)
Andrey V. Masloboev
2014-11-01
Full Text Available Subject of research. The research goal and scope are development of methods and software for mathematical and computer modeling of the regional security information support systems as multilevel hierarchical systems. Such systems are characterized by loosely formalization, multiple-aspect of descendent system processes and their interconnectivity, high level dynamics and uncertainty. The research methodology is based on functional-target approach and principles of multilevel hierarchical system theory. The work considers analysis and structural-algorithmic synthesis problem-solving of the multilevel computer-aided systems intended for management and decision-making information support in the field of regional security. Main results. A hierarchical control multilevel model of regional socio-economic system complex security has been developed. The model is based on functional-target approach and provides both formal statement and solving, and practical implementation of the automated information system structure and control algorithms synthesis problems of regional security management optimal in terms of specified criteria. An approach for intralevel and interlevel coordination problem-solving in the multilevel hierarchical systems has been proposed on the basis of model application. The coordination is provided at the expense of interconnection requirements satisfaction between the functioning quality indexes (objective functions, which are optimized by the different elements of multilevel systems. That gives the possibility for sufficient coherence reaching of the local decisions, being made on the different control levels, under decentralized decision-making and external environment high dynamics. Recurrent model application provides security control mathematical models formation of regional socioeconomic systems, functioning under uncertainty. Practical relevance. The model implementation makes it possible to automate synthesis realization of
CRBA: A Capacity Restricted Model Evolved from BA Model for Complex Network
Directory of Open Access Journals (Sweden)
Xiao-song Zhang
2011-08-01
Full Text Available It is critical to obtain a fine description of the topology of a complex network when modeling its behavior, as the network’s functionality heavily relies on its structure. Capacity Restricted model evolved from BA model (CRBA for complex network proposed in this paper is the first attempt to date to take the node’s capacity distribution into modeling. CRBA is a universal and academic model, we learn it qualitatively and acquire several meaningful outcomes. Then we deduce a practical model from CRBA (CRBAC which has a constant node’s capacity distribution. We make a quantitative comparison of the properties of CRBAC with those of BA model, including the degree distribution, clustering coefficient and the average path length. Since majority of networks in practical are capacity–restricted, our model provides a better description of real-life complex networks.
Complexity and agent-based modelling in urban research
DEFF Research Database (Denmark)
Fertner, Christian
Urbanisation processes are results of a broad variety of actors or actor groups and their behaviour and decisions based on different experiences, knowledge, resources, values etc. The decisions done are often on a micro/individual level but resulting in macro/collective behaviour. In urban research...... influence on the bigger system. Traditional scientific methods or theories often tried to simplify, not accounting complex relations of actors and decision-making. The introduction of computers in simulation made new approaches in modelling, as for example agent-based modelling (ABM), possible, dealing...
Time-dependent models of dense PDRs with complex molecules
Morata, O.; Herbst, E.
2008-01-01
We present a study of the chemistry of a dense photon-dominated region (PDR) using a time-dependent chemical model. Our major interest is to study the spatial distribution of complex molecules such as hydrocarbons and cyanopolyynes in the cool dense material bordering regions where star formation has taken place. Our standard model uses a homogeneous cloud of density 2x10e4 cm-3 and temperature T=40 K, which is irradiated by a far-ultraviolet radiation field of intermediate intensity, given b...
Stochastic modeling of unresolved scales in complex systems
Institute of Scientific and Technical Information of China (English)
Jinqiao DUAN
2009-01-01
Model uncertainties or simulation uncertainties occur in math-ematical modeling of multiscale complex systems, since some mechanisms or scales are not represented (i.e., 'unresolved') due to a lack in our understand-ing of these mechanisms or limitations in computational power. The impact of these unresolved scales on the resolved scales needs to be parameterized or taken into account. A stochastic scheme is devised to take the effects of unresolved scales into account, in the context of solving nonlinear partial differential equations. An example is presented to demonstrate this strategy.
Computational molecular basis for improved silica surface complexation models
Energy Technology Data Exchange (ETDEWEB)
Sahai, Nita; Rosso, Kevin M.
2006-06-06
The acidity and reactivity of surface sites on amorphous and crystalline polymorphs of silica and other oxides control their thermodynamic stability and kinetic reactivity towards reactants in surface-controlled processes of environmental, industrial, biomedical and technological relevance. Recent advances in computational methodologies such as CPMD and increasing computer power combined with spectroscopic measurements are now making it possible to link, with an impressive degree of accuracy, the molecular-level description of these processes to phenomenological, surface complexation models The future challenge now lies in linking mesoscale properties at the nanometer scale to phenomenological models that will afford a more intuitive understanding of the systems under consideration.
Automorphisms and Generalized Involution Models of Finite Complex Reflection Groups
Marberg, Eric
2010-01-01
We prove that a finite complex reflection group has a generalized involution model, as defined by Bump and Ginzburg, if and only if each of its irreducible factors is either $G(r,p,n)$ with $\\gcd(p,n)=1$; $G(r,p,2)$ with $r/p$ odd; or $G_{23}$, the Coxeter group of type $H_3$. We additionally provide explicit formulas for all automorphisms of $G(r,p,n)$, and construct new Gelfand models for the groups $G(r,p,n)$ with $\\gcd(p,n)=1$.
Transmembrane potentials of canine AV junctional tissues.
Tse, W W
1986-06-01
The atrioventricular (AV) junction comprises the AV node, His bundle (HB), and specialized tissues proximal to the node called paranodal fibers (PNF). In the present study, an in vitro, dissection-exposed canine right atrial (RA), transitional fiber (TF), AV junctional preparation was used. The TF and PNF formed a pathway running along the base of the septal cusp of the tricuspid valve (SCTV). In the first experiment, impulses elicited at the RA were monitored to propagate sequentially through the TF, PNF, AV node, and then the HB. This functional evidence supports the concept that a conduction pathway connecting the RA and the AV node exists along the base of the SCTV. This internodal pathway is referred to as the septal cusp pathway. In another experiment, transmembrane potentials and Vmax were determined on each of the AV junctional tissues. Results showed that PNF had the lowest Vmax (2.5 V/sec), followed by AV node (7.0 V/sec) and HB (33 V/sec). This finding showed that PNF, and not the AV node, has the lowest Vmax, suggesting that the PNF has the lowest conductivity among the AV junctional tissues, and this study advances our understanding on the mechanism of AV conduction delay in dog hearts.
Quantitative modeling of degree-degree correlation in complex networks
Niño, Alfonso
2013-01-01
This paper presents an approach to the modeling of degree-degree correlation in complex networks. Thus, a simple function, \\Delta(k', k), describing specific degree-to- degree correlations is considered. The function is well suited to graphically depict assortative and disassortative variations within networks. To quantify degree correlation variations, the joint probability distribution between nodes with arbitrary degrees, P(k', k), is used. Introduction of the end-degree probability function as a basic variable allows using group theory to derive mathematical models for P(k', k). In this form, an expression, representing a family of seven models, is constructed with the needed normalization conditions. Applied to \\Delta(k', k), this expression predicts a nonuniform distribution of degree correlation in networks, organized in two assortative and two disassortative zones. This structure is actually observed in a set of four modeled, technological, social, and biological networks. A regression study performed...
Semiotic aspects of control and modeling relations in complex systems
Energy Technology Data Exchange (ETDEWEB)
Joslyn, C.
1996-08-01
A conceptual analysis of the semiotic nature of control is provided with the goal of elucidating its nature in complex systems. Control is identified as a canonical form of semiotic relation of a system to its environment. As a form of constraint between a system and its environment, its necessary and sufficient conditions are established, and the stabilities resulting from control are distinguished from other forms of stability. These result from the presence of semantic coding relations, and thus the class of control systems is hypothesized to be equivalent to that of semiotic systems. Control systems are contrasted with models, which, while they have the same measurement functions as control systems, do not necessarily require semantic relations because of the lack of the requirement of an interpreter. A hybrid construction of models in control systems is detailed. Towards the goal of considering the nature of control in complex systems, the possible relations among collections of control systems are considered. Powers arguments on conflict among control systems and the possible nature of control in social systems are reviewed, and reconsidered based on our observations about hierarchical control. Finally, we discuss the necessary semantic functions which must be present in complex systems for control in this sense to be present at all.
DEFF Research Database (Denmark)
VanWinkle, W Barry; Snuggs, Mark B; De Hostos, Eugenio L
2002-01-01
Syndecan-4 (syn-4), a transmembrane heparan sulfate-containing proteoglycan, is unique among the four members of the syndecan family in its specific cellular localization to complex cytoskeletal adhesion sites, i.e., focal adhesions. During early phenotypic redifferentiation of neonatal cardiomyo...
van Gestel, Aukje; Severens, Johan L.; Webers, Carroll A. B.; Beckers, Henny J. M.; Jansonius, Nomdo M.; Schouten, Jan S. A. G.
2010-01-01
Objective: Discrete event simulation (DES) modeling has several advantages over simpler modeling techniques in health economics, such as increased flexibility and the ability to model complex systems. Nevertheless, these benefits may come at the cost of reduced transparency, which may compromise the
A Tractable Complex Network Model based on the Stochastic Mean-field Model of Distance
Aldous, David J.
2003-01-01
Much recent research activity has been devoted to empirical study and theoretical models of complex networks (random graphs) with three qualitative features: power-law degree distribution, local clustering of edges, and small diameter. We point out a new (in this context) platform for such models -- the stochastic mean-field model of distance -- and within this platform study a simple two-parameter proportional attachment model. The model is mathematicallly natural, permits a wide variety of ...
Sensitivity Analysis in a Complex Marine Ecological Model
Directory of Open Access Journals (Sweden)
Marcos D. Mateus
2015-05-01
Full Text Available Sensitivity analysis (SA has long been recognized as part of best practices to assess if any particular model can be suitable to inform decisions, despite its uncertainties. SA is a commonly used approach for identifying important parameters that dominate model behavior. As such, SA address two elementary questions in the modeling exercise, namely, how sensitive is the model to changes in individual parameter values, and which parameters or associated processes have more influence on the results. In this paper we report on a local SA performed on a complex marine biogeochemical model that simulates oxygen, organic matter and nutrient cycles (N, P and Si in the water column, and well as the dynamics of biological groups such as producers, consumers and decomposers. SA was performed using a “one at a time” parameter perturbation method, and a color-code matrix was developed for result visualization. The outcome of this study was the identification of key parameters influencing model performance, a particularly helpful insight for the subsequent calibration exercise. Also, the color-code matrix methodology proved to be effective for a clear identification of the parameters with most impact on selected variables of the model.
An efficient algorithm for corona simulation with complex chemical models
Villa, Andrea; Barbieri, Luca; Gondola, Marco; Leon-Garzon, Andres R.; Malgesini, Roberto
2017-05-01
The simulation of cold plasma discharges is a leading field of applied sciences with many applications ranging from pollutant control to surface treatment. Many of these applications call for the development of novel numerical techniques to implement fully three-dimensional corona solvers that can utilize complex and physically detailed chemical databases. This is a challenging task since it multiplies the difficulties inherent to a three-dimensional approach by the complexity of databases comprising tens of chemical species and hundreds of reactions. In this paper a novel approach, capable of reducing significantly the computational burden, is developed. The proposed method is based on a proper time stepping algorithm capable of decomposing the original problem into simpler ones: each of them has then been tackled with either finite element, finite volume or ordinary differential equations solvers. This last solver deals with the chemical model and its efficient implementation is one of the main contributions of this work.
Fisher's zeros, complex RG flows and confinement in LGT models
Denbleyker, Alan; Du, Daping; Liu, Yuzhi; Meurice, Yannick; Zou, Haiyuan
2011-01-01
The zeros of the partition function in the complex beta plane (Fisher's zeros) play an important role in our understanding of phase transitions and RG flows. Recently, we argued that they act as gates or separatrices for complex RG flows. Using histogram reweighting to construct the density of states, we calculate the Fisher's zeros for pure gauge SU(2) and U(1) on L^4 lattices. For SU(2), these zeros appear to move almost horizontally when the volume increases. They stay away from the real axis which indicates a confining theory at zero temperature. We discuss the effect of an adjoint term on these results. In contrast, using recent multicanonical simulations for the U(1) model for L up to 8 we find that the zeros pinch the real axis near beta =1.0113. Preliminary results concerning U(1) at larger volumes, SU(3) with 3 light flavors and plans to delimit the boundary of the conformal window are briefly discussed.
Pinning control of a generalized complex dynamical network model
Institute of Scientific and Technical Information of China (English)
Huizhong YANG; Li SHENG
2009-01-01
This paper investigates the local and global synchronization of a generalized complex dynamical network model with constant and delayed coupling.Without assuming symmetry of the couplings,we proved that a single controller can pin the generalized complex network to a homogenous solution.Some previous synchronization results are generalized.In this paper,we first discuss how to pin an array of delayed neural networks to the synchronous solution by adding only one controller.Next,by using the Lyapunov functional method,some sufficient conditions are derived for the local and global synchronization of the coupled systems.The obtained results are expressed in terms of LMIs,which can be efficiently checked by the Matlab LMI toolbox.Finally,an example is given to illustrate the theoretical results.
Bloch-Redfield equations for modeling light-harvesting complexes.
Jeske, Jan; Ing, David J; Plenio, Martin B; Huelga, Susana F; Cole, Jared H
2015-02-14
We challenge the misconception that Bloch-Redfield equations are a less powerful tool than phenomenological Lindblad equations for modeling exciton transport in photosynthetic complexes. This view predominantly originates from an indiscriminate use of the secular approximation. We provide a detailed description of how to model both coherent oscillations and several types of noise, giving explicit examples. All issues with non-positivity are overcome by a consistent straightforward physical noise model. Herein also lies the strength of the Bloch-Redfield approach because it facilitates the analysis of noise-effects by linking them back to physical parameters of the noise environment. This includes temporal and spatial correlations and the strength and type of interaction between the noise and the system of interest. Finally, we analyze a prototypical dimer system as well as a 7-site Fenna-Matthews-Olson complex in regards to spatial correlation length of the noise, noise strength, temperature, and their connection to the transfer time and transfer probability.
IDMS: inert dark matter model with a complex singlet
Bonilla, Cesar; Sokolowska, Dorota; Darvishi, Neda; Diaz-Cruz, J. Lorenzo; Krawczyk, Maria
2016-06-01
We study an extension of the inert doublet model (IDM) that includes an extra complex singlet of the scalars fields, which we call the IDMS. In this model there are three Higgs particles, among them a SM-like Higgs particle, and the lightest neutral scalar, from the inert sector, remains a viable dark matter (DM) candidate. We assume a non-zero complex vacuum expectation value for the singlet, so that the visible sector can introduce extra sources of CP violation. We construct the scalar potential of IDMS, assuming an exact Z 2 symmetry, with the new singlet being Z 2-even, as well as a softly broken U(1) symmetry, which allows a reduced number of free parameters in the potential. In this paper we explore the foundations of the model, in particular the masses and interactions of scalar particles for a few benchmark scenarios. Constraints from collider physics, in particular from the Higgs signal observed at the Large Hadron Collider with {M}h≈ 125 {{GeV}}, as well as constraints from the DM experiments, such as relic density measurements and direct detection limits, are included in the analysis. We observe significant differences with respect to the IDM in relic density values from additional annihilation channels, interference and resonance effects due to the extended Higgs sector.
A computational model for cancer growth by using complex networks
Galvão, Viviane; Miranda, José G. V.
2008-09-01
In this work we propose a computational model to investigate the proliferation of cancerous cell by using complex networks. In our model the network represents the structure of available space in the cancer propagation. The computational scheme considers a cancerous cell randomly included in the complex network. When the system evolves the cells can assume three states: proliferative, non-proliferative, and necrotic. Our results were compared with experimental data obtained from three human lung carcinoma cell lines. The computational simulations show that the cancerous cells have a Gompertzian growth. Also, our model simulates the formation of necrosis, increase of density, and resources diffusion to regions of lower nutrient concentration. We obtain that the cancer growth is very similar in random and small-world networks. On the other hand, the topological structure of the small-world network is more affected. The scale-free network has the largest rates of cancer growth due to hub formation. Finally, our results indicate that for different average degrees the rate of cancer growth is related to the available space in the network.
A Review of Kinetic Modeling Methodologies for Complex Processes
Directory of Open Access Journals (Sweden)
de Oliveira Luís P.
2016-05-01
Full Text Available In this paper, kinetic modeling techniques for complex chemical processes are reviewed. After a brief historical overview of chemical kinetics, an overview is given of the theoretical background of kinetic modeling of elementary steps and of multistep reactions. Classic lumping techniques are introduced and analyzed. Two examples of lumped kinetic models (atmospheric gasoil hydrotreating and residue hydroprocessing developed at IFP Energies nouvelles (IFPEN are presented. The largest part of this review describes advanced kinetic modeling strategies, in which the molecular detail is retained, i.e. the reactions are represented between molecules or even subdivided into elementary steps. To be able to retain this molecular level throughout the kinetic model and the reactor simulations, several hurdles have to be cleared first: (i the feedstock needs to be described in terms of molecules, (ii large reaction networks need to be automatically generated, and (iii a large number of rate equations with their rate parameters need to be derived. For these three obstacles, molecular reconstruction techniques, deterministic or stochastic network generation programs, and single-event micro-kinetics and/or linear free energy relationships have been applied at IFPEN, as illustrated by several examples of kinetic models for industrial refining processes.
Modeling the propagation of mobile phone virus under complex network.
Yang, Wei; Wei, Xi-liang; Guo, Hao; An, Gang; Guo, Lei; Yao, Yu
2014-01-01
Mobile phone virus is a rogue program written to propagate from one phone to another, which can take control of a mobile device by exploiting its vulnerabilities. In this paper the propagation model of mobile phone virus is tackled to understand how particular factors can affect its propagation and design effective containment strategies to suppress mobile phone virus. Two different propagation models of mobile phone viruses under the complex network are proposed in this paper. One is intended to describe the propagation of user-tricking virus, and the other is to describe the propagation of the vulnerability-exploiting virus. Based on the traditional epidemic models, the characteristics of mobile phone viruses and the network topology structure are incorporated into our models. A detailed analysis is conducted to analyze the propagation models. Through analysis, the stable infection-free equilibrium point and the stability condition are derived. Finally, considering the network topology, the numerical and simulation experiments are carried out. Results indicate that both models are correct and suitable for describing the spread of two different mobile phone viruses, respectively.
Surface complexation model of uranyl sorption on Georgia kaolinite
Payne, T.E.; Davis, J.A.; Lumpkin, G.R.; Chisari, R.; Waite, T.D.
2004-01-01
The adsorption of uranyl on standard Georgia kaolinites (KGa-1 and KGa-1B) was studied as a function of pH (3-10), total U (1 and 10 ??mol/l), and mass loading of clay (4 and 40 g/l). The uptake of uranyl in air-equilibrated systems increased with pH and reached a maximum in the near-neutral pH range. At higher pH values, the sorption decreased due to the presence of aqueous uranyl carbonate complexes. One kaolinite sample was examined after the uranyl uptake experiments by transmission electron microscopy (TEM), using energy dispersive X-ray spectroscopy (EDS) to determine the U content. It was found that uranium was preferentially adsorbed by Ti-rich impurity phases (predominantly anatase), which are present in the kaolinite samples. Uranyl sorption on the Georgia kaolinites was simulated with U sorption reactions on both titanol and aluminol sites, using a simple non-electrostatic surface complexation model (SCM). The relative amounts of U-binding >TiOH and >AlOH sites were estimated from the TEM/EDS results. A ternary uranyl carbonate complex on the titanol site improved the fit to the experimental data in the higher pH range. The final model contained only three optimised log K values, and was able to simulate adsorption data across a wide range of experimental conditions. The >TiOH (anatase) sites appear to play an important role in retaining U at low uranyl concentrations. As kaolinite often contains trace TiO2, its presence may need to be taken into account when modelling the results of sorption experiments with radionuclides or trace metals on kaolinite. ?? 2004 Elsevier B.V. All rights reserved.
TSSOM：Transmembrane Segments Prediction by Self—Organizing Map
Institute of Scientific and Technical Information of China (English)
LIUQi; ZHUYisheng; WANGBaohua; LIYixue
2003-01-01
A novel method ealled TSSOM(Transmembrane segments prediction by self-organizing map)is presented in the paper.The main idea of the method lies in the application of self-organizing feature map together with special visualization techniques to classify the multivariate "time" series of transmembrane proteins into flve classes.Through the analysis of resulting trajectories on the map,frequent patterns of transmembrane segments are detected and even some kind of "new"knowledge about membrane insertion mechanism is acquired.The discovered patterns and the knowledge are then used to predict transmembrane segments for auery sequence.The prediction results not only show that the method is powerful,but also prove that the patterns and the knowledge about the interaction bwtween the patterns are effective and acceptable.
The role of lipophilicity in transmembrane anion transport
Saggiomo, Vittorio; Otto, Sijbren; Marques, Igor; Felix, Vitor; Torroba, Tomas; Quesada, Roberto
2012-01-01
The transmembrane anion transport activity of a series of synthetic molecules inspired by the structure of tambjamine alkaloids can be tuned by varying the lipophilicity of the receptor, with carriers within a certain log P range performing best.
Lipid bilayer microarray for parallel recording of transmembrane ion currents.
Le Pioufle, Bruno; Suzuki, Hiroaki; Tabata, Kazuhito V; Noji, Hiroyuki; Takeuchi, Shoji
2008-01-01
This paper describes a multiwell biochip for simultaneous parallel recording of ion current through transmembrane pores reconstituted in planar lipid bilayer arrays. Use of a thin poly(p-xylylene) (parylene) film having micrometer-sized apertures (phi=15-50 microm, t=20 microm) led to formation of highly stable bilayer lipid membranes (BLMs) for incorporation of transmembrane pores; thus, a large number of BLMs could be arrayed without any skillful technique. We optically confirmed the simultaneous formation of BLMs in a 5x5 matrix, and in our durability test, the BLM lasted more than 15 h. Simultaneous parallel recording of alamethicin and gramicidin transmembrane pores in multiple contiguous recording sites demonstrated the feasibility of high-throughput screening of transmembrane ion currents in artificial lipid bilayers.
The Lantibiotic Nisin Induces Transmembrane Movement of a Fluorescent Phospholipid
Moll, Gert N.; Konings, Wil N.; Driessen, Arnold J.M.
1998-01-01
Nisin is a pore-forming antimicrobial peptide. The capacity of nisin to induce transmembrane movement of a fluorescent phospholipid in lipid vesicles was investigated. Unilamellar phospholipid vesicles that contained a fluorescent phospholipid
Trabanino, Rene J; Vaidehi, Nagarajan; Hall, Spencer E; Goddard, William A; Floriano, Wely
2013-02-05
The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling method, such as hydrophobicity analysis, to provide a fast and accurate procedure for predicting transmembrane regions. Methods and apparatus of the invention are useful to screen protein or polynucleotide databases for encoded proteins with transmembrane regions, such as GPCRs.
Sparse Estimation Using Bayesian Hierarchical Prior Modeling for Real and Complex Linear Models
DEFF Research Database (Denmark)
Pedersen, Niels Lovmand; Manchón, Carles Navarro; Badiu, Mihai Alin;
2015-01-01
In sparse Bayesian learning (SBL), Gaussian scale mixtures (GSMs) have been used to model sparsity-inducing priors that realize a class of concave penalty functions for the regression task in real-valued signal models. Motivated by the relative scarcity of formal tools for SBL in complex-valued m......In sparse Bayesian learning (SBL), Gaussian scale mixtures (GSMs) have been used to model sparsity-inducing priors that realize a class of concave penalty functions for the regression task in real-valued signal models. Motivated by the relative scarcity of formal tools for SBL in complex...
Complex saddles in the Gross-Witten-Wadia matrix model
Álvarez, Gabriel; Medina, Elena
2016-01-01
We give an exhaustive characterization of the complex saddle point configurations of the Gross-Witten-Wadia matrix model in the large-N limit. In particular, we characterize the cases in which the saddles accumulate in one, two, or three arcs, in terms of the values of the coupling constant and of the fraction of the total unit density that is supported in one of the arcs, and derive an explicit condition for gap closing associated to nonvacuum saddles. By applying the idea of large-N instanton we also give direct analytic derivations of the weak-coupling and strong-coupling instanton actions.
Complex Data Modeling and Computationally Intensive Statistical Methods
Mantovan, Pietro
2010-01-01
The last years have seen the advent and development of many devices able to record and store an always increasing amount of complex and high dimensional data; 3D images generated by medical scanners or satellite remote sensing, DNA microarrays, real time financial data, system control datasets. The analysis of this data poses new challenging problems and requires the development of novel statistical models and computational methods, fueling many fascinating and fast growing research areas of modern statistics. The book offers a wide variety of statistical methods and is addressed to statistici
Complex Dynamics of an Adnascent-Type Game Model
Directory of Open Access Journals (Sweden)
Baogui Xin
2008-01-01
Full Text Available The paper presents a nonlinear discrete game model for two oligopolistic firms whose products are adnascent. (In biology, the term adnascent has only one sense, “growing to or on something else,” e.g., “moss is an adnascent plant.” See Webster's Revised Unabridged Dictionary published in 1913 by C. & G. Merriam Co., edited by Noah Porter. The bifurcation of its Nash equilibrium is analyzed with Schwarzian derivative and normal form theory. Its complex dynamics is demonstrated by means of the largest Lyapunov exponents, fractal dimensions, bifurcation diagrams, and phase portraits. At last, bifurcation and chaos anticontrol of this system are studied.
Does model performance improve with complexity? A case study with three hydrological models
Orth, Rene; Staudinger, Maria; Seneviratne, Sonia I.; Seibert, Jan; Zappa, Massimiliano
2015-04-01
In recent decades considerable progress has been made in climate model development. Following the massive increase in computational power, models became more sophisticated. At the same time also simple conceptual models have advanced. In this study we validate and compare three hydrological models of different complexity to investigate whether their performance varies accordingly. For this purpose we use runoff and also soil moisture measurements, which allow a truly independent validation, from several sites across Switzerland. The models are calibrated in similar ways with the same runoff data. Our results show that the more complex models HBV and PREVAH outperform the simple water balance model (SWBM) in case of runoff but not for soil moisture. Furthermore the most sophisticated PREVAH model shows an added value compared to the HBV model only in case of soil moisture. Focusing on extreme events we find generally improved performance of the SWBM during drought conditions and degraded agreement with observations during wet extremes. For the more complex models we find the opposite behavior, probably because they were primarily developed for prediction of runoff extremes. As expected given their complexity, HBV and PREVAH have more problems with over-fitting. All models show a tendency towards better performance in lower altitudes as opposed to (pre-) alpine sites. The results vary considerably across the investigated sites. In contrast, the different metrics we consider to estimate the agreement between models and observations lead to similar conclusions, indicating that the performance of the considered models is similar at different time scales as well as for anomalies and long-term means. We conclude that added complexity does not necessarily lead to improved performance of hydrological models, and that performance can vary greatly depending on the considered hydrological variable (e.g. runoff vs. soil moisture) or hydrological conditions (floods vs. droughts).
Virgilio, Kelley M; Martin, Kyle S; Peirce, Shayn M; Blemker, Silvia S
2015-04-06
Computational models have been increasingly used to study the tissue-level constitutive properties of muscle microstructure; however, these models were not created to study or incorporate the influence of disease-associated modifications in muscle. The purpose of this paper was to develop a novel multiscale muscle modelling framework to elucidate the relationship between microstructural disease adaptations and modifications in both mechanical properties of muscle and strain in the cell membrane. We used an agent-based model to randomly generate new muscle fibre geometries and mapped them into a finite-element model representing a cross section of a muscle fascicle. The framework enabled us to explore variability in the shape and arrangement of fibres, as well as to incorporate disease-related changes. We applied this method to reveal the trade-offs between mechanical properties and damage susceptibility in Duchenne muscular dystrophy (DMD). DMD is a fatal genetic disease caused by a lack of the transmembrane protein dystrophin, leading to muscle wasting and death due to cardiac or pulmonary complications. The most prevalent microstructural variations in DMD include: lack of transmembrane proteins, fibrosis, fatty infiltration and variation in fibre cross-sectional area. A parameter analysis of these variations and case study of DMD revealed that the nature of fibrosis and density of transmembrane proteins strongly affected the stiffness of the muscle and susceptibility to membrane damage.
Socio-Environmental Resilience and Complex Urban Systems Modeling
Deal, Brian; Petri, Aaron; Pan, Haozhi; Goldenberg, Romain; Kalantari, Zahra; Cvetkovic, Vladimir
2017-04-01
The increasing pressure of climate change has inspired two normative agendas; socio-technical transitions and socio-ecological resilience, both sharing a complex-systems epistemology (Gillard et al. 2016). Socio-technical solutions include a continuous, massive data gathering exercise now underway in urban places under the guise of developing a 'smart'(er) city. This has led to the creation of data-rich environments where large data sets have become central to monitoring and forming a response to anomalies. Some have argued that these kinds of data sets can help in planning for resilient cities (Norberg and Cumming 2008; Batty 2013). In this paper, we focus on a more nuanced, ecologically based, socio-environmental perspective of resilience planning that is often given less consideration. Here, we broadly discuss (and model) the tightly linked, mutually influenced, social and biophysical subsystems that are critical for understanding urban resilience. We argue for the need to incorporate these sub system linkages into the resilience planning lexicon through the integration of systems models and planning support systems. We make our case by first providing a context for urban resilience from a socio-ecological and planning perspective. We highlight the data needs for this type of resilient planning and compare it to currently collected data streams in various smart city efforts. This helps to define an approach for operationalizing socio-environmental resilience planning using robust systems models and planning support systems. For this, we draw from our experiences in coupling a spatio-temporal land use model (the Landuse Evolution and impact Assessment Model (LEAM)) with water quality and quantity models in Stockholm Sweden. We describe the coupling of these systems models using a robust Planning Support System (PSS) structural framework. We use the coupled model simulations and PSS to analyze the connection between urban land use transformation (social) and water
The Eemian climate simulated by two models of different complexities
Nikolova, Irina; Yin, Qiuzhen; Berger, Andre; Singh, Umesh; Karami, Pasha
2013-04-01
The Eemian period, also known as MIS-5, experienced warmer than today climate, reduction in ice sheets and important sea-level rise. These interesting features have made the Eemian appropriate to evaluate climate models when forced with astronomical and greenhouse gas forcings different from today. In this work, we present the simulated Eemian climate by two climate models of different complexities, LOVECLIM (LLN Earth system model of intermediate complexity) and CCSM3 (NCAR atmosphere-ocean general circulation model). Feedbacks from sea ice, vegetation, monsoon and ENSO phenomena are discussed to explain the regional similarities/dissimilarities in both models with respect to the pre-industrial (PI) climate. Significant warming (cooling) over almost all the continents during boreal summer (winter) leads to a largely increased (reduced) seasonal contrast in the northern (southern) hemisphere, mainly due to the much higher (lower) insolation received by the whole Earth in boreal summer (winter). The arctic is warmer than at PI through the whole year, resulting from its much higher summer insolation and its remnant effect in the following fall-winter through the interactions between atmosphere, ocean and sea ice. Regional discrepancies exist in the sea-ice formation zones between the two models. Excessive sea-ice formation in CCSM3 results in intense regional cooling. In both models intensified African monsoon and vegetation feedback are responsible for the cooling during summer in North Africa and on the Arabian Peninsula. Over India precipitation maximum is found further west, while in Africa the precipitation maximum migrates further north. Trees and grassland expand north in Sahel/Sahara, trees being more abundant in the results from LOVECLIM than from CCSM3. A mix of forest and grassland occupies continents and expand deep in the high northern latitudes in line with proxy records. Desert areas reduce significantly in Northern Hemisphere, but increase in North
The independent spreaders involved SIR Rumor model in complex networks
Qian, Zhen; Tang, Shaoting; Zhang, Xiao; Zheng, Zhiming
2015-07-01
Recent studies of rumor or information diffusion process in complex networks show that in contrast to traditional comprehension, individuals who participate in rumor spreading within one network do not always get the rumor from their neighbors. They can obtain the rumor from different sources like online social networks and then publish it on their personal sites. In our paper, we discuss this phenomenon in complex networks by adopting the concept of independent spreaders. Rather than getting the rumor from neighbors, independent spreaders learn it from other channels. We further develop the classic "ignorant-spreaders-stiflers" or SIR model of rumor diffusion process in complex networks. A steady-state analysis is conducted to investigate the final spectrum of the rumor spreading under various spreading rate, stifling rate, density of independent spreaders and average degree of the network. Results show that independent spreaders effectively enhance the rumor diffusion process, by delivering the rumor to regions far away from the current rumor infected regions. And though the rumor spreading process in SF networks is faster than that in ER networks, the final size of rumor spreading in ER networks is larger than that in SF networks.
A RANGE BASED METHOD FOR COMPLEX FACADE MODELING
Directory of Open Access Journals (Sweden)
A. Adami
2012-09-01
Full Text Available 3d modelling of Architectural Heritage does not follow a very well-defined way, but it goes through different algorithms and digital form according to the shape complexity of the object, to the main goal of the representation and to the starting data. Even if the process starts from the same data, such as a pointcloud acquired by laser scanner, there are different possibilities to realize a digital model. In particular we can choose between two different attitudes: the mesh and the solid model. In the first case the complexity of architecture is represented by a dense net of triangular surfaces which approximates the real surface of the object. In the other -opposite- case the 3d digital model can be realized by the use of simple geometrical shapes, by the use of sweeping algorithm and the Boolean operations. Obviously these two models are not the same and each one is characterized by some peculiarities concerning the way of modelling (the choice of a particular triangulation algorithm or the quasi-automatic modelling by known shapes and the final results (a more detailed and complex mesh versus an approximate and more simple solid model. Usually the expected final representation and the possibility of publishing lead to one way or the other. In this paper we want to suggest a semiautomatic process to build 3d digital models of the facades of complex architecture to be used for example in city models or in other large scale representations. This way of modelling guarantees also to obtain small files to be published on the web or to be transmitted. The modelling procedure starts from laser scanner data which can be processed in the well known way. Usually more than one scan is necessary to describe a complex architecture and to avoid some shadows on the facades. These have to be registered in a single reference system by the use of targets which are surveyed by topography and then to be filtered in order to obtain a well controlled and
Schöniger, Anneli; Illman, Walter A.; Wöhling, Thomas; Nowak, Wolfgang
2015-12-01
Groundwater modelers face the challenge of how to assign representative parameter values to the studied aquifer. Several approaches are available to parameterize spatial heterogeneity in aquifer parameters. They differ in their conceptualization and complexity, ranging from homogeneous models to heterogeneous random fields. While it is common practice to invest more effort into data collection for models with a finer resolution of heterogeneities, there is a lack of advice which amount of data is required to justify a certain level of model complexity. In this study, we propose to use concepts related to Bayesian model selection to identify this balance. We demonstrate our approach on the characterization of a heterogeneous aquifer via hydraulic tomography in a sandbox experiment (Illman et al., 2010). We consider four increasingly complex parameterizations of hydraulic conductivity: (1) Effective homogeneous medium, (2) geology-based zonation, (3) interpolation by pilot points, and (4) geostatistical random fields. First, we investigate the shift in justified complexity with increasing amount of available data by constructing a model confusion matrix. This matrix indicates the maximum level of complexity that can be justified given a specific experimental setup. Second, we determine which parameterization is most adequate given the observed drawdown data. Third, we test how the different parameterizations perform in a validation setup. The results of our test case indicate that aquifer characterization via hydraulic tomography does not necessarily require (or justify) a geostatistical description. Instead, a zonation-based model might be a more robust choice, but only if the zonation is geologically adequate.
Simultaneous prediction of protein secondary structure and transmembrane spans.
Leman, Julia Koehler; Mueller, Ralf; Karakas, Mert; Woetzel, Nils; Meiler, Jens
2013-07-01
Prediction of transmembrane spans and secondary structure from the protein sequence is generally the first step in the structural characterization of (membrane) proteins. Preference of a stretch of amino acids in a protein to form secondary structure and being placed in the membrane are correlated. Nevertheless, current methods predict either secondary structure or individual transmembrane states. We introduce a method that simultaneously predicts the secondary structure and transmembrane spans from the protein sequence. This approach not only eliminates the necessity to create a consensus prediction from possibly contradicting outputs of several predictors but bears the potential to predict conformational switches, i.e., sequence regions that have a high probability to change for example from a coil conformation in solution to an α-helical transmembrane state. An artificial neural network was trained on databases of 177 membrane proteins and 6048 soluble proteins. The output is a 3 × 3 dimensional probability matrix for each residue in the sequence that combines three secondary structure types (helix, strand, coil) and three environment types (membrane core, interface, solution). The prediction accuracies are 70.3% for nine possible states, 73.2% for three-state secondary structure prediction, and 94.8% for three-state transmembrane span prediction. These accuracies are comparable to state-of-the-art predictors of secondary structure (e.g., Psipred) or transmembrane placement (e.g., OCTOPUS). The method is available as web server and for download at www.meilerlab.org.
Energy Technology Data Exchange (ETDEWEB)
Torgerson, P.M.; Drickamer, H.G.; Weber, G.
1979-07-10
Certain protein-ligand complexes are destabilized by application of pressures of the order of 5 to 10 kbar while others are stabilized. This divergent behavior is attributed to differences in compressibility of the protein binding sites. Pressure-stabilized binding is thought by us to be characteristic of soft binding sites, sites in which rotation about backbone bonds permits reduction of the site dimensions under pressure. In contradistinction, hard binding sites do not decrease their size when pressure is applied. As a model for this latter kind we have measured the changes in equilibrium with pressure of complexes of poly-..beta..-cyclodextrin with two fluorescent probes: 8-anilinonaphthalene-1-sulfonate and 6-propionyl-2-(dimethylamino)naphthalene. The standard volume change upon formation of the complexes at 1 atm is similar in both (+9.3 mL/mol), and as expected the incompressibility of the cyclodextrin rings results in a site from which the probes are dissociated by pressure. On the assmption of incompressibility of the binding site, the experimental data permit the calculation of the pressure vs volume curves (compressibility curves) for the probes molecularly dispersed in water. These curves are in broad agreement with those of liquid aliphatic and aromatic hydrocarbons in the low-pressure range (1 to 4 kbar) but indicate a reduced compressibility at the higher pressures. Considerations of relative compressibility offer a quantitative alternative to the usual qualitative discussion of the effects of high pressures upon proteins in terms of the participation of hydrophobic and other bonds.
Thermohaline feedbacks in ocean-climate models of varying complexity
den Toom, M.
2013-03-01
explicitly resolves eddies, and a model in which eddies are parameterized. It is found that the behavior of an eddy-resolving model is qualitatively different from that of a non-eddying model. What is clear at this point, is that the AMOC is governed by non-linear dynamics. As a result, its simulated behavior depends in a non-trivial way on how unresolved processes are represented in a model. As demonstrated in this thesis, model fidelity can be effectively assessed by examining models of varying complexity.
Simple models for studying complex spatiotemporal patterns of animal behavior
Tyutyunov, Yuri V.; Titova, Lyudmila I.
2017-06-01
Minimal mathematical models able to explain complex patterns of animal behavior are essential parts of simulation systems describing large-scale spatiotemporal dynamics of trophic communities, particularly those with wide-ranging species, such as occur in pelagic environments. We present results obtained with three different modelling approaches: (i) an individual-based model of animal spatial behavior; (ii) a continuous taxis-diffusion-reaction system of partial-difference equations; (iii) a 'hybrid' approach combining the individual-based algorithm of organism movements with explicit description of decay and diffusion of the movement stimuli. Though the models are based on extremely simple rules, they all allow description of spatial movements of animals in a predator-prey system within a closed habitat, reproducing some typical patterns of the pursuit-evasion behavior observed in natural populations. In all three models, at each spatial position the animal movements are determined by local conditions only, so the pattern of collective behavior emerges due to self-organization. The movement velocities of animals are proportional to the density gradients of specific cues emitted by individuals of the antagonistic species (pheromones, exometabolites or mechanical waves of the media, e.g., sound). These cues play a role of taxis stimuli: prey attract predators, while predators repel prey. Depending on the nature and the properties of the movement stimulus we propose using either a simplified individual-based model, a continuous taxis pursuit-evasion system, or a little more detailed 'hybrid' approach that combines simulation of the individual movements with the continuous model describing diffusion and decay of the stimuli in an explicit way. These can be used to improve movement models for many species, including large marine predators.
MODELING AND AVAILABILITY ANALYZES OF A COMPLEX GAS PIPELINE NETWORK
Energy Technology Data Exchange (ETDEWEB)
Ainouche, A.; Ainouche, H.
2007-07-01
The network reliability, in the way of security of supply of international markets, is proved to be an essential criterion for the conservation of the market shares and the conquest of new customers. In relation with the importance and the existing configurations diversity of gas pipelines networks, the obtaining of a global availability model of a network is difficult to implement by the use of a classic approach based on the analysis of the whole of failure risks, the definition of their probability and the estimation of their impact in term of productivity. This because mainly of the huge dimensions of the phase space that would result from such a conception. To get round this problem we implemented a systemic type approach for the modeling of the availability of a complex gas pipelines network. The approach of modeling is of 'bottom-up' type. The model of coordination is a model of flow maximization whose formalization requires the representation of the gas pipeline network by the graphs theory. The developed tool can also be used as a stand of experimentation and to define by simulation the impact of every decision having the tendency to improve the availability of the network. (auth)
Complex Wall Boundary Conditions for Modeling Combustion in Catalytic Channels
Zhu, Huayang; Jackson, Gregory
2000-11-01
Monolith catalytic reactors for exothermic oxidation are being used in automobile exhaust clean-up and ultra-low emissions combustion systems. The reactors present a unique coupling between mass, heat, and momentum transport in a channel flow configuration. The use of porous catalytic coatings along the channel wall presents a complex boundary condition when modeled with the two-dimensional channel flow. This current work presents a 2-D transient model for predicting the performance of catalytic combustion systems for methane oxidation on Pd catalysts. The model solves the 2-D compressible transport equations for momentum, species, and energy, which are solved with a porous washcoat model for the wall boundary conditions. A time-splitting algorithm is used to separate the stiff chemical reactions from the convective/diffusive equations for the channel flow. A detailed surface chemistry mechanism is incorporated for the catalytic wall model and is used to predict transient ignition and steady-state conversion of CH4-air flows in the catalytic reactor.
Complex system modelling and control through intelligent soft computations
Azar, Ahmad
2015-01-01
The book offers a snapshot of the theories and applications of soft computing in the area of complex systems modeling and control. It presents the most important findings discussed during the 5th International Conference on Modelling, Identification and Control, held in Cairo, from August 31-September 2, 2013. The book consists of twenty-nine selected contributions, which have been thoroughly reviewed and extended before their inclusion in the volume. The different chapters, written by active researchers in the field, report on both current theories and important applications of soft-computing. Besides providing the readers with soft-computing fundamentals, and soft-computing based inductive methodologies/algorithms, the book also discusses key industrial soft-computing applications, as well as multidisciplinary solutions developed for a variety of purposes, like windup control, waste management, security issues, biomedical applications and many others. It is a perfect reference guide for graduate students, r...
Complex fluid flow modeling with SPH on GPU
Bilotta, Giuseppe; Hérault, Alexis; Del Negro, Ciro; Russo, Giovanni; Vicari, Annamaria
2010-05-01
We describe an implementation of the Smoothed Particle Hydrodynamics (SPH) method for the simulation of complex fluid flows. The algorithm is entirely executed on Graphic Processing Units (GPUs) using the Compute Unified Device Architecture (CUDA) developed by NVIDIA and fully exploiting their computational power. An increase of one to two orders of magnitude in simulation speed over equivalent CPU code is achieved. A complete modeling of the flow of a complex fluid such as lava is challenging from the modelistic, numerical and computational points of view. The natural topography irregularities, the dynamic free boundaries and phenomena such as solidification, presence of floating solid bodies or other obstacles and their eventual fragmentation make the problem difficult to solve using traditional numerical methods (finite volumes, finite elements): the need to refine the discretization grid in correspondence of high gradients, when possible, is computationally expensive and with an often inadequate control of the error; for real-world applications, moreover, the information needed by the grid refinement may not be available (e.g. because the Digital Elevation Models are too coarse); boundary tracking is also problematic with Eulerian discretizations, more so with complex fluids due to the presence of internal boundaries given by fluid inhomogeneity and presence of solidification fronts. An alternative approach is offered by mesh-free particle methods, that solve most of the problems connected to the dynamics of complex fluids in a natural way. Particle methods discretize the fluid using nodes which are not forced on a given topological structure: boundary treatment is therefore implicit and automatic; the movement freedom of the particles also permits the treatment of deformations without incurring in any significant penalty; finally, the accuracy is easily controlled by the insertion of new particles where needed. Our team has developed a new model based on the
Modeling pedestrian's conformity violation behavior: a complex network based approach.
Zhou, Zhuping; Hu, Qizhou; Wang, Wei
2014-01-01
Pedestrian injuries and fatalities present a problem all over the world. Pedestrian conformity violation behaviors, which lead to many pedestrian crashes, are common phenomena at the signalized intersections in China. The concepts and metrics of complex networks are applied to analyze the structural characteristics and evolution rules of pedestrian network about the conformity violation crossings. First, a network of pedestrians crossing the street is established, and the network's degree distributions are analyzed. Then, by using the basic idea of SI model, a spreading model of pedestrian illegal crossing behavior is proposed. Finally, through simulation analysis, pedestrian's illegal crossing behavior trends are obtained in different network structures and different spreading rates. Some conclusions are drawn: as the waiting time increases, more pedestrians will join in the violation crossing once a pedestrian crosses on red firstly. And pedestrian's conformity violation behavior will increase as the spreading rate increases.
Using Stochastic Model Checking to Provision Complex Business Services
DEFF Research Database (Denmark)
Herbert, Luke Thomas; Sharp, Robin
2012-01-01
bounds on resources consumed during execution of business processes. Accurate resource provisioning is often central to ensuring the safe execution of a process. We first introduce a formalised core subset of the Business Process Modelling and Notation (BPMN), which we extend with probabilistic and non......We present a framework for modelling and analysis of real-world business workflows. Business processes regularly form the basis for the design of software services, and frequently display complex stochastic behaviour. The accurate evaluation of their qualitative aspects can allow for determining...... of business processes including transient probabilities, timing, occurrence and ordering of events, and best- and worst-case scenarios. The developments presented are illustrated using an example from the health-care industry....
Graph spectral characterisation of the XY model on complex networks
Expert, Paul; Takaguchi, Taro; Lambiotte, Renaud
2016-01-01
There is recent evidence that the $XY$ spin model on complex networks can display three different macroscopic states in response to the topology of the network underpinning the interactions of the spins. In this work, we present a novel way to characterise the macroscopic states of the $XY$ spin model based on the spectral decomposition of time series using topological information about the underlying networks. We use three different classes of networks to generate time series of the spins for the three possible macroscopic states. We then use the temporal Graph Signal Transform technique to decompose the time series of the spins on the eigenbasis of the Laplacian. From this decomposition, we produce spatial power spectra, which summarise the activation of structural modes by the non-linear dynamics, and thus coherent patterns of activity of the spins. These signatures of the macroscopic states are independent of the underlying networks and can thus be used as universal signatures for the macroscopic states. ...
Responses of Transmembrane Peptide and Lipid Chains to Hydrophobic Mismatch
Institute of Scientific and Technical Information of China (English)
YANG Lei; LI Jian-tao; QI Hai-yan; LI Fei
2012-01-01
Hydrophobic mismatch between the hydrophobic length of membrane proteins and hydrophobic thickness of membranes is a crucial factor in controlling protein function and assembly.We combined fluorescence with circular dichroism(CD) and attenuated total reflection infrared(ATR-IR) spectroscopic methods to investigate the behaviors of the peptide and lipids under hydrophobic mismatch using a model peptide from the fourth transmembrane domain of natural resistance-associated macrophage protein 1 (Nramp 1),the phosphatidylcholines(PCs) and phosphatidylglycerols(PGs) with different lengths of acyl chains(14:0,16:0 and 18:0).In all PG lipid membranes,the peptide forms stable α-helix structure,and the helix axis is parallel to lipid chains.The helical span and orientation hardly change in varying thickness of PG membranes,while the lipid chains can deform to accommodate to the hydrophobic surface of embedded peptide.By comparison,the helical structures of the model peptide in PC lipid membranes are less stable.Upon incorporation with PC lipid membranes,the peptide can deform itself to accommodate to the hydrophobic thickness of lipid membranes in response to hydrophobic mismatch.In addition,hydrophobic mismatch can increase the aggregation propensity of the peptide in both PC and PG lipid membranes and the peptide in PC membranes has more aggregation tendency than that in PG membranes.
COMPLEX PROGRAMS FOR MODELING HIGHWAY: WAY AND STREAM
Directory of Open Access Journals (Sweden)
A. V. Skrypnikov
2014-01-01
Full Text Available The complexity of the operation of the road caused by continuously varying from picket to picket road conditions caused by a variety of parameters projected (existing road , the variety of types of cars, their technical and economic parameters , a variety of climatic and weather conditions required to develop a complex simulation programs . This paper describes a set of programs that form the core of the subsystem "driver-vehicle-road environment". Optimization of the design solutions developed modules contribute WAY type and columns, not using indicators averaged transport - road performance, and detailed process model of functioning of the road. WAY module provides continuous sequence modeling perception of road elements mechanical subsystem "road-car " (by continuous formation and solution of the equations of motion and the characteristics of this mode. WAY module (with module PARK brings the technical contradiction between the 20-year term of road design and use of existing practices in their justification of design decisions technical parameters of cars today. The complexity of the operation of the road due to the random nature of traffic demanded inclusion in the computer -aided design of roads STREAM module. STREAM module allows to obtain simulation results of a random process, sufficient to optimize the design decisions in general and in the areas of local variation of the plan, longitudinal section, the way the situation, etc. Varie ty of road conditions possible to classify on the specifics of the formation of the flow regimes. This builds on the results of study of the process of movement of cars in the stream.
Alpha Decay in the Complex Energy Shell Model
Betan, R Id
2012-01-01
Alpha emission from a nucleus is a fundamental decay process in which the alpha particle formed inside the nucleus tunnels out through the potential barrier. We describe alpha decay of $^{212}$Po and $^{104}$Te by means of the configuration interaction approach. To compute the preformation factor and penetrability, we use the complex-energy shell model with a separable T=1 interaction. The single-particle space is expanded in a Woods-Saxon basis that consists of bound and unbound resonant states. Special attention is paid to the treatment of the norm kernel appearing in the definition of the formation amplitude that guarantees the normalization of the channel function. Without explicitly considering the alpha-cluster component in the wave function of the parent nucleus, we reproduce the experimental alpha-decay width of $^{212}$Po and predict an upper limit of T_{1/2}=5.5x10^{-7} sec for the half-life of $^{104}$Te. The complex-energy shell model in a large valence configuration space is capable of providing ...
Mutual information model for link prediction in heterogeneous complex networks
Shakibian, Hadi; Moghadam Charkari, Nasrollah
2017-01-01
Recently, a number of meta-path based similarity indices like PathSim, HeteSim, and random walk have been proposed for link prediction in heterogeneous complex networks. However, these indices suffer from two major drawbacks. Firstly, they are primarily dependent on the connectivity degrees of node pairs without considering the further information provided by the given meta-path. Secondly, most of them are required to use a single and usually symmetric meta-path in advance. Hence, employing a set of different meta-paths is not straightforward. To tackle with these problems, we propose a mutual information model for link prediction in heterogeneous complex networks. The proposed model, called as Meta-path based Mutual Information Index (MMI), introduces meta-path based link entropy to estimate the link likelihood and could be carried on a set of available meta-paths. This estimation measures the amount of information through the paths instead of measuring the amount of connectivity between the node pairs. The experimental results on a Bibliography network show that the MMI obtains high prediction accuracy compared with other popular similarity indices. PMID:28344326
Phase-separation models for swimming enhancement in complex fluids
Man, Yi
2015-01-01
Swimming cells often have to self-propel through fluids displaying non-Newtonian rheology. While past theoretical work seems to indicate that stresses arising from complex fluids should systematically hinder low-Reynolds number locomotion, experimental observations suggest that locomotion enhancement is possible. In this paper we propose a physical mechanism for locomotion enhancement of microscopic swimmers in a complex fluid. It is based on the fact that micro-structured fluids will generically phase-separate near surfaces, leading to the presence of low-viscosity layers which promote slip and decrease viscous friction near the surface of the swimmer. We use two models to address the consequence of this phase separation: a nonzero apparent slip length for the fluid and then an explicit modeling of the change of viscosity in a thin layer near the swimmer. Considering two canonical setups for low-Reynolds number locomotion, namely the waving locomotion of a two-dimensional sheet and that of a three-dimensiona...
Uncertainty quantification for quantum chemical models of complex reaction networks.
Proppe, Jonny; Husch, Tamara; Simm, Gregor N; Reiher, Markus
2016-12-22
For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.
Green IT engineering concepts, models, complex systems architectures
Kondratenko, Yuriy; Kacprzyk, Janusz
2017-01-01
This volume provides a comprehensive state of the art overview of a series of advanced trends and concepts that have recently been proposed in the area of green information technologies engineering as well as of design and development methodologies for models and complex systems architectures and their intelligent components. The contributions included in the volume have their roots in the authors’ presentations, and vivid discussions that have followed the presentations, at a series of workshop and seminars held within the international TEMPUS-project GreenCo project in United Kingdom, Italy, Portugal, Sweden and the Ukraine, during 2013-2015 and at the 1st - 5th Workshops on Green and Safe Computing (GreenSCom) held in Russia, Slovakia and the Ukraine. The book presents a systematic exposition of research on principles, models, components and complex systems and a description of industry- and society-oriented aspects of the green IT engineering. A chapter-oriented structure has been adopted for this book ...
Directory of Open Access Journals (Sweden)
Taras Gout
2012-01-01
Full Text Available The CFTR gene is unique within the ATP-binding cassette (ABC protein family, predominantly of transporters, by coding a chloride channel. The gating mechanism of ABC proteins has been characterized by the ATP Switch model in terms cycles of dimer formation and dissociation linked to ATP binding and hydrolysis, respectively. It would be of interest to assess the extent that Cystic Fibrosis Transmembrane Conductance Regulator (CFTR, a functional channel, fits the ATP Switch model for ABC transporters. Additional transporter mechanisms, namely those of Pgp and HlyB, are discussed for perspective. Literature search of databases selected key references in comparing and contrasting the gating mechanism. CFTR is a functional chloride channel facilitating transmembrane anion flow down electrochemical gradients. A dysfunctional CFTR protein results in cystic fibrosis, a fatal pleiotropic disease currently managed symptomatically. Understanding the gating mechanism will help target drug development aimed at alleviating and curing the disease.
Modelling methodology for engineering of complex sociotechnical systems
CSIR Research Space (South Africa)
Oosthuizen, R
2014-10-01
Full Text Available Different systems engineering techniques and approaches are applied to design and develop complex sociotechnical systems for complex problems. In a complex sociotechnical system cognitive and social humans use information technology to make sense...
Modelling microbial metabolic rewiring during growth in a complex medium.
Fondi, Marco; Bosi, Emanuele; Presta, Luana; Natoli, Diletta; Fani, Renato
2016-11-24
In their natural environment, bacteria face a wide range of environmental conditions that change over time and that impose continuous rearrangements at all the cellular levels (e.g. gene expression, metabolism). When facing a nutritionally rich environment, for example, microbes first use the preferred compound(s) and only later start metabolizing the other one(s). A systemic re-organization of the overall microbial metabolic network in response to a variation in the composition/concentration of the surrounding nutrients has been suggested, although the range and the entity of such modifications in organisms other than a few model microbes has been scarcely described up to now. We used multi-step constraint-based metabolic modelling to simulate the growth in a complex medium over several time steps of the Antarctic model organism Pseudoalteromonas haloplanktis TAC125. As each of these phases is characterized by a specific set of amino acids to be used as carbon and energy source our modelling framework describes the major consequences of nutrients switching at the system level. The model predicts that a deep metabolic reprogramming might be required to achieve optimal biomass production in different stages of growth (different medium composition), with at least half of the cellular metabolic network involved (more than 50% of the metabolic genes). Additionally, we show that our modelling framework is able to capture metabolic functional association and/or common regulatory features of the genes embedded in our reconstruction (e.g. the presence of common regulatory motifs). Finally, to explore the possibility of a sub-optimal biomass objective function (i.e. that cells use resources in alternative metabolic processes at the expense of optimal growth) we have implemented a MOMA-based approach (called nutritional-MOMA) and compared the outcomes with those obtained with Flux Balance Analysis (FBA). Growth simulations under this scenario revealed the deep impact of
Surface Complexation Modelling in Metal-Mineral-Bacteria Systems
Johnson, K. J.; Fein, J. B.
2002-12-01
The reactive surfaces of bacteria and minerals can determine the fate, transport, and bioavailability of aqueous heavy metal cations. Geochemical models are instrumental in accurately accounting for the partitioning of the metals between mineral surfaces and bacteria cell walls. Previous research has shown that surface complexation modelling (SCM) is accurate in two-component systems (metal:mineral and metal:bacteria); however, the ability of SCMs to account for metal distribution in mixed metal-mineral-bacteria systems has not been tested. In this study, we measure aqueous Cd distributions in water-bacteria-mineral systems, and compare these observations with predicted distributions based on a surface complexation modelling approach. We measured Cd adsorption in 2- and 3-component batch adsorption experiments. In the 2-component experiments, we measured the extent of adsorption of 10 ppm aqueous Cd onto either a bacterial or hydrous ferric oxide sorbent. The metal:bacteria experiments contained 1 g/L (wet wt.) of B. subtilis, and were conducted as a function of pH; the metal:mineral experiments were conducted as a function of both pH and HFO content. Two types of 3-component Cd adsorption experiments were also conducted in which both mineral powder and bacteria were present as sorbents: 1) one in which the HFO was physically but not chemically isolated from the system using sealed dialysis tubing, and 2) others where the HFO, Cd and B. subtilis were all in physical contact. The dialysis tubing approach enabled the direct determination of the concentration of Cd on each sorbing surface, after separation and acidification of each sorbent. The experiments indicate that both bacteria and mineral surfaces can dominate adsorption in the system, depending on pH and bacteria:mineral ratio. The stability constants, determined using the data from the 2-component systems, along with those for other surface and aqueous species in the systems, were used with FITEQL to
Gershenson, Carlos
2011-01-01
The term complexity derives etymologically from the Latin plexus, which means interwoven. Intuitively, this implies that something complex is composed by elements that are difficult to separate. This difficulty arises from the relevant interactions that take place between components. This lack of separability is at odds with the classical scientific method - which has been used since the times of Galileo, Newton, Descartes, and Laplace - and has also influenced philosophy and engineering. In recent decades, the scientific study of complexity and complex systems has proposed a paradigm shift in science and philosophy, proposing novel methods that take into account relevant interactions.
Wind Power Curve Modeling in Simple and Complex Terrain
Energy Technology Data Exchange (ETDEWEB)
Bulaevskaya, V. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wharton, S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Irons, Z. [Enel Green Power North America, Andover, MA (United States); Qualley, G. [Pentalum, Colleyville, TX (United States)
2015-02-09
Our previous work on wind power curve modeling using statistical models focused on a location with a moderately complex terrain in the Altamont Pass region in northern California (CA). The work described here is the follow-up to that work, but at a location with a simple terrain in northern Oklahoma (OK). The goal of the present analysis was to determine the gain in predictive ability afforded by adding information beyond the hub-height wind speed, such as wind speeds at other heights, as well as other atmospheric variables, to the power prediction model at this new location and compare the results to those obtained at the CA site in the previous study. While we reach some of the same conclusions at both sites, many results reported for the CA site do not hold at the OK site. In particular, using the entire vertical profile of wind speeds improves the accuracy of wind power prediction relative to using the hub-height wind speed alone at both sites. However, in contrast to the CA site, the rotor equivalent wind speed (REWS) performs almost as well as the entire profile at the OK site. Another difference is that at the CA site, adding wind veer as a predictor significantly improved the power prediction accuracy. The same was true for that site when air density was added to the model separately instead of using the standard air density adjustment. At the OK site, these additional variables result in no significant benefit for the prediction accuracy.
Coevolving complex networks in the model of social interactions
Raducha, Tomasz; Gubiec, Tomasz
2017-04-01
We analyze Axelrod's model of social interactions on coevolving complex networks. We introduce four extensions with different mechanisms of edge rewiring. The models are intended to catch two kinds of interactions-preferential attachment, which can be observed in scientists or actors collaborations, and local rewiring, which can be observed in friendship formation in everyday relations. Numerical simulations show that proposed dynamics can lead to the power-law distribution of nodes' degree and high value of the clustering coefficient, while still retaining the small-world effect in three models. All models are characterized by two phase transitions of a different nature. In case of local rewiring we obtain order-disorder discontinuous phase transition even in the thermodynamic limit, while in case of long-distance switching discontinuity disappears in the thermodynamic limit, leaving one continuous phase transition. In addition, we discover a new and universal characteristic of the second transition point-an abrupt increase of the clustering coefficient, due to formation of many small complete subgraphs inside the network.
Influence of magnesium sulfate on HCO3/Cl transmembrane exchange rate in human erythrocytes.
Chernyshova, Ekaterina S; Zaikina, Yulia S; Tsvetovskaya, Galina A; Strokotov, Dmitry I; Yurkin, Maxim A; Serebrennikova, Elena S; Volkov, Leonid; Maltsev, Valeri P; Chernyshev, Andrei V
2016-03-21
Magnesium sulfate (MgSO4) is widely used in medicine but molecular mechanisms of its protection through influence on erythrocytes are not fully understood and are considerably controversial. Using scanning flow cytometry, in this work for the first time we observed experimentally (both in situ and in vitro) a significant increase of HCO3(-)/Cl(-) transmembrane exchange rate of human erythrocytes in the presence of MgSO4 in blood. For a quantitative analysis of the obtained experimental data, we introduced and verified a molecular kinetic model, which describes activation of major anion exchanger Band 3 (or AE1) by its complexation with free intracellular Mg(2+) (taking into account Mg(2+) membrane transport and intracellular buffering). Fitting the model to our in vitro experimental data, we observed a good correspondence between theoretical and experimental kinetic curves that allowed us to evaluate the model parameters and to estimate for the first time the association constant of Mg(2+) with Band 3 as KB~0.07mM, which is in agreement with known values of the apparent Mg(2+) dissociation constant (from 0.01 to 0.1mM) that reflects experiments on enrichment of Mg(2+) at the inner erythrocyte membrane (Gunther, 2007). Results of this work partly clarify the molecular mechanisms of MgSO4 action in human erythrocytes. The method developed allows one to estimate quantitatively a perspective of MgSO4 treatment for a patient. It should be particularly helpful in prenatal medicine for early detection of pathologies associated with the risk of fetal hypoxia.
Spectroscopic studies of molybdenum complexes as models for nitrogenase
Energy Technology Data Exchange (ETDEWEB)
Walker, T.P.
1981-05-01
Because biological nitrogen fixation requires Mo, there is an interest in inorganic Mo complexes which mimic the reactions of nitrogen-fixing enzymes. Two such complexes are the dimer Mo/sub 2/O/sub 4/ (cysteine)/sub 2//sup 2 -/ and trans-Mo(N/sub 2/)/sub 2/(dppe)/sub 2/ (dppe = 1,2-bis(diphenylphosphino)ethane). The H/sup 1/ and C/sup 13/ NMR of solutions of Mo/sub 2/O/sub 4/(cys)/sub 2//sup 2 -/ are described. It is shown that in aqueous solution the cysteine ligands assume at least three distinct configurations. A step-wise dissociation of the cysteine ligand is proposed to explain the data. The Extended X-ray Absorption Fine Structure (EXAFS) of trans-Mo(N/sub 2/)/sub 2/(dppe)/sub 2/ is described and compared to the EXAFS of MoH/sub 4/(dppe)/sub 2/. The spectra are fitted to amplitude and phase parameters developed at Bell Laboratories. On the basis of this analysis, one can determine (1) that the dinitrogen complex contains nitrogen and the hydride complex does not and (2) the correct Mo-N distance. This is significant because the Mo inn both complexes is coordinated by four P atoms which dominate the EXAFS. A similar sort of interference is present in nitrogenase due to S coordination of the Mo in the enzyme. This model experiment indicates that, given adequate signal to noise ratios, the presence or absence of dinitrogen coordination to Mo in the enzyme may be determined by EXAFS using existing data analysis techniques. A new reaction between Mo/sub 2/O/sub 4/(cys)/sub 2//sup 2 -/ and acetylene is described to the extent it is presently understood. A strong EPR signal is observed, suggesting the production of stable Mo(V) monomers. EXAFS studies support this suggestion. The Mo K-edge is described. The edge data suggests Mo(VI) is also produced in the reaction. Ultraviolet spectra suggest that cysteine is released in the course of the reaction.
DEFF Research Database (Denmark)
Sikder, K. U.; Stone, K. A.; Kumar, P. B. S.
2014-01-01
We investigate the combined effects of transmembrane proteins and the subjacent cytoskeleton on the dynamics of phase separation in multicomponent lipid bilayers using computer simulations of a particle-based implicit solvent model for lipid membranes with soft-core interactions. We find that mic...... that microphase separation can be achieved by the protein confinement by the cytoskeleton. Our results have relevance to the finite size of lipid rafts in the plasma membrane of mammalian cells. (C) 2014 AIP Publishing LLC....
Sikder, Md. Kabir Uddin; Stone, Kyle A.; Kumar, P. B. Sunil; Laradji, Mohamed
2014-08-01
We investigate the combined effects of transmembrane proteins and the subjacent cytoskeleton on the dynamics of phase separation in multicomponent lipid bilayers using computer simulations of a particle-based implicit solvent model for lipid membranes with soft-core interactions. We find that microphase separation can be achieved by the protein confinement by the cytoskeleton. Our results have relevance to the finite size of lipid rafts in the plasma membrane of mammalian cells.
Siegfried, Robert
2014-01-01
Robert Siegfried presents a framework for efficient agent-based modeling and simulation of complex systems. He compares different approaches for describing structure and dynamics of agent-based models in detail. Based on this evaluation the author introduces the "General Reference Model for Agent-based Modeling and Simulation" (GRAMS). Furthermore he presents parallel and distributed simulation approaches for execution of agent-based models -from small scale to very large scale. The author shows how agent-based models may be executed by different simulation engines that utilize underlying hard
A Tractable Complex Network Model Based onthe Stochastic Mean-Field Model of Distance
Aldous, David J.
Much recent research activity has been devoted to empirical study and theoretical models of complex networks (random graphs) possessing three qualitative features: power-law degree distributions, local clustering, and slowly-growing diameter. We point out a new (in this context) platform for such models - the stochastic mean-field model of distances - and within this platform study a simple two-parameter proportional attachment (or copying) model. The model is mathematically natural, permits a wide variety of explicit calculations, has the desired three qualitative features, and fits the complete range of degree scaling exponents and clustering parameters; in these respects it compares favorably with existing models.
Structural organization and interactions of transmembrane domains in tetraspanin proteins
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DeGrado William F
2005-06-01
Full Text Available Abstract Background Proteins of the tetraspanin family contain four transmembrane domains (TM1-4 linked by two extracellular loops and a short intracellular loop, and have short intracellular N- and C-termini. While structure and function analysis of the larger extracellular loop has been performed, the organization and role of transmembrane domains have not been systematically assessed. Results Among 28 human tetraspanin proteins, the TM1-3 sequences display a distinct heptad repeat motif (abcdefgn. In TM1, position a is occupied by structurally conserved bulky residues and position d contains highly conserved Asn and Gly residues. In TM2, position a is occupied by conserved small residues (Gly/Ala/Thr, and position d has a conserved Gly and two bulky aliphatic residues. In TM3, three a positions of the heptad repeat are filled by two leucines and a glutamate/glutamine residue, and two d positions are occupied by either Phe/Tyr or Val/Ile/Leu residues. No heptad motif is apparent in TM4 sequences. Mutations of conserved glycines in human CD9 (Gly25 and Gly32 in TM1; Gly67 and Gly74 in TM2 caused aggregation of mutant proteins inside the cell. Modeling of the TM1-TM2 interface in CD9, using a novel algorithm, predicts tight packing of conserved bulky residues against conserved Gly residues along the two helices. The homodimeric interface of CD9 was mapped, by disulfide cross-linking of single-cysteine mutants, to the vicinity of residues Leu14 and Phe17 in TM1 (positions g and c and Gly77, Gly80 and Ala81 in TM2 (positions d, g and a, respectively. Mutations of a and d residues in both TM1 and TM2 (Gly25, Gly32, Gly67 and Gly74, involved in intramolecular TM1-TM2 interaction, also strongly diminished intermolecular interaction, as assessed by cross-linking of Cys80. Conclusion Our results suggest that tetraspanin intra- and intermolecular interactions are mediated by conserved residues in adjacent, but distinct regions of TM1 and TM2. A key
Structure of FGFR3 transmembrane domain dimer: implications for signaling and human pathologies.
Bocharov, Eduard V; Lesovoy, Dmitry M; Goncharuk, Sergey A; Goncharuk, Marina V; Hristova, Kalina; Arseniev, Alexander S
2013-11-05
Fibroblast growth factor receptor 3 (FGFR3) transduces biochemical signals via lateral dimerization in the plasma membrane, and plays an important role in human development and disease. Eight different pathogenic mutations, implicated in cancers and growth disorders, have been identified in the FGFR3 transmembrane segment. Here, we describe the dimerization of the FGFR3 transmembrane domain in membrane-mimicking DPC/SDS (9/1) micelles. In the solved NMR structure, the two transmembrane helices pack into a symmetric left-handed dimer, with intermolecular stacking interactions occurring in the dimer central region. Some pathogenic mutations fall within the helix-helix interface, whereas others are located within a putative alternative interface. This implies that although the observed dimer structure is important for FGFR3 signaling, the mechanism of FGFR3-mediated transduction across the membrane is complex. We propose an FGFR3 signaling mechanism that is based on the solved structure, available structures of isolated soluble FGFR domains, and published biochemical and biophysical data.
Complex Model Structure - SAHG | LSDB Archive [Life Science Database Archive metadata
Lifescience Database Archive (English)
Full Text Available List Contact us SAHG Complex Model Structure Data detail Data name Complex Model Structure DOI 10.18908/lsdb...a.nbdc01193-007 Description of data contents Predicted protein compex structure (PDB format). Data file File name: complex..._model_structure.zip File URL: ftp://ftp.biosciencedbc.jp/archive/sahg/LATEST/complex_model_st...rget sequence was related to a given subunit of a template complex in PQS database with >=80% sequence ident...ity by the BLAST search and all the other subunits were related to any target sequences, the complex model w
Directory of Open Access Journals (Sweden)
CHEN Zhanlong
2016-02-01
Full Text Available A method about shape similarity measurement of complex holed objects is proposed in this paper. The method extracts features including centroid distance, multilevel chord length, bending degree and concavity-convexity of a geometric object, to construct complex functions based on multilevel bending degree and radius. The complex functions are capable of describing geometry shape from entirety to part. The similarity between geometric objects can be measured by the shape descriptor which is based on the fast Fourier transform of the complex functions. Meanwhile, the matching degree of each scene of complex holed polygons can be got by scene completeness and shape similarity model. And using the feature of multi-level can accomplish the shape similarity measurement among complex geometric objects. Experimenting on geometric objects of different space complexity, the results match human's perceive and show that this method is simple with precision.
Elements of complexity in subsurface modeling, exemplified with three case studies
Freedman, Vicky L.; Truex, Michael J.; Rockhold, Mark L.; Bacon, Diana H.; Freshley, Mark D.; Wellman, Dawn M.
2017-09-01
There are complexity elements to consider when applying subsurface flow and transport models to support environmental analyses. Modelers balance the benefits and costs of modeling along the spectrum of complexity, taking into account the attributes of more simple models (e.g., lower cost, faster execution, easier to explain, less mechanistic) and the attributes of more complex models (higher cost, slower execution, harder to explain, more mechanistic and technically defensible). In this report, modeling complexity is examined with respect to considering this balance. The discussion of modeling complexity is organized into three primary elements: (1) modeling approach, (2) description of process, and (3) description of heterogeneity. Three examples are used to examine these complexity elements. Two of the examples use simulations generated from a complex model to develop simpler models for efficient use in model applications. The first example is designed to support performance evaluation of soil-vapor-extraction remediation in terms of groundwater protection. The second example investigates the importance of simulating different categories of geochemical reactions for carbon sequestration and selecting appropriate simplifications for use in evaluating sequestration scenarios. In the third example, the modeling history for a uranium-contaminated site demonstrates that conservative parameter estimates were inadequate surrogates for complex, critical processes and there is discussion on the selection of more appropriate model complexity for this application. All three examples highlight how complexity considerations are essential to create scientifically defensible models that achieve a balance between model simplification and complexity.
Low-complexity energy disaggregation using appliance load modelling
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Hana Altrabalsi
2016-01-01
Full Text Available Large-scale smart metering deployments and energy saving targets across the world have ignited renewed interest in residential non-intrusive appliance load monitoring (NALM, that is, disaggregating total household’s energy consumption down to individual appliances, using purely analytical tools. Despite increased research efforts, NALM techniques that can disaggregate power loads at low sampling rates are still not accurate and/or practical enough, requiring substantial customer input and long training periods. In this paper, we address these challenges via a practical low-complexity lowrate NALM, by proposing two approaches based on a combination of the following machine learning techniques: k-means clustering and Support Vector Machine, exploiting their strengths and addressing their individual weaknesses. The first proposed supervised approach is a low-complexity method that requires very short training period and is fairly accurate even in the presence of labelling errors. The second approach relies on a database of appliance signatures that we designed using publicly available datasets. The database compactly represents over 200 appliances using statistical modelling of measured active power. Experimental results on three datasets from US, Italy, Austria and UK, demonstrate the reliability and practicality.
A model for transgenerational imprinting variation in complex traits.
Wang, Chenguang; Wang, Zhong; Luo, Jiangtao; Li, Qin; Li, Yao; Ahn, Kwangmi; Prows, Daniel R; Wu, Rongling
2010-07-14
Despite the fact that genetic imprinting, i.e., differential expression of the same allele due to its different parental origins, plays a pivotal role in controlling complex traits or diseases, the origin, action and transmission mode of imprinted genes have still remained largely unexplored. We present a new strategy for studying these properties of genetic imprinting with a two-stage reciprocal F mating design, initiated with two contrasting inbred lines. This strategy maps quantitative trait loci that are imprinted (i.e., iQTLs) based on their segregation and transmission across different generations. By incorporating the allelic configuration of an iQTL genotype into a mixture model framework, this strategy provides a path to trace the parental origin of alleles from previous generations. The imprinting effects of iQTLs and their interactions with other traditionally defined genetic effects, expressed in different generations, are estimated and tested by implementing the EM algorithm. The strategy was used to map iQTLs responsible for survival time with four reciprocal F populations and test whether and how the detected iQTLs inherit their imprinting effects into the next generation. The new strategy will provide a tool for quantifying the role of imprinting effects in the creation and maintenance of phenotypic diversity and elucidating a comprehensive picture of the genetic architecture of complex traits and diseases.
A model for transgenerational imprinting variation in complex traits.
Directory of Open Access Journals (Sweden)
Chenguang Wang
Full Text Available Despite the fact that genetic imprinting, i.e., differential expression of the same allele due to its different parental origins, plays a pivotal role in controlling complex traits or diseases, the origin, action and transmission mode of imprinted genes have still remained largely unexplored. We present a new strategy for studying these properties of genetic imprinting with a two-stage reciprocal F mating design, initiated with two contrasting inbred lines. This strategy maps quantitative trait loci that are imprinted (i.e., iQTLs based on their segregation and transmission across different generations. By incorporating the allelic configuration of an iQTL genotype into a mixture model framework, this strategy provides a path to trace the parental origin of alleles from previous generations. The imprinting effects of iQTLs and their interactions with other traditionally defined genetic effects, expressed in different generations, are estimated and tested by implementing the EM algorithm. The strategy was used to map iQTLs responsible for survival time with four reciprocal F populations and test whether and how the detected iQTLs inherit their imprinting effects into the next generation. The new strategy will provide a tool for quantifying the role of imprinting effects in the creation and maintenance of phenotypic diversity and elucidating a comprehensive picture of the genetic architecture of complex traits and diseases.
Modeling Cu2+-Aβ complexes from computational approaches
Alí-Torres, Jorge; Mirats, Andrea; Maréchal, Jean-Didier; Rodríguez-Santiago, Luis; Sodupe, Mariona
2015-09-01
Amyloid plaques formation and oxidative stress are two key events in the pathology of the Alzheimer disease (AD), in which metal cations have been shown to play an important role. In particular, the interaction of the redox active Cu2+ metal cation with Aβ has been found to interfere in amyloid aggregation and to lead to reactive oxygen species (ROS). A detailed knowledge of the electronic and molecular structure of Cu2+-Aβ complexes is thus important to get a better understanding of the role of these complexes in the development and progression of the AD disease. The computational treatment of these systems requires a combination of several available computational methodologies, because two fundamental aspects have to be addressed: the metal coordination sphere and the conformation adopted by the peptide upon copper binding. In this paper we review the main computational strategies used to deal with the Cu2+-Aβ coordination and build plausible Cu2+-Aβ models that will afterwards allow determining physicochemical properties of interest, such as their redox potential.
Modeling Cu2+-Aβ complexes from computational approaches
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Jorge Alí-Torres
2015-09-01
Full Text Available Amyloid plaques formation and oxidative stress are two key events in the pathology of the Alzheimer disease (AD, in which metal cations have been shown to play an important role. In particular, the interaction of the redox active Cu2+ metal cation with Aβ has been found to interfere in amyloid aggregation and to lead to reactive oxygen species (ROS. A detailed knowledge of the electronic and molecular structure of Cu2+-Aβ complexes is thus important to get a better understanding of the role of these complexes in the development and progression of the AD disease. The computational treatment of these systems requires a combination of several available computational methodologies, because two fundamental aspects have to be addressed: the metal coordination sphere and the conformation adopted by the peptide upon copper binding. In this paper we review the main computational strategies used to deal with the Cu2+-Aβ coordination and build plausible Cu2+-Aβ models that will afterwards allow determining physicochemical properties of interest, such as their redox potential.
Modeling Cu{sup 2+}-Aβ complexes from computational approaches
Energy Technology Data Exchange (ETDEWEB)
Alí-Torres, Jorge [Departamento de Química, Universidad Nacional de Colombia- Sede Bogotá, 111321 (Colombia); Mirats, Andrea; Maréchal, Jean-Didier; Rodríguez-Santiago, Luis; Sodupe, Mariona, E-mail: Mariona.Sodupe@uab.cat [Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)
2015-09-15
Amyloid plaques formation and oxidative stress are two key events in the pathology of the Alzheimer disease (AD), in which metal cations have been shown to play an important role. In particular, the interaction of the redox active Cu{sup 2+} metal cation with Aβ has been found to interfere in amyloid aggregation and to lead to reactive oxygen species (ROS). A detailed knowledge of the electronic and molecular structure of Cu{sup 2+}-Aβ complexes is thus important to get a better understanding of the role of these complexes in the development and progression of the AD disease. The computational treatment of these systems requires a combination of several available computational methodologies, because two fundamental aspects have to be addressed: the metal coordination sphere and the conformation adopted by the peptide upon copper binding. In this paper we review the main computational strategies used to deal with the Cu{sup 2+}-Aβ coordination and build plausible Cu{sup 2+}-Aβ models that will afterwards allow determining physicochemical properties of interest, such as their redox potential.
NEUROCOMPUTATIONAL MODEL OF EEG COMPLEXITY DURING MIND WANDERING
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Antonio José Ibáñez-Molina
2016-03-01
Full Text Available Mind wandering (MW can be understood as a transient state in which attention drifts from an external task to internal self-generated thoughts. MW has been associated with the activation of the Default Mode Network (DMN. In addition, it has been shown that the activity of the DMN is anti-correlated with activation in brain networks related to the processing of external events (e.g., Salience network, SN. In this study, we present a mean field model based on weakly coupled Kuramoto oscillators. We simulated the oscillatory activity of the entire brain and explored the role of the interaction between the nodes from the DMN and SN in MW states. External stimulation was added to the network model in two opposite conditions. Stimuli could be presented when oscillators in the SN showed more internal coherence (synchrony than in the DMN, or, on the contrary, when the coherence in the SN was lower than in the DMN. The resulting phases of the oscillators were analyzed and used to simulate EEG signals. Our results showed that the structural complexity from both simulated and real data was higher when the model was stimulated during periods in which DMN was more coherent than the SN. Overall, our results provided a plausible mechanistic explanation to MW as a state in which high coherence in the DMN partially suppresses the capacity of the system to process external stimuli.
Time-dependent models of dense PDRs with complex molecules
Morata, O
2008-01-01
We present a study of the chemistry of a dense photon-dominated region (PDR) using a time-dependent chemical model. Our major interest is to study the spatial distribution of complex molecules such as hydrocarbons and cyanopolyynes in the cool dense material bordering regions where star formation has taken place. Our standard model uses a homogeneous cloud of density 2x10e4 cm-3 and temperature T=40 K, which is irradiated by a far-ultraviolet radiation field of intermediate intensity, given by X=100. We find that over a range of times unsaturated hydrocarbons (e.g., C2H, C4H, C3H2) have relatively high fractional abundances in the more external layers of the PDR, whereas their abundances in the innermost layers are several orders of magnitudes lower. On the other hand, molecules that are typical of late-time chemistry are usually more abundant in the inner parts of the PDR. We also present results for models with different density, temperature, intensity of the radiation field and initial fractional abundance...
Evolution of complexity in a resource-based model
Fernández, Lenin; Campos, Paulo R. A.
2017-02-01
Through a resource-based modelling the evolution of organismal complexity is studied. In the model, the cells are characterized by their metabolic rates which, together with the availability of resource, determine the rate at which they divide. The population is structured in groups. Groups are also autonomous entities regarding reproduction and propagation, and so they correspond to a higher biological organization level. The model assumes reproductive altruism as there exists a fitness transfer from the cell level to the group level. Reproductive altruism comes about by inflicting a higher energetic cost to cells belonging to larger groups. On the other hand, larger groups are less prone to extinction. The strength of this benefit arising from group augmentation can be tuned by the synergistic parameter γ. Through extensive computer simulations we make a thorough exploration of the parameter space to find out the domain in which the formation of larger groups is allowed. We show that formation of small groups can be obtained for a low level of synergy. Larger group sizes can only be attained as synergistic interactions surpass a given level of strength. Although the total resource influx rate plays a key role in determining the number of groups coexisting at the equilibrium, its function on driving group size is minor. On the other hand, how the resource is seized by the groups matters.
A model for navigational errors in complex environmental fields.
Postlethwaite, Claire M; Walker, Michael M
2014-12-21
Many animals are believed to navigate using environmental signals such as light, sound, odours and magnetic fields. However, animals rarely navigate directly to their target location, but instead make a series of navigational errors which are corrected during transit. In previous work, we introduced a model showing that differences between an animal׳s 'cognitive map' of the environmental signals used for navigation and the true nature of these signals caused a systematic pattern in orientation errors when navigation begins. The model successfully predicted the pattern of errors seen in previously collected data from homing pigeons, but underestimated the amplitude of the errors. In this paper, we extend our previous model to include more complicated distortions of the contour lines of the environmental signals. Specifically, we consider the occurrence of critical points in the fields describing the signals. We consider three scenarios and compute orientation errors as parameters are varied in each case. We show that the occurrence of critical points can be associated with large variations in initial orientation errors over a small geographic area. We discuss the implications that these results have on predicting how animals will behave when encountering complex distortions in any environmental signals they use to navigate.
Integrated modeling tool for performance engineering of complex computer systems
Wright, Gary; Ball, Duane; Hoyt, Susan; Steele, Oscar
1989-01-01
This report summarizes Advanced System Technologies' accomplishments on the Phase 2 SBIR contract NAS7-995. The technical objectives of the report are: (1) to develop an evaluation version of a graphical, integrated modeling language according to the specification resulting from the Phase 2 research; and (2) to determine the degree to which the language meets its objectives by evaluating ease of use, utility of two sets of performance predictions, and the power of the language constructs. The technical approach followed to meet these objectives was to design, develop, and test an evaluation prototype of a graphical, performance prediction tool. The utility of the prototype was then evaluated by applying it to a variety of test cases found in the literature and in AST case histories. Numerous models were constructed and successfully tested. The major conclusion of this Phase 2 SBIR research and development effort is that complex, real-time computer systems can be specified in a non-procedural manner using combinations of icons, windows, menus, and dialogs. Such a specification technique provides an interface that system designers and architects find natural and easy to use. In addition, PEDESTAL's multiview approach provides system engineers with the capability to perform the trade-offs necessary to produce a design that meets timing performance requirements. Sample system designs analyzed during the development effort showed that models could be constructed in a fraction of the time required by non-visual system design capture tools.
Atmospheric dispersion modelling over complex terrain at small scale
Nosek, S.; Janour, Z.; Kukacka, L.; Jurcakova, K.; Kellnerova, R.; Gulikova, E.
2014-03-01
Previous study concerned of qualitative modelling neutrally stratified flow over open-cut coal mine and important surrounding topography at meso-scale (1:9000) revealed an important area for quantitative modelling of atmospheric dispersion at small-scale (1:3300). The selected area includes a necessary part of the coal mine topography with respect to its future expansion and surrounding populated areas. At this small-scale simultaneous measurement of velocity components and concentrations in specified points of vertical and horizontal planes were performed by two-dimensional Laser Doppler Anemometry (LDA) and Fast-Response Flame Ionization Detector (FFID), respectively. The impact of the complex terrain on passive pollutant dispersion with respect to the prevailing wind direction was observed and the prediction of the air quality at populated areas is discussed. The measured data will be used for comparison with another model taking into account the future coal mine transformation. Thus, the impact of coal mine transformation on pollutant dispersion can be observed.
Neurocomputational Model of EEG Complexity during Mind Wandering.
Ibáñez-Molina, Antonio J; Iglesias-Parro, Sergio
2016-01-01
Mind wandering (MW) can be understood as a transient state in which attention drifts from an external task to internal self-generated thoughts. MW has been associated with the activation of the Default Mode Network (DMN). In addition, it has been shown that the activity of the DMN is anti-correlated with activation in brain networks related to the processing of external events (e.g., Salience network, SN). In this study, we present a mean field model based on weakly coupled Kuramoto oscillators. We simulated the oscillatory activity of the entire brain and explored the role of the interaction between the nodes from the DMN and SN in MW states. External stimulation was added to the network model in two opposite conditions. Stimuli could be presented when oscillators in the SN showed more internal coherence (synchrony) than in the DMN, or, on the contrary, when the coherence in the SN was lower than in the DMN. The resulting phases of the oscillators were analyzed and used to simulate EEG signals. Our results showed that the structural complexity from both simulated and real data was higher when the model was stimulated during periods in which DMN was more coherent than the SN. Overall, our results provided a plausible mechanistic explanation to MW as a state in which high coherence in the DMN partially suppresses the capacity of the system to process external stimuli.
Beyond pure parasystole: promises and problems in modeling complex arrhythmias.
Courtemanche, M; Glass, L; Rosengarten, M D; Goldberger, A L
1989-08-01
The dynamics of pure parasystole, a cardiac arrhythmia in which two competing pacemakers fire independently, have recently been fully characterized. This model is now extended in an attempt to account for the more complex dynamics occurring with modulated parasystole, in which there exists nonlinear interaction between the sinus node and the ectopic ventricular focus. Theoretical analysis of modulated parasystole reveals three types of dynamics: entrainment, quasiperiodicity, and chaos. Rhythms associated with quasiperiodicity obey a set of rules derived from pure parasystole. This model is applied to the interpretation of continuous electrocardiographic data sets from three patients with complicated patterns of ventricular ectopic activity. We describe several new statistical properties of these records, related to the number of intervening sinus beats between ectopic events, that are essential in characterizing the dynamics and testing mathematical models. Detailed comparison between data and theory in these cases show substantial areas of agreement as well as potentially important discrepancies. These findings have implications for understanding the dynamics of the heartbeat in normal and pathological conditions.
Deposition parameterizations for the Industrial Source Complex (ISC3) model
Energy Technology Data Exchange (ETDEWEB)
Wesely, Marvin L. [Argonne National Lab. (ANL), Argonne, IL (United States); Doskey, Paul V. [Argonne National Lab. (ANL), Argonne, IL (United States); Shannon, J. D. [Argonne National Lab. (ANL), Argonne, IL (United States)
2002-06-01
Improved algorithms have been developed to simulate the dry and wet deposition of hazardous air pollutants (HAPs) with the Industrial Source Complex version 3 (ISC3) model system. The dry deposition velocities (concentrations divided by downward flux at a specified height) of the gaseous HAPs are modeled with algorithms adapted from existing dry deposition modules. The dry deposition velocities are described in a conventional resistance scheme, for which micrometeorological formulas are applied to describe the aerodynamic resistances above the surface. Pathways to uptake at the ground and in vegetative canopies are depicted with several resistances that are affected by variations in air temperature, humidity, solar irradiance, and soil moisture. The role of soil moisture variations in affecting the uptake of gases through vegetative plant leaf stomata is assessed with the relative available soil moisture, which is estimated with a rudimentary budget of soil moisture content. Some of the procedures and equations are simplified to be commensurate with the type and extent of information on atmospheric and surface conditions available to the ISC3 model system user. For example, standardized land use types and seasonal categories provide sets of resistances to uptake by various components of the surface. To describe the dry deposition of the large number of gaseous organic HAPS, a new technique based on laboratory study results and theoretical considerations has been developed providing a means of evaluating the role of lipid solubility in uptake by the waxy outer cuticle of vegetative plant leaves.
Critical noise of majority-vote model on complex networks
Chen, Hanshuang; He, Gang; Zhang, Haifeng; Hou, Zhonghuai
2016-01-01
The majority-vote model with noise is one of the simplest nonequilibrium statistical model that has been extensively studied in the context of complex networks. However, the relationship between the critical noise where the order-disorder phase transition takes place and the topology of the underlying networks is still lacking. In the paper, we use the heterogeneous mean-field theory to derive the rate equation for governing the model's dynamics that can analytically determine the critical noise $f_c$ in the limit of infinite network size $N\\rightarrow \\infty$. The result shows that $f_c$ depends on the ratio of ${\\left\\langle k \\right\\rangle }$ to ${\\left\\langle k^{3/2} \\right\\rangle }$, where ${\\left\\langle k \\right\\rangle }$ and ${\\left\\langle k^{3/2} \\right\\rangle }$ are the average degree and the $3/2$ order moment of degree distribution, respectively. Furthermore, we consider the finite size effect where the stochastic fluctuation should be involved. To the end, we derive the Langevin equation and obtai...
CP violation in the Standard Model with a complex singlet
Darvishi, Neda
2016-01-01
CP violation of the Standard Model (SM) is insufficient to explain the baryon asymmetry in the Universe and therefore an additional source of CP violation is needed. Here we consider the extension of the SM by a neutral complex singlet and discuss the physical conditions for a spontaneous CP violation in such model. In the model there are three neutral Higgs particles. Assuming the lightest one to be the 125 GeV Higgs boson found at LHC we calculate masses of the additional Higgs scalars and perform a numerical study of the allowed region of parameters. The scenario according to which the SM-like Higgs particle comes mostly from the SM-like SU(2) doublet, with a small modification coming from the singlet, is in agreement with the newest $R_{\\gamma \\gamma}$ and precise EW (parameters S, T) data. We have found that the Jarlskog invariant, measuring the strength of the CP violation, can be enhanced as compared to the one in the SM, at the same time there is no corresponding enhancements expected for the Electric...
Toxicological risk assessment of complex mixtures through the Wtox model
Directory of Open Access Journals (Sweden)
William Gerson Matias
2015-01-01
Full Text Available Mathematical models are important tools for environmental management and risk assessment. Predictions about the toxicity of chemical mixtures must be enhanced due to the complexity of eects that can be caused to the living species. In this work, the environmental risk was accessed addressing the need to study the relationship between the organism and xenobiotics. Therefore, ve toxicological endpoints were applied through the WTox Model, and with this methodology we obtained the risk classication of potentially toxic substances. Acute and chronic toxicity, citotoxicity and genotoxicity were observed in the organisms Daphnia magna, Vibrio scheri and Oreochromis niloticus. A case study was conducted with solid wastes from textile, metal-mechanic and pulp and paper industries. The results have shown that several industrial wastes induced mortality, reproductive eects, micronucleus formation and increases in the rate of lipid peroxidation and DNA methylation of the organisms tested. These results, analyzed together through the WTox Model, allowed the classication of the environmental risk of industrial wastes. The evaluation showed that the toxicological environmental risk of the samples analyzed can be classied as signicant or critical.
Random field Ising model and community structure in complex networks
Son, S.-W.; Jeong, H.; Noh, J. D.
2006-04-01
We propose a method to determine the community structure of a complex network. In this method the ground state problem of a ferromagnetic random field Ising model is considered on the network with the magnetic field Bs = +∞, Bt = -∞, and Bi≠s,t=0 for a node pair s and t. The ground state problem is equivalent to the so-called maximum flow problem, which can be solved exactly numerically with the help of a combinatorial optimization algorithm. The community structure is then identified from the ground state Ising spin domains for all pairs of s and t. Our method provides a criterion for the existence of the community structure, and is applicable equally well to unweighted and weighted networks. We demonstrate the performance of the method by applying it to the Barabási-Albert network, Zachary karate club network, the scientific collaboration network, and the stock price correlation network. (Ising, Potts, etc.)
Numerical simulations and mathematical models of flows in complex geometries
DEFF Research Database (Denmark)
Hernandez Garcia, Anier
, anomalous transport features of Lagrangian trajectories are investigated. Several statistical properties of both Lagrangian and Eulerian velocities are also examined. Based on these measurements, an eective model is considered to assess the role of the pressure gradient on the transport of Lagrangian......The research work of the present thesis was mainly aimed at exploiting one of the strengths of the Lattice Boltzmann methods, namely, the ability to handle complicated geometries to accurately simulate flows in complex geometries. In this thesis, we perform a very detailed theoretical analysis...... of the finite volume unstructured lattice Boltzmann method (ULBM) in three dimensions, considering the Bhatnagar-Gross-Krook (BGK) relaxation time approximation for the collision operator, one of the more commonly used by the community. Regarding this scheme, two time integration methods are considered...
The inherent complexity in nonlinear business cycle model in resonance
Energy Technology Data Exchange (ETDEWEB)
Ma Junhai [School of Management, Tianjin University, Tianjin 300072 (China) and Tianjin University of Finance and Economics, Tianjin 300222 (China)], E-mail: lzqsly@126.com; Sun Tao; Liu Lixia [School of Management, Tianjin University, Tianjin 300072 (China)
2008-08-15
Based on Abraham C.-L. Chian's research, we applied nonlinear dynamic system theory to study the first-order and second-order approximate solutions to one category of the nonlinear business cycle model in resonance condition. We have also analyzed the relation between amplitude and phase of second-order approximate solutions as well as the relation between outer excitements' amplitude, frequency approximate solutions, and system bifurcation parameters. Then we studied the system quasi-periodical solutions, annulus periodical solutions and the path leading to system bifurcation and chaotic state with different parameter combinations. Finally, we conducted some numerical simulations for various complicated circumstances. Therefore this research will lay solid foundation for detecting the complexity of business cycles and systems in the future.
Social Complexity: can it be analyzed and modelled?
Kaski, Kimmo
2010-01-01
Over the past decade network theory has turned out to be a powerful methodology to investigate complex systems of various sorts. Through data analysis, modeling, and simulation quite an unparalleled insight into their structure, function, and response can be obtained. In human societies individuals are linked through social interactions, which today are increasingly mediated electronically by modern Information Communication Technology thus leaving "footprints" of human behaviour as digital records. For these datasets the network theory approach is a natural one as we have demonstrated by analysing the dataset of multi-million user mobile phone communication-logs. This social network turned out to be modular in structure showing communities where individuals are connected with stronger ties and between communities with weaker ties. Also the network topology and the weighted links for pairs of individuals turned out to be related.These empirical findings inspired us to take the next step in network theory, by ...
Nie, Kun; Zhang, Xue-Zhu; Zhao, Lan; Jia, Yu-Jie; Han, Jing-Xian
2014-08-01
To reveal the transmembrane signal pathway participating in regulating neuron functions of treating Alzheimer's disease (AD) by acupuncture. SAMP8 mice was used for AD animal model. The effect of acupuncture method for qi benefiting, blood regulating, health supporting, and root strengthening on the amount and varieties of transmembrane signal proteins from hippocampal lipid rafts in SAMP8 mice was detected using HPLC MS/MS proteomics method. Compared with the control group, acupuncture increased 39 transmembrane signal proteins from hippocampal lipid rafts in SAMP8 mice, of them, 14 belonged to ionophorous protein, 8 to G protein, 8 to transmembrane signal receptor, and 9 to kinase protein. Totally 3 main cell signal pathways were involved, including G-protein-coupled receptors signal, enzyme linked receptor signal, and ion-channel mediated signal. Compared with the sham-acupuncture group, acupuncture resulted in significant increase of kinase signal protein amount. From the aspect of functions, they were dominant in regulating synapse functions relevant to cytoskeleton and secreting neurotransmitters. The cell biological mechanism for treating AD by acupuncture might be achieved by improving synapse functions and promoting the secretion of neurotransmitters through transmembrane signal transduction, thus improving cognitive function of AD patients.
Dynamical complexity in the perception-based network formation model
Jo, Hang-Hyun; Moon, Eunyoung
2016-12-01
Many link formation mechanisms for the evolution of social networks have been successful to reproduce various empirical findings in social networks. However, they have largely ignored the fact that individuals make decisions on whether to create links to other individuals based on cost and benefit of linking, and the fact that individuals may use perception of the network in their decision making. In this paper, we study the evolution of social networks in terms of perception-based strategic link formation. Here each individual has her own perception of the actual network, and uses it to decide whether to create a link to another individual. An individual with the least perception accuracy can benefit from updating her perception using that of the most accurate individual via a new link. This benefit is compared to the cost of linking in decision making. Once a new link is created, it affects the accuracies of other individuals' perceptions, leading to a further evolution of the actual network. As for initial actual networks, we consider both homogeneous and heterogeneous cases. The homogeneous initial actual network is modeled by Erdős-Rényi (ER) random networks, while we take a star network for the heterogeneous case. In any cases, individual perceptions of the actual network are modeled by ER random networks with controllable linking probability. Then the stable link density of the actual network is found to show discontinuous transitions or jumps according to the cost of linking. As the number of jumps is the consequence of the dynamical complexity, we discuss the effect of initial conditions on the number of jumps to find that the dynamical complexity strongly depends on how much individuals initially overestimate or underestimate the link density of the actual network. For the heterogeneous case, the role of the highly connected individual as an information spreader is also discussed.
Kajiwara, Tsuyoshi; Sasaki, Toru; Takeuchi, Yasuhiro
2015-02-01
We present a constructive method for Lyapunov functions for ordinary differential equation models of infectious diseases in vivo. We consider models derived from the Nowak-Bangham models. We construct Lyapunov functions for complex models using those of simpler models. Especially, we construct Lyapunov functions for models with an immune variable from those for models without an immune variable, a Lyapunov functions of a model with absorption effect from that for a model without absorption effect. We make the construction clear for Lyapunov functions proposed previously, and present new results with our method.
African Journals Online (AJOL)
CLEMENT O BEWAJI
Schiff bases and their complex compounds have been studied for their .... establishing coordination of the N–(2 – hydroxybenzyl) - L - α - valine Schiff base ..... (1967); “Spectrophotometric Identification of Organic Compounds”, Willey, New.
Directory of Open Access Journals (Sweden)
Bryan D Moyer
Full Text Available BACKGROUND: Using fungiform (FG and circumvallate (CV taste buds isolated by laser capture microdissection and analyzed using gene arrays, we previously constructed a comprehensive database of gene expression in primates, which revealed over 2,300 taste bud-associated genes. Bioinformatics analyses identified hundreds of genes predicted to encode multi-transmembrane domain proteins with no previous association with taste function. A first step in elucidating the roles these gene products play in gustation is to identify the specific taste cell types in which they are expressed. METHODOLOGY/PRINCIPAL FINDINGS: Using double label in situ hybridization analyses, we identified seven new genes expressed in specific taste cell types, including sweet, bitter, and umami cells (TRPM5-positive, sour cells (PKD2L1-positive, as well as other taste cell populations. Transmembrane protein 44 (TMEM44, a protein with seven predicted transmembrane domains with no homology to GPCRs, is expressed in a TRPM5-negative and PKD2L1-negative population that is enriched in the bottom portion of taste buds and may represent developmentally immature taste cells. Calcium homeostasis modulator 1 (CALHM1, a component of a novel calcium channel, along with family members CALHM2 and CALHM3; multiple C2 domains; transmembrane 1 (MCTP1, a calcium-binding transmembrane protein; and anoctamin 7 (ANO7, a member of the recently identified calcium-gated chloride channel family, are all expressed in TRPM5 cells. These proteins may modulate and effect calcium signalling stemming from sweet, bitter, and umami receptor activation. Synaptic vesicle glycoprotein 2B (SV2B, a regulator of synaptic vesicle exocytosis, is expressed in PKD2L1 cells, suggesting that this taste cell population transmits tastant information to gustatory afferent nerve fibers via exocytic neurotransmitter release. CONCLUSIONS/SIGNIFICANCE: Identification of genes encoding multi-transmembrane domain proteins
Multilevel complexity of calcium signaling:Modeling angiogenesis
Institute of Scientific and Technical Information of China (English)
Luca; Munaron; Marco; Scianna
2012-01-01
Intracellular calcium signaling is a universal,evolutionary conserved and versatile regulator of cell biochemistry.The complexity of calcium signaling and related cell machinery can be investigated by the use of experimental strategies,as well as by computational approaches.Vascular endothelium is a fascinating model to study the specific properties and roles of calcium signals at multiple biological levels.During the past 20 years,live cell imaging,patch clamp and other techniques have allowed us to detect and interfere with calcium signaling in endothelial cells(ECs),providing a huge amount of information on the regulation of vascularization(angiogenesis) in normal and tumoral tissues.These data range from the spatiotemporal dynamics of calcium within different cell microcompartments to those in entire multicellular and organized EC networks.Beside experimental strategies,in silico endothelial models,specifically designed for simulating calcium signaling,are contributing to our knowledge of vascular physiol-ogy and pathology.They help to investigate and predict the quantitative features of proangiogenic events moving through subcellular,cellular and supracellular levels.This review focuses on some recent developments of computational approaches for proangiogenic endothelial calcium signaling.In particular,we discuss the creation of hybrid simulation environments,which combine and integrate discrete Cellular Potts Models.They are able to capture the phenomenological mechanisms of cell morphological reorganization,migration,and intercellular adhesion,with single-cell spatiotemporal models,based on reaction-diffusion equations that describe the agonist-induced intracellular calcium events.
Rumor spreading model with noise interference in complex social networks
Zhu, Liang; Wang, Youguo
2017-03-01
In this paper, a modified susceptible-infected-removed (SIR) model has been proposed to explore rumor diffusion on complex social networks. We take variation of connectivity into consideration and assume the variation as noise. On the basis of related literature on virus networks, the noise is described as standard Brownian motion while stochastic differential equations (SDE) have been derived to characterize dynamics of rumor diffusion both on homogeneous networks and heterogeneous networks. Then, theoretical analysis on homogeneous networks has been demonstrated to investigate the solution of SDE model and the steady state of rumor diffusion. Simulations both on Barabási-Albert (BA) network and Watts-Strogatz (WS) network display that the addition of noise accelerates rumor diffusion and expands diffusion size, meanwhile, the spreading speed on BA network is much faster than on WS network under the same noise intensity. In addition, there exists a rumor diffusion threshold in statistical average meaning on homogeneous network which is absent on heterogeneous network. Finally, we find a positive correlation between peak value of infected individuals and noise intensity while a negative correlation between rumor lifecycle and noise intensity overall.
Permutation Complexity and Coupling Measures in Hidden Markov Models
Directory of Open Access Journals (Sweden)
Taichi Haruna
2013-09-01
Full Text Available Recently, the duality between values (words and orderings (permutations has been proposed by the authors as a basis to discuss the relationship between information theoretic measures for finite-alphabet stationary stochastic processes and their permutatio nanalogues. It has been used to give a simple proof of the equality between the entropy rate and the permutation entropy rate for any finite-alphabet stationary stochastic process and to show some results on the excess entropy and the transfer entropy for finite-alphabet stationary ergodic Markov processes. In this paper, we extend our previous results to hidden Markov models and show the equalities between various information theoretic complexity and coupling measures and their permutation analogues. In particular, we show the following two results within the realm of hidden Markov models with ergodic internal processes: the two permutation analogues of the transfer entropy, the symbolic transfer entropy and the transfer entropy on rank vectors, are both equivalent to the transfer entropy if they are considered as the rates, and the directed information theory can be captured by the permutation entropy approach.
On the Modeling of Musical Solos as Complex Networks
Ferretti, Stefano
2016-01-01
Notes in a musical piece are building blocks employed in non-random ways to create melodies. It is the "interaction" among a limited amount of notes that allows constructing the variety of musical compositions that have been written in centuries and within different cultures. Networks are a modeling tool that is commonly employed to represent a set of entities interacting in some way. Thus, notes composing a melody can be seen as nodes of a network that are connected whenever these are played in sequence. The outcome of such a process results in a directed graph. By using complex network theory, some main metrics of musical graphs can be measured, which characterize the related musical pieces. In this paper, we define a framework to represent melodies as networks. Then, we provide an analysis on a set of guitar solos performed by main musicians. Results of this study indicate that the presented model can have an impact on audio and multimedia applications such as music classification, identification, e-learni...
Analysis of a Mouse Skin Model of Tuberous Sclerosis Complex
Guo, Yanan; Dreier, John R.; Cao, Juxiang; Du, Heng; Granter, Scott R.; Kwiatkowski, David J.
2016-01-01
Tuberous Sclerosis Complex (TSC) is an autosomal dominant tumor suppressor gene syndrome in which patients develop several types of tumors, including facial angiofibroma, subungual fibroma, Shagreen patch, angiomyolipomas, and lymphangioleiomyomatosis. It is due to inactivating mutations in TSC1 or TSC2. We sought to generate a mouse model of one or more of these tumor types by targeting deletion of the Tsc1 gene to fibroblasts using the Fsp-Cre allele. Mutant, Tsc1ccFsp-Cre+ mice survived a median of nearly a year, and developed tumors in multiple sites but did not develop angiomyolipoma or lymphangioleiomyomatosis. They did develop a prominent skin phenotype with marked thickening of the dermis with accumulation of mast cells, that was minimally responsive to systemic rapamycin therapy, and was quite different from the pathology seen in human TSC skin lesions. Recombination and loss of Tsc1 was demonstrated in skin fibroblasts in vivo and in cultured skin fibroblasts. Loss of Tsc1 in fibroblasts in mice does not lead to a model of angiomyolipoma or lymphangioleiomyomatosis. PMID:27907099
Reliable modeling of the electronic spectra of realistic uranium complexes
Tecmer, Paweł; Govind, Niranjan; Kowalski, Karol; de Jong, Wibe A.; Visscher, Lucas
2013-07-01
We present an EOMCCSD (equation of motion coupled cluster with singles and doubles) study of excited states of the small [UO2]2+ and [UO2]+ model systems as well as the larger UVIO2(saldien) complex. In addition, the triples contribution within the EOMCCSDT and CR-EOMCCSD(T) (completely renormalized EOMCCSD with non-iterative triples) approaches for the [UO2]2+ and [UO2]+ systems as well as the active-space variant of the CR-EOMCCSD(T) method—CR-EOMCCSd(t)—for the UVIO2(saldien) molecule are investigated. The coupled cluster data were employed as benchmark to choose the "best" appropriate exchange-correlation functional for subsequent time-dependent density functional (TD-DFT) studies on the transition energies for closed-shell species. Furthermore, the influence of the saldien ligands on the electronic structure and excitation energies of the [UO2]+ molecule is discussed. The electronic excitations as well as their oscillator dipole strengths modeled with TD-DFT approach using the CAM-B3LYP exchange-correlation functional for the [UVO2(saldien)]- with explicit inclusion of two dimethyl sulfoxide molecules are in good agreement with the experimental data of Takao et al. [Inorg. Chem. 49, 2349 (2010), 10.1021/ic902225f].
Electromagnetic modelling of Ground Penetrating Radar responses to complex targets
Pajewski, Lara; Giannopoulos, Antonis
2014-05-01
This work deals with the electromagnetic modelling of composite structures for Ground Penetrating Radar (GPR) applications. It was developed within the Short-Term Scientific Mission ECOST-STSM-TU1208-211013-035660, funded by COST Action TU1208 "Civil Engineering Applications of Ground Penetrating Radar". The Authors define a set of test concrete structures, hereinafter called cells. The size of each cell is 60 x 100 x 18 cm and the content varies with growing complexity, from a simple cell with few rebars of different diameters embedded in concrete at increasing depths, to a final cell with a quite complicated pattern, including a layer of tendons between two overlying meshes of rebars. Other cells, of intermediate complexity, contain pvc ducts (air filled or hosting rebars), steel objects commonly used in civil engineering (as a pipe, an angle bar, a box section and an u-channel), as well as void and honeycombing defects. One of the cells has a steel mesh embedded in it, overlying two rebars placed diagonally across the comers of the structure. Two cells include a couple of rebars bent into a right angle and placed on top of each other, with a square/round circle lying at the base of the concrete slab. Inspiration for some of these cells is taken from the very interesting experimental work presented in Ref. [1]. For each cell, a subset of models with growing complexity is defined, starting from a simple representation of the cell and ending with a more realistic one. In particular, the model's complexity increases from the geometrical point of view, as well as in terms of how the constitutive parameters of involved media and GPR antennas are described. Some cells can be simulated in both two and three dimensions; the concrete slab can be approximated as a finite-thickness layer having infinite extension on the transverse plane, thus neglecting how edges affect radargrams, or else its finite size can be fully taken into account. The permittivity of concrete can be
Italian Case Studies Modelling Complex Earthquake Sources In PSHA
Gee, Robin; Peruzza, Laura; Pagani, Marco
2017-04-01
This study presents two examples of modelling complex seismic sources in Italy, done in the framework of regional probabilistic seismic hazard assessment (PSHA). The first case study is for an area centred around Collalto Stoccaggio, a natural gas storage facility in Northern Italy, located within a system of potentially seismogenic thrust faults in the Venetian Plain. The storage exploits a depleted natural gas reservoir located within an actively growing anticline, which is likely driven by the Montello Fault, the underlying blind thrust. This fault has been well identified by microseismic activity (Mseismological information. We explore the sensitivity of the hazard results to various parameters affected by epistemic uncertainty, such as ground motions prediction equations with different rupture-to-site distance metrics, fault geometry, and maximum magnitude. The second case is an innovative study, where we perform aftershock probabilistic seismic hazard assessment (APSHA) in Central Italy, following the Amatrice M6.1 earthquake of August 24th, 2016 (298 casualties) and the subsequent earthquakes of Oct 26th and 30th (M6.1 and M6.6 respectively, no deaths). The aftershock hazard is modelled using a fault source with complex geometry, based on literature data and field evidence associated with the August mainshock. Earthquake activity rates during the very first weeks after the deadly earthquake were used to calibrated an Omori-Utsu decay curve, and the magnitude distribution of aftershocks is assumed to follow a Gutenberg-Richter distribution. We apply uniform and non-uniform spatial distribution of the seismicity across the fault source, by modulating the rates as a decreasing function of distance from the mainshock. The hazard results are computed for short-exposure periods (1 month, before the occurrences of October earthquakes) and compared to the background hazard given by law (MPS04), and to observations at some reference sites. We also show the results of
Robustness and Optimization of Complex Networks: Reconstructability, Algorithms and Modeling
Liu, D.
2013-01-01
The infrastructure networks, including the Internet, telecommunication networks, electrical power grids, transportation networks (road, railway, waterway, and airway networks), gas networks and water networks, are becoming more and more complex. The complex infrastructure networks are crucial to our
Investigating Patterns for the Process-Oriented Modelling and Simulation of Space in Complex Systems
Sampson, Adam T.; Welch, Peter H.; Warren, Douglas N.; Andrews, Paul S.; Bjørndalen, John Markus; Stepney, Susan; Timmis, Jon
2008-01-01
Complex systems modelling and simulation is becoming increasingly important to numerous disciplines. The CoSMoS project aims to produce a unified infrastructure for modelling and simulating all sorts of complex systems, making use of design patterns and the process-oriented programming model. We provide a description of CoSMoS and present a case study into the modelling of space in complex systems. We describe how two models - absolute geometric space and relational network space - can be cap...
Artificial Diels–Alderase based on the transmembrane protein FhuA
Beckerle, Klaus; Arlt, Marcus; Himiyama, Tomoki; Polen, Tino; Onoda, Akira; Schwaneberg, Ulrich; Hayashi, Takashi
2016-01-01
Summary Copper(I) and copper(II) complexes were covalently linked to an engineered variant of the transmembrane protein Ferric hydroxamate uptake protein component A (FhuA ΔCVFtev). Copper(I) was incorporated using an N-heterocyclic carbene (NHC) ligand equipped with a maleimide group on the side arm at the imidazole nitrogen. Copper(II) was attached by coordination to a terpyridyl ligand. The spacer length was varied in the back of the ligand framework. These biohybrid catalysts were shown to be active in the Diels–Alder reaction of a chalcone derivative with cyclopentadiene to preferentially give the endo product. PMID:27559380
Artificial Diels-Alderase based on the transmembrane protein FhuA.
Osseili, Hassan; Sauer, Daniel F; Beckerle, Klaus; Arlt, Marcus; Himiyama, Tomoki; Polen, Tino; Onoda, Akira; Schwaneberg, Ulrich; Hayashi, Takashi; Okuda, Jun
2016-01-01
Copper(I) and copper(II) complexes were covalently linked to an engineered variant of the transmembrane protein Ferric hydroxamate uptake protein component A (FhuA ΔCVF(tev)). Copper(I) was incorporated using an N-heterocyclic carbene (NHC) ligand equipped with a maleimide group on the side arm at the imidazole nitrogen. Copper(II) was attached by coordination to a terpyridyl ligand. The spacer length was varied in the back of the ligand framework. These biohybrid catalysts were shown to be active in the Diels-Alder reaction of a chalcone derivative with cyclopentadiene to preferentially give the endo product.
DEFF Research Database (Denmark)
Gurtovenko, Andrey A; Vattulainen, Ilpo
2009-01-01
Using atomic-scale molecular dynamics simulations, we consider the intrinsic cell membrane potential that is found to originate from a subtle interplay between lipid transmembrane asymmetry and the asymmetric distribution of monovalent salt ions on the two sides of the cell membrane. It turns out......Cl saline solution and the PE leaflet is exposed to KCl, the outcome is that the effects of asymmetric lipid and salt ion distributions essentially cancel one another almost completely. Overall, our study highlights the complex nature of the intrinsic potential of cell membranes under physiological...
Artificial Diels–Alderase based on the transmembrane protein FhuA
Directory of Open Access Journals (Sweden)
Hassan Osseili
2016-06-01
Full Text Available Copper(I and copper(II complexes were covalently linked to an engineered variant of the transmembrane protein Ferric hydroxamate uptake protein component A (FhuA ΔCVFtev. Copper(I was incorporated using an N-heterocyclic carbene (NHC ligand equipped with a maleimide group on the side arm at the imidazole nitrogen. Copper(II was attached by coordination to a terpyridyl ligand. The spacer length was varied in the back of the ligand framework. These biohybrid catalysts were shown to be active in the Diels–Alder reaction of a chalcone derivative with cyclopentadiene to preferentially give the endo product.
Atmospheric Modelling for Air Quality Study over the complex Himalayas
Surapipith, Vanisa; Panday, Arnico; Mukherji, Aditi; Banmali Pradhan, Bidya; Blumer, Sandro
2014-05-01
An Atmospheric Modelling System has been set up at International Centre for Integrated Mountain Development (ICIMOD) for the assessment of Air Quality across the Himalaya mountain ranges. The Weather Research and Forecasting (WRF) model version 3.5 has been implemented over the regional domain, stretching across 4995 x 4455 km2 centred at Ichhyakamana , the ICIMOD newly setting-up mountain-peak station (1860 m) in central Nepal, and covering terrains from sea-level to the Everest (8848 m). Simulation is carried out for the winter time period, i.e. December 2012 to February 2013, when there was an intensive field campaign SusKat, where at least 7 super stations were collecting meteorology and chemical parameters on various sites. The very complex terrain requires a high horizontal resolution (1 × 1 km2), which is achieved by nesting the domain of interest, e.g. Kathmandu Valley, into 3 coarser ones (27, 9, 3 km resolution). Model validation is performed against the field data as well as satellite data, and the challenge of capturing the necessary atmospheric processes is discussed, before moving forward with the fully coupled chemistry module (WRF-Chem), having local and regional emission databases as input. The effort aims at finding a better understanding of the atmospheric processes and air quality impact on the mountain population, as well as the impact of the long-range transport, particularly of Black Carbon aerosol deposition, to the radiative budget over the Himalayan glaciers. The higher rate of snowcap melting, and shrinkage of permafrost as noticed by glaciologists is a concern. Better prediction will supply crucial information to form the proper mitigation and adaptation strategies for saving people lives across the Himalayas in the changing climate.
Thermophysical Model of S-complex NEAs: 1627 Ivar
Crowell, Jenna; Howell, Ellen S.; Magri, Christopher; Fernandez, Yanga R.; Marshall, Sean E.; Warner, Brian D.; Vervack, Ronald J., Jr.
2016-01-01
We present an updated thermophysical model of 1627 Ivar, an Amor class near Earth asteroid (NEA) with a taxonomic type of Sqw [1]. Ivar's large size and close approach to Earth in 2013 (minimum distance 0.32 AU) provided an opportunity to observe the asteroid over many different viewing angles for an extended period of time, which we have utilized to generate a shape and thermophysical model of Ivar, allowing us to discuss the implications that these results have on the regolith of this asteroid. Using the software SHAPE [2,3], we updated the nonconvex shape model of Ivar, which was constructed by Kaasalainen et al. [4] using photometry. We incorporated 2013 radar data and CCD lightcurves using the Arecibo Observatory's 2380Mz radar and the 0.35m telescope at the Palmer Divide Station respectively, to create a shape model with higher surface detail. We found Ivar to be elongated with maximum extended lengths along principal axes of 12 x 5 x 6 km and a rotation rate of 4.795162 ± 5.4 * 10-6 hrs [5]. In addition to these radar data and lightcurves, we also observed Ivar in the near IR using the SpeX instrument at the NASA IRTF. These data cover a wide range of Ivar's rotational longitudes and viewing geometries. We have used SHERMAN [6,7] with input parameters such as the asteroid's IR emissivity, optical scattering law, and thermal inertia, in order to complete thermal computations based on our shape model and known spin state. Using this procedure, we find which reflective, thermal, and surface properties best reproduce the observed spectra. This allows us to characterize properties of the asteroid's regolith and study heterogeneity of the surface. We will compare these results with those of other S-complex asteroids to better understand this asteroid type and the uniqueness of 1627 Ivar.[1] DeMeo et al. 2009, Icarus 202, 160-180 [2] Magri, C. et al. 2011, Icarus 214, 210-227. [3] Crowell, J. et al. 2014, AAS/DPS 46 [4] Kaasalainen, M. et al. 2004, Icarus 167, 178
Agent-oriented modeling of the dynamics of complex biological processes I: single agent models
Jonker, C.M.; Treur, J.
2008-01-01
In the pair of papers of which this is Part I, the agent-oriented modeling perspective to cope with biological complexity is discussed. Three levels of dynamics are distinguished and related to each other: dynamics of externally observable agent behavior, dynamics of internal agent processes, and dy
The effects of model and data complexity on predictions from species distributions models
DEFF Research Database (Denmark)
García-Callejas, David; Bastos, Miguel
2016-01-01
study contradicts the widely held view that the complexity of species distributions models has significant effects in their predictive ability while findings support for previous observations that the properties of species distributions data and their relationship with the environment are strong...
Optimizing an emperical scoring function for transmembrane protein structure determination.
Energy Technology Data Exchange (ETDEWEB)
Young, Malin M.; Sale, Kenneth L.; Gray, Genetha Anne; Kolda, Tamara Gibson
2003-10-01
We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.
Optimizing an emperical scoring function for transmembrane protein structure determination.
Energy Technology Data Exchange (ETDEWEB)
Young, Malin M.; Sale, Kenneth L.; Gray, Genetha Anne; Kolda, Tamara Gibson
2003-10-01
We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.
Bonten, Luc T C; Groenenberg, Jan E; Meesenburg, Henning; de Vries, Wim
2011-10-01
Various dynamic soil chemistry models have been developed to gain insight into impacts of atmospheric deposition of sulphur, nitrogen and other elements on soil and soil solution chemistry. Sorption parameters for anions and cations are generally calibrated for each site, which hampers extrapolation in space and time. On the other hand, recently developed surface complexation models (SCMs) have been successful in predicting ion sorption for static systems using generic parameter sets. This study reports the inclusion of an assemblage of these SCMs in the dynamic soil chemistry model SMARTml and applies this model to a spruce forest site in Solling Germany. Parameters for SCMs were taken from generic datasets and not calibrated. Nevertheless, modelling results for major elements matched observations well. Further, trace metals were included in the model, also using the existing framework of SCMs. The model predicted sorption for most trace elements well.
A New Approach to Modelling Student Retention through an Application of Complexity Thinking
Forsman, Jonas; Linder, Cedric; Moll, Rachel; Fraser, Duncan; Andersson, Staffan
2014-01-01
Complexity thinking is relatively new to education research and has rarely been used to examine complex issues in physics and engineering education. Issues in higher education such as student retention have been approached from a multiplicity of perspectives and are recognized as complex. The complex system of student retention modelling in higher…
Using Models to Inform Policy: Insights from Modeling the Complexities of Global Polio Eradication
Thompson, Kimberly M.
Drawing on over 20 years of experience modeling risks in complex systems, this talk will challenge SBP participants to develop models that provide timely and useful answers to critical policy questions when decision makers need them. The talk will include reflections on the opportunities and challenges associated with developing integrated models for complex problems and communicating their results effectively. Dr. Thompson will focus the talk largely on collaborative modeling related to global polio eradication and the application of system dynamics tools. After successful global eradication of wild polioviruses, live polioviruses will still present risks that could potentially lead to paralytic polio cases. This talk will present the insights of efforts to use integrated dynamic, probabilistic risk, decision, and economic models to address critical policy questions related to managing global polio risks. Using a dynamic disease transmission model combined with probabilistic model inputs that characterize uncertainty for a stratified world to account for variability, we find that global health leaders will face some difficult choices, but that they can take actions that will manage the risks effectively. The talk will emphasize the need for true collaboration between modelers and subject matter experts, and the importance of working with decision makers as partners to ensure the development of useful models that actually get used.
Gong, Wei; Duan, Qingyun; Li, Jianduo; Wang, Chen; Di, Zhenhua; Ye, Aizhong; Miao, Chiyuan; Dai, Yongjiu
2016-03-01
Parameter specification is an important source of uncertainty in large, complex geophysical models. These models generally have multiple model outputs that require multiobjective optimization algorithms. Although such algorithms have long been available, they usually require a large number of model runs and are therefore computationally expensive for large, complex dynamic models. In this paper, a multiobjective adaptive surrogate modeling-based optimization (MO-ASMO) algorithm is introduced that aims to reduce computational cost while maintaining optimization effectiveness. Geophysical dynamic models usually have a prior parameterization scheme derived from the physical processes involved, and our goal is to improve all of the objectives by parameter calibration. In this study, we developed a method for directing the search processes toward the region that can improve all of the objectives simultaneously. We tested the MO-ASMO algorithm against NSGA-II and SUMO with 13 test functions and a land surface model - the Common Land Model (CoLM). The results demonstrated the effectiveness and efficiency of MO-ASMO.
Directory of Open Access Journals (Sweden)
Fraser Paul E
2008-01-01
Full Text Available Abstract Background Amyloid precursor protein (APP is enzymatically cleaved by γ-secretase to form two peptide products, either Aβ40 or the more neurotoxic Aβ42. The Aβ42/40 ratio is increased in many cases of familial Alzheimer's disease (FAD. The transmembrane domain (TM of APP contains the known dimerization motif GXXXA. We have investigated the dimerization of both wild type and FAD mutant APP transmembrane domains. Results Using synthetic peptides derived from the APP-TM domain, we show that this segment is capable of forming stable transmembrane dimers. A model of a dimeric APP-TM domain reveals a putative dimerization interface, and interestingly, majority of FAD mutations in APP are localized to this interface region. We find that FAD-APP mutations destabilize the APP-TM dimer and increase the population of APP peptide monomers. Conclusion The dissociation constants are correlated to both the Aβ42/Aβ40 ratio and the mean age of disease onset in AD patients. We also show that these TM-peptides reduce Aβ production and Aβ42/Aβ40 ratios when added to HEK293 cells overexpressing the Swedish FAD mutation and γ-secretase components, potentially revealing a new class of γ-secretase inhibitors.
Directory of Open Access Journals (Sweden)
Balda Maria S
2009-12-01
Full Text Available Abstract Background Tight junctions are an intercellular adhesion complex of epithelial and endothelial cells, and form a paracellular barrier that restricts the diffusion of solutes on the basis of size and charge. Tight junctions are formed by multiprotein complexes containing cytosolic and transmembrane proteins. How these components work together to form functional tight junctions is still not well understood and will require a complete understanding of the molecular composition of the junction. Results Here we identify a new transmembrane component of tight junctions: MarvelD3, a four-span transmembrane protein. Its predicted transmembrane helices form a Marvel (MAL and related proteins for vesicle traffic and membrane link domain, a structural motif originally discovered in proteins involved in membrane apposition and fusion events, such as the tight junction proteins occludin and tricellulin. In mammals, MarvelD3 is expressed as two alternatively spliced isoforms. Both isoforms exhibit a broad tissue distribution and are expressed by different types of epithelial as well as endothelial cells. MarvelD3 co-localises with occludin at tight junctions in intestinal and corneal epithelial cells. RNA interference experiments in Caco-2 cells indicate that normal MarvelD3 expression is not required for the formation of functional tight junctions but depletion results in monolayers with increased transepithelial electrical resistance. Conclusions Our data indicate that MarvelD3 is a third member of the tight junction-associated occludin family of transmembrane proteins. Similar to occludin, normal expression of MarvelD3 is not essential for the formation of functional tight junctions. However, MarvelD3 functions as a determinant of epithelial paracellular permeability properties.
Warren, Dan L; Seifert, Stephanie N
2011-03-01
Maxent, one of the most commonly used methods for inferring species distributions and environmental tolerances from occurrence data, allows users to fit models of arbitrary complexity. Model complexity is typically constrained via a process known as L1 regularization, but at present little guidance is available for setting the appropriate level of regularization, and the effects of inappropriately complex or simple models are largely unknown. In this study, we demonstrate the use of information criterion approaches to setting regularization in Maxent, and we compare models selected using information criteria to models selected using other criteria that are common in the literature. We evaluate model performance using occurrence data generated from a known "true" initial Maxent model, using several different metrics for model quality and transferability. We demonstrate that models that are inappropriately complex or inappropriately simple show reduced ability to infer habitat quality, reduced ability to infer the relative importance of variables in constraining species' distributions, and reduced transferability to other time periods. We also demonstrate that information criteria may offer significant advantages over the methods commonly used in the literature.
Determining the appropriate model complexity for patient-specific advice on mechanical ventilation
DEFF Research Database (Denmark)
Rees, Stephen E.; Karbing, Dan S.
2017-01-01
Mathematical physiological models can be applied in medical decision support systems. To do so requires consideration of the necessary model complexity. Models that simulate changes in the individual patient are required, meaning that models should have a complexity where parameters can be unique...
How Good Are Statistical Models at Approximating Complex Fitness Landscapes?
du Plessis, Louis; Leventhal, Gabriel E.; Bonhoeffer, Sebastian
2016-01-01
Fitness landscapes determine the course of adaptation by constraining and shaping evolutionary trajectories. Knowledge of the structure of a fitness landscape can thus predict evolutionary outcomes. Empirical fitness landscapes, however, have so far only offered limited insight into real-world questions, as the high dimensionality of sequence spaces makes it impossible to exhaustively measure the fitness of all variants of biologically meaningful sequences. We must therefore revert to statistical descriptions of fitness landscapes that are based on a sparse sample of fitness measurements. It remains unclear, however, how much data are required for such statistical descriptions to be useful. Here, we assess the ability of regression models accounting for single and pairwise mutations to correctly approximate a complex quasi-empirical fitness landscape. We compare approximations based on various sampling regimes of an RNA landscape and find that the sampling regime strongly influences the quality of the regression. On the one hand it is generally impossible to generate sufficient samples to achieve a good approximation of the complete fitness landscape, and on the other hand systematic sampling schemes can only provide a good description of the immediate neighborhood of a sequence of interest. Nevertheless, we obtain a remarkably good and unbiased fit to the local landscape when using sequences from a population that has evolved under strong selection. Thus, current statistical methods can provide a good approximation to the landscape of naturally evolving populations. PMID:27189564
Solvent-Dependent Pyranopterin Cyclization in Molybdenum Cofactor Model Complexes.
Williams, Benjamin R; Gisewhite, Douglas; Kalinsky, Anna; Esmail, Alisha; Burgmayer, Sharon J Nieter
2015-09-08
The conserved pterin dithiolene ligand that coordinates molybdenum (Mo) in the cofactor (Moco) of mononuclear Mo enzymes can exist in both a tricyclic pyranopterin dithiolene form and as a bicyclic pterin-dithiolene form as observed in protein crystal structures of several bacterial molybdoenzymes. Interconversion between the tricyclic and bicyclic forms via pyran scission and cyclization has been hypothesized to play a role in the catalytic mechanism of Moco. Therefore, understanding the interconversion between the tricyclic and bicyclic forms, a type of ring-chain tautomerism, is an important aspect of study to understand its role in catalysis. In this study, equilibrium constants (K(eq)) as well as enthalpy, entropy, and free energy values are obtained for pyran ring tautomerism exhibited by two Moco model complexes, namely, (Et4N)[Tp*Mo(O)(S2BMOPP)] (1) and (Et4N)[Tp*Mo(O)(S2PEOPP)] (2), as a solvent-dependent equilibrium process. Keq values obtained from (1)H NMR data in seven deuterated solvents show a correlation between solvent polarity and tautomer form, where solvents with higher polarity parameters favor the pyran form.
Complex network model of the Treatise on Cold Damage Disorders
Shao, Feng-jing; Sui, Yi; Zhou, Yong-hong; Sun, Ren-cheng
2016-10-01
Investigating the underlying principles of the Treatise on Cold Damage Disorder is meaningful and interesting. In this study, we investigated the symptoms, herbal formulae, herbal drugs, and their relationships in this treatise based on a multi-subnet composited complex network model (MCCN). Syndrome subnets were constructed for the symptoms and a formula subnet for herbal drugs. By subnet compounding using MCCN, a composited network was obtained that described the treatment relationships between syndromes and formulae. The results obtained by topological analysis suggested some prescription laws that could be validated in clinics. After subnet reduction using the MCCN, six channel (Tai-yang, Yang-ming, Shao-yang, Tai-yin, Shao-yin, and Jue-yin) subnets were obtained. By analyzing the strengths of the relationships among these six channel subnets, we found that the Tai-yang channel and Yang-ming channel were related most strongly with each other, and we found symptoms that implied pathogen movements and transformations among the six channels. This study could help therapists to obtain a deeper understanding of this ancient treatise.
How Good Are Statistical Models at Approximating Complex Fitness Landscapes?
du Plessis, Louis; Leventhal, Gabriel E; Bonhoeffer, Sebastian
2016-09-01
Fitness landscapes determine the course of adaptation by constraining and shaping evolutionary trajectories. Knowledge of the structure of a fitness landscape can thus predict evolutionary outcomes. Empirical fitness landscapes, however, have so far only offered limited insight into real-world questions, as the high dimensionality of sequence spaces makes it impossible to exhaustively measure the fitness of all variants of biologically meaningful sequences. We must therefore revert to statistical descriptions of fitness landscapes that are based on a sparse sample of fitness measurements. It remains unclear, however, how much data are required for such statistical descriptions to be useful. Here, we assess the ability of regression models accounting for single and pairwise mutations to correctly approximate a complex quasi-empirical fitness landscape. We compare approximations based on various sampling regimes of an RNA landscape and find that the sampling regime strongly influences the quality of the regression. On the one hand it is generally impossible to generate sufficient samples to achieve a good approximation of the complete fitness landscape, and on the other hand systematic sampling schemes can only provide a good description of the immediate neighborhood of a sequence of interest. Nevertheless, we obtain a remarkably good and unbiased fit to the local landscape when using sequences from a population that has evolved under strong selection. Thus, current statistical methods can provide a good approximation to the landscape of naturally evolving populations.
MODELING AND ANALYSIS OF ENERGY SYSTEM BASED ON COMPLEX ADAPTIVE SYSTEM
Institute of Scientific and Technical Information of China (English)
QIU Shiming; GU Peiliang
2004-01-01
Complex adaptive system (CAS) is a kind of complex system in natural and artificial systems. In this paper, the theory of complex adaptive system is introduced at first. Considering the characteristic of energy system, it can be regarded as a complex adaptive system. After the evolutionary law is analysed, the energy complex system model is established based on CAS and application tool SWARM, which is a simulation software platform. The model differs from the models as well as methods developed before. As an application, China's energy system is simulated with the model established above.China's future total energy demand in the future, energy structure and related in fiuence on environment are presented.
Lu, Xiaohui; Gross, Alec W; Lodish, Harvey F
2006-03-17
In the absence of erythropoietin (Epo) cell surface Epo receptors (EpoR) are dimeric; dimerization is mediated mainly by the transmembrane domain. Binding of Epo changes the orientation of the two receptor subunits. This conformational change is transmitted through the juxtamembrane and transmembrane domains, leading to activation of JAK2 kinase and induction of proliferation and survival signals. To define the active EpoR conformation(s) we screened libraries of EpoRs with random mutations in the transmembrane domain and identified several point mutations that activate the EpoR in the absence of ligand, including changes of either of the first two transmembrane domain residues (Leu(226) and Ile(227)) to cysteine. Following this discovery, we performed cysteine-scanning mutagenesis in the EpoR juxtamembrane and transmembrane domains. Many mutants formed disulfide-linked receptor dimers, but only EpoR dimers linked by cysteines at positions 223, 226, or 227 activated EpoR signal transduction pathways and supported proliferation of Ba/F3 cells in the absence of cytokines. These data suggest that activation of dimeric EpoR by Epo binding is achieved by reorienting the EpoR transmembrane and the connected cytosolic domains and that certain disulfide-bonded dimers represent the activated dimeric conformation of the EpoR, constitutively activating downstream signaling. Based on our data and the previously determined structure of Epo bound to a dimer of the EpoR extracellular domain, we present a model of the active and inactive conformations of the Epo receptor.
DEFF Research Database (Denmark)
Eby, M.; Weaver, A. J.; Alexander, K.;
2013-01-01
and continue through to 2005. The standard simulations include changes in forcing from solar luminosity, Earth's orbital configuration, CO2, additional greenhouse gases, land use, and sulphate and volcanic aerosols. In spite of very different modelled pre-industrial global surface air temperatures, overall 20......Both historical and idealized climate model experiments are performed with a variety of Earth system models of intermediate complexity (EMICs) as part of a community contribution to the Intergovernmental Panel on Climate Change Fifth Assessment Report. Historical simulations start at 850 CE...
Openings: the Act of Modelizing and the Question of Complexity
Directory of Open Access Journals (Sweden)
Emilie Janton
2010-02-01
Full Text Available Richard Powers’ novels are commonly associated with “systems novels” as Tom LeClair first described them, notably because of the constant compositional use the novelist makes of different extra-textual systems (including various fields such as biology, computer science, or more extensively chaos theory.To what extent do those modelized systems, apparently meant to supply structuring tools to readers keen for interpretive keys, contribute to the novels’ inner complexity, and how does their installation in the texts take place? The way I have chosen to address this issue is to look into the openings of the novels as privileged locations where formal guidelines are provided. Focusing on the openings helps point out functional variations in the use of models, which appear to be essential to the continuous development of complexity throughout the texts. The openings therefore seem not only to have programmatic virtues, but also to offer disorienting elements whose impact on the global scale (that is that of the novel as a whole forces us to reconsider the scope of the models at stake in Richard Powers’ writing.Les romans de Richard Powers sont souvent associés aux « romans systémiques » tels que Tom LeClair a pu les décrire, et ce notamment en raison de l’usage répété que le romancier fait, dans la composition de ses textes, de divers systèmes extra-textuels (dont la biologie, l’informatique et, plus largement, la théorie du chaos.Dans quelle mesure ces systèmes modélisés, apparemment destinés à donner aux lecteurs avides de clés interprétatives des outils propres à dégager des structures, participent-ils de la complexité interne des romans, et comment ces systèmes sont-ils mis en place dans les textes ? Le présent article aborde ces questions en analysant l’ouverture de plusieurs romans, lieu privilégié de l’instauration de lignes de force structurelles. L’étude de ces ouvertures permet de mettre en
The Lantibiotic Nisin Induces Transmembrane Movement of a Fluorescent Phospholipid
Moll, Gert N.; Konings, Wil N.; Driessen, Arnold J.M.
1998-01-01
Nisin is a pore-forming antimicrobial peptide. The capacity of nisin to induce transmembrane movement of a fluorescent phospholipid in lipid vesicles was investigated. Unilamellar phospholipid vesicles that contained a fluorescent phospholipid (1-acyl-2-{6-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]ca
Regulation of cytoskeletal organization by syndecan transmembrane proteoglycans
DEFF Research Database (Denmark)
Yoneda, Atsuko; Couchman, John R
2003-01-01
Syndecans, a family of transmembrane proteoglycans, interact with numerous extracellular ligands through specific sequences in their heparan sulfate chains and have been considered to be co-receptors for matrix molecules and growth factors. In addition to their roles as co-receptors, many studies...
Evolution Methods of Formation of Neuronet Models of Complex Economic Systems
Directory of Open Access Journals (Sweden)
Khemelyov Oleksandr H.
2014-01-01
Full Text Available The article analyses principles of formation of neuronet models of complex economic systems. It justifies prospectiveness of use of artificial intellect methods when modelling complex economic systems. It shows a possibility of use of evolution methods when forming neuronet models of complex economic systems for ensuring invariance of their generalising properties. It offers an algorithm with a genome from operons of fixed length. It considers all operons from the point of view of functional positions. It notes a specific feature of the algorithm, which allows excluding anthropogenic factors when selecting the neuronet models architecture. It proves adequacy of the formed neuronet models of complex economic systems.
Joseph, Benesh; Jeschke, Gunnar; Goetz, Birke A; Locher, Kaspar P; Bordignon, Enrica
2011-11-25
ATP-binding cassette (ABC) transporters are ubiquitous integral membrane proteins that translocate substrates across cell membranes. The alternating access of their transmembrane domains to opposite sides of the membrane powered by the closure and reopening of the nucleotide binding domains is proposed to drive the translocation events. Despite clear structural similarities, evidence for considerable mechanistic diversity starts to accumulate within the importers subfamily. We present here a detailed study of the gating mechanism of a type II ABC importer, the BtuCD-F vitamin B(12) importer from Escherichia coli, elucidated by EPR spectroscopy. Distance changes at key positions in the translocation gates in the nucleotide-free, ATP- and ADP-bound conformations of the transporter were measured in detergent micelles and liposomes. The translocation gates of the BtuCD-F complex undergo conformational changes in line with a "two-state" alternating access model. We provide the first direct evidence that binding of ATP drives the gates to an inward-facing conformation, in contrast to type I importers specific for maltose, molybdate, or methionine. Following ATP hydrolysis, the translocation gates restore to an apo-like conformation. In the presence of ATP, an excess of vitamin B(12) promotes the reopening of the gates toward the periplasm and the dislodgment of BtuF from the transporter. The EPR data allow a productive translocation cycle of the vitamin B(12) transporter to be modeled.
Dynamics of Symmetric Conserved Mass Aggregation Model on Complex Networks
Institute of Scientific and Technical Information of China (English)
HUA Da-Yin
2009-01-01
We investigate the dynamical behaviour of the aggregation process in the symmetric conserved mass aggregation model under three different topological structures. The dispersion σ(t, L) = (∑i(mi - ρ0)2/L)1/2 is defined to describe the dynamical behaviour where ρ0 is the density of particle and mi is the particle number on a site. It is found numerically that for a regular lattice and a scale-free network, σ(t, L) follows a power-law scaling σ(t, L) ～ tδ1 and σ(t, L) ～ tδ4 from a random initial condition to the stationary states, respectively. However, for a small-world network, there are two power-law scaling regimes, σ(t, L) ～ tδ2 when t＜T and a(t, L) ～ tδ3 when tT. Moreover, it is found numerically that δ2 is near to δ1 for small rewiring probability q, and δ3 hardly changes with varying q and it is almost the same as δ4. We speculate that the aggregation of the connection degree accelerates the mass aggregation in the initial relaxation stage and the existence of the long-distance interactions in the complex networks results in the acceleration of the mass aggregation when tT for the small-world networks. We also show that the relaxation time T follows a power-law scaling τ Lz and σ(t, L) in the stationary state follows a power-law σs(L) ～ Lσ for three different structures.
Probabilistic Multi-Factor Interaction Model for Complex Material Behavior
Abumeri, Galib H.; Chamis, Christos C.
2010-01-01
Complex material behavior is represented by a single equation of product form to account for interaction among the various factors. The factors are selected by the physics of the problem and the environment that the model is to represent. For example, different factors will be required for each to represent temperature, moisture, erosion, corrosion, etc. It is important that the equation represent the physics of the behavior in its entirety accurately. The Multi-Factor Interaction Model (MFIM) is used to evaluate the divot weight (foam weight ejected) from the external launch tanks. The multi-factor has sufficient degrees of freedom to evaluate a large number of factors that may contribute to the divot ejection. It also accommodates all interactions by its product form. Each factor has an exponent that satisfies only two points - the initial and final points. The exponent describes a monotonic path from the initial condition to the final. The exponent values are selected so that the described path makes sense in the absence of experimental data. In the present investigation, the data used were obtained by testing simulated specimens in launching conditions. Results show that the MFIM is an effective method of describing the divot weight ejected under the conditions investigated. The problem lies in how to represent the divot weight with a single equation. A unique solution to this problem is a multi-factor equation of product form. Each factor is of the following form (1 xi/xf)ei, where xi is the initial value, usually at ambient conditions, xf the final value, and ei the exponent that makes the curve represented unimodal that meets the initial and final values. The exponents are either evaluated by test data or by technical judgment. A minor disadvantage may be the selection of exponents in the absence of any empirical data. This form has been used successfully in describing the foam ejected in simulated space environmental conditions. Seven factors were required
Modeling Complex Organic Molecules in dense regions: Eley-Rideal and complex induced reaction
Ruaud, M; Hickson, K M; Gratier, P; Hersant, F; Wakelam, V
2014-01-01
Recent observations have revealed the existence of Complex Organic Molecules (COMs) in cold dense cores and prestellar cores. The presence of these molecules in such cold conditions is not well understood and remains a matter of debate since the previously proposed "warm- up" scenario cannot explain these observations. In this article, we study the effect of Eley- Rideal and complex induced reaction mechanisms of gas-phase carbon atoms with the main ice components of dust grains on the formation of COMs in cold and dense regions. Based on recent experiments we use a low value for the chemical desorption efficiency (which was previously invoked to explain the observed COM abundances). We show that our introduced mechanisms are efficient enough to produce a large amount of complex organic molecules in the gas-phase at temperatures as low as 10K.
Mattern, Jann Paul; Edwards, Christopher A.
2017-01-01
Parameter estimation is an important part of numerical modeling and often required when a coupled physical-biogeochemical ocean model is first deployed. However, 3-dimensional ocean model simulations are computationally expensive and models typically contain upwards of 10 parameters suitable for estimation. Hence, manual parameter tuning can be lengthy and cumbersome. Here, we present four easy to implement and flexible parameter estimation techniques and apply them to two 3-dimensional biogeochemical models of different complexities. Based on a Monte Carlo experiment, we first develop a cost function measuring the model-observation misfit based on multiple data types. The parameter estimation techniques are then applied and yield a substantial cost reduction over ∼ 100 simulations. Based on the outcome of multiple replicate experiments, they perform on average better than random, uninformed parameter search but performance declines when more than 40 parameters are estimated together. Our results emphasize the complex cost function structure for biogeochemical parameters and highlight dependencies between different parameters as well as different cost function formulations.
VV&A and confidence assessment of a complex giant system simulation model
Institute of Scientific and Technical Information of China (English)
伞冶; 陈建明
2004-01-01
It is difficult or even impossible for a pure mathematical model to represent a complex giant system because of the complexity, activity, uncertainty in such a system. The meta-synthesis methodology and the generalized modelling method are used to model a complex giant system. This paper has an in-depth study on the confidence assessment of a complex giant system simulation model that is built based on the meta-synthesis methodology and the generalized modelling method. A new definition of VV&A for complex system is given, on which is based a -step reference model and proposed for VV&A purpose. Furthermore, the principle andmethod of intelligent boundary interval intermediate assessment is proposed for the harmonization of modelling and model-validation.
Architecture of mammalian respiratory complex I.
Vinothkumar, Kutti R; Zhu, Jiapeng; Hirst, Judy
2014-11-06
Complex I (NADH:ubiquinone oxidoreductase) is essential for oxidative phosphorylation in mammalian mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the energy-transducing inner membrane, providing electrons for respiration and driving ATP synthesis. Mammalian complex I contains 44 different nuclear- and mitochondrial-encoded subunits, with a combined mass of 1 MDa. The 14 conserved 'core' subunits have been structurally defined in the minimal, bacterial complex, but the structures and arrangement of the 30 'supernumerary' subunits are unknown. Here we describe a 5 Å resolution structure of complex I from Bos taurus heart mitochondria, a close relative of the human enzyme, determined by single-particle electron cryo-microscopy. We present the structures of the mammalian core subunits that contain eight iron-sulphur clusters and 60 transmembrane helices, identify 18 supernumerary transmembrane helices, and assign and model 14 supernumerary subunits. Thus, we considerably advance knowledge of the structure of mammalian complex I and the architecture of its supernumerary ensemble around the core domains. Our structure provides insights into the roles of the supernumerary subunits in regulation, assembly and homeostasis, and a basis for understanding the effects of mutations that cause a diverse range of human diseases.
Complex Automated Negotiations Theories, Models, and Software Competitions
Zhang, Minjie; Robu, Valentin; Matsuo, Tokuro
2013-01-01
Complex Automated Negotiations are a widely studied, emerging area in the field of Autonomous Agents and Multi-Agent Systems. In general, automated negotiations can be complex, since there are a lot of factors that characterize such negotiations. For this book, we solicited papers on all aspects of such complex automated negotiations, which are studied in the field of Autonomous Agents and Multi-Agent Systems. This book includes two parts, which are Part I: Agent-based Complex Automated Negotiations and Part II: Automated Negotiation Agents Competition. Each chapter in Part I is an extended version of ACAN 2011 papers after peer reviews by three PC members. Part II includes ANAC 2011 (The Second Automated Negotiating Agents Competition), in which automated agents who have different negotiation strategies and implemented by different developers are automatically negotiate in the several negotiation domains. ANAC is an international competition in which automated negotiation strategies, submitted by a number of...
Application of surface complexation models to anion adsorption by natural materials
Various chemical models of ion adsorption will be presented and discussed. Chemical models, such as surface complexation models, provide a molecular description of anion adsorption reactions using an equilibrium approach. Two such models, the constant capacitance model and the triple layer model w...
Combined Mechanistic and Transport Modelling of Metal Humate Complexes
DEFF Research Database (Denmark)
Bryan, N. D.; Jones, D.; Griffin, D.
1999-01-01
RMC-Environmental Contribution to Task 4, (Model Development and Testing). Reporting period 1998.......RMC-Environmental Contribution to Task 4, (Model Development and Testing). Reporting period 1998....
Modelling tidal influence on sea breezes with models of different complexity
Directory of Open Access Journals (Sweden)
Jana Fischereit
2016-09-01
Full Text Available Tides influence both the formation and development of sea breezes. The aim of this study is to investigate the tidal influence to decide which model complexity is needed to reproduce the main influence of tides in a numerical model of coastal meteorology. Two processes are considered: (a the influence of tides on sea breezes through the effect of tidal currents on the surface wind and (b the thermal influence through the flooding and drying of mudflats in the intertidal area. The processes are considered separately by representing the ocean in the non-hydrostatic mesoscale atmosphere model METRAS with different complexity, ranging from a homogeneous stationary surface to a shallow-water model coupled to METRAS with a two-way exchange of momentum. The model system is applied in a case study to the German Bight, where large mudflats exist at low tide.The results show that the main influence of tides originates from a change in the mudflat heat budget through flooding and drying. The influence of tidal currents on the surface wind is small. Therefore, we conclude that no coupled atmosphere-ocean model is needed to reproduce the main influence of tides on sea breezes in a numerical model. Instead, we suggest to use an atmosphere model which simulates the change of surface cover in the intertidal area and includes a realistic spatial sea surface temperature distribution. For this it is essential to simulate the change in surface cover with the correct timing because the results show that the atmosphere reacts very sensitively to that change.
Zhao, Yuejie; Singh, Arunima; Xu, Yongmei; Zong, Chengli; Zhang, Fuming; Boons, Geert-Jan; Liu, Jian; Linhardt, Robert J.; Woods, Robert J.; Amster, I. Jonathan
2016-09-01
Fibroblast growth factors (FGFs) regulate several cellular developmental processes by interacting with cell surface heparan proteoglycans and transmembrane cell surface receptors (FGFR). The interaction of FGF with heparan sulfate (HS) is known to induce protein oligomerization, increase the affinity of FGF towards its receptor FGFR, promoting the formation of the HS-FGF-FGFR signaling complex. Although the role of HS in the signaling pathways is well recognized, the details of FGF oligomerization and formation of the ternary signaling complex are still not clear, with several conflicting models proposed in literature. Here, we examine the effect of size and sulfation pattern of HS upon FGF1 oligomerization, binding stoichiometry and conformational stability, through a combination of ion mobility (IM) and theoretical modeling approaches. Ion mobility-mass spectrometry (IMMS) of FGF1 in the presence of several HS fragments ranging from tetrasaccharide (dp4) to dodecasaccharide (dp12) in length was performed. A comparison of the binding stoichiometry of variably sulfated dp4 HS to FGF1 confirmed the significance of the previously known high-affinity binding motif in FGF1 dimerization, and demonstrated that certain tetrasaccharide-length fragments are also capable of inducing dimerization of FGF1. The degree of oligomerization was found to increase in the presence of dp12 HS, and a general lack of specificity for longer HS was observed. Additionally, collision cross-sections (CCSs) of several FGF1-HS complexes were calculated, and were found to be in close agreement with experimental results. Based on the (CCSs) a number of plausible binding modes of 2:1 and 3:1 FGF1-HS are proposed.
Zhao, Yuejie; Singh, Arunima; Xu, Yongmei; Zong, Chengli; Zhang, Fuming; Boons, Geert-Jan; Liu, Jian; Linhardt, Robert J.; Woods, Robert J.; Amster, I. Jonathan
2017-01-01
Fibroblast growth factors (FGFs) regulate several cellular developmental processes by interacting with cell surface heparan proteoglycans and transmembrane cell surface receptors (FGFR). The interaction of FGF with heparan sulfate (HS) is known to induce protein oligomerization, increase the affinity of FGF towards its receptor FGFR, promoting the formation of the HS-FGF-FGFR signaling complex. Although the role of HS in the signaling pathways is well recognized, the details of FGF oligomerization and formation of the ternary signaling complex are still not clear, with several conflicting models proposed in literature. Here, we examine the effect of size and sulfation pattern of HS upon FGF1 oligomerization, binding stoichiometry and conformational stability, through a combination of ion mobility (IM) and theoretical modeling approaches. Ion mobility-mass spectrometry (IMMS) of FGF1 in the presence of several HS fragments ranging from tetrasaccharide (dp4) to dodecasaccharide (dp12) in length was performed. A comparison of the binding stoichiometry of variably sulfated dp4 HS to FGF1 confirmed the significance of the previously known high-affinity binding motif in FGF1 dimerization, and demonstrated that certain tetrasaccharide-length fragments are also capable of inducing dimerization of FGF1. The degree of oligomerization was found to increase in the presence of dp12 HS, and a general lack of specificity for longer HS was observed. Additionally, collision cross-sections (CCSs) of several FGF1-HS complexes were calculated, and were found to be in close agreement with experimental results. Based on the (CCSs) a number of plausible binding modes of 2:1 and 3:1 FGF1-HS are proposed.
A note on the Dirichlet problem for model complex partial differential equations
Ashyralyev, Allaberen; Karaca, Bahriye
2016-08-01
Complex model partial differential equations of arbitrary order are considered. The uniqueness of the Dirichlet problem is studied. It is proved that the Dirichlet problem for higher order of complex partial differential equations with one complex variable has infinitely many solutions.
Numerical simulations and mathematical models of flows in complex geometries
DEFF Research Database (Denmark)
Hernandez Garcia, Anier
The research work of the present thesis was mainly aimed at exploiting one of the strengths of the Lattice Boltzmann methods, namely, the ability to handle complicated geometries to accurately simulate flows in complex geometries. In this thesis, we perform a very detailed theoretical analysis...... and through the Chapman-Enskog multi-scale expansion technique the dependence of the kinetic viscosity on each scheme is investigated. Seeking for optimal numerical schemes to eciently simulate a wide range of complex flows a variant of the finite element, off-lattice Boltzmann method [5], which uses...... the characteristic based integration is also implemented. Using the latter scheme, numerical simulations are conducted in flows of different complexities: flow in a (real) porous network and turbulent flows in ducts with wall irregularities. From the simulations of flows in porous media driven by pressure gradients...