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Sample records for model biomembranes complex

  1. Modeling biomembranes.

    SciTech Connect

    Plimpton, Steven James; Heffernan, Julieanne; Sasaki, Darryl Yoshio; Frischknecht, Amalie Lucile; Stevens, Mark Jackson; Frink, Laura J. Douglas

    2005-11-01

    Understanding the properties and behavior of biomembranes is fundamental to many biological processes and technologies. Microdomains in biomembranes or ''lipid rafts'' are now known to be an integral part of cell signaling, vesicle formation, fusion processes, protein trafficking, and viral and toxin infection processes. Understanding how microdomains form, how they depend on membrane constituents, and how they act not only has biological implications, but also will impact Sandia's effort in development of membranes that structurally adapt to their environment in a controlled manner. To provide such understanding, we created physically-based models of biomembranes. Molecular dynamics (MD) simulations and classical density functional theory (DFT) calculations using these models were applied to phenomena such as microdomain formation, membrane fusion, pattern formation, and protein insertion. Because lipid dynamics and self-organization in membranes occur on length and time scales beyond atomistic MD, we used coarse-grained models of double tail lipid molecules that spontaneously self-assemble into bilayers. DFT provided equilibrium information on membrane structure. Experimental work was performed to further help elucidate the fundamental membrane organization principles.

  2. Interaction of Complex Liquids with Lipid Biomembranes

    NASA Astrophysics Data System (ADS)

    Jing, Benxin; Zhu, Y.

    2013-03-01

    With the emerging of smart molecular probes and functional nanocolloids for various biomedical applications, it becomes critical to understand the interaction of complex liquids with cell biomembranes in order to effectively use them with minimal cytotoxicity. Deciphered mainly by fluorescence imaging and fluorescence correlation spectroscopy, this poster will emphasize some recent studies in our group of how ionic liquids, macroionic nanoclusters, and nanocolloids interact with cell biomembrane. Using lipid bilayers as model biomembranes, I will show that adsorbed molecules and nanocolloids can not only disrupt the morphology of lipid bilayers, but also induce their phase transition due to sufficiently strong electrostatic attraction. With ionic liquids and macroionic nanoclusters whose dimensions are comparable to lipids, intriguing supramolecular assembly is also observed at lipid bilayer interface, showing a strong dependence on the chemical makeup of adsorbed ionic species.

  3. Structure and physical properties of biomembranes and model membranes

    NASA Astrophysics Data System (ADS)

    Hianik, T.

    2006-12-01

    Biomembranes belong to the most important structures of the cell and the cell organels. They play not only structural role of the barrier separating the external and internal part of the membrane but contain also various functional molecules, like receptors, ionic channels, carriers and enzymes. The cell membrane also preserves non-equillibrium state in a cell which is crucial for maintaining its excitability and other signaling functions. The growing interest to the biomembranes is also due to their unique physical properties. From physical point of view the biomembranes, that are composed of lipid bilayer into which are incorporated integral proteins and on their surface are anchored peripheral proteins and polysaccharides, represent liquid scrystal of smectic type. The biomembranes are characterized by anisotropy of structural and physical properties. The complex structure of biomembranes makes the study of their physical properties rather difficult. Therefore several model systems that mimic the structure of biomembranes were developed. Among them the lipid monolayers at an air-water interphase, bilayer lipid membranes (BLM), supported bilayer lipid membranes (sBLM) and liposomes are most known. This work is focused on the introduction into the "physical word" of the biomembranes and their models. After introduction to the membrane structure and the history of its establishment, the physical properties of the biomembranes and their models areare stepwise presented. The most focus is on the properties of lipid monolayers, BLM, sBLM and liposomes that were most detailed studied. This contribution has tutorial character that may be usefull for undergraduate and graduate students in the area of biophysics, biochemistry, molecular biology and bioengineering, however it contains also original work of the author and his co-worker and PhD students, that may be usefull also for specialists working in the field of biomembranes and model membranes.

  4. Simple models for biomembrane structure and dynamics

    NASA Astrophysics Data System (ADS)

    Brown, Frank L. H.

    2007-07-01

    Simulation of biomembranes over length and time scales relevant to cellular biology is not currently feasible with molecular dynamics including full atomic detail. Barring an unforeseen revolution in the computer industry, this situation will not change for many decades. We present two coarse grained simulation models for biomembranes that treat water implicitly (i.e. no water molecules appear in our simulations. The hydrophobic effect, hydrodynamics and related properties are approximately included without simulation of solvent). These models enable the study of systems and phenomena previously intractable to simulation. The influence of membrane bound proteins on lipid ordering and the diffusion of membrane bound proteins is discussed.

  5. Biomembranes

    SciTech Connect

    Packer, L.

    1986-01-01

    This book contains 58 selections. Some of the selection titles are: Nuclear magnetic resonance study of water interactions with proteins, biomolecules, membranes, and tissues; Quantitation of water in membranes by neutron diffraction and x-ray techniques; Proton movements in inorganic materials; Solid-phase protein hydration studies; Cell water viscosity; Water channels; and Proton permeation through model membranes.

  6. Introductory lecture: basic quantities in model biomembranes.

    PubMed

    Nagle, John F

    2013-01-01

    One of the many aspects of membrane biophysics dealt with in this Faraday Discussion regards the material moduli that describe energies at a supramolecular level. This introductory lecture first critically reviews differences in reported numerical values of the bending modulus K(C), which is a central property for the biologically important flexibility of membranes. It is speculated that there may be a reason that the shape analysis method tends to give larger values of K(C) than the micromechanical manipulation method or the more recent X-ray method that agree very well with each other. Another theme of membrane biophysics is the use of simulations to provide exquisite detail of structures and processes. This lecture critically reviews the application of atomic level simulations to the quantitative structure of simple single component lipid bilayers and diagnostics are introduced to evaluate simulations. Another theme of this Faraday Discussion was lateral heterogeneity in biomembranes with many different lipids. Coarse grained simulations and analytical theories promise to synergistically enhance experimental studies when their interaction parameters are tuned to agree with experimental data, such as the slopes of experimental tie lines in ternary phase diagrams. Finally, attention is called to contributions that add relevant biological molecules to bilayers and to contributions that study the exciting shape changes and different non-bilayer structures with different lipids.

  7. Ferroelectric active models of ion channels in biomembranes.

    PubMed

    Bystrov, V S; Lakhno, V D; Molchanov, M

    1994-06-21

    Ferroactive models of ion channels in the theory of biological membranes are presented. The main equations are derived and their possible solutions are shown. The estimates of some experimentally measured parameters are given. Possible physical consequences of the suggested models are listed and the possibility of their experimental finding is discussed. The functioning of the biomembrane's ion channel is qualitatively described on the basis of the suggested ferroactive models. The main directions and prospects for development of the ferroactive approach to the theory of biological membranes and their structures are indicated.

  8. Peridynamic Modeling of Ruptures in Biomembranes

    PubMed Central

    Jesorka, Aldo; Bertoldi, Katia

    2016-01-01

    We simulate the formation of spontaneous ruptures in supported phospholipid double bilayer membranes, using peridynamic modeling. Experiments performed on spreading double bilayers typically show two distinct kinds of ruptures, floral and fractal, which form spontaneously in the distal (upper) bilayer at late stages of double bilayer formation on high energy substrates. It is, however, currently unresolved which factors govern the occurrence of either rupture type. Variations in the distance between the two bilayers, and the occurrence of interconnections (“pinning sites”) are suspected of contributing to the process. Our new simulations indicate that the pinned regions which form, presumably due to Ca2+ ions serving as bridging agent between the distal and the proximal bilayer, act as nucleation sites for the ruptures. Moreover, assuming that the pinning sites cause a non-zero shear modulus, our simulations also show that they change the rupture mode from floral to fractal. At zero shear modulus the pores appear to be circular, subsequently evolving into floral pores. With increasing shear modulus the pore edges start to branch, favoring fractal morphologies. We conclude that the pinning sites may indirectly determine the rupture morphology by contributing to shear stress in the distal membrane. PMID:27829001

  9. Conjugation of squalene to acyclovir improves the affinity for biomembrane models.

    PubMed

    Sarpietro, Maria Grazia; Micieli, Dorotea; Rocco, Flavio; Ceruti, Maurizio; Castelli, Francesco

    2009-12-01

    Differential scanning calorimetry was used to study the interaction of acyclovir and its prodrug squalenoyl-acyclovir (obtained by conjugation of 1,1',2-tris-nor-squalene acid (squaleneCOOH) with acyclovir) with biomembrane models made of DMPC multilamellar vesicles with the aim to verify whether a stronger interaction of the prodrug with respect to the free drug can be obtained. Multilamellar vesicles were prepared in the presence of increasing molar fractions of acyclovir, squaleneCOOH or prodrug and the effect of the compounds on the thermotropic behavior of vesicles was researched, revealing no effect of acyclovir but a strong effect of squaleneCOOH and prodrug. To evaluate if acyclovir, squaleneCOOH and prodrug can be absorbed by the biomembrane model, an experiment was carried out in which the considered compounds were left in contact with the biomembrane model and their eventual uptake was evaluated analyzing the effect on the thermotropic behavior of the biomembrane model. A very small uptake was revealed for all the compounds. To check the potential use of liposomes as a delivery system for the prodrug, the biomembrane models were incubated with liposomes loaded with the compounds and the compounds transferring from the loaded liposomes to the unloaded biomembrane model was followed. The results suggest that liposomes could be used to deliver the squalenoyl-acyclovir to the biomembrane model.

  10. Imitation of biomembranes on the basis of cholic acid and endogenic thermostable protein complex in biopartitioning micellar chromatography.

    PubMed

    Rukhadze, Marina; Dzidziguri, Diana; Giorgobiani, Nana; Kerkenjia, Salome

    2011-12-01

    The structure of biomembranes was imitated by introducing nonionic surfactant polyoxyethylene (23) dodecylether, cholic acid and endogenic thermostable protein complex (14-65 kDa) into the mobile phase. The influence of concentration of these additives on the retention of the model compounds was studied. The competing interaction of cholic acid and endogenic thermostable protein complex in the lipid bilayer model was revealed on the basis of chromatographic data. The values of efficiency of the chromatographic column regarding solutes were increased by addition of endogenic thermostable protein complex to the mobile phase containing Brij-35 and cholic acid.

  11. Element-specific density profiles in interacting biomembrane models

    NASA Astrophysics Data System (ADS)

    Schneck, Emanuel; Rodriguez-Loureiro, Ignacio; Bertinetti, Luca; Marin, Egor; Novikov, Dmitri; Konovalov, Oleg; Gochev, Georgi

    2017-03-01

    Surface interactions involving biomembranes, such as cell-cell interactions or membrane contacts inside cells play important roles in numerous biological processes. Structural insight into the interacting surfaces is a prerequisite to understand the interaction characteristics as well as the underlying physical mechanisms. Here, we work with simplified planar experimental models of membrane surfaces, composed of lipids and lipopolymers. Their interaction is quantified in terms of pressure-distance curves using ellipsometry at controlled dehydrating (interaction) pressures. For selected pressures, their internal structure is investigated by standing-wave x-ray fluorescence (SWXF). This technique yields specific density profiles of the chemical elements P and S belonging to lipid headgroups and polymer chains, as well as counter-ion profiles for charged surfaces.

  12. Biomembrane models and drug-biomembrane interaction studies: Involvement in drug design and development

    PubMed Central

    Pignatello, R.; Musumeci, T.; Basile, L.; Carbone, C.; Puglisi, G.

    2011-01-01

    Contact with many different biological membranes goes along the destiny of a drug after its systemic administration. From the circulating macrophage cells to the vessel endothelium, to more complex absorption barriers, the interaction of a biomolecule with these membranes largely affects its rate and time of biodistribution in the body and at the target sites. Therefore, investigating the phenomena occurring on the cell membranes, as well as their different interaction with drugs in the physiological or pathological conditions, is important to exploit the molecular basis of many diseases and to identify new potential therapeutic strategies. Of course, the complexity of the structure and functions of biological and cell membranes, has pushed researchers toward the proposition and validation of simpler two- and three-dimensional membrane models, whose utility and drawbacks will be discussed. This review also describes the analytical methods used to look at the interactions among bioactive compounds with biological membrane models, with a particular accent on the calorimetric techniques. These studies can be considered as a powerful tool for medicinal chemistry and pharmaceutical technology, in the steps of designing new drugs and optimizing the activity and safety profile of compounds already used in the therapy. PMID:21430952

  13. Absorption of nitro-polycyclic aromatic hydrocarbons by biomembrane models: effect of the medium lipophilicity.

    PubMed

    Castelli, Francesco; Micieli, Dorotea; Ottimo, Sara; Minniti, Zelica; Sarpietro, Maria Grazia; Librando, Vito

    2008-10-01

    To demonstrate the relationship between the structure of nitro-polycyclic aromatic hydrocarbons and their effect on biomembranes, we have investigated the influence of three structurally different nitro-polycyclic aromatic hydrocarbons, 2-nitrofluorene, 2,7-dinitrofluorene and 3-nitrofluoranthene, on the thermotropic behavior of dimyristoylphosphatidylcholine multilamellar vesicles, used as biomembrane models, by means of differential scanning calorimetry. The obtained results indicate that the studied nitro-polycyclic aromatic hydrocarbons affected the thermotropic behavior of multilamellar vesicles to various extents, modifying the pretransition and the main phase transition peaks and shifting them to lower temperatures. The effect of the aqueous and lipophilic medium on the absorption process of these compounds by the biomembrane models has been also investigated revealing that the process is hindered by the aqueous medium but strongly allowed by the lipophilic medium.

  14. [Quinones and their interactions with enzyme complexes of energy-transducing biomembranes].

    PubMed

    Oleskin, A V; Samuilov, V D

    1988-10-01

    The functionally essential properties of biomembrane quinones and the mechanism of their interaction with protein components are discussed. The hypotheses on the mobile quinone pool or the ability of protein-bound quinones to transfer redox equivalents in biomembranes are discussed. The idea of quinone domains is invoked, and evidence is provided for the presence of such domains in operative biomembranes.

  15. Interaction of α-Hexylcinnamaldehyde with a Biomembrane Model: A Possible MDR Reversal Mechanism.

    PubMed

    Sarpietro, Maria Grazia; Di Sotto, Antonella; Accolla, Maria Lorena; Castelli, Francesco

    2015-05-22

    The ability of the naturally derived compound α-hexylcinnamaldehyde (1) to interact with biomembranes and to modulate their permeability has been investigated as a strategy to reverse multidrug resistance (MDR) in cancer cells. Dimyristoylphosphatidylcholine (DMPC) multilamellar vesicles (MLVs) were used as biomembrane models, and differential scanning calorimetry was applied to measure the effect of 1 on the thermotropic behavior of DMPC MLVs. The effect of an aqueous medium or a lipid carrier on the uptake of 1 by the biomembrane was also characterized. Furthermore, taking into account that MDR is strictly regulated by redox signaling, the pro-oxidant and/or antioxidant effects of 1 were evaluated by the crocin-bleaching assay, in both hydrophilic and lipophilic environments. Compound 1 was uniformly distributed in the phospholipid bilayers and deeply interacted with DMPC MLVs, intercalating among the phospholipid acyl chains and thus decreasing their cooperativity. The lipophilic medium allowed the absorption of 1 into the phospholipid membrane. In the crocin-bleaching assay, the substance produced no pro-oxidant effects in both hydrophilic and lipophilic environments; conversely, a significant inhibition of AAPH-induced oxidation was exerted in hydrophilic medium. These results suggest a possible role of 1 as a chemopreventive and chemosensitizing agent for fighting cancer.

  16. Effect of tetracaine on DMPC and DMPC+cholesterol biomembrane models: liposomes and monolayers.

    PubMed

    Serro, A P; Galante, R; Kozica, A; Paradiso, P; da Silva, A M P S Gonçalves; Luzyanin, K V; Fernandes, A C; Saramago, B

    2014-04-01

    Different types of lipid bilayers/monolayers have been used to simulate the cellular membranes in the investigation of the interactions between drugs and cells. However, to our knowledge, very few studies focused on the influence of the chosen membrane model upon the obtained results. The main objective of this work is to understand how do the nature and immobilization state of the biomembrane models influence the action of the local anaesthetic tetracaine (TTC) upon the lipid membranes. The interaction of TTC with different biomembrane models of dimyristoylphosphatidylcholine (DMPC) with and without cholesterol (CHOL) was investigated through several techniques. A quartz crystal microbalance with dissipation (QCM-D) was used to study the effect on immobilized liposomes, while phosphorus nuclear magnetic resonance ((31)P-NMR) and differential scanning calorimetry (DSC) were applied to liposomes in suspension. The effect of TTC on Langmuir monolayers of lipids was also investigated through surface pressure-area measurements at the air-water interface. The general conclusion was that TTC has a fluidizing effect on the lipid membranes and, above certain concentrations, induces membrane swelling or even solubilization. However, different models led to variable responses to the TTC action. The intensity of the disordering effect caused by TTC increased in the following order: supported liposomes

  17. Metal Transport across Biomembranes: Emerging Models for a Distinct Chemistry*

    PubMed Central

    Argüello, José M.; Raimunda, Daniel; González-Guerrero, Manuel

    2012-01-01

    Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models. PMID:22389499

  18. Metal transport across biomembranes: emerging models for a distinct chemistry.

    PubMed

    Argüello, José M; Raimunda, Daniel; González-Guerrero, Manuel

    2012-04-20

    Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models.

  19. Calorimetry and Langmuir-Blodgett studies on the interaction of a lipophilic prodrug of LHRH with biomembrane models.

    PubMed

    Sarpietro, Maria G; Accolla, Maria L; Santoro, Nancy; Mansfeld, Friederike M; Pignatello, Rosario; Toth, Istvan; Castelli, Francesco

    2014-05-01

    The interaction between an amphiphilic luteinizing hormone-releasing hormone (LHRH) prodrug that incorporated a lipoamino acid moiety (C12-LAA) with biological membrane models that consisted of multilamellar liposomes (MLVs) and phospholipid monolayers, was studied using Differential Scanning Calorimetry (DSC) and Langmuir-Blodgett film techniques. The effect of the prodrug C12[Q1]LHRH on the lipid layers was compared with the results obtained with the pure precursors, LHRH and C12-LAA. Conjugation of LHRH with a LAA promoiety showed to improve the peptide interaction with biomembrane models. Basing on the calorimetric findings, the LAA moiety aided the transfer of the prodrug from an aqueous solution to the biomembrane model.

  20. Phase separation and bistability in a three-dimensional model for protein domain formation at biomembranes

    NASA Astrophysics Data System (ADS)

    Alonso, Sergio; Bär, Markus

    2010-12-01

    Proteins in living cells interact with membranes. They may bind to or unbind from the membrane to the cytosol depending on the lipid composition of the membrane and their interaction with cytosolic enzymes. Moreover, proteins can accumulate at the membrane and assemble in spatial domains. Here, a simple model of protein cycling at biomembranes is studied, when the total number of proteins is conserved. Specifically, we consider the spatio-temporal dynamics of MARCKS proteins and their interactions with enzymes facilitating translocation from and rebinding to the membrane. The model exhibits two qualitatively different mechanisms of protein domain formation: phase separation related to a long-wave instability of a membrane state with homogeneous protein coverage and stable coexistence of two states with different homogeneous protein coverage in bistable media. We evaluate the impact of the cytosolic volume on the occurrence of protein pattern formation by simulations in a three-dimensional model. We show that the explicit treatment of the volume in the model leads to an effective rescaling of the reaction rates. For a simplified model of protein cycling, we can derive analytical expressions for the rescaling coefficients and verify them by direct simulations with the complete three-dimensional model.

  1. Temperature-pressure phase diagram of a heterogeneous anionic model biomembrane system: results from a combined calorimetry, spectroscopy and microscopy study.

    PubMed

    Kapoor, Shobhna; Werkmüller, Alexander; Denter, Christian; Zhai, Yong; Markgraf, Jonas; Weise, Katrin; Opitz, Norbert; Winter, Roland

    2011-04-01

    By using Fourier transform infrared (FT-IR) spectroscopy in combination with differential scanning calorimetry (DSC) coupled with pressure perturbation calorimetry (PPC), ultrasound velocimetry, Laurdan fluorescence spectroscopy, fluorescence microscopy and atomic force microscopy (AFM), the temperature and pressure dependent phase behavior of the five-component anionic model raft lipid mixture DOPC/DOPG/DPPC/DPPG/cholesterol (20:5:45:5:25 mol%) was investigated. A temperature range from 5 to 65 °C and a pressure range up to 16 kbar were covered to establish the temperature-pressure phase diagram of this heterogeneous model biomembrane system. Incorporation of 10-20 mol% PG still leads to liquid-ordered (l(o))-liquid-disordered (l(d)) phase coexistence regions over a wide range of temperatures and pressures. Compared to the corresponding neutral model raft mixture (DOPC/DPPC/Chol 25:50:25 mol%), the p,T-phase diagram is - as expected and in accordance with the Gibbs phase rule - more complex, the phase sequence as a function of temperature and pressure is largely similar, however. This anionic heterogeneous model membrane system will serve as a more realistic model biomembrane system to study protein interactions with anionic lipid bilayers displaying liquid-disordered/liquid-ordered domain coexistence over a wide range of the temperature-pressure plane, thus allowing also studies of biologically relevant systems encountered under extreme environmental conditions.

  2. Preparation, property of the complex of carboxymethyl chitosan grafted copolymer with iodine and application of it in cervical antibacterial biomembrane.

    PubMed

    Chen, Yu; Yang, Yumin; Liao, Qingping; Yang, Wei; Ma, Wanfeng; Zhao, Jian; Zheng, Xionggao; Yang, Yang; Chen, Rui

    2016-10-01

    Cervical erosion is one of the common diseases of women. The loop electrosurgical excisional procedure (LEEP) has been used widely in the treatment of the cervical diseases. However, there are no effective wound dressings for the postoperative care to protect the wound area from further infection, leading to increased secretion and longer healing time. Iodine is a widely used inorganic antibacterial agent with many advantages. However, the carrier for stable iodine complex antibacterial agents is lack. In the present study, a novel iodine carrier, Carboxymethyl chitosan-g-(poly(sodium acrylate)-co-polyvinylpyrrolidone) (CMCTS-g-(PAANa-co-PVP), was prepared by graft copolymerization of sodium acrylate (AANa) and N-vinylpyrrolidone (NVP) to a carboxymethyl chitosan (CMCTS) skeleton. The obtained structure could combine prominent property of poly(sodium acrylate) (PAANa) anionic polyelectrolyte segment and good complex property of polyvinylpyrrolidone (PVP) segment to iodine. The bioactivity of CMCTS could also be kept. The properties of the complex, CMCTS-g-(PAANa-co-PVP)-I2, were studied. The in vitro experiment shows that it has broad-spectrum bactericidal effects to virus, fungus, gram-positive bacteria and gram-negative bacteria. A CMCTS-g-(PAANa-co-PVP)-I2 complex contained cervical antibacterial biomembrane (CABM) was prepared. The iodine release from the CABM is pH-dependent. The clinic trial results indicate that CABM has better treatment effectiveness than the conventional treatment in the postoperative care of the LEEP operation. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Structure effect on the interaction of phenylurea herbicides with model biomembrane as an environmental mobility parameter.

    PubMed

    Librando, Vito; Forte, Stefano; Sarpietro, Maria G

    2004-01-15

    During recent years, intensive use of herbicides has raised increasing concern mainly due to their massive pollution of the environment. As these herbicides are directly or indirectly toxic to a wide range of organisms, their potential for contaminating soil, surface water, and groundwater makes these xenobiotics of special interest from a health and environmental point of view. Knowledge of the mechanisms by which they exert their toxic effects is becoming a need. Because of the herbicides' lipophilicity, a possible site of interaction in the cell is represented by biomembranes. The interaction of four herbicides, difenoxuron, diuron, linuron, and metoxuron, with model membranes constituted of dimyristoylphosphatidylcholine multilamellar vesicles was investigated by the differential scanning calorimetry technique. The aim was to study the effects exerted by an increasing amount of the examined compounds on thermotropic behavior of the model phospholipid membranes and to correlate the obtained results with structural features of the herbicides due to their environmental mobility. Among the herbicides studied, linuron is the most effective in perturbing the ordinate structure of vesicles forming phospholipids, whereas metoxuron is the least effective and the others exert an intermediate effect. Linuron exerts its effect both on the transition temperature of the gel to the liquid crystalline phase and on the enthalpy change. Difenoxuron, diuron, and metoxuron cause a change in the transition temperature but have an insignificant effect on the enthalpy change. The calorimetric results, correlated with the structural features of the herbicides, are consistent with their partition coefficient, log K(ow), suggesting that the more hydrophobic compound character causes a greater liposolubility and consequential cellular absorption with more effectiveness on the membrane order.

  4. Engineering and validation of a novel lipid thin film for biomembrane modeling in lipophilicity determination of drugs and xenobiotics

    PubMed Central

    Idowu, Sunday Olakunle; Adeyemo, Morenikeji Ambali; Ogbonna, Udochi Ihechiluru

    2009-01-01

    Background Determination of lipophilicity as a tool for predicting pharmacokinetic molecular behavior is limited by the predictive power of available experimental models of the biomembrane. There is current interest, therefore, in models that accurately simulate the biomembrane structure and function. A novel bio-device; a lipid thin film, was engineered as an alternative approach to the previous use of hydrocarbon thin films in biomembrane modeling. Results Retention behavior of four structurally diverse model compounds; 4-amino-3,5-dinitrobenzoic acid (ADBA), naproxen (NPX), nabumetone (NBT) and halofantrine (HF), representing 4 broad classes of varying molecular polarities and aqueous solubility behavior, was investigated on the lipid film, liquid paraffin, and octadecylsilane layers. Computational, thermodynamic and image analysis confirms the peculiar amphiphilic configuration of the lipid film. Effect of solute-type, layer-type and variables interactions on retention behavior was delineated by 2-way analysis of variance (ANOVA) and quantitative structure property relationships (QSPR). Validation of the lipid film was implemented by statistical correlation of a unique chromatographic metric with Log P (octanol/water) and several calculated molecular descriptors of bulk and solubility properties. Conclusion The lipid film signifies a biomimetic artificial biological interface capable of both hydrophobic and specific electrostatic interactions. It captures the hydrophilic-lipophilic balance (HLB) in the determination of lipophilicity of molecules unlike the pure hydrocarbon film of the prior art. The potentials and performance of the bio-device gives the promise of its utility as a predictive analytic tool for early-stage drug discovery science. PMID:19735551

  5. Evaluation of the interaction of coumarins with biomembrane models studied by differential scanning calorimetry and Langmuir-Blodgett techniques.

    PubMed

    Sarpietro, Maria Grazia; Giuffrida, Maria Chiara; Ottimo, Sara; Micieli, Dorotea; Castelli, Francesco

    2011-04-25

    Three coumarins, scopoletin (1), esculetin (2), and esculin (3), were investigated by differential scanning calorimetry and Langmuir-Blodgett techniques to gain information about the interaction of these compounds with cellular membranes. Phospholipids assembled as multilamellar vesicles or monolayers (at the air-water interface) were used as biomembrane models. Differential scanning calorimetry was employed to study the interaction of these coumarins with multilamellar vesicles and to evaluate their absorption by multilamellar vesicles. These experiments indicated that 1-3 interact in this manner to different extents. The Langmuir-Blodgett technique was used to study the effect of these coumarins on the organization of phospholipids assembled as a monolayer. The data obtained were in agreement with those obtained in the calorimetric experiments.

  6. X-ray scattering reveals molecular tilt is an order parameter for the main phase transition in a model biomembrane

    NASA Astrophysics Data System (ADS)

    Nagle, John F.

    2017-09-01

    Synchrotron diffuse x-ray scattering data reveal a dramatic softening of the molecular tilt modulus Kθ of the model biomembrane composed of DMPC lipids as the temperature is lowered towards the main phase transition temperature at TM=24∘C . Spontaneous tilt occurs below TM, suggesting that tilt is a symmetry breaking order parameter. Consistent with this hypothesis, it is also found that a different lipid POPS has no spontaneous tilt below its TM at 14∘C and correspondingly its tilt modulus did not soften as TM was approached from above. As previously known, the bending modulus KC of DMPC also softens close to TM, but unlike the tilt modulus, KC has a maximum 3∘ above TM, which also marks the limit of the well-known anomalous swelling regime. Tilt adds a different perspective to our previous understanding of the main phase transition in lipid bilayers.

  7. Interaction study of three overlapping synthetic peptides belonging to E2 protein of GBV-C/HGV with liposomes as biomembrane models

    NASA Astrophysics Data System (ADS)

    Rojo, N.; Muñoz, M.; Pujol, M.; Alsina, M. A.; Haro, I.

    2004-12-01

    In this work we studied by DSC the interaction of three antigenic overlapping peptides belonging to the E2 envelope protein of Hepatitis G virus, namely E2(39-53), E2(32-53) and E2(26-53), with liposomes of different lipid composition (DPPC, DMPC and DMPG) as biomembrane models. The effect of the three selected peptides on the thermotropic behaviour of lipid bilayers has been evaluated.

  8. An adaptive meshfree method for phase-field models of biomembranes. Part I: Approximation with maximum-entropy basis functions

    NASA Astrophysics Data System (ADS)

    Rosolen, A.; Peco, C.; Arroyo, M.

    2013-09-01

    We present an adaptive meshfree method to approximate phase-field models of biomembranes. In such models, the Helfrich curvature elastic energy, the surface area, and the enclosed volume of a vesicle are written as functionals of a continuous phase-field, which describes the interface in a smeared manner. Such functionals involve up to second-order spatial derivatives of the phase-field, leading to fourth-order Euler-Lagrange partial differential equations (PDE). The solutions develop sharp internal layers in the vicinity of the putative interface, and are nearly constant elsewhere. Thanks to the smoothness of the local maximum-entropy (max-ent) meshfree basis functions, we approximate numerically this high-order phase-field model with a direct Ritz-Galerkin method. The flexibility of the meshfree method allows us to easily adapt the grid to resolve the sharp features of the solutions. Thus, the proposed approach is more efficient than common tensor product methods (e.g. finite differences or spectral methods), and simpler than unstructured C0 finite element methods, applicable by reformulating the model as a system of second-order PDE. The proposed method, implemented here under the assumption of axisymmetry, allows us to show numerical evidence of convergence of the phase-field solutions to the sharp interface limit as the regularization parameter approaches zero. In a companion paper, we present a Lagrangian method based on the approximants analyzed here to study the dynamics of vesicles embedded in a viscous fluid.

  9. Differential scanning calorimetry approach to investigate the transfer of the multitarget opioid analgesic LP1 to biomembrane model.

    PubMed

    Accolla, Maria Lorena; Turnaturi, Rita; Sarpietro, Maria Grazia; Ronsisvalle, Simone; Castelli, Francesco; Pasquinucci, Lorella

    2014-04-22

    An emerging approach in pain management is the use of multitarget opioid ligands, owing an improved analgesic effect coupled to a reduced incidence of side effects. With a mu opioid receptor agonist/delta opioid receptor antagonist profile, the benzomorphan-based compound LP1 belongs to multitarget ligands class. Previous in vivo investigations showed that LP1 - subcutaneously administered as oxalate salt - was an antinociceptive agent as potent as morphine with a low tolerance-inducing capability. Because the renal toxicity of oxalate is known, an alternative approach allowing the administration of LP1 freebase could be more biocompatible. In this study the interaction of LP1 freebase and LP1 oxalate salt with multilamellar vesicles, as membrane model, was evaluated using differential scanning calorimetry technique. Despite the good membrane interaction showed by LP1 freebase, it was not capable to diffuse in the aqueous medium and to be uptaken by multilamellar vesicles. On the other hand, LP1 freebase possessed a good transfer profile by a liposomal carrier to a biomembrane model. Considering our findings and the need of safe formulations, studies for the development of a suitable carrier for a systemic administration of LP1 freebase are in progress. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  10. Biomimetic approach to biomembrane models studies: medium influence on the interaction kinetics of some phenylurea derivatives herbicides.

    PubMed

    Librando, Vito; Sarpietro, Maria Grazia; Minniti, Zelica; Micieli, Dorotea; Castelli, Francesco

    2006-04-01

    The ability of herbicides to interact with cell membranes outer lipid layer and subsequently to penetrate inside cells can be a prerequisite for exhibiting a toxic activity for both the directly exposed workers and the end consumers as the herbicides are present in the soil and water. The effect exerted by fenuron, chlorotoluron, metobromuron, monolinuron, and chlorbromuron, five structurally similar phenylurea herbicides, on the thermotropic behavior of model membranes, represented by dimyristoylphosphatidylcholine (DMPC) vesicles, was investigated by differential scanning calorimetry. The examined compounds, when dispersed in liposomes during their preparation, exerted a different action on the gel-to-liquid crystal phase transition of DMPC multilamellar vesicles. The ability of phenylurea herbicides, as a finely powdered solid, to migrate through an aqueous medium and interact with biomembrane models was also studied. This transfer process was compared with these compounds intermembrane transfer from herbicide-loaded liposomes to empty ones. These processes can mimic absorption kinetics mediated by hydrophilic or lipophilic media. Different rate and entity of interaction occurred between model membranes and solid phenylurea herbicides. Different behavior was observed by considering the time-dependent studies carried out by contacting, for increasing times, equivalent amounts of empty DMPC vesicles with phenylurea herbicide-loaded ones; all compounds were able to migrate from loaded to empty DMPC vesicles. Thus, phenylurea herbicides are able to reach and penetrate biological membranes when dispersed in a lipophilic or hydrophilic medium; these processes are related to the substituents present on the compounds backbone. The obtained experimental results seem to validate the employed strategy to study the ability of bioactive compounds to both interact with biological membranes and be adsorbed inside a membrane mimicking a biological cell when dispersed in a

  11. Nanodomains in Biomembranes with Recycling.

    PubMed

    Berger, Mareike; Manghi, Manoel; Destainville, Nicolas

    2016-10-13

    Cell membranes are out of thermodynamic equilibrium notably because of membrane recycling, i.e., active exchange of material with the cytosol. We propose an analytically tractable model of biomembrane predicting the effects of recycling on the size of protein nanodomains also called protein clusters. The model includes a short-range attraction between proteins and a weaker long-range repulsion which ensures the existence of so-called cluster phases in equilibrium, where monomeric proteins coexist with finite-size domains. Our main finding is that, when taking recycling into account, the typical cluster size at steady state increases logarithmically with the recycling rate at fixed protein concentration. Using physically realistic model parameters, the predicted 2-fold increase due to recycling in living cells is most likely experimentally measurable with the help of super-resolution microscopy.

  12. Rigid-rod molecules in biomembrane models: from hydrogen-bonded chains to synthetic multifunctional pores.

    PubMed

    Sakai, Naomi; Mareda, Jiri; Matile, Stefan

    2005-02-01

    Synthetic ion channels and pores formed by rigid-rod molecules are summarized. This includes work on hydrogen-bonded chains installed along membrane-spanning rigid-rod scaffolds to transport protons. As a second topic, programmed assembly of p-septiphenyls with terminal iminodiacetate-copper complexes for potassium transport by cation-pi interactions is described. The third topic concerns rigid push-pull rods as fluorescent alpha-helix mimics to probe the importance of dipole-potential interactions for voltage gating, both on the functional and the structural level. Topic number four deals with p-octiphenyl staves as key scaffolds for the synthesis of rigid-rod beta-barrel pores. The description of internal and external design strategies for these rigid-rod beta-barrels covers a rich collection of pH-, pM-, voltage-, ligand-, and enzyme-gated synthetic multifunctional pores that can act as hosts, sensors, and catalysts. As far as practical applications are concerned, the possibility to detect chemical reactions with synthetic multifunctional pores appears most attractive. Recent molecular mechanics simulations are presented as a valuable approach to insights on the elusive suprastructures of multifunctional pores made from rigid rods.

  13. Travelling lipid domains in a dynamic model for protein-induced pattern formation in biomembranes

    NASA Astrophysics Data System (ADS)

    John, Karin; Bär, Markus

    2005-06-01

    Cell membranes are composed of a mixture of lipids. Many biological processes require the formation of spatial domains in the lipid distribution of the plasma membrane. We have developed a mathematical model that describes the dynamic spatial distribution of acidic lipids in response to the presence of GMC proteins and regulating enzymes. The model encompasses diffusion of lipids and GMC proteins, electrostatic attraction between acidic lipids and GMC proteins as well as the kinetics of membrane attachment/detachment of GMC proteins. If the lipid-protein interaction is strong enough, phase separation occurs in the membrane as a result of free energy minimization and protein/lipid domains are formed. The picture is changed if a constant activity of enzymes is included into the model. We chose the myristoyl-electrostatic switch as a regulatory module. It consists of a protein kinase C that phosphorylates and removes the GMC proteins from the membrane and a phosphatase that dephosphorylates the proteins and enables them to rebind to the membrane. For sufficiently high enzymatic activity, the phase separation is replaced by travelling domains of acidic lipids and proteins. The latter active process is typical for nonequilibrium systems. It allows for a faster restructuring and polarization of the membrane since it acts on a larger length scale than the passive phase separation. The travelling domains can be pinned by spatial gradients in the activity; thus the membrane is able to detect spatial clues and can adapt its polarity dynamically to changes in the environment.

  14. Differential scanning calorimetry as a tool to investigate the transfer of anticancer drugs to biomembrane model.

    PubMed

    Sarpietro, Maria Grazia; Accolla, Maria Lorena; Celia, Christian; Grattoni, Alessandro; Castelli, Francesco; Fresta, Massimo; Ferrari, Mauro; Paolino, Donatella

    2013-08-01

    Different anticancer drugs clinically approved by international regulatory organizations present poor water solubility and low stability after systemic injection. Their administration requires suitable carriers capable of maximizing therapeutic efficacy. Lipid and polymeric nanotherapeutics, particularly liposomes, are widely used to deliver chemotherapeutics in the clinic. The interaction between chemotherapeutics and biocompatible lipids and polymers can affect their efficacy and play a pivotal role in chemotherapy. Phospholipids are the main components of liposomes and their interactions with therapeutic agents are widely investigated in the pharmaceutical field using differential scanning calorimetry (DSC). In this work, DSC was exploited to investigate the interaction between hydrophobic chemotherapeutics, i.e. docetaxel, tamoxifen and lapatinib, with lipid vesicles. Lipid carriers are prepared using dimyristoylphosphatidylcholine (DMPC), a phosphatidylcholine derivative, showing the same physicochemical features of the main lipids in the biological membranes. DMPC was used as a biological membrane model to evaluate interaction, passage, diffusion, and adsorption of chemotherapeutics. These processes were evaluated through the variation of thermotropic parameters of the biological membrane model. DSC studies were carried out in heating and cooling mode. Results demonstrated a modification of calorimetric curves and this effect is strictly related to the molar fraction and physicochemical features of chemotherapeutics. Furthermore, the interaction between chemotherapeutics and biological membranes affects their internalization and distribution inside tumors and this process depends on gel-liquid crystal transition of phospholipids. DSC results provide suitable information about this effect and can be used as tool to predict further interaction between chemotherapeutics and biological membranes.

  15. New Insights on the Biophysical Interaction of Resveratrol with Biomembrane Models: Relevance for Its Biological Effects.

    PubMed

    Neves, Ana Rute; Nunes, Cláudia; Reis, Salette

    2015-09-03

    Resveratrol has been widely studied because of its pleiotropic effects in cancer therapy, neuroprotection, and cardioprotection. It is believed that the interaction of resveratrol with biological membranes may play a key role in its therapeutic activity. The capacity of resveratrol to partition into lipid bilayers, its possible location within the membrane, and the influence of this compound on the membrane fluidity were investigated using membrane mimetic systems composed of egg l-α-phosphatidylcholine (EPC), cholesterol (CHOL), and sphingomyelin (SM). The results showed that resveratrol has greater affinity for the EPC bilayers than for EPC:CHOL [4:1] and EPC:CHOL:SM [1:1:1] membrane models. The increased difficulty in penetrating tight packed membranes is also demonstrated by fluorescence quenching of probes and by fluorescence anisotropy measurements. Resveratrol may be involved in the regulation of cell membrane fluidity, thereby contributing for cell homeostasis.

  16. The SPASIBA force field of model compounds related to lipids of biomembranes

    NASA Astrophysics Data System (ADS)

    Chhiba, M.; Vergoten, G.

    1996-10-01

    The vibrational spectroscopic force field SPASIBA (Spectroscopic Potential Algorithm for SImulating Biomolecular conformational Adaptability), which has been shown to exhibit unique properties over the whole molecular potential energy surface rather than in the vicinity of minima (as current force fields do), has been developed for a series of model compounds related to the lipid component of biological membranes. The structures, relative energies and vibrational spectra of several phosphate anions, acetylcholine cations, phosphorylcholine and some of their deuterated analogs have been investigated in detail. In particular, the root mean square deviation of 11 cm -1 between the observed and the calculated vibrational frequency lends some confidence to the expectation that this force field will give meaningful results when used in molecular dynamics simulations.

  17. Binding of LL-37 to model biomembranes: insight into target vs host cell recognition.

    PubMed

    Sood, Rohit; Domanov, Yegor; Pietiäinen, Milla; Kontinen, Vesa P; Kinnunen, Paavo K J

    2008-04-01

    Pursuing the molecular mechanisms of the concentration dependent cytotoxic and hemolytic effects of the human antimicrobial peptide LL-37 on cells, we investigated the interactions of this peptide with lipids using different model membranes, together with fluorescence spectroscopy for the Trp-containing mutant LL-37(F27W). Minimum concentrations inhibiting bacterial growth and lipid interactions assessed by dynamic light scattering and monolayer penetration revealed the mutant to retain the characteristics of native LL-37. Although both LL-37 and the mutant intercalated effectively into zwitterionic phosphatidylcholine membranes the presence of acidic phospholipids caused augmented membrane binding. Interestingly, strongly attenuated intercalation of LL-37 into membranes containing both cholesterol and sphingomyelin (both at X=0.3) was observed. Accordingly, the distinction between target and host cells by LL-37 is likely to derive from i) acidic phospholipids causing enhanced association with the former cells as well as ii) from attenuated interactions with the outer surface of the plasma membrane of the peptide secreting host, imposed by its high content of cholesterol and sphingomyelin. Our results further suggest that LL-37 may exert its antimicrobial effects by compromising the membrane barrier properties of the target microbes by a mechanism involving cytotoxic oligomers, similarly to other peptides forming amyloid-like fibers in the presence of acidic phospholipids.

  18. Quenching of fluorescein-conjugated lipids by antibodies. Quantitative recognition and binding of lipid-bound haptens in biomembrane models, formation of two-dimensional protein domains and molecular dynamics simulations.

    PubMed Central

    Ahlers, M; Grainger, D W; Herron, J N; Lim, K; Ringsdorf, H; Salesse, C

    1992-01-01

    Three model biomembrane systems, monolayers, micelles, and vesicles, have been used to study the influence of chemical and physical variables of hapten presentation at membrane interfaces on antibody binding. Hapten recognition and binding were monitored for the anti-fluorescein monoclonal antibody 4-4-20 generated against the hapten, fluorescein, in these membrane models as a function of fluorescein-conjugated lipid architecture. Specific recognition and binding in this system are conveniently monitored by quenching of fluorescein emission upon penetration of fluorescein into the antibody's active site. Lipid structure was shown to play a large role in affecting antibody quenching. Interestingly, the observed degrees of quenching were nearly independent of the lipid membrane model studied, but directly correlated with the chemical structure of the lipids. In all cases, the antibody recognized and quenched most efficiently a lipid based on dioctadecylamine where fluorescein is attached to the headgroup via a long, flexible hydrophilic spacer. Dipalmitoyl phosphatidylethanolamine containing a fluorescein headgroup demonstrated only partial binding/quenching. Egg phosphatidylethanolamine with a fluorescein headgroup showed no susceptibility to antibody recognition, binding, or quenching. Formation of two-dimensional protein domains upon antibody binding to the fluorescein-lipids in monolayers is also presented. Chemical and physical requirements for these antibody-hapten complexes at membrane surfaces have been discussed in terms of molecular dynamics simulations based on recent crystallographic models for this antibody-hapten complex (Herron et al., 1989. Proteins Struct. Funct. Genet. 5:271-280). Images FIGURE 7 FIGURE 8 PMID:1420916

  19. Biomembrane and receptor mechanisms

    SciTech Connect

    Chapman, D.; Bertoli, E.

    1987-01-01

    This book cover the reviews on biomembrane dynamics; recent spectroscopic studies. Topics covered are freeze fracture: Seeing and thinking biological membranes, membrane proteins and receptors: structure and organisation; techniques to determine the transbilayer distribution and mobility of phospholipids in biological membranes, transbilayer organisation of phospholipids in the plasma membranes of pro-erythroblasts and normal and abnormal red cells, aminophospholipid translocation in the erythroctye membrane is mediated by a specific AIP-dependent enzyme; membrane protein interactions, lipid-protein interactions: selectively and receptor binding, membrane fluidity in the regulation of membrane-linked enzymes, the lipid regulation of receptor functions, microheterogencity of biological membrane: structural and functional implications, fusion-fission reactions in biological membranes and in phospholpid bilayers, methods for studying the structure and function of the mitochondrial uncoupling protein, methods for studying metabolite transport in mitochondria, transport of metabolites in mitochondria, membrane gangliosides and allied glycosphingolipids: Biochemical features and physicochemical properties, the use of merocyanine 540 for monitoring aggregation properties of sialogangliosides in solution, hormone reception at the cell surface - an overview, double role for GIP in the stimulus secretion sequence of mast cells and neurophils, tumor promoters and hormone receptor coupling mechanisms in the anterior pituitary. The regulation of hormone-dependent adenylate cyclase in native membranes and systems reconstituted from purified components.- Immunological tools for the study of plasma membrane receptors.

  20. Molecular dynamics simulation of biomembranes in aqueous solution

    NASA Astrophysics Data System (ADS)

    Bostick, David Lee

    In recent years, the developments in classical molecular dynamics simulation have allowed for an atomistic depiction of mesoscopic biological systems. With the awareness of such developments, the natural strive of the scientific community has been to increase the size of such simulated systems [70]. Nonetheless, the subtleties in the properties of biomembranes require an unusually thoughtful approach [70, 203]. In this work, a hierarchical approach is taken, with respect to system complexity, in the classical molecular dynamics simulation of biomembrane systems in aqueous solution. A progression of simulation studies is presented that begins with the analysis of the interfacial properties of neat bilayers composed of zwitterionic (phosphatidylcholine) lipids in both pure water and in electrolyte. We move on to study mixed bilayers containing zwitterionic (phosphatidylcholine) and acidic (phosphatidylserine) lipids with counterions immersed in electrolyte. Yet another layer of complexity is added to the problem by studying hydrated bilayers containing phosphatidylcholine lipids and cholesterol. Finally, we address the semipermeable nature of biomembranes by studying two membrane-channel systems. We start with a simple model membrane-channel consisting of a six-helix alamethicin bundle embedded in a hydrated phosphatidylcholine bilayer. The knowledge gained from this study is then carried over to the simulation of a large membrane-embedded prokaryotic ClC Cl-/H + antiporter, utilizing a free-energetic analysis to reveal the role of protons in the Cl- transport mechanism. Throughout the progression, methods are developed and used in the analysis of interfacial aqueous solution structure, ion-membrane binding, lipid structural properties, inter-lipid hydrogen bonded complexation, and electrostatics at the membrane interface. The developments reveal the layered nature of water near the rugged, molecularscale aqueous solution/membrane interface and its electrostatic

  1. Towards the understanding of the behavior of single-chained ether phospholipids in model biomembranes: interactions with phosphatidylethanolamines in Langmuir monolayers.

    PubMed

    Hąc-Wydro, Katarzyna; Flasiński, Michał; Wydro, Paweł; Dynarowicz-Łątka, Patrycja

    2012-09-01

    Three single-chained ether lipids of comparable chemical structure but different biological activities (namely natural platelet activating factor - PAF, its deacetylated precursor - lyso-PAF and synthetic compound - edelfosine - ED) have been investigated in mixed Langmuir monolayers with phosphatidylethanolamines, PEs (DSPE, SOPE and DOPE), serving as model of inner shell of cellular membrane. The aim of undertaken studies was to verify the correlation between minor differences in chemical structures of the investigated ether lipids and their behavior in membrane-mimicking environment. To reach this goal the interactions between particular ether lipids and PEs have been analyzed with ΔG(Exc) values derived from the surface pressure-area isotherms. To get insight into miscibility between film components, Brewster angle microscopy, enabling direct visualization of monolayers structure, has been applied. The obtained results prove significant differences in both mixing properties and the interactions in the investigated systems. On one hand, they are related to the structure of polar head-groups of the studied ether lipids, which determine their capability of hydrogen bond(s) formation with head-groups of PEs. Edelfosine, lacking this property, interacts with PEs the most unfavorably among all the investigated compounds. Another important parameter in this context is the structure of PEs monolayers - the most closely packed DSPE film was found to be most unfavorable for incorporation of ether lipid molecules. Our results prove that the analysis of the interaction between ether lipids and components of biomembrane in Langmuir monolayers is a potent method to explain differences in biological activity of the investigated ether lipids. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Effect of mucoadhesive polymers on the in vitro performance of insulin-loaded silica nanoparticles: Interactions with mucin and biomembrane models.

    PubMed

    Andreani, Tatiana; Miziara, Leonardo; Lorenzón, Esteban N; de Souza, Ana Luiza R; Kiill, Charlene P; Fangueiro, Joana F; Garcia, Maria L; Gremião, Palmira D; Silva, Amélia M; Souto, Eliana B

    2015-06-01

    The present paper focuses on the development and characterization of silica nanoparticles (SiNP) coated with hydrophilic polymers as mucoadhesive carriers for oral administration of insulin. SiNP were prepared by sol-gel technology under mild conditions and coated with different hydrophilic polymers, namely, chitosan, sodium alginate or poly(ethylene glycol) (PEG) with low and high molecular weight (PEG 6000 and PEG 20000) to increase the residence time at intestinal mucosa. The mean size and size distribution, association efficiency, insulin structure and insulin thermal denaturation have been determined. The mean nanoparticle diameter ranged from 289 nm to 625 nm with a PI between 0.251 and 0.580. The insulin association efficiency in SiNP was recorded above 70%. After coating, the association efficiency of insulin increased up to 90%, showing the high affinity of the protein to the hydrophilic polymer chains. Circular dichroism (CD) indicated that no conformation changes of insulin structure occurred after loading the peptide into SiNP. Nano-differential scanning calorimetry (nDSC) showed that SiNP shifted the insulin endothermic peak to higher temperatures. The influence of coating on the interaction of nanoparticles with dipalmitoylphosphatidylcholine (DPPC) biomembrane models was also evaluated by nDSC. The increase of ΔH values suggested a strong association of non-coated SiNP and those PEGylated nanoparticles coated with DPPC polar heads by forming hydrogen bonds and/or by electrostatic interaction. The mucoadhesive properties of nanoparticles were examined by studying the interaction with mucin in aqueous solution. SiNP coated with alginate or chitosan showed high contact with mucin. On the other hand, non-coated SiNP and PEGylated SiNP showed lower interaction with mucin, indicating that these nanoparticles can interdiffuse across mucus network. The results of the present work provide valuable data in assessing the in vitro performance of insulin

  3. Langmuir monolayers and Differential Scanning Calorimetry for the study of the interactions between camptothecin drugs and biomembrane models.

    PubMed

    Casadó, Ana; Giuffrida, M Chiara; Sagristá, M Lluïsa; Castelli, Francesco; Pujol, Montserrat; Alsina, M Asunción; Mora, Margarita

    2016-02-01

    CPT-11 and SN-38 are camptothecins with strong antitumor activity. Nevertheless, their severe side effects and the chemical instability of their lactone ring have questioned the usual forms for its administration and have focused the current research on the development of new suitable pharmaceutical formulations. This work presents a biophysical study of the interfacial interactions of CPT-11 and SN-38 with membrane mimetic models by using monolayer techniques and Differential Scanning Calorimetry. The aim is to get new insights for the understanding of the bilayer mechanics after drug incorporation and to optimize the design of drug delivery systems based on the formation of stable bilayer structures. Moreover, from our knowledge, the molecular interactions between camptothecins and phospholipids have not been investigated in detail, despite their importance in the context of drug action. The results show that neither CPT-11 nor SN-38 disturbs the structure of the complex liposome bilayers, despite their different solubility, that CPT-11, positively charged in its piperidine group, interacts electrostatically with DOPS, making stable the incorporation of a high percentage of CPT-11 into liposomes and that SN-38 establishes weak repulsive interactions with lipid molecules that modify the compressibility of the bilayer without affecting significantly neither the lipid collapse pressure nor the miscibility pattern of drug-lipid mixed monolayers. The suitability of a binary and a ternary lipid mixture for encapsulating SN-38 and CPT-11, respectively, has been demonstrated. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Phase Studies of Model Biomembranes: Complex Behavior of DSPC/DOPC/Cholesterol

    PubMed Central

    Zhao, Jiang; Wu, Jing; Heberle, Frederick A.; Mills, Thalia T.; Klawitter, Paul; Huang, Grace; Costanza, Greg; Feigenson, Gerald W.

    2009-01-01

    We have undertaken a series of experiments to examine the behavior of individual components of cell membranes. Here we report an initial stage of these experiments, in which the properties of a chemically simple lipid mixture are carefully mapped onto a phase diagram. Four different experimental methods were used to establish the phase behavior of the 3-component mixture DSPC/DOPC/chol: (1) confocal fluorescence microscopy observation of giant unilamellar vesicles, GUVs; (2) FRET from perylene to C20:0-DiI; (3) fluorescence of dilute dyes C18:2-DiO and C20:0-DiI; and (4) wide angle x-ray diffraction. This particular 3-component mixture was chosen, in part, for a high level of immiscibility of the components in order to facilitate solving the phase behavior at all compositions. At 23 °C, a large fraction of the possible compositions for this mixture give rise to a solid phase. A region of 3-phase coexistence of {Lα + Lβ + Lo} was detected and defined based on a combination of fluorescence microscopy of GUVs, FRET, and dilute C20:0-DiI fluorescence. At very low cholesterol concentrations, the solid phase is the tilted-chain phase Lβ′. Most of the phase boundaries have been determined to within a few percent of the composition. Measurements of the perturbations of the boundaries of this accurate phase diagram could serve as a means to understand the behaviors of a range of added lipids and proteins. PMID:17825247

  5. Intelligent biomembrane obtained by irradiation techniques

    NASA Astrophysics Data System (ADS)

    Kaetsu, Isao; Uchida, Kumao; Sutani, Kouichi; Sakata, Shoei

    2000-03-01

    An intelligent biomembrane for environment-responsive feedback releases has been developed using radiation techniques. Various fine-porous base membranes (polyester, polycarbonate, silicon) were prepared by hole fabrication techniques with excimer-laser, ion-beam etching and photo-lithography etching. Then, various monomeric mixture of stimuli-sensitive hydrogels with or without immobilized enzymes were coated and polymerized on the porous membrane by UV, γ-ray or electron beam. The product showed the intelligent feedback release functions of model substance (methylene blue) in response to the on-off switching of signals such as pH changes and introduction of electric field. The responsiveness was remarkably improved by radiation induced IPN (interpenetrating polymer network) formation. Intelligent release controlled by a computer program was also studied and proved.

  6. Statistical Thermodynamics of Biomembranes

    PubMed Central

    Devireddy, Ram V.

    2010-01-01

    An overview of the major issues involved in the statistical thermodynamic treatment of phospholipid membranes at the atomistic level is summarized: thermodynamic ensembles, initial configuration (or the physical system being modeled), force field representation as well as the representation of long-range interactions. This is followed by a description of the various ways that the simulated ensembles can be analyzed: area of the lipid, mass density profiles, radial distribution functions (RDFs), water orientation profile, Deuteurium order parameter, free energy profiles and void (pore) formation; with particular focus on the results obtained from our recent molecular dynamic (MD) simulations of phospholipids interacting with dimethylsulfoxide (Me2SO), a commonly used cryoprotective agent (CPA). PMID:19460363

  7. Protein crowding on biomembranes: Analysis of contour instabilities

    NASA Astrophysics Data System (ADS)

    Manyuhina, O. V.

    2014-08-01

    Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as the anchoring forces exerted on a membrane by layer of proteins. We show analytically that such anisotropic interactions can drive membrane bending, resulting in nontrivial equilibrium morphologies. The predicted instabilities can advance our conceptual understanding of physical mechanisms behind collective phenomena in biological systems, in particular those with inherent anisotropy.

  8. Cytotoxicity of methyl methacrylate (MMA) and related compounds and their interaction with dipalmitoylphosphatidylcholine (DPPC) liposomes as a model for biomembranes.

    PubMed

    Fujisawa, S; Atsumi, T; Kadoma, Y

    2000-07-01

    To clarify the potential mechanism of action of methyl methacrylate (MMA) and related compounds to membranes of living cells, compared with their interaction with dipalmitoylphosphatidylcholine (DPPC) liposomes as a model for biological membranes. For (meth)acrylates, MMA, ethyl acrylate(EA), n-butyl acrylate (BA) and n-butyl methacrylate (BMA) and for living cells, primary human gingival fibroblast (HGF), human submandibular gland adenocarcinoma cell line (HSG) and human erythrocytes were used. The physicochemical changes in DPPC liposomes induced by (meth)acrylates were studied using differential scanning calorimetry (DSC) and nuclear magnetic resonance spectroscopy (NMR). Cytotoxicity decreased as follows: BA > BMA > EA > MMA. Changes in phase transition properties (temperature Tm, enthalpy delta H and Height/Half-Height Width (H/HHW) of DSC peak were decreased as follows: BA > EA > MMA. BMA enhanced H/HHW and increased Tm slightly. NMR-shielding effect decreased as follows: BMA > MMA > BA, EA. BA and BMA exhibited large cytotoxicity and high DPPC-interaction due to their lipophilicity, compared to EA or MMA. MMA showed little cytotoxicity and small changes in DPPC liposomes, whereas BA showed large cytotoxicity and large changes in the liposomes characterized by the membrane disturbance. Haemolytic activity and cytotoxicity of acrylates were higher than those of methacrylates. The physico-chemical properties (Log P or Q sigma) of (meth)acrylates affect the lipid bilayer in biological membranes.

  9. Hydration-induced changes of structure and vibrational frequencies of methylphosphocholine studied as a model of biomembrane lipids.

    PubMed

    Mrázková, E; Hobza, P; Bohl, M; Gauger, D R; Pohle, W

    2005-08-11

    The chemical characteristics of the polar parts of phospholipids as the main components of biological membranes were investigated by using infrared (IR) spectroscopy and theoretical calculations with water as a probe molecule. The logical key molecule used in this study is methylphosphocholine (MePC) as it is not only a representative model for a polar lipid headgroup but itself has biological significance. Isolated MePC forms a compact (folded) structure which is essentially stabilized by two intramolecular C-H...O type hydrogen bonds. At lower hydration, considerable wavenumber shifts were revealed by IR spectroscopy: the frequencies of the (O-P-O)- stretches were strongly redshifted, whereas methyl and methylene C-H and O-P-O stretches shifted surprisingly to blue. The origin of both red- and blueshifts was rationalized, on the basis of molecular-dynamics and quantum-chemistry calculations. In more detail, the hydration-induced blueshifts of C-H stretches could be shown to arise from several origins: disruption of the intramolecular C-H...O hydrogen bonds, formation of intermolecular C-H...O(water) H-bonds. The stepwise disruption of the intramolecular hydrogen bonds appeared to be the main feature that causes partial unfolding of the compact structure. However, the transition from a folded to extended MePC structure was completed only at high hydration. One might hypothesize that the mechanism of hydration-driven conformational changes as described here for MePC could be transferred to other zwitterions with relevant internal C-H...O hydrogen bonds.

  10. Kinetics of Hole Nucleation in Biomembrane Rupture

    PubMed Central

    Evans, Evan; Smith, Benjamin A

    2011-01-01

    The core component of a biological membrane is a fluid-lipid bilayer held together by interfacial-hydrophobic and van der Waals interactions, which are balanced for the most part by acyl chain entropy confinement. If biomembranes are subjected to persistent tensions, an unstable (nanoscale) hole will emerge at some time to cause rupture. Because of the large energy required to create a hole, thermal activation appears to be requisite for initiating a hole and the activation energy is expected to depend significantly on mechanical tension. Although models exist for the kinetic process of hole nucleation in tense membranes, studies of membrane survival have failed to cover the ranges of tension and lifetime needed to critically examine nucleation theory. Hence, rupturing giant (~20 μm) membrane vesicles ultra-slowly to ultra-quickly with slow to fast ramps of tension, we demonstrate a method to directly quantify kinetic rates at which unstable holes form in fluid membranes, at the same time providing a range of kinetic rates from < 0.01 s−1 to > 100 s−1. Measuring lifetimes of many hundreds of vesicles, each tensed by precision control of micropipet suction, we have determined the rates of failure for vesicles made from several synthetic phospholipids plus 1:1 mixtures of phospho- and sphingo-lipids with cholesterol, all of which represent prominent constituents of eukaryotic cell membranes. Plotted on a logarithmic scale, the failure rates for vesicles are found to rise dramatically with increase of tension. Converting the experimental profiles of kinetic rates into changes of activation energy versus tension, we show that the results closely match expressions for thermal activation derived from a combination of meso-scale theory and molecular-scale simulations of hole formation. Moreover, we demonstrate a generic approach to transform analytical fits of activation energies obtained from rupture experiments into energy landscapes characterizing the process hole

  11. Lipid Biomembrane in Ionic Liquids

    NASA Astrophysics Data System (ADS)

    Yoo, Brian; Jing, Benxin; Shah, Jindal; Maginn, Ed; Zhu, Y. Elaine; Department of Chemical and Biomolecular Engineering Team

    2014-03-01

    Ionic liquids (ILs) have been recently explored as new ``green'' chemicals in several chemical and biomedical processes. In our pursuit of understanding their toxicities towards aquatic and terrestrial organisms, we have examined the IL interaction with lipid bilayers as model cell membranes. Experimentally by fluorescence microscopy, we have directly observed the disruption of lipid bilayer by added ILs. Depending on the concentration, alkyl chain length, and anion hydrophobicity of ILs, the interaction of ILs with lipid bilayers leads to the formation of micelles, fibrils, and multi-lamellar vesicles for IL-lipid complexes. By MD computer simulations, we have confirmed the insertion of ILs into lipid bilayers to modify the spatial organization of lipids in the membrane. The combined experimental and simulation results correlate well with the bioassay results of IL-induced suppression in bacteria growth, thereby suggesting a possible mechanism behind the IL toxicity. National Science Foundation, Center for Research Computing at Notre Dame.

  12. Uptake and localization mechanisms of fluorescent and colored lipid probes. Part 2. QSAR models that predict localization of fluorescent probes used to identify ("specifically stain") various biomembranes and membranous organelles.

    PubMed

    Horobin, R W; Stockert, J C; Rashid-Doubell, F

    2015-05-01

    We discuss a variety of biological targets including generic biomembranes and the membranes of the endoplasmic reticulum, endosomes/lysosomes, Golgi body, mitochondria (outer and inner membranes) and the plasma membrane of usual fluidity. For each target, we discuss the access of probes to the target membrane, probe uptake into the membrane and the mechanism of selectivity of the probe uptake. A statement of the QSAR decision rule that describes the required physicochemical features of probes that enable selective staining also is provided, followed by comments on exceptions and limits. Examples of probes typically used to demonstrate each target structure are noted and decision rule tabulations are provided for probes that localize in particular targets; these tabulations show distribution of probes in the conceptual space defined by the relevant structure parameters ("parameter space"). Some general implications and limitations of the QSAR models for probe targeting are discussed including the roles of certain cell and protocol factors that play significant roles in lipid staining. A case example illustrates the predictive ability of QSAR models. Key limiting values of the head group hydrophilicity parameter associated with membrane-probe interactions are discussed in an appendix.

  13. Impedance Analysis of Surface-Bound Biomembranes

    DTIC Science & Technology

    1990-06-08

    and identify by block numb (i FIELD GROUP SUB-GROLm--- AC Impedance, Biomembranes, Lipid, Electrod\\) ’CBiosensor - O ( S. &-’te ,,• J ABSTRACT...Instit-ute 57 Union St., Worcester, MA 01608 ABSTRACTElcchria isThe impedance of different electrode substratesElcharacteriz l biomemance atnactuses fomed ...T10 2), indium/tin oxide (ITO) and platinum electrodes that have been "primed" by covalent attachment of long-chained alkyl groups . The electroes were

  14. Biophysical approaches in the study of biomembrane solubilization: quantitative assessment and the role of lateral inhomogeneity.

    PubMed

    Riske, Karin A; Domingues, Cleyton C; Casadei, Bruna R; Mattei, Bruno; Caritá, Amanda C; Lira, Rafael B; Preté, Paulo S C; de Paula, Eneida

    2017-08-23

    Detergents are amphiphilic molecules widely used to solubilize biological membranes and/or extract their components. Nevertheless, because of the complex composition of biomembranes, their solubilization by detergents has not been systematically studied. In this review, we address the solubilization of erythrocytes, which provide a relatively simple, robust and easy to handle biomembrane, and of biomimetic models, to stress the role of the lipid composition on the solubilization process. First, results of a systematic study on the solubilization of human erythrocyte membranes by different series of non-ionic (Triton, CxEy, Brij, Renex, Tween), anionic (bile salts) and zwitterionic (ASB, CHAPS) detergents are shown. Such quantitative approach allowed us to propose Re(sat)-the effective detergent/lipid molar ratio in the membrane for the onset of hemolysis as a new parameter to classify the solubilization efficiency of detergents. Second, detergent-resistant membranes (DRMs) obtained as a result of the partial solubilization of erythrocytes by TX-100, C12E8 and Brij detergents are examined. DRMs were characterized by their cholesterol, sphingolipid and specific proteins content, as well as lipid packing. Finally, lipid bilayers of tuned lipid composition forming liposomes were used to investigate the solubilization process of membranes of different compositions/phases induced by Triton X-100. Optical microscopy of giant unilamellar vesicles revealed that pure phospholipid membranes are fully solubilized, whereas the presence of cholesterol renders the mixture partially or even fully insoluble, depending on the composition. Additionally, Triton X-100 induced phase separation in raft-like mixtures, and selective solubilization of the fluid phase only.

  15. Depolarization Laplace transform analysis of exchangeable hyperpolarized ¹²⁹Xe for detecting ordering phases and cholesterol content of biomembrane models.

    PubMed

    Schnurr, Matthias; Witte, Christopher; Schröder, Leif

    2014-03-18

    We present a highly sensitive nuclear-magnetic resonance technique to study membrane dynamics that combines the temporary encapsulation of spin-hyperpolarized xenon ((129)Xe) atoms in cryptophane-A-monoacid (CrAma) and their indirect detection through chemical exchange saturation transfer. Radiofrequency-labeled Xe@CrAma complexes exhibit characteristic differences in chemical exchange saturation transfer-driven depolarization when interacting with binary membrane models composed of different molecular ratios of DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine). The method is also applied to mixtures of cholesterol and POPC. The existence of domains that fluctuate in cluster size in DPPC/POPC models at a high (75-98%) DPPC content induces up to a fivefold increase in spin depolarization time τ at 297 K. In POPC/cholesterol model membranes, the parameter τ depends linearly on the cholesterol content at 310 K and allows us to determine the cholesterol content with an accuracy of at least 5%. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  16. On soliton propagation in biomembranes and nerves

    PubMed Central

    Heimburg, Thomas; Jackson, Andrew D.

    2005-01-01

    The lipids of biological membranes and intact biomembranes display chain melting transitions close to temperatures of physiological interest. During this transition the heat capacity, volume and area compressibilities, and relaxation times all reach maxima. Compressibilities are thus nonlinear functions of temperature and pressure in the vicinity of the melting transition, and we show that this feature leads to the possibility of soliton propagation in such membranes. In particular, if the membrane state is above the melting transition solitons will involve changes in lipid state. We discuss solitons in the context of several striking properties of nerve membranes under the influence of the action potential, including mechanical dislocations and temperature changes. PMID:15994235

  17. On soliton propagation in biomembranes and nerves.

    PubMed

    Heimburg, Thomas; Jackson, Andrew D

    2005-07-12

    The lipids of biological membranes and intact biomembranes display chain melting transitions close to temperatures of physiological interest. During this transition the heat capacity, volume and area compressibilities, and relaxation times all reach maxima. Compressibilities are thus nonlinear functions of temperature and pressure in the vicinity of the melting transition, and we show that this feature leads to the possibility of soliton propagation in such membranes. In particular, if the membrane state is above the melting transition solitons will involve changes in lipid state. We discuss solitons in the context of several striking properties of nerve membranes under the influence of the action potential, including mechanical dislocations and temperature changes.

  18. Biomembranes research using thermal and cold neutrons.

    PubMed

    Heberle, F A; Myles, D A A; Katsaras, J

    2015-11-01

    In 1932 James Chadwick discovered the neutron using a polonium source and a beryllium target (Chadwick, 1932). In a letter to Niels Bohr dated February 24, 1932, Chadwick wrote: "whatever the radiation from Be may be, it has most remarkable properties." Where it concerns hydrogen-rich biological materials, the "most remarkable" property is the neutron's differential sensitivity for hydrogen and its isotope deuterium. Such differential sensitivity is unique to neutron scattering, which unlike X-ray scattering, arises from nuclear forces. Consequently, the coherent neutron scattering length can experience a dramatic change in magnitude and phase as a result of resonance scattering, imparting sensitivity to both light and heavy atoms, and in favorable cases to their isotopic variants. This article describes recent biomembranes research using a variety of neutron scattering techniques.

  19. Biomembranes research using thermal and cold neutrons

    SciTech Connect

    Heberle, Frederick A.; Myles, Dean A. A.; Katsaras, John

    2015-08-01

    In 1932 James Chadwick discovered the neutron using a polonium source and a beryllium target (Chadwick, 1932). In a letter to Niels Bohr dated February 24, 1932, Chadwick wrote: “whatever the radiation from Be may be, it has most remarkable properties.” Where it concerns hydrogen-rich biological materials, the “most remarkable” property is the neutron’s differential sensitivity for hydrogen and its isotope deuterium. Such differential sensitivity is unique to neutron scattering, which unlike X-ray scattering, arises from nuclear forces. Consequently, the coherent neutron scattering length can experience a dramatic change in magnitude and phase as a result of resonance scattering, imparting sensitivity to both light and heavy atoms, and in favorable cases to their isotopic variants. Furthermore, this article describes recent biomembranes research using a variety of neutron scattering techniques.

  20. Biomembranes research using thermal and cold neutrons

    DOE PAGES

    Heberle, Frederick A.; Myles, Dean A. A.; Katsaras, John

    2015-08-01

    In 1932 James Chadwick discovered the neutron using a polonium source and a beryllium target (Chadwick, 1932). In a letter to Niels Bohr dated February 24, 1932, Chadwick wrote: “whatever the radiation from Be may be, it has most remarkable properties.” Where it concerns hydrogen-rich biological materials, the “most remarkable” property is the neutron’s differential sensitivity for hydrogen and its isotope deuterium. Such differential sensitivity is unique to neutron scattering, which unlike X-ray scattering, arises from nuclear forces. Consequently, the coherent neutron scattering length can experience a dramatic change in magnitude and phase as a result of resonance scattering, impartingmore » sensitivity to both light and heavy atoms, and in favorable cases to their isotopic variants. Furthermore, this article describes recent biomembranes research using a variety of neutron scattering techniques.« less

  1. The decreasing of corn root biomembrane penetration for acetochlor with vermicompost amendment

    NASA Astrophysics Data System (ADS)

    Sytnyk, Svitlana; Wiche, Oliver

    2016-04-01

    One of the topical environmental security issues is management and control of anthropogenic (artificially synthesized) chemical agents usage and utilization. Protection systems development against toxic effects of herbicides should be based on studies of biological indication mechanisms for identification of stressors effect in organisms. Lipid degradation is non-specific reaction to exogenous chemical agents effects. Therefore it is important to study responses of lipid components depending on the stressor type. We studied physiological and biochemical characteristics of lipid metabolism under action of herbicides of chloracetamide group. Corn at different stages of ontogenesis was used as testing object during model laboratory and microfield experiments. Cattle manure treated with earth worms Essenia Foetida was used as compost fertilizer to add to chain: chernozem (black soil) -corn system. It was found several acetochlor actions as following: -decreasing of sterols, phospholipids, phosphatidylcholines and phosphatidylethanolamines content; -increasing pool of available fatty acids and phosphatidic acids associated with intensification of hydrolysis processes; -lypase activity stimulation under effect of stressor in low concentrations; -lypase activity inhibition under effect of high stressor level; -decreasing of polyenoic free fatty acids indicating biomembrane degradation; -accumulation of phospholipids degradation products (phosphatidic acids); -decreasing of high-molecular compounds (phosphatidylcholin and phosphatidylinositol) concentrations; -change in the index of unsaturated and saturated free fatty acids ratio in biomembranes structure; It was established that incorporation of vermicompost in dose 0.4 kg/m2 in black soil lead to corn roots biomembrane restoration. It was fixed the decreasing roots biomembrane penetration for acetochlor in trial with vermicompost. Second compost substances antidote effect is the soil microorganism's activation

  2. A Molecular Understanding of the Toxic Interactions of Ionic Liquids Towards a Lipid Biomembrane

    NASA Astrophysics Data System (ADS)

    Yoo, Brian; Maginn, Edward; Zhu, Yingxi

    2015-03-01

    There is a growing urgency to understand the toxicity of ionic liquids (ILs) due to their potential leakage into aquatic environment via aqueous waste streams in many large-scale commercial applications. Better understanding in the molecular interactions of ILs, primarily those in the popular imidazolium-class, with biological systems can serve as a physical foundation for their future design into ecologically benign ones. Here we investigate the toxic interaction of IL aqueous solutions with a supported lipid bilayer as a model cell membrane, using a combined experimental (fluorescence microscopic measurements) and multiscale simulation-based analysis. Both experimental and computer simulation studies have shown that the interactions of ILs with a supported lipid bilayer can lead to the insertion of ILs into the lipid bilayer, causing biomembrane morphological changes into multilayers, fibers, and/or vesicles with a strong dependence on the alkyl side chain length of IL cations. Using atomistic and coarse grained simulations, we have examined the potential of mean force of IL upon approaching a lipid bilayer and resulting changes in the mechanical compliance of lipid bilayer induced by IL interactions. We find that the resulting IL-lipid bilayer complexes can be strongly dependent on the ILs' ability to form cationic micelles. National Science Foundation (CBET-1134238).

  3. CdSe magic-sized quantum dots incorporated in biomembrane models at the air-water interface composed of components of tumorigenic and non-tumorigenic cells.

    PubMed

    Goto, Thiago E; Lopes, Carla C; Nader, Helena B; Silva, Anielle C A; Dantas, Noelio O; Siqueira, José R; Caseli, Luciano

    2016-07-01

    Cadmium selenide (CdSe) magic-sized quantum dots (MSQDs) are semiconductor nanocrystals with stable luminescence that are feasible for biomedical applications, especially for in vivo and in vitro imaging of tumor cells. In this work, we investigated the specific interaction of CdSe MSQDs with tumorigenic and non-tumorigenic cells using Langmuir monolayers and Langmuir-Blodgett (LB) films of lipids as membrane models for diagnosis of cancerous cells. Surface pressure-area isotherms and polarization modulation reflection-absorption spectroscopy (PM-IRRAS) showed an intrinsic interaction between the quantum dots, inserted in the aqueous subphase, and Langmuir monolayers constituted either of selected lipids or of tumorigenic and non-tumorigenic cell extracts. The films were transferred to solid supports to obtain microscopic images, providing information on their morphology. Similarity between films with different compositions representing cell membranes, with or without the quantum dots, was evaluated by atomic force microscopy (AFM) and confocal microscopy. This study demonstrates that the affinity of quantum dots for models representing cancer cells permits the use of these systems as devices for cancer diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Surface complexation modeling

    USDA-ARS?s Scientific Manuscript database

    Adsorption-desorption reactions are important processes that affect the transport of contaminants in the environment. Surface complexation models are chemical models that can account for the effects of variable chemical conditions, such as pH, on adsorption reactions. These models define specific ...

  5. Performance of skeleton-reinforced biomembranes in locomotion

    NASA Astrophysics Data System (ADS)

    Zhu, Qiang; Shoele, Kourosh

    2008-11-01

    Skeleton-reinforced biomembranes are ubiquitous in nature and play critical roles in many biological functions. Representative examples include insect wings, cell membranes, and mollusk nacres. In this study we focus on the ray fins of fish and investigate the effects of anisotropic flexibility on their performance. Employing a fluid-structure interaction algorithm by coupling a boundary-element model with a nonlinear structural model, we examined the dynamics of a membrane that is geometrically and structurally similar to a caudal fin. Several locomotion modes that closely resemble caudal fin kinematics reported in the literature are applied. Our results show that the flexibility of the fin significantly increases its capacity of thrust generation, manifested as increased efficiency, reduced transverse force, and reduced sensitivity to kinematic parameters. This design also makes the fin more controllable and deployable. Despite simplifications made in this model in terms of fin geometry, internal structure, and kinematics, detailed features of the simulated flow field are consistent with observations and speculations based upon Particle Image Velocimetry (PIV) measurements of flow around live fish.

  6. Biomembrane disruption by silica-core nanoparticles: effect of surface functional group measured using a tethered bilayer lipid membrane.

    PubMed

    Liu, Ying; Zhang, Zhen; Zhang, Quanxuan; Baker, Gregory L; Worden, R Mark

    2014-01-01

    Engineered nanomaterials (ENM) have desirable properties that make them well suited for many commercial applications. However, a limited understanding of how ENM's properties influence their molecular interactions with biomembranes hampers efforts to design ENM that are both safe and effective. This paper describes the use of a tethered bilayer lipid membrane (tBLM) to characterize biomembrane disruption by functionalized silica-core nanoparticles. Electrochemical impedance spectroscopy was used to measure the time trajectory of tBLM resistance following nanoparticle exposure. Statistical analysis of parameters from an exponential resistance decay model was then used to quantify and analyze differences between the impedance profiles of nanoparticles that were unfunctionalized, amine-functionalized, or carboxyl-functionalized. All of the nanoparticles triggered a decrease in membrane resistance, indicating nanoparticle-induced disruption of the tBLM. Hierarchical clustering allowed the potency of nanoparticles for reducing tBLM resistance to be ranked in the order amine>carboxyl~bare silica. Dynamic light scattering analysis revealed that tBLM exposure triggered minor coalescence for bare and amine-functionalized silica nanoparticles but not for carboxyl-functionalized silica nanoparticles. These results indicate that the tBLM method can reproducibly characterize ENM-induced biomembrane disruption and can distinguish the BLM-disruption patterns of nanoparticles that are identical except for their surface functional groups. The method provides insight into mechanisms of molecular interaction involving biomembranes and is suitable for miniaturization and automation for high-throughput applications to help assess the health risk of nanomaterial exposure or identify ENM having a desired mode of interaction with biomembranes. © 2013. Published by Elsevier B.V. All rights reserved.

  7. Differentiation of photoreceptor cells and morphogenetic function of biomembranes.

    PubMed

    Vinnikov, Y A

    1974-01-01

    Photoreceptor cells of eyes in vertebrate animals have been chosen as an example to illustrate the morphogenetic function of biomembranes in differentiation of the eye outer segments -- rods and cones. Morphogenetic function of biomembranes in photoreceptor cells involves an insertion of the heterogeneous molecule of visual pigment into the original plasma membrane. Depending on some features of visual pigment in one case cones may be produced or rods as more complicated structures may be differentiated in the other one. Some evolution aspects of photoreceptor cell differentiation have also been under discussion.

  8. Modeling complexes of modeled proteins.

    PubMed

    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.

  9. Sporadic meteoroid complex: Modeling

    NASA Astrophysics Data System (ADS)

    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.

  10. Use of inverse theory algorithms in the analysis of biomembrane NMR data.

    PubMed

    Sternin, Edward

    2007-01-01

    Treating the analysis of experimental spectroscopic data as an inverse problem and using regularization techniques to obtain stable pseudoinverse solutions, allows access to previously unavailable level of spectroscopic detail. The data is mapped into an appropriate physically relevant parameter space, leading to better qualitative and quantitative understanding of the underlying physics, and in turn, to better and more detailed models. A brief survey of relevant inverse methods is illustrated by several successful applications to the analysis of nuclear magnetic resonance data, yielding new insight into the structure and dynamics of biomembrane lipids.

  11. How lidocaine influences the bilayer thickness and bending elasticity of biomembranes

    NASA Astrophysics Data System (ADS)

    Yi, Zheng; Nagao, Michihiro; Bossev, Dobrin P.

    2010-11-01

    We have studied how local anesthetics influence the structural and dynamical properties of model bio-membranes. The measurements of small-angle neutron scattering have been performed on 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) unilamellar vesicles with different concentrations of lidocaine in D2O to determine the bilayer thickness as a function of the lidocaine concentration. The neutron-spin echo spectroscopy (NSE) has been used to study the influence of lidocaine on the bending elasticity of DMPC bilayers in fluid crystal phase (Lα) and the ripple gel (Pβ') phase.

  12. Predictive Surface Complexation Modeling

    SciTech Connect

    Sverjensky, Dimitri A.

    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 CO2 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.

  13. Debating complexity in modeling

    USGS Publications Warehouse

    Hunt, Randall J.; Zheng, Chunmiao

    1999-01-01

    As scientists trying to understand the natural world, how should our effort be apportioned? We know that the natural world is characterized by complex and interrelated processes. Yet do we need to explicitly incorporate these intricacies to perform the tasks we are charged with? In this era of expanding computer power and development of sophisticated preprocessors and postprocessors, are bigger machines making better models? Put another way, do we understand the natural world better now with all these advancements in our simulation ability? Today the public's patience for long-term projects producing indeterminate results is wearing thin. This increases pressure on the investigator to use the appropriate technology efficiently. On the other hand, bringing scientific results into the legal arena opens up a new dimension to the issue: to the layperson, a tool that includes more of the complexity known to exist in the real world is expected to provide the more scientifically valid answer.

  14. Biomembranes in atomistic and coarse-grained simulations

    NASA Astrophysics Data System (ADS)

    Pluhackova, Kristyna; Böckmann, Rainer A.

    2015-08-01

    The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.

  15. Response of biomembrane domains to external stimuli

    NASA Astrophysics Data System (ADS)

    Urbancic, Iztok

    To enrich our knowledge about membrane domains, new measurement techniques with extended spatial and temporal windows are being vigorously developed by combining various approaches. Following such efforts of the scientific community, we set up fluorescence microspectroscopy (FMS), bridging two well established methods: fluorescence microscopy, which enables imaging of the samples with spatial resolution down to 200 nm, and fluorescence spectroscopy that provides molecular information of the environment at nanometer and nanosecond scale. The combined method therefore allows us to localize this type of information with the precision suitable for studying various cellular structures. Faced with weak available fluorescence signals, we have put considerable efforts into optimization of measurement processes and analysis of the data. By introducing a novel acquisition scheme and by fitting the data with a mathematical model, we preserved the spectral resolution, characteristic for spectroscopic measurements of bulk samples, also at microscopic level. We have at the same time overcome the effects of photobleaching, which had previously considerably distorted the measured spectral lineshape of photosensitive dyes and consequently hindered the reliability of FMS. Our new approach has therefore greatly extended the range of applicable environmentally sensitive probes, which can now be designed to better accommodate the needs of each particular experiment. Moreover, photobleaching of fluorescence signal can now even be exploited to obtain new valuable information about molecular environment of the probes, as bleaching rates of certain probes also depend on physical and chemical properties of the local surroundings. In this manner we increased the number of available spatially localized spectral parameters, which becomes invaluable when investigating complex biological systems that can only be adequately characterized by several independent variables. Applying the developed

  16. Dynamics of bio-membranes investigated by neutron spin echo: Effects of phospholipid conformations and presence of lidocaine

    NASA Astrophysics Data System (ADS)

    Yi, Zheng

    Bio-membranes of the natural living cells are made of bilayers of phospholipids molecules embedded with other constituents, such as cholesterol and membrane proteins, which help to accomplish a broad range of functions. Vesicles made of lipid bilayers can serve as good model systems for bio-membranes. Therefore these systems have been extensively characterized and much is known about their shape, size, porosity and functionality. In this dissertation we report the studies of the effects of the phosoholipid conformation, such as hydrocarbon number and presence of double bond in hydrophobic tails on dynamics of phospholipids bilayers studied by neutron spin echo (NSE) technique. We have investigated how lidocaine, the most medically used local anesthetics (LA), influence the structural and dynamical properties of model bio-membranes by small angle neutron scattering (SANS), NSE and differential scanning calorimetry (DSC). To investigate the influence of phospholipid conformation on bio-membranes, the bending elasticities kappac of seven saturated and monounsaturated phospholipid bilayers were investigated by NSE spectroscopy. kappa c of phosphatidylcholines (PCS) in liquid crystalline (L alpha) phase ranges from 0.38x10-19 J for 1,2-Dimyristoyl- sn-Glycero-3-Phosphocholine (14:0 PC) to 0.64x10-19 J for 1,2-Dieicosenoyl-sn-Glycero-3-Phosphocholine (20:1 PC). It was confirmed that when the area modulus KA varies little with chain unsaturation or length, the elastic ratios (kappac/ KA)1/2 of bilayers varies linearly with lipid hydrophobic thickness d. For the study of the influence of LA on bio-membranes, SANS measurements have been performed on 14:0 PC bilayers with different concentrations of lidocaine to determine the bilayer thickness dL as a function of the lidocaine concentration. NSE has been used to study the influence of lidocaine on the bending elasticity of 14:0 PC bilayers in Lalpha and ripple gel (Pbeta') phases. Our results confirmed that the molecules of

  17. 57 Fe Mössbauer probe of spin crossover thin films on a bio-membrane

    NASA Astrophysics Data System (ADS)

    Naik, Anil D.; Garcia, Yann

    2012-03-01

    An illustrious complex [Fe(ptz)6](BF4)2 (ptz = 1-propyl-tetrazole) ( 1) which was produced in the form of submicron crystals and thin film on Allium cepa membrane was probed by 57Fe Mossbauer spectroscopy in order to follow its intrinsic spin crossover. In addition to a weak signal that corresponds to neat SCO compound significant amount of other iron compounds are found that could have morphed from 1 due to specific host-guest interaction on the lipid-bilayer of bio-membrane. Further complimentary information about biogenic role of membrane, was obtained from variable temperature Mossbauer spectroscopy on a ~5% enriched [57Fe(H2O)6](BF4)2 salt on this membrane.

  18. A bola-phospholipid bearing tetrafluorophenylazido chromophore as a promising lipid probe for biomembrane photolabeling studies.

    PubMed

    Xia, Yi; Sengupta, Kheya; Maggiani, Alain; Qu, Fanqi; Peng, Ling

    2013-08-14

    A bola-phospholipid probe, carrying a tetrafluorophenylazido chromophore in the middle of the transmembrane diacyl chain, was synthesized and characterized with a view to studying biomembranes by a photolabeling approach. This probe shows the advantageous stability of bola-lipids in giant vesicle formation alongside excellent photochemical properties conferred by the tetrafluorophenylazido chromophore, and thus constitutes a promising probe for biomembrane photolabeling studies.

  19. Action of the multifunctional peptide BP100 on native biomembranes examined by solid-state NMR.

    PubMed

    Misiewicz, Julia; Afonin, Sergii; Grage, Stephan L; van den Berg, Jonas; Strandberg, Erik; Wadhwani, Parvesh; Ulrich, Anne S

    2015-04-01

    Membrane composition is a key factor that regulates the destructive activity of antimicrobial peptides and the non-leaky permeation of cell penetrating peptides in vivo. Hence, the choice of model membrane is a crucial aspect in NMR studies and should reflect the biological situation as closely as possible. Here, we explore the structure and dynamics of the short multifunctional peptide BP100 using a multinuclear solid-state NMR approach. The membrane alignment and mobility of this 11 amino acid peptide was studied in various synthetic lipid bilayers with different net charge, fluidity, and thickness, as well as in native biomembranes harvested from prokaryotic and eukaryotic cells. (19)F-NMR provided the high sensitivity and lack of natural abundance background that are necessary to observe a labelled peptide even in protoplast membranes from Micrococcus luteus and in erythrocyte ghosts. Six selectively (19)F-labeled BP100 analogues gave remarkably similar spectra in all of the macroscopically oriented membrane systems, which were studied under quasi-native conditions of ambient temperature and full hydration. This similarity suggests that BP100 has the same surface-bound helical structure and high mobility in the different biomembranes and model membranes alike, independent of charge, thickness or cholesterol content of the system. (31)P-NMR spectra of the phospholipid components did not indicate any bilayer perturbation, so the formation of toroidal wormholes or micellarization can be excluded as a mechanism of its antimicrobial or cell penetrating action. However, (2)H-NMR analysis of the acyl chain order parameter profiles showed that BP100 leads to considerable membrane thinning and thereby local destabilization.

  20. Tools for characterizing biomembranes : final LDRD report.

    SciTech Connect

    Alam, Todd Michael; Stevens, Mark; Holland, Gregory P.; McIntyre, Sarah K.

    2007-10-01

    A suite of experimental nuclear magnetic resonance (NMR) spectroscopy tools were developed to investigate lipid structure and dynamics in model membrane systems. By utilizing both multinuclear and multidimensional NMR experiments a range of different intra- and inter-molecular contacts were probed within the membranes. Examples on pure single component lipid membranes and on the canonical raft forming mixture of DOPC/SM/Chol are presented. A unique gel phase pretransition in SM was also identified and characterized using these NMR techniques. In addition molecular dynamics into the hydrogen bonding network unique to sphingomyelin containing membranes were evaluated as a function of temperature, and are discussed.

  1. Dynamic Tension Spectroscopy and Strength of Biomembranes

    PubMed Central

    Evans, Evan; Heinrich, Volkmar; Ludwig, Florian; Rawicz, Wieslawa

    2003-01-01

    Rupturing fluid membrane vesicles with a steady ramp of micropipette suction produces a distribution of breakage tensions governed by the kinetic process of membrane failure. When plotted as a function of log(tension loading rate), the locations of distribution peaks define a dynamic tension spectrum with distinct regimes that reflect passage of prominent energy barriers along the kinetic pathway. Using tests on five types of giant phosphatidylcholine lipid vesicles over loading rates(tension/time) from 0.01–100 mN/m/s, we show that the kinetic process of membrane breakage can be modeled by a causal sequence of two thermally-activated transitions. At fast loading rates, a steep linear regime appears in each spectrum which implies that membrane failure starts with nucleation of a rare precursor defect. The slope and projected intercept of this regime are set by defect size and frequency of spontaneous formation, respectively. But at slow loading rates, each spectrum crosses over to a shallow-curved regime where rupture tension changes weakly with rate. This regime is predicted by the classical cavitation theory for opening an unstable hole in a two-dimensional film within the lifetime of the defect state. Under slow loading, membrane edge energy and the frequency scale for thermal fluctuations in hole size are the principal factors that govern the level of tension at failure. To critically test the model and obtain the parameters governing the rates of transition under stress, distributions of rupture tension were computed and matched to the measured histograms through solution of the kinetic master (Markov) equations for defect formation and annihilation or evolution to an unstable hole under a ramp of tension. As key predictors of membrane strength, the results for spontaneous frequencies of defect formation and hole edge energies were found to correlate with membrane thicknesses and elastic bending moduli, respectively. PMID:14507698

  2. The thermodynamics of simple biomembrane mimetic systems

    PubMed Central

    Raudino, Antonio; Sarpietro, Maria Grazia; Pannuzzo, Martina

    2011-01-01

    Insight into the forces governing a system is essential for understanding its behavior and function. Thermodynamic investigations provide a wealth of information that is not, or is hardly, available from other methods. This article reviews thermodynamic approaches and assays to measure collective properties such as heat adsorption / emission and volume variations. These methods can be successfully applied to the study of lipid vesicles (liposomes) and biological membranes. With respect to instrumentation, differential scanning calorimetry, pressure perturbation calorimetry, isothermal titration calorimetry, dilatometry, and acoustic techniques aimed at measuring the isothermal and adiabatic processes, two- and three-dimensional compressibilities are considered. Applications of these techniques to lipid systems include the measurement of different thermodynamic parameters and a detailed characterization of thermotropic, barotropic, and lyotropic phase behavior. The membrane binding and / or partitioning of solutes (proteins, peptides, drugs, surfactants, ions, etc.) can also be quantified and modeled. Many thermodynamic assays are available for studying the effect of proteins and other additives on membranes, characterizing non-ideal mixing, domain formation, bilayer stability, curvature strain, permeability, solubilization, and fusion. Studies of membrane proteins in lipid environments elucidate lipid–protein interactions in membranes. Finally, a plethora of relaxation phenomena toward equilibrium thermodynamic structures can be also investigated. The systems are described in terms of enthalpic and entropic forces, equilibrium constants, heat capacities, partial volume changes, volume and area compressibility, and so on, also shedding light on the stability of the structures and the molecular origin and mechanism of the structural changes. PMID:21430953

  3. Measured depletion of ions at the biomembrane interface.

    PubMed

    Petrache, Horia I; Kimchi, Itamar; Harries, Daniel; Parsegian, V Adrian

    2005-08-24

    Expected from theory and simulations, depletion of ions at fuzzy biomembrane interfaces has long eluded experiments. Here, we show how salt exclusion can be accurately measured by surprisingly simple yet accurate benchtop measurements. Multilamellar aggregates of common phospholipids sink in low salt but float in salt solutions that are much less dense than the lipid itself. By manipulating bath and lipid densities, using heavy water and varied lipid chain length, we obtain accurate exclusion curves over a wide range of KCl and KBr concentrations. While maintaining a constant width at low salt, the exclusion layer decreases in high salt, following the Debye screening length. Consistent with interfacial accumulation of polarizable ions, bromide salts are less excluded than chloride, with an attraction of approximately 2kBT per Br- ion. So far neglected in theoretical descriptions, the competition between salt exclusion and binding is critical to understanding membrane interactions and specific ionic effects.

  4. Field theoretical approach for bio-membrane coupled with flow field

    NASA Astrophysics Data System (ADS)

    Oya, Y.; Kawakatsu, T.

    2013-02-01

    Shape deformation of bio-membranes in flow field is well known phenomenon in biological systems, for example red blood cell in blood vessel. To simulate such deformation with use of field theoretical approach, we derived the dynamical equation of phase field for shape of membrane and coupled the equation with Navier-Stokes equation for flow field. In 2-dimensional simulations, we found that a bio-membrane in a Poiseuille flow takes a parachute shape similar to the red blood cells.

  5. Atmospheric modeling in complex terrain

    SciTech Connect

    Williams, M. D.; Streit, G. E.

    1990-05-01

    Los Alamos investigators have developed several models which are relevant to modeling Mexico City air quality. The collection of models includes: meteorological models, dispersion models, air chemistry models, and visibility models. The models have been applied in several different contexts. They have been developed primarily to address the complexities posed by complex terrain. HOTMAC is the meteorological model which requires terrain and limited meteorological information. HOTMAC incorporates a relatively complete description of atmospheric physics to give good descriptions of the wind, temperature, and turbulence fields. RAPTAD is a dispersion code which uses random particle transport and kernel representations to efficiently provide accurate pollutant concentration fields. RAPTAD provides a much better description of tracer dispersion than do Gaussian puff models which fail to properly represent the effects of the wind profile near the surface. ATMOS and LAVM treat photochemistry and visibility respectively. ATMOS has been used to describe wintertime chemistry of the Denver brown cloud. Its description provided reasonable agreement with measurements for the high altitude of Denver. LAVM can provide both numerical indices or pictoral representations of visibility effects of pollutants. 15 refs., 74 figs.

  6. BOOK REVIEW: Modeling Complex Systems

    NASA Astrophysics Data System (ADS)

    Schreckenberg, M.

    2004-10-01

    This book by Nino Boccara presents a compilation of model systems commonly termed as `complex'. It starts with a definition of the systems under consideration and how to build up a model to describe the complex dynamics. The subsequent chapters are devoted to various categories of mean-field type models (differential and recurrence equations, chaos) and of agent-based models (cellular automata, networks and power-law distributions). Each chapter is supplemented by a number of exercises and their solutions. The table of contents looks a little arbitrary but the author took the most prominent model systems investigated over the years (and up until now there has been no unified theory covering the various aspects of complex dynamics). The model systems are explained by looking at a number of applications in various fields. The book is written as a textbook for interested students as well as serving as a compehensive reference for experts. It is an ideal source for topics to be presented in a lecture on dynamics of complex systems. This is the first book on this `wide' topic and I have long awaited such a book (in fact I planned to write it myself but this is much better than I could ever have written it!). Only section 6 on cellular automata is a little too limited to the author's point of view and one would have expected more about the famous Domany--Kinzel model (and more accurate citation!). In my opinion this is one of the best textbooks published during the last decade and even experts can learn a lot from it. Hopefully there will be an actualization after, say, five years since this field is growing so quickly. The price is too high for students but this, unfortunately, is the normal case today. Nevertheless I think it will be a great success!

  7. Speciation analysis, bioavailability and risk assessment of trace metals in herbal decoctions using a combined technique of in Vitro digestion and biomembrane filtration as sample pretreatment method.

    PubMed

    Li, Shun-Xing; Lin, Lu-xiu; Lin, Jing; Zheng, Feng-Ying; Wang, Qing-Xiang; Weng, Wen

    2010-01-01

    Sample preparation is the first crucial step in the speciation analysis, bioavailability and risk assessment of trace metals in plant samples such as herb and vegetables. Two bionic technologies titled 'in vitro digestion' and 'extraction with biomembrane' were developed for pre-treatment of herbal decoction. The decoctions of Aconiteum carmichaeli and Paeonia lactiflora were digested at body temperature, at the acidity of the stomach or intestine and with inorganic and organic materials (digestive enzymes were included for whole-bionic and excluded for semi-bionic) found in the stomach or intestine. Being similar to the biomembrane between the gastrointestinal tract and blood vessels, monolayer liposome was used as a biomembrane model. Affinity-monolayer liposome metals and water-soluble metals were used for speciation analysis and bioavailability assessment of copper and zinc in herbal decoction. In the decoction of Aconiteum carmichaeli and Paeonia lactiflora, Zn was mainly absorbed in the intestine and Cu was mainly absorbed by both stomach and intestine. The safe dosage for males and females is below 257.1 g/day Aconiteum carmichaeli and 529.4 g/day Paeonia lactiflora. Copyright © 2010 John Wiley & Sons, Ltd.

  8. Phospholipid bilayer-perturbing properties underlying lysis induced by pH-sensitive cationic lysine-based surfactants in biomembranes.

    PubMed

    Nogueira, Daniele Rubert; Mitjans, Montserrat; Busquets, M Antonia; Pérez, Lourdes; Vinardell, M Pilar

    2012-08-14

    Amino acid-based surfactants constitute an important class of natural surface-active biomolecules with an unpredictable number of industrial applications. To gain a better mechanistic understanding of surfactant-induced membrane destabilization, we assessed the phospholipid bilayer-perturbing properties of new cationic lysine-based surfactants. We used erythrocytes as biomembrane models to study the hemolytic activity of surfactants and their effects on cells' osmotic resistance and morphology, as well as on membrane fluidity and membrane protein profile with varying pH. The antihemolytic capacity of amphiphiles correlated negatively with the length of the alkyl chain. Anisotropy measurements showed that the pH-sensitive surfactants, with the positive charge on the α-amino group of lysine, significantly increased membrane fluidity at acidic conditions. SDS-PAGE analysis revealed that surfactants induced significant degradation of membrane proteins in hypo-osmotic medium and at pH 5.4. By scanning electron microscopy examinations, we corroborated the interaction of surfactants with lipid bilayer. We found that varying the surfactant chemical structure is a way to modulate the positioning of the molecule inside bilayer and, thus, the overall effect on the membrane. Our work showed that pH-sensitive lysine-based surfactants significantly disturb the lipid bilayer of biomembranes especially at acidic conditions, which suggests that these compounds are promising as a new class of multifunctional bioactive excipients for active intracellular drug delivery.

  9. Modeling phototaxis in complex networks

    NASA Astrophysics Data System (ADS)

    Kuksenok, Olga; Balazs, Anna C.

    2006-03-01

    Phototaxis is the movement of organisms towards or away from light. It is one of the most important photo-biological processes, which in turn are responsible for light reception and the use of photons as a source of information. We briefly review current models of phototaxis of biological organisms and we develop a simple, minimal model for synthetic microscale units that can undergo phototactic motion. We then use this model to simulate the collective motion of such photosensitive artificial objects within a complex network, which is illuminated in a non-uniform manner by an external light.

  10. Complex Networks in Psychological Models

    NASA Astrophysics Data System (ADS)

    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.

  11. Modeling wildfire incident complexity dynamics.

    PubMed

    Thompson, Matthew P

    2013-01-01

    Wildfire management in the United States and elsewhere is challenged by substantial uncertainty regarding the location and timing of fire events, the socioeconomic and ecological consequences of these events, and the costs of suppression. Escalating U.S. Forest Service suppression expenditures is of particular concern at a time of fiscal austerity as swelling fire management budgets lead to decreases for non-fire programs, and as the likelihood of disruptive within-season borrowing potentially increases. Thus there is a strong interest in better understanding factors influencing suppression decisions and in turn their influence on suppression costs. As a step in that direction, this paper presents a probabilistic analysis of geographic and temporal variation in incident management team response to wildfires. The specific focus is incident complexity dynamics through time for fires managed by the U.S. Forest Service. The modeling framework is based on the recognition that large wildfire management entails recurrent decisions across time in response to changing conditions, which can be represented as a stochastic dynamic system. Daily incident complexity dynamics are modeled according to a first-order Markov chain, with containment represented as an absorbing state. A statistically significant difference in complexity dynamics between Forest Service Regions is demonstrated. Incident complexity probability transition matrices and expected times until containment are presented at national and regional levels. Results of this analysis can help improve understanding of geographic variation in incident management and associated cost structures, and can be incorporated into future analyses examining the economic efficiency of wildfire management.

  12. Artificial biomembrane morphology: a dissipative particle dynamics study.

    PubMed

    Becton, Matthew; Averett, Rodney; Wang, Xianqiao

    2017-09-18

    Artificial membranes mimicking biological structures are rapidly breaking new ground in the areas of medicine and soft-matter physics. In this endeavor, we use dissipative particle dynamics simulation to investigate the morphology and behavior of lipid-based biomembranes under conditions of varied lipid density and self-interaction. Our results show that a less-than-normal initial lipid density does not create the traditional membrane; but instead results in the formation of a 'net', or at very low densities, a series of disparate 'clumps' similar to the micelles formed by lipids in nature. When the initial lipid density is high, a membrane forms, but due to the large number of lipids, the naturally formed membrane would be larger than the simulation box, leading to 'rippling' behavior as the excess repulsive force of the membrane interior overcomes the bending energy of the membrane. Once the density reaches a certain point however, 'bubbles' appear inside the membrane, reducing the rippling behavior and eventually generating a relatively flat, but thick, structure with micelles of water inside the membrane itself. Our simulations also demonstrate that the interaction parameter between individual lipids plays a significant role in the formation and behavior of lipid membrane assemblies, creating similar structures as the initial lipid density distribution. This work provides a comprehensive approach to the intricacies of lipid membranes, and offers a guideline to design biological or polymeric membranes through self-assembly processes as well as develop novel cellular manipulation and destruction techniques.

  13. Morphological and Physical Analysis of Natural Phospholipids-Based Biomembranes

    PubMed Central

    Jacquot, Adrien; Francius, Grégory; Razafitianamaharavo, Angelina; Dehghani, Fariba; Tamayol, Ali; Linder, Michel; Arab-Tehrany, Elmira

    2014-01-01

    Background Liposomes are currently an important part of biological, pharmaceutical, medical and nutritional research, as they are considered to be among the most effective carriers for the introduction of various types of bioactive agents into target cells. Scope of Review In this work, we study the lipid organization and mechanical properties of biomembranes made of marine and plant phospholipids. Membranes based on phospholipids extracted from rapeseed and salmon are studied in the form of liposome and as supported lipid bilayer. Dioleylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC) are used as references to determine the lipid organization of marine and plant phospholipid based membranes. Atomic force microscopy (AFM) imaging and force spectroscopy measurements are performed to investigate the membranes' topography at the micrometer scale and to determine their mechanical properties. Major Conclusions The mechanical properties of the membranes are correlated to the fatty acid composition, the morphology, the electrophoretic mobility and the membrane fluidity. Thus, soft and homogeneous mechanical properties are evidenced for salmon phospholipids membrane containing various polyunsaturated fatty acids. Besides, phase segregation in rapeseed membrane and more important mechanical properties were emphasized for this type of membranes by contrast to the marine phospholipids based membranes. General Significance This paper provides new information on the nanomechanical and morphological properties of membrane in form of liposome by AFM. The originality of this work is to characterize the physico-chemical properties of the nanoliposome from the natural sources containing various fatty acids and polar head. PMID:25238543

  14. Nanometer-resolved radio-frequency absorption and heating in biomembrane hydration layers.

    PubMed

    Gekle, Stephan; Netz, Roland R

    2014-05-08

    Radio-frequency (RF) electromagnetic fields are readily absorbed in biological matter and lead to dielectric heating. To understand how RF radiation interacts with macromolecular structures and possibly influences biological function, a quantitative description of dielectric absorption and heating at nanometer resolution beyond the usual effective medium approach is crucial. We report an exemplary multiscale theoretical study for biomembranes that combines (i) atomistic simulations for the spatially resolved absorption spectrum at a single planar DPPC lipid bilayer immersed in water, (ii) calculation of the electric field distribution in planar and spherical cell models, and (iii) prediction of the nanometer resolved temperature profiles under steady RF radiation. Our atomistic simulations show that the only 2 nm thick lipid hydration layer strongly absorbs in a wide RF range between 10 MHz and 100 GHz. The absorption strength, however, strongly depends on the direction of the incident wave. This requires modeling of the electric field distribution using tensorial dielectric spectral functions. For a spherical cell model, we find a strongly enhanced RF absorption on an equatorial ring, which gives rise to temperature gradients inside a single cell under radiation. Although absolute temperature elevation is small under conditions of typical telecommunication usage, our study points to hitherto neglected temperature gradient effects and allows thermal RF effects to be predicted on an atomistically resolved level. In addition to a refined physiological risk assessment of RF fields, technological applications for controlling temperature profiles in nanodevices are possible.

  15. Modeling Wildfire Incident Complexity Dynamics

    PubMed Central

    Thompson, Matthew P.

    2013-01-01

    Wildfire management in the United States and elsewhere is challenged by substantial uncertainty regarding the location and timing of fire events, the socioeconomic and ecological consequences of these events, and the costs of suppression. Escalating U.S. Forest Service suppression expenditures is of particular concern at a time of fiscal austerity as swelling fire management budgets lead to decreases for non-fire programs, and as the likelihood of disruptive within-season borrowing potentially increases. Thus there is a strong interest in better understanding factors influencing suppression decisions and in turn their influence on suppression costs. As a step in that direction, this paper presents a probabilistic analysis of geographic and temporal variation in incident management team response to wildfires. The specific focus is incident complexity dynamics through time for fires managed by the U.S. Forest Service. The modeling framework is based on the recognition that large wildfire management entails recurrent decisions across time in response to changing conditions, which can be represented as a stochastic dynamic system. Daily incident complexity dynamics are modeled according to a first-order Markov chain, with containment represented as an absorbing state. A statistically significant difference in complexity dynamics between Forest Service Regions is demonstrated. Incident complexity probability transition matrices and expected times until containment are presented at national and regional levels. Results of this analysis can help improve understanding of geographic variation in incident management and associated cost structures, and can be incorporated into future analyses examining the economic efficiency of wildfire management. PMID:23691014

  16. On the Way to Appropriate Model Complexity

    NASA Astrophysics Data System (ADS)

    Höge, M.

    2016-12-01

    When statistical models are used to represent natural phenomena they are often too simple or too complex - this is known. But what exactly is model complexity? Among many other definitions, the complexity of a model can be conceptualized as a measure of statistical dependence between observations and parameters (Van der Linde, 2014). However, several issues remain when working with model complexity: A unique definition for model complexity is missing. Assuming a definition is accepted, how can model complexity be quantified? How can we use a quantified complexity to the better of modeling? Generally defined, "complexity is a measure of the information needed to specify the relationships between the elements of organized systems" (Bawden & Robinson, 2015). The complexity of a system changes as the knowledge about the system changes. For models this means that complexity is not a static concept: With more data or higher spatio-temporal resolution of parameters, the complexity of a model changes. There are essentially three categories into which all commonly used complexity measures can be classified: (1) An explicit representation of model complexity as "Degrees of freedom" of a model, e.g. effective number of parameters. (2) Model complexity as code length, a.k.a. "Kolmogorov complexity": The longer the shortest model code, the higher its complexity (e.g. in bits). (3) Complexity defined via information entropy of parametric or predictive uncertainty. Preliminary results show that Bayes theorem allows for incorporating all parts of the non-static concept of model complexity like data quality and quantity or parametric uncertainty. Therefore, we test how different approaches for measuring model complexity perform in comparison to a fully Bayesian model selection procedure. Ultimately, we want to find a measure that helps to assess the most appropriate model.

  17. Hepatocellular biomembrane peroxidation in copper-induced injury

    SciTech Connect

    Homer, B.L.

    1986-01-01

    The pathogenesis of Cu-induced hepatocellular biomembrane peroxidation was studied in male Fischer rats by analyzing hepatic morphologic alterations, measuring the activity of hepatic free radical scavenger enzymes, and determining the distribution of hepatic cytosolic Cu bound to high and low molecular weight proteins. Seventy-five weanling rats were divided into 3 group of 25 each and injected once daily with either 6.25 mg/kg or 12.5 mg/kg cupric chloride, or 0.2 ml/100 gm saline. Five rats from each group were killed after 3, 14, 28, 42, and 70 consecutive days of injections. The level of malondialdehyde was elevated after 3 days of Cu injections and continued to increase until it peaked in the high-dose group after 28 days and in the low-dose group after 42 days. The density of catalase-containing peroxisomes was reduced in Cu-treated rats, correlating with a reduced activity of hepatic catalase. Catalase activity in Cu-treated rats was reduced after 3 days, and always remained < or = to the activity in control rats. The activity of glutathione peroxidase in high-dose rats always was < or = to the level in control rats, while the activity in control rats always was < or = to the level in low-dose rats. Meanwhile, the activity of superoxide dismutase increase in Cu-treated rats after 28 days. The concentration of cytosolic low molecular weight protein-bound Cu was elevated after 3 days in both Cu-treated groups and continued to increase, leveling off or peaking after 42 days. Regression analysis and in vitro studies, involving the peroxidation of erythrocyte ghost membranes, demonstrated that Cu bound to low molecular weight proteins was less likely to induce lipoperoxidation than copper bound to high molecular weight proteins.

  18. Molecular modeling of polynucleotide complexes.

    PubMed

    Meneksedag-Erol, Deniz; Tang, Tian; Uludağ, Hasan

    2014-08-01

    Delivery of polynucleotides into patient cells is a promising strategy for treatment of genetic disorders. Gene therapy aims to either synthesize desired proteins (DNA delivery) or suppress expression of endogenous genes (siRNA delivery). Carriers constitute an important part of gene therapeutics due to limitations arising from the pharmacokinetics of polynucleotides. Non-viral carriers such as polymers and lipids protect polynucleotides from intra and extracellular threats and facilitate formation of cell-permeable nanoparticles through shielding and/or bridging multiple polynucleotide molecules. Formation of nanoparticulate systems with optimal features, their cellular uptake and intracellular trafficking are crucial steps for an effective gene therapy. Despite the great amount of experimental work pursued, critical features of the nanoparticles as well as their processing mechanisms are still under debate due to the lack of instrumentation at atomic resolution. Molecular modeling based computational approaches can shed light onto the atomic level details of gene delivery systems, thus provide valuable input that cannot be readily obtained with experimental techniques. Here, we review the molecular modeling research pursued on critical gene therapy steps, highlight the knowledge gaps in the field and providing future perspectives. Existing modeling studies revealed several important aspects of gene delivery, such as nanoparticle formation dynamics with various carriers, effect of carrier properties on complexation, carrier conformations in endosomal stages, and release of polynucleotides from carriers. Rate-limiting steps related to cellular events (i.e. internalization, endosomal escape, and nuclear uptake) are now beginning to be addressed by computational approaches. Limitations arising from current computational power and accuracy of modeling have been hindering the development of more realistic models. With the help of rapidly-growing computational power

  19. The improved efficacy of Sifuvirtide compared with enfuvirtide might be related to its selectivity for the rigid biomembrane, as determined through surface plasmon resonance

    PubMed Central

    Cao, Ping; Dou, Guifang

    2017-01-01

    Most mechanistic studies on human immunodeficiency virus (HIV) peptide fusion inhibitors have focused on the interactions between fusion inhibitors and viral envelope proteins. However, the interactions of fusion inhibitors with viral membranes are also essential for the efficacy of these drugs. Here, we utilized surface plasmon resonance (SPR) technology to study the interactions between the HIV fusion inhibitor peptides sifuvirtide and enfuvirtide and biomembrane models. Sifuvirtide presented selectivity toward biomembrane models composed of saturated dipalmitoylphosphatidylcholine (DPPC) (32-fold higher compared with unsaturated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine [POPC]) and sphingomyelin (SM) (31-fold higher compared with POPC), which are rigid compositions enriched in the HIV viral membrane. In contrast, enfuvirtide showed no significant selectively toward these rigid membrane models. Furthermore, the bindings of sifuvirtide and enfuvirtide to SM bilayers were markedly higher than those to monolayers (14-fold and 23-fold, respectively), indicating that the inner leaflet influences the binding of these drugs to SM bilayers. No obvious differences were noted in the bindings of either peptide to the other mono- and bilayer models tested, illustrating that both peptides interact with these membranes through surface-binding. The bindings of the inhibitor peptides to biomembranes were found to be driven predominantly by hydrophobic interactions rather than electrostatic interactions, as determined by comparing their affinities to those of positively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-ethylphosphocholine (EPC) to zwitterionic membrane models. The improved efficiency of sifuvirtide relative to enfuvirtide might be related to its ability to adsorb on rigid lipidic areas, such as the viral envelope and lipid rafts, which results in an increased sifuvirtide concentration at the fusion site. PMID:28207776

  20. The improved efficacy of Sifuvirtide compared with enfuvirtide might be related to its selectivity for the rigid biomembrane, as determined through surface plasmon resonance.

    PubMed

    Cao, Ping; Dou, Guifang; Cheng, Yuanguo; Che, Jinjing

    2017-01-01

    Most mechanistic studies on human immunodeficiency virus (HIV) peptide fusion inhibitors have focused on the interactions between fusion inhibitors and viral envelope proteins. However, the interactions of fusion inhibitors with viral membranes are also essential for the efficacy of these drugs. Here, we utilized surface plasmon resonance (SPR) technology to study the interactions between the HIV fusion inhibitor peptides sifuvirtide and enfuvirtide and biomembrane models. Sifuvirtide presented selectivity toward biomembrane models composed of saturated dipalmitoylphosphatidylcholine (DPPC) (32-fold higher compared with unsaturated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine [POPC]) and sphingomyelin (SM) (31-fold higher compared with POPC), which are rigid compositions enriched in the HIV viral membrane. In contrast, enfuvirtide showed no significant selectively toward these rigid membrane models. Furthermore, the bindings of sifuvirtide and enfuvirtide to SM bilayers were markedly higher than those to monolayers (14-fold and 23-fold, respectively), indicating that the inner leaflet influences the binding of these drugs to SM bilayers. No obvious differences were noted in the bindings of either peptide to the other mono- and bilayer models tested, illustrating that both peptides interact with these membranes through surface-binding. The bindings of the inhibitor peptides to biomembranes were found to be driven predominantly by hydrophobic interactions rather than electrostatic interactions, as determined by comparing their affinities to those of positively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-ethylphosphocholine (EPC) to zwitterionic membrane models. The improved efficiency of sifuvirtide relative to enfuvirtide might be related to its ability to adsorb on rigid lipidic areas, such as the viral envelope and lipid rafts, which results in an increased sifuvirtide concentration at the fusion site.

  1. Alleviation of capsular formations on silicone implants in rats using biomembrane-mimicking coatings.

    PubMed

    Park, Ji Ung; Ham, Jiyeon; Kim, Sukwha; Seo, Ji-Hun; Kim, Sang-Hyon; Lee, Seonju; Min, Hye Jeong; Choi, Sunghyun; Choi, Ra Mi; Kim, Heejin; Oh, Sohee; Hur, Ji An; Choi, Tae Hyun; Lee, Yan

    2014-10-01

    Despite their popular use in breast augmentation and reconstruction surgeries, the limited biocompatibility of silicone implants can induce severe side effects, including capsular contracture - an excessive foreign body reaction that forms a tight and hard fibrous capsule around the implant. This study examines the effects of using biomembrane-mimicking surface coatings to prevent capsular formations on silicone implants. The covalently attached biomembrane-mimicking polymer, poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC), prevented nonspecific protein adsorption and fibroblast adhesion on the silicone surface. More importantly, in vivo capsule formations around PMPC-grafted silicone implants in rats were significantly thinner and exhibited lower collagen densities and more regular collagen alignments than bare silicone implants. The observed decrease in α-smooth muscle actin also supported the alleviation of capsular formations by the biomembrane-mimicking coating. Decreases in inflammation-related cells, myeloperoxidase and transforming growth factor-β resulted in reduced inflammation in the capsular tissue. The biomembrane-mimicking coatings used on these silicone implants demonstrate great potential for preventing capsular contracture and developing biocompatible materials for various biomedical applications.

  2. Teacher Modeling Using Complex Informational Texts

    ERIC Educational Resources Information Center

    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.

  3. Teacher Modeling Using Complex Informational Texts

    ERIC Educational Resources Information Center

    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.

  4. "Computational Modeling of Actinide Complexes"

    SciTech Connect

    Balasubramanian, K

    2007-03-07

    We will present our recent studies on computational actinide chemistry of complexes which are not only interesting from the standpoint of actinide coordination chemistry but also of relevance to environmental management of high-level nuclear wastes. We will be discussing our recent collaborative efforts with Professor Heino Nitsche of LBNL whose research group has been actively carrying out experimental studies on these species. Computations of actinide complexes are also quintessential to our understanding of the complexes found in geochemical, biochemical environments and actinide chemistry relevant to advanced nuclear systems. In particular we have been studying uranyl, plutonyl, and Cm(III) complexes are in aqueous solution. These studies are made with a variety of relativistic methods such as coupled cluster methods, DFT, and complete active space multi-configuration self-consistent-field (CASSCF) followed by large-scale CI computations and relativistic CI (RCI) computations up to 60 million configurations. Our computational studies on actinide complexes were motivated by ongoing EXAFS studies of speciated complexes in geo and biochemical environments carried out by Prof Heino Nitsche's group at Berkeley, Dr. David Clark at Los Alamos and Dr. Gibson's work on small actinide molecules at ORNL. The hydrolysis reactions of urnayl, neputyl and plutonyl complexes have received considerable attention due to their geochemical and biochemical importance but the results of free energies in solution and the mechanism of deprotonation have been topic of considerable uncertainty. We have computed deprotonating and migration of one water molecule from the first solvation shell to the second shell in UO{sub 2}(H{sub 2}O){sub 5}{sup 2+}, UO{sub 2}(H{sub 2}O){sub 5}{sup 2+}NpO{sub 2}(H{sub 2}O){sub 6}{sup +}, and PuO{sub 2}(H{sub 2}O){sub 5}{sup 2+} complexes. Our computed Gibbs free energy(7.27 kcal/m) in solution for the first time agrees with the experiment (7.1 kcal

  5. Capturing Complexity through Maturity Modelling

    ERIC Educational Resources Information Center

    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…

  6. Capturing Complexity through Maturity Modelling

    ERIC Educational Resources Information Center

    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…

  7. Molecular simulation and modeling of complex I.

    PubMed

    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.

  8. Hierarchical Models of the Nearshore Complex System

    DTIC Science & Technology

    2004-01-01

    unclassified unclassified /,andard Form 7 7Qien. -pii Prescrbed by ANS Sid 239-18 zgB -10z Hierarchical Models of the Nearshore Complex System: Final...TITLE AND SUBTITLE S. FUNDING NUMBERS Hierarchical Models of the Nearshore Complex System N00014-02-1-0358 6. AUTHOR(S) Brad Werner 7. PERFORMING...8217 ........... The long-term goal of this reasearch was to develop and test predictive models for nearshore processes. This grant was terminaton funding for the

  9. Scaffolding in Complex Modelling Situations

    ERIC Educational Resources Information Center

    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…

  10. Scaffolding in Complex Modelling Situations

    ERIC Educational Resources Information Center

    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…

  11. Role models for complex networks

    NASA Astrophysics Data System (ADS)

    Reichardt, J.; White, D. R.

    2007-11-01

    We present a framework for automatically decomposing (“block-modeling”) the functional classes of agents within a complex network. These classes are represented by the nodes of an image graph (“block model”) depicting the main patterns of connectivity and thus functional roles in the network. Using a first principles approach, we derive a measure for the fit of a network to any given image graph allowing objective hypothesis testing. From the properties of an optimal fit, we derive how to find the best fitting image graph directly from the network and present a criterion to avoid overfitting. The method can handle both two-mode and one-mode data, directed and undirected as well as weighted networks and allows for different types of links to be dealt with simultaneously. It is non-parametric and computationally efficient. The concepts of structural equivalence and modularity are found as special cases of our approach. We apply our method to the world trade network and analyze the roles individual countries play in the global economy.

  12. Complex Parameter Landscape for a Complex Neuron Model

    PubMed Central

    Achard, Pablo; De Schutter, Erik

    2006-01-01

    The electrical activity of a neuron is strongly dependent on the ionic channels present in its membrane. Modifying the maximal conductances from these channels can have a dramatic impact on neuron behavior. But the effect of such modifications can also be cancelled out by compensatory mechanisms among different channels. We used an evolution strategy with a fitness function based on phase-plane analysis to obtain 20 very different computational models of the cerebellar Purkinje cell. All these models produced very similar outputs to current injections, including tiny details of the complex firing pattern. These models were not completely isolated in the parameter space, but neither did they belong to a large continuum of good models that would exist if weak compensations between channels were sufficient. The parameter landscape of good models can best be described as a set of loosely connected hyperplanes. Our method is efficient in finding good models in this complex landscape. Unraveling the landscape is an important step towards the understanding of functional homeostasis of neurons. PMID:16848639

  13. Tether-Supported Biomembranes with Alpha-Helical Peptide-Based Anchoring Constructs

    PubMed Central

    Zhong, Lina; Tu, Raymond; Gilchrist, M. Lane

    2013-01-01

    The strict requirement of constructing a native lipid environment to preserve the structure and functionality of membrane proteins is the starting constraint when building biomaterials and sensor systems from these biomolecules. In order to enhance the viability of supported biomembranes systems and build new ligand display interfaces, we apply rationally-designed peptides partitioned into the lipid bilayer interface. Peptides designed to form membrane-spanning alpha-helical anchoring domains are synthesized using solid-phase peptide synthesis. K3A4L2A7L2A3K2-FITC is synthesized at 100 mg scale for use as a biomembrane anchoring molecules, where orthogonal side-chain modifications allows us to introduce probes enabling peptide localization within supported bilayers. The peptides are found to form alpha-helical domains within liposomes as assessed with circular dichroism spectroscopy. These peptides are designed to incorporate into lipid bilayers supported by microspheres and serve as biomembrane anchoring moieties to amino-terminated surfaces. Here, the silica bead surface (4.7 μm diameter) is activated with homobifunctional NHS-PEG3000-NHS as “polymer cushion” spacers. This tethering to a subset of the K3A4L2A7L2A3K2-FITC molecules present in the bilayer is achieved by fusion of liposomes followed by coupling of the peptide amino groups to the NHS presented from the silica microsphere surfaces. The biomembrane distributions of tethered and untethered K3A4L2A7L2A3K2-FITC is probed with confocal microscopy and found to give 3D reconstructions consistent with largely homogeneous supported biomembranes. The fluidity of the untethered fraction of the peptides within supported membranes is quantified using the fluorescence recovery after photobleaching (FRAP) technique. The presence of the PEG3000 polymer cushion facilitated a 28.9% increase in peptide diffusivity over untethered bilayers at the lowest peptide to lipid ratio we examined. We show that rationally

  14. Agent-based modeling of complex infrastructures

    SciTech Connect

    North, M. J.

    2001-06-01

    Complex Adaptive Systems (CAS) can be applied to investigate complex infrastructures and infrastructure interdependencies. The CAS model agents within the Spot Market Agent Research Tool (SMART) and Flexible Agent Simulation Toolkit (FAST) allow investigation of the electric power infrastructure, the natural gas infrastructure and their interdependencies.

  15. Modeling the complex bromate-iodine reaction.

    PubMed

    Machado, Priscilla B; Faria, Roberto B

    2009-05-07

    In this article, it is shown that the FLEK model (ref 5 ) is able to model the experimental results of the bromate-iodine clock reaction. Five different complex chemical systems, the bromate-iodide clock and oscillating reactions, the bromite-iodide clock and oscillating reactions, and now the bromate-iodine clock reaction are adequately accounted for by the FLEK model.

  16. Numerical models of complex diapirs

    NASA Astrophysics Data System (ADS)

    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.

  17. Slip complexity in earthquake fault models.

    PubMed

    Rice, J R; Ben-Zion, Y

    1996-04-30

    We summarize studies of earthquake fault models that give rise to slip complexities like those in natural earthquakes. For models of smooth faults between elastically deformable continua, it is critical that the friction laws involve a characteristic distance for slip weakening or evolution of surface state. That results in a finite nucleation size, or coherent slip patch size, h*. Models of smooth faults, using numerical cell size properly small compared to h*, show periodic response or complex and apparently chaotic histories of large events but have not been found to show small event complexity like the self-similar (power law) Gutenberg-Richter frequency-size statistics. This conclusion is supported in the present paper by fully inertial elastodynamic modeling of earthquake sequences. In contrast, some models of locally heterogeneous faults with quasi-independent fault segments, represented approximately by simulations with cell size larger than h* so that the model becomes "inherently discrete," do show small event complexity of the Gutenberg-Richter type. Models based on classical friction laws without a weakening length scale or for which the numerical procedure imposes an abrupt strength drop at the onset of slip have h* = 0 and hence always fall into the inherently discrete class. We suggest that the small-event complexity that some such models show will not survive regularization of the constitutive description, by inclusion of an appropriate length scale leading to a finite h*, and a corresponding reduction of numerical grid size.

  18. Mathematical modeling of complex regulatory networks.

    PubMed

    Stelling, Jörg; Gilles, Ernst Dieter

    2004-09-01

    Cellular regulation comprises overwhelmingly complex interactions between genes and proteins that ultimately will only be rendered understandable by employing formal approaches. Developing large-scale mathematical models of such systems in an efficient and reliable way, however, requires careful evaluation of structuring principles for the models, of the description of the system dynamics, and of the experimental data basis for adjusting the models to reality. We discuss these three aspects of model development using the example of cell cycle regulation in yeast and suggest that capturing complex dynamic networks is feasible despite incomplete (quantitative) biological knowledge.

  19. Preferential urn model and nongrowing complex networks.

    PubMed

    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.

  20. New illumination technique for IR-video guided patch-clamp recording from neurons in slice cultures on biomembrane.

    PubMed

    Alix, Philippe; Winterer, Jochen; Müller, Wolfgang

    2003-09-30

    Slice cultures on biomembrane are the method of choice for studying Ca2+-dependent plastic changes occurring over several days to weeks. Using IR-differential interference contrast, good visualization of neurons in biomembrane slice cultures has been achieved despite a negative optical effect of the biomembrane, but epifluorescence imaging requires removal of a Wollaston prism and the analyzer. Here, we describe a novel illumination method to overcome this problem. Using optic fiber illumination at a shallow angle from the top of the slice culture, with or without additional illumination from the bottom, we obtained good cellular resolution of neurons in biomembrane slice cultures as well as in acute slices with an infrared-video camera. With this technique, we demonstrate visually guided whole-cell patch-clamp recording of Na+- and K+-currents as well as combination of whole-cell recording with fluorescence imaging of hippocampal and entorhinal cortex neurons in biomembrane slice cultures. Our inexpensive method should prove very useful for studying in vitro effects of long-term manipulations on membrane currents and intracellular Ca2+-signaling.

  1. Complex system modelling for veterinary epidemiology.

    PubMed

    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.

  2. Modelling Canopy Flows over Complex Terrain

    NASA Astrophysics Data System (ADS)

    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.

  3. A differential model of the complex cell.

    PubMed

    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.

  4. From Complex to Simple: Interdisciplinary Stochastic Models

    ERIC Educational Resources Information Center

    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…

  5. From Complex to Simple: Interdisciplinary Stochastic Models

    ERIC Educational Resources Information Center

    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…

  6. Modeling the chemistry of complex petroleum mixtures.

    PubMed

    Quann, R J

    1998-12-01

    Determining the complete molecular composition of petroleum and its refined products is not feasible with current analytical techniques because of the astronomical number of molecular components. Modeling the composition and behavior of such complex mixtures in refinery processes has accordingly evolved along a simplifying concept called lumping. Lumping reduces the complexity of the problem to a manageable form by grouping the entire set of molecular components into a handful of lumps. This traditional approach does not have a molecular basis and therefore excludes important aspects of process chemistry and molecular property fundamentals from the model's formulation. A new approach called structure-oriented lumping has been developed to model the composition and chemistry of complex mixtures at a molecular level. The central concept is to represent an individual molecular or a set of closely related isomers as a mathematical construct of certain specific and repeating structural groups. A complex mixture such as petroleum can then be represented as thousands of distinct molecular components, each having a mathematical identity. This enables the automated construction of large complex reaction networks with tens of thousands of specific reactions for simulating the chemistry of complex mixtures. Further, the method provides a convenient framework for incorporating molecular physical property correlations, existing group contribution methods, molecular thermodynamic properties, and the structure--activity relationships of chemical kinetics in the development of models.

  7. Modeling the chemistry of complex petroleum mixtures.

    PubMed Central

    Quann, R J

    1998-01-01

    Determining the complete molecular composition of petroleum and its refined products is not feasible with current analytical techniques because of the astronomical number of molecular components. Modeling the composition and behavior of such complex mixtures in refinery processes has accordingly evolved along a simplifying concept called lumping. Lumping reduces the complexity of the problem to a manageable form by grouping the entire set of molecular components into a handful of lumps. This traditional approach does not have a molecular basis and therefore excludes important aspects of process chemistry and molecular property fundamentals from the model's formulation. A new approach called structure-oriented lumping has been developed to model the composition and chemistry of complex mixtures at a molecular level. The central concept is to represent an individual molecular or a set of closely related isomers as a mathematical construct of certain specific and repeating structural groups. A complex mixture such as petroleum can then be represented as thousands of distinct molecular components, each having a mathematical identity. This enables the automated construction of large complex reaction networks with tens of thousands of specific reactions for simulating the chemistry of complex mixtures. Further, the method provides a convenient framework for incorporating molecular physical property correlations, existing group contribution methods, molecular thermodynamic properties, and the structure--activity relationships of chemical kinetics in the development of models. PMID:9860903

  8. Updating the debate on model complexity

    USGS Publications Warehouse

    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.”

  9. Multifaceted Modelling of Complex Business Enterprises.

    PubMed

    Chakraborty, Subrata; Mengersen, Kerrie; Fidge, Colin; Ma, Lin; Lassen, David

    2015-01-01

    We formalise and present a new generic multifaceted complex system approach for modelling complex business enterprises. Our method has a strong focus on integrating the various data types available in an enterprise which represent the diverse perspectives of various stakeholders. We explain the challenges faced and define a novel approach to converting diverse data types into usable Bayesian probability forms. The data types that can be integrated include historic data, survey data, and management planning data, expert knowledge and incomplete data. The structural complexities of the complex system modelling process, based on various decision contexts, are also explained along with a solution. This new application of complex system models as a management tool for decision making is demonstrated using a railway transport case study. The case study demonstrates how the new approach can be utilised to develop a customised decision support model for a specific enterprise. Various decision scenarios are also provided to illustrate the versatility of the decision model at different phases of enterprise operations such as planning and control.

  10. Multifaceted Modelling of Complex Business Enterprises

    PubMed Central

    2015-01-01

    We formalise and present a new generic multifaceted complex system approach for modelling complex business enterprises. Our method has a strong focus on integrating the various data types available in an enterprise which represent the diverse perspectives of various stakeholders. We explain the challenges faced and define a novel approach to converting diverse data types into usable Bayesian probability forms. The data types that can be integrated include historic data, survey data, and management planning data, expert knowledge and incomplete data. The structural complexities of the complex system modelling process, based on various decision contexts, are also explained along with a solution. This new application of complex system models as a management tool for decision making is demonstrated using a railway transport case study. The case study demonstrates how the new approach can be utilised to develop a customised decision support model for a specific enterprise. Various decision scenarios are also provided to illustrate the versatility of the decision model at different phases of enterprise operations such as planning and control. PMID:26247591

  11. Complex quantum network model of energy transfer in photosynthetic complexes.

    PubMed

    Ai, Bao-Quan; Zhu, Shi-Liang

    2012-12-01

    The quantum network model with real variables is usually used to describe the excitation energy transfer (EET) in the Fenna-Matthews-Olson (FMO) complexes. In this paper we add the quantum phase factors to the hopping terms and find that the quantum phase factors play an important role in the EET. The quantum phase factors allow us to consider the space structure of the pigments. It is found that phase coherence within the complexes would allow quantum interference to affect the dynamics of the EET. There exist some optimal phase regions where the transfer efficiency takes its maxima, which indicates that when the pigments are optimally spaced, the exciton can pass through the FMO with perfect efficiency. Moreover, the optimal phase regions almost do not change with the environments. In addition, we find that the phase factors are useful in the EET just in the case of multiple pathways. Therefore, we demonstrate that the quantum phases may bring the other two factors, the optimal space of the pigments and multiple pathways, together to contribute the EET in photosynthetic complexes with perfect efficiency.

  12. Fully implicit methodology for the dynamics of biomembranes and capillary interfaces by combining the level set and Newton methods

    NASA Astrophysics Data System (ADS)

    Laadhari, Aymen; Saramito, Pierre; Misbah, Chaouqi; Székely, Gábor

    2017-08-01

    This framework is concerned with the numerical modeling of the dynamics of individual biomembranes and capillary interfaces in a surrounding Newtonian fluid. A level set approach helps to follow the interface motion. Our method features the use of high order fully implicit time integration schemes that enable to overcome stability issues related to the explicit discretization of the highly non-linear bending force or capillary force. At each time step, the tangent systems are derived and the resulting nonlinear problems are solved by a Newton-Raphson method. Based on the signed distance assumption, several inexact Newton strategies are employed to solve the capillary and vesicle problems and guarantee the second-order convergence behavior. We address in detail the main features of the proposed method, and we report several experiments in the two-dimensional case with the aim of illustrating its accuracy and efficiency. Comparative investigations with respect to the fully explicit scheme depict the stabilizing effect of the new method, which allows to use significantly larger time step sizes.

  13. Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble.

    PubMed

    Coimbra, João T S; Sousa, Sérgio F; Fernandes, Pedro A; Rangel, Maria; Ramos, Maria J

    2014-01-01

    The AMBER family of force fields is one of the most commonly used alternatives to describe proteins and drug-like molecules in molecular dynamics simulations. However, the absence of a specific set of parameters for lipids has been limiting the widespread application of this force field in biomembrane simulations, including membrane protein simulations and drug-membrane simulations. Here, we report the systematic parameterization of 12 common lipid types consistent with the General Amber Force Field (GAFF), with charge-parameters determined with RESP at the HF/6-31G(d) level of theory, to be consistent with AMBER. The accuracy of the scheme was evaluated by comparing predicted and experimental values for structural lipid properties in MD simulations in an NPT ensemble with explicit solvent in 100:100 bilayer systems. Globally, a consistent agreement with experimental reference data on membrane structures was achieved for some lipid types when using the typical MD conditions normally employed when handling membrane proteins and drug-membrane simulations (a tensionless NPT ensemble, 310 K), without the application of any of the constraints often used in other biomembrane simulations (such as the surface tension and the total simulation box area). The present set of parameters and the universal approach used in the parameterization of all the lipid types described here, as well as the consistency with the AMBER force field family, together with the tensionless NPT ensemble used, opens the door to systematic studies combining lipid components with small drug-like molecules or membrane proteins and show the potential of GAFF in dealing with biomembranes.

  14. Slip complexity in earthquake fault models.

    PubMed Central

    Rice, J R; Ben-Zion, Y

    1996-01-01

    We summarize studies of earthquake fault models that give rise to slip complexities like those in natural earthquakes. For models of smooth faults between elastically deformable continua, it is critical that the friction laws involve a characteristic distance for slip weakening or evolution of surface state. That results in a finite nucleation size, or coherent slip patch size, h*. Models of smooth faults, using numerical cell size properly small compared to h*, show periodic response or complex and apparently chaotic histories of large events but have not been found to show small event complexity like the self-similar (power law) Gutenberg-Richter frequency-size statistics. This conclusion is supported in the present paper by fully inertial elastodynamic modeling of earthquake sequences. In contrast, some models of locally heterogeneous faults with quasi-independent fault segments, represented approximately by simulations with cell size larger than h* so that the model becomes "inherently discrete," do show small event complexity of the Gutenberg-Richter type. Models based on classical friction laws without a weakening length scale or for which the numerical procedure imposes an abrupt strength drop at the onset of slip have h* = 0 and hence always fall into the inherently discrete class. We suggest that the small-event complexity that some such models show will not survive regularization of the constitutive description, by inclusion of an appropriate length scale leading to a finite h*, and a corresponding reduction of numerical grid size. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:11607669

  15. Minimum-complexity helicopter simulation math model

    NASA Technical Reports Server (NTRS)

    Heffley, Robert K.; Mnich, Marc A.

    1988-01-01

    An example of a minimal complexity simulation helicopter math model is presented. Motivating factors are the computational delays, cost, and inflexibility of the very sophisticated math models now in common use. A helicopter model form is given which addresses each of these factors and provides better engineering understanding of the specific handling qualities features which are apparent to the simulator pilot. The technical approach begins with specification of features which are to be modeled, followed by a build up of individual vehicle components and definition of equations. Model matching and estimation procedures are given which enable the modeling of specific helicopters from basic data sources such as flight manuals. Checkout procedures are given which provide for total model validation. A number of possible model extensions and refinement are discussed. Math model computer programs are defined and listed.

  16. Experimentally tractable, pseudo-elastic constitutive law for biomembranes: II. Application.

    PubMed

    Criscione, John C; Sacks, Michael S; Hunter, William C

    2003-02-01

    This is the second paper of a 2 part series. In the first, a theoretical framework is developed that provides 3 enhancements for the constitutive theory of biomembranes. 1) Covariance amongst response terms is minimized, 2) the pseudo-strain-energy potential is redefined so as to be measurable, and 3) the stress response is decomposed into 2 parts--a hyperelastic part plus a hypoelastic-stress-residual. This paper illustrates the experimental advantages of this novel constitutive theory via analysis of biaxial test data obtained from chemically treated bovine pericardium.

  17. Trends in modeling Biomedical Complex Systems

    PubMed Central

    Milanesi, Luciano; Romano, Paolo; Castellani, Gastone; Remondini, Daniel; Liò, Petro

    2009-01-01

    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. PMID:19828068

  18. Constructing minimal models for complex system dynamics

    NASA Astrophysics Data System (ADS)

    Barzel, Baruch; Liu, Yang-Yu; Barabási, Albert-László

    2015-05-01

    One of the strengths of statistical physics is the ability to reduce macroscopic observations into microscopic models, offering a mechanistic description of a system's dynamics. This paradigm, rooted in Boltzmann's gas theory, has found applications from magnetic phenomena to subcellular processes and epidemic spreading. Yet, each of these advances were the result of decades of meticulous model building and validation, which are impossible to replicate in most complex biological, social or technological systems that lack accurate microscopic models. Here we develop a method to infer the microscopic dynamics of a complex system from observations of its response to external perturbations, allowing us to construct the most general class of nonlinear pairwise dynamics that are guaranteed to recover the observed behaviour. The result, which we test against both numerical and empirical data, is an effective dynamic model that can predict the system's behaviour and provide crucial insights into its inner workings.

  19. Refiners Switch to RFG Complex Model

    EIA Publications

    1998-01-01

    On January 1, 1998, domestic and foreign refineries and importers must stop using the "simple" model and begin using the "complex" model to calculate emissions of volatile organic compounds (VOC), toxic air pollutants (TAP), and nitrogen oxides (NOx) from motor gasoline. The primary differences between application of the two models is that some refineries may have to meet stricter standards for the sulfur and olefin content of the reformulated gasoline (RFG) they produce and all refineries will now be held accountable for NOx emissions. Requirements for calculating emissions from conventional gasoline under the anti-dumping rule similarly change for exhaust TAP and NOx. However, the change to the complex model is not expected to result in an increase in the price premium for RFG or constrain supplies.

  20. Modeling acuity for optotypes varying in complexity.

    PubMed

    Watson, Andrew B; Ahumada, Albert J

    2012-09-29

    Watson and Ahumada (2008) described a template model of visual acuity based on an ideal-observer limited by optical filtering, neural filtering, and noise. They computed predictions for selected optotypes and optical aberrations. Here we compare this model's predictions to acuity data for six human observers, each viewing seven different optotype sets, consisting of one set of Sloan letters and six sets of Chinese characters, differing in complexity (Zhang, Zhang, Xue, Liu, & Yu, 2007). Since optical aberrations for the six observers were unknown, we constructed 200 model observers using aberrations collected from 200 normal human eyes (Thibos, Hong, Bradley, & Cheng, 2002). For each condition (observer, optotype set, model observer) we estimated the model noise required to match the data. Expressed as efficiency, performance for Chinese characters was 1.4 to 2.7 times lower than for Sloan letters. Efficiency was weakly and inversely related to perimetric complexity of optotype set. We also compared confusion matrices for human and model observers. Correlations for off-diagonal elements ranged from 0.5 to 0.8 for different sets, and the average correlation for the template model was superior to a geometrical moment model with a comparable number of parameters (Liu, Klein, Xue, Zhang, & Yu, 2009). The template model performed well overall. Estimated psychometric function slopes matched the data, and noise estimates agreed roughly with those obtained independently from contrast sensitivity to Gabor targets. For optotypes of low complexity, the model accurately predicted relative performance. This suggests the model may be used to compare acuities measured with different sets of simple optotypes.

  1. The Kuramoto model in complex networks

    NASA Astrophysics Data System (ADS)

    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.

  2. Modelling biological complexity: a physical scientist's perspective.

    PubMed

    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

  3. Modelling biological complexity: a physical scientist's perspective

    PubMed Central

    Coveney, Peter V; Fowler, Philip W

    2005-01-01

    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

  4. Comparing flood loss models of different complexity

    NASA Astrophysics Data System (ADS)

    Schröter, Kai; Kreibich, Heidi; Vogel, Kristin; Riggelsen, Carsten; Scherbaum, Frank; Merz, Bruno

    2013-04-01

    Any deliberation on flood risk requires the consideration of potential flood losses. In particular, reliable flood loss models are needed to evaluate cost-effectiveness of mitigation measures, to assess vulnerability, for comparative risk analysis and financial appraisal during and after floods. In recent years, considerable improvements have been made both concerning the data basis and the methodological approaches used for the development of flood loss models. Despite of that, flood loss models remain an important source of uncertainty. Likewise the temporal and spatial transferability of flood loss models is still limited. This contribution investigates the predictive capability of different flood loss models in a split sample cross regional validation approach. For this purpose, flood loss models of different complexity, i.e. based on different numbers of explaining variables, are learned from a set of damage records that was obtained from a survey after the Elbe flood in 2002. The validation of model predictions is carried out for different flood events in the Elbe and Danube river basins in 2002, 2005 and 2006 for which damage records are available from surveys after the flood events. The models investigated are a stage-damage model, the rule based model FLEMOps+r as well as novel model approaches which are derived using data mining techniques of regression trees and Bayesian networks. The Bayesian network approach to flood loss modelling provides attractive additional information concerning the probability distribution of both model predictions and explaining variables.

  5. Study of filtering Ag liquid sample by chitosan biomembrane using laser-induced breakdown spectroscopy (LIBS)

    NASA Astrophysics Data System (ADS)

    Rupiasih, Ni Nyoman; Suyanto, Hery; Sumadiyasa, Made; Purwanto, Christine Prita; Purnomo, Rendra Rustam

    2013-09-01

    The capability of Laser-Induced Breakdown Spectroscopy (LIBS) to resolve filtration process of Ag liquid sample by chitosan biomembrane is demonstrated. The biomembrane was prepared by inversion method used to filter Ag liquid using pressurized technique samples which were then analyzed by monitoring the emission corresponding to Ag (I) at wavelength of 328 nm. The experiment was conducted by varying the laser energy i.e. 80, 120, and 160 mJ, where, subsequently, and its effect on the depth-profile from 20 - 200 μm was characterized by LIBS. The results showed that the physical processes of pressurized filtration led a homogeneous Ag in the membrane from the surface to a depth of 200 μm. The optimum condition was obtained at laser energy of 120 mJ. The adsorption occurred only on the surface of the membrane i.e. 20 μm depth, but there was no inclusion. Improvement of the detection performance of adsorption process was done by heating the dripped membrane at 35 °C and was resulting in increase in emission intensity as expected.

  6. Label-free characterization of biomembranes: from structure to dynamics.

    PubMed

    Mashaghi, Alireza; Mashaghi, Samaneh; Reviakine, Ilya; Heeren, Ron M A; Sandoghdar, Vahid; Bonn, Mischa

    2014-02-07

    We review recent progress in the study of the structure and dynamics of phospholipid membranes and associated proteins, using novel label-free analytical tools. We describe these techniques and illustrate them with examples highlighting current capabilities and limitations. Recent advances in applying such techniques to biological and model membranes for biophysical studies and biosensing applications are presented, and future prospects are discussed.

  7. Modeling Electromagnetic Scattering From Complex Inhomogeneous Objects

    NASA Technical Reports Server (NTRS)

    Deshpande, Manohar; Reddy, C. J.

    2011-01-01

    This software innovation is designed to develop a mathematical formulation to estimate the electromagnetic scattering characteristics of complex, inhomogeneous objects using the finite-element-method (FEM) and method-of-moments (MoM) concepts, as well as to develop a FORTRAN code called FEMOM3DS (Finite Element Method and Method of Moments for 3-Dimensional Scattering), which will implement the steps that are described in the mathematical formulation. Very complex objects can be easily modeled, and the operator of the code is not required to know the details of electromagnetic theory to study electromagnetic scattering.

  8. Flowgraph Models for Complex Multistate System Reliabiliy.

    SciTech Connect

    Williams, B. J.; Huzurbazar, A. V.

    2005-01-01

    This chapter reviews flowgraph models for complex multistate systems. The focus is on modeling data from semi-Markov processes and constructing likelihoods when different portions of the system data are censored and incomplete. Semi-Markov models play an important role in the analysis of time to event data. However, in practice, data analysis for semi-Markov processes can be quite difficult and many simplifying assumptions are made. Flowgraph models are multistate models that provide a data analytic method for semi-Markov processes. Flowgraphs are useful for estimating Bayes predictive densities, predictive reliability functions, and predictive hazard functions for waiting times of interest in the presence of censored and incomplete data. This chapter reviews data analysis for flowgraph models and then presents methods for constructing likelihoods when portions of the system data are missing.

  9. Complexity.

    PubMed

    Gómez-Hernández, J Jaime

    2006-01-01

    It is difficult to define complexity in modeling. Complexity is often associated with uncertainty since modeling uncertainty is an intrinsically difficult task. However, modeling uncertainty does not require, necessarily, complex models, in the sense of a model requiring an unmanageable number of degrees of freedom to characterize the aquifer. The relationship between complexity, uncertainty, heterogeneity, and stochastic modeling is not simple. Aquifer models should be able to quantify the uncertainty of their predictions, which can be done using stochastic models that produce heterogeneous realizations of aquifer parameters. This is the type of complexity addressed in this article.

  10. Human driven transitions in complex model ecosystems

    NASA Astrophysics Data System (ADS)

    Harfoot, Mike; Newbold, Tim; Tittinsor, Derek; Purves, Drew

    2015-04-01

    Human activities have been observed to be impacting ecosystems across the globe, leading to reduced ecosystem functioning, altered trophic and biomass structure and ultimately ecosystem collapse. Previous attempts to understand global human impacts on ecosystems have usually relied on statistical models, which do not explicitly model the processes underlying the functioning of ecosystems, represent only a small proportion of organisms and do not adequately capture complex non-linear and dynamic responses of ecosystems to perturbations. We use a mechanistic ecosystem model (1), which simulates the underlying processes structuring ecosystems and can thus capture complex and dynamic interactions, to investigate boundaries of complex ecosystems to human perturbation. We explore several drivers including human appropriation of net primary production and harvesting of animal biomass. We also present an analysis of the key interactions between biotic, societal and abiotic earth system components, considering why and how we might think about these couplings. References: M. B. J. Harfoot et al., Emergent global patterns of ecosystem structure and function from a mechanistic general ecosystem model., PLoS Biol. 12, e1001841 (2014).

  11. Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes

    PubMed Central

    Orsi, Mario; Noro, Massimo G.; Essex, Jonathan W.

    2011-01-01

    Triclocarban and triclosan, two potent antibacterial molecules present in many consumer products, have been subject to growing debate on a number of issues, particularly in relation to their possible role in causing microbial resistance. In this computational study, we present molecular-level insights into the interaction between these antimicrobial agents and hydrated phospholipid bilayers (taken as a simple model for the cell membrane). Simulations are conducted by a novel ‘dual-resolution’ molecular dynamics approach which combines accuracy with efficiency: the antimicrobials, modelled atomistically, are mixed with simplified (coarse-grain) models of lipids and water. A first set of calculations is run to study the antimicrobials' transfer free energies and orientations as a function of depth inside the membrane. Both molecules are predicted to preferentially accumulate in the lipid headgroup–glycerol region; this finding, which reproduces corresponding experimental data, is also discussed in terms of a general relation between solute partitioning and the intramembrane distribution of pressure. A second set of runs involves membranes incorporated with different molar concentrations of antimicrobial molecules (up to one antimicrobial per two lipids). We study the effects induced on fundamental membrane properties, such as the electron density, lateral pressure and electrical potential profiles. In particular, the analysis of the spontaneous curvature indicates that increasing antimicrobial concentrations promote a ‘destabilizing’ tendency towards non-bilayer phases, as observed experimentally. The antimicrobials' influence on the self-assembly process is also investigated. The significance of our results in the context of current theories of antimicrobial action is discussed. PMID:21131331

  12. Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations

    PubMed Central

    2015-01-01

    The bilayer bending modulus (Kc) is one of the most important physical constants characterizing lipid membranes, but precisely measuring it is a challenge, both experimentally and computationally. Experimental measurements on chemically identical bilayers often differ depending upon the techniques employed, and robust simulation results have previously been limited to coarse-grained models (at varying levels of resolution). This Communication demonstrates the extraction of Kc from fully atomistic molecular dynamics simulations for three different single-component lipid bilayers (DPPC, DOPC, and DOPE). The results agree quantitatively with experiments that measure thermal shape fluctuations in giant unilamellar vesicles. Lipid tilt, twist, and compression moduli are also reported. PMID:25202918

  13. Constitutive modeling of pia-arachnoid complex.

    PubMed

    Jin, Xin; Mao, Haojie; Yang, King H; King, Albert I

    2014-04-01

    The pia-arachnoid complex (PAC) covering the brain plays an important role in the mechanical response of the brain during impact or inertial loading. Recent studies have revealed the complicated material behavior of the PAC. In this study, the nonlinear viscoelastic, transversely isotropic material properties of the PAC were modeled as Mooney-Rivlin ground substance with collagen fibers strengthening within the meningeal plane through an exponential model. The material constants needed were determined using experimental data from in-plane tension, normal traction, and shear tests conducted on bovine specimens. Results from this study provide essential information to properly model the PAC membrane, an important component in the skull/brain interface, in a computational brain model. Such an improved representation of the skull/brain interface will enhance the accuracy of finite element models used in brain injury mechanism studies under various loading conditions.

  14. BDI-modelling of complex intracellular dynamics.

    PubMed

    Jonker, C M; Snoep, J L; Treur, J; Westerhoff, H V; Wijngaards, W C A

    2008-03-07

    A BDI-based continuous-time modelling approach for intracellular dynamics is presented. It is shown how temporalized BDI-models make it possible to model intracellular biochemical processes as decision processes. By abstracting from some of the details of the biochemical pathways, the model achieves understanding in nearly intuitive terms, without losing veracity: classical intentional state properties such as beliefs, desires and intentions are founded in reality through precise biochemical relations. In an extensive example, the complex regulation of Escherichia coli vis-à-vis lactose, glucose and oxygen is simulated as a discrete-state, continuous-time temporal decision manager. Thus a bridge is introduced between two different scientific areas: the area of BDI-modelling and the area of intracellular dynamics.

  15. A Practical Philosophy of Complex Climate Modelling

    NASA Technical Reports Server (NTRS)

    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.

  16. A Practical Philosophy of Complex Climate Modelling

    NASA Technical Reports Server (NTRS)

    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.

  17. Intrinsic Uncertainties in Modeling Complex Systems.

    SciTech Connect

    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.

  18. Lateral diffusion induced by active proteins in a biomembrane

    NASA Astrophysics Data System (ADS)

    Hosaka, Yuto; Yasuda, Kento; Okamoto, Ryuichi; Komura, Shigeyuki

    2017-05-01

    We discuss the hydrodynamic collective effects due to active protein molecules that are immersed in lipid bilayer membranes and modeled as stochastic force dipoles. We specifically take into account the presence of the bulk solvent that surrounds the two-dimensional fluid membrane. Two membrane geometries are considered: the free membrane case and the confined membrane case. Using the generalized membrane mobility tensors, we estimate the active diffusion coefficient and the drift velocity as a function of the size of a diffusing object. The hydrodynamic screening lengths distinguish the two asymptotic regimes of these quantities. Furthermore, the competition between the thermal and nonthermal contributions in the total diffusion coefficient is characterized by two length scales corresponding to the two membrane geometries. These characteristic lengths describe the crossover between different asymptotic behaviors when they are larger than the hydrodynamic screening lengths.

  19. Different Epidemic Models on Complex Networks

    NASA Astrophysics Data System (ADS)

    Zhang, Hai-Feng; Small, Michael; Fu, Xin-Chu

    2009-07-01

    Models for diseases spreading are not just limited to SIS or SIR. For instance, for the spreading of AIDS/HIV, the susceptible individuals can be classified into different cases according to their immunity, and similarly, the infected individuals can be sorted into different classes according to their infectivity. Moreover, some diseases may develop through several stages. Many authors have shown that the individuals' relation can be viewed as a complex network. So in this paper, in order to better explain the dynamical behavior of epidemics, we consider different epidemic models on complex networks, and obtain the epidemic threshold for each case. Finally, we present numerical simulations for each case to verify our results.

  20. Noncommutative complex Grosse-Wulkenhaar model

    SciTech Connect

    Hounkonnou, Mahouton Norbert; Samary, Dine Ousmane

    2008-11-18

    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.

  1. Color appearance models and complex visual stimuli.

    PubMed

    Fairchild, Mark D

    2010-01-01

    Teeth in a patient's mouth in a dental office, or in the natural environment, represent very complex stimuli for the human color vision system. Predicting their perceived color is a daunting task at best. Colorimetry is designed mainly for the evaluation of uniform, flat, opaque, materials of fairly large size viewed on a medium-grey background under near-daylight sources of fairly high luminance. On the contrary, in situ teeth vary spatially, are curved and ridged, translucent, relatively small, and viewed against a variable background under nonuniform, and typically nonstandard, illumination. These differences in stimuli and viewing conditions summarize the difficulty in predicting the color appearance of teeth. The field of color science has extended basic colorimetry, as represented by CIE XYZ and CIELAB coordinates, to more complex visual stimuli and viewing environments. The CIECAM02 color appearance model accurately addresses issues of chromatic adaptation, luminance effects and adaptation, background and surround effects, and the higher dimensionality of color appearance. Such models represent a significant advance and are used successfully in a variety of applications. However, many stimuli vary in space and time at scales not addressed by typical color appearance models. For example, high-definition video images would fall into such a category and so would in situ human teeth. More recently, color appearance models and image quality metrics have been combined to create image appearance models for even more complex visual stimuli. This paper provides an overview of fundamental and advanced colorimetry leading up to color appearance and image appearance models and their potential application in dentistry. Copyright © 2010 Elsevier Ltd. All rights reserved.

  2. The noisy voter model on complex networks

    PubMed Central

    Carro, Adrián; Toral, Raúl; San Miguel, Maxi

    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 annealed approximation for uncorrelated networks, 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 inferring the degree heterogeneity of the underlying network by observing only the aggregate behavior of the system as a whole, an issue of interest for systems where only macroscopic, population level variables can be measured. PMID:27094773

  3. Complex Constructivism: A Theoretical Model of Complexity and Cognition

    ERIC Educational Resources Information Center

    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…

  4. Magnetic modeling of the Bushveld Igneous Complex

    NASA Astrophysics Data System (ADS)

    Webb, S. J.; Cole, J.; Letts, S. A.; Finn, C.; Torsvik, T. H.; Lee, M. D.

    2009-12-01

    Magnetic modeling of the 2.06 Ga Bushveld Complex presents special challenges due a variety of magnetic effects. These include strong remanence in the Main Zone and extremely high magnetic susceptibilities in the Upper Zone, which exhibit self-demagnetization. Recent palaeomagnetic results have resolved a long standing discrepancy between age data, which constrain the emplacement to within 1 million years, and older palaeomagnetic data which suggested ~50 million years for emplacement. The new palaeomagnetic results agree with the age data and present a single consistent pole, as opposed to a long polar wander path, for the Bushveld for all of the Zones and all of the limbs. These results also pass a fold test indicating the Bushveld Complex was emplaced horizontally lending support to arguments for connectivity. The magnetic signature of the Bushveld Complex provides an ideal mapping tool as the UZ has high susceptibility values and is well layered showing up as distinct anomalies on new high resolution magnetic data. However, this signature is similar to the highly magnetic BIFs found in the Transvaal and in the Witwatersrand Supergroups. Through careful mapping using new high resolution aeromagnetic data, we have been able to map the Bushveld UZ in complicated geological regions and identify a characteristic signature with well defined layers. The Main Zone, which has a more subdued magnetic signature, does have a strong remanent component and exhibits several magnetic reversals. The magnetic layers of the UZ contain layers of magnetitite with as much as 80-90% pure magnetite with large crystals (1-2 cm). While these layers are not strongly remanent, they have extremely high magnetic susceptibilities, and the self demagnetization effect must be taken into account when modeling these layers. Because the Bushveld Complex is so large, the geometry of the Earth’s magnetic field relative to the layers of the UZ Bushveld Complex changes orientation, creating

  5. Structured analysis and modeling of complex systems

    NASA Technical Reports Server (NTRS)

    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.

  6. Project trades model for complex space missions

    NASA Technical Reports Server (NTRS)

    Girerd, Andre R.; Shishko, Roberto

    2003-01-01

    A Project Trades Model (PTM) is a collection of tools/simulations linked together to rapidly perform integrated system trade studies of performance, cost, risk, and mission effectiveness. An operating PTM captures the interactions between various targeted systems and subsystems through an exchange of computed variables of the constituent models. Selection and implementation of the order, method of interaction, model type, and envisioned operation of the ensemble of tools rpresents the key system engineering challenge of the approach. This paper describes an approach to building a PTM and using it to perform top-level system trades for a complex space mission. In particular, the PTM discussed here is for a future Mars mission involving a large rover.

  7. The Intermediate Complexity Atmospheric Research Model

    NASA Astrophysics Data System (ADS)

    Gutmann, Ethan; Clark, Martyn; Rasmussen, Roy; Arnold, Jeffrey; Brekke, Levi

    2015-04-01

    The high-resolution, non-hydrostatic atmospheric models often used for dynamical downscaling are extremely computationally expensive, and, for a certain class of problems, their complexity hinders our ability to ask key scientific questions, particularly those related to hydrology and climate change. For changes in precipitation in particular, an atmospheric model grid spacing capable of resolving the structure of mountain ranges is of critical importance, yet such simulations can not currently be performed with an advanced regional climate model for long time periods, over large areas, and forced by many climate models. Here we present the newly developed Intermediate Complexity Atmospheric Research model (ICAR) capable of simulating critical atmospheric processes two to three orders of magnitude faster than a state of the art regional climate model. ICAR uses a simplified dynamical formulation based off of linear theory, combined with the circulation field from a low-resolution climate model. The resulting three-dimensional wind field is used to advect heat and moisture within the domain, while sub-grid physics (e.g. microphysics) are processed by standard and simplified physics schemes from the Weather Research and Forecasting (WRF) model. ICAR is tested in comparison to WRF by downscaling a climate change scenario over the Colorado Rockies. Both atmospheric models predict increases in precipitation across the domain with a greater increase on the western half. In contrast, statistically downscaled precipitation using multiple common statistical methods predict decreases in precipitation over the western half of the domain. Finally, we apply ICAR to multiple CMIP5 climate models and scenarios with multiple parameterization options to investigate the importance of uncertainty in sub-grid physics as compared to the uncertainty in the large scale climate scenario. ICAR is a useful tool for climate change and weather forecast downscaling, particularly for orographic

  8. Glass Durability Modeling, Activated Complex Theory (ACT)

    SciTech Connect

    CAROL, JANTZEN

    2005-02-04

    dissolution modeling using simple atomic ratios is shown to represent the structural effects of the glass on the dissolution and the formation of activated complexes in the glass leached layer. This provides two different methods by which a linear glass durability model can be formulated. One based on the quasi- crystalline mineral species in a glass and one based on cation ratios in the glass: both are related to the activated complexes on the surface by the law of mass action. The former would allow a new Thermodynamic Hydration Energy Model to be developed based on the hydration of the quasi-crystalline mineral species if all the pertinent thermodynamic data were available. Since the pertinent thermodynamic data is not available, the quasi-crystalline mineral species and the activated complexes can be related to cation ratios in the glass by the law of mass action. The cation ratio model can, thus, be used by waste form producers to formulate durable glasses based on fundamental structural and activated complex theories. Moreover, glass durability model based on atomic ratios simplifies HLW glass process control in that the measured ratios of only a few waste components and glass formers can be used to predict complex HLW glass performance with a high degree of accuracy, e.g. an R{sup 2} approximately 0.97.

  9. Thermal reversal of polyvalent choline phosphate, a multivalent universal biomembrane adhesive.

    PubMed

    Yu, Xifei; Zou, Yuquan; Horte, Sonja; Janzen, Johan; Kizhakkedathu, Jayachandran N; Brooks, Donald E

    2013-08-12

    Multivalent macromolecular associations are widely observed in biological systems and are increasingly being utilized in bioengineering, nanomedicine, and biomaterial applications. Control over such associations usually demands an ability to reverse the multivalent binding. While in principle this can be done with binding site competitive inhibitors, dissociation is difficult in practice due to limited site accessibility when the macromolecule is bound. We demonstrate here efficient binding reversal of multivalent linear copolymers that adhere to any mammalian cell via the universal mechanism based on choline phosphate (CP) groups binding to phosphatidyl choline (PC)-containing biomembranes. Using a smart linear polymer exhibiting a lower critical solution temperature (LCST), we take advantage of the thermal contraction of the polymer above the LCST, which reduces accessibility of the CP groups to cell membrane PC lipids. The polymer construct can then desorb from the cell surface, reversing all effects of multivalent polymer adhesion on the cell.

  10. BFPTool: a software tool for analysis of Biomembrane Force Probe experiments.

    PubMed

    Šmít, Daniel; Fouquet, Coralie; Doulazmi, Mohamed; Pincet, Frédéric; Trembleau, Alain; Zapotocky, Martin

    2017-01-01

    The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Experiments are typically repeated many times, conditions are often not optimal, the captured video can be unstable and lose focus; this makes efficient analysis challenging, while out-of-the-box non-proprietary solutions are not freely available. This dedicated tool was developed to integrate and simplify the image processing and analysis of videomicroscopy recordings from BFP experiments. A novel processing feature, allowing the tracking of the pipette, was incorporated to address a limitation of preceding methods. Emphasis was placed on versatility and comprehensible user interface implemented in a graphical form. An integrated analytical tool was implemented to provide a faster, simpler and more convenient way to process and analyse BFP experiments.

  11. Modeling the human prothrombinase complex components

    NASA Astrophysics Data System (ADS)

    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.

  12. Chitosan-collagen biomembrane embedded with calcium-aluminate enhances dentinogenic potential of pulp cells.

    PubMed

    Soares, Diana Gabriela; Rosseto, Hebert Luís; Basso, Fernanda Gonçalves; Scheffel, Débora Salles; Hebling, Josimeri; Costa, Carlos Alberto de Souza

    2016-01-01

    The development of biomaterials capable of driving dental pulp stem cell differentiation into odontoblast-like cells able to secrete reparative dentin is the goal of current conservative dentistry. In the present investigation, a biomembrane (BM) composed of a chitosan/collagen matrix embedded with calcium-aluminate microparticles was tested. The BM was produced by mixing collagen gel with a chitosan solution (2:1), and then adding bioactive calcium-aluminate cement as the mineral phase. An inert material (polystyrene) was used as the negative control. Human dental pulp cells were seeded onto the surface of certain materials, and the cytocompatibility was evaluated by cell proliferation and cell morphology, assessed after 1, 7, 14 and 28 days in culture. The odontoblastic differentiation was evaluated by measuring alkaline phosphatase (ALP) activity, total protein production, gene expression of DMP-1/DSPP and mineralized nodule deposition. The pulp cells were able to attach onto the BM surface and spread, displaying a faster proliferative rate at initial periods than that of the control cells. The BM also acted on the cells to induce more intense ALP activity, protein production at 14 days, and higher gene expression of DSPP and DMP-1 at 28 days, leading to the deposition of about five times more mineralized matrix than the cells in the control group. Therefore, the experimental biomembrane induced the differentiation of pulp cells into odontoblast-like cells featuring a highly secretory phenotype. This innovative bioactive material can drive other protocols for dental pulp exposure treatment by inducing the regeneration of dentin tissue mediated by resident cells.

  13. The inflammatory stimulus of a natural latex biomembrane improves healing in mice.

    PubMed

    Andrade, T A M; Iyer, A; Das, P K; Foss, N T; Garcia, S B; Coutinho-Netto, J; Jordão-Jr, A A; Frade, M A C

    2011-10-01

    The aim of the present study was to compare healing obtained with biomembranes with the natural healing process (sham) using biochemical and immunohistological assays. C57BL/6 mice were divided into 4 groups of 15 mice each and received different subcutaneous implants: natural latex biomembrane (NLB), denatured latex (DL), expanded polytetrafluorethylene (ePTFE), or sham. On the 2nd, 7th, and 14th days post-treatment, 5 mice per group were sacrificed and biopsied for the following measurements: oxidative stress based on malondialdehyde (MDA), myeloperoxidase (MPO) and hydrogen peroxide by the method of ferrous oxidation-xylenol orange (FOX), as well as glutathione and total proteins; histological evaluation to enumerate inflammatory cells, fibroblasts, blood vessels, and collagen, and immunohistochemical staining for inducible nitric oxide synthase, interleukin-1β, vascular endothelial growth factor (VEGF), and transforming growth factor-β1 (TGF-β1). On day 2 post-treatment, NLB stimulated a dense inflammatory infiltrate mainly consisting of polymorphonuclear cells, as indicated by increased MPO (P < 0.05), but oxidative stress due to MDA was not observed until the 7th day (P < 0.05). The number of blood vessels was greater in NLB (P < 0.05) and DL (P < 0.05) mice compared to sham animals on day 14. NLB induced fibroplasia by day 14 (P < 0.05) with low expression of TGF-β1 and collagenesis. Thus, NLB significantly induced the inflammatory phase of healing mediated by oxidative stress, which appeared to influence the subsequent phases such as angiogenesis (with low expression of VEGF) and fibroplasia (independent of TGF-β1) without influencing collagenesis.

  14. On Complexity of the Quantum Ising Model

    NASA Astrophysics Data System (ADS)

    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.

  15. Wind and Diffusion Modeling for Complex Terrain.

    NASA Astrophysics Data System (ADS)

    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

  16. Inexpensive Complex Hand Model Twenty Years Later.

    PubMed

    Frenger, Paul

    2015-01-01

    Twenty years ago the author unveiled his inexpensive complex hand model, which reproduced every motion of the human hand. A control system programmed in the Forth language operated its actuators and sensors. Follow-on papers for this popular project were next presented in Texas, Canada and Germany. From this hand grew the author’s meter-tall robot (nicknamed ANNIE: Android With Neural Networks, Intellect and Emotions). It received machine vision, facial expressiveness, speech synthesis and speech recognition; a simian version also received a dexterous ape foot. New artificial intelligence features included op-amp neurons for OCR and simulated emotions, hormone emulation, endocannabinoid receptors, fear-trust-love mechanisms, a Grandmother Cell recognizer and artificial consciousness. Simulated illnesses included narcotic addiction, autism, PTSD, fibromyalgia and Alzheimer’s disease. The author gave 13 robotics-AI presentations at NASA in Houston since 2006. A meter-tall simian robot was proposed with gripping hand-feet for use with space vehicles and to explore distant planets and moons. Also proposed were: intelligent motorized exoskeletons for astronaut force multiplication; a cognitive prosthesis to detect and alleviate decreased crew mental performance; and a gynoid robot medic to tend astronauts in deep space missions. What began as a complex hand model evolved into an innovative robot-AI within two decades.

  17. Complex Educational Design: A Course Design Model Based on Complexity

    ERIC Educational Resources Information Center

    Freire, Maximina Maria

    2013-01-01

    Purpose: This article aims at presenting a conceptual framework which, theoretically grounded on complexity, provides the basis to conceive of online language courses that intend to respond to the needs of students and society. Design/methodology/approach: This paper is introduced by reflections on distance education and on the paradigmatic view…

  18. Lattice Boltzmann model for the complex Ginzburg-Landau equation.

    PubMed

    Zhang, Jianying; Yan, Guangwu

    2010-06-01

    A lattice Boltzmann model with complex distribution function for the complex Ginzburg-Landau equation (CGLE) is proposed. By using multiscale technique and the Chapman-Enskog expansion on complex variables, we obtain a series of complex partial differential equations. Then, complex equilibrium distribution function and its complex moments are obtained. Based on this model, the rotation and oscillation properties of stable spiral waves and the breaking-up behavior of unstable spiral waves in CGLE are investigated in detail.

  19. Delineating parameter unidentifiabilities in complex models

    NASA Astrophysics Data System (ADS)

    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.

  20. Using Perspective to Model Complex Processes

    SciTech Connect

    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.

  1. Clinical Complexity in Medicine: A Measurement Model of Task and Patient Complexity.

    PubMed

    Islam, R; Weir, C; Del Fiol, G

    2016-01-01

    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. 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 the infectious disease domain. The measurement model was adapted and modified for the healthcare domain. 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 processes 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. 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. 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.

  2. Ants (Formicidae): models for social complexity.

    PubMed

    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.

  3. Reducing Spatial Data Complexity for Classification Models

    NASA Astrophysics Data System (ADS)

    Ruta, Dymitr; Gabrys, Bogdan

    2007-11-01

    Intelligent data analytics gradually becomes a day-to-day reality of today's businesses. However, despite rapidly increasing storage and computational power current state-of-the-art predictive models still can not handle massive and noisy corporate data warehouses. What is more adaptive and real-time operational environment requires multiple models to be frequently retrained which further hinders their use. Various data reduction techniques ranging from data sampling up to density retention models attempt to address this challenge by capturing a summarised data structure, yet they either do not account for labelled data or degrade the classification performance of the model trained on the condensed dataset. Our response is a proposition of a new general framework for reducing the complexity of labelled data by means of controlled spatial redistribution of class densities in the input space. On the example of Parzen Labelled Data Compressor (PLDC) we demonstrate a simulatory data condensation process directly inspired by the electrostatic field interaction where the data are moved and merged following the attracting and repelling interactions with the other labelled data. The process is controlled by the class density function built on the original data that acts as a class-sensitive potential field ensuring preservation of the original class density distributions, yet allowing data to rearrange and merge joining together their soft class partitions. As a result we achieved a model that reduces the labelled datasets much further than any competitive approaches yet with the maximum retention of the original class densities and hence the classification performance. PLDC leaves the reduced dataset with the soft accumulative class weights allowing for efficient online updates and as shown in a series of experiments if coupled with Parzen Density Classifier (PDC) significantly outperforms competitive data condensation methods in terms of classification performance at the

  4. Reducing Spatial Data Complexity for Classification Models

    SciTech Connect

    Ruta, Dymitr; Gabrys, Bogdan

    2007-11-29

    Intelligent data analytics gradually becomes a day-to-day reality of today's businesses. However, despite rapidly increasing storage and computational power current state-of-the-art predictive models still can not handle massive and noisy corporate data warehouses. What is more adaptive and real-time operational environment requires multiple models to be frequently retrained which further hinders their use. Various data reduction techniques ranging from data sampling up to density retention models attempt to address this challenge by capturing a summarised data structure, yet they either do not account for labelled data or degrade the classification performance of the model trained on the condensed dataset. Our response is a proposition of a new general framework for reducing the complexity of labelled data by means of controlled spatial redistribution of class densities in the input space. On the example of Parzen Labelled Data Compressor (PLDC) we demonstrate a simulatory data condensation process directly inspired by the electrostatic field interaction where the data are moved and merged following the attracting and repelling interactions with the other labelled data. The process is controlled by the class density function built on the original data that acts as a class-sensitive potential field ensuring preservation of the original class density distributions, yet allowing data to rearrange and merge joining together their soft class partitions. As a result we achieved a model that reduces the labelled datasets much further than any competitive approaches yet with the maximum retention of the original class densities and hence the classification performance. PLDC leaves the reduced dataset with the soft accumulative class weights allowing for efficient online updates and as shown in a series of experiments if coupled with Parzen Density Classifier (PDC) significantly outperforms competitive data condensation methods in terms of classification performance at the

  5. Hybrid elastic and discrete-particle approach to biomembrane dynamics with application to the mobility of curved integral membrane proteins.

    PubMed

    Naji, Ali; Atzberger, Paul J; Brown, Frank L H

    2009-04-03

    We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral membrane proteins that impart a curvature on the bilayer surrounding them. Such proteins exhibit a substantial reduction in diffusion coefficient relative to "flat" proteins; this effect is explained by elementary hydrodynamic considerations.

  6. Parallel Scene Generation/Electromagnetic Modeling of Complex Targets in Complex Clutter and Propagation Environments

    DTIC Science & Technology

    2005-10-01

    COMPLEX TARGETS IN COMPLEX CLUTTER AND PROPAGATION ENVIRONMENTS Black River Systems Company APPROVED FOR PUBLIC RELEASE... PROPAGATION ENVIRONMENTS 6. AUTHOR(S) Milissa Benincasa, Tapan Sarkar, Christopher Card, Carl Thomas, Eric Mokole, Douglas Taylor, Richard Schneible, Ravi...targets (today’s capability) to accurate modeling of complex targets in complex environments with all their associated scattering and propagation

  7. Advanced Combustion Modeling for Complex Turbulent Flows

    NASA Technical Reports Server (NTRS)

    Ham, Frank Stanford

    2005-01-01

    The next generation of aircraft engines will need to pass stricter efficiency and emission tests. NASA's Ultra-Efficient Engine Technology (UEET) program has set an ambitious goal of 70% reduction of NO(x) emissions and a 15% increase in fuel efficiency of aircraft engines. We will demonstrate the state-of-the-art combustion tools developed a t Stanford's Center for Turbulence Research (CTR) as part of this program. In the last decade, CTR has spear-headed a multi-physics-based combustion modeling program. Key technologies have been transferred to the aerospace industry and are currently being used for engine simulations. In this demo, we will showcase the next-generation combustion modeling tools that integrate a very high level of detailed physics into advanced flow simulation codes. Combustor flows involve multi-phase physics with liquid fuel jet breakup, evaporation, and eventual combustion. Individual components of the simulation are verified against complex test cases and show excellent agreement with experimental data.

  8. Advanced Combustion Modeling for Complex Turbulent Flows

    NASA Technical Reports Server (NTRS)

    Ham, Frank Stanford

    2005-01-01

    The next generation of aircraft engines will need to pass stricter efficiency and emission tests. NASA's Ultra-Efficient Engine Technology (UEET) program has set an ambitious goal of 70% reduction of NO(x) emissions and a 15% increase in fuel efficiency of aircraft engines. We will demonstrate the state-of-the-art combustion tools developed a t Stanford's Center for Turbulence Research (CTR) as part of this program. In the last decade, CTR has spear-headed a multi-physics-based combustion modeling program. Key technologies have been transferred to the aerospace industry and are currently being used for engine simulations. In this demo, we will showcase the next-generation combustion modeling tools that integrate a very high level of detailed physics into advanced flow simulation codes. Combustor flows involve multi-phase physics with liquid fuel jet breakup, evaporation, and eventual combustion. Individual components of the simulation are verified against complex test cases and show excellent agreement with experimental data.

  9. Discrete Element Modeling of Complex Granular Flows

    NASA Astrophysics Data System (ADS)

    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

  10. Natural lipid extracts and biomembrane-mimicking lipid compositions are disposed to form nonlamellar phases, and they release DNA from lipoplexes most efficiently

    SciTech Connect

    Koynova, Rumiana; MacDonald, Robert C.

    2010-01-18

    A viewpoint now emerging is that a critical factor in lipid-mediated transfection (lipofection) is the structural evolution of lipoplexes upon interacting and mixing with cellular lipids. Here we report our finding that lipid mixtures mimicking biomembrane lipid compositions are superior to pure anionic liposomes in their ability to release DNA from lipoplexes (cationic lipid/DNA complexes), even though they have a much lower negative charge density (and thus lower capacity to neutralize the positive charge of the lipoplex lipids). Flow fluorometry revealed that the portion of DNA released after a 30-min incubation of the cationic O-ethylphosphatidylcholine lipoplexes with the anionic phosphatidylserine or phosphatidylglycerol was 19% and 37%, respectively, whereas a mixture mimicking biomembranes (MM: phosphatidylcholine/phosphatidylethanolamine/phosphatidylserine /cholesterol 45:20:20:15 w/w) and polar lipid extract from bovine liver released 62% and 74%, respectively, of the DNA content. A possible reason for this superior power in releasing DNA by the natural lipid mixtures was suggested by structural experiments: while pure anionic lipids typically form lamellae, the natural lipid mixtures exhibited a surprising predilection to form nonlamellar phases. Thus, the MM mixture arranged into lamellar arrays at physiological temperature, but began to convert to the hexagonal phase at a slightly higher temperature, {approx} 40-45 C. A propensity to form nonlamellar phases (hexagonal, cubic, micellar) at close to physiological temperatures was also found with the lipid extracts from natural tissues (from bovine liver, brain, and heart). This result reveals that electrostatic interactions are only one of the factors involved in lipid-mediated DNA delivery. The tendency of lipid bilayers to form nonlamellar phases has been described in terms of bilayer 'frustration' which imposes a nonzero intrinsic curvature of the two opposing monolayers. Because the stored curvature

  11. Modeling competitive substitution in a polyelectrolyte complex

    SciTech Connect

    Peng, B.; Muthukumar, M.

    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.

  12. Ultrasonic ray models for complex geometries

    NASA Astrophysics Data System (ADS)

    Schumm, A.

    2000-05-01

    Computer Aided Design techniques have become an inherent part of many industrial applications and are also gaining popularity in Nondestructive Testing. In sound field calculations, CAD representations can contribute to one of the generic problem in ultrasonic modeling, the wave propagation in complex geometries. Ray tracing codes were the first to take account of the geometry, providing qualitative information on beam propagation, such as geometrical echoes, multiple sound paths and possible conversions between wave modes. The forward ray tracing approach is intuitive and straightforward and can evolve towards a more quantitative code if transmission, divergence and polarization information is added. If used to evaluate the impulse response of a given geometry, an approximated time-dependent received signal can be obtained after convolution with the excitation signal. The more accurate reconstruction of a sound field after interaction with a geometrical interface according to ray theory requires inverse (or Fermat) ray-tracing to obtain the contribution of each elementary point source to the field at a given observation point. The resulting field of a finite transducer can then be obtained after integration over all point sources. While conceptionally close to classical ray tracing, this approach puts more stringent requirements on the CAD representation employed and is more difficult to extend towards multiple interfaces. In this communication we present examples for both approaches. In a prospective step, the link between both ray techniques is shown, and we illustrate how a combination of both approaches contributes to the solution of an industrial problem.

  13. Complex networks repair strategies: Dynamic models

    NASA Astrophysics Data System (ADS)

    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 < k > and enhances network invulnerability.

  14. Modeling competitive substitution in a polyelectrolyte complex

    NASA Astrophysics Data System (ADS)

    Peng, B.; Muthukumar, M.

    2015-12-01

    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.

  15. Room-temperature ionic liquids meet bio-membranes: the state-of-the-art.

    PubMed

    Benedetto, Antonio

    2017-08-04

    Room-temperature ionic liquids (RTIL) are a new class of organic salts whose melting temperature falls below the conventional limit of 100 °C. Their low vapor pressure, moreover, has made these ionic compounds the solvents of choice of the so-called green chemistry. For these and other peculiar characteristics, they are increasingly used in industrial applications. However, studies of their interaction with living organisms have highlighted mild to severe health hazards. Since their cytotoxicity shows a positive correlation with their lipophilicity, several chemical-physical studies of their interactions with biomembranes have been carried out in the last few years, aiming to identify the molecular mechanisms behind their toxicity. Cation chain length and anion nature of RTILs have seemed to affect lipophilicity and, in turn, their toxicity. However, the emerging picture raises new questions, points to the need to assess toxicity on a case-by-case basis, but also suggests a potential positive role of RTILs in pharmacology, bio-medicine and bio-nanotechnology. Here, we review this new subject of research, and comment on the future and the potential importance of this emerging field of study.

  16. Wound healing modulation by a latex protein-containing polyvinyl alcohol biomembrane.

    PubMed

    Ramos, Márcio V; de Alencar, Nylane Maria N; de Oliveira, Raquel S B; Freitas, Lyara B N; Aragão, Karoline S; de Andrade, Thiago Antônio M; Frade, Marco Andrey C; Brito, Gerly Anne C; de Figueiredo, Ingrid Samantha T

    2016-07-01

    In a previous study, we performed the chemical characterization of a polyvinyl alcohol (PVA) membrane supplemented with latex proteins (LP) displaying wound healing activity, and its efficacy as a delivery system was demonstrated. Here, we report on aspects of the mechanism underlying the performance of the PVA-latex protein biomembrane on wound healing. LP-PVA, but not PVA, induced more intense leukocyte (neutrophil) migration and mast cell degranulation during the inflammatory phase of the cicatricial process. Likewise, LP-PVA induced an increase in key markers and mediators of the inflammatory response (myeloperoxidase activity, nitric oxide, TNF, and IL-1β). These results demonstrated that LP-PVA significantly accelerates the early phase of the inflammatory process by upregulating cytokine release. This remarkable effect improves the subsequent phases of the healing process. The polyvinyl alcohol membrane was fully absorbed as an inert support while LP was shown to be active. It is therefore concluded that the LP-PVA is a suitable bioresource for biomedical engineering.

  17. Biomembrane-mimicking lipid bilayer system as a mechanically tunable cell substrate

    PubMed Central

    Lin, C. Y.; Auernheimer, V.; Naumann, C.; Goldmann, W. H.; Fabry, B.

    2014-01-01

    Cell behavior such as cell adhesion, spreading, and contraction critically depends on the elastic properties of the extracellular matrix. It is not known, however, how cells respond to viscoelastic or plastic material properties that more closely resemble the mechanical environment that cells encounter in the body. In this report, we employ viscoelastic and plastic biomembrane-mimicking cell substrates. The compliance of the substrates can be tuned by increasing the number of polymer-tethered bilayers. This leaves the density and conformation of adhesive ligands on the top bilayer unaltered. We then observe the response of fibroblasts to these property changes. For comparison, we also study the cells on soft polyacrylamide and hard glass surfaces. Cell morphology, motility, cell stiffness, contractile forces and adhesive contact size all decrease on more compliant matrices but are less sensitive to changes in matrix dissipative properties. These data suggest that cells are able to feel and respond predominantly to the effective matrix compliance, which arises as a combination of substrate and adhesive ligand mechanical properties. PMID:24439398

  18. How Local Anesthetics affect the structural and dynamical properties of bio-membranes

    NASA Astrophysics Data System (ADS)

    Yi, Zheng; Nagao, Michihiro; Bossev, Dobrin

    2009-03-01

    To address the question of how local anesthetics influences the structural and dynamical properties of bio-membranes, neutron-spin echo spectroscopy (NSE) has been performed on 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC) unilamellar vesicles (ULV) with different concentrations of Lidocaine in D2O to study the influence of Lidocaine on the bending elasticity of DMPC ULV bilayers in fluid crystal (L&_slash;alpha) phase and the ripple gel (P&_slash;beta') phase; The measurement of small-angle neutron scattering (SANS) has been performed to determine the bilayer thickness as a function of the concentration of Lidocaine. In the existence of molecules of Lidocaine the bending elasticity of DMPC bilayers was increased 30&%slash; -100&%slash; in L&_slash;alpha phase. The NSE data confirmed that fluid crystal/ripple gel transition temperature of DMPC bilayers was depressed by the addition of local anesthetics, which has also been examined via differential scanning calorimetry (DSC).

  19. Challenge for spectroscopic tomography of biomembrane using imaging type two-dimensional Fourier spectroscopy

    NASA Astrophysics Data System (ADS)

    Qi, Wei; Ishimaru, Ichiro

    2010-02-01

    We propose an image-producing Fourier spectroscopic technology that enables two-dimensional spectroscopic images to be obtained within the focusing plane alone. This technology incorporates auto-correlational phase-shift interferometry that uses only object light generated by the bright points that optically make up the object. We are currently involved in studies of non-invasive technologies used to measure blood components such as glucose and lipids, which are measured for use in daily living. Previous studies have investigated non-invasive technologies that measure blood glucose levels by utilizing near-infrared light that permeates the skin well. It has been confirmed that subtle changes in the concentration of a glucose solution, a sample used to measure the glucose level, can be measured by analyzing the spectroscopic characteristics of near-infrared light; however, when applied to a biomembrane, technology such as this is incapable of precisely measuring the glucose level because light diffusion within the skin disturbs the measurement. Our proposed technology enables two-dimensional spectroscopy to a limited depth below the skin covered by the measurement. Specifically, our technology concentrates only on the vascular territory near the skin surface, which is only minimally affected by light diffusion, as discussed previously; the spectroscopic characteristics of this territory are obtained and the glucose level can be measured with good sensitivity. In this paper we propose an image-producing Fourier spectroscopy method that is used as the measuring technology in producing a three-dimensional spectroscopic image.

  20. Applying a potential across a biomembrane: electrostatic contribution to the bending rigidity and membrane instability.

    PubMed

    Ambjörnsson, Tobias; Lomholt, Michael A; Hansen, Per Lyngs

    2007-05-01

    We investigate the effect on biomembrane mechanical properties due to the presence an external potential for a nonconductive incompressible membrane surrounded by different electrolytes. By solving the Debye-Hückel and Laplace equations for the electrostatic potential and using the relevant stress-tensor we find (1) in the small screening length limit, where the Debye screening length is smaller than the distance between the electrodes, the screening certifies that all electrostatic interactions are short range and the major effect of the applied potential is to decrease the membrane tension and increase the bending rigidity; explicit expressions for electrostatic contribution to the tension and bending rigidity are derived as a function of the applied potential, the Debye screening lengths, and the dielectric constants of the membrane and the solvents. For sufficiently large voltages the negative contribution to the tension is expected to cause a membrane stretching instability. (2) For the dielectric limit, i.e., no salt (and small wave vectors compared to the distance between the electrodes), when the dielectric constant on the two sides are different the applied potential induces an effective (unscreened) membrane charge density, whose long-range interaction is expected to lead to a membrane undulation instability.

  1. Probing protein-protein interaction in biomembranes using Fourier transform infrared spectroscopy.

    PubMed

    Haris, Parvez I

    2013-10-01

    The position, intensity and width of bands in infrared spectra that arise from vibrational modes within a protein can be used to probe protein secondary structure, amino acid side chain structure as well as protein dynamics and stability. FTIR spectroscopic studies on protein-protein interaction have been severely limited due to extensive overlap of peaks, from the interacting proteins. This problem is being addressed by combining data processing and acquisition techniques (difference spectroscopy and two-dimensional spectroscopy) with judicious modifications in the protein primary structure through molecular biological and chemical methods. These include the ability to modify amino acids (site-directed mutagenesis; chemical synthesis) and produce isotopically labelled proteins and peptides. Whilst great progress is being made towards overcoming the congestion of overlapping peaks, the slow progress in the assignment of bands continues to be a major hindrance in the use of infrared spectroscopy for obtaining highly accurate and precise information on protein structure. This review discusses some of these problems and presents examples of infrared studies on protein-protein interaction in biomembrane systems. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.

  2. Modeling Complex Chemical Systems: Problems and Solutions

    NASA Astrophysics Data System (ADS)

    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.

  3. Clinical complexity in medicine: A measurement model of task and patient complexity

    PubMed Central

    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

  4. Power Curve Modeling in Complex Terrain Using Statistical Models

    NASA Astrophysics Data System (ADS)

    Bulaevskaya, V.; Wharton, S.; Clifton, A.; Qualley, G.; Miller, W.

    2014-12-01

    Traditional power output curves typically model power only as a function of the wind speed at the turbine hub height. While the latter is an essential predictor of power output, wind speed information in other parts of the vertical profile, as well as additional atmospheric variables, are also important determinants of power. The goal of this work was to determine the gain in predictive ability afforded by adding wind speed information at other heights, as well as other atmospheric variables, to the power prediction model. Using data from a wind farm with a moderately complex terrain in the Altamont Pass region in California, we trained three statistical models, a neural network, a random forest and a Gaussian process model, to predict power output from various sets of aforementioned predictors. The comparison of these predictions to the observed power data revealed that considerable improvements in prediction accuracy can be achieved both through the addition of predictors other than the hub-height wind speed and the use of statistical models. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344 and was funded by Wind Uncertainty Quantification Laboratory Directed Research and Development Project at LLNL under project tracking code 12-ERD-069.

  5. Models of electron-transfer reactions at a biological-membrane-covered electrode-solution interface

    SciTech Connect

    Khan, S.U.

    1988-05-05

    Three models of electron-transfer processes at a biological-membrane-covered electrode-solution interface are put forward to explain the observed current density-overpotential dependences. The wet protein embedded in the biomembrane is assumed to act as a semiconductor. In model A, the transition of an electron is assumed as due to a transport (diffusion and drift) process in the biomembrane. A direct tunneling of electrons from the underlying metal surface through the barrier in the biomembrane to redox species in solution is assumed in model B. In model C, a resonance tunneling of electron from the metal surface via the resonance states in the band gap of the semiconducting protein in the biomembrane to the species in the solution is assumed. The current density-overpotential dependences from the transport model (model A) agree well with the experimental results. For biomembrane thickness of 70 A, the results of current density from the resonance tunneling model (model C) agree fairly with the experimental findings. The agreement between the results of theory and experiment suggest that electrons can, in fact, transfer through the biomembrane and react with the redox species in a solution.

  6. Spatiotemporal Organization of Spin-Coated Supported Model Membranes

    NASA Astrophysics Data System (ADS)

    Simonsen, Adam Cohen

    All cells of living organisms are separated from their surroundings and organized internally by means of flexible lipid membranes. In fact, there is consensus that the minimal requirements for self-replicating life processes include the following three features: (1) information carriers (DNA, RNA), (2) a metabolic system, and (3) encapsulation in a container structure [1]. Therefore, encapsulation can be regarded as an essential part of life itself. In nature, membranes are highly diverse interfacial structures that compartmentalize cells [2]. While prokaryotic cells only have an outer plasma membrane and a less-well-developed internal membrane structure, eukaryotic cells have a number of internal membranes associated with the organelles and the nucleus. Many of these membrane structures, including the plasma membrane, are complex layered systems, but with the basic structure of a lipid bilayer. Biomembranes contain hundreds of different lipid species in addition to embedded or peripherally associated membrane proteins and connections to scaffolds such as the cytoskeleton. In vitro, lipid bilayers are spontaneously self-organized structures formed by a large group of amphiphilic lipid molecules in aqueous suspensions. Bilayer formation is driven by the entropic properties of the hydrogen bond network in water in combination with the amphiphilic nature of the lipids. The molecular shapes of the lipid constituents play a crucial role in bilayer formation, and only lipids with approximately cylindrical shapes are able to form extended bilayers. The bilayer structure of biomembranes was discovered by Gorter and Grendel in 1925 [3] using monolayer studies of lipid extracts from red blood cells. Later, a number of conceptual models were developed to rationalize the organization of lipids and proteins in biological membranes. One of the most celebrated is the fluid-mosaic model by Singer and Nicolson (1972) [4]. According to this model, the lipid bilayer component of

  7. Modeling Complex Workflow in Molecular Diagnostics

    PubMed Central

    Gomah, Mohamed E.; Turley, James P.; Lu, Huimin; Jones, Dan

    2010-01-01

    One of the hurdles to achieving personalized medicine has been implementing the laboratory processes for performing and reporting complex molecular tests. The rapidly changing test rosters and complex analysis platforms in molecular diagnostics have meant that many clinical laboratories still use labor-intensive manual processing and testing without the level of automation seen in high-volume chemistry and hematology testing. We provide here a discussion of design requirements and the results of implementation of a suite of lab management tools that incorporate the many elements required for use of molecular diagnostics in personalized medicine, particularly in cancer. These applications provide the functionality required for sample accessioning and tracking, material generation, and testing that are particular to the evolving needs of individualized molecular diagnostics. On implementation, the applications described here resulted in improvements in the turn-around time for reporting of more complex molecular test sets, and significant changes in the workflow. Therefore, careful mapping of workflow can permit design of software applications that simplify even the complex demands of specialized molecular testing. By incorporating design features for order review, software tools can permit a more personalized approach to sample handling and test selection without compromising efficiency. PMID:20007844

  8. Living bio-membrane bi-template route for simultaneous synthesis of lead selenide nanorods and nanotubes

    NASA Astrophysics Data System (ADS)

    Li, Li; Wu, Qing-Sheng; Ding, Ya-Ping

    2004-12-01

    In this paper, a novel method is reported by which semiconductor materials are synthesized via controlled organism membranes. Semiconductor lead selenide nanorods and nanotubes have been successfully prepared simultaneously through living bio-membrane bi-templates of the mungbean sprout. The lead selenide nanorods are approximately 45 nm in diameter, and up to 1100 nm in length; all of them are single crystalline in structure. Lead selenide nanotubes are 50 nm in diameter, and up to 2000 nm in length, and are poly-crystalline in structure. The characteristics of the products are illustrated by various means, and their possible formation mechanism is explored.

  9. Dispersion Modeling in Complex Urban Systems

    EPA Science Inventory

    Models are used to represent real systems in an understandable way. They take many forms. A conceptual model explains the way a system works. In environmental studies, for example, a conceptual model may delineate all the factors and parameters for determining how a particle move...

  10. Specifying and Refining a Complex Measurement Model.

    ERIC Educational Resources Information Center

    Levy, Roy; Mislevy, Robert J.

    This paper aims to describe a Bayesian approach to modeling and estimating cognitive models both in terms of statistical machinery and actual instrument development. Such a method taps the knowledge of experts to provide initial estimates for the probabilistic relationships among the variables in a multivariate latent variable model and refines…

  11. Acquisition of Complex Systemic Thinking: Mental Models of Evolution

    ERIC Educational Resources Information Center

    d'Apollonia, Sylvia T.; Charles, Elizabeth S.; Boyd, Gary M.

    2004-01-01

    We investigated the impact of introducing college students to complex adaptive systems on their subsequent mental models of evolution compared to those of students taught in the same manner but with no reference to complex systems. The students' mental models (derived from similarity ratings of 12 evolutionary terms using the pathfinder algorithm)…

  12. Acquisition of Complex Systemic Thinking: Mental Models of Evolution

    ERIC Educational Resources Information Center

    d'Apollonia, Sylvia T.; Charles, Elizabeth S.; Boyd, Gary M.

    2004-01-01

    We investigated the impact of introducing college students to complex adaptive systems on their subsequent mental models of evolution compared to those of students taught in the same manner but with no reference to complex systems. The students' mental models (derived from similarity ratings of 12 evolutionary terms using the pathfinder algorithm)…

  13. Modeling Electronic Properties of Complex Oxides

    NASA Astrophysics Data System (ADS)

    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.

  14. Complexity reduction in context-dependent DNA substitution models.

    PubMed

    Majoros, William H; Ohler, Uwe

    2009-01-15

    The modeling of conservation patterns in genomic DNA has become increasingly popular for a number of bioinformatic applications. While several systems developed to date incorporate context-dependence in their substitution models, the impact on computational complexity and generalization ability of the resulting higher order models invites the question of whether simpler approaches to context modeling might permit appreciable reductions in model complexity and computational cost, without sacrificing prediction accuracy. We formulate several alternative methods for context modeling based on windowed Bayesian networks, and compare their effects on both accuracy and computational complexity for the task of discriminating functionally distinct segments in vertebrate DNA. Our results show that substantial reductions in the complexity of both the model and the associated inference algorithm can be achieved without reducing predictive accuracy.

  15. Complex Systems and Human Performance Modeling

    DTIC Science & Technology

    2013-12-01

    human communication patterns can be implemented in a task network modeling tool. Although queues are a basic feature in many task network modeling...time. MODELING COMMUNICATIVE BEHAVIOR Barabasi (2010) argues that human communication patterns are “bursty”; that is, the inter-event arrival...Having implemented the methods advocated by Clauset et al. in C3TRACE, we have grown more confident that the human communication data discussed above

  16. Multiscale Computational Models of Complex Biological Systems

    PubMed Central

    Walpole, Joseph; Papin, Jason A.; Peirce, Shayn M.

    2014-01-01

    Integration of data across spatial, temporal, and functional scales is a primary focus of biomedical engineering efforts. The advent of powerful computing platforms, coupled with quantitative data from high-throughput experimental platforms, has allowed multiscale modeling to expand as a means to more comprehensively investigate biological phenomena in experimentally relevant ways. This review aims to highlight recently published multiscale models of biological systems while using their successes to propose the best practices for future model development. We demonstrate that coupling continuous and discrete systems best captures biological information across spatial scales by selecting modeling techniques that are suited to the task. Further, we suggest how to best leverage these multiscale models to gain insight into biological systems using quantitative, biomedical engineering methods to analyze data in non-intuitive ways. These topics are discussed with a focus on the future of the field, the current challenges encountered, and opportunities yet to be realized. PMID:23642247

  17. Information, complexity and efficiency: The automobile model

    SciTech Connect

    Allenby, B. |

    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.

  18. Modeling Power Systems as Complex Adaptive Systems

    SciTech Connect

    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.

  19. Integrated Modeling of Complex Optomechanical Systems

    NASA Astrophysics Data System (ADS)

    Andersen, Torben; Enmark, Anita

    2011-09-01

    Mathematical modeling and performance simulation are playing an increasing role in large, high-technology projects. There are two reasons; first, projects are now larger than they were before, and the high cost calls for detailed performance prediction before construction. Second, in particular for space-related designs, it is often difficult to test systems under realistic conditions beforehand, and mathematical modeling is then needed to verify in advance that a system will work as planned. Computers have become much more powerful, permitting calculations that were not possible before. At the same time mathematical tools have been further developed and found acceptance in the community. Particular progress has been made in the fields of structural mechanics, optics and control engineering, where new methods have gained importance over the last few decades. Also, methods for combining optical, structural and control system models into global models have found widespread use. Such combined models are usually called integrated models and were the subject of this symposium. The objective was to bring together people working in the fields of groundbased optical telescopes, ground-based radio telescopes, and space telescopes. We succeeded in doing so and had 39 interesting presentations and many fruitful discussions during coffee and lunch breaks and social arrangements. We are grateful that so many top ranked specialists found their way to Kiruna and we believe that these proceedings will prove valuable during much future work.

  20. Slip complexity in dynamic models of earthquake faults.

    PubMed Central

    Langer, J S; Carlson, J M; Myers, C R; Shaw, B E

    1996-01-01

    We summarize recent evidence that models of earthquake faults with dynamically unstable friction laws but no externally imposed heterogeneities can exhibit slip complexity. Two models are described here. The first is a one-dimensional model with velocity-weakening stick-slip friction; the second is a two-dimensional elastodynamic model with slip-weakening friction. Both exhibit small-event complexity and chaotic sequences of large characteristic events. The large events in both models are composed of Heaton pulses. We argue that the key ingredients of these models are reasonably accurate representations of the properties of real faults. PMID:11607671

  1. Modeling complex systems in the geosciences

    NASA Astrophysics Data System (ADS)

    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.

  2. Complex networks and simple models in biology

    PubMed Central

    de Silva, Eric; Stumpf, Michael P.H

    2005-01-01

    The analysis of molecular networks, such as transcriptional, metabolic and protein interaction networks, has progressed substantially because of the power of models from statistical physics. Increasingly, the data are becoming so detailed—though not always complete or correct—that the simple models are reaching the limits of their usefulness. Here, we will discuss how network information can be described and to some extent quantified. In particular statistics offers a range of tools, such as model selection, which have not yet been widely applied in the analysis of biological networks. We will also outline a number of present challenges posed by biological network data in systems biology, and the extent to which these can be addressed by new developments in statistics, physics and applied mathematics. PMID:16849202

  3. Reduced-Complexity Models for Network Performance Prediction

    DTIC Science & Technology

    2005-05-01

    traffic over the network . To understand such a complex system it is necessary to develop accurate, yet simple, models to describe the performance...interconnected in complex ways, with millions of users sending traffic over the network . To understand such a complex system, it is necessary to develop...number of downloaders . . . . . . . . . . . . . . . . . 17 11 A network of ISP clouds. In this figure, the ISPs are connected via peering points, denoted

  4. A simple model clarifies the complicated relationships of complex networks

    PubMed Central

    Zheng, Bojin; Wu, Hongrun; Kuang, Li; Qin, Jun; Du, Wenhua; Wang, Jianmin; Li, Deyi

    2014-01-01

    Real-world networks such as the Internet and WWW have many common traits. Until now, hundreds of models were proposed to characterize these traits for understanding the networks. Because different models used very different mechanisms, it is widely believed that these traits origin from different causes. However, we find that a simple model based on optimisation can produce many traits, including scale-free, small-world, ultra small-world, Delta-distribution, compact, fractal, regular and random networks. Moreover, by revising the proposed model, the community-structure networks are generated. By this model and the revised versions, the complicated relationships of complex networks are illustrated. The model brings a new universal perspective to the understanding of complex networks and provide a universal method to model complex networks from the viewpoint of optimisation. PMID:25160506

  5. Complex Chebyshev-polynomial-based unified model (CCPBUM) neural networks

    NASA Astrophysics Data System (ADS)

    Jeng, Jin-Tsong; Lee, Tsu-Tian

    1998-03-01

    In this paper, we propose complex Chebyshev Polynomial Based unified model neural network for the approximation of complex- valued function. Based on this approximate transformable technique, we have derived the relationship between the single-layered neural network and multi-layered perceptron neural network. It is shown that the complex Chebyshev Polynomial Based unified model neural network can be represented as a functional link network that are based on Chebyshev polynomial. We also derived a new learning algorithm for the proposed network. It turns out that the complex Chebyshev Polynomial Based unified model neural network not only has the same capability of universal approximator, but also has faster learning speed than conventional complex feedforward/recurrent neural network.

  6. A musculoskeletal model of the elbow joint complex

    NASA Technical Reports Server (NTRS)

    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.

  7. Cellular Potts modeling of complex multicellular behaviors in tissue morphogenesis.

    PubMed

    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.

  8. An elementary method for implementing complex biokinetic models.

    PubMed

    Leggett, R W; Eckerman, K F; Williams, L R

    1993-03-01

    Recent efforts to incorporate greater anatomical and physiological realism into biokinetic models have resulted in many cases in mathematically complex formulations that limit routine application of the models. This paper describes an elementary, computer-efficient technique for implementing complex compartmental models, with attention focused primarily on biokinetic models involving time-dependent transfer rates and recycling. The technique applies, in particular, to the physiologically based, age-specific biokinetic models recommended in Publication No. 56 of the International Commission on Radiological Protection, Age-Dependent Doses to Members of the Public from Intake of Radionuclides.

  9. Realistic modeling of complex oxide materials

    NASA Astrophysics Data System (ADS)

    Solovyev, I. V.

    2011-01-01

    Since electronic and magnetic properties of many transition-metal oxides can be efficiently controlled by external factors such as the temperature, pressure, electric or magnetic field, they are regarded as promising materials for various applications. From the viewpoint of the electronic structure, these phenomena are frequently related to the behavior of a small group of states located near the Fermi level. The basic idea of this project is to construct a model for the low-energy states, derive all the parameters rigorously on the basis of density functional theory (DFT), and to study this model by modern techniques. After a brief review of the method, the abilities of this approach will be illustrated on a number of examples, including multiferroic manganites and spin-orbital-lattice coupled phenomena in RVO 3 (where R is the three-valent element).

  10. Complex Network Modeling with an Emulab HPC

    DTIC Science & Technology

    2012-09-01

    field. Actual Joint Tactical Radio System (JTRS) radios, Operations Network ( OPNET ) emulations, and GNU (recursive definition for GNU is Not Unix...open-source software-defined-radio software/ firmware/ hardware emulations can be accommodated. Index Terms—network emulation, Emulab, OPNET I...other hand, simulation tools such as MATLAB, Optimized Network Engineering Tools ( OPNET ), NS2, and CORE (a modeling environment from Vitech

  11. Toward Modeling the Intrinsic Complexity of Test Problems

    ERIC Educational Resources Information Center

    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…

  12. Classrooms as Complex Adaptive Systems: A Relational Model

    ERIC Educational Resources Information Center

    Burns, Anne; Knox, John S.

    2011-01-01

    In this article, we describe and model the language classroom as a complex adaptive system (see Logan & Schumann, 2005). We argue that linear, categorical descriptions of classroom processes and interactions do not sufficiently explain the complex nature of classrooms, and cannot account for how classroom change occurs (or does not occur), over…

  13. Computational Modeling of Uranium Hydriding and Complexes

    SciTech Connect

    Balasubramanian, K; Siekhaus, W J; McLean, W

    2003-02-03

    Uranium hydriding is one of the most important processes that has received considerable attention over many years. Although many experimental and modeling studies have been carried out concerning thermochemistry, diffusion kinetics and mechanisms of U-hydriding, very little is known about the electronic structure and electronic features that govern the U-hydriding process. Yet it is the electronic feature that controls the activation barrier and thus the rate of hydriding. Moreover the role of impurities and the role of the product UH{sub 3} on hydriding rating are not fully understood. An early study by Condon and Larson concerns with the kinetics of U-hydrogen system and a mathematical model for the U-hydriding process. They proposed that diffusion in the reactant phase by hydrogen before nucleation to form hydride phase and that the reaction is first order for hydriding and zero order for dehydriding. Condon has also calculated and measures the reaction rates of U-hydriding and proposed a diffusion model for the U-hydriding. This model was found to be in excellent agreement with the experimental reaction rates. From the slopes of the Arrhenius plot the activation energy was calculated as 6.35 kcal/mole. In a subsequent study Kirkpatrick formulated a close-form for approximate solution to Condon's equation. Bloch and Mintz have proposed the kinetics and mechanism for the U-H reaction over a wide range of pressures and temperatures. They have discussed their results through two models, one, which considers hydrogen diffusion through a protective UH{sub 3} product layer, and the second where hydride growth occurs at the hydride-metal interface. These authors obtained two-dimensional fits of experimental data to the pressure-temperature reactions. Kirkpatrick and Condon have obtained a linear solution to hydriding of uranium. These authors showed that the calculated reaction rates compared quite well with the experimental data at a hydrogen pressure of 1 atm. Powell

  14. Model complexity and performance: How far can we simplify?

    NASA Astrophysics Data System (ADS)

    Raick, C.; Soetaert, K.; Grégoire, M.

    2006-07-01

    Handling model complexity and reliability is a key area of research today. While complex models containing sufficient detail have become possible due to increased computing power, they often lead to too much uncertainty. On the other hand, very simple models often crudely oversimplify the real ecosystem and can not be used for management purposes. Starting from a complex and validated 1D pelagic ecosystem model of the Ligurian Sea (NW Mediterranean Sea), we derived simplified aggregated models in which either the unbalanced algal growth, the functional group diversity or the explicit description of the microbial loop was sacrificed. To overcome the problem of data availability with adequate spatial and temporal resolution, the outputs of the complex model are used as the baseline of perfect knowledge to calibrate the simplified models. Objective criteria of model performance were used to compare the simplified models’ results to the complex model output and to the available data at the DYFAMED station in the central Ligurian Sea. We show that even the simplest (NPZD) model is able to represent the global ecosystem features described by the complex model (e.g. primary and secondary productions, particulate organic matter export flux, etc.). However, a certain degree of sophistication in the formulation of some biogeochemical processes is required to produce realistic behaviors (e.g. the phytoplankton competition, the potential carbon or nitrogen limitation of the zooplankton ingestion, the model trophic closure, etc.). In general, a 9 state-variable model that has the functional group diversity removed, but which retains the bacterial loop and the unbalanced algal growth, performs best.

  15. Prequential Analysis of Complex Data with Adaptive Model Reselection.

    PubMed

    Clarke, Jennifer; Clarke, Bertrand

    2009-11-01

    In Prequential analysis, an inference method is viewed as a forecasting system, and the quality of the inference method is based on the quality of its predictions. This is an alternative approach to more traditional statistical methods that focus on the inference of parameters of the data generating distribution. In this paper, we introduce adaptive combined average predictors (ACAPs) for the Prequential analysis of complex data. That is, we use convex combinations of two different model averages to form a predictor at each time step in a sequence. A novel feature of our strategy is that the models in each average are re-chosen adaptively at each time step. To assess the complexity of a given data set, we introduce measures of data complexity for continuous response data. We validate our measures in several simulated contexts prior to using them in real data examples. The performance of ACAPs is compared with the performances of predictors based on stacking or likelihood weighted averaging in several model classes and in both simulated and real data sets. Our results suggest that ACAPs achieve a better trade off between model list bias and model list variability in cases where the data is very complex. This implies that the choices of model class and averaging method should be guided by a concept of complexity matching, i.e. the analysis of a complex data set may require a more complex model class and averaging strategy than the analysis of a simpler data set. We propose that complexity matching is akin to a bias-variance tradeoff in statistical modeling.

  16. Theoretical Modeling and Electromagnetic Response of Complex Metamaterials

    DTIC Science & Technology

    2017-03-06

    AFRL-AFOSR-VA-TR-2017-0042 Theoretical Modeling and Electromagnetic Response of Complex Metamaterials Andrea Alu UNIVERSITY OF TEXAS AT AUSTIN Final...Nov 2016 4. TITLE AND SUBTITLE Theoretical Modeling and Electromagnetic Response of Complex Metamaterials 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER...based on parity-time symmetric metasurfaces, and various advances in electromagnetic and acoustic theory and applications. Our findings have opened

  17. Model Analysis of Complex Systems Behavior using MADS

    NASA Astrophysics Data System (ADS)

    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.

  18. Do complex models increase prediction of complex behaviours? Predicting driving ability in people with brain disorders.

    PubMed

    Innes, Carrie R H; Lee, Dominic; Chen, Chen; Ponder-Sutton, Agate M; Melzer, Tracy R; Jones, Richard D

    2011-09-01

    Prediction of complex behavioural tasks via relatively simple modelling techniques, such as logistic regression and discriminant analysis, often has limited success. We hypothesized that to more accurately model complex behaviour, more complex models, such as kernel-based methods, would be needed. To test this hypothesis, we assessed the value of six modelling approaches for predicting driving ability based on performance on computerized sensory-motor and cognitive tests (SMCTests™) in 501 people with brain disorders. The models included three models previously used to predict driving ability (discriminant analysis, DA; binary logistic regression, BLR; and nonlinear causal resource analysis, NCRA) and three kernel methods (support vector machine, SVM; product kernel density, PK; and kernel product density, KP). At the classification level, two kernel methods were substantially more accurate at classifying on-road pass or fail (SVM 99.6%, PK 99.8%) than the other models (DA 76%, BLR 78%, NCRA 74%, KP 81%). However, accuracy decreased substantially for all of the kernel models when cross-validation techniques were used to estimate prediction of on-road pass or fail in an independent referral group (SVM 73-76%, PK 72-73%, KP 71-72%) but decreased only slightly for DA (74-75%) and BLR (75-76%). Cross-validation of NCRA was not possible. In conclusion, while kernel-based models are successful at modelling complex data at a classification level, this is likely to be due to overfitting of the data, which does not lead to an improvement in accuracy in independent data over and above the accuracy of other less complex modelling techniques.

  19. Size and complexity in model financial systems.

    PubMed

    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.

  20. Size and complexity in model financial systems

    PubMed Central

    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

  1. Modeling a Ca2+ Channel/BKCa Channel Complex at the Single-Complex Level

    PubMed Central

    Cox, Daniel H.

    2014-01-01

    BKCa-channel activity often affects the firing properties of neurons, the shapes of neuronal action potentials (APs), and in some cases the extent of neurotransmitter release. It has become clear that BKCa channels often form complexes with voltage-gated Ca2+ channels (CaV channels) such that when a CaV channel is activated, the ensuing influx of Ca2+ activates its closely associated BKCa channel. Thus, in modeling the electrical properties of neurons, it would be useful to have quantitative models of CaV/BKCa complexes. Furthermore, in a population of CaV/BKCa complexes, all BKCa channels are not exposed to the same Ca2+ concentration at the same time. Thus, stochastic rather than deterministic models are required. To date, however, no such models have been described. Here, however, I present a stochastic model of a CaV2.1/BKCa(α-only) complex, as might be found in a central nerve terminal. The CaV2.1/BKCa model is based on kinetic modeling of its two component channels at physiological temperature. Surprisingly, The CaV2.1/BKCa model predicts that although the CaV channel will open nearly every time during a typical cortical AP, its associated BKCa channel is expected to open in only 30% of trials, and this percentage is very sensitive to the duration of the AP, the distance between the two channels in the complex, and the presence of fast internal Ca2+ buffers. Also, the model predicts that the kinetics of the BKCa currents of a population of CaV2.1/BKCa complexes will not be limited by the kinetics of the CaV2.1 channel, and during a train of APs, the current response of the complex is expected to faithfully follow even very rapid trains. Aside from providing insight into how these complexes are likely to behave in vivo, the models presented here could also be of use more generally as components of higher-level models of neural function. PMID:25517147

  2. Generalized complex geometry, generalized branes and the Hitchin sigma model

    NASA Astrophysics Data System (ADS)

    Zucchini, Roberto

    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.

  3. Experimental porcine model of complex fistula-in-ano

    PubMed Central

    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 < 0.05). CONCLUSION Rubber band ligation is a stable and reliable method to establish complex fistula-in-ano models. Large animal models of complex anal fistulas can be used for the diagnosis and treatment of anal fistulas. PMID:28348488

  4. Finite element analysis to model complex mitral valve repair.

    PubMed

    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.

  5. Interaction of lipophilic gemcitabine prodrugs with biomembrane models studied by Langmuir-Blodgett technique.

    PubMed

    Castelli, Francesco; Sarpietro, Maria Grazia; Rocco, Flavio; Ceruti, Maurizio; Cattel, Luigi

    2007-09-01

    The stability and bioavailability of anticancer agents, such as gemcitabine, can be increased by forming prodrugs. Gemcitabine is rapidly deaminated to the inactive metabolite (2('),2(')-difluorodeoxyuridine), thus to improve its stability a series of increasingly lipophilic gemcitabine prodrugs linked through the 4-amino group to valeroyl, lauroyl, and stearoyl acyl chains were synthesized. Studies of monolayer properties are important to improve understanding of biological phenomena involving lipid/gemcitabine or lipid/gemcitabine derivative interactions. The interfacial behavior of monolayers constituted by DMPC plus gemcitabine or lipophilic gemcitabine prodrugs at increasing molar fractions was studied at the air/water interface at temperatures below (10 degrees C) and above (37 degrees C) the lipid phase transition. The effect of the hydrophobic chain length of gemcitabine derivatives on the isotherm of pure DMPC was investigated by surface tension measurement, and the results are reported as molar fractions as a function of mean molecular area per molecule. The results show that the compounds interact with DMPC producing mixed monolayers that are subject to an expansion effect, depending on the prodrug chain length. The results give useful hints of the interaction of these prodrugs with biological membranes and increase knowledge on the incorporation site of such compounds, as a function of their lipophilicity, in a lipid carrier; they may lead to improved liposomal formulation design.

  6. Reactivity and activation of dioxygen-derived species in aprotic media (a model matrix for biomembranes).

    PubMed

    Sawyer, D T; Roberts, J L; Calderwood, T S; Sugimoto, H; McDowell, M S

    1985-12-17

    In aprotic media the electrochemical reduction of dioxygen yields superoxide ion (O2-), which is an effective Brønsted base, nucleophile, one-electron reductant, and one-electron oxidant of reduced transition metal ions. With electrophilic substrates (organic halides and carbonyl carbons) O2- displaces a leaving group to form a peroxy radical (ROO.) in the primary process. Superoxide ion oxidizes the activated hydrogen atoms of ascorbic acid, catechols, hydrophenazines and hydroflavins. Combination of O2- with 1,2-diphenylhydrazine yields the anion radical of azobenzene, which reacts with O2 to give azobenzene and O2- (an example of O2--induced autoxidation). With phenylhydrazine, O2- produces phenyl radicals. The in situ formation of HO2. (O2- plus a proton source) results in H-atom abstraction from allylic and other groups with weak heteroatom--H bonds (binding energy (b.e.) less than 335 kJ). This is a competitive process with the facile second-order disproportionation of HO2. to H2O2 and O2 (kbi approximately equal to 10(4) mol-1 s-1 in Me2SO). Addition of [FeII(MeCN)4] (ClO4)2 to solutions of hydrogen peroxide in dry acetonitrile catalyses a rapid disproportionation of H2O2 via the initial formation of an adduct [FeII(H2O2)2+----Fe(O)(H2O)2+], which oxidizes a second H2O2 to oxygen. In the presence of organic substrates such as 1,4-cyclohexadiene, 1,2-diphenylhydrazine, catechols and thiols the FeII-H2O2/MeCN system yields dehydrogenated products; with alcohols, aldehydes, methylstyrene, thioethers, sulphoxides, and phosphines, the FeII(H2O2)2+ adduct promotes their monoxygenation. The product from the FeO2+-H2O2 reaction, [FeII(H2O2)22+], exhibits chemistry that is closely similar to that for singlet oxygen (1O2), which has been confirmed by the stoichiometric dioxygenation of diphenylisobenzofuran, 9,10-diphenylanthracene, rubrene and electron-rich unsaturated carbon-carbon bonds (Ph2C = CPh2, PhC = CPh and cis-PhCH = CHPh). In dry ligand-free acetonitrile (MeCN), anhydrous ferric chloride (FeIIICl3) activates hydrogen peroxide for the efficient epoxidation of alkenes. The FeIIICl3 further catalyses the dimerization of the resulting epoxides to dioxanes. These observations indicate that strong Lewis acids that are coordinatively unsaturated, [FeII(MeCN)4]2+ and [FeIIICl3], activate H2O2 to form an effective oxygenation and dehydrogenation agent.(ABSTRACT TRUNCATED AT 400 WORDS)

  7. Penetration of Milk-Derived Antimicrobial Peptides into Phospholipid Monolayers as Model Biomembranes

    PubMed Central

    Rogalska, Ewa; Więcław-Czapla, Katarzyna

    2013-01-01

    Three antimicrobial peptides derived from bovine milk proteins were examined with regard to penetration into insoluble monolayers formed with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) or 1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol) sodium salt (DPPG). Effects on surface pressure (Π) and electric surface potential (ΔV) were measured, Π with a platinum Wilhelmy plate and ΔV with a vibrating plate. The penetration measurements were performed under stationary diffusion conditions and upon the compression of the monolayers. The two type measurements showed greatly different effects of the peptide-lipid interactions. Results of the stationary penetration show that the peptide interactions with DPPC monolayer are weak, repulsive, and nonspecific while the interactions with DPPG monolayer are significant, attractive, and specific. These results are in accord with the fact that antimicrobial peptides disrupt bacteria membranes (negative) while no significant effect on the host membranes (neutral) is observed. No such discrimination was revealed from the compression isotherms. The latter indicate that squeezing the penetrant out of the monolayer upon compression does not allow for establishing the penetration equilibrium, so the monolayer remains supersaturated with the penetrant and shows an under-equilibrium orientation within the entire compression range, practically. PMID:24455264

  8. Effect of charged lidocaine on static and dynamic properties of model bio-membranes.

    PubMed

    Yi, Zheng; Nagao, Michihiro; Bossev, Dobrin P

    2012-01-01

    The effect of the charged lidocaine on the structure and dynamics of DMPC/DMPG (mass fraction of 95/5) unilamellar vesicles has been investigated. Changes in membrane organization caused by the presence of lidocaine were detected through small angle neutron scattering experiments. Our results suggest that the presence of lidocaine in the vicinity of the headgroups of lipid membranes leads to an increase of the area per lipid molecule and to a decrease of membrane thickness. Such changes in membrane structure may induce disordering of the tail group. This scenario explains the reduction of the main transition temperature of lipid membranes, as the fraction of lidocaine per lipid molecules increases, which was evident from differential scanning calorimetry results. Furthermore neutron spin echo spectroscopy was used for the dynamics measurements and the results reveal that presence of charged lidocaine increases the bending elasticity of the lipid membranes in the fluid phase and slows the temperature-dependent change of bending elasticity across the main transition temperature.

  9. Bladder Cancer: A Simple Model Becomes Complex

    PubMed Central

    Pierro, Giovanni Battista Di; Gulia, Caterina; Cristini, Cristiano; Fraietta, Giorgio; Marini, Lorenzo; Grande, Pietro; Gentile, Vincenzo; Piergentili, Roberto

    2012-01-01

    Bladder cancer is one of the most frequent malignancies in developed countries and it is also characterized by a high number of recurrences. Despite this, several authors in the past reported that only two altered molecular pathways may genetically explain all cases of bladder cancer: one involving the FGFR3 gene, and the other involving the TP53 gene. Mutations in any of these two genes are usually predictive of the malignancy final outcome. This cancer may also be further classified as low-grade tumors, which is always papillary and in most cases superficial, and high-grade tumors, not necessarily papillary and often invasive. This simple way of considering this pathology has strongly changed in the last few years, with the development of genome-wide studies on expression profiling and the discovery of small non-coding RNA affecting gene expression. An easy search in the OMIM (On-line Mendelian Inheritance in Man) database using “bladder cancer” as a query reveals that genes in some way connected to this pathology are approximately 150, and some authors report that altered gene expression (up- or down-regulation) in this disease may involve up to 500 coding sequences for low-grade tumors and up to 2300 for high-grade tumors. In many clinical cases, mutations inside the coding sequences of the above mentioned two genes were not found, but their expression changed; this indicates that also epigenetic modifications may play an important role in its development. Indeed, several reports were published about genome-wide methylation in these neoplastic tissues, and an increasing number of small non-coding RNA are either up- or down-regulated in bladder cancer, indicating that impaired gene expression may also pass through these metabolic pathways. Taken together, these data reveal that bladder cancer is far to be considered a simple model of malignancy. In the present review, we summarize recent progress in the genome-wide analysis of bladder cancer, and analyse non

  10. Reassessing Geophysical Models of the Bushveld Complex in 3D

    NASA Astrophysics Data System (ADS)

    Cole, J.; Webb, S. J.; Finn, C.

    2012-12-01

    Conceptual geophysical models of the Bushveld Igneous Complex show three possible geometries for its mafic component: 1) Separate intrusions with vertical feeders for the eastern and western lobes (Cousins, 1959) 2) Separate dipping sheets for the two lobes (Du Plessis and Kleywegt, 1987) 3) A single saucer-shaped unit connected at depth in the central part between the two lobes (Cawthorn et al, 1998) Model three incorporates isostatic adjustment of the crust in response to the weight of the dense mafic material. The model was corroborated by results of a broadband seismic array over southern Africa, known as the Southern African Seismic Experiment (SASE) (Nguuri, et al, 2001; Webb et al, 2004). This new information about the crustal thickness only became available in the last decade and could not be considered in the earlier models. Nevertheless, there is still on-going debate as to which model is correct. All of the models published up to now have been done in 2 or 2.5 dimensions. This is not well suited to modelling the complex geometry of the Bushveld intrusion. 3D modelling takes into account effects of variations in geometry and geophysical properties of lithologies in a full three dimensional sense and therefore affects the shape and amplitude of calculated fields. The main question is how the new knowledge of the increased crustal thickness, as well as the complexity of the Bushveld Complex, will impact on the gravity fields calculated for the existing conceptual models, when modelling in 3D. The three published geophysical models were remodelled using full 3Dl potential field modelling software, and including crustal thickness obtained from the SASE. The aim was not to construct very detailed models, but to test the existing conceptual models in an equally conceptual way. Firstly a specific 2D model was recreated in 3D, without crustal thickening, to establish the difference between 2D and 3D results. Then the thicker crust was added. Including the less

  11. The Use of Behavior Models for Predicting Complex Operations

    NASA Technical Reports Server (NTRS)

    Gore, Brian F.

    2010-01-01

    Modeling and simulation (M&S) plays an important role when complex human-system notions are being proposed, developed and tested within the system design process. National Aeronautics and Space Administration (NASA) as an agency uses many different types of M&S approaches for predicting human-system interactions, especially when it is early in the development phase of a conceptual design. NASA Ames Research Center possesses a number of M&S capabilities ranging from airflow, flight path models, aircraft models, scheduling models, human performance models (HPMs), and bioinformatics models among a host of other kinds of M&S capabilities that are used for predicting whether the proposed designs will benefit the specific mission criteria. The Man-Machine Integration Design and Analysis System (MIDAS) is a NASA ARC HPM software tool that integrates many models of human behavior with environment models, equipment models, and procedural / task models. The challenge to model comprehensibility is heightened as the number of models that are integrated and the requisite fidelity of the procedural sets are increased. Model transparency is needed for some of the more complex HPMs to maintain comprehensibility of the integrated model performance. This will be exemplified in a recent MIDAS v5 application model and plans for future model refinements will be presented.

  12. Modeling of Protein Binary Complexes Using Structural Mass Spectrometry Data

    SciTech Connect

    Amisha Kamal,J.; Chance, M.

    2008-01-01

    In this article, we describe a general approach to modeling the structure of binary protein complexes using structural mass spectrometry data combined with molecular docking. In the first step, hydroxyl radical mediated oxidative protein footprinting is used to identify residues that experience conformational reorganization due to binding or participate in the binding interface. In the second step, a three-dimensional atomic structure of the complex is derived by computational modeling. Homology modeling approaches are used to define the structures of the individual proteins if footprinting detects significant conformational reorganization as a function of complex formation. A three-dimensional model of the complex is constructed from these binary partners using the ClusPro program, which is composed of docking, energy filtering, and clustering steps. Footprinting data are used to incorporate constraints--positive and/or negative--in the docking step and are also used to decide the type of energy filter--electrostatics or desolvation--in the successive energy-filtering step. By using this approach, we examine the structure of a number of binary complexes of monomeric actin and compare the results to crystallographic data. Based on docking alone, a number of competing models with widely varying structures are observed, one of which is likely to agree with crystallographic data. When the docking steps are guided by footprinting data, accurate models emerge as top scoring. We demonstrate this method with the actin/gelsolin segment-1 complex. We also provide a structural model for the actin/cofilin complex using this approach which does not have a crystal or NMR structure.

  13. Geometric modeling of subcellular structures, organelles, and multiprotein complexes

    PubMed Central

    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

  14. Geometric modeling of subcellular structures, organelles, and multiprotein complexes.

    PubMed

    Feng, Xin; Xia, Kelin; Tong, Yiying; Wei, Guo-Wei

    2012-12-01

    Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multiprotein 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. Copyright © 2012 John Wiley & Sons, Ltd.

  15. Between complexity of modelling and modelling of complexity: An essay on econophysics

    NASA Astrophysics Data System (ADS)

    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.

  16. Using fMRI to Test Models of Complex Cognition

    ERIC Educational Resources Information Center

    Anderson, John R.; Carter, Cameron S.; Fincham, Jon M.; Qin, Yulin; Ravizza, Susan M.; Rosenberg-Lee, Miriam

    2008-01-01

    This article investigates the potential of fMRI to test assumptions about different components in models of complex cognitive tasks. If the components of a model can be associated with specific brain regions, one can make predictions for the temporal course of the BOLD response in these regions. An event-locked procedure is described for dealing…

  17. Network model of bilateral power markets based on complex networks

    NASA Astrophysics Data System (ADS)

    Wu, Yang; Liu, Junyong; Li, Furong; Yan, Zhanxin; Zhang, Li

    2014-06-01

    The bilateral power transaction (BPT) mode becomes a typical market organization with the restructuring of electric power industry, the proper model which could capture its characteristics is in urgent need. However, the model is lacking because of this market organization's complexity. As a promising approach to modeling complex systems, complex networks could provide a sound theoretical framework for developing proper simulation model. In this paper, a complex network model of the BPT market is proposed. In this model, price advantage mechanism is a precondition. Unlike other general commodity transactions, both of the financial layer and the physical layer are considered in the model. Through simulation analysis, the feasibility and validity of the model are verified. At same time, some typical statistical features of BPT network are identified. Namely, the degree distribution follows the power law, the clustering coefficient is low and the average path length is a bit long. Moreover, the topological stability of the BPT network is tested. The results show that the network displays a topological robustness to random market member's failures while it is fragile against deliberate attacks, and the network could resist cascading failure to some extent. These features are helpful for making decisions and risk management in BPT markets.

  18. Using fMRI to Test Models of Complex Cognition

    ERIC Educational Resources Information Center

    Anderson, John R.; Carter, Cameron S.; Fincham, Jon M.; Qin, Yulin; Ravizza, Susan M.; Rosenberg-Lee, Miriam

    2008-01-01

    This article investigates the potential of fMRI to test assumptions about different components in models of complex cognitive tasks. If the components of a model can be associated with specific brain regions, one can make predictions for the temporal course of the BOLD response in these regions. An event-locked procedure is described for dealing…

  19. Tips on Creating Complex Geometry Using Solid Modeling Software

    ERIC Educational Resources Information Center

    Gow, George

    2008-01-01

    Three-dimensional computer-aided drafting (CAD) software, sometimes referred to as "solid modeling" software, is easy to learn, fun to use, and becoming the standard in industry. However, many users have difficulty creating complex geometry with the solid modeling software. And the problem is not entirely a student problem. Even some teachers and…

  20. Tips on Creating Complex Geometry Using Solid Modeling Software

    ERIC Educational Resources Information Center

    Gow, George

    2008-01-01

    Three-dimensional computer-aided drafting (CAD) software, sometimes referred to as "solid modeling" software, is easy to learn, fun to use, and becoming the standard in industry. However, many users have difficulty creating complex geometry with the solid modeling software. And the problem is not entirely a student problem. Even some teachers and…

  1. Zebrafish as an emerging model for studying complex brain disorders

    PubMed Central

    Kalueff, Allan V.; Stewart, Adam Michael; Gerlai, Robert

    2014-01-01

    The zebrafish (Danio rerio) is rapidly becoming a popular model organism in pharmacogenetics and neuropharmacology. Both larval and adult zebrafish are currently used to increase our understanding of brain function, dysfunction, and their genetic and pharmacological modulation. Here we review the developing utility of zebrafish in the analysis of complex brain disorders (including, for example, depression, autism, psychoses, drug abuse and cognitive disorders), also covering zebrafish applications towards the goal of modeling major human neuropsychiatric and drug-induced syndromes. We argue that zebrafish models of complex brain disorders and drug-induced conditions have become a rapidly emerging critical field in translational neuropharmacology research. PMID:24412421

  2. Dynamic bio-adhesion of polymer nanoparticles on MDCK epithelial cells and its impact on bio-membranes, endocytosis and paracytosis.

    PubMed

    He, Bing; Yuan, Lan; Dai, Wenbing; Gao, Wei; Zhang, Hua; Wang, Xueqing; Fang, Weigang; Zhang, Qiang

    2016-03-21

    Nowadays, concern about the use of nanotechnology for biomedical application is unprecedentedly increasing. In fact, nanosystems applied for various potential clinical uses always have to cross the primary biological barrier consisting of epithelial cells. However, little is really known currently in terms of the influence of the dynamic bio-adhesion of nanosystems on bio-membranes as well as on endocytosis and transcytosis. This was investigated here using polymer nanoparticles (PNs) and MDCK epithelial cells as the models. Firstly, the adhesion of PNs on cell membranes was found to be time-dependent with a shift of both location and dispersion pattern, from the lateral adhesion of mainly mono-dispersed PNs initially to the apical coverage of the PN aggregate later. Then, it was interesting to observe in this study that the dynamic bio-adhesion of PNs only affected their endocytosis but not their transcytosis. It was important to find that the endocytosis of PNs was not a constant process. A GM1 dependent CDE (caveolae dependent endocytosis) pathway was dominant in the preliminary stage, followed by the co-existence of a CME (clathrin-mediated endocytosis) pathway for the PN aggregate at a later stage, in accordance with the adhesion features of PNs, suggesting the modification of PN adhesion patterns on the endocytosis pathways. Next, the PN adhesion was noticed to affect the structure of cell junctions, via altering the extra- and intra-cellular calcium levels, leading to the enhanced paracellular transport of small molecules, but not favorably enough for the obviously increased passing of PNs themselves. Finally, FRAP and other techniques all demonstrated the obvious impact of PN adhesion on the membrane confirmation, independent of the adhesion location and time, which might lower the threshold for the internalization of PNs, even their aggregates. Generally, these findings confirm that the transport pathway mechanism of PNs through epithelial cells is rather

  3. Dynamic bio-adhesion of polymer nanoparticles on MDCK epithelial cells and its impact on bio-membranes, endocytosis and paracytosis

    NASA Astrophysics Data System (ADS)

    He, Bing; Yuan, Lan; Dai, Wenbing; Gao, Wei; Zhang, Hua; Wang, Xueqing; Fang, Weigang; Zhang, Qiang

    2016-03-01

    Nowadays, concern about the use of nanotechnology for biomedical application is unprecedentedly increasing. In fact, nanosystems applied for various potential clinical uses always have to cross the primary biological barrier consisting of epithelial cells. However, little is really known currently in terms of the influence of the dynamic bio-adhesion of nanosystems on bio-membranes as well as on endocytosis and transcytosis. This was investigated here using polymer nanoparticles (PNs) and MDCK epithelial cells as the models. Firstly, the adhesion of PNs on cell membranes was found to be time-dependent with a shift of both location and dispersion pattern, from the lateral adhesion of mainly mono-dispersed PNs initially to the apical coverage of the PN aggregate later. Then, it was interesting to observe in this study that the dynamic bio-adhesion of PNs only affected their endocytosis but not their transcytosis. It was important to find that the endocytosis of PNs was not a constant process. A GM1 dependent CDE (caveolae dependent endocytosis) pathway was dominant in the preliminary stage, followed by the co-existence of a CME (clathrin-mediated endocytosis) pathway for the PN aggregate at a later stage, in accordance with the adhesion features of PNs, suggesting the modification of PN adhesion patterns on the endocytosis pathways. Next, the PN adhesion was noticed to affect the structure of cell junctions, via altering the extra- and intra-cellular calcium levels, leading to the enhanced paracellular transport of small molecules, but not favorably enough for the obviously increased passing of PNs themselves. Finally, FRAP and other techniques all demonstrated the obvious impact of PN adhesion on the membrane confirmation, independent of the adhesion location and time, which might lower the threshold for the internalization of PNs, even their aggregates. Generally, these findings confirm that the transport pathway mechanism of PNs through epithelial cells is rather

  4. Hypothesis of potential active components in Angelica sinensis by using biomembrane extraction and high performance liquid chromatography.

    PubMed

    Dong, Z B; Li, S P; Hong, M; Zhu, Q

    2005-07-15

    The screening and analysis of bioactive components in traditional Chinese medicines (TCMs) is very important not only for the quality control of crude drugs but also for elucidating the therapeutic principle. In this study, a method for screening potential active components from TCMs was developed by using biomembrane extraction and high performance liquid chromatography. Based on the methodology, aqueous extract of Angelica sinensis (WEAS) was used, and four compounds were detected by HPLC in the desorption eluate of red cell membrane extraction for WEAS. The compounds were identified as ferulic acid, ligustilide, senkyunolide H and senkyunolide I based on their UV, MS and NMR spectra. Actually, ferulic acid and ligustilide are considered as major active components in Angelica sinensis. Therefore, this method may be applied to predict the potential bioactivities of multiple compounds in TCMs simultaneously.

  5. Complexation and molecular modeling studies of europium(III)-gallic acid-amino acid complexes.

    PubMed

    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.

  6. Artificial biomembranes stabilized over spin coated hydrogel scaffolds. Crosslinking agent nature induces wrinkled or flat surfaces on the hydrogel.

    PubMed

    González-Henríquez, C M; Pizarro-Guerra, G C; Córdova-Alarcón, E N; Sarabia-Vallejos, M A; Terraza-Inostroza, C A

    2016-03-01

    Hydrogel films possess the ability of retain water and deliver it to a phospholipid bilayer mainly composed by DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine); moisture of the medium favors the stability of an artificial biomembrane when it is subjected to repetitive heating cycles. This hypothesis is valid when the hydrogel film, used as scaffold, present a flat surface morphology and a high ability for water releasing. On the other hand, when the sample presents a wrinkle topography (periodic undulations), free lateral molecular movement of the bilayer becomes lower, disfavoring the occurrence of clear phases/phase transitions according to applied temperature. Hydrogel films were prepared using HEMA (hydroxyethylmetacrylate), different crosslinking agents and initiators. This reaction mixture was spread over hydrophilic silicon wafers using spin coating technique. Resultant films were then exposed to UV light favoring polymeric chain crosslinking and interactions between hydrogel and substrate; this process is also known to generate tensile stress mismatch between different hydrogel strata, producing out-of-plane net force that generate ordered undulations or collapsed crystals at surface level. DPPC bilayers were then placed over hydrogel using Langmuir-Blodgett technique. Surface morphology was detected in order to clarify the behavior of these films. Obtained data corroborate DPPC membrane stability making possible to detect phases/phase transitions by ellipsometric methods and Atomic Force Microscopy due to their high hydration level. This system is intended to be used as biosensor through the insertion of transmembrane proteins or peptides that detect minimal variations of some analyte in the environment; artificial biomembrane stability and behavior is fundamental for this purpose. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. Bim Automation: Advanced Modeling Generative Process for Complex Structures

    NASA Astrophysics Data System (ADS)

    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.

  8. Pedigree models for complex human traits involving the mitochrondrial genome

    SciTech Connect

    Schork, N.J.; Guo, S.W. )

    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.

  9. Multiscale Model for the Assembly Kinetics of Protein Complexes.

    PubMed

    Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

    2016-02-04

    The assembly of proteins into high-order complexes is a general mechanism for these biomolecules to implement their versatile functions in cells. Natural evolution has developed various assembling pathways for specific protein complexes to maintain their stability and proper activities. Previous studies have provided numerous examples of the misassembly of protein complexes leading to severe biological consequences. Although the research focusing on protein complexes has started to move beyond the static representation of quaternary structures to the dynamic aspect of their assembly, the current understanding of the assembly mechanism of protein complexes is still largely limited. To tackle this problem, we developed a new multiscale modeling framework. This framework combines a lower-resolution rigid-body-based simulation with a higher-resolution Cα-based simulation method so that protein complexes can be assembled with both structural details and computational efficiency. We applied this model to a homotrimer and a heterotetramer as simple test systems. Consistent with experimental observations, our simulations indicated very different kinetics between protein oligomerization and dimerization. The formation of protein oligomers is a multistep process that is much slower than dimerization but thermodynamically more stable. Moreover, we showed that even the same protein quaternary structure can have very diverse assembly pathways under different binding constants between subunits, which is important for regulating the functions of protein complexes. Finally, we revealed that the binding between subunits in a complex can be synergistically strengthened during assembly without considering allosteric regulation or conformational changes. Therefore, our model provides a useful tool to understand the general principles of protein complex assembly.

  10. Emulator-assisted data assimilation in complex models

    NASA Astrophysics Data System (ADS)

    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.

  11. Systems Engineering Metrics: Organizational Complexity and Product Quality Modeling

    NASA Technical Reports Server (NTRS)

    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.

  12. Calibration of Complex Subsurface Reaction Models Using a Surrogate-Model Approach

    EPA Science Inventory

    Application of model assessment techniques to complex subsurface reaction models involves numerous difficulties, including non-trivial model selection, parameter non-uniqueness, and excessive computational burden. To overcome these difficulties, this study introduces SAMM (Simult...

  13. Calibration of Complex Subsurface Reaction Models Using a Surrogate-Model Approach

    EPA Science Inventory

    Application of model assessment techniques to complex subsurface reaction models involves numerous difficulties, including non-trivial model selection, parameter non-uniqueness, and excessive computational burden. To overcome these difficulties, this study introduces SAMM (Simult...

  14. Modeling of Complex Adaptive Systems in Air Operations

    DTIC Science & Technology

    2006-09-01

    control of C3 in an increasingly complex military environment. Control theory is a multidisciplinary science associated with dynamic systems and, while...AFRL-IF-RS-TR-2006-282 In- House Final Technical Report September 2006 MODELING OF COMPLEX ADAPTIVE SYSTEMS IN AIR OPERATIONS...NOTICE AND SIGNATURE PAGE Using Government drawings, specifications, or other data included in this document for any purpose other than Government

  15. Improving a regional model using reduced complexity and parameter estimation

    USGS Publications Warehouse

    Kelson, Victor A.; Hunt, Randall J.; Haitjema, Henk M.

    2002-01-01

    The availability of powerful desktop computers and graphical user interfaces for ground water flow models makes possible the construction of ever more complex models. A proposed copper-zinc sulfide mine in northern Wisconsin offers a unique case in which the same hydrologic system has been modeled using a variety of techniques covering a wide range of sophistication and complexity. Early in the permitting process, simple numerical models were used to evaluate the necessary amount of water to be pumped from the mine, reductions in streamflow, and the drawdowns in the regional aquifer. More complex models have subsequently been used in an attempt to refine the predictions. Even after so much modeling effort, questions regarding the accuracy and reliability of the predictions remain. We have performed a new analysis of the proposed mine using the two-dimensional analytic element code GFLOW coupled with the nonlinear parameter estimation code UCODE. The new model is parsimonious, containing fewer than 10 parameters, and covers a region several times larger in areal extent than any of the previous models. The model demonstrates the suitability of analytic element codes for use with parameter estimation codes. The simplified model results are similar to the more complex models; predicted mine inflows and UCODE-derived 95% confidence intervals are consistent with the previous predictions. More important, the large areal extent of the model allowed us to examine hydrological features not included in the previous models, resulting in new insights about the effects that far-field boundary conditions can have on near-field model calibration and parameterization. In this case, the addition of surface water runoff into a lake in the headwaters of a stream while holding recharge constant moved a regional ground watershed divide and resulted in some of the added water being captured by the adjoining basin. Finally, a simple analytical solution was used to clarify the GFLOW model

  16. On explicit algebraic stress models for complex turbulent flows

    NASA Technical Reports Server (NTRS)

    Gatski, T. B.; Speziale, C. G.

    1992-01-01

    Explicit algebraic stress models that are valid for three-dimensional turbulent flows in noninertial frames are systematically derived from a hierarchy of second-order closure models. This represents a generalization of the model derived by Pope who based his analysis on the Launder, Reece, and Rodi model restricted to two-dimensional turbulent flows in an inertial frame. The relationship between the new models and traditional algebraic stress models -- as well as anistropic eddy visosity models -- is theoretically established. The need for regularization is demonstrated in an effort to explain why traditional algebraic stress models have failed in complex flows. It is also shown that these explicit algebraic stress models can shed new light on what second-order closure models predict for the equilibrium states of homogeneous turbulent flows and can serve as a useful alternative in practical computations.

  17. Complex groundwater flow systems as traveling agent models

    PubMed Central

    Padilla, Pablo; Escolero, Oscar; González, Tomas; Morales-Casique, Eric; Osorio-Olvera, Luis

    2014-01-01

    Analyzing field data from pumping tests, we show that as with many other natural phenomena, groundwater flow exhibits 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. PMID:25337455

  18. Complex groundwater flow systems as traveling agent models.

    PubMed

    López Corona, Oliver; Padilla, Pablo; Escolero, Oscar; González, Tomas; Morales-Casique, Eric; Osorio-Olvera, Luis

    2014-01-01

    Analyzing field data from pumping tests, we show that as with many other natural phenomena, groundwater flow exhibits 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.

  19. A Complex Systems Model Approach to Quantified Mineral Resource Appraisal

    USGS Publications Warehouse

    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.

  20. Dockground: A comprehensive data resource for modeling of protein complexes.

    PubMed

    Kundrotas, Petras J; Anishchenko, Ivan; Dauzhenka, Taras; Kotthoff, Ian; Mnevets, Daniil; Copeland, Matthew M; Vakser, Ilya A

    2017-09-10

    Characterization of life processes at the molecular level requires structural details of protein interactions. The number of experimentally determined structures of protein-protein complexes accounts only for a fraction of known protein interactions. This gap in structural description of the interactome has to be bridged by modeling. An essential part of the development of structural modeling/docking techniques for protein interactions is databases of protein-protein complexes. They are necessary for studying protein interfaces, providing a knowledge base for docking algorithms, developing intermolecular potentials, search procedures, and scoring functions. Development of protein-protein docking techniques requires thorough benchmarking of different parts of the docking protocols on carefully curated sets of protein-protein complexes. We present a comprehensive description of the Dockground resource (http://dockground.compbio.ku.edu) for structural modeling of protein interactions, including previously unpublished unbound docking benchmark set 4, and the X-ray docking decoy set 2. The resource offers a variety of interconnected datasets of protein-protein complexes and other data for the development and testing of different aspects of protein docking methodologies. Based on protein-protein complexes extracted from the PDB biounit files, Dockground offers sets of X-ray unbound, simulated unbound, model, and docking decoy structures. All datasets are freely available for download, as a whole or selecting specific structures, through a user-friendly interface on one integrated website. This article is protected by copyright. All rights reserved. © 2017 The Protein Society.

  1. Mathematical approaches for complexity/predictivity trade-offs in complex system models : LDRD final report.

    SciTech Connect

    Goldsby, Michael E.; Mayo, Jackson R.; Bhattacharyya, Arnab; 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.

  2. SEE Rate Estimation: Model Complexity and Data Requirements

    NASA Technical Reports Server (NTRS)

    Ladbury, Ray

    2008-01-01

    Statistical Methods outlined in [Ladbury, TNS20071 can be generalized for Monte Carlo Rate Calculation Methods Two Monte Carlo Approaches: a) Rate based on vendor-supplied (or reverse-engineered) model SEE testing and statistical analysis performed to validate model; b) Rate calculated based on model fit to SEE data Statistical analysis very similar to case for CREME96. Information Theory allows simultaneous consideration of multiple models with different complexities: a) Model with lowest AIC usually has greatest predictive power; b) Model averaging using AIC weights may give better performance if several models have similar good performance; and c) Rates can be bounded for a given confidence level over multiple models, as well as over the parameter space of a model.

  3. Multikernel linear mixed models for complex phenotype prediction

    PubMed Central

    Weissbrod, Omer; Geiger, Dan; Rosset, Saharon

    2016-01-01

    Linear mixed models (LMMs) and their extensions have recently become the method of choice in phenotype prediction for complex traits. However, LMM use to date has typically been limited by assuming simple genetic architectures. Here, we present multikernel linear mixed model (MKLMM), a predictive modeling framework that extends the standard LMM using multiple-kernel machine learning approaches. MKLMM can model genetic interactions and is particularly suitable for modeling complex local interactions between nearby variants. We additionally present MKLMM-Adapt, which automatically infers interaction types across multiple genomic regions. In an analysis of eight case-control data sets from the Wellcome Trust Case Control Consortium and more than a hundred mouse phenotypes, MKLMM-Adapt consistently outperforms competing methods in phenotype prediction. MKLMM is as computationally efficient as standard LMMs and does not require storage of genotypes, thus achieving state-of-the-art predictive power without compromising computational feasibility or genomic privacy. PMID:27302636

  4. Modelling nutrient reduction targets - model structure complexity vs. data availability

    NASA Astrophysics Data System (ADS)

    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.

  5. On the dangers of model complexity without ecological justification in species distribution modeling

    Treesearch

    David M. Bell; Daniel R. Schlaepfer

    2016-01-01

    Although biogeographic patterns are the product of complex ecological processes, the increasing com-plexity of correlative species distribution models (SDMs) is not always motivated by ecological theory,but by model fit. The validity of model projections, such as shifts in a species’ climatic niche, becomesquestionable particularly during extrapolations, such as for...

  6. A Compact Model for the Complex Plant Circadian Clock

    PubMed Central

    De Caluwé, Joëlle; Xiao, Qiying; Hermans, Christian; Verbruggen, Nathalie; Leloup, Jean-Christophe; Gonze, Didier

    2016-01-01

    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 gene mRNA/protein 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-24 h 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 core clock as well as clock-dependent processes. PMID:26904049

  7. Vacuum structure of the Higgs complex singlet-doublet model

    NASA Astrophysics Data System (ADS)

    Ferreira, P. M.

    2016-11-01

    The complex singlet-doublet model is a popular theory to account for dark matter and electroweak baryogenesis, wherein the Standard Model particle content is supplemented by a complex scalar gauge singlet, with certain discrete symmetries imposed. The scalar potential which results thereof can have seven different types of minima at tree level, which may coexist for specific choices of parameters. There is therefore the possibility that a given minimum is not global but rather a local one, and may tunnel to a deeper extremum, thus causing vacuum instability. This rich vacuum structure is explained and discussed in detail.

  8. Further thoughts on simplicity and complexity in population projection models.

    PubMed

    Smith, S K

    1997-12-01

    "This article is a review of--and response to--a special issue of Mathematical Population Studies that focused on the relative performance of simpler vs. more complex population projection models. I do not attempt to summarize or comment on each of the articles in the special issue, but rather present an additional perspective on several points: definitions of simplicity and complexity, empirical evidence regarding population forecast accuracy, the costs and benefits of disaggregation, the potential benefits of combining forecasts, criteria for evaluating projection models, and issues of economic efficiency in the production of population projections."

  9. Model complexity versus ensemble size: allocating resources for climate prediction.

    PubMed

    Ferro, Christopher A T; Jupp, Tim E; Lambert, F Hugo; Huntingford, Chris; Cox, Peter M

    2012-03-13

    A perennial question in modern weather forecasting and climate prediction is whether to invest resources in more complex numerical models or in larger ensembles of simulations. If this question is to be addressed quantitatively, then information is needed about how changes in model complexity and ensemble size will affect predictive performance. Information about the effects of ensemble size is often available, but information about the effects of model complexity is much rarer. An illustration is provided of the sort of analysis that might be conducted for the simplified case in which model complexity is judged in terms of grid resolution and ensemble members are constructed only by perturbing their initial conditions. The effects of resolution and ensemble size on the performance of climate simulations are described with a simple mathematical model, which is then used to define an optimal allocation of computational resources for a range of hypothetical prediction problems. The optimal resolution and ensemble size both increase with available resources, but their respective rates of increase depend on the values of two parameters that can be determined from a small number of simulations. The potential for such analyses to guide future investment decisions in climate prediction is discussed.

  10. (Relatively) Simple Models of Flow in Complex Terrain

    NASA Astrophysics Data System (ADS)

    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.

  11. Surface complexation modeling of inositol hexaphosphate sorption onto gibbsite.

    PubMed

    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

  12. Predictive modelling of complex agronomic and biological systems.

    PubMed

    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.

  13. A model of clutter for complex, multivariate geospatial displays.

    PubMed

    Lohrenz, Maura C; Trafton, J Gregory; Beck, R Melissa; Gendron, Marlin L

    2009-02-01

    A novel model of measuring clutter in complex geospatial displays was compared with human ratings of subjective clutter as a measure of convergent validity. The new model is called the color-clustering clutter (C3) model. Clutter is a known problem in displays of complex data and has been shown to affect target search performance. Previous clutter models are discussed and compared with the C3 model. Two experiments were performed. In Experiment 1, participants performed subjective clutter ratings on six classes of information visualizations. Empirical results were used to set two free parameters in the model. In Experiment 2, participants performed subjective clutter ratings on aeronautical charts. Both experiments compared and correlated empirical data to model predictions. The first experiment resulted in a .76 correlation between ratings and C3. The second experiment resulted in a .86 correlation, significantly better than results from a model developed by Rosenholtz et al. Outliers to our correlation suggest further improvements to C3. We suggest that (a) the C3 model is a good predictor of subjective impressions of clutter in geospatial displays, (b) geospatial clutter is a function of color density and saliency (primary C3 components), and (c) pattern analysis techniques could further improve C3. The C3 model could be used to improve the design of electronic geospatial displays by suggesting when a display will be too cluttered for its intended audience.

  14. Complexity, accuracy and practical applicability of different biogeochemical model versions

    NASA Astrophysics Data System (ADS)

    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

  15. Assessing Complexity in Learning Outcomes--A Comparison between the SOLO Taxonomy and the Model of Hierarchical Complexity

    ERIC Educational Resources Information Center

    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…

  16. Assessing Complexity in Learning Outcomes--A Comparison between the SOLO Taxonomy and the Model of Hierarchical Complexity

    ERIC Educational Resources Information Center

    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…

  17. Modeling the propagation of mobile malware on complex networks

    NASA Astrophysics Data System (ADS)

    Liu, Wanping; Liu, Chao; Yang, Zheng; Liu, Xiaoyang; Zhang, Yihao; Wei, Zuxue

    2016-08-01

    In this paper, the spreading behavior of malware across mobile devices is addressed. By introducing complex networks to model mobile networks, which follows the power-law degree distribution, a novel epidemic model for mobile malware propagation is proposed. The spreading threshold that guarantees the dynamics of the model is calculated. Theoretically, the asymptotic stability of the malware-free equilibrium is confirmed when the threshold is below the unity, and the global stability is further proved under some sufficient conditions. The influences of different model parameters as well as the network topology on malware propagation are also analyzed. Our theoretical studies and numerical simulations show that networks with higher heterogeneity conduce to the diffusion of malware, and complex networks with lower power-law exponents benefit malware spreading.

  18. Computer models of complex multiloop branched pipeline systems

    NASA Astrophysics Data System (ADS)

    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.

  19. Singularities in mixture models and upper bounds of stochastic complexity.

    PubMed

    Yamazaki, Keisuke; Watanabe, Sumio

    2003-09-01

    A learning machine which is a mixture of several distributions, for example, a gaussian mixture or a mixture of experts, has a wide range of applications. However, such a machine is a non-identifiable statistical model with a lot of singularities in the parameter space, hence its generalization property is left unknown. Recently an algebraic geometrical method has been developed which enables us to treat such learning machines mathematically. Based on this method, this paper rigorously proves that a mixture learning machine has the smaller Bayesian stochastic complexity than regular statistical models. Since the generalization error of a learning machine is equal to the increase of the stochastic complexity, the result of this paper shows that the mixture model can attain the more precise prediction than regular statistical models if Bayesian estimation is applied in statistical inference.

  20. P-wave complexity in normal subjects and computer models.

    PubMed

    Potse, Mark; Lankveld, Theo A R; Zeemering, Stef; Dagnelie, Pieter C; Stehouwer, Coen D A; Henry, Ronald M; Linnenbank, André C; Kuijpers, Nico H L; Schotten, Ulrich

    2016-01-01

    P waves reported in electrocardiology literature uniformly appear smooth. Computer simulation and signal analysis studies have shown much more complex shapes. We systematically investigated P-wave complexity in normal volunteers using high-fidelity electrocardiographic techniques without filtering. We recorded 5-min multichannel ECGs in 16 healthy volunteers. Noise and interference were reduced by averaging over 300 beats per recording. In addition, normal P waves were simulated with a realistic model of the human atria. Measured P waves had an average of 4.1 peaks (range 1-10) that were reproducible between recordings. Simulated P waves demonstrated similar complexity, which was related to structural discontinuities in the computer model of the atria. The true shape of the P wave is very irregular and is best seen in ECGs averaged over many beats. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  1. Surface complexation modeling or organic acid sorption to goethite

    SciTech Connect

    Evanko, C.R.; Dzombak, D.A.

    1999-06-15

    Surface complexation modeling was performed using the Generalized Two-Layer Model for a series of low molecular weight organic acids. Sorption of these organic acids to goethite was investigated in a previous study to assess the influence of particular structural features on sorption. Here, the ability to describe the observed sorption behavior for compounds with similar structural features using surface complexation modeling was investigated. A set of surface reactions and equilibrium constants yielding optimal data fits was obtained for each organic acid over a range of total sorbate concentrations. Surface complexation modeling successfully described sorption of a number of the simple organic acids, but an additional hydrophobic component was needed to describe sorption behavior of some compounds with significant hydrophobic character. These compounds exhibited sorption behavior of some compounds with significant hydrophobic character. These compounds exhibited sorption behavior that was inconsistent with ligand exchange mechanisms since sorption behavior of some compounds with significant hydrophobic character. These compounds exhibited sorption behavior that was inconsistent with ligand exchange mechanisms since sorption did not decrease with increasing total sorbate concentration and/or exceeded surface site saturation. Hydrophobic interactions appeared to be most significant for the compound containing a 5-carbon aliphatic chain. Comparison of optimized equilibrium constants for similar surface species showed that model results were consistent with observed sorption behavior: equilibrium constants were highest for compounds having adjacent carboxylic groups, lower for compounds with adjacent phenolic groups, and lowest for compounds with phenolic groups in the ortho position relative to a carboxylic group. Surface complexation modeling was also performed to fit sorption data for Suwannee River fulvic acid. The data could be described well using reactions and

  2. Surface Complexation Modeling of Organic Acid Sorption to Goethite.

    PubMed

    Evanko; Dzombak

    1999-06-15

    Surface complexation modeling was performed using the Generalized Two-Layer Model for a series of low molecular weight organic acids. Sorption of these organic acids to goethite was investigated in a previous study to assess the influence of particular structural features on sorption. Here, the ability to describe the observed sorption behavior for compounds with similar structural features using surface complexation modeling was investigated. A set of surface reactions and equilibrium constants yielding optimal data fits was obtained for each organic acid over a range of total sorbate concentrations. Surface complexation modeling successfully described sorption of a number of the simple organic acids, but an additional hydrophobic component was needed to describe sorption behavior of some compounds with significant hydrophobic character. These compounds exhibited sorption behavior that was inconsistent with ligand exchange mechanisms since sorption did not decrease with increasing total sorbate concentration and/or exceeded surface site saturation. Hydrophobic interactions appeared to be most significant for the compound containing a 5-carbon aliphatic chain. Comparison of optimized equilibrium constants for similar surface species showed that model results were consistent with observed sorption behavior: equilibrium constants were highest for compounds having adjacent carboxylic groups, lower for compounds with adjacent phenolic groups, and lowest for compounds with phenolic groups in the ortho position relative to a carboxylic group. Surface complexation modeling was also performed to fit sorption data for Suwannee River fulvic acid. The data could be described well using reactions and constants similar to those for pyromellitic acid. This four-carboxyl group compound may be useful as a model for fulvic acid with respect to sorption. Other simple organic acids having multiple carboxylic and phenolic functional groups were identified as potential models for humic

  3. Petri net model for analysis of concurrently processed complex algorithms

    NASA Technical Reports Server (NTRS)

    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.

  4. Graphical Models as Surrogates for Complex Ground Motion Models

    NASA Astrophysics Data System (ADS)

    Vogel, K.; Riggelsen, C.; Kuehn, N.; Scherbaum, F.

    2012-04-01

    An essential part of the probabilistic seismic hazard analysis (PSHA) is the ground motion model, which estimates the conditional probability of a ground motion parameter, such as (horizontal) peak ground acceleration or spectral acceleration, given earthquake and site related predictor variables. For a reliable seismic hazard estimation the ground motion model has to keep the epistemic uncertainty small, while the aleatory uncertainty of the ground motion is covered by the model. In regions of well recorded seismicity the most popular modeling approach is to fit a regression function to the observed data, where the functional form is determined by expert knowledge. In regions, where we lack a sufficient amount of data, it is popular to fit the regression function to a data set generated by a so-called stochastic model, which distorts the shape of a random time series according to physical principles to obtain a time series with properties that match ground-motion characteristics. The stochastic model does not have nice analytical properties nor does it come in a form amenable for easy analytical handling and evaluation as needed for PSHA. Therefore a surrogate model, which describes the stochastic model in a more abstract sense (e.g. regression) is often used instead. We show how Directed Graphical Models (DGM) may be seen as a viable alternative to the classical regression approach. They describe a joint probability distribution of a set of variables, decomposing it into a product of (local) conditional probability distributions according to a directed acyclic graph. Graphical models have proven to be a all-round pre/descriptive probabilistic framework for many problems. Their transparent nature is attractive from a domain perspective allowing for a better understanding and gives direct insight into the relationships and workings of a system. DGMs learn the dependency structure of the parameters from the data and do not need, but can include prior expert

  5. Interactive Visualizations of Complex Seismic Data and Models

    NASA Astrophysics Data System (ADS)

    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

  6. Fischer and Schrock Carbene Complexes: A Molecular Modeling Exercise

    ERIC Educational Resources Information Center

    Montgomery, Craig D.

    2015-01-01

    An exercise in molecular modeling that demonstrates the distinctive features of Fischer and Schrock carbene complexes is presented. Semi-empirical calculations (PM3) demonstrate the singlet ground electronic state, restricted rotation about the C-Y bond, the positive charge on the carbon atom, and hence, the electrophilic nature of the Fischer…

  7. Soliton solutions for quintic complex Ginzburg-Landau model

    NASA Astrophysics Data System (ADS)

    Nawaz, B.; Ali, K.; Rizvi, S. T. R.; Younis, M.

    2017-10-01

    In this paper, we find the rational function solution, confluent hypergeometric functions solutions and solitary wave solutions for quintic complex Ginzburg-Landau (CGLQ) model by using extended trial equation method. We also find some new solitary wave soliton solutions for CGLQ equation by using modified extended tanh-function method.

  8. Performance of Random Effects Model Estimators under Complex Sampling Designs

    ERIC Educational Resources Information Center

    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…

  9. Performance of Random Effects Model Estimators under Complex Sampling Designs

    ERIC Educational Resources Information Center

    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…

  10. Fischer and Schrock Carbene Complexes: A Molecular Modeling Exercise

    ERIC Educational Resources Information Center

    Montgomery, Craig D.

    2015-01-01

    An exercise in molecular modeling that demonstrates the distinctive features of Fischer and Schrock carbene complexes is presented. Semi-empirical calculations (PM3) demonstrate the singlet ground electronic state, restricted rotation about the C-Y bond, the positive charge on the carbon atom, and hence, the electrophilic nature of the Fischer…

  11. Fitting Meta-Analytic Structural Equation Models with Complex Datasets

    ERIC Educational Resources Information Center

    Wilson, Sandra Jo; Polanin, Joshua R.; Lipsey, Mark W.

    2016-01-01

    A modification of the first stage of the standard procedure for two-stage meta-analytic structural equation modeling for use with large complex datasets is presented. This modification addresses two common problems that arise in such meta-analyses: (a) primary studies that provide multiple measures of the same construct and (b) the correlation…

  12. The Complexity of Developmental Predictions from Dual Process Models

    ERIC Educational Resources Information Center

    Stanovich, Keith E.; West, Richard F.; Toplak, Maggie E.

    2011-01-01

    Drawing developmental predictions from dual-process theories is more complex than is commonly realized. Overly simplified predictions drawn from such models may lead to premature rejection of the dual process approach as one of many tools for understanding cognitive development. Misleading predictions can be avoided by paying attention to several…

  13. Surface complexation modeling of americium sorption onto volcanic tuff.

    PubMed

    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. Published by Elsevier Ltd.

  14. Fitting Meta-Analytic Structural Equation Models with Complex Datasets

    ERIC Educational Resources Information Center

    Wilson, Sandra Jo; Polanin, Joshua R.; Lipsey, Mark W.

    2016-01-01

    A modification of the first stage of the standard procedure for two-stage meta-analytic structural equation modeling for use with large complex datasets is presented. This modification addresses two common problems that arise in such meta-analyses: (a) primary studies that provide multiple measures of the same construct and (b) the correlation…

  15. Conceptual Complexity, Teaching Style and Models of Teaching.

    ERIC Educational Resources Information Center

    Joyce, Bruce; Weil, Marsha

    The focus of this paper is on the relative roles of personality and training in enabling teachers to carry out the kinds of complex learning models which are envisioned by curriculum reformers in the social sciences. The paper surveys some of the major research done in this area and concludes that: 1) Most teachers do not manifest the complex…

  16. A random interacting network model for complex networks

    PubMed Central

    Goswami, Bedartha; Shekatkar, Snehal M.; Rheinwalt, Aljoscha; Ambika, G.; Kurths, Jürgen

    2015-01-01

    We propose a RAndom Interacting Network (RAIN) model to study the interactions between a pair of complex networks. The model involves two major steps: (i) the selection of a pair of nodes, one from each network, based on intra-network node-based characteristics, and (ii) the placement of a link between selected nodes based on the similarity of their relative importance in their respective networks. Node selection is based on a selection fitness function and node linkage is based on a linkage probability defined on the linkage scores of nodes. The model allows us to relate within-network characteristics to between-network structure. We apply the model to the interaction between the USA and Schengen airline transportation networks (ATNs). Our results indicate that two mechanisms: degree-based preferential node selection and degree-assortative link placement are necessary to replicate the observed inter-network degree distributions as well as the observed inter-network assortativity. The RAIN model offers the possibility to test multiple hypotheses regarding the mechanisms underlying network interactions. It can also incorporate complex interaction topologies. Furthermore, the framework of the RAIN model is general and can be potentially adapted to various real-world complex systems. PMID:26657032

  17. A perspective on modeling and simulation of complex dynamical systems

    NASA Astrophysics Data System (ADS)

    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.

  18. Bayesian Case-deletion Model Complexity and Information Criterion

    PubMed Central

    Zhu, Hongtu; Ibrahim, Joseph G.; Chen, Qingxia

    2015-01-01

    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. PMID:26180578

  19. Bayesian Case-deletion Model Complexity and Information Criterion.

    PubMed

    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.

  20. Complexity vs. simplicity: groundwater model ranking using information criteria.

    PubMed

    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.

  1. On Using Meta-Modeling and Multi-Modeling to Address Complex Problems

    ERIC Educational Resources Information Center

    Abu Jbara, Ahmed

    2013-01-01

    Models, created using different modeling techniques, usually serve different purposes and provide unique insights. While each modeling technique might be capable of answering specific questions, complex problems require multiple models interoperating to complement/supplement each other; we call this Multi-Modeling. To address the syntactic and…

  2. On Using Meta-Modeling and Multi-Modeling to Address Complex Problems

    ERIC Educational Resources Information Center

    Abu Jbara, Ahmed

    2013-01-01

    Models, created using different modeling techniques, usually serve different purposes and provide unique insights. While each modeling technique might be capable of answering specific questions, complex problems require multiple models interoperating to complement/supplement each other; we call this Multi-Modeling. To address the syntactic and…

  3. Modeling Stochastic Complexity in Complex Adaptive Systems: Non-Kolmogorov Probability and the Process Algebra Approach.

    PubMed

    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.

  4. Probabilistic Analysis Techniques Applied to Complex Spacecraft Power System Modeling

    NASA Technical Reports Server (NTRS)

    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).

  5. Evaluation of a puff dispersion model in complex terrain

    SciTech Connect

    Thuillier, R.H. )

    1992-03-01

    California's Pacific Gas and Electric Company has many power plant operations situated in complex terrain, prominent examples being the Geysers geothermal plant in Lake and Sonoma Counties, and the Diablo Canyon nuclear plant in San Luis Obispo County. Procedures ranging from plant licensing to emergency response require a dispersion modeling capability in a complex terrain environment. This paper describes the performance evaluation of such a capability, the Pacific Gas and Electric Company Modeling System (PGEMS), a fast response Gaussian puff model with a three-dimensional wind field generator. Performance of the model was evaluated for ground level and short stack elevated release on the basis of a special intensive tracer experiment in the complex coastal terrain surrounding the Diablo Canyon Nuclear Power Plant in San Luis Obispo County, California. The model performed well under a variety of meteorological and release conditions within the test region of 20-kilometer radius surrounding the nuclear plant, and turned in a superior performance in the wake of the nuclear plant, using a new wake correction algorithm for ground level and roof-vent releases a that location.

  6. Probabilistic Analysis Techniques Applied to Complex Spacecraft Power System Modeling

    NASA Technical Reports Server (NTRS)

    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).

  7. Boolean modeling of collective effects in complex networks

    PubMed Central

    Norrell, Johannes; Socolar, Joshua E. S.

    2009-01-01

    Complex systems are often modeled as Boolean networks in attempts to capture their logical structure and reveal its dynamical consequences. Approximating the dynamics of continuous variables by discrete values and Boolean logic gates may, however, introduce dynamical possibilities that are not accessible to the original system. We show that large random networks of variables coupled through continuous transfer functions often fail to exhibit the complex dynamics of corresponding Boolean models in the disordered (chaotic) regime, even when each individual function appears to be a good candidate for Boolean idealization. A suitably modified Boolean theory explains the behavior of systems in which information does not propagate faithfully down certain chains of nodes. Model networks incorporating calculated or directly measured transfer functions reported in the literature on transcriptional regulation of genes are described by the modified theory. PMID:19658525

  8. Activity-Dependent Neuronal Model on Complex Networks

    PubMed Central

    de Arcangelis, Lucilla; Herrmann, Hans J.

    2012-01-01

    Neuronal avalanches are a novel mode of activity in neuronal networks, experimentally found in vitro and in vivo, and exhibit a robust critical behavior: these avalanches are characterized by a power law distribution for the size and duration, features found in other problems in the context of the physics of complex systems. We present a recent model inspired in self-organized criticality, which consists of an electrical network with threshold firing, refractory period, and activity-dependent synaptic plasticity. The model reproduces the critical behavior of the distribution of avalanche sizes and durations measured experimentally. Moreover, the power spectra of the electrical signal reproduce very robustly the power law behavior found in human electroencephalogram (EEG) spectra. We implement this model on a variety of complex networks, i.e., regular, small-world, and scale-free and verify the robustness of the critical behavior. PMID:22470347

  9. Deciphering the complexity of acute inflammation using mathematical models.

    PubMed

    Vodovotz, Yoram

    2006-01-01

    Various stresses elicit an acute, complex inflammatory response, leading to healing but sometimes also to organ dysfunction and death. We constructed both equation-based models (EBM) and agent-based models (ABM) of various degrees of granularity--which encompass the dynamics of relevant cells, cytokines, and the resulting global tissue dysfunction--in order to begin to unravel these inflammatory interactions. The EBMs describe and predict various features of septic shock and trauma/hemorrhage (including the response to anthrax, preconditioning phenomena, and irreversible hemorrhage) and were used to simulate anti-inflammatory strategies in clinical trials. The ABMs that describe the interrelationship between inflammation and wound healing yielded insights into intestinal healing in necrotizing enterocolitis, vocal fold healing during phonotrauma, and skin healing in the setting of diabetic foot ulcers. Modeling may help in understanding the complex interactions among the components of inflammation and response to stress, and therefore aid in the development of novel therapies and diagnostics.

  10. Entropy, complexity, and Markov diagrams for random walk cancer models

    NASA Astrophysics Data System (ADS)

    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.

  11. Entropy, complexity, and Markov diagrams for random walk cancer models

    PubMed Central

    Newton, Paul K.; Mason, Jeremy; Hurt, Brian; Bethel, Kelly; Bazhenova, Lyudmila; Nieva, Jorge; Kuhn, Peter

    2014-01-01

    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. PMID:25523357

  12. Entropy, complexity, and Markov diagrams for random walk cancer models.

    PubMed

    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.

  13. Simple charge-transfer model for metallic complexes.

    PubMed

    Ramírez-Ramírez, José-Zeferino; Vargas, Rubicelia; Garza, Jorge; Gázquez, José L

    2010-08-05

    In the chemistry of metallic complexes, two important concepts have been used to rationalize the recognition and selectivity of a host by a guest: preorganization and complementarity. Both of these concepts stem from geometrical features. Less explored in the literature has been the interactional complementarity, where mainly the electronic factors in the intermolecular forces are involved. Because the charge transfer between a species rich in electrons (ligand) and another deficient in them (cation) is one of the main intermolecular factors that control the binding energies in metallic complexes, for such systems, we propose a simple model based on density functional theory. We define an interactional energy in which the geometrical energy changes are subtracted from the binding energies and just the electronic factors are taken into account. The model is tested for the complexation between bidentate and cyclic ligands and Ca, Pb, and Hg metal dications. The charge-transfer energy described by our model fits nicely with the interactional energy. Thus, when the geometrical changes do not contribute in a significant way to the complexation energy, the interactional energy is dominated by charge-transfer effects.

  14. Quantum scattering model of energy transfer in photosynthetic complexes

    NASA Astrophysics Data System (ADS)

    Ai, Bao-quan; Zhu, Shi-Liang

    2015-12-01

    We develop a quantum scattering model to describe the exciton transport through the Fenna-Matthews-Olson (FMO) complex. It is found that the exciton transport involving the optimal quantum coherence is more efficient than that involving classical behaviour alone. Furthermore, we also find that the quantum resonance condition is easier to be fulfilled in multiple pathways than that in one pathway. We then definitely demonstrate that the optimal distribution of the pigments, the multitude of energy delivery pathways and the quantum effects are combined together to contribute to the perfect energy transport in the FMO complex.

  15. Complex reaction noise in a molecular quasispecies model

    NASA Astrophysics Data System (ADS)

    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.

  16. Modeling and Algorithmic Approaches to Constitutively-Complex, Microstructured Fluids

    SciTech Connect

    Miller, Gregory H.; Forest, Gregory

    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.

  17. Modeling of Carbohydrate Binding Modules Complexed to Cellulose

    SciTech Connect

    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.

  18. Complex Behavior in Simple Models of Biological Coevolution

    NASA Astrophysics Data System (ADS)

    Rikvold, Per Arne

    We explore the complex dynamical behavior of simple predator-prey models of biological coevolution that account for interspecific and intraspecific competition for resources, as well as adaptive foraging behavior. In long kinetic Monte Carlo simulations of these models we find quite robust 1/f-like noise in species diversity and population sizes, as well as power-law distributions for the lifetimes of individual species and the durations of quiet periods of relative evolutionary stasis. In one model, based on the Holling Type II functional response, adaptive foraging produces a metastable low-diversity phase and a stable high-diversity phase.

  19. Rethinking the Psychogenic Model of Complex Regional Pain Syndrome: Somatoform Disorders and Complex Regional Pain Syndrome

    PubMed Central

    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

  20. Rethinking the psychogenic model of complex regional pain syndrome: somatoform disorders and complex regional pain syndrome.

    PubMed

    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.

  1. Development of Conceptual Benchmark Models to Evaluate Complex Hydrologic Model Calibration in Managed Basins Using Python

    NASA Astrophysics Data System (ADS)

    Hughes, J. D.; White, J.

    2013-12-01

    For many numerical hydrologic models it is a challenge to quantitatively demonstrate that complex models are preferable to simpler models. Typically, a decision is made to develop and calibrate a complex model at the beginning of a study. The value of selecting a complex model over simpler models is commonly inferred from use of a model with fewer simplifications of the governing equations because it can be time consuming to develop another numerical code with data processing and parameter estimation functionality. High-level programming languages like Python can greatly reduce the effort required to develop and calibrate simple models that can be used to quantitatively demonstrate the increased value of a complex model. We have developed and calibrated a spatially-distributed surface-water/groundwater flow model for managed basins in southeast Florida, USA, to (1) evaluate the effect of municipal groundwater pumpage on surface-water/groundwater exchange, (2) investigate how the study area will respond to sea-level rise, and (3) explore combinations of these forcing functions. To demonstrate the increased value of this complex model, we developed a two-parameter conceptual-benchmark-discharge model for each basin in the study area. The conceptual-benchmark-discharge model includes seasonal scaling and lag parameters and is driven by basin rainfall. The conceptual-benchmark-discharge models were developed in the Python programming language and used weekly rainfall data. Calibration was implemented with the Broyden-Fletcher-Goldfarb-Shanno method available in the Scientific Python (SciPy) library. Normalized benchmark efficiencies calculated using output from the complex model and the corresponding conceptual-benchmark-discharge model indicate that the complex model has more explanatory power than the simple model driven only by rainfall.

  2. Mathematical and Computational Modeling in Complex Biological Systems

    PubMed Central

    Li, Wenyang; Zhu, Xiaoliang

    2017-01-01

    The biological process and molecular functions involved in the cancer progression remain difficult to understand for biologists and clinical doctors. Recent developments in high-throughput technologies urge the systems biology to achieve more precise models for complex diseases. Computational and mathematical models are gradually being used to help us understand the omics data produced by high-throughput experimental techniques. The use of computational models in systems biology allows us to explore the pathogenesis of complex diseases, improve our understanding of the latent molecular mechanisms, and promote treatment strategy optimization and new drug discovery. Currently, it is urgent to bridge the gap between the developments of high-throughput technologies and systemic modeling of the biological process in cancer research. In this review, we firstly studied several typical mathematical modeling approaches of biological systems in different scales and deeply analyzed their characteristics, advantages, applications, and limitations. Next, three potential research directions in systems modeling were summarized. To conclude, this review provides an update of important solutions using computational modeling approaches in systems biology. PMID:28386558

  3. Bridging Mechanistic and Phenomenological Models of Complex Biological Systems

    PubMed Central

    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

  4. An efficient fluctuating charge model for transition metal complexes.

    PubMed

    Comba, Peter; Martin, Bodo; Sanyal, Avik

    2013-07-05

    A fluctuating charge model for transition metal complexes, based on the Hirshfeld partitioning scheme, spectroscopic energy data from the NIST Atomic Spectroscopy Database and the electronegativity equalization approach, has been developed and parameterized for organic ligands and their high- and low-spin Fe(II) and Fe(III), low-spin Co(III) and Cu(II) complexes, using atom types defined in the Momec force field. Based on large training sets comprising a variety of transition metal complexes, a general parameter set has been developed and independently validated which allows the efficient computation of geometry-dependent charge distributions in the field of transition metal coordination compounds. Copyright © 2013 Wiley Periodicals, Inc.

  5. Mathematical modelling of complex contagion on clustered networks

    NASA Astrophysics Data System (ADS)

    O'sullivan, David J.; O'Keeffe, Gary; Fennell, Peter; Gleeson, James

    2015-09-01

    The spreading of behavior, such as the adoption of a new innovation, is influenced bythe structure of social networks that interconnect the population. In the experiments of Centola (Science, 2010), adoption of new behavior was shown to spread further and faster across clustered-lattice networks than across corresponding random networks. This implies that the “complex contagion” effects of social reinforcement are important in such diffusion, in contrast to “simple” contagion models of disease-spread which predict that epidemics would grow more efficiently on random networks than on clustered networks. To accurately model complex contagion on clustered networks remains a challenge because the usual assumptions (e.g. of mean-field theory) regarding tree-like networks are invalidated by the presence of triangles in the network; the triangles are, however, crucial to the social reinforcement mechanism, which posits an increased probability of a person adopting behavior that has been adopted by two or more neighbors. In this paper we modify the analytical approach that was introduced by Hebert-Dufresne et al. (Phys. Rev. E, 2010), to study disease-spread on clustered networks. We show how the approximation method can be adapted to a complex contagion model, and confirm the accuracy of the method with numerical simulations. The analytical results of the model enable us to quantify the level of social reinforcement that is required to observe—as in Centola’s experiments—faster diffusion on clustered topologies than on random networks.

  6. An Adaptive Complex Network Model for Brain Functional Networks

    PubMed Central

    Gomez Portillo, Ignacio J.; Gleiser, Pablo M.

    2009-01-01

    Brain functional networks are graph representations of activity in the brain, where the vertices represent anatomical regions and the edges their functional connectivity. These networks present a robust small world topological structure, characterized by highly integrated modules connected sparsely by long range links. Recent studies showed that other topological properties such as the degree distribution and the presence (or absence) of a hierarchical structure are not robust, and show different intriguing behaviors. In order to understand the basic ingredients necessary for the emergence of these complex network structures we present an adaptive complex network model for human brain functional networks. The microscopic units of the model are dynamical nodes that represent active regions of the brain, whose interaction gives rise to complex network structures. The links between the nodes are chosen following an adaptive algorithm that establishes connections between dynamical elements with similar internal states. We show that the model is able to describe topological characteristics of human brain networks obtained from functional magnetic resonance imaging studies. In particular, when the dynamical rules of the model allow for integrated processing over the entire network scale-free non-hierarchical networks with well defined communities emerge. On the other hand, when the dynamical rules restrict the information to a local neighborhood, communities cluster together into larger ones, giving rise to a hierarchical structure, with a truncated power law degree distribution. PMID:19738902

  7. Simplifying complex clinical element models to encourage adoption.

    PubMed

    Freimuth, Robert R; Zhu, Qian; Pathak, Jyotishman; Chute, Christopher G

    2014-01-01

    Clinical Element Models (CEMs) were developed to provide a normalized form for the exchange of clinical data. The CEM specification is quite complex and specialized knowledge is required to understand and implement the models, which presents a significant barrier to investigators and study designers. To encourage the adoption of CEMs at the time of data collection and reduce the need for retrospective normalization efforts, we developed an approach that provides a simplified view of CEMs for non-experts while retaining the full semantic detail of the underlying logical models. This allows investigators to approach CEMs through generalized representations that are intended to be more intuitive than the native models, and it permits them to think conceptually about their data elements without worrying about details related to the CEM logical models and syntax. We demonstrate our approach using data elements from the Pharmacogenomics Research Network (PGRN).

  8. Lateral organization of complex lipid mixtures from multiscale modeling

    NASA Astrophysics Data System (ADS)

    Tumaneng, Paul W.; Pandit, Sagar A.; Zhao, Guijun; Scott, H. L.

    2010-02-01

    The organizational properties of complex lipid mixtures can give rise to functionally important structures in cell membranes. In model membranes, ternary lipid-cholesterol (CHOL) mixtures are often used as representative systems to investigate the formation and stabilization of localized structural domains ("rafts"). In this work, we describe a self-consistent mean-field model that builds on molecular dynamics simulations to incorporate multiple lipid components and to investigate the lateral organization of such mixtures. The model predictions reveal regions of bimodal order on ternary plots that are in good agreement with experiment. Specifically, we have applied the model to ternary mixtures composed of dioleoylphosphatidylcholine:18:0 sphingomyelin:CHOL. This work provides insight into the specific intermolecular interactions that drive the formation of localized domains in these mixtures. The model makes use of molecular dynamics simulations to extract interaction parameters and to provide chain configuration order parameter libraries.

  9. The semiotics of control and modeling relations in complex systems.

    PubMed

    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.

  10. RHIC injector complex online model status and plans

    SciTech Connect

    Schoefer,V.; Ahrens, L.; Brown, K.; Morris, J.; Nemesure, S.

    2009-05-04

    An online modeling system is being developed for the RHIC injector complex, which consists of the Booster, the AGS and the transfer lines connecting the Booster to the AGS and the AGS to RHIC. Historically the injectors have been operated using static values from design specifications or offline model runs, but tighter beam optics constraints required by polarized proton operations (e.g, accelerating with near-integer tunes) have necessitated a more dynamic system. An online model server for the AGS has been implemented using MAD-X [1] as the model engine, with plans to extend the system to the Booster and the injector transfer lines and to add the option of calculating optics using the Polymorphic Tracking Code (PTC [2]) as the model engine.

  11. Mechanistic modeling confronts the complexity of molecular cell biology.

    PubMed

    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.

  12. Cx-02 Program, workshop on modeling complex systems

    USGS Publications Warehouse

    Mossotti, Victor G.; Barragan, Jo Ann; Westergard, Todd D.

    2003-01-01

    This publication contains the abstracts and program for the workshop on complex systems that was held on November 19-21, 2002, in Reno, Nevada. Complex systems are ubiquitous within the realm of the earth sciences. Geological systems consist of a multiplicity of linked components with nested feedback loops; the dynamics of these systems are non-linear, iterative, multi-scale, and operate far from equilibrium. That notwithstanding, It appears that, with the exception of papers on seismic studies, geology and geophysics work has been disproportionally underrepresented at regional and national meetings on complex systems relative to papers in the life sciences. This is somewhat puzzling because geologists and geophysicists are, in many ways, preadapted to thinking of complex system mechanisms. Geologists and geophysicists think about processes involving large volumes of rock below the sunlit surface of Earth, the accumulated consequence of processes extending hundreds of millions of years in the past. Not only do geologists think in the abstract by virtue of the vast time spans, most of the evidence is out-of-sight. A primary goal of this workshop is to begin to bridge the gap between the Earth sciences and life sciences through demonstration of the universality of complex systems science, both philosophically and in model structures.

  13. Interaction of Ionic Liquids with Lipid Biomembrane: Implication from Supramolecular Assembly to Cytotoxicity

    NASA Astrophysics Data System (ADS)

    Jing, Benxin; Lan, Nan; Zhu, Y. Elaine

    2013-03-01

    An explosion in the research activities using ionic liquids (ILs) as new ``green'' chemicals in several chemical and biomedical processes has resulted in the urgent need to understand their impact in term of their transport and toxicity towards aquatic organisms. Though a few experimental toxicology studies have reported that some ionic liquids are toxic with increased hydrophobicity of ILs while others are not, our understanding of the molecular level mechanism of IL toxicity remains poorly understood. In this talk, we will discuss our recent study of the interaction of ionic liquids with model cell membranes. We have found that the ILs could induce morphological change of lipid bilayers when a critical concentration is exceeded, leading to the swelling and tube-like formation of lipid bilayers. The critical concentration shows a strong dependence on the length of hydrocarbon tails and hydrophobic counterions. By SAXS, Langmuir-Blodgett (LB) and fluorescence microscopic measurement, we have confirmed that tube-like lipid complexes result from the insertion of ILs with long hydrocarbon chains to minimize the hydrophobic interaction with aqueous media. This finding could give insight to the modification and adoption of ILs for the engineering of micro-organisms.

  14. Computational and analytical modeling of cationic lipid-DNA complexes.

    PubMed

    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

  15. Reduced Complexity Modeling (RCM): toward more use of less

    NASA Astrophysics Data System (ADS)

    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

  16. GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking.

    PubMed

    Heo, Lim; Lee, Hasup; Seok, Chaok

    2016-08-18

    Protein-protein docking methods have been widely used to gain an atomic-level understanding of protein interactions. However, docking methods that employ low-resolution energy functions are popular because of computational efficiency. Low-resolution docking tends to generate protein complex structures that are not fully optimized. GalaxyRefineComplex takes such low-resolution docking structures and refines them to improve model accuracy in terms of both interface contact and inter-protein orientation. This refinement method allows flexibility at the protein interface and in the overall docking structure to capture conformational changes that occur upon binding. Symmetric refinement is also provided for symmetric homo-complexes. This method was validated by refining models produced by available docking programs, including ZDOCK and M-ZDOCK, and was successfully applied to CAPRI targets in a blind fashion. An example of using the refinement method with an existing docking method for ligand binding mode prediction of a drug target is also presented. A web server that implements the method is freely available at http://galaxy.seoklab.org/refinecomplex.

  17. GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking

    PubMed Central

    Heo, Lim; Lee, Hasup; Seok, Chaok

    2016-01-01

    Protein-protein docking methods have been widely used to gain an atomic-level understanding of protein interactions. However, docking methods that employ low-resolution energy functions are popular because of computational efficiency. Low-resolution docking tends to generate protein complex structures that are not fully optimized. GalaxyRefineComplex takes such low-resolution docking structures and refines them to improve model accuracy in terms of both interface contact and inter-protein orientation. This refinement method allows flexibility at the protein interface and in the overall docking structure to capture conformational changes that occur upon binding. Symmetric refinement is also provided for symmetric homo-complexes. This method was validated by refining models produced by available docking programs, including ZDOCK and M-ZDOCK, and was successfully applied to CAPRI targets in a blind fashion. An example of using the refinement method with an existing docking method for ligand binding mode prediction of a drug target is also presented. A web server that implements the method is freely available at http://galaxy.seoklab.org/refinecomplex. PMID:27535582

  18. Modelling of Rare Earth Elements Complexation With Humic Acid

    NASA Astrophysics Data System (ADS)

    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

  19. Mathematic modeling of complex aquifer: Evian Natural Mineral Water case study considering lumped and distributed models.

    NASA Astrophysics Data System (ADS)

    Henriot, abel; Blavoux, bernard; Travi, yves; Lachassagne, patrick; Beon, olivier; Dewandel, benoit; Ladouche, bernard

    2013-04-01

    The Evian Natural Mineral Water (NMW) aquifer is a highly heterogeneous Quaternary glacial deposits complex composed of three main units, from bottom to top: - The "Inferior Complex" mainly composed of basal and impermeable till lying on the Alpine rocks. It outcrops only at the higher altitudes but is known in depth through drilled holes. - The "Gavot Plateau Complex" is an interstratified complex of mainly basal and lateral till up to 400 m thick. It outcrops at heights above approximately 850 m a.m.s.l. and up to 1200 m a.m.s.l. over a 30 km² area. It is the main recharge area known for the hydromineral system. - The "Terminal Complex" from which the Evian NMW is emerging at 410 m a.m.s.l. It is composed of sand and gravel Kame terraces that allow water to flow from the deep "Gavot Plateau Complex" permeable layers to the "Terminal Complex". A thick and impermeable terminal till caps and seals the system. Aquifer is then confined at its downstream area. Because of heterogeneity and complexity of this hydrosystem, distributed modeling tools are difficult to implement at the whole system scale: important hypothesis would have to be made about geometry, hydraulic properties, boundary conditions for example and extrapolation would lead with no doubt to unacceptable errors. Consequently a modeling strategy is being developed and leads also to improve the conceptual model of the hydrosystem. Lumped models mainly based on tritium time series allow the whole hydrosystem to be modeled combining in series: an exponential model (superficial aquifers of the "Gavot Plateau Complex"), a dispersive model (Gavot Plateau interstratified complex) and a piston flow model (sand and gravel from the Kame terraces) respectively 8, 60 and 2.5 years of mean transit time. These models provide insight on the governing parameters for the whole mineral aquifer. They help improving the current conceptual model and are to be improved with other environmental tracers such as CFC, SF6. A

  20. A Corticothalamic Circuit Model for Sound Identification in Complex Scenes

    PubMed Central

    Otazu, Gonzalo H.; Leibold, Christian

    2011-01-01

    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. PMID:21931668

  1. An Ontology for Modeling Complex Inter-relational Organizations

    NASA Astrophysics Data System (ADS)

    Wautelet, Yves; Neysen, Nicolas; Kolp, Manuel

    This paper presents an ontology for organizational modeling through multiple complementary aspects. The primary goal of the ontology is to dispose of an adequate set of related concepts for studying complex organizations involved in a lot of relationships at the same time. In this paper, we define complex organizations as networked organizations involved in a market eco-system that are playing several roles simultaneously. In such a context, traditional approaches focus on the macro analytic level of transactions; this is supplemented here with a micro analytic study of the actors' rationale. At first, the paper overviews enterprise ontologies literature to position our proposal and exposes its contributions and limitations. The ontology is then brought to an advanced level of formalization: a meta-model in the form of a UML class diagram allows to overview the ontology concepts and their relationships which are formally defined. Finally, the paper presents the case study on which the ontology has been validated.

  2. Polygonal Shapes Detection in 3d Models of Complex Architectures

    NASA Astrophysics Data System (ADS)

    Benciolini, G. B.; Vitti, A.

    2015-02-01

    A sequential application of two global models defined on a variational framework is proposed for the detection of polygonal shapes in 3D models of complex architectures. As a first step, the procedure involves the use of the Mumford and Shah (1989) 1st-order variational model in dimension two (gridded height data are processed). In the Mumford-Shah model an auxiliary function detects the sharp changes, i.e., the discontinuities, of a piecewise smooth approximation of the data. The Mumford-Shah model requires the global minimization of a specific functional to simultaneously produce both the smooth approximation and its discontinuities. In the proposed procedure, the edges of the smooth approximation derived by a specific processing of the auxiliary function are then processed using the Blake and Zisserman (1987) 2nd-order variational model in dimension one (edges are processed in the plane). This second step permits to describe the edges of an object by means of piecewise almost-linear approximation of the input edges themselves and to detects sharp changes of the first-derivative of the edges so to detect corners. The Mumford-Shah variational model is used in two dimensions accepting the original data as primary input. The Blake-Zisserman variational model is used in one dimension for the refinement of the description of the edges. The selection among all the boundaries detected by the Mumford-Shah model of those that present a shape close to a polygon is performed by considering only those boundaries for which the Blake-Zisserman model identified discontinuities in their first derivative. The output of the procedure are hence shapes, coming from 3D geometric data, that can be considered as polygons. The application of the procedure is suitable for, but not limited to, the detection of objects such as foot-print of polygonal buildings, building facade boundaries or windows contours. v The procedure is applied to a height model of the building of the Engineering

  3. A computational framework for modeling targets as complex adaptive systems

    NASA Astrophysics Data System (ADS)

    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.

  4. A Hybridization Model for the Plasmon Response of Complex Nanostructures

    NASA Astrophysics Data System (ADS)

    Prodan, E.; Radloff, C.; Halas, N. J.; Nordlander, P.

    2003-10-01

    We present a simple and intuitive picture, an electromagnetic analog of molecular orbital theory, that describes the plasmon response of complex nanostructures of arbitrary shape. Our model can be understood as the interaction or ``hybridization'' of elementary plasmons supported by nanostructures of elementary geometries. As an example, the approach is applied to the important case of a four-layer concentric nanoshell, where the hybridization of the plasmons of the inner and outer nanoshells determines the resonant frequencies of the multilayer nanostructure.

  5. A hybridization model for the plasmon response of complex nanostructures.

    PubMed

    Prodan, E; Radloff, C; Halas, N J; Nordlander, P

    2003-10-17

    We present a simple and intuitive picture, an electromagnetic analog of molecular orbital theory, that describes the plasmon response of complex nanostructures of arbitrary shape. Our model can be understood as the interaction or "hybridization" of elementary plasmons supported by nanostructures of elementary geometries. As an example, the approach is applied to the important case of a four-layer concentric nanoshell, where the hybridization of the plasmons of the inner and outer nanoshells determines the resonant frequencies of the multilayer nanostructure.

  6. CFD Modeling of Local Scour under Complex Free Surface Flow

    NASA Astrophysics Data System (ADS)

    Bihs, Hans; Ahmad, Nadeem; Kamath, Arun; Arntsen, Øivind A.

    2017-04-01

    In the present study the open-source three-dimensional numerical model REEF3D is used to calculate the complex free surface flow over a spillway, the corresponding hydraulic jump downstream of the spillway and the resulting local scour. The numerical results are compared with experimental data. The transcritical flow changes from supercritical to subcritical after the hydraulic structure, which results in the hydraulic jump. The flow of the hydraulic jump is characterised by the its violent nature and the large amount of turbulence production. While the downstream area of a spillway is typically protected by a concrete apron, scour can still occur downstream of this protection. REEF3D has advanced interface capturing capabilities, with which it is possible to simulate the complex free surface dynamics. With the level set method free surface is modeled as the zero level set of a scalar signed distance function. The flow velocities are calculated together with the pressure on a staggered grid, ensuring a tight velocity-pressure coupling. Complex geometries are modeled with a ghost cell immersed boundary method. The convective terms of the momentum equations, the level set function and the equations of the k-ω turbulence model are discretized with the fifth-order finite difference WENO scheme. Parallelization of the numerical scheme is achieved by using the domain decomposition framework together with the MPI library. The topography of the sediment bed is implicitly described by a level set function. Based on bedload and suspended load transport formulations, the sediment continuity defect in the bed cells is converted into the rate of change of the vertical bed elevation. This strategy has two major advantages: the topology is a well defined surface when calculating the incipient motion on the sloping bed and the sand avalanche. In addition, the numerically error prone re-meshing can be avoided, because the complex boundary surface is accounted for by the immersed

  7. Modeling Dynamic Perceptual Attention in Complex Virtual Environments

    DTIC Science & Technology

    2005-01-01

    Modeling Dynamic Perceptual Attention in Complex Virtual Environments Youngjun Kim, Martin van Velsen and Randall W. Hill, Jr. Institute for...Youngjun Kim, Martin van Velsen and Randall W. Hill, Jr. the human realm. Spatial cognition and especially spatial attention has allowed humans to make...At any point in time, the virtual human must recognize which object is the most salient among those 4 Youngjun Kim, Martin van Velsen and

  8. Termination of Multipartite Graph Series Arising from Complex Network Modelling

    NASA Astrophysics Data System (ADS)

    Latapy, Matthieu; Phan, Thi Ha Duong; Crespelle, Christophe; Nguyen, Thanh Qui

    An intense activity is nowadays devoted to the definition of models capturing the properties of complex networks. Among the most promising approaches, it has been proposed to model these graphs via their clique incidence bipartite graphs. However, this approach has, until now, severe limitations resulting from its incapacity to reproduce a key property of this object: the overlapping nature of cliques in complex networks. In order to get rid of these limitations we propose to encode the structure of clique overlaps in a network thanks to a process consisting in iteratively factorising the maximal bicliques between the upper level and the other levels of a multipartite graph. We show that the most natural definition of this factorising process leads to infinite series for some instances. Our main result is to design a restriction of this process that terminates for any arbitrary graph. Moreover, we show that the resulting multipartite graph has remarkable combinatorial properties and is closely related to another fundamental combinatorial object. Finally, we show that, in practice, this multipartite graph is computationally tractable and has a size that makes it suitable for complex network modelling.

  9. A Simple Model for Complex Dynamical Transitions in Epidemics

    NASA Astrophysics Data System (ADS)

    Earn, David J. D.; Rohani, Pejman; Bolker, Benjamin M.; Grenfell, Bryan T.

    2000-01-01

    Dramatic changes in patterns of epidemics have been observed throughout this century. For childhood infectious diseases such as measles, the major transitions are between regular cycles and irregular, possibly chaotic epidemics, and from regionally synchronized oscillations to complex, spatially incoherent epidemics. A simple model can explain both kinds of transitions as the consequences of changes in birth and vaccination rates. Measles is a natural ecological system that exhibits different dynamical transitions at different times and places, yet all of these transitions can be predicted as bifurcations of a single nonlinear model.

  10. The evaluative imaging of mental models - Visual representations of complexity

    NASA Technical Reports Server (NTRS)

    Dede, Christopher

    1989-01-01

    The paper deals with some design issues involved in building a system that could visually represent the semantic structures of training materials and their underlying mental models. In particular, hypermedia-based semantic networks that instantiate classification problem solving strategies are thought to be a useful formalism for such representations; the complexity of these web structures can be best managed through visual depictions. It is also noted that a useful approach to implement in these hypermedia models would be some metrics of conceptual distance.

  11. The evaluative imaging of mental models - Visual representations of complexity

    NASA Technical Reports Server (NTRS)

    Dede, Christopher

    1989-01-01

    The paper deals with some design issues involved in building a system that could visually represent the semantic structures of training materials and their underlying mental models. In particular, hypermedia-based semantic networks that instantiate classification problem solving strategies are thought to be a useful formalism for such representations; the complexity of these web structures can be best managed through visual depictions. It is also noted that a useful approach to implement in these hypermedia models would be some metrics of conceptual distance.

  12. Model for complex heart rate dynamics in health and diseases

    NASA Astrophysics Data System (ADS)

    Kotani, Kiyoshi; Struzik, Zbigniew R.; Takamasu, Kiyoshi; Stanley, H. Eugene; Yamamoto, Yoshiharu

    2005-10-01

    A physiologically motivated, dynamical model of cardiovascular autonomic regulation is shown to be capable of generating long-range correlated and multifractal heart rate. Virtual disease simulations are carried out systematically to account for the disease-induced relative dysfunction of the parasympathetic and the sympathetic branches of the autonomic control. Statistical agreement of the simulation results with those of real life data is reached, suggesting the possible use of the model as a state-of-the-art basis for further understanding of the physiological correlates of complex heart rate dynamics.

  13. Complex tephra dispersion from 3D plume modeling using ATHAM

    NASA Astrophysics Data System (ADS)

    Nicholson, B. C.; Kobs-Nawotniak, S. E.

    2014-12-01

    Most volcanic hazard assessments are based on a classic inversion tool for tephra deposits that relies on a simple integral model to explain the eruption plume. While this tool is adequate for first-order predictions of tephra deposition under no-wind conditions, the simplifying assumptions make it unreliable for ambient winds >10 m/s. Advances in computational power now make it possible to improve the inversion tool using 3D fluid dynamics. We do this with the physics-based Active Tracer High-resolution Atmospheric Model (ATHAM) to model tephra dispersion and deposition from volcanic eruption columns. The model, when run in 3D, is able to capture the complex morphology of bent plumes. Tephra distributions produced by these morphologies differ significantly from distributions created by idealized advection solutions, reflecting the effects of counter-rotating vortex pairs, puffing modes, or plume bifurcation. The modeled tephra deposition better captures the complex effects of wind-plume interaction, allowing us to update classic inversion tools with more realistic weak plume conditions consistent with typical historical explosive eruptions.

  14. Anti-inflammatory and Antibacterial Effects of Covalently Attached Biomembrane-Mimic Polymer Grafts on Gore-Tex Implants.

    PubMed

    Jin, Young Ju; Kang, Sunah; Park, Pona; Choi, Dongkil; Kim, Dae Woo; Jung, Dongwook; Koh, Jaemoon; Jeon, Joohee; Lee, Myoungjin; Ham, Jiyeon; Seo, Ji-Hun; Jin, Hong-Ryul; Lee, Yan

    2017-06-07

    Expanded polytetrafluoroethylene (ePTFE), also known as Gore-Tex, is widely used as an implantable biomaterial in biomedical applications because of its favorable mechanical properties and biochemical inertness. However, infection and inflammation are two major complications with ePTFE implantations, because pathogenic bacteria can inhabit the microsized pores, without clearance by host immune cells, and the limited biocompatibility can induce foreign body reactions. To minimize these complications, we covalently grafted a biomembrane-mimic polymer, poly(2-methacryloyloxylethyl phosphorylcholine) (PMPC), by partial defluorination followed by UV-induced polymerization with cross-linkers on the ePTFE surface. PMPC grafting greatly reduced serum protein adsorption as well as fibroblast adhesion on the ePTFE surface. Moreover, the PMPC-grafted ePTFE surface exhibited a dramatic inhibition of the adhesion and growth of Staphylococcus aureus, a typical pathogenic bacterium in ePTFE implants, in the porous network. On the basis of an analysis of immune cells and inflammation-related factors, i.e., transforming growth factor-β (TGF-β) and myeloperoxidase (MPO), we confirmed that inflammation was efficiently alleviated in tissues around PMPC-grafted ePTFE plates implanted in the backs of rats. Covalent PMPC may be an effective strategy for promoting anti-inflammatory and antibacterial functions in ePTFE implants and to reduce side effects in biomedical applications of ePTFE.

  15. Interaction of Local Anesthetics with Biomembranes Consisting of Phospholipids and Cholesterol: Mechanistic and Clinical Implications for Anesthetic and Cardiotoxic Effects

    PubMed Central

    2013-01-01

    Despite a long history in medical and dental application, the molecular mechanism and precise site of action are still arguable for local anesthetics. Their effects are considered to be induced by acting on functional proteins, on membrane lipids, or on both. Local anesthetics primarily interact with sodium channels embedded in cell membranes to reduce the excitability of nerve cells and cardiomyocytes or produce a malfunction of the cardiovascular system. However, the membrane protein-interacting theory cannot explain all of the pharmacological and toxicological features of local anesthetics. The administered drug molecules must diffuse through the lipid barriers of nerve sheaths and penetrate into or across the lipid bilayers of cell membranes to reach the acting site on transmembrane proteins. Amphiphilic local anesthetics interact hydrophobically and electrostatically with lipid bilayers and modify their physicochemical property, with the direct inhibition of membrane functions, and with the resultant alteration of the membrane lipid environments surrounding transmembrane proteins and the subsequent protein conformational change, leading to the inhibition of channel functions. We review recent studies on the interaction of local anesthetics with biomembranes consisting of phospholipids and cholesterol. Understanding the membrane interactivity of local anesthetics would provide novel insights into their anesthetic and cardiotoxic effects. PMID:24174934

  16. Amelioration of oxidative stress in bio-membranes and macromolecules by non-toxic dye from Morinda tinctoria (Roxb.) roots.

    PubMed

    Bhakta, Dipita; Siva, Ramamoorthy

    2012-06-01

    Plant dyes have been in use for coloring and varied purposes since prehistoric times. A red dye found in the roots of plants belonging to genus Morinda is a well recognized coloring ingredient. The dye fraction obtained from the methanolic extract of the roots of Morinda tinctoria was explored for its role in attenuating damages caused by H(2)O(2)-induced oxidative stress. The antioxidant potential of the dye fraction was assessed through DPPH radical scavenging, deoxyribose degradation and inhibition of lipid peroxidation in mice liver. It was subsequently screened for its efficiency in extenuating damage incurred to biomembrane (using erythrocytes and their ghost membranes) and macromolecules (pBR322 DNA, lipids and proteins) from exposure to hydrogen peroxide. In addition, the non-toxic nature of the dye was supported by the histological evaluation conducted on the tissue sections from the major organs of Swiss Albino mice as well as effect on Hep3B cell line (human hepatic carcinoma). The LC-MS confirms the dye fraction to be morindone. Our study strongly suggests that morindone present in the root extracts of M. tinctoria, in addition to being a colorant, definitely holds promise in the pharmaceutical industry. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Hierarchical Model for the Evolution of Cloud Complexes

    NASA Astrophysics Data System (ADS)

    Sánchez D., Néstor M.; Parravano, Antonio

    1999-01-01

    The structure of cloud complexes appears to be well described by a tree structure (i.e., a simplified ``stick man'') 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. The model follows the mass evolution of each substructure by computing its mass exchange with its parent and children. The parent-child mass exchange (evaporation or condensation) depends on the radiation density at the interphase. At the end of the ``lineage,'' stars may be born or die, so that there is a nonstationary mass flow in the hierarchical structure. For a variety of parameter sets the system follows the same series of steps to transform diffuse gas into stars, and the regulation of the mass flux in the tree by previously formed stars dominates the evolution of the star formation. For the set of parameters used here as a reference model, the system tends to produce initial mass functions (IMFs) that have a maximum at a mass that is too high (~2 Msolar) and the characteristic times for evolution seem too long. We show that these undesired properties can be improved by adjusting the model parameters. The model requires further physics (e.g., allowing for multiple stellar systems and clump collisions) before a definitive comparison with observations can be made. Instead, the emphasis here is to illustrate some general properties of this kind of complex nonlinear model for the star formation process. Notwithstanding the simplifications involved, the model reveals an essential feature that will likely remain if additional physical processes are included, that is, the detailed behavior of the system is very sensitive to the variations on the initial and external conditions, suggesting that a ``universal'' IMF is very unlikely. When an ensemble of IMFs corresponding to a

  18. Complex hybrid models combining deterministic and machine learning components for numerical climate modeling and weather prediction.

    PubMed

    Krasnopolsky, Vladimir M; Fox-Rabinovitz, Michael S

    2006-03-01

    A new practical application of neural network (NN) techniques to environmental numerical modeling has been developed. Namely, a new type of numerical model, a complex hybrid environmental model based on a synergetic combination of deterministic and machine learning model components, has been introduced. Conceptual and practical possibilities of developing hybrid models are discussed in this paper for applications to climate modeling and weather prediction. The approach presented here uses NN as a statistical or machine learning technique to develop highly accurate and fast emulations for time consuming model physics components (model physics parameterizations). The NN emulations of the most time consuming model physics components, short and long wave radiation parameterizations or full model radiation, presented in this paper are combined with the remaining deterministic components (like model dynamics) of the original complex environmental model--a general circulation model or global climate model (GCM)--to constitute a hybrid GCM (HGCM). The parallel GCM and HGCM simulations produce very similar results but HGCM is significantly faster. The speed-up of model calculations opens the opportunity for model improvement. Examples of developed HGCMs illustrate the feasibility and efficiency of the new approach for modeling complex multidimensional interdisciplinary systems.

  19. Hybrid Structural Model of the Complete Human ESCRT-0 Complex

    SciTech Connect

    Ren, Xuefeng; Kloer, Daniel P.; Kim, Young C.; Ghirlando, Rodolfo; Saidi, Layla F.; Hummer, Gerhard; Hurley, James H.

    2009-03-31

    The human Hrs and STAM proteins comprise the ESCRT-0 complex, which sorts ubiquitinated cell surface receptors to lysosomes for degradation. Here we report a model for the complete ESCRT-0 complex based on the crystal structure of the Hrs-STAM core complex, previously solved domain structures, hydrodynamic measurements, and Monte Carlo simulations. ESCRT-0 expressed in insect cells has a hydrodynamic radius of R{sub H} = 7.9 nm and is a 1:1 heterodimer. The 2.3 {angstrom} crystal structure of the ESCRT-0 core complex reveals two domain-swapped GAT domains and an antiparallel two-stranded coiled-coil, similar to yeast ESCRT-0. ESCRT-0 typifies a class of biomolecular assemblies that combine structured and unstructured elements, and have dynamic and open conformations to ensure versatility in target recognition. Coarse-grained Monte Carlo simulations constrained by experimental R{sub H} values for ESCRT-0 reveal a dynamic ensemble of conformations well suited for diverse functions.

  20. Context dependent preferential attachment model for complex networks

    NASA Astrophysics Data System (ADS)

    Pandey, Pradumn Kumar; Adhikari, Bibhas

    2015-10-01

    In this paper, we propose a growing random complex network model, which we call context dependent preferential attachment model (CDPAM), when the preference of a new node to get attached to old nodes is determined by the local and global property of the old nodes. We consider that local and global properties of a node as the degree and relative average degree of the node respectively. We prove that the degree distribution of complex networks generated by CDPAM follow power law with exponent lies in the interval [2,3] and the expected diameter grows logarithmically with the size of new nodes added to the initial small network. Numerical results show that the expected diameter stabilizes when alike weights to the local and global properties are assigned by the new nodes. Computing various measures including clustering coefficient, assortativity, number of triangles, algebraic connectivity, spectral radius, we show that the proposed model replicates properties of real networks when alike weights are given to local and global property. Finally, we observe that the BA model is a limiting case of CDPAM when new nodes tend to give large weight to the local property compared to the weight given to the global property during link formation.

  1. Parameter estimation for distributed parameter models of complex, flexible structures

    NASA Technical Reports Server (NTRS)

    Taylor, Lawrence W., Jr.

    1991-01-01

    Distributed parameter modeling of structural dynamics has been limited to simple spacecraft configurations because of the difficulty of handling several distributed parameter systems linked at their boundaries. Although there is other computer software able to generate such models or complex, flexible spacecraft, unfortunately, neither is suitable for parameter estimation. Because of this limitation the computer software PDEMOD is being developed for the express purposes of modeling, control system analysis, parameter estimation and structure optimization. PDEMOD is capable of modeling complex, flexible spacecraft which consist of a three-dimensional network of flexible beams and rigid bodies. Each beam has bending (Bernoulli-Euler or Timoshenko) in two directions, torsion, and elongation degrees of freedom. The rigid bodies can be attached to the beam ends at any angle or body location. PDEMOD is also capable of performing parameter estimation based on matching experimental modal frequencies and static deflection test data. The underlying formulation and the results of using this approach for test data of the Mini-MAST truss will be discussed. The resulting accuracy of the parameter estimates when using such limited data can impact significantly the instrumentation requirements for on-orbit tests.

  2. Molecular modeling of the neurophysin I/oxytocin complex

    NASA Astrophysics Data System (ADS)

    Kazmierkiewicz, R.; Czaplewski, C.; Lammek, B.; Ciarkowski, J.

    1997-01-01

    Neurophysins I and II (NPI and NPII) act in the neurosecretory granules as carrier proteinsfor the neurophyseal hormones oxytocin (OT) and vasopressin (VP), respectively. The NPI/OTfunctional unit, believed to be an (NPI/OT)2 heterotetramer, was modeled using low-resolution structure information, viz. the Cα carbon atom coordinates of the homologousNPII/dipeptide complex (file 1BN2 in the Brookhaven Protein Databank) as a template. Itsall-atom representation was obtained using standard modeling tools available within theINSIGHT/Biopolymer modules supplied by Biosym Technologies Inc. A conformation of theNPI-bound OT, similar to that recently proposed in a transfer NOE experiment, was dockedinto the ligand-binding site by a superposition of its Cys1-Tyr2 fragment onto the equivalentportion of the dipeptide in the template. The starting complex for the initial refinements wasprepared by two alternative strategies, termed Model I and Model II, each ending with a˜100 ps molecular dynamics (MD) simulation in water using the AMBER 4.1 force field. The freehomodimer NPI2 was obtained by removal of the two OT subunits from their sites, followedby a similar structure refinement. The use of Model I, consisting of a constrained simulatedannealing, resulted in a structure remarkably similar to both the NPII/dipeptide complex anda recently published solid-state structure of the NPII/OT complex. Thus, Model I isrecommended as the method of choice for the preparation of the starting all-atom data forMD. The MD simulations indicate that, both in the homodimer and in the heterotetramer, the310-helices demonstrate an increased mobility relative to the remaining body of the protein.Also, the C-terminal domains in the NPI2 homodimer are more mobile than the N-terminalones. Finally, a distinct intermonomer interaction is identified, concentrated around its mostprominent, although not unique, contribution provided by an H-bond from Ser25Oγ in one NPI unit to Glu81 Oɛ in the other

  3. Semiotic aspects of control and modeling relations in complex systems

    SciTech Connect

    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.

  4. Modeling the Self-assembly of the Cellulosome Enzyme Complex*

    PubMed Central

    Bomble, Yannick J.; Beckham, Gregg T.; Matthews, James F.; Nimlos, Mark R.; Himmel, Michael E.; Crowley, Michael F.

    2011-01-01

    Most bacteria use free enzymes to degrade plant cell walls in nature. However, some bacteria have adopted a different strategy wherein enzymes can either be free or tethered on a protein scaffold forming a complex called a cellulosome. The study of the structure and mechanism of these large macromolecular complexes is an active and ongoing research topic, with the goal of finding ways to improve biomass conversion using cellulosomes. Several mechanisms involved in cellulosome formation remain unknown, including how cellulosomal enzymes assemble on the scaffoldin and what governs the population of cellulosomes created during self-assembly. Here, we present a coarse-grained model to study the self-assembly of cellulosomes. The model captures most of the physical characteristics of three cellulosomal enzymes (Cel5B, CelS, and CbhA) and the scaffoldin (CipA) from Clostridium thermocellum. The protein structures are represented by beads connected by restraints to mimic the flexibility and shapes of these proteins. From a large simulation set, the assembly of cellulosomal enzyme complexes is shown to be dominated by their shape and modularity. The multimodular enzyme, CbhA, binds statistically more frequently to the scaffoldin than CelS or Cel5B. The enhanced binding is attributed to the flexible nature and multimodularity of this enzyme, providing a longer residence time around the scaffoldin. The characterization of the factors influencing the cellulosome assembly process may enable new strategies to create designers cellulosomes. PMID:21098021

  5. Rubber particles from four different species, examined by transmission electron microscopy and electron-paramagnetic-resonance spin labeling, are found to consist of a homogeneous rubber core enclosed by a contiguous, monolayer biomembrane

    PubMed

    Cornish; Wood; Windle

    1999-11-01

    The physical characteristics of rubber particles from the four rubber (cis-1,4-polyisoprene) producing species Euphorbia lactiflua Phil., Ficus elastica Roxb., Hevea brasiliensis Mull. Arg., and Parthenium argentatum Gray, were investigated using transmission electron microscopy (TEM) and electron-paramagnetic-resonance (EPR) spin labeling spectroscopy. Transmission electron microscopy showed the rubber particles to be composed of a spherical, homogeneous, core of rubber enclosed by a contiguous, electron-dense, single-track surface layer. The biochemical composition of the surface layer and its single-track TEM suggested that a monolayer biomembrane was the surface structure most compatible with the hydrophobic rubber core. The EPR spectra for a series of positional isomers of doxyl stearic acid, used to label the surface layer of the rubber particles, exhibited flexibility gradients and evidence for lipid-protein interactions for all four rubber particle types that is consistent with a biomembrane-like surface. The EPR spectra confirmed that the surface biomembrane is a monolayer. Thus, rubber particles appear similar to oil bodies in their basic architecture. The EPR spectra also provided information on protein location and degree of biomembrane penetration that correlated with the known properties of the rubber-particle-bound proteins. The monolayer biomembrane serves as an interface between the hydrophobic rubber interior and the aqueous cytosol and prevents aggregation of the particles. An unexpected observation for the probes in pure polyisoprene was evidence of an intrinsic flexibility gradient associated with the stearic acid molecule itself.

  6. Complexity in modeling and understanding protonation states: computational titration of HIV-1-protease-inhibitor complexes.

    PubMed

    Tripathi, Ashutosh; Fornabaio, Micaela; Spyrakis, Francesca; Mozzarelli, Andrea; Cozzini, Pietro; Kellogg, Glen E

    2007-11-01

    The computational-titration (CT) algorithm based on the 'natural' Hydropathic INTeractions (HINT) force field is described. The HINT software model is an empirical, non-Newtonian force field derived from experimentally measured partition coefficients for solvent transfer between octanol and H(2)O (log P(o/w)). The CT algorithm allows the identification, modeling, and optimization of multiple protonation states of residues and ligand functional groups at the protein-ligand active site. The importance of taking into account pH and ionization states of residues, which strongly affect the process of ligand binding, for correctly predicting binding free energies is discussed. The application of the CT protocol to a set of six cyclic inhibitors in their complexes with HIV-1 protease is presented, and the advance of HINT as a virtual-screening tool is outlined.

  7. A Qualitative Model of Human Interaction with Complex Dynamic Systems

    NASA Technical Reports Server (NTRS)

    Hess, Ronald A.

    1987-01-01

    A qualitative model describing human interaction with complex dynamic systems is developed. The model is hierarchical in nature and consists of three parts: a behavior generator, an internal model, and a sensory information processor. The behavior generator is responsible for action decomposition, turning higher level goals or missions into physical action at the human-machine interface. The internal model is an internal representation of the environment which the human is assumed to possess and is divided into four submodel categories. The sensory information processor is responsible for sensory composition. All three parts of the model act in consort to allow anticipatory behavior on the part of the human in goal-directed interaction with dynamic systems. Human workload and error are interpreted in this framework, and the familiar example of an automobile commute is used to illustrate the nature of the activity in the three model elements. Finally, with the qualitative model as a guide, verbal protocols from a manned simulation study of a helicopter instrument landing task are analyzed with particular emphasis on the effect of automation on human-machine performance.

  8. A qualitative model of human interaction with complex dynamic systems

    NASA Technical Reports Server (NTRS)

    Hess, Ronald A.

    1987-01-01

    A qualitative model describing human interaction with complex dynamic systems is developed. The model is hierarchical in nature and consists of three parts: a behavior generator, an internal model, and a sensory information processor. The behavior generator is responsible for action decomposition, turning higher level goals or missions into physical action at the human-machine interface. The internal model is an internal representation of the environment which the human is assumed to possess and is divided into four submodel categories. The sensory information processor is responsible for sensory composition. All three parts of the model act in consort to allow anticipatory behavior on the part of the human in goal-directed interaction with dynamic systems. Human workload and error are interpreted in this framework, and the familiar example of an automobile commute is used to illustrate the nature of the activity in the three model elements. Finally, with the qualitative model as a guide, verbal protocols from a manned simulation study of a helicopter instrument landing task are analyzed with particular emphasis on the effect of automation on human-machine performance.

  9. Spatio-temporal modelling of lightning climatologies for complex terrain

    NASA Astrophysics Data System (ADS)

    Simon, Thorsten; Umlauf, Nikolaus; Zeileis, Achim; Mayr, Georg J.; Schulz, Wolfgang; Diendorfer, Gerhard

    2017-03-01

    This study develops methods for estimating lightning climatologies on the day-1 km-2 scale for regions with complex terrain and applies them to summertime observations (2010-2015) of the lightning location system ALDIS in the Austrian state of Carinthia in the Eastern Alps. Generalized additive models (GAMs) are used to model both the probability of occurrence and the intensity of lightning. Additive effects are set up for altitude, day of the year (season) and geographical location (longitude/latitude). The performance of the models is verified by 6-fold cross-validation. The altitude effect of the occurrence model suggests higher probabilities of lightning for locations on higher elevations. The seasonal effect peaks in mid-July. The spatial effect models several local features, but there is a pronounced minimum in the north-west and a clear maximum in the eastern part of Carinthia. The estimated effects of the intensity model reveal similar features, though they are not equal. The main difference is that the spatial effect varies more strongly than the analogous effect of the occurrence model. A major asset of the introduced method is that the resulting climatological information varies smoothly over space, time and altitude. Thus, the climatology is capable of serving as a useful tool in quantitative applications, i.e. risk assessment and weather prediction.

  10. Wrapped-around models for the lac operon complex.

    PubMed

    La Penna, Giovanni; Perico, Angelo

    2010-06-16

    The protein-DNA complex, involved in the lac operon of enteric bacteria, is paradigmatic in understanding the extent of DNA bending and plasticity due to interactions with protein assemblies acting as DNA regulators. For the lac operon, two classes of structures have been proposed: 1), with the protein tetramer lying away from the DNA loop (wrapped-away model); and 2), with the protein tetramer lying inside the DNA loop (wrapped-around model). A recently developed electrostatic analytical model shows that the size and net charge of the Lac protein tetramer allow the bending of DNA, which is consistent with another wrapped-around model from the literature. Coarse-grained models, designed based on this observation, are extensively investigated and show three kinds of wrapped-around arrangements of DNA and a lower propensity for wrapped-away configurations. Molecular dynamics simulations of an all-atom model, built on the basis of the most tightly collapsed coarse-grained model, show that most of the DNA double-helical architecture is maintained in the region between O3 and O1 DNA operators, that the DNA distortion is concentrated in the chain beyond the O1 operator, and that the protein tetramer can adapt the N-terminal domains to the DNA tension.

  11. Are more complex physiological models of forest ecosystems better choices for plot and regional predictions?

    Treesearch

    Wenchi Jin; Hong S. He; Frank R. Thompson

    2016-01-01

    Process-based forest ecosystem models vary from simple physiological, complex physiological, to hybrid empirical-physiological models. Previous studies indicate that complex models provide the best prediction at plot scale with a temporal extent of less than 10 years, however, it is largely untested as to whether complex models outperform the other two types of models...

  12. An efficient algorithm for corona simulation with complex chemical models

    NASA Astrophysics Data System (ADS)

    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.

  13. Modeling Uncertainty and Its Implications in Complex Interdependent Networks

    DTIC Science & Technology

    2016-04-30

    risks to facilitate this analysis. Networked applications often operate under uncertainty in environmental response and the temporal state and action...Operating environment: uncertainty , complexity, rapid change and persistent conflict. • Integrated approach (WSARA 2009). • Definition: • Cascading risk ...qÜáêíÉÉåíÜ=^ååì~ä= ^Åèìáëáíáçå=oÉëÉ~êÅÜ= póãéçëáìã= qÜìêëÇ~ó=pÉëëáçåë= sçäìãÉ=ff= = Modeling Uncertainty and Its Implications in Complex Interdependent

  14. 3D model of amphioxus steroid receptor complexed with estradiol

    SciTech Connect

    Baker, Michael E.; Chang, David J.

    2009-08-28

    The origins of signaling by vertebrate steroids are not fully understood. An important advance was the report that an estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates. To investigate the evolution of estrogen-binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with estradiol. This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human ER{alpha} are not conserved in the SR, which can explain the low affinity of estradiol for the SR. These differences between the SR and ER{alpha} in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the SR. The 3D model predicts that mutation of Glu-346 to Gln will increase the affinity of testosterone for amphioxus SR and elucidate the evolution of steroid-binding to nuclear receptors.

  15. Emission spectra of LH2 complex: full Hamiltonian model

    NASA Astrophysics Data System (ADS)

    Heřman, Pavel; Zapletal, David; Horák, Milan

    2013-05-01

    In the present contribution we study the absorption and steady-state fluorescence spectra for ring molecular system, which can model B850 ring of peripheral light-harvesting complex LH2 from purple bacterium Rhodopseudomonas acidophila (Rhodoblastus acidophilus). LH2 is a highly symmetric ring of nine pigment-protein subunits, each containing two transmembrane polypeptide helixes and three bacteriochlorophylls (BChl). The uncorrelated diagonal static disorder with Gaussian distribution (fluctuations of local excitation energies) simultaneously with the diagonal dynamic disorder (interaction with a bath) in Markovian approximation is used in our simulations. We compare calculated absorption and steady state fluorescence spectra obtained within the full Hamiltonian model of the B850 ring with our previous results calculated within the nearest neighbour approximation model and also with experimental data.

  16. A two-level complex network model and its application

    NASA Astrophysics Data System (ADS)

    Yang, Jianmei; Wang, Wenjie; Chen, Guanrong

    2009-06-01

    This paper investigates the competitive relationship and rivalry of industrial markets, using Chinese household electrical appliance firms as a platform for the study. The common complex network models belong to one-level networks in layered classification, while this paper formulates and evaluates a new two-level network model, in which the first level is the whole unweighted-undirected network useful for macro-analyzing the industrial market structure while the second level is a local weighted-directed network capable of micro-analyzing the inter-firm rivalry in the market. It is believed that the relationship is determined by objective factors whereas the action is rather subjective, and the idea in this paper lies in that the objective relationship and the subjective action subjected to this relationship are being simultaneously considered but at deferent levels of the model which may be applicable to many real applications.

  17. NMR-derived model for a peptide-antibody complex

    SciTech Connect

    Zilber, B.; Scherf, T.; Anglister, J. ); Levitt, M. )

    1990-10-01

    The TE34 monoclonal antibody against cholera toxin peptide 3 (CTP3; VEVPGSQHIDSQKKA) was sequenced and investigated by two-dimensional transferred NOE difference spectroscopy and molecular modeling. The V{sub H} sequence of TE34, which does not bind cholera toxin, shares remarkable homology to that of TE32 and TE33, which are both anti-CTP3 antibodies that bind the toxin. However, due to a shortened heavy chain CDR3, TE34 assumes a radically different combining site structure. The assignment of the combining site interactions to specific peptide residues was completed by use of AcIDSQRKA, a truncated peptide analogue in which lysine-13 was substituted by arginine, specific deuteration of individual polypeptide chains of the antibody, and a computer model for the Fv fragment of TE34. NMR-derived distance restraints were then applied to the calculated model of the Fv to generate a three-dimensional structure of the TE34/CTP3 complex. The combining site was found to be a very hydrophobic cavity composed of seven aromatic residues. Charged residues are found in the periphery of the combining site. The peptide residues HIDSQKKA form a {beta}-turn inside the combining site. The contact area between the peptide and the TE34 antibody is 388 {Angstrom}{sup 2}, about half of the contact area observed in protein-antibody complexes.

  18. A computational model for cancer growth by using complex networks

    NASA Astrophysics Data System (ADS)

    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.

  19. Multiagent model and mean field theory of complex auction dynamics

    NASA Astrophysics Data System (ADS)

    Chen, Qinghua; Huang, Zi-Gang; Wang, Yougui; Lai, Ying-Cheng

    2015-09-01

    Recent years have witnessed a growing interest in analyzing a variety of socio-economic phenomena using methods from statistical and nonlinear physics. We study a class of complex systems arising from economics, the lowest unique bid auction (LUBA) systems, which is a recently emerged class of online auction game systems. Through analyzing large, empirical data sets of LUBA, we identify a general feature of the bid price distribution: an inverted J-shaped function with exponential decay in the large bid price region. To account for the distribution, we propose a multi-agent model in which each agent bids stochastically in the field of winner’s attractiveness, and develop a theoretical framework to obtain analytic solutions of the model based on mean field analysis. The theory produces bid-price distributions that are in excellent agreement with those from the real data. Our model and theory capture the essential features of human behaviors in the competitive environment as exemplified by LUBA, and may provide significant quantitative insights into complex socio-economic phenomena.

  20. Troposphere-lower-stratosphere connection in an intermediate complexity model.

    NASA Astrophysics Data System (ADS)

    Ruggieri, Paolo; King, Martin; Kucharski, Fred; Buizza, Roberto; Visconti, Guido

    2016-04-01

    The dynamical coupling between the troposphere and the lower stratosphere has been investigated using a low-top, intermediate complexity model provided by the Abdus Salam International Centre for Theoretical Physics (SPEEDY). The key question that we wanted to address is whether a simple model like SPEEDY can be used to understand troposphere-stratosphere interactions, e.g. forced by changes of sea-ice concentration in polar arctic regions. Three sets of experiments have been performed. Firstly, a potential vorticity perspective has been applied to understand the wave-like forcing of the troposphere on the stratosphere and to provide quantitative information on the sub seasonal variability of the coupling. Then, the zonally asymmetric, near-surface response to a lower-stratospheric forcing has been analysed in a set of forced experiments with an artificial heating imposed in the extra-tropical lower stratosphere. Finally, the lower-stratosphere response sensitivity to tropospheric initial conditions has been examined. Results indicate how SPEEDY captures the physics of the troposphere-stratosphere connection but also show the lack of stratospheric variability. Results also suggest that intermediate-complexity models such as SPEEDY could be used to investigate the effects that surface forcing (e.g. due to sea-ice concentration changes) have on the troposphere and the lower stratosphere.

  1. Preconditioning the bidomain model with almost linear complexity

    NASA Astrophysics Data System (ADS)

    Pierre, Charles

    2012-01-01

    The bidomain model is widely used in electro-cardiology to simulate spreading of excitation in the myocardium and electrocardiograms. It consists of a system of two parabolic reaction diffusion equations coupled with an ODE system. Its discretisation displays an ill-conditioned system matrix to be inverted at each time step: simulations based on the bidomain model therefore are associated with high computational costs. In this paper we propose a preconditioning for the bidomain model either for an isolated heart or in an extended framework including a coupling with the surrounding tissues (the torso). The preconditioning is based on a formulation of the discrete problem that is shown to be symmetric positive semi-definite. A block LU decomposition of the system together with a heuristic approximation (referred to as the monodomain approximation) are the key ingredients for the preconditioning definition. Numerical results are provided for two test cases: a 2D test case on a realistic slice of the thorax based on a segmented heart medical image geometry, a 3D test case involving a small cubic slab of tissue with orthotropic anisotropy. The analysis of the resulting computational cost (both in terms of CPU time and of iteration number) shows an almost linear complexity with the problem size, i.e. of type nlog α( n) (for some constant α) which is optimal complexity for such problems.

  2. Bloch-Redfield equations for modeling light-harvesting complexes.

    PubMed

    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.

  3. An ice sheet model of reduced complexity for paleoclimate studies

    NASA Astrophysics Data System (ADS)

    Neff, Basil; Born, Andreas; Stocker, Thomas F.

    2016-04-01

    IceBern2D is a vertically integrated ice sheet model to investigate the ice distribution on long timescales under different climatic conditions. It is forced by simulated fields of surface temperature and precipitation of the Last Glacial Maximum and present-day climate from a comprehensive climate model. This constant forcing is adjusted to changes in ice elevation. Due to its reduced complexity and computational efficiency, the model is well suited for extensive sensitivity studies and ensemble simulations on extensive temporal and spatial scales. It shows good quantitative agreement with standardized benchmarks on an artificial domain (EISMINT). Present-day and Last Glacial Maximum ice distributions in the Northern Hemisphere are also simulated with good agreement. Glacial ice volume in Eurasia is underestimated due to the lack of ice shelves in our model. The efficiency of the model is utilized by running an ensemble of 400 simulations with perturbed model parameters and two different estimates of the climate at the Last Glacial Maximum. The sensitivity to the imposed climate boundary conditions and the positive degree-day factor β, i.e., the surface mass balance, outweighs the influence of parameters that disturb the flow of ice. This justifies the use of simplified dynamics as a means to achieve computational efficiency for simulations that cover several glacial cycles. Hysteresis simulations over 5 million years illustrate the stability of the simulated ice sheets to variations in surface air temperature.

  4. Modeling the propagation of mobile phone virus under complex network.

    PubMed

    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.

  5. MOVIE - A Software Environment For Modeling Complex Adaptive Systems

    NASA Astrophysics Data System (ADS)

    Furmanski, Wojtek; Fox, Geoffrey J.

    1990-02-01

    We discuss here the basic elements of the new software system for large scale computation -MOVIE- (Metashell based Object oriented Visual Interactive Environment), recently designed and implemented at Caltech within the Caltech Concurrent Computation Program. From the research perspective, the goal of the MOVIE project is to create a simulation environment for modeling complex systems, with the focus on computational structures capable to adapt and act "intelligently", such as ensembles of image processing, early vision, neural network and Artificial Intelligence modules, integrated in the form of "neural robots". The high level MOVIE model, based on portable communication and computation protocol is suitable for large scale "intelligence engineering" by modeling such systems in distributed heterogeneous multicomputer environment and porting successful implementations to dedicated massively parallel hardware. From the software engineering point of view, the MOVIE model offers a platform for unifying elements of contemporary computing such as networking, windowing, parallelism, number crunching and symbolic processing. The basic idea, borrowed from Sun NeWS, is to use an appropriately extended PostScript as the unifying language. The MOVIE extension aims at promoting PostScript to a general purpose high level object oriented language with a high performance user expandable computational sector, fully compatible with the Adobe model for 2D graphics and the Sun X11 /NeWS model for windowing and multitasking.

  6. When do evolutionary food web models generate complex networks?

    PubMed

    Allhoff, Korinna T; Drossel, Barbara

    2013-10-07

    Evolutionary foodweb models are used to build food webs by the repeated addition of new species. Population dynamics leads to the extinction or establishment of a newly added species, and possibly to the extinction of other species. The food web structure that emerges after some time is a highly nontrivial result of the evolutionary and dynamical rules. We investigate the evolutionary food web model introduced by Loeuille and Loreau (2005), which characterizes species by their body mass as the only evolving trait. Our goal is to find the reasons behind the model's remarkable robustness and its capability to generate various and stable networks. In contrast to other evolutionary food web models, this model requires neither adaptive foraging nor allometric scaling of metabolic rates with body mass in order to produce complex networks that do not eventually collapse to trivial structures. Our study shows that this is essentially due to the fact that the difference in niche value between predator and prey as well as the feeding range are constrained so that they remain within narrow limits under evolution. Furthermore, competition between similar species is sufficiently strong, so that a trophic level can accommodate several species. We discuss the implications of these findings and argue that the conditions that stabilize other evolutionary food web models have similar effects because they also prevent the occurrence of extreme specialists or extreme generalists that have in general a higher fitness than species with a moderate niche width.

  7. Modeling the Propagation of Mobile Phone Virus under Complex Network

    PubMed Central

    Yang, Wei; Wei, Xi-liang; Guo, Hao; An, Gang; Guo, Lei

    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. PMID:25133209

  8. Surface complexation model of uranyl sorption on Georgia kaolinite

    USGS Publications Warehouse

    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.

  9. Model Complexity in Diffusion Modeling: Benefits of Making the Model More Parsimonious

    PubMed Central

    Lerche, Veronika; Voss, Andreas

    2016-01-01

    The diffusion model (Ratcliff, 1978) takes into account the reaction time distributions of both correct and erroneous responses from binary decision tasks. This high degree of information usage allows the estimation of different parameters mapping cognitive components such as speed of information accumulation or decision bias. For three of the four main parameters (drift rate, starting point, and non-decision time) trial-to-trial variability is allowed. We investigated the influence of these variability parameters both drawing on simulation studies and on data from an empirical test-retest study using different optimization criteria and different trial numbers. Our results suggest that less complex models (fixing intertrial variabilities of the drift rate and the starting point at zero) can improve the estimation of the psychologically most interesting parameters (drift rate, threshold separation, starting point, and non-decision time). PMID:27679585

  10. Application of Peterson's stray light model to complex optical instruments

    NASA Astrophysics Data System (ADS)

    Fray, S.; Goepel, M.; Kroneberger, M.

    2016-07-01

    Gary L. Peterson (Breault Research Organization) presented a simple analytical model for in- field stray light evaluation of axial optical systems. We exploited this idea for more complex optical instruments of the Meteosat Third Generation (MTG) mission. For the Flexible Combined Imager (FCI) we evaluated the in-field stray light of its three-mirroranastigmat telescope, while for the Infrared Sounder (IRS) we performed an end-to-end analysis including the front telescope, interferometer and back telescope assembly and the cold optics. A comparison to simulations will be presented. The authors acknowledge the support by ESA and Thales Alenia Space through the MTG satellites program.

  11. Optimizing complex phenotypes through model-guided multiplex genome engineering

    DOE PAGES

    Kuznetsov, Gleb; Goodman, Daniel B.; Filsinger, Gabriel T.; ...

    2017-05-25

    Here, we present a method for identifying genomic modifications that optimize a complex phenotype through multiplex genome engineering and predictive modeling. We apply our method to identify six single nucleotide mutations that recover 59% of the fitness defect exhibited by the 63-codon E. coli strain C321.ΔA. By introducing targeted combinations of changes in multiplex we generate rich genotypic and phenotypic diversity and characterize clones using whole-genome sequencing and doubling time measurements. Regularized multivariate linear regression accurately quantifies individual allelic effects and overcomes bias from hitchhiking mutations and context-dependence of genome editing efficiency that would confound other strategies.

  12. The modeling of complex continua: Fundamental obstacles and grand challenges

    SciTech Connect

    Not Available

    1993-01-01

    The research is divided into: discontinuities and adaptive computation, chaotic flows, dispersion of flow in porous media, and nonlinear waves and nonlinear materials. The research program has emphasized innovative computation and theory. The approach depends on abstracting mathematical concepts and computational methods from individual applications to a wide range of problems involving complex continua. The generic difficulties in the modeling of continua that guide this abstraction are multiple length and time scales, microstructures (bubbles, droplets, vortices, crystal defects), and chaotic or random phenomena described by a statistical formulation.

  13. Modeling and Visualizing Flow of Chemical Agents Across Complex Terrain

    NASA Technical Reports Server (NTRS)

    Kao, David; Kramer, Marc; Chaderjian, Neal

    2005-01-01

    Release of chemical agents across complex terrain presents a real threat to homeland security. Modeling and visualization tools are being developed that capture flow fluid terrain interaction as well as point dispersal downstream flow paths. These analytic tools when coupled with UAV atmospheric observations provide predictive capabilities to allow for rapid emergency response as well as developing a comprehensive preemptive counter-threat evacuation plan. The visualization tools involve high-end computing and massive parallel processing combined with texture mapping. We demonstrate our approach across a mountainous portion of North California under two contrasting meteorological conditions. Animations depicting flow over this geographical location provide immediate assistance in decision support and crisis management.

  14. Modeling and Visualizing Flow of Chemical Agents Across Complex Terrain

    NASA Technical Reports Server (NTRS)

    Kao, David; Kramer, Marc; Chaderjian, Neal

    2005-01-01

    Release of chemical agents across complex terrain presents a real threat to homeland security. Modeling and visualization tools are being developed that capture flow fluid terrain interaction as well as point dispersal downstream flow paths. These analytic tools when coupled with UAV atmospheric observations provide predictive capabilities to allow for rapid emergency response as well as developing a comprehensive preemptive counter-threat evacuation plan. The visualization tools involve high-end computing and massive parallel processing combined with texture mapping. We demonstrate our approach across a mountainous portion of North California under two contrasting meteorological conditions. Animations depicting flow over this geographical location provide immediate assistance in decision support and crisis management.

  15. Does model performance improve with complexity? A case study with three hydrological models

    NASA Astrophysics Data System (ADS)

    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).

  16. The Eemian climate simulated by two models of different complexities

    NASA Astrophysics Data System (ADS)

    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

  17. Socio-Environmental Resilience and Complex Urban Systems Modeling

    NASA Astrophysics Data System (ADS)

    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

  18. Gene 5 protein-DNA complex: modeling binding interactions.

    PubMed

    Hutchinson, D L; Barnett, B L; Bobst, A M

    1990-08-01

    A helical (not toroidal) complex consisting of eight gene 5 protein dimers per turn is proposed for the extension of DNA from dimer to dimer using known bond length constraints, postulated protein-nucleic acid interactions (determined from NMR and chemical modification studies), other physical properties of the complex, and data from electron micrographs. The binding channel has been dictated by these known parameters and the relative ease of geometrically fitting these constituents. This channel is different from that previously reported by other modelers. The channel lies underneath the long arm "claw-like" extension of the monomer, so that it rests inside the outer surface of the protein complex. An explanation is proposed for the two binding modes, n = 4 (the predominate mode) and n = 3, based on the weak binding interaction of Tyrosine 34. Also, the site of the less mobile nucleic acid base as reported from ESR studies (S.-C. Kao, E.V. Bobst, G.T. Pauly and A.M. Bobst, J. Biom. Struc. Dyn. 3,261 (1985)) is postulated as involving the fourth nucleotide, and this particular base is stacked between Tyrosine 34 and Phenylalanine 73'.

  19. The independent spreaders involved SIR Rumor model in complex networks

    NASA Astrophysics Data System (ADS)

    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.

  20. a Range Based Method for Complex Facade Modeling

    NASA Astrophysics Data System (ADS)

    Adami, A.; Fregonese, L.; Taffurelli, L.

    2011-09-01

    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 homogeneous point cloud of

  1. Finding the right balance between groundwater model complexity and experimental effort via Bayesian model selection

    NASA Astrophysics Data System (ADS)

    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.

  2. Thermohaline feedbacks in ocean-climate models of varying complexity

    NASA Astrophysics Data System (ADS)

    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.

  3. Simple models for studying complex spatiotemporal patterns of animal behavior

    NASA Astrophysics Data System (ADS)

    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.

  4. 3-D physical modeling of a complex salt canopy

    SciTech Connect

    Wiley, R.W.; Sekharan, K.K.

    1996-12-31

    Recent drilling has confirmed both significant reservoir potential and the presence of commercial hydrocarbons below salt structures in the Gulf of Mexico. Obtaining definitive seismic images with standard processing schemes beneath these salt structures is very difficult if not impossible. Because of the complicated seismic behavior of these structures, full volume 3-D prestack depth migration is required. Unfortunately, carrying out the multitude of calculations needed to create a proper image requires the largest and fastest supercomputers and rather complex numerical algorithms. Furthermore, developing and testing the imaging algorithms is quite involved and requires appropriate test data sets. To better understand the problems and issues of subsalt imaging, Marathon Oil Company and Louisiana Land and Exploration Company contracted with the University of Houston`s Allied Geophysical Laboratories (AGL) to construct a salt canopy physical model. The model is patterned after the SEG/EAEG Salt Model and is made from synthetic materials. It is a full three-dimensional model with an irregularly shaped, lateral salt structure embedded in five distinct sedimentary layers. The model was used to acquire a multi-offset 3-D marine-style survey. These data are being used to address problems of subsalt imaging. In addition to standard processing techniques, the authors investigate algorithms for multiple removal and prestack depth migration.

  5. Modeling of the formation of complex molecules in protostellar objects

    NASA Astrophysics Data System (ADS)

    Kochina, O. V.; Wiebe, D. S.; Kalenskii, S. V.; Vasyunin, A. I.

    2013-11-01

    The results of molecular composition modeling are presented for the well studied low-mass star-forming region TMC-1 and the massive star-forming region DR21(OH), which is poorly studied from a chemical point of view. The column densities of dozens of molecules, ranging from simple diatomic to complex organic molecules, are reproduced to within an order of magnitude using a one-dimensional model for the physical and chemical structure of these regions. The chemical ages of the regions are approximately 105 years in both cases. The main desorption mechanisms that are usually included in chemical models (photodesorption, thermal desorption, and cosmic-ray-induced desorption) do not provide sufficient gasphase abundances of molecules that are synthesized in surface reactions; however, this shortcoming can be removed by introducing small amount of reactive desorption into the model. It is possible to reproduce the properties of the TMC-1 chemical composition in a standard model, without requiring additional assumptions about an anomalous C/O ratio or the recent accretion of matter enriched with atomic carbon, as has been proposed by some researchers.

  6. Complex Wall Boundary Conditions for Modeling Combustion in Catalytic Channels

    NASA Astrophysics Data System (ADS)

    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.

  7. A subsurface model of the beaver meadow complex

    NASA Astrophysics Data System (ADS)

    Nash, C.; Grant, G.; Flinchum, B. A.; Lancaster, J.; Holbrook, W. S.; Davis, L. G.; Lewis, S.

    2015-12-01

    Wet meadows are a vital component of arid and semi-arid environments. These valley spanning, seasonally inundated wetlands provide critical habitat and refugia for wildlife, and may potentially mediate catchment-scale hydrology in otherwise "water challenged" landscapes. In the last 150 years, these meadows have begun incising rapidly, causing the wetlands to drain and much of the ecological benefit to be lost. The mechanisms driving this incision are poorly understood, with proposed means ranging from cattle grazing to climate change, to the removal of beaver. There is considerable interest in identifying cost-effective strategies to restore the hydrologic and ecological conditions of these meadows at a meaningful scale, but effective process based restoration first requires a thorough understanding of the constructional history of these ubiquitous features. There is emerging evidence to suggest that the North American beaver may have had a considerable role in shaping this landscape through the building of dams. This "beaver meadow complex hypothesis" posits that as beaver dams filled with fine-grained sediments, they became large wet meadows on which new dams, and new complexes, were formed, thereby aggrading valley bottoms. A pioneering study done in Yellowstone indicated that 32-50% of the alluvial sediment was deposited in ponded environments. The observed aggradation rates were highly heterogeneous, suggesting spatial variability in the depositional process - all consistent with the beaver meadow complex hypothesis (Polvi and Wohl, 2012). To expand on this initial work, we have probed deeper into these meadow complexes using a combination of geophysical techniques, coring methods and numerical modeling to create a 3-dimensional representation of the subsurface environments. This imaging has given us a unique view into the patterns and processes responsible for the landforms, and may shed further light on the role of beaver in shaping these landscapes.

  8. Industrial processing of complex fluids: Formulation and modeling

    SciTech Connect

    Scovel, J.C.; Bleasdale, S.; Forest, G.M.; Bechtel, S.

    1997-08-01

    The production of many important commercial materials involves the evolution of a complex fluid through a cooling phase into a hardened product. Textile fibers, high-strength fibers(KEVLAR, VECTRAN), plastics, chopped-fiber compounds, and fiber optical cable are such materials. Industry desires to replace experiments with on-line, real time models of these processes. Solutions to the problems are not just a matter of technology transfer, but require a fundamental description and simulation of the processes. Goals of the project are to develop models that can be used to optimize macroscopic properties of the solid product, to identify sources of undesirable defects, and to seek boundary-temperature and flow-and-material controls to optimize desired properties.

  9. Modeling pedestrian's conformity violation behavior: a complex network based approach.

    PubMed

    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.

  10. Modeling Pedestrian's Conformity Violation Behavior: A Complex Network Based Approach

    PubMed Central

    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. PMID:25530755

  11. On the effect of scaling conceptual model complexity on stochastic response for water quality modeling.

    PubMed

    Parker, G T

    2011-01-01

    This paper extends previous work comparing the response of water quality models under uncertainty. A new model, the River Water Quality Model no. 1 (RWQM1), is compared to the previous work of two commonly used water quality models. Additionally, the effect of conceptual model scaling within a single modelling framework, as allowed by RWQM1, is explored under uncertainty. Model predictions are examined using against real-world data for the Potomac River with a Generalized Likelihood Uncertainty Estimation used to assess model response surfaces to uncertainty. Generally, it was found that there are tangible model characteristics that are closely tied to model complexity and thresholds for these characteristics were discussed. The novel work has yielded an illustrative example but also a conceptually scaleable water quality modelling tool, alongside defined metrics to assess when scaling is required under uncertainty. The resulting framework holds substantial, unique, promise for a new generation of modelling tools that are capable of addressing classically intractable problems.

  12. Fish locomotion: insights from both simple and complex mechanical models

    NASA Astrophysics Data System (ADS)

    Lauder, George

    2015-11-01

    Fishes are well-known for their ability to swim and maneuver effectively in the water, and recent years have seen great progress in understanding the hydrodynamics of aquatic locomotion. But studying freely-swimming fishes is challenging due to difficulties in controlling fish behavior. Mechanical models of aquatic locomotion have many advantages over studying live animals, including the ability to manipulate and control individual structural or kinematic factors, easier measurement of forces and torques, and the ability to abstract complex animal designs into simpler components. Such simplifications, while not without their drawbacks, facilitate interpretation of how individual traits alter swimming performance and the discovery of underlying physical principles. In this presentation I will discuss the use of a variety of mechanical models for fish locomotion, ranging from simple flexing panels to complex biomimetic designs incorporating flexible, actively moved, fin rays on multiple fins. Mechanical devices have provided great insight into the dynamics of aquatic propulsion and, integrated with studies of locomotion in freely-swimming fishes, provide new insights into how fishes move through the water.

  13. Uncertainty quantification for quantum chemical models of complex reaction networks.

    PubMed

    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.

  14. Mutual information model for link prediction in heterogeneous complex networks

    PubMed Central

    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

  15. Interaction of cholesterol-conjugated ionizable amino lipids with biomembranes: lipid polymorphism, structure-activity relationship, and implications for siRNA delivery.

    PubMed

    Zhang, Jingtao; Fan, Haihong; Levorse, Dorothy A; Crocker, Louis S

    2011-08-02

    Delivery of siRNA is a major obstacle to the advancement of RNAi as a novel therapeutic modality. Lipid nanoparticles (LNP) consisting of ionizable amino lipids are being developed as an important delivery platform for siRNAs, and significant efforts are being made to understand the structure-activity relationship (SAR) of the lipids. This article uses a combination of small-angle X-ray scattering (SAXS) and differential scanning calorimetry (DSC) to evaluate the interaction between cholesterol-conjugated ionizable amino lipids and biomembranes, focusing on an important area of lipid SAR--the ability of lipids to destabilize membrane bilayer structures and facilitate endosomal escape. In this study, cholesterol-conjugated amino lipids were found to be effective in increasing the order of biomembranes and also highly effective in inducing phase changes in biological membranes in vitro (i.e., the lamellar to inverted hexagonal phase transition). The phase transition temperatures, determined using SAXS and DSC, serve as an indicator for ranking the potency of lipids to destabilize endosomal membranes. It was found that the bilayer disruption ability of amino lipids depends strongly on the amino lipid concentration in membranes. Amino lipids with systematic variations in headgroups, the extent of ionization, tail length, the degree of unsaturation, and tail asymmetry were evaluated for their bilayer disruption ability to establish SAR. Overall, it was found that the impact of these lipid structure changes on their bilayer disruption ability agrees well with the results from a conceptual molecular "shape" analysis. Implications of the findings from this study for siRNA delivery are discussed. The methods reported here can be used to support the SAR screening of cationic lipids for siRNA delivery, and the information revealed through the study of the interaction between cationic lipids and biomembranes will contribute significantly to the design of more efficient si

  16. Modelling microbial metabolic rewiring during growth in a complex medium.

    PubMed

    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

  17. Surface Complexation Modelling in Metal-Mineral-Bacteria Systems

    NASA Astrophysics Data System (ADS)

    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

  18. A modeling process to understand complex system architectures

    NASA Astrophysics Data System (ADS)

    Robinson, Santiago Balestrini

    2009-12-01

    In recent decades, several tools have been developed by the armed forces, and their contractors, to test the capability of a force. These campaign level analysis tools, often times characterized as constructive simulations are generally expensive to create and execute, and at best they are extremely difficult to verify and validate. This central observation, that the analysts are relying more and more on constructive simulations to predict the performance of future networks of systems, leads to the two central objectives of this thesis: (1) to enable the quantitative comparison of architectures in terms of their ability to satisfy a capability without resorting to constructive simulations, and (2) when constructive simulations must be created, to quantitatively determine how to spend the modeling effort amongst the different system classes. The first objective led to Hypothesis A, the first main hypotheses, which states that by studying the relationships between the entities that compose an architecture, one can infer how well it will perform a given capability. The method used to test the hypothesis is based on two assumptions: (1) the capability can be defined as a cycle of functions, and that it (2) must be possible to estimate the probability that a function-based relationship occurs between any two types of entities. If these two requirements are met, then by creating random functional networks, different architectures can be compared in terms of their ability to satisfy a capability. In order to test this hypothesis, a novel process for creating representative functional networks of large-scale system architectures was developed. The process, named the Digraph Modeling for Architectures (DiMA), was tested by comparing its results to those of complex constructive simulations. Results indicate that if the inputs assigned to DiMA are correct (in the tests they were based on time-averaged data obtained from the ABM), DiMA is able to identify which of any two

  19. Coevolving complex networks in the model of social interactions

    NASA Astrophysics Data System (ADS)

    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.

  20. Wind Power Curve Modeling in Simple and Complex Terrain

    SciTech Connect

    Bulaevskaya, V.; Wharton, S.; Irons, Z.; Qualley, G.

    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.

  1. Lupus Nephritis: Animal Modeling of a Complex Disease Syndrome Pathology

    PubMed Central

    McGaha, Tracy L; Madaio, Michael P.

    2014-01-01

    Nephritis as a result of autoimmunity is a common morbidity associated with Systemic Lupus Erythematosus (SLE). There is substantial clinical and industry interest in medicinal intervention in the SLE nephritic process; however, clinical trials to specifically treat lupus nephritis have not resulted in complete and sustained remission in all patients. Multiple mouse models have been used to investigate the pathologic interactions between autoimmune reactivity and SLE pathology. While several models bear a remarkable similarity to SLE-driven nephritis, there are limitations for each that can make the task of choosing the appropriate model for a particular aspect of SLE pathology challenging. This is not surprising given the variable and diverse nature of human disease. In many respects, features among murine strains mimic some (but never all) of the autoimmune and pathologic features of lupus patients. Although the diversity often limits universal conclusions relevant to pathogenesis, they provide insights into the complex process that result in phenotypic manifestations of nephritis. Thus nephritis represents a microcosm of systemic disease, with variable lesions and clinical features. In this review, we discuss some of the most commonly used models of lupus nephritis (LN) and immune-mediated glomerular damage examining their relative strengths and weaknesses, which may provide insight in the human condition. PMID:25722732

  2. Complex Geometry Creation and Turbulent Conjugate Heat Transfer Modeling

    SciTech Connect

    Bodey, Isaac T; Arimilli, Rao V; Freels, James D

    2011-01-01

    The multiphysics capabilities of COMSOL provide the necessary tools to simulate the turbulent thermal-fluid aspects of the High Flux Isotope Reactor (HFIR). Version 4.1, and later, of COMSOL provides three different turbulence models: the standard k-{var_epsilon} closure model, the low Reynolds number (LRN) k-{var_epsilon} model, and the Spalart-Allmaras model. The LRN meets the needs of the nominal HFIR thermal-hydraulic requirements for 2D and 3D simulations. COMSOL also has the capability to create complex geometries. The circular involute fuel plates used in the HFIR require the use of algebraic equations to generate an accurate geometrical representation in the simulation environment. The best-estimate simulation results show that the maximum fuel plate clad surface temperatures are lower than those predicted by the legacy thermal safety code used at HFIR by approximately 17 K. The best-estimate temperature distribution determined by COMSOL was then used to determine the necessary increase in the magnitude of the power density profile (PDP) to produce a similar clad surface temperature as compared to the legacy thermal safety code. It was determined and verified that a 19% power increase was sufficient to bring the two temperature profiles to relatively good agreement.

  3. Spectroscopic studies of molybdenum complexes as models for nitrogenase

    SciTech Connect

    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.

  4. A Tractable Complex Network Model Based onthe Stochastic Mean-Field Model of Distance

    NASA Astrophysics Data System (ADS)

    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.

  5. Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models.

    PubMed

    El Houasli, Marwa; Maigret, Bernard; Devignes, Marie-Dominique; Ghoorah, Anisah W; Grudinin, Sergei; Ritchie, David W

    2017-03-01

    Many of the modeling targets in the blind CASP-11/CAPRI-30 experiment were protein homo-dimers and homo-tetramers. Here, we perform a retrospective docking-based analysis of the perfectly symmetrical CAPRI Round 30 targets whose crystal structures have been published. Starting from the CASP "stage-2" fold prediction models, we show that using our recently developed "SAM" polar Fourier symmetry docking algorithm combined with NAMD energy minimization often gives acceptable or better 3D models of the target complexes. We also use SAM to analyze the overall quality of all CASP structural models for the selected targets from a docking-based perspective. We demonstrate that docking only CASP "center" structures for the selected targets provides a fruitful and economical docking strategy. Furthermore, our results show that many of the CASP models are dockable in the sense that they can lead to acceptable or better models of symmetrical complexes. Even though SAM is very fast, using docking and NAMD energy minimization to pull out acceptable docking models from a large ensemble of docked CASP models is computationally expensive. Nonetheless, thanks to our SAM docking algorithm, we expect that applying our docking protocol on a modern computer cluster will give us the ability to routinely model 3D structures of symmetrical protein complexes from CASP-quality models. Proteins 2017; 85:463-469. © 2016 Wiley Periodicals, Inc.

  6. Exploring the shape deformation of biomembrane tubes with theoretical analysis and computer simulation.

    PubMed

    Liu, Xuejuan; Tian, Falin; Yue, Tongtao; Zhang, Xianren; Zhong, Chongli

    2016-11-09

    The shape deformation of membrane nanotubes is studied by a combination of theoretical analysis and molecular simulation. First we perform free energy analysis to demonstrate the effects of various factors on two ideal states for the pearling transition, and then we carry out dissipative particle dynamics simulations, through which various types of membrane tube deformation are found, including membrane pearling, buckling, and bulging. Different models for inducing tube deformation, including the osmotic pressure, area difference and spontaneous curvature models, are considered to investigate tubular instabilities. Combined with free energy analysis, our simulations show that the origin of the deformation of membrane tubes in different models can be classified into two categories: effective spontaneous curvature and membrane tension. We further demonstrate that for different models, a positive membrane tension is required for the pearling transition. Finally we show that different models can be coupled to effectively deform the membrane tube.

  7. Water Balance Modelling - Does The Required Model Complexity Change With Scale?

    NASA Astrophysics Data System (ADS)

    Blöschl, G.; Merz, R.

    An important issue in modelling the water balance of catchments is what is the suitable model complexity. Anecdotal evidence suggests that the model complexity required to model the water balance accurately decreases with catchment scale but so far very few studies have quantified these possible effects. In this paper we examine the model per- formance as a function of catchment scale for a given model complexity which allows us to infer, whether the required model complexity changes with scale. We also exam- ine whether the calibrated parameter values change with scale or are scale invariant. In a case study we analysed 700 catchments in Austria with catchment sizes ranging from 10 to 100 000 km2. 30 years of daily data (runoff, precipitation, air temperature, air humidity) were analysed. A spatially lumped, conceptual, HBV style soil mois- ture accounting scheme was used which involved fifteen model parameters including snow processes. Five parameters were preset and ten parameters were calibrated on observed daily streamflow. The calibration period was about 10 years and the verifi- cation period was about 20 years. Model performance (in terms of Nash-Sutcliffe effi- ciency) was examined both for the calibration and the verification periods. The mean efficiency over all catchments only decreased slightly when moving from the calibra- tion to the verification (from R2 = 0.65 to 0.60). The results suggest that the model efficiencies (both for the calibration and the verification) do not change which catch- ment scale for scales smaller than 10 000 km2 but beyond this scale there is a slight decrease in model performance. This means that for these very large scales, a spatial subdivision of the lumped model is needed to allow for spatial differences in rainfall. The results also suggest that the model parameters are not scale dependent. We con- clude that the complexity required for water balance models of catchments does not change with scale for catchment sizes

  8. Elements of complexity in subsurface modeling, exemplified with three case studies

    NASA Astrophysics Data System (ADS)

    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.

  9. Elements of complexity in subsurface modeling, exemplified with three case studies

    NASA Astrophysics Data System (ADS)

    Freedman, Vicky L.; Truex, Michael J.; Rockhold, Mark L.; Bacon, Diana H.; Freshley, Mark D.; Wellman, Dawn M.

    2017-04-01

    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.

  10. Wind Tunnel Modeling Of Wind Flow Over Complex Terrain

    NASA Astrophysics Data System (ADS)

    Banks, D.; Cochran, B.

    2010-12-01

    This presentation will describe the finding of an atmospheric boundary layer (ABL) wind tunnel study conducted as part of the Bolund Experiment. This experiment was sponsored by Risø DTU (National Laboratory for Sustainable Energy, Technical University of Denmark) during the fall of 2009 to enable a blind comparison of various air flow models in an attempt to validate their performance in predicting airflow over complex terrain. Bohlund hill sits 12 m above the water level at the end of a narrow isthmus. The island features a steep escarpment on one side, over which the airflow can be expected to separate. The island was equipped with several anemometer towers, and the approach flow over the water was well characterized. This study was one of only two only physical model studies included in the blind model comparison, the other being a water plume study. The remainder were computational fluid dynamics (CFD) simulations, including both RANS and LES. Physical modeling of air flow over topographical features has been used since the middle of the 20th century, and the methods required are well understood and well documented. Several books have been written describing how to properly perform ABL wind tunnel studies, including ASCE manual of engineering practice 67. Boundary layer wind tunnel tests are the only modelling method deemed acceptable in ASCE 7-10, the most recent edition of the American Society of Civil Engineers standard that provides wind loads for buildings and other structures for buildings codes across the US. Since the 1970’s, most tall structures undergo testing in a boundary layer wind tunnel to accurately determine the wind induced loading. When compared to CFD, the US EPA considers a properly executed wind tunnel study to be equivalent to a CFD model with infinitesimal grid resolution and near infinite memory. One key reason for this widespread acceptance is that properly executed ABL wind tunnel studies will accurately simulate flow separation

  11. Modeling Cu{sup 2+}-Aβ complexes from computational approaches

    SciTech Connect

    Alí-Torres, Jorge; Mirats, Andrea; Maréchal, Jean-Didier; Rodríguez-Santiago, Luis; Sodupe, Mariona

    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.

  12. Modeling Cu2+-Aβ complexes from computational approaches

    NASA Astrophysics Data System (ADS)

    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.

  13. Complex dynamics in the Oregonator model with linear delayed feedback

    NASA Astrophysics Data System (ADS)

    Sriram, K.; Bernard, S.

    2008-06-01

    The Belousov-Zhabotinsky (BZ) reaction can display a rich dynamics when a delayed feedback is applied. We used the Oregonator model of the oscillating BZ reaction to explore the dynamics brought about by a linear delayed feedback. The time-delayed feedback can generate a succession of complex dynamics: period-doubling bifurcation route to chaos; amplitude death; fat, wrinkled, fractal, and broken tori; and mixed-mode oscillations. We observed that this dynamics arises due to a delay-driven transition, or toggling of the system between large and small amplitude oscillations, through a canard bifurcation. We used a combination of numerical bifurcation continuation techniques and other numerical methods to explore the dynamics in the strength of feedback-delay space. We observed that the period-doubling and quasiperiodic route to chaos span a low-dimensional subspace, perhaps due to the trapping of the trajectories in the small amplitude regime near the canard; and the trapped chaotic trajectories get ejected from the small amplitude regime due to a crowding effect to generate chaotic-excitable spikes. We also qualitatively explained the observed dynamics by projecting a three-dimensional phase portrait of the delayed dynamics on the two-dimensional nullclines. This is the first instance in which it is shown that the interaction of delay and canard can bring about complex dynamics.

  14. Integrated modeling tool for performance engineering of complex computer systems

    NASA Technical Reports Server (NTRS)

    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.

  15. A resistive force model for complex intrusion in granular media

    NASA Astrophysics Data System (ADS)

    Zhang, Tingnan; Li, Chen; Goldman, Daniel

    2012-11-01

    Intrusion forces in granular media (GM) are best understood for simple shapes (like disks and rods) undergoing vertical penetration and horizontal drag. Inspired by a resistive force theory for sand-swimming, we develop a new two-dimensional resistive force model for intruders of arbitrary shape and intrusion path into GM in the vertical plane. We divide an intruder of complex geometry into small segments and approximate segmental forces by measuring forces on small flat plates in experiments. Both lift and drag forces on the plates are proportional to penetration depth, and depend sensitively on the angle of attack and the direction of motion. Summation of segmental forces over the intruder predicts the net forces on a c-leg, a flat leg, and a reversed c-leg rotated into GM about a fixed axle. The stress profiles are similar for GM of different particle sizes, densities, coefficients of friction, and volume fractions. We propose a universal scaling law applicable to all tested GM. By combining the new force model with a multi-body simulator, we can also predict the locomotion dynamics of a small legged robot on GM. Our force laws can provide a strict test of hydrodynamic-like approaches to model dense granular flows. Also affiliated to: School of Physics, Georgia Institute of Technology.

  16. Beyond pure parasystole: promises and problems in modeling complex arrhythmias.

    PubMed

    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.

  17. Modeling the Complex Dynamics and Changing Correlations of Epileptic Events

    PubMed Central

    Wulsin, Drausin F.; Fox, Emily B.; Litt, Brian

    2014-01-01

    Patients with epilepsy can manifest short, sub-clinical epileptic “bursts” in addition to full-blown clinical seizures. We believe the relationship between these two classes of events—something not previously studied quantitatively—could yield important insights into the nature and intrinsic dynamics of seizures. A goal of our work is to parse these complex epileptic events into distinct dynamic regimes. A challenge posed by the intracranial EEG (iEEG) data we study is the fact that the number and placement of electrodes can vary between patients. We develop a Bayesian nonparametric Markov switching process that allows for (i) shared dynamic regimes between a variable number of channels, (ii) asynchronous regime-switching, and (iii) an unknown dictionary of dynamic regimes. We encode a sparse and changing set of dependencies between the channels using a Markov-switching Gaussian graphical model for the innovations process driving the channel dynamics and demonstrate the importance of this model in parsing and out-of-sample predictions of iEEG data. We show that our model produces intuitive state assignments that can help automate clinical analysis of seizures and enable the comparison of sub-clinical bursts and full clinical seizures. PMID:25284825

  18. Neurocomputational Model of EEG Complexity during Mind Wandering

    PubMed Central

    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. PMID:26973505

  19. Genotoxicity of model and complex mixtures of polycyclic aromatic hydrocarbons

    SciTech Connect

    Donnelly, K.C.; Phillips, T.D.; Onufrock, A.M.; Collie, S.L.; Huebner, H.J.; Washburn, K.S.

    1996-12-31

    Polycyclic aromatic hydrocarbons (PAHs) are one of the most ubiquitous classes of environmental carcinogens; however, limited information is available to describe their potential genotoxic interactions. This manuscript reports on the interactions of PAHs in complex mixtures as determined in microbial mutagenicity assays. Samples analyzed included separate 2-, 3-, and 4-ring PAH individual model fractions (IMFs) constructed to simulate the composition of a model coal tar. These were tested individually and in various combinations, including a reconstituted model fraction (RMF) composed of all three IMFs. A solvent extract of coal tar and a benzo(a)pyrene-amended extract of coal tar were also tested. The maximum mutagenic response of 1,089 revertants was induced by the RMF at a dose of 90 {micro}g/plate with metabolic activation. At the four lowest dose levels, the response observed in the RMF sample was increased when compared to the 4-ring-IMF sample alone. However, the response observed with the RMF sample at the highest dose tested was less than was observed in the 4-ring-IMF sample tested independently. When IMF samples were combined or mixed with individual chemicals, some inhibition was observed. These data indicate that mixtures of PAHs can exhibit a variety of mutagenic interactions controlled by both the metabolism of the PAHs and by their concentration in the mixture.

  20. Deposition parameterizations for the Industrial Source Complex (ISC3) model

    SciTech Connect

    Wesely, Marvin L.; Doskey, Paul V.; Shannon, J. D.

    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.

  1. Simulation and Processing Seismic Data in Complex Geological Models

    NASA Astrophysics Data System (ADS)

    Forestieri da Gama Rodrigues, S.; Moreira Lupinacci, W.; Martins de Assis, C. A.

    2014-12-01

    Seismic simulations in complex geological models are interesting to verify some limitations of seismic data. In this project, different geological models were designed to analyze some difficulties encountered in the interpretation of seismic data. Another idea is these data become available for LENEP/UENF students to test new tools to assist in seismic data processing. The geological models were created considering some characteristics found in oil exploration. We simulated geological medium with volcanic intrusions, salt domes, fault, pinch out and layers more distante from surface (Kanao, 2012). We used the software Tesseral Pro to simulate the seismic acquisitions. The acquisition geometries simulated were of the type common offset, end-on and split-spread. (Figure 1) Data acquired with constant offset require less processing routines. The processing flow used with tools available in Seismic Unix package (for more details, see Pennington et al., 2005) was geometric spreading correction, deconvolution, attenuation correction and post-stack depth migration. In processing of the data acquired with end-on and split-spread geometries, we included velocity analysis and NMO correction routines. Although we analyze synthetic data and carefully applied each processing routine, we can observe some limitations of the seismic reflection in imaging thin layers, great surface depth layers, layers with low impedance contrast and faults.

  2. Evolution of complexity in a resource-based model

    NASA Astrophysics Data System (ADS)

    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.

  3. Methods of Information Geometry to model complex shapes

    NASA Astrophysics Data System (ADS)

    De Sanctis, A.; Gattone, S. A.

    2016-09-01

    In this paper, a new statistical method to model patterns emerging in complex systems is proposed. A framework for shape analysis of 2- dimensional landmark data is introduced, in which each landmark is represented by a bivariate Gaussian distribution. From Information Geometry we know that Fisher-Rao metric endows the statistical manifold of parameters of a family of probability distributions with a Riemannian metric. Thus this approach allows to reconstruct the intermediate steps in the evolution between observed shapes by computing the geodesic, with respect to the Fisher-Rao metric, between the corresponding distributions. Furthermore, the geodesic path can be used for shape predictions. As application, we study the evolution of the rat skull shape. A future application in Ophthalmology is introduced.

  4. Inverse Problems in Complex Models and Applications to Earth Sciences

    NASA Astrophysics Data System (ADS)

    Bosch, M. E.

    2015-12-01

    The inference of the subsurface earth structure and properties requires the integration of different types of data, information and knowledge, by combined processes of analysis and synthesis. To support the process of integrating information, the regular concept of data inversion is evolving to expand its application to models with multiple inner components (properties, scales, structural parameters) that explain multiple data (geophysical survey data, well-logs, core data). The probabilistic inference methods provide the natural framework for the formulation of these problems, considering a posterior probability density function (PDF) that combines the information from a prior information PDF and the new sets of observations. To formulate the posterior PDF in the context of multiple datasets, the data likelihood functions are factorized assuming independence of uncertainties for data originating across different surveys. A realistic description of the earth medium requires modeling several properties and structural parameters, which relate to each other according to dependency and independency notions. Thus, conditional probabilities across model components also factorize. A common setting proceeds by structuring the model parameter space in hierarchical layers. A primary layer (e.g. lithology) conditions a secondary layer (e.g. physical medium properties), which conditions a third layer (e.g. geophysical data). In general, less structured relations within model components and data emerge from the analysis of other inverse problems. They can be described with flexibility via direct acyclic graphs, which are graphs that map dependency relations between the model components. Examples of inverse problems in complex models can be shown at various scales. At local scale, for example, the distribution of gas saturation is inferred from pre-stack seismic data and a calibrated rock-physics model. At regional scale, joint inversion of gravity and magnetic data is applied

  5. Complex events in a fault model with interacting asperities

    NASA Astrophysics Data System (ADS)

    Dragoni, Michele; Tallarico, Andrea

    2016-08-01

    The dynamics of a fault with heterogeneous friction is studied by employing a discrete fault model with two asperities of different strengths. The average values of stress, friction and slip on each asperity are considered and the state of the fault is described by the slip deficits of the asperities as functions of time. The fault has three different slipping modes, corresponding to the asperities slipping one at a time or simultaneously. Any seismic event produced by the fault is a sequence of n slipping modes. According to initial conditions, seismic events can be different sequences of slipping modes, implying different moment rates and seismic moments. Each event can be represented geometrically in the state space by an orbit that is the union of n damped Lissajous curves. We focus our interest on events that are sequences of two or more slipping modes: they show a complex stress interchange between the asperities and a complex temporal pattern of slip rate. The initial stress distribution producing these events is not uniform on the fault. We calculate the stress drop, the moment rate and the frequency spectrum of the events, showing how these quantities depend on initial conditions. These events have the greatest seismic moments that can be produced by fault slip. As an example, we model the moment rate of the 1992 Landers, California, earthquake that can be described as the consecutive failure of two asperities, one of which has a double strength than the other, and evaluate the evolution of stress distribution on the fault during the event.

  6. Dynamical complexity in the perception-based network formation model

    NASA Astrophysics Data System (ADS)

    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.

  7. Construction of Lyapunov functions for some models of infectious diseases in vivo: from simple models to complex models.

    PubMed

    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.

  8. Complex Environmental Data Modelling Using Adaptive General Regression Neural Networks

    NASA Astrophysics Data System (ADS)

    Kanevski, Mikhail

    2015-04-01

    The research deals with an adaptation and application of Adaptive General Regression Neural Networks (GRNN) to high dimensional environmental data. GRNN [1,2,3] are efficient modelling tools both for spatial and temporal data and are based on nonparametric kernel methods closely related to classical Nadaraya-Watson estimator. Adaptive GRNN, using anisotropic kernels, can be also applied for features selection tasks when working with high dimensional data [1,3]. In the present research Adaptive GRNN are used to study geospatial data predictability and relevant feature selection using both simulated and real data case studies. The original raw data were either three dimensional monthly precipitation data or monthly wind speeds embedded into 13 dimensional space constructed by geographical coordinates and geo-features calculated from digital elevation model. GRNN were applied in two different ways: 1) adaptive GRNN with the resulting list of features ordered according to their relevancy; and 2) adaptive GRNN applied to evaluate all possible models N [in case of wind fields N=(2^13 -1)=8191] and rank them according to the cross-validation error. In both cases training were carried out applying leave-one-out procedure. An important result of the study is that the set of the most relevant features depends on the month (strong seasonal effect) and year. The predictabilities of precipitation and wind field patterns, estimated using the cross-validation and testing errors of raw and shuffled data, were studied in detail. The results of both approaches were qualitatively and quantitatively compared. In conclusion, Adaptive GRNN with their ability to select features and efficient modelling of complex high dimensional data can be widely used in automatic/on-line mapping and as an integrated part of environmental decision support systems. 1. Kanevski M., Pozdnoukhov A., Timonin V. Machine Learning for Spatial Environmental Data. Theory, applications and software. EPFL Press

  9. Thermophysical Model of S-complex NEAs: 1627 Ivar

    NASA Astrophysics Data System (ADS)

    Crowell, Jenna L.; Howell, Ellen S.; Magri, Christopher; Fernandez, Yan R.; Marshall, Sean E.; Warner, Brian D.; Vervack, Ronald J.

    2015-11-01

    We present updates to the thermophysical model of asteroid 1627 Ivar. Ivar is an Amor class near Earth asteroid (NEA) with a taxonomic type of Sqw [1] and a rotation rate of 4.795162 ± 5.4 * 10-6 hours [2]. In 2013, our group observed Ivar in radar, in CCD lightcurves, and in the near-IR’s reflected and thermal regimes (0.8 - 4.1 µm) using the Arecibo Observatory’s 2380 MHz radar, the Palmer Divide Station’s 0.35m telescope, and the SpeX instrument at the NASA IRTF respectively. Using these radar and lightcurve data, we generated a detailed shape model of Ivar using the software SHAPE [3,4]. Our shape model reveals more surface detail compared to earlier models [5] and we found Ivar to be an elongated asteroid with the maximum extended length along the three body-fixed coordinates being 12 x 11.76 x 6 km. For our thermophysical modeling, 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 the known spin state. We then create synthetic near-IR spectra that can be compared to our observed spectra, which cover a wide range of Ivar’s rotational longitudes and viewing geometries. As has been noted [6,8], the use of an accurate shape model is often crucial for correctly interpreting multi-epoch thermal emission observations. We will present what SHERMAN has let us determine about the reflective, thermal, and surface properties for Ivar that best reproduce our spectra. From our derived best-fit thermal parameters, we will learn more about the regolith, surface properties, and heterogeneity of Ivar and how those properties compare to those of other S-complex asteroids. References: [1] DeMeo et al. 2009, Icarus 202, 160-180 [2] Crowell, J. et al. 2015, LPSC 46 [3] Magri C. et al. 2007, Icarus 186, 152-177 [4] Crowell, J. et al. 2014, AAS/DPS 46 [5] Kaasalainen, M. et al. 2004, Icarus 167, 178-196 [6] Crowell, J. et

  10. Compartmental models for apical efflux by P-glycoprotein. Part 1. Evaluation of model complexity

    PubMed Central

    Nagar, Swati; Tucker, Jalia; Weiskircher, Erica A.; Bhoopathy, Siddhartha; Hidalgo, Ismael J.; Korzekwa, Ken

    2013-01-01

    Purpose With the goal of quantifying P-gp transport kinetics, Part 1 of these manuscripts evaluates different compartmental models and Part 2 applies these models to kinetic data. Methods Models were developed to simulate the effect of apical efflux transporters on intracellular concentrations of six drugs. The effect of experimental variability on model predictions was evaluated. Several models were evaluated, and characteristics including membrane configuration, lipid content, and apical surface area (asa) were varied. Results Passive permeabilities from MDCK-MDR1 cells in the presence of cyclosporine gave lower model errors than from MDCK control cells. Consistent with the results in Part 2, model configuration had little impact on calculated model errors. The 5-compartment model was the simplest model that reproduced experimental lag times. Lipid content and asa had minimal effect on model errors, predicted lag times, and intracellular concentrations. Including endogenous basolateral uptake activity can decrease model errors. Models with and without explicit membrane barriers differed markedly in their predicted intracellular concentrations for basolateral drug exposure. Single point data resulted in clearances similar to time course data. Conclusions Compartmental models are useful to evaluate the impact of efflux transporters on intracellular concentrations. Whereas a 3-compartment model may be sufficient to predict the impact of transporters that efflux drugs from the cell, a 5-compartment model with explicit membranes may be required to predict intracellular concentrations when efflux occurs from the membrane. More complex models including additional compartments may be unnecessary. PMID:24019023

  11. Dynamics of vortices in complex wakes: Modeling, analysis, and experiments

    NASA Astrophysics Data System (ADS)

    Basu, Saikat

    The thesis develops singly-periodic mathematical models for complex laminar wakes which are formed behind vortex-shedding bluff bodies. These wake structures exhibit a variety of patterns as the bodies oscillate or are in close proximity of one another. The most well-known formation comprises two counter-rotating vortices in each shedding cycle and is popularly known as the von Karman vortex street. Of the more complex configurations, as a specific example, this thesis investigates one of the most commonly occurring wake arrangements, which consists of two pairs of vortices in each shedding period. The paired vortices are, in general, counter-rotating and belong to a more general definition of the 2P mode, which involves periodic release of four vortices into the flow. The 2P arrangement can, primarily, be sub-classed into two types: one with a symmetric orientation of the two vortex pairs about the streamwise direction in a periodic domain and the other in which the two vortex pairs per period are placed in a staggered geometry about the wake centerline. The thesis explores the governing dynamics of such wakes and characterizes the corresponding relative vortex motion. In general, for both the symmetric as well as the staggered four vortex periodic arrangements, the thesis develops two-dimensional potential flow models (consisting of an integrable Hamiltonian system of point vortices) that consider spatially periodic arrays of four vortices with their strengths being +/-Gamma1 and +/-Gamma2. Vortex formations observed in the experiments inspire the assumed spatial symmetry. The models demonstrate a number of dynamic modes that are classified using a bifurcation analysis of the phase space topology, consisting of level curves of the Hamiltonian. Despite the vortex strengths in each pair being unequal in magnitude, some initial conditions lead to relative equilibrium when the vortex configuration moves with invariant size and shape. The scaled comparisons of the

  12. Grafted biomembranes containing membrane proteins--the case of the leucine transporter.

    PubMed

    Jagalski, Vivien; Barker, Robert D; Thygesen, Mikkel B; Gotfryd, Kamil; Krüger, Mie B; Shi, Lei; Maric, Selma; Bovet, Nicolas; Moulin, Martine; Haertlein, Michael; Pomorski, Thomas Günther; Loland, Claus J; Cárdenas, Marité

    2015-10-21

    Here, we bind the sodium dependent amino acid transporter on nitrilotriacetic acid/polyethylene glycol functionalized gold sensors in detergents and perform a detergent-lipid exchange with phosphatidylcholine. We characterize the LeuT structure in the adsorbed film by magnetic contrast neutron reflection using the predicted model from molecular dynamic simulations.

  13. Rumor spreading model with noise interference in complex social networks

    NASA Astrophysics Data System (ADS)

    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.

  14. Electromagnetic modelling of Ground Penetrating Radar responses to complex targets

    NASA Astrophysics Data System (ADS)

    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

  15. The complexity of model checking for belief revision and update

    SciTech Connect

    Liberatore, P.; Schaerf, M.

    1996-12-31

    One of the main challenges in the formal modeling of common-sense reasoning is the ability to cope with the dynamic nature of the world. Among the approaches put forward to address this problem are belief revision and update. Given a knowledge base T, representing our knowledge of the {open_quotes}state of affairs{close_quotes} of the world of interest, it is possible that we are lead to trust another piece of information P, possibly inconsistent with the old one T. The aim of revision and update operators is to characterize the revised knowledge base T{prime} that incorporates the new formula P into the old one T while preserving consistency and, at the same time, avoiding the loss of too much information in this process. In this paper we study the computational complexity of one of the main computational problems of belief revision and update: deciding if an interpretation M is a model of the revised knowledge base.

  16. Fitting meta-analytic structural equation models with complex datasets.

    PubMed

    Wilson, Sandra Jo; Polanin, Joshua R; Lipsey, Mark W

    2016-06-01

    A modification of the first stage of the standard procedure for two-stage meta-analytic structural equation modeling for use with large complex datasets is presented. This modification addresses two common problems that arise in such meta-analyses: (a) primary studies that provide multiple measures of the same construct and (b) the correlation coefficients that exhibit substantial heterogeneity, some of which obscures the relationships between the constructs of interest or undermines the comparability of the correlations across the cells. One component of this approach is a three-level random effects model capable of synthesizing a pooled correlation matrix with dependent correlation coefficients. Another component is a meta-regression that can be used to generate covariate-adjusted correlation coefficients that reduce the influence of selected unevenly distributed moderator variables. A non-technical presentation of these techniques is given, along with an illustration of the procedures with a meta-analytic dataset. Copyright © 2016 John Wiley & Sons, Ltd.

  17. Analysis of a Mouse Skin Model of Tuberous Sclerosis Complex

    PubMed Central

    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

  18. A minimal model for congestion phenomena on complex networks

    NASA Astrophysics Data System (ADS)

    DeMartino, Daniele; Dall'Asta, Luca; Bianconi, Ginestra; Marsili, Matteo

    2009-08-01

    We study a minimal model of traffic flows in complex networks, simple enough for getting analytical results, but with a very rich phenomenology, presenting continuous, discontinuous as well as hybrid phase transitions between a free-flow phase and a congested phase, critical points and different behaviors of scaling with the system size. It consists of random walkers on a queuing network with one-range repulsion, where particles can be destroyed only if they can move. We focus on the dependence on the topology as well as on the level of traffic control. We are able to obtain transition curves and phase diagrams at an analytical level for the ensemble of uncorrelated networks and numerically for single instances. We find that traffic control improves global performance, enlarging the free-flow region in parameter space only in heterogeneous networks. Traffic control introduces non-linear effects and, beyond a critical strength, may trigger the appearance of a congested phase in a discontinuous manner. The model also reproduces the crossover in the scaling of traffic fluctuations empirically observed in the Internet, and moreover, a conserved version can reproduce qualitatively some stylized facts of traffic in transportation networks.

  19. Reliable modeling of the electronic spectra of realistic uranium complexes

    NASA Astrophysics Data System (ADS)

    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].

  20. Entropy of biogeochemical compartment models: complexity and information content as a tool for model development

    NASA Astrophysics Data System (ADS)

    Metzler, Holger; Sierra, Carlos A.

    2017-04-01

    Most soil organic matter decomposition models consist of a number of compartments describing the dynamics of substrate and microbial biomass pools. The fluxes of mass between the compartments are usually described by a system of ordinary differential equations, in which the number of compartments and the connections among them define the complexity of the model and the number of biological processes that need to be described. With this approach, it is difficult to determine the level of detail that is required to describe a given system, and it is also difficult to compare models against each other due to large differences in their level of complexity. Here, we propose entropy as a tool to determine the level of complexity required to describe a biogeochemical system and to compare the information content of different models. Instead of entire masses on bulk soil level, we look at such models from the point of view of a single particle on the molecular level. This particle enters the system, cycles through it, and leaves it at some point later in time, thereby following a path through the system. We think of this path as a particular stochastic process, a Markov renewal process. If we consider this path as a random variable in a path space, its Shannon information entropy describes its information content, i.e. how much we learn when we observe the entire path of a particle traveling through the system. In other words, it tells us how hard it is to predict this path and thus how much we do not know about what is going to happen to one single particle. The entropy as a measure of model complexity can help us to decide whether a model is not complex enough to represent the information that we have about a system or whether it is too complex. The concept of maximum entropy provides a powerful tool to develop unbiased models, i.e. models that contain the exact amount of information that we have about the system. In addition, differences between a soil organic matter

  1. Chitosan and alginate types of bio-membrane in fuel cell application: An overview

    NASA Astrophysics Data System (ADS)

    Shaari, N.; Kamarudin, S. K.

    2015-09-01

    The major problems of polymer electrolyte membrane fuel cell technology that need to be highlighted are fuel crossovers (e.g., methanol or hydrogen leaking across fuel cell membranes), CO poisoning, low durability, and high cost. Chitosan and alginate-based biopolymer membranes have recently been used to solve these problems with promising results. Current research in biopolymer membrane materials and systems has focused on the following: 1) the development of novel and efficient biopolymer materials; and 2) increasing the processing capacity of membrane operations. Consequently, chitosan and alginate-based biopolymers seek to enhance fuel cell performance by improving proton conductivity, membrane durability, and reducing fuel crossover and electro-osmotic drag. There are four groups of chitosan-based membranes (categorized according to their reaction and preparation): self-cross-linked and salt-complexed chitosans, chitosan-based polymer blends, chitosan/inorganic filler composites, and chitosan/polymer composites. There are only three alginate-based membranes that have been synthesized for fuel cell application. This work aims to review the state-of-the-art in the growth of chitosan and alginate-based biopolymer membranes for fuel cell applications.

  2. Combined effect of cortical cytoskeleton and transmembrane proteins on domain formation in biomembranes

    NASA Astrophysics Data System (ADS)

    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.

  3. Combined effect of cortical cytoskeleton and transmembrane proteins on domain formation in biomembranes

    PubMed Central

    Sikder, Md. Kabir Uddin; Stone, Kyle A.; Kumar, P. B. Sunil; Laradji, Mohamed

    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 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. PMID:25106608

  4. Modeling CO2 Migration at Sleipner Using Models of Varying Complexity

    NASA Astrophysics Data System (ADS)

    Bandilla, K.; Celia, M. A.; Leister, E.; Guo, B.

    2014-12-01

    The goal of geologic carbon sequestration (GCS) is to store carbon dioxide (CO2) in the subsurface for time periods on the order of thousands of years. To ensure the safe storage of CO2 in the subsurface, the migration of CO2 and resident brine needs to be predicted. Mathematical modeling is an important tool to predict the migration of both CO2 and brine. Many modeling approaches with different levels of complexity have been applied to the problem of GCS ranging from simple analytic solutions to full three-dimensional reservoir simulators. The choice of modeling approach is often a function of the spatial and temporal scales of the problem, reservoir properties, data availability, available computational resources, and the familiarity of the modeler with a specific modeling approach.The Utsira Formation off the coast of Norway is the target formation of the Sleipner Project, where approximately 1 million tons of CO2 are injected per year. The Utsira Sand consists of a Pliocene sandstone with high permeability and porosity, interbedded with thin mudstone layers that act as baffles for vertical flow. CO2 is injected at the bottom of the formation and collects under the mudstone baffles as it migrates to the top of the formation. The layer of sandstone between the topmost mudstone baffle and caprock is termed the 9th layer. Geometrical and petro-physical data of the 9th layer have been made publicly available, and are the basis for this modeling study.In this study we apply a series of models with different levels of model complexity to the 9th layer of the Utsira Sand. The list of modeling approaches includes (from least complex to most complex): macroscopic invasion percolation model, numerical vertical-equilibrium model with sharp-interface, numerical vertical-equilibrium model with capillary transition zone, vertically-integrated model with dynamic vertical pressure and saturation reconstruction, and full three-dimensional model. The models are compared based on

  5. Atmospheric Modelling for Air Quality Study over the complex Himalayas

    NASA Astrophysics Data System (ADS)

    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.

  6. Thermophysical Model of S-complex NEAs: 1627 Ivar

    NASA Astrophysics Data System (ADS)

    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

  7. Italian Case Studies Modelling Complex Earthquake Sources In PSHA

    NASA Astrophysics Data System (ADS)

    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 (M<2) detected by a local seismometric network installed in 2012 (http://rete-collalto.crs.inogs.it/). At this time, no correlation can be identified between the gas storage activity and local seismicity, so we proceed with a PSHA that considers only natural seismicity, where the rates of earthquakes are assumed to be time-independent. The source model consists of faults and distributed seismicity to consider earthquakes that cannot be associated to specific structures. All potentially active faults within 50 km of the site are considered, and are modelled as 3D listric surfaces, consistent with the proposed geometry of the Montello Fault. Slip rates are constrained using available geological, geophysical and seismological 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

  8. Biomembrane phospholipid-oxide surface interactions: crystal chemical and thermodynamic basis.

    PubMed

    Sahai, Nita

    2002-08-15

    Quartz has the least favored surface among many oxides for bacterial attachment and for lipid bilayer or micelle interactions. Tetrahedrally coordinated crystalline silica polymorphs are membranolytic toward liposomes, lysosomes, erythrocytes, and macrophages. Amorphous silica, the octahedral silica polymorph, (stishovite), and oxides such as Al2O3, Fe2 O3, and TiO2 are less cytotoxic. Existing theories for membrane rupture that invoke interactions between oxide surfaces and cell membrane phospholipids (PLs) do not adequately explain these differences in membranolytic potential of the oxides. The author presents a crystal chemical, thermodynamic model for the initial interaction of oxide surfaces with the quaternary ammonium component of the PL's polar head group. The model includes solvation energy changes and electrostatic forces during adsorption, represented by the dielectric constant of the solid and the charge-to-radius ratio of the adsorbing solute. The nature of oxide-solute interactions compared with oxide-water, solute-water, and water-water interactions determines the membranolytic activity of the oxide, where the solute is TMA+, the quaternary ammonium moeity. Significant membrane rupture, as on quartz, requires unfavorable adsorption entropy (DeltaS(ads,TMA+)<0) to maximize disruption of normal membrane structure and requires favorable Gibbs free energy of exchange between TMA+ and the ambient Na+ ions (DeltaG(exc,TMA+/Na+) = DeltaG(ads,TMA+)-DeltaG(ads,Na+)<0) to maximize the extent of membrane affected. For amorphous silica, DeltaS(ads,TMA+) >0, so disruption of structure is limited, even though G(exc,TMA+/Na+) is <0. Stishovite and other oxides have DeltaS(ads,TMA+) <0, but now DeltaG(exc,TMA+/Na+) is>0 at the acidic to circumneutral pHs of cellular and subcellular organelle fluids. The model predicts the correct sequence of membranolytic ability: quartz > or = amorphous SiO2 >Al2O3 >Fe2O3 >TiO2. The model thus explains the relatively poor adhesion

  9. Using advanced surface complexation models for modelling soil chemistry under forests: Solling forest, Germany.

    PubMed

    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.

  10. A New Approach to Modelling Student Retention through an Application of Complexity Thinking

    ERIC Educational Resources Information Center

    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…

  11. A New Approach to