WorldWideScience

Sample records for biological transport model

  1. Biological transportation networks: Modeling and simulation

    KAUST Repository

    Albi, Giacomo

    2015-09-15

    We present a model for biological network formation originally introduced by Cai and Hu [Adaptation and optimization of biological transport networks, Phys. Rev. Lett. 111 (2013) 138701]. The modeling of fluid transportation (e.g., leaf venation and angiogenesis) and ion transportation networks (e.g., neural networks) is explained in detail and basic analytical features like the gradient flow structure of the fluid transportation network model and the impact of the model parameters on the geometry and topology of network formation are analyzed. We also present a numerical finite-element based discretization scheme and discuss sample cases of network formation simulations.

  2. Documentation of TRU biological transport model (BIOTRAN)

    International Nuclear Information System (INIS)

    Gallegos, A.F.; Garcia, B.J.; Sutton, C.M.

    1980-01-01

    Inclusive of Appendices, this document describes the purpose, rationale, construction, and operation of a biological transport model (BIOTRAN). This model is used to predict the flow of transuranic elements (TRU) through specified plant and animal environments using biomass as a vector. The appendices are: (A) Flows of moisture, biomass, and TRU; (B) Intermediate variables affecting flows; (C) Mnemonic equivalents (code) for variables; (D) Variable library (code); (E) BIOTRAN code (Fortran); (F) Plants simulated; (G) BIOTRAN code documentation; (H) Operating instructions for BIOTRAN code. The main text is presented with a specific format which uses a minimum of space, yet is adequate for tracking most relationships from their first appearance to their formulation in the code. Because relationships are treated individually in this manner, and rely heavily on Appendix material for understanding, it is advised that the reader familiarize himself with these materials before proceeding with the main text

  3. Documentation of TRU biological transport model (BIOTRAN)

    Energy Technology Data Exchange (ETDEWEB)

    Gallegos, A.F.; Garcia, B.J.; Sutton, C.M.

    1980-01-01

    Inclusive of Appendices, this document describes the purpose, rationale, construction, and operation of a biological transport model (BIOTRAN). This model is used to predict the flow of transuranic elements (TRU) through specified plant and animal environments using biomass as a vector. The appendices are: (A) Flows of moisture, biomass, and TRU; (B) Intermediate variables affecting flows; (C) Mnemonic equivalents (code) for variables; (D) Variable library (code); (E) BIOTRAN code (Fortran); (F) Plants simulated; (G) BIOTRAN code documentation; (H) Operating instructions for BIOTRAN code. The main text is presented with a specific format which uses a minimum of space, yet is adequate for tracking most relationships from their first appearance to their formulation in the code. Because relationships are treated individually in this manner, and rely heavily on Appendix material for understanding, it is advised that the reader familiarize himself with these materials before proceeding with the main text.

  4. Continuous Modeling of Calcium Transport Through Biological Membranes

    Science.gov (United States)

    Jasielec, J. J.; Filipek, R.; Szyszkiewicz, K.; Sokalski, T.; Lewenstam, A.

    2016-08-01

    In this work an approach to the modeling of the biological membranes where a membrane is treated as a continuous medium is presented. The Nernst-Planck-Poisson model including Poisson equation for electric potential is used to describe transport of ions in the mitochondrial membrane—the interface which joins mitochondrial matrix with cellular cytosis. The transport of calcium ions is considered. Concentration of calcium inside the mitochondrion is not known accurately because different analytical methods give dramatically different results. We explain mathematically these differences assuming the complexing reaction inside mitochondrion and the existence of the calcium set-point (concentration of calcium in cytosis below which calcium stops entering the mitochondrion).

  5. Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study

    Directory of Open Access Journals (Sweden)

    King John R

    2010-03-01

    Full Text Available Abstract Background Stochastic and asymptotic methods are powerful tools in developing multiscale systems biology models; however, little has been done in this context to compare the efficacy of these methods. The majority of current systems biology modelling research, including that of auxin transport, uses numerical simulations to study the behaviour of large systems of deterministic ordinary differential equations, with little consideration of alternative modelling frameworks. Results In this case study, we solve an auxin-transport model using analytical methods, deterministic numerical simulations and stochastic numerical simulations. Although the three approaches in general predict the same behaviour, the approaches provide different information that we use to gain distinct insights into the modelled biological system. We show in particular that the analytical approach readily provides straightforward mathematical expressions for the concentrations and transport speeds, while the stochastic simulations naturally provide information on the variability of the system. Conclusions Our study provides a constructive comparison which highlights the advantages and disadvantages of each of the considered modelling approaches. This will prove helpful to researchers when weighing up which modelling approach to select. In addition, the paper goes some way to bridging the gap between these approaches, which in the future we hope will lead to integrative hybrid models.

  6. Constructing Soliton and Kink Solutions of PDE Models in Transport and Biology

    Directory of Open Access Journals (Sweden)

    Vsevolod A. Vladimirov

    2006-06-01

    Full Text Available We present a review of our recent works directed towards discovery of a periodic, kink-like and soliton-like travelling wave solutions within the models of transport phenomena and the mathematical biology. Analytical description of these wave patterns is carried out by means of our modification of the direct algebraic balance method. In the case when the analytical description fails, we propose to approximate invariant travelling wave solutions by means of an infinite series of exponential functions. The effectiveness of the method of approximation is demonstrated on a hyperbolic modification of Burgers equation.

  7. Experimental validation of convection-diffusion discretisation scheme employed for computational modelling of biological mass transport

    Directory of Open Access Journals (Sweden)

    Ku David N

    2010-07-01

    Full Text Available Abstract Background The finite volume solver Fluent (Lebanon, NH, USA is a computational fluid dynamics software employed to analyse biological mass-transport in the vasculature. A principal consideration for computational modelling of blood-side mass-transport is convection-diffusion discretisation scheme selection. Due to numerous discretisation schemes available when developing a mass-transport numerical model, the results obtained should either be validated against benchmark theoretical solutions or experimentally obtained results. Methods An idealised aneurysm model was selected for the experimental and computational mass-transport analysis of species concentration due to its well-defined recirculation region within the aneurysmal sac, allowing species concentration to vary slowly with time. The experimental results were obtained from fluid samples extracted from a glass aneurysm model, using the direct spectrophometric concentration measurement technique. The computational analysis was conducted using the four convection-diffusion discretisation schemes available to the Fluent user, including the First-Order Upwind, the Power Law, the Second-Order Upwind and the Quadratic Upstream Interpolation for Convective Kinetics (QUICK schemes. The fluid has a diffusivity of 3.125 × 10-10 m2/s in water, resulting in a Peclet number of 2,560,000, indicating strongly convection-dominated flow. Results The discretisation scheme applied to the solution of the convection-diffusion equation, for blood-side mass-transport within the vasculature, has a significant influence on the resultant species concentration field. The First-Order Upwind and the Power Law schemes produce similar results. The Second-Order Upwind and QUICK schemes also correlate well but differ considerably from the concentration contour plots of the First-Order Upwind and Power Law schemes. The computational results were then compared to the experimental findings. An average error of 140

  8. Experimental validation of convection-diffusion discretisation scheme employed for computational modelling of biological mass transport.

    Science.gov (United States)

    Carroll, Gráinne T; Devereux, Paul D; Ku, David N; McGloughlin, Timothy M; Walsh, Michael T

    2010-07-19

    The finite volume solver Fluent (Lebanon, NH, USA) is a computational fluid dynamics software employed to analyse biological mass-transport in the vasculature. A principal consideration for computational modelling of blood-side mass-transport is convection-diffusion discretisation scheme selection. Due to numerous discretisation schemes available when developing a mass-transport numerical model, the results obtained should either be validated against benchmark theoretical solutions or experimentally obtained results. An idealised aneurysm model was selected for the experimental and computational mass-transport analysis of species concentration due to its well-defined recirculation region within the aneurysmal sac, allowing species concentration to vary slowly with time. The experimental results were obtained from fluid samples extracted from a glass aneurysm model, using the direct spectrophometric concentration measurement technique. The computational analysis was conducted using the four convection-diffusion discretisation schemes available to the Fluent user, including the First-Order Upwind, the Power Law, the Second-Order Upwind and the Quadratic Upstream Interpolation for Convective Kinetics (QUICK) schemes. The fluid has a diffusivity of 3.125 x 10-10 m2/s in water, resulting in a Peclet number of 2,560,000, indicating strongly convection-dominated flow. The discretisation scheme applied to the solution of the convection-diffusion equation, for blood-side mass-transport within the vasculature, has a significant influence on the resultant species concentration field. The First-Order Upwind and the Power Law schemes produce similar results. The Second-Order Upwind and QUICK schemes also correlate well but differ considerably from the concentration contour plots of the First-Order Upwind and Power Law schemes. The computational results were then compared to the experimental findings. An average error of 140% and 116% was demonstrated between the experimental

  9. Quantitative Modeling of Membrane Transport and Anisogamy by Small Groups Within a Large-Enrollment Organismal Biology Course

    Directory of Open Access Journals (Sweden)

    Eric S. Haag

    2016-12-01

    Full Text Available Quantitative modeling is not a standard part of undergraduate biology education, yet is routine in the physical sciences. Because of the obvious biophysical aspects, classes in anatomy and physiology offer an opportunity to introduce modeling approaches to the introductory curriculum. Here, we describe two in-class exercises for small groups working within a large-enrollment introductory course in organismal biology. Both build and derive biological insights from quantitative models, implemented using spreadsheets. One exercise models the evolution of anisogamy (i.e., small sperm and large eggs from an initial state of isogamy. Groups of four students work on Excel spreadsheets (from one to four laptops per group. The other exercise uses an online simulator to generate data related to membrane transport of a solute, and a cloud-based spreadsheet to analyze them. We provide tips for implementing these exercises gleaned from two years of experience.

  10. Zebrafish as a visual and dynamic model to study the transport of nanosized drug delivery systems across the biological barriers.

    Science.gov (United States)

    Li, Ye; Miao, Xiaoqing; Chen, Tongkai; Yi, Xiang; Wang, Ruibing; Zhao, Haitao; Lee, Simon Ming-Yuen; Wang, Xueqing; Zheng, Ying

    2017-08-01

    With the wide application of nanotechnology to drug delivery systems, a simple, dynamic and visual in vivo model for high-throughput screening of novel formulations with fluorescence markers across biological barriers is desperately needed. In vitro cell culture models have been widely used, although they are far from a complimentary in vivo system. Mammalian animal models are common predictive models to study transport, but they are costly and time consuming. Zebrafish (Danio rerio), a small vertebrate model, have the potential to be developed as an "intermediate" model for quick evaluations. Based on our previously established coumarin 6 nanocrystals (C6-NCs), which have two different sizes, the present study investigates the transportation of C6-NCs across four biological barriers, including the chorion, blood brain barrier (BBB), blood retinal barrier (BRB) and gastrointestinal (GI) barrier, using zebrafish embryos and larvae as in vivo models. The biodistribution and elimination of C6 from different organs were quantified in adult zebrafish. The results showed that compared to 200nm C6-NCs, 70nm C6-NCs showed better permeability across these biological barriers. A FRET study suggested that intact C6-NCs together with the free dissolved form of C6 were absorbed into the larval zebrafish. More C6 was accumulated in different organs after incubation with small sized NCs via lipid raft-mediated endocytosis in adult zebrafish, which is consistent with the findings from in vitro cell monolayers and the zebrafish larvae model. C6-NCs could be gradually eliminated in each organ over time. This study demonstrated the successful application of zebrafish as a simple and dynamic model to simultaneously assess the transport of nanosized drug delivery systems across several biological barriers and biodistribution in different organs, especially in the brain, which could be used for central nervous system (CNS) drug and delivery system screening. Copyright © 2017 Elsevier B

  11. Modeling large scale cohesive sediment transport affected by small scale biological activity

    NARCIS (Netherlands)

    Borsje, Bastiaan Wijnand; de Vries, Mindert; Hulscher, Suzanne J.M.H.; de Boer, Gerben J.

    2008-01-01

    Biological activity on the bottom of the seabed is known to have significant influence on the dynamics of cohesive sediment on a small spatial and temporal scale. In this study, we aim to understand the large-scale effects of small-scale biological activity. Hereto, effects of biology are

  12. Survey and discussion of models applicable to the transport and fate thrust area of the Department of Energy Chemical and Biological Nonproliferation Program

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-09-01

    The availability and easy production of toxic chemical and biological agents by domestic and international terrorists pose a serious threat to US national security, especially to civilian populations in and around urban areas. To address this threat, the Department of Energy (DOE) has established the Chemical and Biological Nonproliferation Program (CBNP) with the goal of focusing the DOE`s technical resources and expertise on capabilities to deny, deter, mitigate and respond to clandestine releases of chemical and biological agents. With the intent to build on DOE core competencies, the DOE has established six technology thrust areas within the CBNP Program: Biological Information Resources; Point Sensor Systems; Stand-off Detection; Transport and Fate; Decontamination; and Systems Analysis and Integration. The purpose of the Transport and Fate Thrust is to accurately predict the dispersion, concentration and ultimate fate of chemical and biological agents released into the urban and suburban environments and has two major goals: (1) to develop an integrated and validated state-of-the-art atmospheric transport and fate modeling capability for chemical and biological agent releases within the complex urban environment from the regional scale down to building and subway interiors, and (2) to apply this modeling capability in a broad range of simulation case studies of chemical and biological agent release scenarios in suburban, urban and confined (buildings and subways) environments and provide analysis for the incident response user community. Sections of this report discuss subway transport and fate models; buildings interior transport and fate modeling; models for flow and transport around buildings; and local-regional meteorology and dispersion models.

  13. Mathematical modeling of biological processes

    CERN Document Server

    Friedman, Avner

    2014-01-01

    This book on mathematical modeling of biological processes includes a wide selection of biological topics that demonstrate the power of mathematics and computational codes in setting up biological processes with a rigorous and predictive framework. Topics include: enzyme dynamics, spread of disease, harvesting bacteria, competition among live species, neuronal oscillations, transport of neurofilaments in axon, cancer and cancer therapy, and granulomas. Complete with a description of the biological background and biological question that requires the use of mathematics, this book is developed for graduate students and advanced undergraduate students with only basic knowledge of ordinary differential equations and partial differential equations; background in biology is not required. Students will gain knowledge on how to program with MATLAB without previous programming experience and how to use codes in order to test biological hypothesis.

  14. Lithium transport across biological membranes

    DEFF Research Database (Denmark)

    Holstein-Rathlou, N H

    1990-01-01

    Li+ is actively transported out of cells, and across different epithelia of both mammalian and amphibian origin. Due to the low affinity of the Na+/K(+)-ATPase for Li+, the transport is most likely energized by exchange and/or cotransport processes. The detailed mechanism by which Li+ is reabsorbed...

  15. Lithium transport across biological membranes

    DEFF Research Database (Denmark)

    Holstein-Rathlou, N H

    1990-01-01

    Li+ is actively transported out of cells, and across different epithelia of both mammalian and amphibian origin. Due to the low affinity of the Na+/K(+)-ATPase for Li+, the transport is most likely energized by exchange and/or cotransport processes. The detailed mechanism by which Li+ is reabsorb...

  16. Laboratory of Biological Modeling

    Data.gov (United States)

    Federal Laboratory Consortium — The Laboratory of Biological Modeling is defined by both its methodologies and its areas of application. We use mathematical modeling in many forms and apply it to a...

  17. Modelling of Transport Phenomena

    OpenAIRE

    K., Itoh; S.-I., Itoh; A., Fukuyama

    1993-01-01

    In this review article, we discuss key features of the transport phenomena and theoretical modelling to understand them. Experimental observations have revealed the nature of anomalous transport, i.e., the enhancement of the transport coefficients by the gradients of the plasma profiles, the pinch phenomena, the radial profile of the apomalous transport coefficients, the variation of the transport among the Bohm diffusion, Pseudo-classical confinement, L-mode and variety of improved confineme...

  18. UZ Colloid Transport Model

    International Nuclear Information System (INIS)

    McGraw, M.

    2000-01-01

    The UZ Colloid Transport model development plan states that the objective of this Analysis/Model Report (AMR) is to document the development of a model for simulating unsaturated colloid transport. This objective includes the following: (1) use of a process level model to evaluate the potential mechanisms for colloid transport at Yucca Mountain; (2) Provide ranges of parameters for significant colloid transport processes to Performance Assessment (PA) for the unsaturated zone (UZ); (3) Provide a basis for development of an abstracted model for use in PA calculations

  19. Stochastic transport processes in discrete biological systems

    CERN Document Server

    Frehland, Eckart

    1982-01-01

    These notes are in part based on a course for advanced students in the applications of stochastic processes held in 1978 at the University of Konstanz. These notes contain the results of re­ cent studies on the stochastic description of ion transport through biological membranes. In particular, they serve as an introduction to an unified theory of fluctuations in complex biological transport systems. We emphasize that the subject of this volume is not to introduce the mathematics of stochastic processes but to present a field of theoretical biophysics in which stochastic methods are important. In the last years the study of membrane noise has become an important method in biophysics. Valuable information on the ion transport mechanisms in membranes can be obtained from noise analysis. A number of different processes such as the opening and closing of ion channels have been shown to be sources of the measured current or voltage fluctuations. Bio­ logical 'transport systems can be complex. For example, the tr...

  20. Gas transport processes in sea ice: How convection and diffusion processes might affect biological imprints, a challenge for modellers

    DEFF Research Database (Denmark)

    Tison, J.-L.; Zhou, Shaola J. G.; Thomas, D. N.

    2012-01-01

    ice cover. These rates were however obtained surmising that neither convection, nor diffusion had affected the gas concentration profiles in the ice between discrete ice core collections. This paper discusses examples from three different field surveys (the above-mentioned Barrow experiment......, the INTERICE IV tank experiment in Hamburg and a short field survey close to the Kapisilit locality in the South-East Greenland fjords) where convection or diffusion processes have clearly affected the temporal evolution of the gas profiles in the ice, therefore potentially affecting biological signatures....... The INTERICE IV and Barrow experiment show that the initial equilibrium dissolved gas entrapment within the skeletal layer basically governs most of the profiles higher up in the sea ice cover during the active sea ice growth. However, as the ice layers age and cool down under the temperature gradient, bubble...

  1. Intracellular transport: from physics to ... biology.

    Science.gov (United States)

    Roux, Aurélien; Cuvelier, Damien; Bassereau, Patricia; Goud, Bruno

    2008-03-01

    Considerable effort over the past three decades has allowed the identification of the protein families that control the cellular machinery responsible for intracellular transport within eukaryotic cells. These proteins are estimated to represent about 10-20% of the human "proteome." The complexity of intracellular transport makes useful the development of model membranes. We describe here experimental systems based on lipid giant unilamellar vesicles (GUVs), which are attached to kinesin molecules. These systems give rise to thin membrane tubes and to complex tubular networks when incubated in vitro with microtubules and ATP. This type of assay, which mimics key events occurring during intracellular transport, allows physicists and biologists to understand how the unique mechanical properties of lipid membranes could be involved in the budding process, the sorting of cargo proteins and lipids, and the separation of the buds from a donor membrane.

  2. Anomalous transport in the crowded world of biological cells

    International Nuclear Information System (INIS)

    Höfling, Felix; Franosch, Thomas

    2013-01-01

    A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important

  3. Anomalous transport in the crowded world of biological cells.

    Science.gov (United States)

    Höfling, Felix; Franosch, Thomas

    2013-04-01

    A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important

  4. New calculation of derived limits for the 1960 radiation protection guides reflecting updated models for dosimetry and biological transport

    International Nuclear Information System (INIS)

    Eckerman, K.F.; Watson, S.B.; Nelson, C.B.; Nelson, D.R.; Richardson, A.C.B.; Sullivan, R.E.

    1984-12-01

    This report presents revised values for the radioactivity concentration guides (RCGs), based on the 1960 primary radiation protection guides (RPGs) for occupational exposure (FRC 1960) and for underground uranium miners (EPA 1971a) using the updated dosimetric models developed to prepare ICRP Publication 30. Unlike the derived quantities presented in Publication 30, which are based on limitation of the weighted sum of doses to all irradiated tissues, these RCGs are based on the ''critical organ'' approach of the 1960 guidance, which was a single limit for the most critically irradiated organ or tissue. This report provides revised guides for the 1960 Federal guidance which are consistent with current dosimetric relationships. 2 figs., 4 tabs

  5. Validation of systems biology models

    NARCIS (Netherlands)

    Hasdemir, D.

    2015-01-01

    The paradigm shift from qualitative to quantitative analysis of biological systems brought a substantial number of modeling approaches to the stage of molecular biology research. These include but certainly are not limited to nonlinear kinetic models, static network models and models obtained by the

  6. Normal and impaired charge transport in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, John H., E-mail: jhmiller@uh.edu [Department of Physics & Texas Center for Superconductivity, University of Houston, Houston, TX 77204-5005 (United States); Villagrán, Martha Y. Suárez; Maric, Sladjana [Department of Physics & Texas Center for Superconductivity, University of Houston, Houston, TX 77204-5005 (United States); Briggs, James M. [Department of Biology & Biochemistry, University of Houston, Houston, TX 77204-5001 (United States)

    2015-03-01

    We examine the physics behind some of the causes (e.g., hole migration and localization that cause incorrect base pairing in DNA) and effects (due to amino acid replacements affecting mitochondrial charge transport) of disease-implicated point mutations, with emphasis on mutations affecting mitochondrial DNA (mtDNA). First we discuss hole transport and localization in DNA, including some of our quantum mechanical modeling results, as they relate to certain mutations in cancer. Next, we give an overview of electron and proton transport in the mitochondrial electron transport chain, and how such transport can become impaired by mutations implicated in neurodegenerative diseases, cancer, and other major illnesses. In particular, we report on our molecular dynamics (MD) studies of a leucine→arginine amino acid replacement in ATP synthase, encoded by the T→G point mutation at locus 8993 of mtDNA. This mutation causes Leigh syndrome, a devastating maternally inherited neuromuscular disorder, and has been found to trigger rapid tumor growth in prostate cancer cell lines. Our MD results suggest, for the first time, that this mutation adversely affects water channels that transport protons to and from the c-ring of the rotary motor ATP synthase, thus impairing the ability of the motor to produce ATP. Finally, we discuss possible future research topics for biological physics, such as mitochondrial complex I, a large proton-pumping machine whose physics remains poorly understood.

  7. Issues in Biological Shape Modelling

    DEFF Research Database (Denmark)

    Hilger, Klaus Baggesen

    This talk reflects parts of the current research at informatics and Mathematical Modelling at the Technical University of Denmark within biological shape modelling. We illustrate a series of generalizations, modifications, and applications of the elements of constructing models of shape or appear......This talk reflects parts of the current research at informatics and Mathematical Modelling at the Technical University of Denmark within biological shape modelling. We illustrate a series of generalizations, modifications, and applications of the elements of constructing models of shape...

  8. Mesoscopic models of biological membranes

    DEFF Research Database (Denmark)

    Venturoli, M.; Sperotto, Maria Maddalena; Kranenburg, M.

    2006-01-01

    Phospholipids are the main components of biological membranes and dissolved in water these molecules self-assemble into closed structures, of which bilayers are the most relevant from a biological point of view. Lipid bilayers are often used, both in experimental and by theoretical investigations...... to coarse grain a biological membrane. The conclusion of this comparison is that there can be many valid different strategies, but that the results obtained by the various mesoscopic models are surprisingly consistent. A second objective of this review is to illustrate how mesoscopic models can be used...

  9. From biological membranes to biomimetic model membranes

    Directory of Open Access Journals (Sweden)

    Eeman, M.

    2010-01-01

    Full Text Available Biological membranes play an essential role in the cellular protection as well as in the control and the transport of nutrients. Many mechanisms such as molecular recognition, enzymatic catalysis, cellular adhesion and membrane fusion take place into the biological membranes. In 1972, Singer et al. provided a membrane model, called fluid mosaic model, in which each leaflet of the bilayer is formed by a homogeneous environment of lipids in a fluid state including globular assembling of proteins and glycoproteins. Since its conception in 1972, many developments were brought to this model in terms of composition and molecular organization. The main development of the fluid mosaic model was made by Simons et al. (1997 and Brown et al. (1997 who suggested that membrane lipids are organized into lateral microdomains (or lipid rafts with a specific composition and a molecular dynamic that are different to the composition and the dynamic of the surrounding liquid crystalline phase. The discovery of a phase separation in the plane of the membrane has induced an explosion in the research efforts related to the biology of cell membranes but also in the development of new technologies for the study of these biological systems. Due to the high complexity of biological membranes and in order to investigate the biological processes that occur on the membrane surface or within the membrane lipid bilayer, a large number of studies are performed using biomimicking model membranes. This paper aims at revisiting the fundamental properties of biological membranes in terms of membrane composition, membrane dynamic and molecular organization, as well as at describing the most common biomimicking models that are frequently used for investigating biological processes such as membrane fusion, membrane trafficking, pore formation as well as membrane interactions at a molecular level.

  10. Viscous flow through slowly expanding or contracting porous walls with low seepage Reynolds number: a model for transport of biological fluids through vessels.

    Science.gov (United States)

    Dinarvand, Saeed

    2011-10-01

    In this article, the problem of laminar, isothermal, incompressible and viscous flow in a rectangular domain bounded by two moving porous walls, which enable the fluid to enter or exit during successive expansions or contractions, is investigated. The governing non-linear equations and their associated boundary conditions are transformed into a highly non-linear ordinary differential equation. The series solution of the problem is obtained by utilising the homotopy perturbation method. Graphical results are presented to investigate the influence of the non-dimensional wall dilation rate and seepage Reynolds number (Re) on the velocity, normal pressure distribution and wall shear stress. Since the transport of biological fluids through contracting or expanding vessels is characterised by low seepage Res, the current study focuses on the viscous flow driven by small wall contractions and expansions of two weakly permeable walls.

  11. Stochastic models of intracellular transport

    KAUST Repository

    Bressloff, Paul C.

    2013-01-09

    The interior of a living cell is a crowded, heterogenuous, fluctuating environment. Hence, a major challenge in modeling intracellular transport is to analyze stochastic processes within complex environments. Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an overdamped Brownian particle. On the other hand, active transport requires chemical energy, usually in the form of adenosine triphosphate hydrolysis, and can be direction specific, allowing biomolecules to be transported long distances; this is particularly important in neurons due to their complex geometry. In this review a wide range of analytical methods and models of intracellular transport is presented. In the case of diffusive transport, narrow escape problems, diffusion to a small target, confined and single-file diffusion, homogenization theory, and fractional diffusion are considered. In the case of active transport, Brownian ratchets, random walk models, exclusion processes, random intermittent search processes, quasi-steady-state reduction methods, and mean-field approximations are considered. Applications include receptor trafficking, axonal transport, membrane diffusion, nuclear transport, protein-DNA interactions, virus trafficking, and the self-organization of subcellular structures. © 2013 American Physical Society.

  12. Compositional Modeling of Biological Systems

    OpenAIRE

    Zámborszky, Judit

    2010-01-01

    Molecular interactions are wired in a fascinating way resulting in complex behavior of bio-logical systems. Theoretical modeling provides us a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological systems calls for conceptual tools that manage the combinatorial explosion of the set of possible interac-tions. A suitable conceptual tool to attack complexity is compositionality, already success-fully used in the process algebra field ...

  13. Goods Transport Modelling, Vol 1

    DEFF Research Database (Denmark)

    Petersen, Morten Steen (red.); Kristiansen, Jørgen

    The report is a study of data requirements and methodologies for goods transport. The study is intended to provide the basis for general discussion about the application of goods transport models in Denmark. The report provides an overview of different types of models and data availability....

  14. Mesoscopic models of biological membranes

    DEFF Research Database (Denmark)

    Venturoli, M.; Sperotto, Maria Maddalena; Kranenburg, M.

    2006-01-01

    Phospholipids are the main components of biological membranes and dissolved in water these molecules self-assemble into closed structures, of which bilayers are the most relevant from a biological point of view. Lipid bilayers are often used, both in experimental and by theoretical investigations......, as model systems to understand the fundamental properties of biomembranes. The properties of lipid bilayers can be studied at different time and length scales. For some properties it is sufficient to envision a membrane as an elastic sheet, while for others it is important to take into account the details...... to coarse grain a biological membrane. The conclusion of this comparison is that there can be many valid different strategies, but that the results obtained by the various mesoscopic models are surprisingly consistent. A second objective of this review is to illustrate how mesoscopic models can be used...

  15. System Convergence in Transport Modelling

    DEFF Research Database (Denmark)

    Rich, Jeppe; Nielsen, Otto Anker; Cantarella, Guilio E.

    2010-01-01

    A fundamental premise of most applied transport models is the existence and uniqueness of an equilibrium solution that balances demand x(t) and supply t(x). The demand consists of the people that travel in the transport system and on the defined network, whereas the supply consists of the resulting...... level-of-service attributes (e.g., travel time and cost) offered to travellers. An important source of complexity is the congestion, which causes increasing demand to affect travel time in a non-linear way. Transport models most often involve separate models for traffic assignment and demand modelling...

  16. Uranium Transport Modeling

    International Nuclear Information System (INIS)

    Bostick, William D.

    2008-01-01

    Uranium contamination is prevalent at many of the U.S. DOE facilities and at several civilian sites that have supported the nuclear fuel cycle. The potential off-site mobility of uranium depends on the partitioning of uranium between aqueous and solid (soil and sediment) phases. Hexavalent U (as uranyl, UO 2 2+ ) is relatively mobile, forming strong complexes with ubiquitous carbonate ion which renders it appreciably soluble even under mild reducing conditions. In the presence of carbonate, partition of uranyl to ferri-hydrate and select other mineral phases is usually maximum in the near-neutral pH range ∼ 5-8. The surface complexation reaction of uranyl with iron-containing minerals has been used as one means to model subsurface migration, used in conjunction with information on the site water chemistry and hydrology. Partitioning of uranium is often studied by short-term batch 'equilibrium' or long-term soil column testing ; MCLinc has performed both of these methodologies, with selection of method depending upon the requirements of the client or regulatory authority. Speciation of uranium in soil may be determined directly by instrumental techniques (e.g., x-ray photoelectron spectroscopy, XPS; x-ray diffraction, XRD; etc.) or by inference drawn from operational estimates. Often, the technique of choice for evaluating low-level radionuclide partitioning in soils and sediments is the sequential extraction approach. This methodology applies operationally-defined chemical treatments to selectively dissolve specific classes of macro-scale soil or sediment components. These methods recognize that total soil metal inventory is of limited use in understanding bioavailability or metal mobility, and that it is useful to estimate the amount of metal present in different solid-phase forms. Despite some drawbacks, the sequential extraction method can provide a valuable tool to distinguish among trace element fractions of different solubility related to mineral phases

  17. Probabilistic transport models for fusion

    International Nuclear Information System (INIS)

    Milligen, B.Ph. van; Carreras, B.A.; Lynch, V.E.; Sanchez, R.

    2005-01-01

    A generalization of diffusive (Fickian) transport is considered, in which particle motion is described by probability distributions. We design a simple model that includes a critical mechanism to switch between two transport channels, and show that it exhibits various interesting characteristics, suggesting that the ideas of probabilistic transport might provide a framework for the description of a range of unusual transport phenomena observed in fusion plasmas. The model produces power degradation and profile consistency, as well as a scaling of the confinement time with system size reminiscent of the gyro-Bohm/Bohm scalings observed in fusion plasmas, and rapid propagation of disturbances. In the present work we show how this model may also produce on-axis peaking of the profiles with off-axis fuelling. It is important to note that the fluid limit of a simple model like this, characterized by two transport channels, does not correspond to the usual (Fickian) transport models commonly used for modelling transport in fusion plasmas, and behaves in a fundamentally different way. (author)

  18. Mathematical models in biological discovery

    CERN Document Server

    Walter, Charles

    1977-01-01

    When I was asked to help organize an American Association for the Advancement of Science symposium about how mathematical models have con­ tributed to biology, I agreed immediately. The subject is of immense importance and wide-spread interest. However, too often it is discussed in biologically sterile environments by "mutual admiration society" groups of "theoreticians", many of whom have never seen, and most of whom have never done, an original scientific experiment with the biolog­ ical materials they attempt to describe in abstract (and often prejudiced) terms. The opportunity to address the topic during an annual meeting of the AAAS was irresistable. In order to try to maintain the integrity ;,f the original intent of the symposium, it was entitled, "Contributions of Mathematical Models to Biological Discovery". This symposium was organized by Daniel Solomon and myself, held during the 141st annual meeting of the AAAS in New York during January, 1975, sponsored by sections G and N (Biological and Medic...

  19. Modelling an Ammonium Transporter with SCLS

    Directory of Open Access Journals (Sweden)

    Angelo Troina

    2009-10-01

    Full Text Available The Stochastic Calculus of Looping Sequences (SCLS is a recently proposed modelling language for the representation and simulation of biological systems behaviour. It has been designed with the aim of combining the simplicity of notation of rewrite systems with the advantage of compositionality. It also allows a rather simple and accurate description of biological membranes and their interactions with the environment.In this work we apply SCLS to model a newly discovered ammonium transporter. This transporter is believed to play a fundamental role for plant mineral acquisition, which takes place in the arbuscular mycorrhiza, the most wide-spread plant-fungus symbiosis on earth. Due to its potential application in agriculture this kind of symbiosis is one of the main focuses of the BioBITs project. In our experiments the passage of NH3 / NH4+ from the fungus to the plant has been dissected in known and hypothetical mechanisms; with the model so far we have been able to simulate the behaviour of the system under different conditions. Our simulations confirmed some of the latest experimental results about the LjAMT2;2 transporter. The initial simulation results of the modelling of the symbiosis process are promising and indicate new directions for biological investigations.

  20. High Energy Density Nastic Structures Using Biological Transport Mechanisms

    Science.gov (United States)

    2007-02-28

    DATES COVERED Final Progress Report; 9/27/04 to 11/30/06 4. TITLE AND SUBTITLE High Energy Density Nastic Structures Using Biological Transport...permeable membranes. This concept is based on the pressurization of cells similar to the process that plants use to maintain homeostasis and regulate...cell function. In all plant systems, the transport of ions and fluid produce localized pressure changes (called turgor pressure) that perform many

  1. Positron interactions and transport in biologically relevant molecules

    International Nuclear Information System (INIS)

    Makochekanwa, C; Jones, A; Caradonna, P; Slaughter, D; Sullivan, J; Buckman, S; Bankovic, A; Petrovic, Z; Malovic, G; Dujko, S; Marler, J; Nixon, K; Brunger, M

    2009-01-01

    We present new, high-resolution measurements of positron scattering from biologically relevant molecules, such as water and formic acid. The measurements include absolute determinations of total scattering and positronium formation and they have enabled us to assemble a set of cross sections for these molecules which can be used in an investigation of positron transport in these systems.

  2. Estimation of light transport parameters in biological media using ...

    Indian Academy of Sciences (India)

    The suitability of using the angular peak shape of the coherent backscattered light for estimating the light transport parameters of biological media has been investigated. Milk and methylene blue doped milk were used as tissue phantoms for the measurements carried out with a He–Ne laser (632.8 nm). Results indicate that ...

  3. Continuum Modeling of Biological Network Formation

    KAUST Repository

    Albi, Giacomo

    2017-04-10

    We present an overview of recent analytical and numerical results for the elliptic–parabolic system of partial differential equations proposed by Hu and Cai, which models the formation of biological transportation networks. The model describes the pressure field using a Darcy type equation and the dynamics of the conductance network under pressure force effects. Randomness in the material structure is represented by a linear diffusion term and conductance relaxation by an algebraic decay term. We first introduce micro- and mesoscopic models and show how they are connected to the macroscopic PDE system. Then, we provide an overview of analytical results for the PDE model, focusing mainly on the existence of weak and mild solutions and analysis of the steady states. The analytical part is complemented by extensive numerical simulations. We propose a discretization based on finite elements and study the qualitative properties of network structures for various parameter values.

  4. Next Generation Transport Phenomenology Model

    Science.gov (United States)

    Strickland, Douglas J.; Knight, Harold; Evans, J. Scott

    2004-01-01

    This report describes the progress made in Quarter 3 of Contract Year 3 on the development of Aeronomy Phenomenology Modeling Tool (APMT), an open-source, component-based, client-server architecture for distributed modeling, analysis, and simulation activities focused on electron and photon transport for general atmospheres. In the past quarter, column emission rate computations were implemented in Java, preexisting Fortran programs for computing synthetic spectra were embedded into APMT through Java wrappers, and work began on a web-based user interface for setting input parameters and running the photoelectron and auroral electron transport models.

  5. Methods for testing transport models

    International Nuclear Information System (INIS)

    Singer, C.; Cox, D.

    1991-01-01

    Substantial progress has been made over the past year on six aspects of the work supported by this grant. As a result, we have in hand for the first time a fairly complete set of transport models and improved statistical methods for testing them against large databases. We also have initial results of such tests. These results indicate that careful application of presently available transport theories can reasonably well produce a remarkably wide variety of tokamak data

  6. Modelling pollutant transport

    International Nuclear Information System (INIS)

    Gopinath, D.V.

    1994-01-01

    An attempt has been made here to present a brief outline of the major processes and problems in the environmental modelling with special reference to radionuclide migration in surface waters. The intention has been only to provide a bird's eye view of this fertile and socially relevant area of scientific pursuit. (author). 2 figs., 4 tabs

  7. Transport of biological molecules in surfactant-alginate composite hydrogels.

    Science.gov (United States)

    Stoppel, Whitney L; White, Joseph C; Horava, Sarena D; Bhatia, Surita R; Roberts, Susan C

    2011-11-01

    Obstructed transport of biological molecules can result in improper release of pharmaceuticals or biologics from biomedical devices. Recent studies have shown that nonionic surfactants, such as Pluronic® F68 (F68), positively alter biomaterial properties such as mesh size and microcapsule diameter. To further understand the effect of F68 (incorporated at concentrations well above the critical micelle concentration (CMC)) in traditional biomaterials, the transport properties of BSA and riboflavin were investigated in F68-alginate composite hydrogels, formed by both internal and external cross-linking with divalent cations. Results indicate that small molecule transport (represented by riboflavin) was not significantly hindered by F68 in homogeneously (internally) cross-linked hydrogels (up to an 11% decrease in loading capacity and 14% increase in effective diffusion coefficient, D(eff)), while protein transport in homogeneously cross-linked hydrogels (represented by BSA) was significantly affected (up to a 43% decrease in loading capacity and 40% increase in D(eff)). For inhomogeneously cross-linked hydrogels (externally cross-linked by CaCl(2) or BaCl(2)), the D(eff) increased up to 50 and 83% for small molecules and proteins, respectively. Variation in the alginate gelation method was shown to affect transport through measurable changes in swelling ratio (30% decrease) and observable changes in cross-linking structure as well as up to a 3.6- and 11.8-fold difference in D(eff) for riboflavin and BSA, respectively. Aside from the expected significant changes due to the cross-linking method utilized, protein transport properties were altered due to mesh size restrictions (10-25 nm estimated by mechanical properties) and BSA-F68 interaction (DLS). Taken as a whole, these results show that incorporation of a nonionic surfactant at concentrations above the CMC can affect device functionality by impeding the transport of large biological molecules. Copyright © 2011

  8. Time lags in biological models

    CERN Document Server

    MacDonald, Norman

    1978-01-01

    In many biological models it is necessary to allow the rates of change of the variables to depend on the past history, rather than only the current values, of the variables. The models may require discrete lags, with the use of delay-differential equations, or distributed lags, with the use of integro-differential equations. In these lecture notes I discuss the reasons for including lags, especially distributed lags, in biological models. These reasons may be inherent in the system studied, or may be the result of simplifying assumptions made in the model used. I examine some of the techniques available for studying the solution of the equations. A large proportion of the material presented relates to a special method that can be applied to a particular class of distributed lags. This method uses an extended set of ordinary differential equations. I examine the local stability of equilibrium points, and the existence and frequency of periodic solutions. I discuss the qualitative effects of lags, and how these...

  9. Estimation of light transport parameters in biological media using ...

    Indian Academy of Sciences (India)

    the use of the coherent backscattered peak from tissues to estimate the transport parameters has also been suggested [5–7]. ... closely resemble those of tissues and milk has been used to model light transport in brain tissue [15], to study optical imaging [16], .... The dye-doped colloids thus. Pramana – J. Phys., Vol. 54, No.

  10. Frontiers in Cancer Nanomedicine: Directing Mass Transport through Biological Barriers

    Science.gov (United States)

    Ferrari, Mauro

    2010-01-01

    The physics of mass transport within body compartments and across biological barriers differentiates cancers from healthy tissues. Variants of nanoparticles can be manufactured in combinatorially large sets, varying only one transport-affecting design parameter at a time. Nanoparticles can also be used as building blocks for systems that perform sequences of coordinated actions, in accordance to a prescribed logic. These are referred to as Logic-Embedded Vectors “(LEV)” in the following. Nanoparticles and LEVs are ideal probes for the determination of mass transport laws in tumors, acting as imaging contrast enhancers, and can be employed for the lesion-selective delivery of therapy. Their size, shape, density and surface chemistry dominate convective transport in the blood stream, margination, cell adhesion, selective cellular uptake, as well as sub-cellular trafficking and localization. As argued here, the understanding of transport differentials in cancer, termed ‘transport oncophysics’ unveils a new promising frontier in oncology: the development of lesion-specific delivery particulates that exploit mass transport differentials to deploy treatment of greater efficacy and reduced side effects. PMID:20079548

  11. Track structure in biological models.

    Science.gov (United States)

    Curtis, S B

    1986-01-01

    High-energy heavy ions in the galactic cosmic radiation (HZE particles) may pose a special risk during long term manned space flights outside the sheltering confines of the earth's geomagnetic field. These particles are highly ionizing, and they and their nuclear secondaries can penetrate many centimeters of body tissue. The three dimensional patterns of ionizations they create as they lose energy are referred to as their track structure. Several models of biological action on mammalian cells attempt to treat track structure or related quantities in their formulation. The methods by which they do this are reviewed. The proximity function is introduced in connection with the theory of Dual Radiation Action (DRA). The ion-gamma kill (IGK) model introduces the radial energy-density distribution, which is a smooth function characterizing both the magnitude and extension of a charged particle track. The lethal, potentially lethal (LPL) model introduces lambda, the mean distance between relevant ion clusters or biochemical species along the track. Since very localized energy depositions (within approximately 10 nm) are emphasized, the proximity function as defined in the DRA model is not of utility in characterizing track structure in the LPL formulation.

  12. Modeling axisymmetric flow and transport

    Science.gov (United States)

    Langevin, C.D.

    2008-01-01

    Unmodified versions of common computer programs such as MODFLOW, MT3DMS, and SEAWAT that use Cartesian geometry can accurately simulate axially symmetric ground water flow and solute transport. Axisymmetric flow and transport are simulated by adjusting several input parameters to account for the increase in flow area with radial distance from the injection or extraction well. Logarithmic weighting of interblock transmissivity, a standard option in MODFLOW, can be used for axisymmetric models to represent the linear change in hydraulic conductance within a single finite-difference cell. Results from three test problems (ground water extraction, an aquifer push-pull test, and upconing of saline water into an extraction well) show good agreement with analytical solutions or with results from other numerical models designed specifically to simulate the axisymmetric geometry. Axisymmetric models are not commonly used but can offer an efficient alternative to full three-dimensional models, provided the assumption of axial symmetry can be justified. For the upconing problem, the axisymmetric model was more than 1000 times faster than an equivalent three-dimensional model. Computational gains with the axisymmetric models may be useful for quickly determining appropriate levels of grid resolution for three-dimensional models and for estimating aquifer parameters from field tests.

  13. Modeling Radionuclide Transport in Clays

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Liange [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Li, Lianchong [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Rutqvist, Jonny [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Liu, Hui -Hai [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Birkholzer, Jens [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2012-05-01

    tests (e.g. Garcia-Gutierrez et al. 2006, Soler et al. 2008, van Loon et al. 2004, Wu et al. 2009) and numerical modeling (de Windt et al. 2003; 2006), the effects of THMC processes on radionuclide transport are not fully investigated. The objectives of the research activity documented in this report are to improve a modeling capability for coupled THMC processes and to use it to evaluate the THMC impacts on radionuclide transport. This research activity addresses several key Features, Events and Processes (FEPs), including FEP 2.2.08, Hydrologic Processes, FEP 2.2.07, Mechanical Processes and FEP 2.2.09, Chemical Process— Transport, by studying near-field coupled THMC processes in clay/shale repositories and their impacts on radionuclide transport. This report documents the progress that has been made in FY12. Section 2 discusses the development of THMC modeling capability. Section 3 reports modeling results of THMC impacts on radionuclide transport. Planned work for the remaining months of FY12 and proposed work for FY13 are presented in Section 4.

  14. Integrated modelling of physical, chemical and biological weather

    DEFF Research Database (Denmark)

    Kurganskiy, Alexander

    Integrated modelling of physical, chemical and biological weather has been widely considered during the recent decades. Such modelling includes interactions of atmospheric physics and chemical/biological aerosol concentrations. Emitted aerosols are subject to atmospheric transport, dispersion...... and deposition, but in turn they impact the radiation as well as cloud and precipitation formation. The present study focuses on birch pollen modelling as well as on physical and chemical weather with emphasis on black carbon (BC) aerosol modelling. The Enviro-HIRLAM model has been used for the study...

  15. Fast Neutron Transport in the Biological Shielding Model and Other Regions of the VVER-1000 Mock-Up on the LR-0 Research Reactor

    Directory of Open Access Journals (Sweden)

    Košťál Michal

    2016-01-01

    Full Text Available A set of benchmark experiments was carried out in the full scale VVER-1000 mock-up on the reactor LR-0 in order to validate neutron transport calculation methodologies and to perform the optimization of the shape and locations of neutron flux operation monitors channels inside the shielding of the new VVER-1000 type reactors. Compared with previous experiments on the VVER-1000 mock-up on the reactor LR-0, the fast neutron spectra were measured in the extended neutron energy interval (0.1–10 MeV and new calculations were carried out with the MCNPX code using various nuclear data libraries (ENDF/B VII.0, JEFF 3.1, JENDL 3.3, JENDL 4, ROSFOND 2009, and CENDL 3.1. Measurements and calculations were carried out at different points in the mock-up. The calculation and experimental data are compared.

  16. Advanced transport modeling of toroidal plasmas with transport barriers

    International Nuclear Information System (INIS)

    Fukuyama, A.; Murakami, S.; Honda, M.; Izumi, Y.; Yagi, M.; Nakajima, N.; Nakamura, Y.; Ozeki, T.

    2005-01-01

    Transport modeling of toroidal plasmas is one of the most important issue to predict time evolution of burning plasmas and to develop control schemes in reactor plasmas. In order to describe the plasma rotation and rapid transition self-consistently, we have developed an advanced scheme of transport modeling based on dynamical transport equation and applied it to the analysis of transport barrier formation. First we propose a new transport model and examine its behavior by the use of conventional diffusive transport equation. This model includes the electrostatic toroidal ITG mode and the electromagnetic ballooning mode and successfully describes the formation of internal transport barriers. Then the dynamical transport equation is introduced to describe the plasma rotation and the radial electric field self-consistently. The formation of edge transport barriers is systematically studied and compared with experimental observations. The possibility of kinetic transport modeling in velocity space is also examined. Finally the modular structure of integrated modeling code for tokamaks and helical systems is discussed. (author)

  17. Generalized Fokker-Planck theory for electron and photon transport in biological tissues: application to radiotherapy.

    Science.gov (United States)

    Olbrant, Edgar; Frank, Martin

    2010-12-01

    In this paper, we study a deterministic method for particle transport in biological tissues. The method is specifically developed for dose calculations in cancer therapy and for radiological imaging. Generalized Fokker-Planck (GFP) theory [Leakeas and Larsen, Nucl. Sci. Eng. 137 (2001), pp. 236-250] has been developed to improve the Fokker-Planck (FP) equation in cases where scattering is forward-peaked and where there is a sufficient amount of large-angle scattering. We compare grid-based numerical solutions to FP and GFP in realistic medical applications. First, electron dose calculations in heterogeneous parts of the human body are performed. Therefore, accurate electron scattering cross sections are included and their incorporation into our model is extensively described. Second, we solve GFP approximations of the radiative transport equation to investigate reflectance and transmittance of light in biological tissues. All results are compared with either Monte Carlo or discrete-ordinates transport solutions.

  18. Ion transport across the biological membrane by computational protein design

    Science.gov (United States)

    Grigoryan, Gevorg

    The cellular membrane is impermeable to most of the chemicals the cell needs to take in or discard to survive. Therefore, transporters-a class of transmembrane proteins tasked with shuttling cargo chemicals in and out of the cell-are essential to all cellular life. From existing crystal structures, we know transporters to be complex machines, exquisitely tuned for specificity and controllability. But how could membrane-bound life have evolved if it needed such complex machines to exist first? To shed light onto this question, we considered the task of designing a transporter de novo. As our guiding principle, we took the ``alternating-access model''-a conceptual mechanism stating that transporters work by rocking between two conformations, each exposing the cargo-binding site to either the intra- or the extra-cellular environment. A computational design framework was developed to encode an anti-parallel four-helix bundle that rocked between two alternative states to orchestrate the movement of Zn(II) ions across the membrane. The ensemble nature of both states was accounted for using a free energy-based approach, and sequences were chosen based on predicted formation of the targeted topology in the membrane and bi-stability. A single sequence was prepared experimentally and shown to function as a Zn(II) transporter in lipid vesicles. Further, transport was specific to Zn(II) ions and several control peptides supported the underlying design principles. This included a mutant designed to retain all properties but with reduced rocking, which showed greatly depressed transport ability. These results suggest that early transporters could have evolved in the context of simple topologies, to be later tuned by evolution for improved properties and controllability. Our study also serves as an important advance in computational protein design, showing the feasibility of designing functional membrane proteins and of tuning conformational landscapes for desired function

  19. Genetics of traffic assignment models for strategic transport planning

    NARCIS (Netherlands)

    Bliemer, M.C.J.; Raadsen, M.P.H.; Brederode, L.J.N.; Bell, M.G.H.; Wismans, Luc Johannes Josephus; Smith, M.J.

    2016-01-01

    This paper presents a review and classification of traffic assignment models for strategic transport planning purposes by using concepts analogous to genetics in biology. Traffic assignment models share the same theoretical framework (DNA), but differ in capability (genes). We argue that all traffic

  20. Modelling of radon transport in porous media

    NARCIS (Netherlands)

    van der Graaf, E.R.; de Meijer, R.J.; Katase, A; Shimo, M

    1998-01-01

    This paper aims to describe the state of the art of modelling radon transport in soil on basis of multiphase radon transport equations. Emphasis is given to methods to obtain a consistent set of input parameters needed For such models. Model-measurement comparisons with the KVI radon transport

  1. Transport Properties for Combustion Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Brown, N.J.; Bastein, L.; Price, P.N.

    2010-02-19

    This review examines current approximations and approaches that underlie the evaluation of transport properties for combustion modeling applications. Discussed in the review are: the intermolecular potential and its descriptive molecular parameters; various approaches to evaluating collision integrals; supporting data required for the evaluation of transport properties; commonly used computer programs for predicting transport properties; the quality of experimental measurements and their importance for validating or rejecting approximations to property estimation; the interpretation of corresponding states; combination rules that yield pair molecular potential parameters for unlike species from like species parameters; and mixture approximations. The insensitivity of transport properties to intermolecular forces is noted, especially the non-uniqueness of the supporting potential parameters. Viscosity experiments of pure substances and binary mixtures measured post 1970 are used to evaluate a number of approximations; the intermediate temperature range 1 < T* < 10, where T* is kT/{var_epsilon}, is emphasized since this is where rich data sets are available. When suitable potential parameters are used, errors in transport property predictions for pure substances and binary mixtures are less than 5 %, when they are calculated using the approaches of Kee et al.; Mason, Kestin, and Uribe; Paul and Warnatz; or Ern and Giovangigli. Recommendations stemming from the review include (1) revisiting the supporting data required by the various computational approaches, and updating the data sets with accurate potential parameters, dipole moments, and polarizabilities; (2) characterizing the range of parameter space over which the fit to experimental data is good, rather than the current practice of reporting only the parameter set that best fits the data; (3) looking for improved combining rules, since existing rules were found to under-predict the viscosity in most cases; (4

  2. Directions in Radiation Transport Modelling

    Directory of Open Access Journals (Sweden)

    P Nicholas Smith

    2016-12-01

    More exciting advances are on the horizon to increase the power of simulation tools. The advent of high performance computers is allowing bigger, higher fidelity models to be created, if the challenges of parallelization and memory management can be met. 3D whole core transport modelling is becoming possible. Uncertainty quantification is improving with large benefits to be gained from more accurate, less pessimistic estimates of uncertainty. Advanced graphical displays allow the user to assimilate and make sense of the vast amounts of data produced by modern modelling tools. Numerical solvers are being developed that use goal-based adaptivity to adjust the nodalisation of the system to provide the optimum scheme to achieve the user requested accuracy on the results, thus removing the need to perform costly convergence studies in space and angle etc. More use is being made of multi-physics methods in which radiation transport is coupled with other phenomena, such as thermal-hydraulics, structural response, fuel performance and/or chemistry in order to better understand their interplay in reactor cores.

  3. The binding, transport and fate of aluminium in biological cells.

    Science.gov (United States)

    Exley, Christopher; Mold, Matthew J

    2015-04-01

    Aluminium is the most abundant metal in the Earth's crust and yet, paradoxically, it has no known biological function. Aluminium is biochemically reactive, it is simply that it is not required for any essential process in extant biota. There is evidence neither of element-specific nor evolutionarily conserved aluminium biochemistry. This means that there are no ligands or chaperones which are specific to its transport, there are no transporters or channels to selectively facilitate its passage across membranes, there are no intracellular storage proteins to aid its cellular homeostasis and there are no pathways which evolved to enable the metabolism and excretion of aluminium. Of course, aluminium is found in every compartment of every cell of every organism, from virus through to Man. Herein we have investigated each of the 'silent' pathways and metabolic events which together constitute a form of aluminium homeostasis in biota, identifying and evaluating as far as is possible what is known and, equally importantly, what is unknown about its uptake, transport, storage and excretion. Copyright © 2014 Elsevier GmbH. All rights reserved.

  4. Biological transport of curium-243 in dairy animals

    International Nuclear Information System (INIS)

    Sutton, W.W.; Patzer, R.G.; Hahn, P.B.; Potter, G.D.

    1979-04-01

    Lactating cows and goats were used to examine the biological transport of curium-243 in dairy animals. After either single oral or intravenous nuclide doses were administered, samples of milk, urine, blood, and feces were taken over a 144-hr priod, and the curium concentrations were determined by gamma counting. Gastrointestinal uptake of curium was estimated to be 0.02 and 0.006% of the oral dose for cows and goats, respectively. The cumulative percentage of oral dose transported to milk and urine was 4.6 x 10 -4 and 1.9 x 10 -3 , respectively, for a cow and 2.7 x 10 -4 and 1.6 x 10 -4 , respectively, for goats. Plasma concentrations of curium decreased rapidly following all intravenous injections. The average percentage of injected curium transferred to milk, urine, and feces was 2, 8, and 1, respectively, for a cow and 2, 5, and 5, respectively, for goats. All animals were sacrificed one week after dosing. Bovine bone retained the greatest fraction of the administered dose and the next highest was the liver. However, in all three intravenously dosed goats the liver contained the greatest amount of curium. Nuclide deposition in bone and liver was essentially equal for two of the three orally dosed goats while the skeleton contained the most curium in the other animal. Comparisons are presented between curium-243 and americium-241 transport in dairy cows

  5. Up-gradient transport in a probabilistic transport model

    DEFF Research Database (Denmark)

    Gavnholt, J.; Juul Rasmussen, J.; Garcia, O.E.

    2005-01-01

    The transport of particles or heat against the driving gradient is studied by employing a probabilistic transport model with a characteristic particle step length that depends on the local concentration or heat gradient. When this gradient is larger than a prescribed critical value, the standard....... These results supplement recent works by van Milligen [Phys. Plasmas 11, 3787 (2004)], which applied Levy distributed step sizes in the case of supercritical gradients to obtain the up-gradient transport. (c) 2005 American Institute of Physics....

  6. Business Models For Transport eBusiness

    OpenAIRE

    Dragan Cisic; Ivan Franciskovic; Ana Peric

    2003-01-01

    In this paper authors are presenting expectations from electronic commerce and its connotations on transport logistics. Based on trends, the relations between the companies in the international transport have to be strengthened using Internet business models. In the paper authors are investigating e-business information models for usage in transport

  7. The particle in the spider's web: transport through biological hydrogels.

    Science.gov (United States)

    Witten, Jacob; Ribbeck, Katharina

    2017-06-22

    Biological hydrogels such as mucus, extracellular matrix, biofilms, and the nuclear pore have diverse functions and compositions, but all act as selectively permeable barriers to the diffusion of particles. Each barrier has a crosslinked polymeric mesh that blocks penetration of large particles such as pathogens, nanotherapeutics, or macromolecules. These polymeric meshes also employ interactive filtering, in which affinity between solutes and the gel matrix controls permeability. Interactive filtering affects the transport of particles of all sizes including peptides, antibiotics, and nanoparticles and in many cases this filtering can be described in terms of the effects of charge and hydrophobicity. The concepts described in this review can guide strategies to exploit or overcome gel barriers, particularly for applications in diagnostics, pharmacology, biomaterials, and drug delivery.

  8. The biological transport of radionuclides in grassland and freshwater ecosystems

    International Nuclear Information System (INIS)

    Rudge, S.A.

    1989-12-01

    This thesis examines the biological transport of radionuclides through terrestrial and aquatic ecosystems, with particular reference to radiocaesium. The semi-natural grassland habitat was located at Drigg, W. Cumbria, contaminated primarily by radioactive fallout, from several sources over the past decade. Advantage was made of the deposition of radionuclides from the Chernobyl reactor incident, which occurred during the early stages of the investigation. The study examined the distribution of radiocaesium for the major components of the grassland ecosystem, within the soil-plant-invertebrate-small mammal food chain. Data concerning temporal fluctuation of radionuclide transfer factors between food chain components are presented. The final section examines the spatial distribution of radiocaesium in sediment and the freshwater eel (Anguilla anguilla) in a small stream contaminated by radioactive effluent. The relationship between activity levels in eels and the sediments in which they rest and forage was investigated. Factors influencing uptake of radiocaesium in freshwater fish were also examined. (author)

  9. Use of Models in Urban Transportation Planning

    Science.gov (United States)

    1973-04-01

    The report describes the most commonly used models in urban transportation planning. A background on urban transportation planning is given including changes in planning objectives and the effects of Federal legislation. General concepts and problems...

  10. The Organic Anion Transporter (OAT) Family: A Systems Biology Perspective

    Science.gov (United States)

    Nigam, Sanjay K.; Bush, Kevin T.; Martovetsky, Gleb; Ahn, Sun-Young; Liu, Henry C.; Richard, Erin; Bhatnagar, Vibha; Wu, Wei

    2015-01-01

    The organic anion transporter (OAT) subfamily, which constitutes roughly half of the SLC22 (solute carrier 22) transporter family, has received a great deal of attention because of its role in handling of common drugs (antibiotics, antivirals, diuretics, nonsteroidal anti-inflammatory drugs), toxins (mercury, aristolochic acid), and nutrients (vitamins, flavonoids). Oats are expressed in many tissues, including kidney, liver, choroid plexus, olfactory mucosa, brain, retina, and placenta. Recent metabolomics and microarray data from Oat1 [Slc22a6, originally identified as NKT (novel kidney transporter)] and Oat3 (Slc22a8) knockouts, as well as systems biology studies, indicate that this pathway plays a central role in the metabolism and handling of gut microbiome metabolites as well as putative uremic toxins of kidney disease. Nuclear receptors and other transcription factors, such as Hnf4α and Hnf1α, appear to regulate the expression of certain Oats in conjunction with phase I and phase II drug metabolizing enzymes. Some Oats have a strong selectivity for particular signaling molecules, including cyclic nucleotides, conjugated sex steroids, odorants, uric acid, and prostaglandins and/or their metabolites. According to the “Remote Sensing and Signaling Hypothesis,” which is elaborated in detail here, Oats may function in remote interorgan communication by regulating levels of signaling molecules and key metabolites in tissues and body fluids. Oats may also play a major role in interorganismal communication (via movement of small molecules across the intestine, placental barrier, into breast milk, and volatile odorants into the urine). The role of various Oat isoforms in systems physiology appears quite complex, and their ramifications are discussed in the context of remote sensing and signaling. PMID:25540139

  11. Modelling of Transport Projects Uncertainties

    DEFF Research Database (Denmark)

    Salling, Kim Bang; Leleur, Steen

    2009-01-01

    This paper proposes a new way of handling the uncertainties present in transport decision making based on infrastructure appraisals. The paper suggests to combine the principle of Optimism Bias, which depicts the historical tendency of overestimating transport related benefits and underestimating......-based graphs which function as risk-related decision support for the appraised transport infrastructure project....

  12. Integrated modelling of physical, chemical and biological weather

    DEFF Research Database (Denmark)

    Kurganskiy, Alexander

    forecasts. The BC modelling study was performed for a modelling domain covering most of the Northern Hemisphere with focus on the EU and Arctic regions. Verification of BC concentrations against observations showed a good agreement for the EU air quality measurement sites. However, the Arctic region turned......Integrated modelling of physical, chemical and biological weather has been widely considered during the recent decades. Such modelling includes interactions of atmospheric physics and chemical/biological aerosol concentrations. Emitted aerosols are subject to atmospheric transport, dispersion...... and deposition, but in turn they impact the radiation as well as cloud and precipitation formation. The present study focuses on birch pollen modelling as well as on physical and chemical weather with emphasis on black carbon (BC) aerosol modelling. The Enviro-HIRLAM model has been used for the study...

  13. Transport and characterization of ambient biological aerosol near Laurel, MD

    Science.gov (United States)

    Santarpia, J. L.; Cunningham, D.; Gilberry, J.; Kim, S.; Smith, E. E.; Ratnesar-Shumate, S.; Quizon, J.

    2010-09-01

    Bacterial aerosol have been observed and studied in the ambient environment since the mid nineteenth century. These studies have sought to provide a better understanding of the diversity, variability and factors that control the biological aerosol population. In this study, we show comparisons between diversity of culturable bacteria and fungi, using culture and clinical biochemical tests, and 16S rRNA diversity using Affymetrix PhyloChips. Comparing the culturable fraction and surveying the total 16S rRNA of each sample provides a comprehensive look at the bacterial population studied and allows comparison with previous studies. Thirty-six hour back-trajectories of the air parcels sampled, over the two day period beginning 4 November 2008, provide information on the sources of aerosol sampled on the campus of Johns Hopkins University Applied Physics Laboratory in Laurel, MD. This study indicates that back-trajectory modeling of air parcels may provide insights into the observed diversity of biological aerosol.

  14. Piecewise deterministic processes in biological models

    CERN Document Server

    Rudnicki, Ryszard

    2017-01-01

    This book presents a concise introduction to piecewise deterministic Markov processes (PDMPs), with particular emphasis on their applications to biological models. Further, it presents examples of biological phenomena, such as gene activity and population growth, where different types of PDMPs appear: continuous time Markov chains, deterministic processes with jumps, processes with switching dynamics, and point processes. Subsequent chapters present the necessary tools from the theory of stochastic processes and semigroups of linear operators, as well as theoretical results concerning the long-time behaviour of stochastic semigroups induced by PDMPs and their applications to biological models. As such, the book offers a valuable resource for mathematicians and biologists alike. The first group will find new biological models that lead to interesting and often new mathematical questions, while the second can observe how to include seemingly disparate biological processes into a unified mathematical theory, and...

  15. Stochastic modelling of dynamical systems in biology

    NARCIS (Netherlands)

    Pellin, Danilo

    2017-01-01

    In this thesis two relevant biological problems will be addressed from a statistical modelling perspective. The first regards the study of hematopoiesis, a still not well understood biological process rarely observable in humans due to technical and ethical reasons. Hematopoiesis is responsible for

  16. SATURATED ZONE FLOW AND TRANSPORT MODEL ABSTRACTION

    International Nuclear Information System (INIS)

    B.W. ARNOLD

    2004-01-01

    The purpose of the saturated zone (SZ) flow and transport model abstraction task is to provide radionuclide-transport simulation results for use in the total system performance assessment (TSPA) for license application (LA) calculations. This task includes assessment of uncertainty in parameters that pertain to both groundwater flow and radionuclide transport in the models used for this purpose. This model report documents the following: (1) The SZ transport abstraction model, which consists of a set of radionuclide breakthrough curves at the accessible environment for use in the TSPA-LA simulations of radionuclide releases into the biosphere. These radionuclide breakthrough curves contain information on radionuclide-transport times through the SZ. (2) The SZ one-dimensional (I-D) transport model, which is incorporated in the TSPA-LA model to simulate the transport, decay, and ingrowth of radionuclide decay chains in the SZ. (3) The analysis of uncertainty in groundwater-flow and radionuclide-transport input parameters for the SZ transport abstraction model and the SZ 1-D transport model. (4) The analysis of the background concentration of alpha-emitting species in the groundwater of the SZ

  17. Logistics and Transport - a conceptual model

    DEFF Research Database (Denmark)

    Jespersen, Per Homann; Drewes, Lise

    2004-01-01

    This paper describes how the freight transport sector is influenced by logistical principles of production and distribution. It introduces new ways of understanding freight transport as an integrated part of the changing trends of mobility. By introducing a conceptual model for understanding...... the interaction between logistics and transport, it points at ways to over-come inherent methodological difficulties when studying this relation...

  18. RADIONUCLIDE TRANSPORT MODELS UNDER AMBIENT CONDITIONS

    Energy Technology Data Exchange (ETDEWEB)

    S. Magnuson

    2004-11-01

    The purpose of this model report is to document the unsaturated zone (UZ) radionuclide transport model, which evaluates, by means of three-dimensional numerical models, the transport of radioactive solutes and colloids in the UZ, under ambient conditions, from the repository horizon to the water table at Yucca Mountain, Nevada.

  19. Modelling of Transport Projects Uncertainties

    DEFF Research Database (Denmark)

    Salling, Kim Bang; Leleur, Steen

    2012-01-01

    This paper proposes a new way of handling the uncertainties present in transport decision making based on infrastructure appraisals. The paper suggests to combine the principle of Optimism Bias, which depicts the historical tendency of overestimating transport related benefits and underestimating......-based graphs which functions as risk-related decision support for the appraised transport infrastructure project. The presentation of RSF is demonstrated by using an appraisal case concerning a new airfield in the capital of Greenland, Nuuk....

  20. Instance-Based Generative Biological Shape Modeling.

    Science.gov (United States)

    Peng, Tao; Wang, Wei; Rohde, Gustavo K; Murphy, Robert F

    2009-01-01

    Biological shape modeling is an essential task that is required for systems biology efforts to simulate complex cell behaviors. Statistical learning methods have been used to build generative shape models based on reconstructive shape parameters extracted from microscope image collections. However, such parametric modeling approaches are usually limited to simple shapes and easily-modeled parameter distributions. Moreover, to maximize the reconstruction accuracy, significant effort is required to design models for specific datasets or patterns. We have therefore developed an instance-based approach to model biological shapes within a shape space built upon diffeomorphic measurement. We also designed a recursive interpolation algorithm to probabilistically synthesize new shape instances using the shape space model and the original instances. The method is quite generalizable and therefore can be applied to most nuclear, cell and protein object shapes, in both 2D and 3D.

  1. A Sediment Transport Model for Sewers

    DEFF Research Database (Denmark)

    Mark, Ole; Larsson, Johan; Larsen, Torben

    1993-01-01

    This paper describes a mathematical model for transport processes in sewers. The model consists of three sub models, a surface model for the description of the buildup and the washoff of sediment particles from the surface area, a morphological model and an advection-dispersion model. The model...

  2. Integrating interactive computational modeling in biology curricula.

    Directory of Open Access Journals (Sweden)

    Tomáš Helikar

    2015-03-01

    Full Text Available While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

  3. Integrating interactive computational modeling in biology curricula.

    Science.gov (United States)

    Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

    2015-03-01

    While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

  4. Modelling collagen diseases: STRUCTURAL BIOLOGY

    OpenAIRE

    Brodsky, Barbara; Baum, Jean

    2008-01-01

    Mutations in collagen lead to hereditary disorders such as brittle-bone disease. Peptide models for aberrant collagens are beginning to clarify how these amino-acid replacements lead to clinical problems.

  5. Setting Parameters for Biological Models With ANIMO

    NARCIS (Netherlands)

    Schivo, Stefano; Scholma, Jetse; Karperien, Hermanus Bernardus Johannes; Post, Janine Nicole; van de Pol, Jan Cornelis; Langerak, Romanus; André, Étienne; Frehse, Goran

    2014-01-01

    ANIMO (Analysis of Networks with Interactive MOdeling) is a software for modeling biological networks, such as e.g. signaling, metabolic or gene networks. An ANIMO model is essentially the sum of a network topology and a number of interaction parameters. The topology describes the interactions

  6. Ecosystem element transport model for Lake Eckarfjaerden

    Energy Technology Data Exchange (ETDEWEB)

    Konovalenko, L.; Bradshaw, C. [The Department of Ecology, Environment and Plant Sciences, Stockholm University (Sweden); Andersson, E.; Kautsky, U. [Swedish Nuclear Fuel and Waste Management Co. - SKB (Sweden)

    2014-07-01

    The ecosystem transport model of elements was developed for Lake Eckarfjaerden located in the Forsmark area in Sweden. Forsmark has currently a low level repository (SFR) and a repository for spent fuel is planned. A large number of data collected during site-investigation program 2002-2009 for planning the repository were available for the creation of the compartment model based on carbon circulation, physical and biological processes (e.g. primary production, consumption, respiration). The model is site-specific in the sense that the food web model is adapted to the actual food web at the site, and most estimates of biomass and metabolic rates for the organisms and meteorological data originate from site data. The functional organism groups of Lake Eckarfjaerden were considered as separate compartments: bacterio-plankton, benthic bacteria, macro-algae, phytoplankton, zooplankton, fish, benthic fauna. Two functional groups of bacteria were taken into account for the reason that they have the highest biomass of all functional groups during the winter, comprising 36% of the total biomass. Effects of ecological parameters, such as bacteria and algae biomass, on redistribution of a hypothetical radionuclide release in the lake were examined. The ecosystem model was used to estimate the environmental transfer of several elements (U, Th, Ra) and their isotopes (U-238, U-234,Th-232, Ra-226) to various aquatic organisms in the lake, using element-specific distribution coefficients for suspended particle and sediment. Results of chemical analyses of the water, sediment and biota were used for model validation. The model gives estimates of concentration factors for fish based on modelling rather on in situ measurement, which reduces the uncertainties for many radionuclides with scarce of data. Document available in abstract form only. (authors)

  7. Two-Dimensional Subsurface Flow, Fate and Transport of Microbes and Chemicals (2DFATMIC) Model

    Science.gov (United States)

    This model simulates subsurface flow, fate, and transport of contaminants that are undergoing chemical or biological transformations. This model is applicable to transient conditions in both saturated and unsaturated zones.

  8. Three-Dimensional Subsurface Flow, Fate and Transport of Microbes and Chemicals (3DFATMIC) Model

    Science.gov (United States)

    This model simulates subsurface flow, fate and transport of contaminants that are undergoing chemical or biological transformations. The model is applicable to transient conditions in both saturated and unsaturated zones.

  9. Structured population models in biology and epidemiology

    CERN Document Server

    Ruan, Shigui

    2008-01-01

    This book consists of six chapters written by leading researchers in mathematical biology. These chapters present recent and important developments in the study of structured population models in biology and epidemiology. Topics include population models structured by age, size, and spatial position; size-structured models for metapopulations, macroparasitc diseases, and prion proliferation; models for transmission of microparasites between host populations living on non-coincident spatial domains; spatiotemporal patterns of disease spread; method of aggregation of variables in population dynamics; and biofilm models. It is suitable as a textbook for a mathematical biology course or a summer school at the advanced undergraduate and graduate level. It can also serve as a reference book for researchers looking for either interesting and specific problems to work on or useful techniques and discussions of some particular problems.

  10. The european Trans-Tools transport model

    NARCIS (Netherlands)

    Rooijen, T. van; Burgess, A.

    2008-01-01

    The paper presents the use of ArcGIS in the Transtools Transport Model, TRANS-TOOLS, created by an international consortium for the European Commission. The model describe passenger as well as freight transport in Europe with all medium and long distance modes (cars, vans, trucks, train, inland

  11. A Mercury Model of Atmospheric Transport

    Energy Technology Data Exchange (ETDEWEB)

    Christensen, Alex B. [Oregon State Univ., Corvallis, OR (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Chodash, Perry A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Procassini, R. J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2018-01-19

    Using the particle transport code Mercury, accurate models were built of the two sources used in Operation BREN, a series of radiation experiments performed by the United States during the 1960s. In the future, these models will be used to validate Mercury’s ability to simulate atmospheric transport.

  12. Dileptons from transport and hydrodynamical models

    International Nuclear Information System (INIS)

    Huovinen, P.; Koch, V.

    2000-01-01

    Transport and hydrodynamical models used to describe the expansion stage of a heavy-ion collision at the CERN SPS give different dilepton spectrum even if they are tuned to reproduce the observed hadron spectra. To understand the origin of this difference we compare the dilepton emission from transport and hydrodynamical models using similar initial states in both models. We find that the requirement of pion number conservation in a hydrodynamical model does not change the dilepton emission. Also the mass distribution from the transport model indicates faster cooling and longer lifetime of the fireball

  13. Unified data model for biological data

    International Nuclear Information System (INIS)

    Idrees, M.

    2014-01-01

    A data model empowers us to store, retrieve and manipulate data in a unified way. We consider the biological data consists of DNA (De-Oxyribonucleic Acid), RNA (Ribonucleic Acid) and protein structures. In our Bioinformatics Lab (Bioinformatics Lab, Alkhawarizmi Institute of Computer Science, University of Engineering and Technology, Lahore, Pakistan), we have already proposed two data models for DNA and protein structures individually. In this paper, we propose a unified data model by using the data models of TOS (Temporal Object Oriented System) after making some necessary modifications to this data model and our already proposed the two data models. This proposed unified data model can be used for the modeling and maintaining the biological data (i.e. DNA, RNA and protein structures), in a single unified way. (author)

  14. Bridging physics and biology teaching through modeling

    Science.gov (United States)

    Hoskinson, Anne-Marie; Couch, Brian A.; Zwickl, Benjamin M.; Hinko, Kathleen A.; Caballero, Marcos D.

    2014-05-01

    As the frontiers of biology become increasingly interdisciplinary, the physics education community has engaged in ongoing efforts to make physics classes more relevant to life science majors. These efforts are complicated by the many apparent differences between these fields, including the types of systems that each studies, the behavior of those systems, the kinds of measurements that each makes, and the role of mathematics in each field. Nonetheless, physics and biology are both sciences that rely on observations and measurements to construct models of the natural world. In this article, we propose that efforts to bridge the teaching of these two disciplines must emphasize shared scientific practices, particularly scientific modeling. We define modeling using language common to both disciplines and highlight how an understanding of the modeling process can help reconcile apparent differences between the teaching of physics and biology. We elaborate on how models can be used for explanatory, predictive, and functional purposes and present common models from each discipline demonstrating key modeling principles. By framing interdisciplinary teaching in the context of modeling, we aim to bridge physics and biology teaching and to equip students with modeling competencies applicable in any scientific discipline.

  15. Optimal transportation networks models and theory

    CERN Document Server

    Bernot, Marc; Morel, Jean-Michel

    2009-01-01

    The transportation problem can be formalized as the problem of finding the optimal way to transport a given measure into another with the same mass. In contrast to the Monge-Kantorovitch problem, recent approaches model the branched structure of such supply networks as minima of an energy functional whose essential feature is to favour wide roads. Such a branched structure is observable in ground transportation networks, in draining and irrigation systems, in electrical power supply systems and in natural counterparts such as blood vessels or the branches of trees. These lectures provide mathematical proof of several existence, structure and regularity properties empirically observed in transportation networks. The link with previous discrete physical models of irrigation and erosion models in geomorphology and with discrete telecommunication and transportation models is discussed. It will be mathematically proven that the majority fit in the simple model sketched in this volume.

  16. Two-point model for divertor transport

    International Nuclear Information System (INIS)

    Galambos, J.D.; Peng, Y.K.M.

    1984-04-01

    Plasma transport along divertor field lines was investigated using a two-point model. This treatment requires considerably less effort to find solutions to the transport equations than previously used one-dimensional (1-D) models and is useful for studying general trends. It also can be a valuable tool for benchmarking more sophisticated models. The model was used to investigate the possibility of operating in the so-called high density, low temperature regime

  17. Laser interaction with biological material mathematical modeling

    CERN Document Server

    Kulikov, Kirill

    2014-01-01

    This book covers the principles of laser interaction with biological cells and tissues of varying degrees of organization. The problems of biomedical diagnostics are considered. Scattering of laser irradiation of blood cells is modeled for biological structures (dermis, epidermis, vascular plexus). An analytic theory is provided which is based on solving the wave equation for the electromagnetic field. It allows the accurate analysis of interference effects arising from the partial superposition of scattered waves. Treated topics of mathematical modeling are: optical characterization of biological tissue with large-scale and small-scale inhomogeneities in the layers, heating blood vessel under laser irradiation incident on the outer surface of the skin and thermo-chemical denaturation of biological structures at the example of human skin.

  18. Introduction to stochastic models in biology

    DEFF Research Database (Denmark)

    Ditlevsen, Susanne; Samson, Adeline

    2013-01-01

    This chapter is concerned with continuous time processes, which are often modeled as a system of ordinary differential equations (ODEs). These models assume that the observed dynamics are driven exclusively by internal, deterministic mechanisms. However, real biological systems will always be exp...

  19. Notions of similarity for computational biology models

    KAUST Repository

    Waltemath, Dagmar

    2016-03-21

    Computational models used in biology are rapidly increasing in complexity, size, and numbers. To build such large models, researchers need to rely on software tools for model retrieval, model combination, and version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of similarity may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here, we introduce a general notion of quantitative model similarities, survey the use of existing model comparison methods in model building and management, and discuss potential applications of model comparison. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on different model aspects. Potentially relevant aspects of a model comprise its references to biological entities, network structure, mathematical equations and parameters, and dynamic behaviour. Future similarity measures could combine these model aspects in flexible, problem-specific ways in order to mimic users\\' intuition about model similarity, and to support complex model searches in databases.

  20. Stochastic dynamics modeling solute transport in porous media modeling solute transport in porous media

    CERN Document Server

    Kulasiri, Don

    2002-01-01

    Most of the natural and biological phenomena such as solute transport in porous media exhibit variability which can not be modeled by using deterministic approaches. There is evidence in natural phenomena to suggest that some of the observations can not be explained by using the models which give deterministic solutions. Stochastic processes have a rich repository of objects which can be used to express the randomness inherent in the system and the evolution of the system over time. The attractiveness of the stochastic differential equations (SDE) and stochastic partial differential equations (SPDE) come from the fact that we can integrate the variability of the system along with the scientific knowledge pertaining to the system. One of the aims of this book is to explaim some useufl concepts in stochastic dynamics so that the scientists and engineers with a background in undergraduate differential calculus could appreciate the applicability and appropriateness of these developments in mathematics. The ideas ...

  1. Coupled transport/hyperelastic model for nastic materials

    Science.gov (United States)

    Homison, Chris; Weiland, Lisa M.

    2006-03-01

    Nastic materials are high energy density active materials that mimic processes used in the plant kingdom to produce large deformations through the conversion of chemical energy. These materials utilize the controlled transport of charge and fluid across a selectively-permeable membrane to achieve bulk deformation in a process referred to in the plant kingdom as nastic movements. The nastic material being developed consists of synthetic membranes containing biological ion pumps, ion channels, and ion exchangers surrounding fluid-filled cavities embedded within a polymer matrix. In this paper the formulation of a biological transport model and its coupling with a hyperelastic finite element model of the polymer matrix is discussed. The transport model includes contributions from ion pumps, ion exchangers, and solvent flux. This work will form the basis for a feedback loop in material synthesis efforts. The goal of these studies is to determine the relative importance of the various parameters associated with both the polymer matrix and the biological transport components.

  2. Setting Parameters for Biological Models With ANIMO

    Directory of Open Access Journals (Sweden)

    Stefano Schivo

    2014-03-01

    Full Text Available ANIMO (Analysis of Networks with Interactive MOdeling is a software for modeling biological networks, such as e.g. signaling, metabolic or gene networks. An ANIMO model is essentially the sum of a network topology and a number of interaction parameters. The topology describes the interactions between biological entities in form of a graph, while the parameters determine the speed of occurrence of such interactions. When a mismatch is observed between the behavior of an ANIMO model and experimental data, we want to update the model so that it explains the new data. In general, the topology of a model can be expanded with new (known or hypothetical nodes, and enables it to match experimental data. However, the unrestrained addition of new parts to a model causes two problems: models can become too complex too fast, to the point of being intractable, and too many parts marked as "hypothetical" or "not known" make a model unrealistic. Even if changing the topology is normally the easier task, these problems push us to try a better parameter fit as a first step, and resort to modifying the model topology only as a last resource. In this paper we show the support added in ANIMO to ease the task of expanding the knowledge on biological networks, concentrating in particular on the parameter settings.

  3. Multiple mode model of tokamak transport

    International Nuclear Information System (INIS)

    Singer, C.E.; Ghanem, E.S.; Bateman, G.; Stotler, D.P.

    1989-07-01

    Theoretical models for radical transport of energy and particles in tokamaks due to drift waves, rippling modes, and resistive ballooning modes have been combined in a predictive transport code. The resulting unified model has been used to simulate low confinement mode (L-mode) energy confinement scalings. Dependence of global energy confinement on electron density for the resulting model is also described. 26 refs., 1 fig., 2 tabs

  4. Multiple mode model of tokamak transport

    Energy Technology Data Exchange (ETDEWEB)

    Singer, C.E.; Ghanem, E.S.; Bateman, G.; Stotler, D.P.

    1989-07-01

    Theoretical models for radical transport of energy and particles in tokamaks due to drift waves, rippling modes, and resistive ballooning modes have been combined in a predictive transport code. The resulting unified model has been used to simulate low confinement mode (L-mode) energy confinement scalings. Dependence of global energy confinement on electron density for the resulting model is also described. 26 refs., 1 fig., 2 tabs.

  5. Transport phenomena and kinetic theory applications to gases, semiconductors, photons, and biological systems

    CERN Document Server

    Gabetta, Ester

    2007-01-01

    The study of kinetic equations related to gases, semiconductors, photons, traffic flow, and other systems has developed rapidly in recent years because of its role as a mathematical tool in many applications in areas such as engineering, meteorology, biology, chemistry, materials science, nanotechnology, and pharmacy. Written by leading specialists in their respective fields, this book presents an overview of recent developments in the field of mathematical kinetic theory with a focus on modeling complex systems, emphasizing both mathematical properties and their physical meaning. The overall presentation covers not only modeling aspects and qualitative analysis of mathematical problems, but also inverse problems, which lead to a detailed assessment of models in connection with their applications, and to computational problems, which lead to an effective link of models to the analysis of real-world systems. "Transport Phenomena and Kinetic Theory" is an excellent self-study reference for graduate students, re...

  6. Stochastic resonance in biological nonlinear evolution models

    Science.gov (United States)

    Dunkel, Jörn; Hilbert, Stefan; Schimansky-Geier, Lutz; Hänggi, Peter

    2004-05-01

    We investigate stochastic resonance in the nonlinear, one-dimensional Fisher-Eigen model (FEM), which represents an archetypal model for biological evolution based on a global coupling scheme. In doing so we consider different periodically driven fitness functions which govern the evolution of a biological phenotype population. For the case of a simple harmonic fitness function we are able to derive the exact analytic solution for the asymptotic probability density. A distinct feature of this solution is a phase lag between the driving signal and the linear response of the system. Furthermore, for more complex systems a general perturbation theory (linear response approximation) is put forward. Using the latter approach, we investigate stochastic resonance in terms of the spectral amplification measure for a quadratic, a quartic single-peaked, and for a bistable fitness function. Our analytical results are also compared with those of detailed numerical simulations. Our findings vindicate that stochastic resonance does occur in these nonlinear, globally coupled biological systems.

  7. Concept Layout Model of Transportation Terminals

    Directory of Open Access Journals (Sweden)

    Li-ya Yao

    2012-01-01

    Full Text Available Transportation terminal is the key node in transport systems. Efficient terminals can improve operation of passenger transportation networks, adjust the layout of public transportation networks, provide a passenger guidance system, and regulate the development of commercial forms, as well as optimize the assembly and distribution of modern logistic modes, among others. This study aims to clarify the relationship between the function and the structure of transportation terminals and establish the function layout design. The mapping mechanism of demand, function, and structure was analyzed, and a quantitative relationship between function and structure was obtained from a design perspective. Passenger demand and terminal structure were decomposed into several demand units and structural elements following the principle of reverse engineering. The relationship maps between these two kinds of elements were then analyzed. Function-oriented concept layout model of transportation terminals was established using the previous method. Thus, a technique in planning and design of transportation structures was proposed. Meaningful results were obtained from the optimization of transportation terminal facilities, which guide the design of the functional layout of transportation terminals and improve the development of urban passenger transportation systems.

  8. Prospective Tests on Biological Models of Acupuncture

    Directory of Open Access Journals (Sweden)

    Charles Shang

    2009-01-01

    Full Text Available The biological effects of acupuncture include the regulation of a variety of neurohumoral factors and growth control factors. In science, models or hypotheses with confirmed predictions are considered more convincing than models solely based on retrospective explanations. Literature review showed that two biological models of acupuncture have been prospectively tested with independently confirmed predictions: The neurophysiology model on the long-term effects of acupuncture emphasizes the trophic and anti-inflammatory effects of acupuncture. Its prediction on the peripheral effect of endorphin in acupuncture has been confirmed. The growth control model encompasses the neurophysiology model and suggests that a macroscopic growth control system originates from a network of organizers in embryogenesis. The activity of the growth control system is important in the formation, maintenance and regulation of all the physiological systems. Several phenomena of acupuncture such as the distribution of auricular acupuncture points, the long-term effects of acupuncture and the effect of multimodal non-specific stimulation at acupuncture points are consistent with the growth control model. The following predictions of the growth control model have been independently confirmed by research results in both acupuncture and conventional biomedical sciences: (i Acupuncture has extensive growth control effects. (ii Singular point and separatrix exist in morphogenesis. (iii Organizers have high electric conductance, high current density and high density of gap junctions. (iv A high density of gap junctions is distributed as separatrices or boundaries at body surface after early embryogenesis. (v Many acupuncture points are located at transition points or boundaries between different body domains or muscles, coinciding with the connective tissue planes. (vi Some morphogens and organizers continue to function after embryogenesis. Current acupuncture research suggests a

  9. Modelling biological pathway dynamics with Timed Automata

    NARCIS (Netherlands)

    Schivo, Stefano; Scholma, Jetse; Urquidi Camacho, R.A.; Wanders, B.; van der Vet, P.E.; Karperien, Hermanus Bernardus Johannes; Langerak, Romanus; van de Pol, Jan Cornelis; Post, Janine Nicole

    2012-01-01

    When analysing complex interaction networks occurring in biological cells, a biologist needs computational support in order to understand the effects of signalling molecules (e.g. growth factors, drugs). ANIMO (Analysis of Networks with Interactive MOdelling) is a tool that allows the user to create

  10. Highway and interline transportation routing models

    International Nuclear Information System (INIS)

    Joy, D.S.; Johnson, P.E.

    1994-01-01

    The potential impacts associated with the transportation of hazardous materials are important issues to shippers, carriers, and the general public. Since transportation routes are a central characteristic in most of these issues, the prediction of likely routes is the first step toward the resolution of these issues. In addition, US Department of Transportation requirements (HM-164) mandate specific routes for shipments of highway controlled quantities of radioactive materials. In response to these needs, two routing models have been developed at Oak Ridge National Laboratory under the sponsorship of the U.S. Department of Energy (DOE). These models have been designated by DOE's Office of Environmental Restoration and Waste Management, Transportation Management Division (DOE/EM) as the official DOE routing models. Both models, HIGHWAY and INTERLINE, are described

  11. Multimodal transportation best practices and model element.

    Science.gov (United States)

    2014-06-01

    This report provides guidance in developing a multimodal transportation element of a local government comprehensive : plan. Two model elements were developed to address differences in statutory requirements for communities of different : sizes and pl...

  12. NODA for EPA's Updated Ozone Transport Modeling

    Science.gov (United States)

    Find EPA's NODA for the Updated Ozone Transport Modeling Data for the 2008 Ozone National Ambient Air Quality Standard (NAAQS) along with the ExitExtension of Public Comment Period on CSAPR for the 2008 NAAQS.

  13. Agent-based modelling in synthetic biology.

    Science.gov (United States)

    Gorochowski, Thomas E

    2016-11-30

    Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions. © 2016 The Author(s).

  14. Mathematical modeling plasma transport in tokamaks

    International Nuclear Information System (INIS)

    Quiang, Ji

    1995-01-01

    In this work, the author applied a systematic calibration, validation and application procedure based on the methodology of mathematical modeling to international thermonuclear experimental reactor (ITER) ignition studies. The multi-mode plasma transport model used here includes a linear combination of drift wave branch and ballooning branch instabilities with two a priori uncertain constants to account for anomalous plasma transport in tokamaks. A Bayesian parameter estimation method is used including experimental calibration error/model offsets and error bar rescaling factors to determine the two uncertain constants in the transport model with quantitative confidence level estimates for the calibrated parameters, which gives two saturation levels of instabilities. This method is first tested using a gyroBohm multi-mode transport model with a pair of DIII-D discharge experimental data, and then applied to calibrating a nominal multi-mode transport model against a broad database using twelve discharges from seven different tokamaks. The calibrated transport model is then validated on five discharges from JT-60 with no adjustable constants. The results are in a good agreement with experimental data. Finally, the resulting class of multi-mode tokamak plasma transport models is applied to the transport analysis of the ignition probability in a next generation machine, ITER. A reference simulation of basic ITER engineering design activity (EDA) parameters shows that a self-sustained thermonuclear burn with 1.5 GW output power can be achieved provided that impurity control makes radiative losses sufficiently small at an average plasma density of 1.2 X 10 20 /m 3 with 50 MW auxiliary heating. The ignition probability of ITER for the EDA parameters, can be formally as high as 99.9% in the present context. The same probability for concept design activity (CDA) parameters of ITER, which has smaller size and lower current, is only 62.6%

  15. Modeling nonspecific interactions at biological interfaces

    Science.gov (United States)

    White, Andrew D.

    Difficulties in applied biomaterials often arise from the complexities of interactions in biological environments. These interactions can be broadly broken into two categories: those which are important to function (strong binding to a single target) and those which are detrimental to function (weak binding to many targets). These will be referred to as specific and nonspecific interactions, respectively. Nonspecific interactions have been central to failures of biomaterials, sensors, and surface coatings in harsh biological environments. There is little modeling work on studying nonspecific interactions. Modeling all possible nonspecific interactions within a biological system is difficult, yet there are ways to both indirectly model nonspecific interactions and directly model many interactions using machine-learning. This research utilizes bioinformatics, phenomenological modeling, molecular simulations, experiments, and stochastic modeling to study nonspecific interactions. These techniques are used to study the hydration molecules which resist nonspecific interactions, the formation of salt bridges, the chemistry of protein surfaces, nonspecific stabilization of proteins in molecular chaperones, and analysis of high-throughput screening experiments. The common aspect for these systems is that nonspecific interactions are more important than specific interactions. Studying these disparate systems has created a set of principles for resisting nonspecific interactions which have been experimentally demonstrated with the creation and testing of novel materials which resist nonspecific interactions.

  16. Statistical Model Checking for Biological Systems

    DEFF Research Database (Denmark)

    David, Alexandre; Larsen, Kim Guldstrand; Legay, Axel

    2014-01-01

    Statistical Model Checking (SMC) is a highly scalable simulation-based verification approach for testing and estimating the probability that a stochastic system satisfies a given linear temporal property. The technique has been applied to (discrete and continuous time) Markov chains, stochastic...... timed automata and most recently hybrid systems using the tool Uppaal SMC. In this paper we enable the application of SMC to complex biological systems, by combining Uppaal SMC with ANIMO, a plugin of the tool Cytoscape used by biologists, as well as with SimBiology®, a plugin of Matlab to simulate...

  17. K+ transport in plants: physiology and molecular biology.

    Science.gov (United States)

    Szczerba, Mark W; Britto, Dev T; Kronzucker, Herbert J

    2009-03-15

    Potassium (K(+)) is an essential nutrient and the most abundant cation in plant cells. Plants have a wide variety of transport systems for K(+) acquisition, catalyzing K(+) uptake across a wide spectrum of external concentrations, and mediating K(+) movement within the plant as well as its efflux into the environment. K(+) transport responds to variations in external K(+) supply, to the presence of other ions in the root environment, and to a range of plant stresses, via Ca(2+) signaling cascades and regulatory proteins. This review will summarize the molecular identities of known K(+) transporters, and examine how this information supports physiological investigations of K(+) transport and studies of plant stress responses in a changing environment.

  18. Spatial Cell Biology : Dissecting and directing intracellular transport mechanisms

    NARCIS (Netherlands)

    Adrian, M.

    2017-01-01

    Cellular compartmentalization and intracellular transport mechanisms are important to establish and maintain the spatial organisation of proteins and organelles needed to ensure proper cellular functioning. Especially in polarized cells like neurons, the proper distribution of proteins into the

  19. Institute for Multiscale Modeling of Biological Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Paulaitis, Michael E; Garcia-Moreno, Bertrand; Lenhoff, Abraham

    2009-12-26

    The Institute for Multiscale Modeling of Biological Interactions (IMMBI) has two primary goals: Foster interdisciplinary collaborations among faculty and their research laboratories that will lead to novel applications of multiscale simulation and modeling methods in the biological sciences and engineering; and Building on the unique biophysical/biology-based engineering foundations of the participating faculty, train scientists and engineers to apply computational methods that collectively span multiple time and length scales of biological organization. The success of IMMBI will be defined by the following: Size and quality of the applicant pool for pre-doctoral and post-doctoral fellows; Academic performance; Quality of the pre-doctoral and post-doctoral research; Impact of the research broadly and to the DOE (ASCR program) mission; Distinction of the next career step for pre-doctoral and post-doctoral fellows; and Faculty collaborations that result from IMMBI activities. Specific details about accomplishments during the three years of DOE support for IMMBI have been documented in Annual Progress Reports (April 2005, June 2006, and March 2007) and a Report for a National Academy of Sciences Review (October 2005) that were submitted to DOE on the dates indicated. An overview of these accomplishments is provided.

  20. Modeling drug- and chemical- induced hepatotoxicity with systems biology approaches

    Directory of Open Access Journals (Sweden)

    Sudin eBhattacharya

    2012-12-01

    Full Text Available We provide an overview of computational systems biology approaches as applied to the study of chemical- and drug-induced toxicity. The concept of ‘toxicity pathways’ is described in the context of the 2007 US National Academies of Science report, Toxicity testing in the 21st Century: A Vision and A Strategy. Pathway mapping and modeling based on network biology concepts are a key component of the vision laid out in this report for a more biologically-based analysis of dose-response behavior and the safety of chemicals and drugs. We focus on toxicity of the liver (hepatotoxicity – a complex phenotypic response with contributions from a number of different cell types and biological processes. We describe three case studies of complementary multi-scale computational modeling approaches to understand perturbation of toxicity pathways in the human liver as a result of exposure to environmental contaminants and specific drugs. One approach involves development of a spatial, multicellular virtual tissue model of the liver lobule that combines molecular circuits in individual hepatocytes with cell-cell interactions and blood-mediated transport of toxicants through hepatic sinusoids, to enable quantitative, mechanistic prediction of hepatic dose-response for activation of the AhR toxicity pathway. Simultaneously, methods are being developing to extract quantitative maps of intracellular signaling and transcriptional regulatory networks perturbed by environmental contaminants, using a combination of gene expression and genome-wide protein-DNA interaction data. A predictive physiological model (DILIsymTM to understand drug-induced liver injury (DILI, the most common adverse event leading to termination of clinical development programs and regulatory actions on drugs, is also described. The model initially focuses on reactive metabolite-induced DILI in response to administration of acetaminophen, and spans multiple biological scales.

  1. Uncertainty associated with selected environmental transport models

    International Nuclear Information System (INIS)

    Little, C.A.; Miller, C.W.

    1979-11-01

    A description is given of the capabilities of several models to predict accurately either pollutant concentrations in environmental media or radiological dose to human organs. The models are discussed in three sections: aquatic or surface water transport models, atmospheric transport models, and terrestrial and aquatic food chain models. Using data published primarily by model users, model predictions are compared to observations. This procedure is infeasible for food chain models and, therefore, the uncertainty embodied in the models input parameters, rather than the model output, is estimated. Aquatic transport models are divided into one-dimensional, longitudinal-vertical, and longitudinal-horizontal models. Several conclusions were made about the ability of the Gaussian plume atmospheric dispersion model to predict accurately downwind air concentrations from releases under several sets of conditions. It is concluded that no validation study has been conducted to test the predictions of either aquatic or terrestrial food chain models. Using the aquatic pathway from water to fish to an adult for 137 Cs as an example, a 95% one-tailed confidence limit interval for the predicted exposure is calculated by examining the distributions of the input parameters. Such an interval is found to be 16 times the value of the median exposure. A similar one-tailed limit for the air-grass-cow-milk-thyroid for 131 I and infants was 5.6 times the median dose. Of the three model types discussed in this report,the aquatic transport models appear to do the best job of predicting observed concentrations. However, this conclusion is based on many fewer aquatic validation data than were availaable for atmospheric model validation

  2. Reactive species in non-equilibrium atmospheric-pressure plasmas: Generation, transport, and biological effects

    Energy Technology Data Exchange (ETDEWEB)

    Lu, X., E-mail: luxinpei@hotmail.com [State Key Laboratory of Advanced Electromagnetic Engineering and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); IFSA Collaborative Innovation Center, Shanghai Jiao Tong University, Shanghai 200240 (China); Naidis, G.V. [Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow 125412 (Russian Federation); Laroussi, M. [Plasma Engineering & Medicine Institute, Old Dominion University, Norfolk, VA 23529 (United States); Reuter, S. [Leibniz Institute for Plasma Science and Technology, Felix-Hausdorff-Strasse 2, 17489 Greifswald (Germany); Graves, D.B. [Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720 (United States); Ostrikov, K. [Institute for Future Environments, Queensland University of Technology, Brisbane, QLD 4000 (Australia); School of Physics, Chemistry, and Mechanical Engineering, Queensland University of Technology, Brisbane, QLD 4000 (Australia); Commonwealth Scientific and Industrial Research Organization, P.O.Box 218, Lindfield, NSW 2070 (Australia); School of Physics, The University of Sydney, Sydney, NSW 2006 (Australia)

    2016-05-04

    Non-equilibrium atmospheric-pressure plasmas have recently become a topical area of research owing to their diverse applications in health care and medicine, environmental remediation and pollution control, materials processing, electrochemistry, nanotechnology and other fields. This review focuses on the reactive electrons and ionic, atomic, molecular, and radical species that are produced in these plasmas and then transported from the point of generation to the point of interaction with the material, medium, living cells or tissues being processed. The most important mechanisms of generation and transport of the key species in the plasmas of atmospheric-pressure plasma jets and other non-equilibrium atmospheric-pressure plasmas are introduced and examined from the viewpoint of their applications in plasma hygiene and medicine and other relevant fields. Sophisticated high-precision, time-resolved plasma diagnostics approaches and techniques are presented and their applications to monitor the reactive species and plasma dynamics in the plasma jets and other discharges, both in the gas phase and during the plasma interaction with liquid media, are critically reviewed. The large amount of experimental data is supported by the theoretical models of reactive species generation and transport in the plasmas, surrounding gaseous environments, and plasma interaction with liquid media. These models are presented and their limitations are discussed. Special attention is paid to biological effects of the plasma-generated reactive oxygen and nitrogen (and some other) species in basic biological processes such as cell metabolism, proliferation, survival, etc. as well as plasma applications in bacterial inactivation, wound healing, cancer treatment and some others. Challenges and opportunities for theoretical and experimental research are discussed and the authors’ vision for the emerging convergence trends across several disciplines and application domains is presented to

  3. Structural sensitivity of biological models revisited.

    Science.gov (United States)

    Cordoleani, Flora; Flora, Cordoleani; Nerini, David; David, Nerini; Gauduchon, Mathias; Mathias, Gauduchon; Morozov, Andrew; Andrew, Morozov; Poggiale, Jean-Christophe; Jean-Christophe, Poggiale

    2011-08-21

    Enhancing the predictive power of models in biology is a challenging issue. Among the major difficulties impeding model development and implementation are the sensitivity of outcomes to variations in model parameters, the problem of choosing of particular expressions for the parametrization of functional relations, and difficulties in validating models using laboratory data and/or field observations. In this paper, we revisit the phenomenon which is referred to as structural sensitivity of a model. Structural sensitivity arises as a result of the interplay between sensitivity of model outcomes to variations in parameters and sensitivity to the choice of model functions, and this can be somewhat of a bottleneck in improving the models predictive power. We provide a rigorous definition of structural sensitivity and we show how we can quantify the degree of sensitivity of a model based on the Hausdorff distance concept. We propose a simple semi-analytical test of structural sensitivity in an ODE modeling framework. Furthermore, we emphasize the importance of directly linking the variability of field/experimental data and model predictions, and we demonstrate a way of assessing the robustness of modeling predictions with respect to data sampling variability. As an insightful illustrative example, we test our sensitivity analysis methods on a chemostat predator-prey model, where we use laboratory data on the feeding of protozoa to parameterize the predator functional response. Copyright © 2011 Elsevier Ltd. All rights reserved.

  4. Real time model for public transportation management

    Directory of Open Access Journals (Sweden)

    Ireneusz Celiński

    2014-03-01

    Full Text Available Background: The article outlines managing a public transportation fleet in the dynamic aspect. There are currently many technical possibilities of identifying demand in the transportation network. It is also possible to indicate legitimate basis of estimating and steering demand. The article describes a general public transportation fleet management concept based on balancing demand and supply. Material and methods: The presented method utilizes a matrix description of demand for transportation based on telemetric and telecommunication data. Emphasis was placed mainly on a general concept and not the manner in which data was collected by other researchers.  Results: The above model gave results in the form of a system for managing a fleet in real-time. The objective of the system is also to optimally utilize means of transportation at the disposal of service providers. Conclusions: The presented concept enables a new perspective on managing public transportation fleets. In case of implementation, the project would facilitate, among others, designing dynamic timetables, updated based on observed demand, and even designing dynamic points of access to public transportation lines. Further research should encompass so-called rerouting based on dynamic measurements of the characteristics of the transportation system.

  5. Transport properties site descriptive model. Guidelines for evaluation and modelling

    International Nuclear Information System (INIS)

    Berglund, Sten; Selroos, Jan-Olof

    2004-04-01

    This report describes a strategy for the development of Transport Properties Site Descriptive Models within the SKB Site Investigation programme. Similar reports have been produced for the other disciplines in the site descriptive modelling (Geology, Hydrogeology, Hydrogeochemistry, Rock mechanics, Thermal properties, and Surface ecosystems). These reports are intended to guide the site descriptive modelling, but also to provide the authorities with an overview of modelling work that will be performed. The site descriptive modelling of transport properties is presented in this report and in the associated 'Strategy for the use of laboratory methods in the site investigations programme for the transport properties of the rock', which describes laboratory measurements and data evaluations. Specifically, the objectives of the present report are to: Present a description that gives an overview of the strategy for developing Site Descriptive Models, and which sets the transport modelling into this general context. Provide a structure for developing Transport Properties Site Descriptive Models that facilitates efficient modelling and comparisons between different sites. Provide guidelines on specific modelling issues where methodological consistency is judged to be of special importance, or where there is no general consensus on the modelling approach. The objectives of the site descriptive modelling process and the resulting Transport Properties Site Descriptive Models are to: Provide transport parameters for Safety Assessment. Describe the geoscientific basis for the transport model, including the qualitative and quantitative data that are of importance for the assessment of uncertainties and confidence in the transport description, and for the understanding of the processes at the sites. Provide transport parameters for use within other discipline-specific programmes. Contribute to the integrated evaluation of the investigated sites. The site descriptive modelling of

  6. Thermal model of spent fuel transport cask

    International Nuclear Information System (INIS)

    Ahmed, E.E.M.; Rahman, F.A.; Sultan, G.F.; Khalil, E.E.

    1996-01-01

    The investigation provides a theoretical model to represent the thermal behaviour of the spent fuel elements when transported in a dry shipping cask under normal transport conditions. The heat transfer process in the spent fuel elements and within the cask are modeled which include the radiant heat transfer within the cask and the heat transfer by thermal conduction within the spent fuel element. The model considers the net radiant method for radiant heat transfer process from the inner most heated element to the surrounding spent elements. The heat conduction through fuel interior, fuel-clad interface and on clad surface are also presented. (author) 6 figs., 9 refs

  7. Coupling of transport and geochemical models

    International Nuclear Information System (INIS)

    Noy, D.J.

    1986-01-01

    This report considers mass transport in the far-field of a radioactive waste repository, and detailed geochemical modelling of the ground-water in the near-field. A parallel approach to this problem of coupling transport and geochemical codes is the subject of another CEC report (ref. EUR 10226). Both studies were carried out in the framework of the CEC project MIRAGE. (Migration of radionuclides in the geosphere)

  8. Radionuclide Transport Models Under Ambient Conditions

    Energy Technology Data Exchange (ETDEWEB)

    G. Moridis; Q. Hu

    2001-12-20

    The purpose of Revision 00 of this Analysis/Model Report (AMR) is to evaluate (by means of 2-D semianalytical and 3-D numerical models) the transport of radioactive solutes and colloids in the unsaturated zone (UZ) under ambient conditions from the potential repository horizon to the water table at Yucca Mountain (YM), Nevada.

  9. Radionuclide Transport Models Under Ambient Conditions

    International Nuclear Information System (INIS)

    Moridis, G.; Hu, Q.

    2001-01-01

    The purpose of Revision 00 of this Analysis/Model Report (AMR) is to evaluate (by means of 2-D semianalytical and 3-D numerical models) the transport of radioactive solutes and colloids in the unsaturated zone (UZ) under ambient conditions from the potential repository horizon to the water table at Yucca Mountain (YM), Nevada

  10. Regional transport model of atmospheric sulfates

    International Nuclear Information System (INIS)

    Rao, K.S.; Thomson, I.; Egan, B.A.

    1977-01-01

    As part of the Sulfate Regional Experiment (SURE) Design Project, a regional transport model of atmospheric sulfates has been developed. This quasi-Lagrangian three-dimensional grid numerical model uses a detailed SO 2 emission inventory of major anthropogenic sources in the Eastern U.S. region, and observed meteorological data during an episode as inputs. The model accounts for advective transport and turbulent diffusion of the pollutants. The chemical transformation of SO 2 and SO 4 /sup =/ and the deposition of the species at the earth's surface are assumed to be linear processes at specified constant rates. The numerical model can predict the daily average concentrations of SO 2 and SO 4 /sup =/ at all receptor locations in the grid region during the episode. Because of the spatial resolution of the grid, this model is particularly suited to investigate the effect of tall stacks in reducing the ambient concentration levels of sulfur pollutants. This paper presents the formulations and assumptions of the regional sulfate transport model. The model inputs and results are discussed. Isopleths of predicted SO 2 and SO 4 /sup =/ concentrations are compared with the observed ground level values. The bulk of the information in this paper is directed to air pollution meteorologists and environmental engineers interested in the atmospheric transport modeling studies of sulfur oxide pollutants

  11. Commercial Consolidation Model Applied to Transport Infrastructure

    Energy Technology Data Exchange (ETDEWEB)

    Guilherme de Aragão, J.J.; Santos Fontes Pereira, L. dos; Yamashita, Y.

    2016-07-01

    Since the 1990s, transport concessions, including public-private partnerships (PPPs), have been increasingly adopted by governments as an alternative for financing and operations in public investments, especially in transport infrastructure. The advantage pointed out by proponents of these models lies in merging the expertise and capital of the private sector to the public interest. Several arrangements are possible and have been employed in different cases. After the duration of the first PPP contracts in transportation, many authors have analyzed the success and failure factors of partnerships. The occurrence of failures in some stages of the process can greatly encumber the public administration, incurring losses to the fiscal responsibility of the competent bodies. This article aims to propose a new commercial consolidation model applied to transport infrastructure to ensure fiscal sustainability and overcome the weaknesses of current models. Initially, a systematic review of the literature covering studies on transport concessions between 1990 and 2015 is offered, where the different approaches between various countries are compared and the critical success factors indicated in the studies are identified. In the subsequent part of the paper, an approach for the commercial consolidation of the infrastructure concessions is presented, where the concessionary is paid following a finalistic performance model, which includes the overall fiscal balance of regional growth. Finally, the papers analyses the usefulness of the model in coping with the critical success factors explained before. (Author)

  12. A Glimpse of Membrane Transport through Structures-Advances in the Structural Biology of the GLUT Glucose Transporters.

    Science.gov (United States)

    Yan, Nieng

    2017-08-18

    The cellular uptake of glucose is an essential physiological process, and movement of glucose across biological membranes requires specialized transporters. The major facilitator superfamily glucose transporters GLUTs, encoded by the SLC2A genes, have been a paradigm for functional, mechanistic, and structural understanding of solute transport in the past century. This review starts with a glimpse into the structural biology of membrane proteins and particularly membrane transport proteins, enumerating the landmark structures in the past 25years. The recent breakthrough in the structural elucidation of GLUTs is then elaborated following a brief overview of the research history of these archetypal transporters, their functional specificity, and physiological and pathophysiological significances. Structures of GLUT1, GLUT3, and GLUT5 in distinct transport and/or ligand-binding states reveal detailed mechanisms of the alternating access transport cycle and substrate recognition, and thus illuminate a path by which structure-based drug design may be applied to help discover novel therapeutics against several debilitating human diseases associated with GLUT malfunction and/or misregulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Radionuclide Transport Models Under Ambient Conditions

    Energy Technology Data Exchange (ETDEWEB)

    G. Moridis; Q. Hu

    2000-03-12

    The purpose of this Analysis/Model Report (AMR) is to evaluate (by means of 2-D semianalytical and 3-D numerical models) the transport of radioactive solutes and colloids in the unsaturated zone (UZ) under ambient conditions from the potential repository horizon to the water table at Yucca Mountain (YM), Nevada. This is in accordance with the ''AMR Development Plan U0060, Radionuclide Transport Models Under Ambient Conditions'' (CRWMS M and O 1999a). This AMR supports the UZ Flow and Transport Process Model Report (PMR). This AMR documents the UZ Radionuclide Transport Model (RTM). This model considers: the transport of radionuclides through fractured tuffs; the effects of changes in the intensity and configuration of fracturing from hydrogeologic unit to unit; colloid transport; physical and retardation processes and the effects of perched water. In this AMR they document the capabilities of the UZ RTM, which can describe flow (saturated and/or unsaturated) and transport, and accounts for (a) advection, (b) molecular diffusion, (c) hydrodynamic dispersion (with full 3-D tensorial representation), (d) kinetic or equilibrium physical and/or chemical sorption (linear, Langmuir, Freundlich or combined), (e) first-order linear chemical reaction, (f) radioactive decay and tracking of daughters, (g) colloid filtration (equilibrium, kinetic or combined), and (h) colloid-assisted solute transport. Simulations of transport of radioactive solutes and colloids (incorporating the processes described above) from the repository horizon to the water table are performed to support model development and support studies for Performance Assessment (PA). The input files for these simulations include transport parameters obtained from other AMRs (i.e., CRWMS M and O 1999d, e, f, g, h; 2000a, b, c, d). When not available, the parameter values used are obtained from the literature. The results of the simulations are used to evaluate the transport of radioactive

  14. Radionuclide Transport Models Under Ambient Conditions

    International Nuclear Information System (INIS)

    Moridis, G.; Hu, Q.

    2000-01-01

    The purpose of this Analysis/Model Report (AMR) is to evaluate (by means of 2-D semianalytical and 3-D numerical models) the transport of radioactive solutes and colloids in the unsaturated zone (UZ) under ambient conditions from the potential repository horizon to the water table at Yucca Mountain (YM), Nevada. This is in accordance with the ''AMR Development Plan U0060, Radionuclide Transport Models Under Ambient Conditions'' (CRWMS M and O 1999a). This AMR supports the UZ Flow and Transport Process Model Report (PMR). This AMR documents the UZ Radionuclide Transport Model (RTM). This model considers: the transport of radionuclides through fractured tuffs; the effects of changes in the intensity and configuration of fracturing from hydrogeologic unit to unit; colloid transport; physical and retardation processes and the effects of perched water. In this AMR they document the capabilities of the UZ RTM, which can describe flow (saturated and/or unsaturated) and transport, and accounts for (a) advection, (b) molecular diffusion, (c) hydrodynamic dispersion (with full 3-D tensorial representation), (d) kinetic or equilibrium physical and/or chemical sorption (linear, Langmuir, Freundlich or combined), (e) first-order linear chemical reaction, (f) radioactive decay and tracking of daughters, (g) colloid filtration (equilibrium, kinetic or combined), and (h) colloid-assisted solute transport. Simulations of transport of radioactive solutes and colloids (incorporating the processes described above) from the repository horizon to the water table are performed to support model development and support studies for Performance Assessment (PA). The input files for these simulations include transport parameters obtained from other AMRs (i.e., CRWMS M and O 1999d, e, f, g, h; 2000a, b, c, d). When not available, the parameter values used are obtained from the literature. The results of the simulations are used to evaluate the transport of radioactive solutes and colloids, and

  15. Chemo-mechanical model of biological membranes for actuation mechanisms

    Science.gov (United States)

    Sundaresan, Vishnu-Baba; Leo, Donald J.

    2005-05-01

    Plants have the ability to develop large mechanical force from chemical energy available with bio-fuels. The energy released by ATP hydrolysis assists the transport of ions and fluids to achieve volumetric expansion and homeostasis. Materials that develop pressure and hence strain similar to bio-materials are classified as nastic materials. Recent calculations for controlled actuation of an active material inspired by biological transport mechanism demonstrated the feasibility of developing such a material with actuation energy densities on the order of 100 kJ/m3. Our initial investigation was based on capsules that generate pressure thus causing strain in the surrounding matrix material. Our present work focuses on our efforts to fabricate a representative actuation structure and describes the chemo-mechanical constitutive equation for such a material. The actuator considered in this work is a laminated arrangement of a hydraulic actuator plate with microscopic barrels and a fluid reservoir kept separated by a semi-permeable membrane dispersed with biological transporters. We present here our initial design and a mathematical model to predict the fluid flux and strain developed in such an actuator.

  16. Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

    Science.gov (United States)

    Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

    2018-04-01

    Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. From biology to mathematical models and back: teaching modeling to biology students, and biology to math and engineering students.

    Science.gov (United States)

    Chiel, Hillel J; McManus, Jeffrey M; Shaw, Kendrick M

    2010-01-01

    We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a "live" textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology.

  18. A simplified tether model for molecular motor transporting cargo

    International Nuclear Information System (INIS)

    Fang-Zhen, Li; Li-Chun, Jiang

    2010-01-01

    Molecular motors are proteins or protein complexes which function as transporting engines in biological cells. This paper models the tether between motor and its cargo as a symmetric linear potential. Different from Elston and Peskin's work for which performance of the system was discussed only in some limiting cases, this study produces analytic solutions of the problem for general cases by simplifying the transport system into two physical states, which makes it possible to discuss the dynamics of the motor–cargo system in detail. It turns out that the tether strength between motor and cargo should be greater than a threshold or the motor will fail to transport the cargo, which was not discussed by former researchers yet. Value of the threshold depends on the diffusion coefficients of cargo and motor and also on the strength of the Brownian ratchets dragging the system. The threshold approaches a finite constant when the strength of the ratchet tends to infinity. (general)

  19. Hydrogen recycle modeling in transport codes

    International Nuclear Information System (INIS)

    Howe, H.C.

    1979-01-01

    The hydrogen recycling models now used in Tokamak transport codes are reviewed and the method by which realistic recycling models are being added is discussed. Present models use arbitrary recycle coefficients and therefore do not model the actual recycling processes at the wall. A model for the hydrogen concentration in the wall serves two purposes: (1) it allows a better understanding of the density behavior in present gas puff, pellet, and neutral beam heating experiments; and (2) it allows one to extrapolate to long pulse devices such as EBT, ISX-C and reactors where the walls are observed or expected to saturate. Several wall models are presently being studied for inclusion in transport codes

  20. GEOS-5 Chemistry Transport Model User's Guide

    Science.gov (United States)

    Kouatchou, J.; Molod, A.; Nielsen, J. E.; Auer, B.; Putman, W.; Clune, T.

    2015-01-01

    The Goddard Earth Observing System version 5 (GEOS-5) General Circulation Model (GCM) makes use of the Earth System Modeling Framework (ESMF) to enable model configurations with many functions. One of the options of the GEOS-5 GCM is the GEOS-5 Chemistry Transport Model (GEOS-5 CTM), which is an offline simulation of chemistry and constituent transport driven by a specified meteorology and other model output fields. This document describes the basic components of the GEOS-5 CTM, and is a user's guide on to how to obtain and run simulations on the NCCS Discover platform. In addition, we provide information on how to change the model configuration input files to meet users' needs.

  1. Modelling Transition Towards Sustainable Transportation Sector

    DEFF Research Database (Denmark)

    Dominkovic, Dominik Franjo; Bačeković, I.; Mýrdal, Jón Steinar Garðarsson

    2016-01-01

    two energy sectors. In order to deal with the raised issue, authors of this paper developed amethodology for calculation of the transition towards sustainable transport sector, focusing on thesolutions that are already available. Furthermore, as a part of the model, a detailed mapping ofresources......In a transition towards 100% renewable energy system, transportation sector is rarely dealt withusing the holistic approach and measuring its impact on the whole energy system. Furthermore, assolutions for power and heat sectors are clearer, it is a tendency of the researchers to focus on thelatter...... needed has been carried out for each of the alternatives. It was shown that theelectrification of the transportation sector is a crucial point in transition, while for the transportmodes that cannot be electrified, or shifted to different transportation modes, four alternatives weredefined: synthetic...

  2. Models in Planning Urban Public Passenger Transport

    Directory of Open Access Journals (Sweden)

    Gordana Štefančić

    2007-07-01

    Full Text Available The solving of complex problems in public transport requiresthe usage of models that are based on the estimate of demandin planning the transport routes. The intention is to predictwhat is going to happen in the future, if the proposed solutionsare implemented. In the majority of cases, the publictransport system is formed as a network and stored in the computermemory in order to start the evaluation process by specifYingthe number of trip origins and destinations in each zone.The trip distribution model which is used to calculate the numberof trips between each pair in the zone is based on the overalltravel frictions from zone to zone.

  3. Uncertainty calculation in transport models and forecasts

    DEFF Research Database (Denmark)

    Manzo, Stefano; Prato, Carlo Giacomo

    . Forthcoming: European Journal of Transport and Infrastructure Research, 15-3, 64-72. 4 The last paper4 examined uncertainty in the spatial composition of residence and workplace locations in the Danish National Transport Model. Despite the evidence that spatial structure influences travel behaviour...... to increase the quality of the decision process and to develop robust or adaptive plans. In fact, project evaluation processes that do not take into account model uncertainty produce not fully informative and potentially misleading results so increasing the risk inherent to the decision to be taken...

  4. Reactive transport models and simulation with ALLIANCES

    International Nuclear Information System (INIS)

    Leterrier, N.; Deville, E.; Bary, B.; Trotignon, L.; Hedde, T.; Cochepin, B.; Stora, E.

    2009-01-01

    Many chemical processes influence the evolution of nuclear waste storage. As a result, simulations based only upon transport and hydraulic processes fail to describe adequately some industrial scenarios. We need to take into account complex chemical models (mass action laws, kinetics...) which are highly non-linear. In order to simulate the coupling of these chemical reactions with transport, we use a classical Sequential Iterative Approach (SIA), with a fixed point algorithm, within the mainframe of the ALLIANCES platform. This approach allows us to use the various transport and chemical modules available in ALLIANCES, via an operator-splitting method based upon the structure of the chemical system. We present five different applications of reactive transport simulations in the context of nuclear waste storage: 1. A 2D simulation of the lixiviation by rain water of an underground polluted zone high in uranium oxide; 2. The degradation of the steel envelope of a package in contact with clay. Corrosion of the steel creates corrosion products and the altered package becomes a porous medium. We follow the degradation front through kinetic reactions and the coupling with transport; 3. The degradation of a cement-based material by the injection of an aqueous solution of zinc and sulphate ions. In addition to the reactive transport coupling, we take into account in this case the hydraulic retroaction of the porosity variation on the Darcy velocity; 4. The decalcification of a concrete beam in an underground storage structure. In this case, in addition to the reactive transport simulation, we take into account the interaction between chemical degradation and the mechanical forces (cracks...), and the retroactive influence on the structure changes on transport; 5. The degradation of the steel envelope of a package in contact with a clay material under a temperature gradient. In this case the reactive transport simulation is entirely directed by the temperature changes and

  5. Unit testing, model validation, and biological simulation.

    Science.gov (United States)

    Sarma, Gopal P; Jacobs, Travis W; Watts, Mark D; Ghayoomie, S Vahid; Larson, Stephen D; Gerkin, Richard C

    2016-01-01

    The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models.

  6. Multi-compartment Aerosol Transport Model

    Energy Technology Data Exchange (ETDEWEB)

    Hubbard, Joshua Allen; Santarpia, Joshua; Brotherton, Christopher M.; Omana, Michael Alexis; Rivera, Danielle; Lucero, Gabriel Anthony

    2017-06-01

    A simple aerosol transport model was developed for a multi-compartmented cleanroom. Each compartment was treated as a well-mixed volume with ventilating supply and return air. Gravitational settling, intercompartment transport, and leakage of exterior air into the system were included in the model. A set of first order, coupled, ordinary differential equations was derived from the conservation equations of aerosol mass and air mass. The system of ODEs was then solved in MATLAB using pre-existing numerical methods. The model was verified against cases of (1) constant inlet-duct concentration, and (2) exponentially decaying inlet-duct concentration. Numerical methods resulted in normalized error of less than 10 -9 when model solutions were compared to analytical solutions. The model was validated against experimental measurements from a single field test and showed good agreement in the shape and magnitude of the aerosol concentration profile with time.

  7. Error estimation and adaptive chemical transport modeling

    Directory of Open Access Journals (Sweden)

    Malte Braack

    2014-09-01

    Full Text Available We present a numerical method to use several chemical transport models of increasing accuracy and complexity in an adaptive way. In largest parts of the domain, a simplified chemical model may be used, whereas in certain regions a more complex model is needed for accuracy reasons. A mathematically derived error estimator measures the modeling error and provides information where to use more accurate models. The error is measured in terms of output functionals. Therefore, one has to consider adjoint problems which carry sensitivity information. This concept is demonstrated by means of ozone formation and pollution emission.

  8. Proton transport in a membrane protein channel: two-dimensional infrared spectrum modeling.

    NARCIS (Netherlands)

    Liang, C.; Knoester, J.; Jansen, T.L.Th.A.

    2012-01-01

    We model the two-dimensional infrared (2DIR) spectrum of a proton channel to investigate its applicability as a spectroscopy tool to study the proton transport process in biological systems. Proton transport processes in proton channels are involved in numerous fundamental biochemical reactions.

  9. A multiscale analysis of nutrient transport and biological tissue growth in vitro

    KAUST Repository

    O'Dea, R. D.

    2014-10-15

    © The authors 2014. In this paper, we consider the derivation of macroscopic equations appropriate to describe the growth of biological tissue, employing a multiple-scale homogenization method to accommodate explicitly the influence of the underlying microscale structure of the material, and its evolution, on the macroscale dynamics. Such methods have been widely used to study porous and poroelastic materials; however, a distinguishing feature of biological tissue is its ability to remodel continuously in response to local environmental cues. Here, we present the derivation of a model broadly applicable to tissue engineering applications, characterized by cell proliferation and extracellular matrix deposition in porous scaffolds used within tissue culture systems, which we use to study coupling between fluid flow, nutrient transport, and microscale tissue growth. Attention is restricted to surface accretion within a rigid porous medium saturated with a Newtonian fluid; coupling between the various dynamics is achieved by specifying the rate of microscale growth to be dependent upon the uptake of a generic diffusible nutrient. The resulting macroscale model comprises a Darcy-type equation governing fluid flow, with flow characteristics dictated by the assumed periodic microstructure and surface growth rate of the porous medium, coupled to an advection-reaction equation specifying the nutrient concentration. Illustrative numerical simulations are presented to indicate the influence of microscale growth on macroscale dynamics, and to highlight the importance of including experimentally relevant microstructural information to correctly determine flow dynamics and nutrient delivery in tissue engineering applications.

  10. Ion transport through biological membranes an integrated theoretical approach

    CERN Document Server

    Mackey, Michael C

    1975-01-01

    This book illustrates some of the ways physics and mathematics have been, and are being, used to elucidate the underlying mechan­ isms of passive ion movement through biological membranes in general, and the membranes of excltable cells in particular. I have made no effort to be comprehensive in my introduction of biological material and the reader interested in a brief account of single cell electro­ physlology from a physically-oriented biologists viewpoint will find the chapters by Woodbury (1965) an excellent introduction. Part I is introductory in nature, exploring the basic electrical properties of inexcitable and excitable cell plasma membranes. Cable theory is utilized to illustrate the function of the non-decrementing action potential as a signaling mechanism for the long range trans­ mission of information in the nervous system, and to gain some in­ sight into the gross behaviour of neurons. The detailed analysis of Hodgkin and Huxley on the squid giant axon membrane ionic conductance properties...

  11. Spherical Cancer Models in Tumor Biology

    Directory of Open Access Journals (Sweden)

    Louis-Bastien Weiswald

    2015-01-01

    Full Text Available Three-dimensional (3D in vitro models have been used in cancer research as an intermediate model between in vitro cancer cell line cultures and in vivo tumor. Spherical cancer models represent major 3D in vitro models that have been described over the past 4 decades. These models have gained popularity in cancer stem cell research using tumorospheres. Thus, it is crucial to define and clarify the different spherical cancer models thus far described. Here, we focus on in vitro multicellular spheres used in cancer research. All these spherelike structures are characterized by their well-rounded shape, the presence of cancer cells, and their capacity to be maintained as free-floating cultures. We propose a rational classification of the four most commonly used spherical cancer models in cancer research based on culture methods for obtaining them and on subsequent differences in sphere biology: the multicellular tumor spheroid model, first described in the early 70s and obtained by culture of cancer cell lines under nonadherent conditions; tumorospheres, a model of cancer stem cell expansion established in a serum-free medium supplemented with growth factors; tissue-derived tumor spheres and organotypic multicellular spheroids, obtained by tumor tissue mechanical dissociation and cutting. In addition, we describe their applications to and interest in cancer research; in particular, we describe their contribution to chemoresistance, radioresistance, tumorigenicity, and invasion and migration studies. Although these models share a common 3D conformation, each displays its own intrinsic properties. Therefore, the most relevant spherical cancer model must be carefully selected, as a function of the study aim and cancer type.

  12. Spherical cancer models in tumor biology.

    Science.gov (United States)

    Weiswald, Louis-Bastien; Bellet, Dominique; Dangles-Marie, Virginie

    2015-01-01

    Three-dimensional (3D) in vitro models have been used in cancer research as an intermediate model between in vitro cancer cell line cultures and in vivo tumor. Spherical cancer models represent major 3D in vitro models that have been described over the past 4 decades. These models have gained popularity in cancer stem cell research using tumorospheres. Thus, it is crucial to define and clarify the different spherical cancer models thus far described. Here, we focus on in vitro multicellular spheres used in cancer research. All these spherelike structures are characterized by their well-rounded shape, the presence of cancer cells, and their capacity to be maintained as free-floating cultures. We propose a rational classification of the four most commonly used spherical cancer models in cancer research based on culture methods for obtaining them and on subsequent differences in sphere biology: the multicellular tumor spheroid model, first described in the early 70s and obtained by culture of cancer cell lines under nonadherent conditions; tumorospheres, a model of cancer stem cell expansion established in a serum-free medium supplemented with growth factors; tissue-derived tumor spheres and organotypic multicellular spheroids, obtained by tumor tissue mechanical dissociation and cutting. In addition, we describe their applications to and interest in cancer research; in particular, we describe their contribution to chemoresistance, radioresistance, tumorigenicity, and invasion and migration studies. Although these models share a common 3D conformation, each displays its own intrinsic properties. Therefore, the most relevant spherical cancer model must be carefully selected, as a function of the study aim and cancer type. Copyright © 2014 Neoplasia Press, Inc. Published by Elsevier Inc. All rights reserved.

  13. Modelling anisotropic water transport in polymer composite

    Indian Academy of Sciences (India)

    This work reports anisotropic water transport in a polymer composite consisting of an epoxy matrix reinforced with aligned triangular bars made of vinyl ester. By gravimetric experiments, water diffusion in resin and polymer composites were characterized. Parameters for Fickian diffusion and polymer relaxation models were ...

  14. Climate impact of transportation A model comparison

    NARCIS (Netherlands)

    Girod, B.; Vuuren, D.P. van; Grahn, M.; Kitous, A.; Kim, S.H.; Kyle, P.

    2013-01-01

    Transportation contributes to a significant and rising share of global energy use and GHG emissions. Therefore modeling future travel demand, its fuel use, and resulting CO2 emission is highly relevant for climate change mitigation. In this study we compare the baseline projections for global

  15. Logistics Chains in Freight Transport Modelling

    NARCIS (Netherlands)

    Davydenko, I.Y.

    2015-01-01

    The flow of trade is not equal to transport flows, mainly due to the fact that warehouses and distribution facilities are used as intermediary stops on the way from production locations to the points of consumption or further rework of goods. This thesis proposes a logistics chain model, which

  16. Modelling soil transport by wind in drylands

    International Nuclear Information System (INIS)

    Hassan, M.H.A.

    1994-01-01

    Understanding the movement of windblown soil particles and the resulting formation of complex surface features are among the most intriguing problems in dryland research. This understanding can only be achieved trough physical and mathematical modelling and must also involve observational data and laboratory experiments. Some current mathematical models that have contributed to the basic understanding of the transportation and deposition of soil particles by wind are presented and solved in these notes. (author). 26 refs, 5 figs

  17. Multiscale mechanical modeling of soft biological tissues

    Science.gov (United States)

    Stylianopoulos, Triantafyllos

    2008-10-01

    Soft biological tissues include both native and artificial tissues. In the human body, tissues like the articular cartilage, arterial wall, and heart valve leaflets are examples of structures composed of an underlying network of collagen fibers, cells, proteins and molecules. Artificial tissues are less complex than native tissues and mainly consist of a fiber polymer network with the intent of replacing lost or damaged tissue. Understanding of the mechanical function of these materials is essential for many clinical treatments (e.g. arterial clamping, angioplasty), diseases (e.g. arteriosclerosis) and tissue engineering applications (e.g. engineered blood vessels or heart valves). This thesis presents the derivation and application of a multiscale methodology to describe the macroscopic mechanical function of soft biological tissues incorporating directly their structural architecture. The model, which is based on volume averaging theory, accounts for structural parameters such as the network volume fraction and orientation, the realignment of the fibers in response to strain, the interactions among the fibers and the interactions between the fibers and the interstitial fluid in order to predict the overall tissue behavior. Therefore, instead of using a constitutive equation to relate strain to stress, the tissue microstructure is modeled within a representative volume element (RVE) and the macroscopic response at any point in the tissue is determined by solving a micromechanics problem in the RVE. The model was applied successfully to acellular collagen gels, native blood vessels, and electrospun polyurethane scaffolds and provided accurate predictions for permeability calculations in isotropic and oriented fiber networks. The agreement of model predictions with experimentally determined mechanical properties provided insights into the mechanics of tissues and tissue constructs, while discrepancies revealed limitations of the model framework.

  18. Numerical modelling of ion transport in flames

    KAUST Repository

    Han, Jie

    2015-10-20

    This paper presents a modelling framework to compute the diffusivity and mobility of ions in flames. The (n, 6, 4) interaction potential is adopted to model collisions between neutral and charged species. All required parameters in the potential are related to the polarizability of the species pair via semi-empirical formulas, which are derived using the most recently published data or best estimates. The resulting framework permits computation of the transport coefficients of any ion found in a hydrocarbon flame. The accuracy of the proposed method is evaluated by comparing its predictions with experimental data on the mobility of selected ions in single-component neutral gases. Based on this analysis, the value of a model constant available in the literature is modified in order to improve the model\\'s predictions. The newly determined ion transport coefficients are used as part of a previously developed numerical approach to compute the distribution of charged species in a freely propagating premixed lean CH4/O2 flame. Since a significant scatter of polarizability data exists in the literature, the effects of changes in polarizability on ion transport properties and the spatial distribution of ions in flames are explored. Our analysis shows that changes in polarizability propagate with decreasing effect from binary transport coefficients to species number densities. We conclude that the chosen polarizability value has a limited effect on the ion distribution in freely propagating flames. We expect that the modelling framework proposed here will benefit future efforts in modelling the effect of external voltages on flames. Supplemental data for this article can be accessed at http://dx.doi.org/10.1080/13647830.2015.1090018. © 2015 Taylor & Francis.

  19. ACTIVE AND PARTICIPATORY METHODS IN BIOLOGY: MODELING

    Directory of Open Access Journals (Sweden)

    Brînduşa-Antonela SBÎRCEA

    2011-01-01

    Full Text Available By using active and participatory methods it is hoped that pupils will not only come to a deeper understanding of the issues involved, but also that their motivation will be heightened. Pupil involvement in their learning is essential. Moreover, by using a variety of teaching techniques, we can help students make sense of the world in different ways, increasing the likelihood that they will develop a conceptual understanding. The teacher must be a good facilitator, monitoring and supporting group dynamics. Modeling is an instructional strategy in which the teacher demonstrates a new concept or approach to learning and pupils learn by observing. In the teaching of biology the didactic materials are fundamental tools in the teaching-learning process. Reading about scientific concepts or having a teacher explain them is not enough. Research has shown that modeling can be used across disciplines and in all grade and ability level classrooms. Using this type of instruction, teachers encourage learning.

  20. Coupled Modeling of Rhizosphere and Reactive Transport Processes

    Science.gov (United States)

    Roque-Malo, S.; Kumar, P.

    2017-12-01

    The rhizosphere, as a bio-diverse plant root-soil interface, hosts many hydrologic and biochemical processes, including nutrient cycling, hydraulic redistribution, and soil carbon dynamics among others. The biogeochemical function of root networks, including the facilitation of nutrient cycling through absorption and rhizodeposition, interaction with micro-organisms and fungi, contribution to biomass, etc., plays an important role in myriad Critical Zone processes. Despite this knowledge, the role of the rhizosphere on watershed-scale ecohydrologic functions in the Critical Zone has not been fully characterized, and specifically, the extensive capabilities of reactive transport models (RTMs) have not been applied to these hydrobiogeochemical dynamics. This study uniquely links rhizospheric processes with reactive transport modeling to couple soil biogeochemistry, biological processes, hydrologic flow, hydraulic redistribution, and vegetation dynamics. Key factors in the novel modeling approach are: (i) bi-directional effects of root-soil interaction, such as simultaneous root exudation and nutrient absorption; (ii) multi-state biomass fractions in soil (i.e. living, dormant, and dead biological and root materials); (iii) expression of three-dimensional fluxes to represent both vertical and lateral interconnected flows and processes; and (iv) the potential to include the influence of non-stationary external forcing and climatic factors. We anticipate that the resulting model will demonstrate the extensive effects of plant root dynamics on ecohydrologic functions at the watershed scale and will ultimately contribute to a better characterization of efflux from both agricultural and natural systems.

  1. Symposium on unsaturated flow and transport modeling

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, E.M.; Gee, G.W.; Nelson, R.W. (eds.)

    1982-09-01

    This document records the proceedings of a symposium on flow and transport processes in partially saturated groundwater systems, conducted at the Battelle Seattle Research Center on March 22-24, 1982. The symposium was sponsored by the US Nuclear Regulatory Commission for the purpose of assessing the state-of-the-art of flow and transport modeling for use in licensing low-level nuclear waste repositories in partially saturated zones. The first day of the symposium centered around research in flow through partially saturated systems. Papers were presented with the opportunity for questions following each presentation. In addition, after all the talks, a formal panel discussion was held during which written questions were addressed to the panel of the days speakers. The second day of the Symposium was devoted to solute and contaminant transport in partially saturated media in an identical format. Individual papers are abstracted.

  2. Molecular modeling of auxin transport inhibitors

    International Nuclear Information System (INIS)

    Gardner, G.; Black-Schaefer, C.; Bures, M.G.

    1990-01-01

    Molecular modeling techniques have been used to study the chemical and steric properties of auxin transport inhibitors. These bind to a specific site on the plant plasma membrane characterized by its affinity for N-1-naphthylphthalamic acid (NPA). A three-dimensional model was derived from critical features of ligands for the NPA receptor, and a suggested binding conformation is proposed. This model, along with three-dimensional structural searching techniques, was then used to search the Abbott corporate database of chemical structures. Of the 467 compounds that satisfied the search criteria, 77 representative molecules were evaluated for their ability to compete for [ 3 H]NPA binding to corn microsomal membranes. Nineteen showed activity that ranged from 16 to 85% of the maximum NPA binding. Four of the most active of these, from chemical classes not included in the original compound set, also inhibited polar auxin transport through corn coleoptile sections

  3. Model prodrugs for the intestinal oligopeptide transporter

    DEFF Research Database (Denmark)

    Nielsen, C U; Andersen, R; Brodin, Birger

    2001-01-01

    The human intestinal di/tri-peptide carrier, hPepT1, has been suggested as a target for increasing intestinal transport of low permeability compounds by creating prodrugs designed for the transporter. Model ester prodrugs using the stabilized dipeptides D-Glu-Ala and D-Asp-Ala as pro...... with a pH of approximately 6.0, but still release the model drug at the intercellular and blood pH of approximately 7.4. Even though benzyl alcohol is not a low molecular weight drug molecule, these results indicate that the dipeptide prodrug principle is a promising drug delivery concept. However......, the physico-chemical properties such as electronegativity, solubility, and log P of the drug molecule may also have an influence on the potential of these kinds of prodrugs. The purpose of the present study is to investigate whether the model drug electronegativity, estimated as Taft substitution parameter...

  4. Numerical modelling of ion transport in flames

    Science.gov (United States)

    Han, Jie; Belhi, Memdouh; Bisetti, Fabrizio; Mani Sarathy, S.

    2015-11-01

    This paper presents a modelling framework to compute the diffusivity and mobility of ions in flames. The (n, 6, 4) interaction potential is adopted to model collisions between neutral and charged species. All required parameters in the potential are related to the polarizability of the species pair via semi-empirical formulas, which are derived using the most recently published data or best estimates. The resulting framework permits computation of the transport coefficients of any ion found in a hydrocarbon flame. The accuracy of the proposed method is evaluated by comparing its predictions with experimental data on the mobility of selected ions in single-component neutral gases. Based on this analysis, the value of a model constant available in the literature is modified in order to improve the model's predictions. The newly determined ion transport coefficients are used as part of a previously developed numerical approach to compute the distribution of charged species in a freely propagating premixed lean CH4/O2 flame. Since a significant scatter of polarizability data exists in the literature, the effects of changes in polarizability on ion transport properties and the spatial distribution of ions in flames are explored. Our analysis shows that changes in polarizability propagate with decreasing effect from binary transport coefficients to species number densities. We conclude that the chosen polarizability value has a limited effect on the ion distribution in freely propagating flames. We expect that the modelling framework proposed here will benefit future efforts in modelling the effect of external voltages on flames. Supplemental data for this article can be accessed at http://dx.doi.org/10.1080/13647830.2015.1090018.

  5. Biological fate, transport, and ecotoxicity of toxic and hazardous waste in the Mississippi River Basin

    International Nuclear Information System (INIS)

    Abdelghani, A.; Hartley, W.; Bart, H.; Ide, C.; Ellgaard, E.; Sherry, T.; Devall, M.; Thien, L.; Horner, E.; Mizell, M.

    1993-01-01

    The objective of the cluster investigators is to develop a dynamic model for the evaluation of the biological fate, transport, and ecotoxicity from multiple chemical contamination of the Mississippi River Basin. To develop this environmental model, FY 93-94 most of cluster investigators focused on Devil's Swamp Site (DSS), a cypress swamp which lies just Northwest of Baton Rouge, Louisiana, adjacent to the Mississippi River. The DSS which includes a man-made lake has contaminated sediment, water and biota. The DSS receives flood water from the Mississippi River during high flow periods and the Baton Rouge Bayou drains through the DSS. The DSS receives toxic substances and hazardous waste from a wide variety of surrounding industrial operations including an abandoned hazardous waste disposal facility. In addition, some investigators studied Bayou Trepangnier. This research cluster will continue studying Devil Swamp. The large number of investigators in this cluster resulted from incorporating related research proposals based on reviewer recommendations. The specific aims of the cluster for the first year were to conduct a physical, chemical, ecological survey and baseline toxicological characterization of the DSS from existing databases maintained by State and federal agencies, field studies (assessment) of sediment, air, water and biota, and laboratory screening studios. This assessment will provide critical information and focus for the next two years in-depth studies of critical transport and fate processes, ecotoxicity, biomarkers of effect, and uptake, metabolism and distribution of toxicants. The primary significant outcome of the cluster researchers will be the development of an ecological risk assessment model combining biotic and physical/chemical variables for DSS with a projection of model reliability and accuracy for use at other typical Mississippi River Basin sites

  6. Innovation in biological production and upgrading of methane and hydrogen for use as gaseous transport biofuel.

    Science.gov (United States)

    Xia, Ao; Cheng, Jun; Murphy, Jerry D

    2016-01-01

    Biofuels derived from biomass will play a major role in future renewable energy supplies in transport. Gaseous biofuels have superior energy balances, offer greater greenhouse gas emission reductions and produce lower pollutant emissions than liquid biofuels. Biogas derived through fermentation of wet organic substrates will play a major role in future transport systems. Biogas (which is composed of approximately 60% methane/hydrogen and 40% carbon dioxide) requires an upgrading process to reduce the carbon dioxide content to less than 3% before it is used as compressed gas in transport. This paper reviews recent developments in fermentative biogas production and upgrading as a transport fuel. Third generation gaseous biofuels may be generated using marine-based algae via two-stage fermentation, cogenerating hydrogen and methane. Alternative biological upgrading techniques, such as biological methanation and microalgal biogas upgrading, have the potential to simultaneously upgrade biogas, increase gaseous biofuel yield and reduce carbon dioxide emission. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Modelling contaminant transport in saturated aquifers

    International Nuclear Information System (INIS)

    Lakshminarayana, V.; Nayak, T.R.

    1990-01-01

    With the increase in population and industrialization the problem of pollution of groundwater has become critical. The present study deals with modelling of pollutant transport through saturated aquifers. Using this model it is possible to predict the concentration distribution, spatial as well as temporal, in the aquifer. The paper also deals with one of the methods of controlling the pollutant movement, namely by pumping wells. A simulation model is developed to determine the number, location and rate of pumping of a number of wells near the source of pollution so that the concentration is within acceptable limits at the point of interest. (Author) (18 refs., 14 figs., tab.)

  8. Modelling biological invasions: Individual to population scales at interfaces

    KAUST Repository

    Belmonte-Beitia, J.

    2013-10-01

    Extracting the population level behaviour of biological systems from that of the individual is critical in understanding dynamics across multiple scales and thus has been the subject of numerous investigations. Here, the influence of spatial heterogeneity in such contexts is explored for interfaces with a separation of the length scales characterising the individual and the interface, a situation that can arise in applications involving cellular modelling. As an illustrative example, we consider cell movement between white and grey matter in the brain which may be relevant in considering the invasive dynamics of glioma. We show that while one can safely neglect intrinsic noise, at least when considering glioma cell invasion, profound differences in population behaviours emerge in the presence of interfaces with only subtle alterations in the dynamics at the individual level. Transport driven by local cell sensing generates predictions of cell accumulations along interfaces where cell motility changes. This behaviour is not predicted with the commonly used Fickian diffusion transport model, but can be extracted from preliminary observations of specific cell lines in recent, novel, cryo-imaging. Consequently, these findings suggest a need to consider the impact of individual behaviour, spatial heterogeneity and especially interfaces in experimental and modelling frameworks of cellular dynamics, for instance in the characterisation of glioma cell motility. © 2013 Elsevier Ltd.

  9. Modeling tritium transport in the environment

    International Nuclear Information System (INIS)

    Murphy, C.E. Jr.

    1986-01-01

    A model of tritium transport in the environment near an atmospheric source of tritium is presented in the general context of modeling material cycling in ecosystems. The model was developed to test hypotheses about the process involved in tritium cycling. The temporal and spatial scales of the model were picked to allow comparison to environmental monitoring data collected in the vicinity of the Savannah River Plant. Initial simulations with the model showed good agreement with monitoring data, including atmospheric and vegetation tritium concentrations. The model can also simulate values of tritium in vegetation organic matter if the key parameter distributing the source of organic hydrogen is varied to fit the data. However, because of the lack of independent conformation of the distribution parameter, there is still uncertainty about the role of organic movement of tritium in the food chain, and its effect on the dose to man

  10. Airborne biological hazards and urban transport infrastructure: current challenges and future directions.

    Science.gov (United States)

    Nasir, Zaheer Ahmad; Campos, Luiza Cintra; Christie, Nicola; Colbeck, Ian

    2016-08-01

    Exposure to airborne biological hazards in an ever expanding urban transport infrastructure and highly diverse mobile population is of growing concern, in terms of both public health and biosecurity. The existing policies and practices on design, construction and operation of these infrastructures may have severe implications for airborne disease transmission, particularly, in the event of a pandemic or intentional release of biological of agents. This paper reviews existing knowledge on airborne disease transmission in different modes of transport, highlights the factors enhancing the vulnerability of transport infrastructures to airborne disease transmission, discusses the potential protection measures and identifies the research gaps in order to build a bioresilient transport infrastructure. The unification of security and public health research, inclusion of public health security concepts at the design and planning phase, and a holistic system approach involving all the stakeholders over the life cycle of transport infrastructure hold the key to mitigate the challenges posed by biological hazards in the twenty-first century transport infrastructure.

  11. Modelling radioiodine transport across a capillary fringe

    International Nuclear Information System (INIS)

    Mathias, Simon A.; Butler, Adrian P.; Wheater, Howard S.

    2008-01-01

    Due to its long radioactive half-life, iodine-129 is considered to be an important radionuclide in the context of underground radioactive waste disposal safety assessment. Iodine speciates as iodide (I - ) in reducing conditions and iodate (IO 3 - ) in oxidizing conditions. As iodate is more reactive, it is much less mobile than iodide. Consequently, in considering vertically upward transport within a soil profile, iodine will tend to accumulate at the top of the capillary fringe. In this paper, a model of iodine transport across a capillary fringe is developed by coupling equations for variably saturated flow, oxygen dynamics and rate-limited sorption. Model parameters are obtained by consideration of literature values, calibration on soil column data and other supporting laboratory experiments. The results demonstrate the importance of rate kinetics on the migration and bioavailability of radioiodine in the near-surface environment

  12. Modelling radioiodine transport across a capillary fringe.

    Science.gov (United States)

    Mathias, Simon A; Butler, Adrian P; Wheater, Howard S

    2008-04-01

    Due to its long radioactive half-life, iodine-129 is considered to be an important radionuclide in the context of underground radioactive waste disposal safety assessment. Iodine speciates as iodide (I-) in reducing conditions and iodate (IO3-) in oxidizing conditions. As iodate is more reactive, it is much less mobile than iodide. Consequently, in considering vertically upward transport within a soil profile, iodine will tend to accumulate at the top of the capillary fringe. In this paper, a model of iodine transport across a capillary fringe is developed by coupling equations for variably saturated flow, oxygen dynamics and rate-limited sorption. Model parameters are obtained by consideration of literature values, calibration on soil column data and other supporting laboratory experiments. The results demonstrate the importance of rate kinetics on the migration and bioavailability of radioiodine in the near-surface environment.

  13. Nonlinear Rheology in a Model Biological Tissue.

    Science.gov (United States)

    Matoz-Fernandez, D A; Agoritsas, Elisabeth; Barrat, Jean-Louis; Bertin, Eric; Martens, Kirsten

    2017-04-14

    The rheological response of dense active matter is a topic of fundamental importance for many processes in nature such as the mechanics of biological tissues. One prominent way to probe mechanical properties of tissues is to study their response to externally applied forces. Using a particle-based model featuring random apoptosis and environment-dependent division rates, we evidence a crossover from linear flow to a shear-thinning regime with an increasing shear rate. To rationalize this nonlinear flow we derive a theoretical mean-field scenario that accounts for the interplay of mechanical and active noise in local stresses. These noises are, respectively, generated by the elastic response of the cell matrix to cell rearrangements and by the internal activity.

  14. Modeling biological tissue growth: discrete to continuum representations.

    Science.gov (United States)

    Hywood, Jack D; Hackett-Jones, Emily J; Landman, Kerry A

    2013-09-01

    There is much interest in building deterministic continuum models from discrete agent-based models governed by local stochastic rules where an agent represents a biological cell. In developmental biology, cells are able to move and undergo cell division on and within growing tissues. A growing tissue is itself made up of cells which undergo cell division, thereby providing a significant transport mechanism for other cells within it. We develop a discrete agent-based model where domain agents represent tissue cells. Each agent has the ability to undergo a proliferation event whereby an additional domain agent is incorporated into the lattice. If a probability distribution describes the waiting times between proliferation events for an individual agent, then the total length of the domain is a random variable. The average behavior of these stochastically proliferating agents defining the growing lattice is determined in terms of a Fokker-Planck equation, with an advection and diffusion term. The diffusion term differs from the one obtained Landman and Binder [J. Theor. Biol. 259, 541 (2009)] when the rate of growth of the domain is specified, but the choice of agents is random. This discrepancy is reconciled by determining a discrete-time master equation for this process and an associated asymmetric nonexclusion random walk, together with consideration of synchronous and asynchronous updating schemes. All theoretical results are confirmed with numerical simulations. This study furthers our understanding of the relationship between agent-based rules, their implementation, and their associated partial differential equations. Since tissue growth is a significant cellular transport mechanism during embryonic growth, it is important to use the correct partial differential equation description when combining with other cellular functions.

  15. Modelling sediment clasts transport during landscape evolution

    Science.gov (United States)

    Carretier, Sébastien; Martinod, Pierre; Reich, Martin; Godderis, Yves

    2016-03-01

    Over thousands to millions of years, the landscape evolution is predicted by models based on fluxes of eroded, transported and deposited material. The laws describing these fluxes, corresponding to averages over many years, are difficult to prove with the available data. On the other hand, sediment dynamics are often tackled by studying the distribution of certain grain properties in the field (e.g. heavy metals, detrital zircons, 10Be in gravel, magnetic tracers). There is a gap between landscape evolution models based on fluxes and these field data on individual clasts, which prevent the latter from being used to calibrate the former. Here we propose an algorithm coupling the landscape evolution with mobile clasts. Our landscape evolution model predicts local erosion, deposition and transfer fluxes resulting from hillslope and river processes. Clasts of any size are initially spread in the basement and are detached, moved and deposited according to probabilities using these fluxes. Several river and hillslope laws are studied. Although the resulting mean transport rate of the clasts does not depend on the time step or the model cell size, our approach is limited by the fact that their scattering rate is cell-size-dependent. Nevertheless, both their mean transport rate and the shape of the scattering-time curves fit the predictions. Different erosion-transport laws generate different clast movements. These differences show that studying the tracers in the field may provide a way to establish these laws on the hillslopes and in the rivers. Possible applications include the interpretation of cosmogenic nuclides in individual gravel deposits, provenance analyses, placers, sediment coarsening or fining, the relationship between magnetic tracers in rivers and the river planform, and the tracing of weathered sediment.

  16. Turbulence modification and multiphase turbulence transport modeling

    International Nuclear Information System (INIS)

    Besnard, D.C.; Kataoka, I.; Serizawa, A.

    1991-01-01

    It is shown here that in the derivation of turbulence transport models for multiphase flows, terms naturally appear that can be interpreted as related to turbulence modification of one field by the other. We obtain two such terms, one suggesting turbulence enhancement due to instabilities in two-phase flow, the second one showing turbulence damping due to the presence of the other field, both in gas-particle and gas-liquid cases

  17. Abstracts of the symposium on unsaturated flow and transport modeling

    International Nuclear Information System (INIS)

    1982-03-01

    Abstract titles are: Recent developments in modeling variably saturated flow and transport; Unsaturated flow modeling as applied to field problems; Coupled heat and moisture transport in unsaturated soils; Influence of climatic parameters on movement of radionuclides in a multilayered saturated-unsaturated media; Modeling water and solute transport in soil containing roots; Simulation of consolidation in partially saturated soil materials; modeling of water and solute transport in unsaturated heterogeneous fields; Fluid dynamics and mass transfer in variably-saturated porous media; Solute transport through soils; One-dimensional analytical transport modeling; Convective transport of ideal tracers in unsaturated soils; Chemical transport in macropore-mesopore media under partially saturated conditions; Influence of the tension-saturated zone on contaminant migration in shallow water regimes; Influence of the spatial distribution of velocities in porous media on the form of solute transport; Stochastic vs deterministic models for solute movement in the field; and Stochastic analysis of flow and solute transport

  18. Topological Data Analysis of Biological Aggregation Models

    Science.gov (United States)

    Topaz, Chad M.; Ziegelmeier, Lori; Halverson, Tom

    2015-01-01

    We apply tools from topological data analysis to two mathematical models inspired by biological aggregations such as bird flocks, fish schools, and insect swarms. Our data consists of numerical simulation output from the models of Vicsek and D'Orsogna. These models are dynamical systems describing the movement of agents who interact via alignment, attraction, and/or repulsion. Each simulation time frame is a point cloud in position-velocity space. We analyze the topological structure of these point clouds, interpreting the persistent homology by calculating the first few Betti numbers. These Betti numbers count connected components, topological circles, and trapped volumes present in the data. To interpret our results, we introduce a visualization that displays Betti numbers over simulation time and topological persistence scale. We compare our topological results to order parameters typically used to quantify the global behavior of aggregations, such as polarization and angular momentum. The topological calculations reveal events and structure not captured by the order parameters. PMID:25970184

  19. Accelerating Bayesian inference for evolutionary biology models.

    Science.gov (United States)

    Meyer, Xavier; Chopard, Bastien; Salamin, Nicolas

    2017-03-01

    Bayesian inference is widely used nowadays and relies largely on Markov chain Monte Carlo (MCMC) methods. Evolutionary biology has greatly benefited from the developments of MCMC methods, but the design of more complex and realistic models and the ever growing availability of novel data is pushing the limits of the current use of these methods. We present a parallel Metropolis-Hastings (M-H) framework built with a novel combination of enhancements aimed towards parameter-rich and complex models. We show on a parameter-rich macroevolutionary model increases of the sampling speed up to 35 times with 32 processors when compared to a sequential M-H process. More importantly, our framework achieves up to a twentyfold faster convergence to estimate the posterior probability of phylogenetic trees using 32 processors when compared to the well-known software MrBayes for Bayesian inference of phylogenetic trees. https://bitbucket.org/XavMeyer/hogan. nicolas.salamin@unil.ch. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  20. In vitro placental model optimization for nanoparticle transport studies

    Directory of Open Access Journals (Sweden)

    Cartwright L

    2012-01-01

    Full Text Available Laura Cartwright1, Marie Sønnegaard Poulsen2, Hanne Mørck Nielsen3, Giulio Pojana4, Lisbeth E Knudsen2, Margaret Saunders1, Erik Rytting2,51Bristol Initiative for Research of Child Health (BIRCH, Biophysics Research Unit, St Michael's Hospital, UH Bristol NHS Foundation Trust, Bristol, UK; 2University of Copenhagen, Faculty of Health Sciences, Department of Public Health, 3University of Copenhagen, Faculty of Pharmaceutical Sciences, Department of Pharmaceutics and Analytical Chemistry, Copenhagen, Denmark; 4Department of Environmental Sciences, Informatics and Statistics, University Ca' Foscari Venice, Venice, Italy; 5Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, Texas, USABackground: Advances in biomedical nanotechnology raise hopes in patient populations but may also raise questions regarding biodistribution and biocompatibility, especially during pregnancy. Special consideration must be given to the placenta as a biological barrier because a pregnant woman's exposure to nanoparticles could have significant effects on the fetus developing in the womb. Therefore, the purpose of this study is to optimize an in vitro model for characterizing the transport of nanoparticles across human placental trophoblast cells.Methods: The growth of BeWo (clone b30 human placental choriocarcinoma cells for nanoparticle transport studies was characterized in terms of optimized Transwell® insert type and pore size, the investigation of barrier properties by transmission electron microscopy, tight junction staining, transepithelial electrical resistance, and fluorescein sodium transport. Following the determination of nontoxic concentrations of fluorescent polystyrene nanoparticles, the cellular uptake and transport of 50 nm and 100 nm diameter particles was measured using the in vitro BeWo cell model.Results: Particle size measurements, fluorescence readings, and confocal microscopy indicated both cellular uptake of

  1. Modeling sediment transport with an integrated view of the biofilm effects

    Science.gov (United States)

    Fang, H. W.; Lai, H. J.; Cheng, W.; Huang, L.; He, G. J.

    2017-09-01

    Most natural sediment is invariably covered by biofilms in reservoirs and lakes, which have significant influence on bed form dynamics and sediment transport, and also play a crucial role in natural river evolution, pollutant transport, and habitat changes. However, most models for sediment transport are based on experiments using clean sediments without biological materials. In this study, a three-dimensional mathematical model of hydrodynamics and sediment transport is presented with a comprehensive consideration of the biofilm effects. The changes of the bed resistance mainly due to the different bed form dynamics of the biofilm-coated sediment (biosediment), which affect the hydrodynamic characteristics, are considered. Moreover, the variations of parameters related to sediment transport after the biofilm growth are integrated, including the significant changes of the incipient velocity, settling velocity, reference concentration, and equilibrium bed load transport rate. The proposed model is applied to evaluate the effects of biofilms on the hydrodynamic characteristics and sediment transport in laboratory experiments. Results indicate that the mean velocity increases after the biofilm growth, and the turbulence intensity near the river bed decreases under the same flow condition. Meanwhile, biofilm inhibits sediment from moving independently. Thus, the moderate erosion is observed for biosediment resulting in smaller suspended sediment concentrations. The proposed model can reasonably reflect these sediment transport characteristics with biofilms, and the approach to integration of the biological impact could also be used in other modeling of sediment transport, which can be further applied to provide references for the integrated management of natural aqueous systems.

  2. Transport Models for Inland and Coastal Waters

    Science.gov (United States)

    Hamilton, Peter

    This proceedings volume originates from a symposium held at Berkeley, California, in August 1980. The purpose of the symposium was to assess the ability of models to predict surface water flow and the transport of dissolved substances in natural systems. The authors were invited, after an initial call for papers, by a Scientific Committee of the International Association for Hydraulic Research.In this context, predictive modeling is limited to hydrodynamic and transport models as applied to rivers, estuaries, shallow coastal waters, lakes, and reservoirs. This is a large subject, though evidently not the whole story on predictive techniques applied to natural water bodies, and many different models are described with applications to a wide variety of natural systems. There is relatively little overlap of material between chapters. It is noteworthy that 21 out of 24 authors of the chapters are affiliated with institutions outside the United States, and many of these are from large European hydraulic laboratories. A number of the chapters summarize numerical modeling studies undertaken by these institutions and so provide the U.S. reader with valuable references to the European open literature and laboratory technical reports. The latter are not usually readily available in the United States. This bias reflects a greater willingness of European engineers to employ sophisticated hydrodynamic numerical models as tools for the solution of engineering and environmental problems of natural water bodies.

  3. Natural analogues and radionuclide transport model validation

    International Nuclear Information System (INIS)

    Lever, D.A.

    1987-08-01

    In this paper, some possible roles for natural analogues are discussed from the point of view of those involved with the development of mathematical models for radionuclide transport and with the use of these models in repository safety assessments. The characteristic features of a safety assessment are outlined in order to address the questions of where natural analogues can be used to improve our understanding of the processes involved and where they can assist in validating the models that are used. Natural analogues have the potential to provide useful information about some critical processes, especially long-term chemical processes and migration rates. There is likely to be considerable uncertainty and ambiguity associated with the interpretation of natural analogues, and thus it is their general features which should be emphasized, and models with appropriate levels of sophistication should be used. Experience gained in modelling the Koongarra uranium deposit in northern Australia is drawn upon. (author)

  4. Computational Modeling of Biological Systems From Molecules to Pathways

    CERN Document Server

    2012-01-01

    Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

  5. Biologically based multistage modeling of radiation effects

    Energy Technology Data Exchange (ETDEWEB)

    William Hazelton; Suresh Moolgavkar; E. Georg Luebeck

    2005-08-30

    This past year we have made substantial progress in modeling the contribution of homeostatic regulation to low-dose radiation effects and carcinogenesis. We have worked to refine and apply our multistage carcinogenesis models to explicitly incorporate cell cycle states, simple and complex damage, checkpoint delay, slow and fast repair, differentiation, and apoptosis to study the effects of low-dose ionizing radiation in mouse intestinal crypts, as well as in other tissues. We have one paper accepted for publication in ''Advances in Space Research'', and another manuscript in preparation describing this work. I also wrote a chapter describing our combined cell-cycle and multistage carcinogenesis model that will be published in a book on stochastic carcinogenesis models edited by Wei-Yuan Tan. In addition, we organized and held a workshop on ''Biologically Based Modeling of Human Health Effects of Low dose Ionizing Radiation'', July 28-29, 2005 at Fred Hutchinson Cancer Research Center in Seattle, Washington. We had over 20 participants, including Mary Helen Barcellos-Hoff as keynote speaker, talks by most of the low-dose modelers in the DOE low-dose program, experimentalists including Les Redpath (and Mary Helen), Noelle Metting from DOE, and Tony Brooks. It appears that homeostatic regulation may be central to understanding low-dose radiation phenomena. The primary effects of ionizing radiation (IR) are cell killing, delayed cell cycling, and induction of mutations. However, homeostatic regulation causes cells that are killed or damaged by IR to eventually be replaced. Cells with an initiating mutation may have a replacement advantage, leading to clonal expansion of these initiated cells. Thus we have focused particularly on modeling effects that disturb homeostatic regulation as early steps in the carcinogenic process. There are two primary considerations that support our focus on homeostatic regulation. First, a number of

  6. Simulation of biological flow and transport in complex geometries using embedded boundary/volume-of-fluid methods

    International Nuclear Information System (INIS)

    Trebotich, David

    2007-01-01

    We have developed a simulation capability to model multiscale flow and transport in complex biological systems based on algorithms and software infrastructure developed under the SciDAC APDEC CET. The foundation of this work is a new hybrid fluid-particle method for modeling polymer fluids in irregular microscale geometries that enables long-time simulation of validation experiments. Both continuum viscoelastic and discrete particle representations have been used to model the constitutive behavior of polymer fluids. Complex flow environment geometries are represented on Cartesian grids using an implicit function. Direct simulation of flow in the irregular geometry is then possible using embedded boundary/volume-of-fluid methods without loss of geometric detail. This capability has been used to simulate biological flows in a variety of application geometries including biomedical microdevices, anatomical structures and porous media

  7. Glucose Transport in Cultured Animal Cells: An Exercise for the Undergraduate Cell Biology Laboratory

    Science.gov (United States)

    Ledbetter, Mary Lee S.; Lippert, Malcolm J.

    2002-01-01

    Membrane transport is a fundamental concept that undergraduate students of cell biology understand better with laboratory experience. Formal teaching exercises commonly used to illustrate this concept are unbiological, qualitative, or intricate and time consuming to prepare. We have developed an exercise that uses uptake of radiolabeled nutrient…

  8. EXPERIMENTAL STUDIES THERMOELECTRIC SYSTEMS FOR SHORT-TERM STORAGE AND TRANSPORTATION OF BIOLOGICAL MATERIAL

    Directory of Open Access Journals (Sweden)

    T. A. Ismailov

    2013-01-01

    Full Text Available Described a schematic diagram of an experimental stand thermoelectric system for shortterm storage and transportation of biological material. The technique of the pilot study of the thermoelectric system. The results of the pilot study.

  9. Model for radionuclide transport in running waters

    Energy Technology Data Exchange (ETDEWEB)

    Jonsson, Karin; Elert, Mark [Kemakta Konsult AB, Stockholm (Sweden)

    2005-11-15

    Two sites in Sweden are currently under investigation by SKB for their suitability as places for deep repository of radioactive waste, the Forsmark and Simpevarp/Laxemar area. As a part of the safety assessment, SKB has formulated a biosphere model with different sub-models for different parts of the ecosystem in order to be able to predict the dose to humans following a possible radionuclide discharge from a future deep repository. In this report, a new model concept describing radionuclide transport in streams is presented. The main difference from the previous model for running water used by SKB, where only dilution of the inflow of radionuclides was considered, is that the new model includes parameterizations also of the exchange processes present along the stream. This is done in order to be able to investigate the effect of the retention on the transport and to be able to estimate the resulting concentrations in the different parts of the system. The concentrations determined with this new model could later be used for order of magnitude predictions of the dose to humans. The presented model concept is divided in two parts, one hydraulic and one radionuclide transport model. The hydraulic model is used to determine the flow conditions in the stream channel and is based on the assumption of uniform flow and quasi-stationary conditions. The results from the hydraulic model are used in the radionuclide transport model where the concentration is determined in the different parts of the stream ecosystem. The exchange processes considered are exchange with the sediments due to diffusion, advective transport and sedimentation/resuspension and uptake of radionuclides in biota. Transport of both dissolved radionuclides and sorbed onto particulates is considered. Sorption kinetics in the stream water phase is implemented as the time scale of the residence time in the stream water probably is short in comparison to the time scale of the kinetic sorption. In the sediment

  10. Modeling VOC transport in simulated waste drums

    International Nuclear Information System (INIS)

    Liekhus, K.J.; Gresham, G.L.; Peterson, E.S.; Rae, C.; Hotz, N.J.; Connolly, M.J.

    1993-06-01

    A volatile organic compound (VOC) transport model has been developed to describe unsteady-state VOC permeation and diffusion within a waste drum. Model equations account for three primary mechanisms for VOC transport from a void volume within the drum. These mechanisms are VOC permeation across a polymer boundary, VOC diffusion across an opening in a volume boundary, and VOC solubilization in a polymer boundary. A series of lab-scale experiments was performed in which the VOC concentration was measured in simulated waste drums under different conditions. A lab-scale simulated waste drum consisted of a sized-down 55-gal metal drum containing a modified rigid polyethylene drum liner. Four polyethylene bags were sealed inside a large polyethylene bag, supported by a wire cage, and placed inside the drum liner. The small bags were filled with VOC-air gas mixture and the VOC concentration was measured throughout the drum over a period of time. Test variables included the type of VOC-air gas mixtures introduced into the small bags, the small bag closure type, and the presence or absence of a variable external heat source. Model results were calculated for those trials where the VOC permeability had been measured. Permeabilities for five VOCs [methylene chloride, 1,1,2-trichloro-1,2,2-trifluoroethane (Freon-113), 1,1,1-trichloroethane, carbon tetrachloride, and trichloroethylene] were measured across a polyethylene bag. Comparison of model and experimental results of VOC concentration as a function of time indicate that model accurately accounts for significant VOC transport mechanisms in a lab-scale waste drum

  11. Modeling of radon transport in unsaturated soil

    International Nuclear Information System (INIS)

    Chen, C.; Thomas, D.M.; Green, R.

    1995-01-01

    This study applies a recently developed model, LEACHV, to simulate transport of radon through unsaturated soil and compares calculated soil radon activities against field-measured values. For volatile and gas phase transport, LEACHV is modified from LEACHP, a pesticide version of LEACHM, as well-documented one-dimensional model for water and chemical movement through unsaturated soil. LEACHV adds consideration of air temperature changes and air flow driven by barometric pressure change to the other soil variables currently used in LEACHP. It applies diurnal barometric pressure and air temperature changes to reflect more accurately the typical field conditions, Sensitivity analysis and simulated results have clearly demonstrated the relative importance of barometric pressure change, rainfall events, changes in water content, gas advection, and radon source term in radon transport process. Comparisons among simulated results illustrated that the importance of barometric pressure change and its pumping phenomenon produces both fluctuation in soil gas radon activities and an elevation of the long-term average radon activity in shallow soils of an equal magnitude to the disturbed source parameter. Comparisons between measured and simulated soil radon activities showed that LEACHV can provide realistic estimates of radon activity concentration in the soil profile. 41 refs., 10 figs., 2 tabs

  12. Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

    Science.gov (United States)

    Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

    2015-08-21

    In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

  13. 3 Lectures: "Lagrangian Models", "Numerical Transport Schemes", and "Chemical and Transport Models"

    Science.gov (United States)

    Douglass, A.

    2005-01-01

    The topics for the three lectures for the Canadian Summer School are Lagrangian Models, numerical transport schemes, and chemical and transport models. In the first lecture I will explain the basic components of the Lagrangian model (a trajectory code and a photochemical code), the difficulties in using such a model (initialization) and show some applications in interpretation of aircraft and satellite data. If time permits I will show some results concerning inverse modeling which is being used to evaluate sources of tropospheric pollutants. In the second lecture I will discuss one of the core components of any grid point model, the numerical transport scheme. I will explain the basics of shock capturing schemes, and performance criteria. I will include an example of the importance of horizontal resolution to polar processes. We have learned from NASA's global modeling initiative that horizontal resolution matters for predictions of the future evolution of the ozone hole. The numerical scheme will be evaluated using performance metrics based on satellite observations of long-lived tracers. The final lecture will discuss the evolution of chemical transport models over the last decade. Some of the problems with assimilated winds will be demonstrated, using satellite data to evaluate the simulations.

  14. Transport and Stability of Biological Molecules in Surfactant-Alginate Composite Hydrogels

    Science.gov (United States)

    Stoppel, Whitney L.; White, Joseph C.; Horava, Sarena D.; Bhatia, Surita R.; Roberts, Susan C.

    2013-01-01

    Obstructed transport of biological molecules can result in improper release of pharmaceuticals or biologics from biomedical devices. Recent studies have shown that nonionic surfactants, such as Pluronic® F68 (F68), positively alter biomaterial properties, such as mesh size and microcapsule diameter. To further understand the effect of F68 (incorporated at concentrations well above the critical micelle concentration (CMC)) in traditional biomaterials, the transport properties of BSA and riboflavin were investigated in F68-alginate composite hydrogels. Results indicate that small molecule transport (represented by riboflavin) was not significantly hindered by F68 in homogeneously crosslinked hydrogels (up to an 11% decrease in loading capacity and 14% increase in effective diffusion coefficient, Deff), while protein transport in homogeneously crosslinked hydrogels (represented by BSA) was significantly affected (up to a 43% decrease in loading capacity and 40% increase in Deff). For inhomogeneously crosslinked hydrogels (CaCl2 or BaCl2 gelation), the Deff increased up to 50% and 83% for small molecule and proteins, respectively. Variation in the alginate gelation method was shown to affect transport through measurable changes in swelling ratio (30% decrease) and observable changes in crosslinking structure as well as up to a 3.6 and 11.8-fold difference in Deff for riboflavin and BSA, respectively. The change in protein transport properties is a product of mesh size restrictions (10–25 nm estimated by mechanical properties) and BSA-F68 interaction (DLS). Taken as a whole, these results show that incorporation of a nonionic surfactant at concentrations above the CMC can affect device functionality by impeding the transport of large biological molecules. PMID:21798381

  15. Biological darkening of ice: measurements and models

    Science.gov (United States)

    Cook, J.; Tedstone, A.; Hodson, A. J.; Williamson, C.; McCutcheon, J.; Tranter, M.

    2017-12-01

    Biological growth occurs in the ablation zones of glaciers and ice sheets, resulting in a reduction of the ice albedo. Given the critical role of albedo in determining the surface energy balance - and therefore melt rate - of a mass of ice, understanding and quantifying biological albedo reduction is fundamental to predicting future ice dynamics. This may be particularly important on ablating ice on the western Greenland Ice Sheet, where a `dark ice zone' of varying spatial extent may be partly or mostly explained by biological growth. However, our ability to quantify and predict the contribution of biological impurities to the overall energy balance of glacial systems is currently limited by a lack of understanding of the mechanisms of biological darkening, difficulties in determining the spatial extent of biological impurities and uncertainty in isolating biological from non-biological albedo reduction. Here, new spectral measurements are presented for ice containing varying amounts of biological impurities which were obtained on the ground using a field spectrometer and from the air using a purpose built UAV on the Greenland Ice Sheet in summer 2016 and 2017. Distinctive spectral signatures are identified and used to map the spatial extent of algal blooms on the ice surface. A new radiative transfer scheme (BioSNICAR) for predicting the albedo of snow or ice discolored by microbial life is also described, offering insight into the mechanisms of biological darkening. Together, these demonstrate the critical role played by pigmented algae in darkening ice surfaces and provide a framework for predicting biological albedo reduction in future climate scenarios.

  16. INTERVAL OBSERVER FOR A BIOLOGICAL REACTOR MODEL

    Directory of Open Access Journals (Sweden)

    T. A. Kharkovskaia

    2014-05-01

    Full Text Available The method of an interval observer design for nonlinear systems with parametric uncertainties is considered. The interval observer synthesis problem for systems with varying parameters consists in the following. If there is the uncertainty restraint for the state values of the system, limiting the initial conditions of the system and the set of admissible values for the vector of unknown parameters and inputs, the interval existence condition for the estimations of the system state variables, containing the actual state at a given time, needs to be held valid over the whole considered time segment as well. Conditions of the interval observers design for the considered class of systems are shown. They are: limitation of the input and state, the existence of a majorizing function defining the uncertainty vector for the system, Lipschitz continuity or finiteness of this function, the existence of an observer gain with the suitable Lyapunov matrix. The main condition for design of such a device is cooperativity of the interval estimation error dynamics. An individual observer gain matrix selection problem is considered. In order to ensure the property of cooperativity for interval estimation error dynamics, a static transformation of coordinates is proposed. The proposed algorithm is demonstrated by computer modeling of the biological reactor. Possible applications of these interval estimation systems are the spheres of robust control, where the presence of various types of uncertainties in the system dynamics is assumed, biotechnology and environmental systems and processes, mechatronics and robotics, etc.

  17. Risk management model in road transport systems

    Science.gov (United States)

    Sakhapov, R. L.; Nikolaeva, R. V.; Gatiyatullin, M. H.; Makhmutov, M. M.

    2016-08-01

    The article presents the results of a study of road safety indicators that influence the development and operation of the transport system. Road safety is considered as a continuous process of risk management. Authors constructed a model that relates the social risks of a major road safety indicator - the level of motorization. The model gives a fairly accurate assessment of the level of social risk for any given level of motorization. Authors calculated the dependence of the level of socio-economic costs of accidents and injured people in them. The applicability of the concept of socio-economic damage is caused by the presence of a linear relationship between the natural and economic indicators damage from accidents. The optimization of social risk is reduced to finding the extremum of the objective function that characterizes the economic effect of the implementation of measures to improve safety. The calculations make it possible to maximize the net present value, depending on the costs of improving road safety, taking into account socio-economic damage caused by accidents. The proposed econometric models make it possible to quantify the efficiency of the transportation system, allow to simulate the change in road safety indicators.

  18. Network-Based Models in Molecular Biology

    Science.gov (United States)

    Beyer, Andreas

    Biological systems are characterized by a large number of diverse interactions. Interaction maps have been used to abstract those interactions at all biological scales ranging from food webs at the ecosystem level down to protein interaction networks at the molecular scale.

  19. Modeling in transport phenomena a conceptual approach

    CERN Document Server

    Tosun, Ismail

    2007-01-01

    Modeling in Transport Phenomena, Second Edition presents and clearly explains with example problems the basic concepts and their applications to fluid flow, heat transfer, mass transfer, chemical reaction engineering and thermodynamics. A balanced approach is presented between analysis and synthesis, students will understand how to use the solution in engineering analysis. Systematic derivations of the equations and the physical significance of each term are given in detail, for students to easily understand and follow up the material. There is a strong incentive in science and engineering to

  20. Coupling of transport and geochemical models

    International Nuclear Information System (INIS)

    Noy, D.J.

    1985-01-01

    This contract stipulated separate pieces of work to consider mass transport in the far-field of a repository, and more detailed geochemical modelling of the groundwater in the near-field. It was envisaged that the far-field problem would be tackled by numerical solutions to the classical advection-diffusion equation obtained by the finite element method. For the near-field problem the feasibility of coupling existing geochemical equilibrium codes to the three dimensional groundwater flow codes was to be investigated. This report is divided into two sections with one part devoted to each aspect of this contract. (author)

  1. A disaggregate freight transport model of transport chain and shipment size choice

    NARCIS (Netherlands)

    Windisch, E.; De Jong, G.C.; Van Nes, R.; Hoogendoorn, S.P.

    2010-01-01

    The field of freight transport modelling is relatively young compared to passenger transport modelling. However, some key issues in freight policy, like growing freight shares on the road, advanced logistics concepts or emerging strict freight transport regulations, have been creating increasing

  2. Toward university modeling instruction--biology: adapting curricular frameworks from physics to biology.

    Science.gov (United States)

    Manthey, Seth; Brewe, Eric

    2013-06-01

    University Modeling Instruction (UMI) is an approach to curriculum and pedagogy that focuses instruction on engaging students in building, validating, and deploying scientific models. Modeling Instruction has been successfully implemented in both high school and university physics courses. Studies within the physics education research (PER) community have identified UMI's positive impacts on learning gains, equity, attitudinal shifts, and self-efficacy. While the success of this pedagogical approach has been recognized within the physics community, the use of models and modeling practices is still being developed for biology. Drawing from the existing research on UMI in physics, we describe the theoretical foundations of UMI and how UMI can be adapted to include an emphasis on models and modeling for undergraduate introductory biology courses. In particular, we discuss our ongoing work to develop a framework for the first semester of a two-semester introductory biology course sequence by identifying the essential basic models for an introductory biology course sequence.

  3. Toward University Modeling Instruction—Biology: Adapting Curricular Frameworks from Physics to Biology

    Science.gov (United States)

    Manthey, Seth; Brewe, Eric

    2013-01-01

    University Modeling Instruction (UMI) is an approach to curriculum and pedagogy that focuses instruction on engaging students in building, validating, and deploying scientific models. Modeling Instruction has been successfully implemented in both high school and university physics courses. Studies within the physics education research (PER) community have identified UMI's positive impacts on learning gains, equity, attitudinal shifts, and self-efficacy. While the success of this pedagogical approach has been recognized within the physics community, the use of models and modeling practices is still being developed for biology. Drawing from the existing research on UMI in physics, we describe the theoretical foundations of UMI and how UMI can be adapted to include an emphasis on models and modeling for undergraduate introductory biology courses. In particular, we discuss our ongoing work to develop a framework for the first semester of a two-semester introductory biology course sequence by identifying the essential basic models for an introductory biology course sequence. PMID:23737628

  4. Uncertainty in reactive transport geochemical modelling

    International Nuclear Information System (INIS)

    Oedegaard-Jensen, A.; Ekberg, C.

    2005-01-01

    Full text of publication follows: Geochemical modelling is one way of predicting the transport of i.e. radionuclides in a rock formation. In a rock formation there will be fractures in which water and dissolved species can be transported. The composition of the water and the rock can either increase or decrease the mobility of the transported entities. When doing simulations on the mobility or transport of different species one has to know the exact water composition, the exact flow rates in the fracture and in the surrounding rock, the porosity and which minerals the rock is composed of. The problem with simulations on rocks is that the rock itself it not uniform i.e. larger fractures in some areas and smaller in other areas which can give different water flows. The rock composition can be different in different areas. In additions to this variance in the rock there are also problems with measuring the physical parameters used in a simulation. All measurements will perturb the rock and this perturbation will results in more or less correct values of the interesting parameters. The analytical methods used are also encumbered with uncertainties which in this case are added to the uncertainty from the perturbation of the analysed parameters. When doing simulation the effect of the uncertainties must be taken into account. As the computers are getting faster and faster the complexity of simulated systems are increased which also increase the uncertainty in the results from the simulations. In this paper we will show how the uncertainty in the different parameters will effect the solubility and mobility of different species. Small uncertainties in the input parameters can result in large uncertainties in the end. (authors)

  5. Oscillation and stability of delay models in biology

    CERN Document Server

    Agarwal, Ravi P; Saker, Samir H

    2014-01-01

    Environmental variation plays an important role in many biological and ecological dynamical systems. This monograph focuses on the study of oscillation and the stability of delay models occurring in biology. The book presents recent research results on the qualitative behavior of mathematical models under different physical and environmental conditions, covering dynamics including the distribution and consumption of food. Researchers in the fields of mathematical modeling, mathematical biology, and population dynamics will be particularly interested in this material.

  6. Computerised modelling for developmental biology : an exploration with case studies

    NARCIS (Netherlands)

    Bertens, Laura M.F.

    2012-01-01

    Many studies in developmental biology rely on the construction and analysis of models. This research presents a broad view of modelling approaches for developmental biology, with a focus on computational methods. An overview of modelling techniques is given, followed by several case studies. Using

  7. Conceptual and Numerical Models for UZ Flow and Transport

    International Nuclear Information System (INIS)

    Liu, H.

    2000-01-01

    The purpose of this Analysis/Model Report (AMR) is to document the conceptual and numerical models used for modeling of unsaturated zone (UZ) fluid (water and air) flow and solute transport processes. This is in accordance with ''AMR Development Plan for U0030 Conceptual and Numerical Models for Unsaturated Zone (UZ) Flow and Transport Processes, Rev 00''. The conceptual and numerical modeling approaches described in this AMR are used for models of UZ flow and transport in fractured, unsaturated rock under ambient and thermal conditions, which are documented in separate AMRs. This AMR supports the UZ Flow and Transport Process Model Report (PMR), the Near Field Environment PMR, and the following models: Calibrated Properties Model; UZ Flow Models and Submodels; Mountain-Scale Coupled Processes Model; Thermal-Hydrologic-Chemical (THC) Seepage Model; Drift Scale Test (DST) THC Model; Seepage Model for Performance Assessment (PA); and UZ Radionuclide Transport Models

  8. Morphogenesis and pattern formation in biological systems experiments and models

    CERN Document Server

    Noji, Sumihare; Ueno, Naoto; Maini, Philip

    2003-01-01

    A central goal of current biology is to decode the mechanisms that underlie the processes of morphogenesis and pattern formation. Concerned with the analysis of those phenomena, this book covers a broad range of research fields, including developmental biology, molecular biology, plant morphogenesis, ecology, epidemiology, medicine, paleontology, evolutionary biology, mathematical biology, and computational biology. In Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models, experimental and theoretical aspects of biology are integrated for the construction and investigation of models of complex processes. This collection of articles on the latest advances by leading researchers not only brings together work from a wide spectrum of disciplines, but also provides a stepping-stone to the creation of new areas of discovery.

  9. Particle transport model sensitivity on wave-induced processes

    Science.gov (United States)

    Staneva, Joanna; Ricker, Marcel; Krüger, Oliver; Breivik, Oyvind; Stanev, Emil; Schrum, Corinna

    2017-04-01

    Different effects of wind waves on the hydrodynamics in the North Sea are investigated using a coupled wave (WAM) and circulation (NEMO) model system. The terms accounting for the wave-current interaction are: the Stokes-Coriolis force, the sea-state dependent momentum and energy flux. The role of the different Stokes drift parameterizations is investigated using a particle-drift model. Those particles can be considered as simple representations of either oil fractions, or fish larvae. In the ocean circulation models the momentum flux from the atmosphere, which is related to the wind speed, is passed directly to the ocean and this is controlled by the drag coefficient. However, in the real ocean, the waves play also the role of a reservoir for momentum and energy because different amounts of the momentum flux from the atmosphere is taken up by the waves. In the coupled model system the momentum transferred into the ocean model is estimated as the fraction of the total flux that goes directly to the currents plus the momentum lost from wave dissipation. Additionally, we demonstrate that the wave-induced Stokes-Coriolis force leads to a deflection of the current. During the extreme events the Stokes velocity is comparable in magnitude to the current velocity. The resulting wave-induced drift is crucial for the transport of particles in the upper ocean. The performed sensitivity analyses demonstrate that the model skill depends on the chosen processes. The results are validated using surface drifters, ADCP, HF radar data and other in-situ measurements in different regions of the North Sea with a focus on the coastal areas. The using of a coupled model system reveals that the newly introduced wave effects are important for the drift-model performance, especially during extremes. Those effects cannot be neglected by search and rescue, oil-spill, transport of biological material, or larva drift modelling.

  10. A Lagrangian mixing frequency model for transported PDF modeling

    Science.gov (United States)

    Turkeri, Hasret; Zhao, Xinyu

    2017-11-01

    In this study, a Lagrangian mixing frequency model is proposed for molecular mixing models within the framework of transported probability density function (PDF) methods. The model is based on the dissipations of mixture fraction and progress variables obtained from Lagrangian particles in PDF methods. The new model is proposed as a remedy to the difficulty in choosing the optimal model constant parameters when using conventional mixing frequency models. The model is implemented in combination with the Interaction by exchange with the mean (IEM) mixing model. The performance of the new model is examined by performing simulations of Sandia Flame D and the turbulent premixed flame from the Cambridge stratified flame series. The simulations are performed using the pdfFOAM solver which is a LES/PDF solver developed entirely in OpenFOAM. A 16-species reduced mechanism is used to represent methane/air combustion, and in situ adaptive tabulation is employed to accelerate the finite-rate chemistry calculations. The results are compared with experimental measurements as well as with the results obtained using conventional mixing frequency models. Dynamic mixing frequencies are predicted using the new model without solving additional transport equations, and good agreement with experimental data is observed.

  11. Modelling biological and chemically induced precipitation of calcium phosphate in enhanced biological phosphorus removal systems.

    Science.gov (United States)

    Barat, R; Montoya, T; Seco, A; Ferrer, J

    2011-06-01

    The biologically induced precipitation processes can be important in wastewater treatment, in particular treating raw wastewater with high calcium concentration combined with Enhanced Biological Phosphorus Removal. Currently, there is little information and experience in modelling jointly biological and chemical processes. This paper presents a calcium phosphate precipitation model and its inclusion in the Activated Sludge Model No 2d (ASM2d). The proposed precipitation model considers that aqueous phase reactions quickly achieve the chemical equilibrium and that aqueous-solid change is kinetically governed. The model was calibrated using data from four experiments in a Sequencing Batch Reactor (SBR) operated for EBPR and finally validated with two experiments. The precipitation model proposed was able to reproduce the dynamics of amorphous calcium phosphate (ACP) formation and later crystallization to hydroxyapatite (HAP) under different scenarios. The model successfully characterised the EBPR performance of the SBR, including the biological, physical and chemical processes. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Parameter optimization for surface flux transport models

    Science.gov (United States)

    Whitbread, T.; Yeates, A. R.; Muñoz-Jaramillo, A.; Petrie, G. J. D.

    2017-11-01

    Accurate prediction of solar activity calls for precise calibration of solar cycle models. Consequently we aim to find optimal parameters for models which describe the physical processes on the solar surface, which in turn act as proxies for what occurs in the interior and provide source terms for coronal models. We use a genetic algorithm to optimize surface flux transport models using National Solar Observatory (NSO) magnetogram data for Solar Cycle 23. This is applied to both a 1D model that inserts new magnetic flux in the form of idealized bipolar magnetic regions, and also to a 2D model that assimilates specific shapes of real active regions. The genetic algorithm searches for parameter sets (meridional flow speed and profile, supergranular diffusivity, initial magnetic field, and radial decay time) that produce the best fit between observed and simulated butterfly diagrams, weighted by a latitude-dependent error structure which reflects uncertainty in observations. Due to the easily adaptable nature of the 2D model, the optimization process is repeated for Cycles 21, 22, and 24 in order to analyse cycle-to-cycle variation of the optimal solution. We find that the ranges and optimal solutions for the various regimes are in reasonable agreement with results from the literature, both theoretical and observational. The optimal meridional flow profiles for each regime are almost entirely within observational bounds determined by magnetic feature tracking, with the 2D model being able to accommodate the mean observed profile more successfully. Differences between models appear to be important in deciding values for the diffusive and decay terms. In like fashion, differences in the behaviours of different solar cycles lead to contrasts in parameters defining the meridional flow and initial field strength.

  13. OFFl Models: Novel Schema for Dynamical Modeling of Biological Systems.

    Directory of Open Access Journals (Sweden)

    C Brandon Ogbunugafor

    Full Text Available Flow diagrams are a common tool used to help build and interpret models of dynamical systems, often in biological contexts such as consumer-resource models and similar compartmental models. Typically, their usage is intuitive and informal. Here, we present a formalized version of flow diagrams as a kind of weighted directed graph which follow a strict grammar, which translate into a system of ordinary differential equations (ODEs by a single unambiguous rule, and which have an equivalent representation as a relational database. (We abbreviate this schema of "ODEs and formalized flow diagrams" as OFFL. Drawing a diagram within this strict grammar encourages a mental discipline on the part of the modeler in which all dynamical processes of a system are thought of as interactions between dynamical species that draw parcels from one or more source species and deposit them into target species according to a set of transformation rules. From these rules, the net rate of change for each species can be derived. The modeling schema can therefore be understood as both an epistemic and practical heuristic for modeling, serving both as an organizational framework for the model building process and as a mechanism for deriving ODEs. All steps of the schema beyond the initial scientific (intuitive, creative abstraction of natural observations into model variables are algorithmic and easily carried out by a computer, thus enabling the future development of a dedicated software implementation. Such tools would empower the modeler to consider significantly more complex models than practical limitations might have otherwise proscribed, since the modeling framework itself manages that complexity on the modeler's behalf. In this report, we describe the chief motivations for OFFL, carefully outline its implementation, and utilize a range of classic examples from ecology and epidemiology to showcase its features.

  14. Modelling of sediment transport at Muria peninsula coastal, Jepara

    International Nuclear Information System (INIS)

    Heni Susiati; Yarianto SBS; Wahyu Pandoe; Eko Kusratmoko; Aris Poniman

    2010-01-01

    Modelling of transport sediment modelling at Muria Peninsula have been done. In this study we had been used mathematical model that consist of hydrodynamics and sediment transport . Data input for modelling has been used tidal, monsoon wind, and river debit. Simulation result of sediment transport modelling showed that tides pattern and seasonal variations are the main causes of variations in the suspended sediment distribution in Muria Peninsula. (author)

  15. Genome-scale biological models for industrial microbial systems.

    Science.gov (United States)

    Xu, Nan; Ye, Chao; Liu, Liming

    2018-04-01

    The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

  16. A framework for standardizing flight characteristics for separating biology from meteorology in long-range insect transport

    Science.gov (United States)

    Gary L. Achtemeier

    1998-01-01

    Once airborne during long-range transport, to what extent is the final destination determined by the biota? It is well known that a biological mechanism initiates flight and another biological mechanism terminates flight. Therefore, efforts to answer the above question should be focused on en route insect behavior. A strategy is proposed to isolate biology...

  17. Mathematical modeling of the evolution of a simple biological system

    Digital Repository Service at National Institute of Oceanography (India)

    Gonsalves, M.J.B.D.; Neetu, S.; Krishnan, K.P.; Attri, K.; LokaBharathi, P.A.

    Paula, Goa 403 004, India. Phone: +91 0832 2450624, Fax: +91 0832 2450606, e-mail: mjudith@nio.org Introduction In India, classroom education in biology does not generally include an exercise in which the data can be used to develop models.... This has hampered exposure to quantitative tools in biology, much to the disadvantage of students. The purpose of this note is to report an exercise we carried out to expose traditional biologists educated in India to mathematical modelling of biological...

  18. Nonequilibrium thermodynamics transport and rate processes in physical, chemical and biological systems

    CERN Document Server

    Demirel, Yasar

    2014-01-01

    Natural phenomena consist of simultaneously occurring transport processes and chemical reactions. These processes may interact with each other and may lead to self-organized structures, fluctuations, instabilities, and evolutionary systems. Nonequilibrium Thermodynamics, 3rd edition emphasizes the unifying role of thermodynamics in analyzing the natural phenomena. This third edition updates and expands on the first and second editions by focusing on the general balance equations for coupled processes of physical, chemical, and biological systems. The new edition contains a new chapte

  19. Modelling Emission of Pollutants from transportation using mobile sensing data

    DEFF Research Database (Denmark)

    Lehmann, Anders

    to use data acquired from smartphones to im- prove transportation related air quality models and models for climate gas emission from transportation. These models can be used for planning of transportation net- works, monitoring of air quality, and automate transport related green accounting. More...... accurate transportation models can be obtained by using observed travel routes, acquired from smartphone data, rather than indirectly computed routes, as input to a model of route choice in a transportation network. Smartphone data can also be used to gain detailed knowledge of the driving style...... scientific contributions of the dissertation are: • Algorithm for origin destination demand matrix creation from smartphone data. • The development of a novel map matching algorithm suitable for a database. • Using user experienced routes as a seed for a transport model. • Driving mode detection from...

  20. Biochemical Space: A Framework for Systemic Annotation of Biological Models

    Czech Academy of Sciences Publication Activity Database

    Klement, M.; Děd, T.; Šafránek, D.; Červený, Jan; Müller, Stefan; Steuer, Ralf

    2014-01-01

    Roč. 306, JUL (2014), s. 31-44 ISSN 1571-0661 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : biological models * model annotation * systems biology * cyanobacteria Subject RIV: EH - Ecology, Behaviour

  1. Digital Learning Material for Model Building in Molecular Biology

    Science.gov (United States)

    Aegerter-Wilmsen, Tinri; Janssen, Fred; Hartog, Rob; Bisseling, Ton

    2005-01-01

    Building models to describe processes forms an essential part of molecular biology research. However, in molecular biology curricula little attention is generally being paid to the development of this skill. In order to provide students the opportunity to improve their model building skills, we decided to develop a number of digital cases about…

  2. Review of "Stochastic Modelling for Systems Biology" by Darren Wilkinson

    Directory of Open Access Journals (Sweden)

    Bullinger Eric

    2006-12-01

    Full Text Available Abstract "Stochastic Modelling for Systems Biology" by Darren Wilkinson introduces the peculiarities of stochastic modelling in biology. This book is particularly suited to as a textbook or for self-study, and for readers with a theoretical background.

  3. Preservice Biology Teachers' Conceptions about the Tentative Nature of Theories and Models in Biology

    Science.gov (United States)

    Reinisch, Bianca; Krüger, Dirk

    2018-01-01

    In research on the nature of science, there is a need to investigate the role and status of different scientific knowledge forms. Theories and models are two of the most important knowledge forms within biology and are the focus of this study. During interviews, preservice biology teachers (N = 10) were asked about their understanding of theories…

  4. Harnessing biological motors to engineer systems for nanoscale transport and assembly.

    Science.gov (United States)

    Goel, Anita; Vogel, Viola

    2008-08-01

    Living systems use biological nanomotors to build life's essential molecules--such as DNA and proteins--as well as to transport cargo inside cells with both spatial and temporal precision. Each motor is highly specialized and carries out a distinct function within the cell. Some have even evolved sophisticated mechanisms to ensure quality control during nanomanufacturing processes, whether to correct errors in biosynthesis or to detect and permit the repair of damaged transport highways. In general, these nanomotors consume chemical energy in order to undergo a series of shape changes that let them interact sequentially with other molecules. Here we review some of the many tasks that biomotors perform and analyse their underlying design principles from an engineering perspective. We also discuss experiments and strategies to integrate biomotors into synthetic environments for applications such as sensing, transport and assembly.

  5. BROMOC suite: Monte Carlo/Brownian dynamics suite for studies of ion permeation and DNA transport in biological and artificial pores with effective potentials.

    Science.gov (United States)

    De Biase, Pablo M; Markosyan, Suren; Noskov, Sergei

    2015-02-05

    The transport of ions and solutes by biological pores is central for cellular processes and has a variety of applications in modern biotechnology. The time scale involved in the polymer transport across a nanopore is beyond the accessibility of conventional MD simulations. Moreover, experimental studies lack sufficient resolution to provide details on the molecular underpinning of the transport mechanisms. BROMOC, the code presented herein, performs Brownian dynamics simulations, both serial and parallel, up to several milliseconds long. BROMOC can be used to model large biological systems. IMC-MACRO software allows for the development of effective potentials for solute-ion interactions based on radial distribution function from all-atom MD. BROMOC Suite also provides a versatile set of tools to do a wide variety of preprocessing and postsimulation analysis. We illustrate a potential application with ion and ssDNA transport in MspA nanopore. © 2014 Wiley Periodicals, Inc.

  6. Probabilistic finite-size transport models for fusion: Anomalous transport and scaling laws

    International Nuclear Information System (INIS)

    Milligen, B.Ph. van; Sanchez, R.; Carreras, B.A.

    2004-01-01

    Transport in fusion plasmas in the low confinement mode is characterized by several remarkable properties: the anomalous scaling of transport with system size, stiff (or 'canonical') profiles, power degradation, and rapid transport phenomena. The present article explores the possibilities of constructing a unified transport model, based on the continuous-time random walk, in which all these phenomena are handled adequately. The resulting formalism appears to be sufficiently general to provide a sound starting point for the development of a full-blown plasma transport code, capable of incorporating the relevant microscopic transport mechanisms, and allowing predictions of confinement properties

  7. Modelling total solar irradiance using a flux transport model

    Science.gov (United States)

    Dasi Espuig, Maria; Jiang, Jie; Krivova, Natalie; Solanki, Sami

    2014-05-01

    Reconstructions of solar irradiance into the past are of considerable interest for studies of solar influence on climate. Models based on the assumption that irradiance changes are caused by the evolution of the photospheric magnetic field have been the most successful in reproducing the measured irradiance variations. Our SATIRE-S model is one of these. It uses solar full-disc magnetograms as an input, and these are available for less than four decades. Thus, to reconstruct the irradiance back to times when no observed magnetograms are available, we combine the SATIRE-S model with synthetic magnetograms, produced using a surface flux transport model. The model is fed with daily, observed or modelled statistically, records of sunspot positions, areas, and tilt angles. To describe the secular change in the irradiance, we used the concept of overlapping ephemeral region cycles. With this technique TSI can be reconstructed back to 1700.

  8. Modeling the mechanisms of biological GTP hydrolysis

    DEFF Research Database (Denmark)

    Carvalho, Alexandra T.P.; Szeler, Klaudia; Vavitsas, Konstantinos

    2015-01-01

    in which GTP hydrolysis is activated and regulated is still a controversial topic and well-designed simulations can play an important role in resolving and rationalizing the experimental data. In this review, we discuss the contributions of computational biology to our understanding of GTP hydrolysis...

  9. Modeling Oxygen Transport in the Human Placenta

    Science.gov (United States)

    Serov, Alexander; Filoche, Marcel; Salafia, Carolyn; Grebenkov, Denis

    Efficient functioning of the human placenta is crucial for the favorable pregnancy outcome. We construct a 3D model of oxygen transport in the placenta based on its histological cross-sections. The model accounts for both diffusion and convention of oxygen in the intervillous space and allows one to estimate oxygen uptake of a placentone. We demonstrate the existence of an optimal villi density maximizing the uptake and explain it as a trade-off between the incoming oxygen flow and the absorbing villous surface. Calculations performed for arbitrary shapes of fetal villi show that only two geometrical characteristics - villi density and the effective villi radius - are required to predict fetal oxygen uptake. Two combinations of physiological parameters that determine oxygen uptake are also identified: maximal oxygen inflow of a placentone and the Damköhler number. An automatic image analysis method is developed and applied to 22 healthy placental cross-sections demonstrating that villi density of a healthy human placenta lies within 10% of the optimal value, while overall geometry efficiency is rather low (around 30-40%). In a perspective, the model can constitute the base of a reliable tool of post partum oxygen exchange efficiency assessment in the human placenta. Also affiliated with Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA.

  10. A Process-Based Transport-Distance Model of Aeolian Transport

    Science.gov (United States)

    Naylor, A. K.; Okin, G.; Wainwright, J.; Parsons, A. J.

    2017-12-01

    We present a new approach to modeling aeolian transport based on transport distance. Particle fluxes are based on statistical probabilities of particle detachment and distributions of transport lengths, which are functions of particle size classes. A computational saltation model is used to simulate transport distances over a variety of sizes. These are fit to an exponential distribution, which has the advantages of computational economy, concordance with current field measurements, and a meaningful relationship to theoretical assumptions about mean and median particle transport distance. This novel approach includes particle-particle interactions, which are important for sustaining aeolian transport and dust emission. Results from this model are compared with results from both bulk- and particle-sized-specific transport equations as well as empirical wind tunnel studies. The transport-distance approach has been successfully used for hydraulic processes, and extending this methodology from hydraulic to aeolian transport opens up the possibility of modeling joint transport by wind and water using consistent physics. Particularly in nutrient-limited environments, modeling the joint action of aeolian and hydraulic transport is essential for understanding the spatial distribution of biomass across landscapes and how it responds to climatic variability and change.

  11. A biological model of tamponade gases following pneumatic retinopexy.

    Science.gov (United States)

    Hutter, Joseph; Luu, Hoan; Schroeder, LeRoy

    2002-10-01

    Predict the persistence and expansion of intra-ocular tamponade gases used in retinal detachment surgery. Quantify factors that contribute to elevations in the intraocular pressure. We developed a non-equilibrium physiological model of intraocular gas transfer in vitreoretinal surgery. The model was calibrated using published volumetric decay measurements for four perfluorocarbon gases (CF(4), C(2)F(6), C(3)F(8), C( 4)F(10)) injected into the New Zealand red rabbit. We validated the model by comparing predicted and experimental results at different conditions in the rabbit. Using the rabbit results, the model was scaled up to humans. Predictions of gas expansion, half-life, and intraocular pressure in humans were found to correlate very well with clinical results. Gas transfer in the eye was controlled by diffusion through plasma and membranes. Although intraocular pressure depended on several complicating factors such as the physiological condition of the eye as well as the medications being used, prediction of conditions that favor elevations in intraocular pressure were identified based on the transport and thermodynamic properties of the gases. The biological model accurately predicted the dynamics of intraocular gases in the human eye. The major factor affecting the intraocular pressure was the aqueous humor dynamics, which is highly dependent on the physiological conditions in the eye. However, for long duration gases such as perfluoropropane, elevations in intraocular pressure are possible following an increase in volume and/or purity of the injected gas. By injecting a mixture of air with an expansive gas, it is possible to reduce elevations in intraocular pressure in patients with the trade off of a reduced longevity of the gas bubble. For gases that diffuse faster than perfluoropropane, there are minimal effects on intraocular pressure due to these changes.

  12. Sensitivity analysis approaches applied to systems biology models.

    Science.gov (United States)

    Zi, Z

    2011-11-01

    With the rising application of systems biology, sensitivity analysis methods have been widely applied to study the biological systems, including metabolic networks, signalling pathways and genetic circuits. Sensitivity analysis can provide valuable insights about how robust the biological responses are with respect to the changes of biological parameters and which model inputs are the key factors that affect the model outputs. In addition, sensitivity analysis is valuable for guiding experimental analysis, model reduction and parameter estimation. Local and global sensitivity analysis approaches are the two types of sensitivity analysis that are commonly applied in systems biology. Local sensitivity analysis is a classic method that studies the impact of small perturbations on the model outputs. On the other hand, global sensitivity analysis approaches have been applied to understand how the model outputs are affected by large variations of the model input parameters. In this review, the author introduces the basic concepts of sensitivity analysis approaches applied to systems biology models. Moreover, the author discusses the advantages and disadvantages of different sensitivity analysis methods, how to choose a proper sensitivity analysis approach, the available sensitivity analysis tools for systems biology models and the caveats in the interpretation of sensitivity analysis results.

  13. Mathematical interpretation of Brownian motor model: Limit cycles and directed transport phenomena

    Science.gov (United States)

    Yang, Jianqiang; Ma, Hong; Zhong, Suchuang

    2018-03-01

    In this article, we first suggest that the attractor of Brownian motor model is one of the reasons for the directed transport phenomenon of Brownian particle. We take the classical Smoluchowski-Feynman (SF) ratchet model as an example to investigate the relationship between limit cycles and directed transport phenomenon of the Brownian particle. We study the existence and variation rule of limit cycles of SF ratchet model at changing parameters through mathematical methods. The influences of these parameters on the directed transport phenomenon of a Brownian particle are then analyzed through numerical simulations. Reasonable mathematical explanations for the directed transport phenomenon of Brownian particle in SF ratchet model are also formulated on the basis of the existence and variation rule of the limit cycles and numerical simulations. These mathematical explanations provide a theoretical basis for applying these theories in physics, biology, chemistry, and engineering.

  14. Computer Models and Automata Theory in Biology and Medicine

    CERN Document Server

    Baianu, I C

    2004-01-01

    The applications of computers to biological and biomedical problem solving goes back to the very beginnings of computer science, automata theory [1], and mathematical biology [2]. With the advent of more versatile and powerful computers, biological and biomedical applications of computers have proliferated so rapidly that it would be virtually impossible to compile a comprehensive review of all developments in this field. Limitations of computer simulations in biology have also come under close scrutiny, and claims have been made that biological systems have limited information processing power [3]. Such general conjectures do not, however, deter biologists and biomedical researchers from developing new computer applications in biology and medicine. Microprocessors are being widely employed in biological laboratories both for automatic data acquisition/processing and modeling; one particular area, which is of great biomedical interest, involves fast digital image processing and is already established for rout...

  15. A transportable system of models for natural resource damage assessment

    International Nuclear Information System (INIS)

    Reed, M.; French, D.

    1992-01-01

    A system of computer models has been developed for assessment of natural resource economic damages resulting from spills of oil and hazardous materials in marine and fresh water environments. Under USA federal legislation, the results of the model system are presumed correct in damage litigation proceedings. The model can address a wide range of spatial and temporal scales. The equations describing the motion of both pollutants and biota are solved in three dimensions. The model can simulate continuous releases of a contaminant, with representation of complex coastal boundaries, variable bathymetry, multiple shoreline types, and spatially variable ecosystem habitats. A graphic user interface provides easy control of the system in addition to the ability to display elements of the underlying geographical information system data base. The model is implemented on a personal computer and on a UNIX workstation. The structure of the system is such that transport to new geographic regions can be accomplished relatively easily, requiring only the development of the appropriate physical, toxicological, biological, and economic data sets. Applications are currently in progress for USA inland and coastal waters, the Adriatic Sea, the Strait of Sicily, the Gulf of Suez, and the Baltic Sea. 4 refs., 2 figs

  16. A transport model with color confinement

    International Nuclear Information System (INIS)

    Loh, S.

    1997-01-01

    First the mostly important properties of QCD are dealt with. It is made plausible, how the QCD vacuum generates a screening of color charges and is by this responsible for the quark confinement in color singlets. in the following the behaviour of classical color charges and color fields is studied and it is concluded that by this approximation, the neglection of quantum-mechanical fluctuation, the quark confinement cannot be explained, because the mean-field approximation leads to a screening of the color charges. Motivated by this result the Friedberg-Lee soliton model is presented, in which the the color confinement and all further nonperturbative QCD effects are phenomenologically modelled by means of a scalar field. Thereafter a derivation of the transport equations for quarks in the framework of the Wigner-function is presented. An extension of the equation to the Friedberg-Lee model is explained. As results the ground-state properties of the model are studied. Mesonic and baryonic ground-state solutions (soliton solutions) of the equations are constructed, whereby the constituents are both light quarks and heavy quarks. Furthermore the color coupling constant of QCD is fixed by means of the string tension by dynamical separation of the quarks of the meson. The flux tubes formed dynamically in this way are applied, in order to study the interaction of two strings and to calculate a string-string potential. Excited states of the meson (isovectorial modes) are presented as well as the influence of the color confinement on the quark motion. Finally the dynamical formation and the break-up of a string by the production of light and heavy quark pairs is described

  17. Mathematical Modeling of Complex Biological Systems

    OpenAIRE

    Fischer, Hans Peter

    2008-01-01

    To understand complex biological systems such as cells, tissues, or even the human body, it is not sufficient to identify and characterize the individual molecules in the system. It also is necessary to obtain a thorough understanding of the interaction between molecules and pathways. This is even truer for understanding complex diseases such as cancer, Alzheimer’s disease, or alcoholism. With recent technological advances enabling researchers to monitor complex cellular processes on the mole...

  18. Modelling and Inference Strategies for Biological Systems

    OpenAIRE

    Palmisano, Alida

    2010-01-01

    For many years, computers have played an important role in helping scientists to store, manipulate, and analyze data coming from many different disciplines. In recent years, however, new technological capabilities and new ways of thinking about the usefulness of computer science is extending the reach of computers from simple analysis of collected data to hypothesis generation. The aim of this work is to provide a contribution in the Computational Systems Biology field. The main purpose of...

  19. Cellular potts models multiscale extensions and biological applications

    CERN Document Server

    Scianna, Marco

    2013-01-01

    A flexible, cell-level, and lattice-based technique, the cellular Potts model accurately describes the phenomenological mechanisms involved in many biological processes. Cellular Potts Models: Multiscale Extensions and Biological Applications gives an interdisciplinary, accessible treatment of these models, from the original methodologies to the latest developments. The book first explains the biophysical bases, main merits, and limitations of the cellular Potts model. It then proposes several innovative extensions, focusing on ways to integrate and interface the basic cellular Potts model at the mesoscopic scale with approaches that accurately model microscopic dynamics. These extensions are designed to create a nested and hybrid environment, where the evolution of a biological system is realistically driven by the constant interplay and flux of information between the different levels of description. Through several biological examples, the authors demonstrate a qualitative and quantitative agreement with t...

  20. A guide to numerical modelling in systems biology

    CERN Document Server

    Deuflhard, Peter

    2015-01-01

    This book is intended for students of computational systems biology with only a limited background in mathematics. Typical books on systems biology merely mention algorithmic approaches, but without offering a deeper understanding. On the other hand, mathematical books are typically unreadable for computational biologists. The authors of the present book have worked hard to fill this gap. The result is not a book on systems biology, but on computational methods in systems biology. This book originated from courses taught by the authors at Freie Universität Berlin. The guiding idea of the courses was to convey those mathematical insights that are indispensable for systems biology, teaching the necessary mathematical prerequisites by means of many illustrative examples and without any theorems. The three chapters cover the mathematical modelling of biochemical and physiological processes, numerical simulation of the dynamics of biological networks, and identification of model parameters by means of comparisons...

  1. Learning (from) the errors of a systems biology model.

    Science.gov (United States)

    Engelhardt, Benjamin; Frőhlich, Holger; Kschischo, Maik

    2016-02-11

    Mathematical modelling is a labour intensive process involving several iterations of testing on real data and manual model modifications. In biology, the domain knowledge guiding model development is in many cases itself incomplete and uncertain. A major problem in this context is that biological systems are open. Missed or unknown external influences as well as erroneous interactions in the model could thus lead to severely misleading results. Here we introduce the dynamic elastic-net, a data driven mathematical method which automatically detects such model errors in ordinary differential equation (ODE) models. We demonstrate for real and simulated data, how the dynamic elastic-net approach can be used to automatically (i) reconstruct the error signal, (ii) identify the target variables of model error, and (iii) reconstruct the true system state even for incomplete or preliminary models. Our work provides a systematic computational method facilitating modelling of open biological systems under uncertain knowledge.

  2. Survey of research reports in transportation modelling. Part 1

    NARCIS (Netherlands)

    Nijsse, A.; Wamsteker-Andriessen, S.J.

    1993-01-01

    A survey of research reports in transportation modelling in two parts. Part one is devided in reports concerning economic development and car mobility, analyzing large transportation data files and transportation planning and spatial development. Part two consists of reserach reports concerning

  3. Survey of research reports in transportation modelling. Part 2

    NARCIS (Netherlands)

    Nijsse, A.; Wamsteker-Andriessen, S.J.

    1993-01-01

    A survey of research reports in transportation modelling in two parts. Part one is devided in reports concerning economic development and car mobility, analyzing large transportation data files and transportation planning and spatial development. Part two consists of reserach reports concerning

  4. Development of a kinetic model for biological sulphate reduction ...

    African Journals Online (AJOL)

    Further, in the BSR model the end-product sulphide has a gaseous equilibrium not in the UCTADM1 model, and hence the physical gas exchange for sulphide is included. The BSR biological, chemical and physical processes are integrated with those of the UCTADM1 model, to give a complete kinetic model for competitive ...

  5. Three dimensional heat transport modeling in Vossoroca reservoir

    Science.gov (United States)

    Arcie Polli, Bruna; Yoshioka Bernardo, Julio Werner; Hilgert, Stephan; Bleninger, Tobias

    2017-04-01

    Freshwater reservoirs are used for many purposes as hydropower generation, water supply and irrigation. In Brazil, according to the National Energy Balance of 2013, hydropower energy corresponds to 70.1% of the Brazilian demand. Superficial waters (which include rivers, lakes and reservoirs) are the most used source for drinking water supply - 56% of the municipalities use superficial waters as a source of water. The last two years have shown that the Brazilian water and electricity supply is highly vulnerable and that improved management is urgently needed. The construction of reservoirs affects physical, chemical and biological characteristics of the water body, e.g. stratification, temperature, residence time and turbulence reduction. Some water quality issues related to reservoirs are eutrophication, greenhouse gas emission to the atmosphere and dissolved oxygen depletion in the hypolimnion. The understanding of the physical processes in the water body is fundamental to reservoir management. Lakes and reservoirs may present a seasonal behavior and stratify due to hydrological and meteorological conditions, and especially its vertical distribution may be related to water quality. Stratification can control heat and dissolved substances transport. It has been also reported the importance of horizontal temperature gradients, e.g. inflows and its density and processes of mass transfer from shallow to deeper regions of the reservoir, that also may impact water quality. Three dimensional modeling of the heat transport in lakes and reservoirs is an important tool to the understanding and management of these systems. It is possible to estimate periods of large vertical temperature gradients, inhibiting vertical transport and horizontal gradients, which could be responsible for horizontal transport of heat and substances (e.g. differential cooling or inflows). Vossoroca reservoir was constructed in 1949 by the impoundment of São João River and is located near to

  6. Uncertainty in biology a computational modeling approach

    CERN Document Server

    Gomez-Cabrero, David

    2016-01-01

    Computational modeling of biomedical processes is gaining more and more weight in the current research into the etiology of biomedical problems and potential treatment strategies.  Computational modeling allows to reduce, refine and replace animal experimentation as well as to translate findings obtained in these experiments to the human background. However these biomedical problems are inherently complex with a myriad of influencing factors, which strongly complicates the model building and validation process.  This book wants to address four main issues related to the building and validation of computational models of biomedical processes: Modeling establishment under uncertainty Model selection and parameter fitting Sensitivity analysis and model adaptation Model predictions under uncertainty In each of the abovementioned areas, the book discusses a number of key-techniques by means of a general theoretical description followed by one or more practical examples.  This book is intended for graduate stude...

  7. Modeling and analysis of transport in the mammary glands

    Science.gov (United States)

    Quezada, Ana; Vafai, Kambiz

    2014-08-01

    The transport of three toxins moving from the blood stream into the ducts of the mammary glands is analyzed in this work. The model predictions are compared with experimental data from the literature. The utility of the model lies in its potential to improve our understanding of toxin transport as a pre-disposing factor to breast cancer. This work is based on a multi-layer transport model to analyze the toxins present in the breast milk. The breast milk in comparison with other sampling strategies allows us to understand the mass transport of toxins once inside the bloodstream of breastfeeding women. The multi-layer model presented describes the transport of caffeine, DDT and cimetidine. The analysis performed takes into account the unique transport mechanisms for each of the toxins. Our model predicts the movement of toxins and/or drugs within the mammary glands as well as their bioaccumulation in the tissues.

  8. A Modeling Approach to Teaching Evolutionary Biology in High Schools.

    Science.gov (United States)

    Passmore, Cynthia; Stewart, Jim

    2002-01-01

    Describes the commitments and research that went into the design of a 9-week high school course in evolutionary biology designed to bring students to an understanding of the practice of evolutionary biology by engaging them in developing, elaborating, and using one of the discipline's most important explanatory models. (Contains 39 references.)…

  9. UVM Transportation Research Center signature project 1B : integrated land-use, transportation and environmental modeling.

    Science.gov (United States)

    2014-05-01

    Land use and transportation are inextricably linked. Models that capture the dynamics and interactions : of both systems are indispensable for evaluating alternative courses of action in policy and investment. : These models must be spatially disaggr...

  10. Modelling global container freight transport demand

    NARCIS (Netherlands)

    Tavasszy, L.A.; Ivanova, O.; Halim, R.A.

    2015-01-01

    The objective of this chapter is to discuss methods and techniques for a quantitative and descriptive analysis of future container transport demand at a global level. Information on future container transport flows is useful for various purposes. It is instrumental for the assessment of returns of

  11. Modelling multicomponent solute transport in structured soils

    NARCIS (Netherlands)

    Beinum, van G.W.

    2007-01-01

    The mobility of contaminants in soil is an important factor in determining their ability to spread into the wider environment. For non-volatile substances, transport within the soil is generally dominated by transport of dissolved fractions in the soil water phase, via either diffusion or

  12. Spatial Modeling Tools for Cell Biology

    Science.gov (United States)

    2006-10-01

    of the cells total volume. The cytosol contains thousands of enzymes that are responsible for the catalyzation of glycolysis and gluconeogenesis ... dog , swine and pig models [Pantely, 1990, 1991; Stanley 1992]. In these studies, blood flow through the left anterior descending (LAD) coronary...perfusion. In conclusion, even thought our model falls within the (rather large) error bounds of experimental dog , pig and swine models, the

  13. Suitability of Commercial Transport Media for Biological Pathogens under Nonideal Conditions

    Directory of Open Access Journals (Sweden)

    Kyle Hubbard

    2011-01-01

    Full Text Available There is extensive data to support the use of commercial transport media as a stabilizer for known clinical samples; however, there is little information to support their use outside of controlled conditions specified by the manufacturer. Furthermore, there is no data to determine the suitability of said media for biological pathogens, specifically those of interest to the US military. This study evaluates commercial off-the-shelf (COTS transport media based on sample recovery, viability, and quality of nucleic acids and peptides for nonpathogenic strains of Bacillus anthracis, Yersinia pestis, and Venezuelan equine encephalitis virus, in addition to ricin toxin. Samples were stored in COTS, PBST, or no media at various temperatures over an extended test period. The results demonstrate that COTS media, although sufficient for the preservation of nucleic acid and proteinaceous material, are not capable of maintaining an accurate representation of biothreat agents at the time of collection.

  14. Modelling the transport system in China and evaluating the current strategies towards the sustainable transport development

    International Nuclear Information System (INIS)

    Liu, Wen; Lund, Henrik; Mathiesen, Brian Vad

    2013-01-01

    Transport is one of the most challenge sectors when addressing energy security and climate change due to its high reliance on oil products and lack of the alternative fuels. This paper explores the ability of three transport strategies to contribute to the development of a sustainable transport in China. With this purpose in mind, a Chinese transport model has been created and three current transport strategies which are high speed railway (HSR), urban rail transit (URT) and electric vehicle (EV) were evaluated together with a reference transport system in 2020. As conservative results, 13% of the energy saving and 12% of the CO 2 emission reduction can be attained by accomplishing three strategies compared with the reference transport system. However, the energy demand of transport in 2020 with the implementation of three strategies will be about 1.7 times as much as today. The three strategies show the potential of drawing the transport demand to the more energy efficient vehicles; however, more initiatives are needed if the sustainable transport is the long term objective, such as the solutions to stabilise the private vehicle demands, to continuously improve the vehicle efficiency and to boost the alternative fuels produced from the renewable energy sources. - Highlights: • A Chinese transport model was created and three transport strategies were evaluated • Transport is the biggest driver of the oil demand in China not the industry • The energy demand of transport in 2020 will be twice as much as today • Strategies contribute 13% energy saving and 12% CO 2 emission reduction • More initiatives are needed if a sustainable transport is the long-term objective

  15. System Identification Theory Approach to Cohesive Sediment Transport Modelling

    OpenAIRE

    CHEN, HUIXIN

    1997-01-01

    Two aspects of the modelling sediment transport are investigated. One is the univariate time series modelling the current velocity dynamics. The other is the multivariate time series modelling the suspended sediment concentration dynamics. Cohesive sediment dynamics and numerical sediment transport model are reviewed and investigated. The system identification theory and time series analysis method are developed and applied to set up the time series model for current velocity a...

  16. Computational Modeling, Formal Analysis, and Tools for Systems Biology.

    Directory of Open Access Journals (Sweden)

    Ezio Bartocci

    2016-01-01

    Full Text Available As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.

  17. Modeling dynamics of biological and chemical components of aquatic ecosystems

    International Nuclear Information System (INIS)

    Lassiter, R.R.

    1975-05-01

    To provide capability to model aquatic ecosystems or their subsystems as needed for particular research goals, a modeling strategy was developed. Submodels of several processes common to aquatic ecosystems were developed or adapted from previously existing ones. Included are submodels for photosynthesis as a function of light and depth, biological growth rates as a function of temperature, dynamic chemical equilibrium, feeding and growth, and various types of losses to biological populations. These submodels may be used as modules in the construction of models of subsystems or ecosystems. A preliminary model for the nitrogen cycle subsystem was developed using the modeling strategy and applicable submodels. (U.S.)

  18. Characterization of the Hanford 300 area burial grounds. Task IV. Biological transport

    Energy Technology Data Exchange (ETDEWEB)

    Fitzner, R.E.; Gano, K.A.; Rickard, W.H.; Rogers, L.E.

    1979-10-01

    The characteristics of radioactive waste burial sites at the 300 area burial grounds on the Department of Energy's Hanford Site, southeastern Washington were studied. The potential vectors of radionuclide transport studied were vegetation and animals. The overall results showed a low potential for uptake and transport of radionuclides from the 300 area sites. However, additional methods to control physical and biological mechanisms may contribute to the effectiveness of waste burial practices. From the results, the Biological Transport task recommended field studies which include reduction of soil erosion and addition of biobarriers to plants and animals. Vegetation plays a major role in reducing soil erosion, and thereby maintaining the backfill over the burial sites. Of the several species found on the 300 area sites, cheatgrass (Bromus tectorum) appears to be the most desirable as a cover. Besides retarding erosion, it has a shallow root system (does not easily penetrate buried material); it has a low affinity for radionuclide uptake; and its tissues are not easily blown away. Small mammals (specifically, mice) appear to have the most potential for radionuclide exposure and uptake. Small mammals were live-trapped within 10 x 10-meter trap grids. Each animal trapped was surgically implanted with a thermoluminescent dosimeter. When the animal was recaptured, the dosimeter was removed and read for exposure. Exposures were reported in milli-Roentgens. The most consistently trapped small mammals were the Great Basin pocket mouse (Perognathus parvus) and the deer mouse (Peromyscus maniculatus). Results from the dosimeter readings showed that some of those animals had higher than background exposures. Biobarriers to animals could be considered as a mechanism to reduce the potential for radionuclide transport.

  19. Characterization of the Hanford 300 area burial grounds. Task IV. Biological transport

    International Nuclear Information System (INIS)

    Fitzner, R.E.; Gano, K.A.; Rickard, W.H.; Rogers, L.E.

    1979-10-01

    The characteristics of radioactive waste burial sites at the 300 area burial grounds on the Department of Energy's Hanford Site, southeastern Washington were studied. The potential vectors of radionuclide transport studied were vegetation and animals. The overall results showed a low potential for uptake and transport of radionuclides from the 300 area sites. However, additional methods to control physical and biological mechanisms may contribute to the effectiveness of waste burial practices. From the results, the Biological Transport task recommended field studies which include reduction of soil erosion and addition of biobarriers to plants and animals. Vegetation plays a major role in reducing soil erosion, and thereby maintaining the backfill over the burial sites. Of the several species found on the 300 area sites, cheatgrass (Bromus tectorum) appears to be the most desirable as a cover. Besides retarding erosion, it has a shallow root system (does not easily penetrate buried material); it has a low affinity for radionuclide uptake; and its tissues are not easily blown away. Small mammals (specifically, mice) appear to have the most potential for radionuclide exposure and uptake. Small mammals were live-trapped within 10 x 10-meter trap grids. Each animal trapped was surgically implanted with a thermoluminescent dosimeter. When the animal was recaptured, the dosimeter was removed and read for exposure. Exposures were reported in milli-Roentgens. The most consistently trapped small mammals were the Great Basin pocket mouse (Perognathus parvus) and the deer mouse (Peromyscus maniculatus). Results from the dosimeter readings showed that some of those animals had higher than background exposures. Biobarriers to animals could be considered as a mechanism to reduce the potential for radionuclide transport

  20. Simulation of a relativistic heavy ions beam transport in the matter: contribution of the fragmentation process and biological implications

    International Nuclear Information System (INIS)

    Ibnouzahir, M.

    1995-03-01

    The study of relativistic heavy ion collisions permit an approach of the properties of dense and not hadronic matter, and an analysis of the reaction mechanisms. Such studies are also interesting on the biological point of view, since there exist now well defined projects concerning the radiotherapy with high LET particles as neutrons, protons, heavy ions. It is thus necessary to have a good understanding of the processes which occur in the propagation of a relativistic heavy ion beam (E≥ 100 A.MeV) in matter. We have elaborated a three dimensional transport code, using a Monte Carlo method, in order to describe the propagation of Ne and Ar ions in water. Violent nuclear collisions giving fragmentation process have been taken into account by use of the FREESCO program. We have tested the validity of our transport model and we show an important change of the energy deposition at the vicinity of the Bragg peak; such a distortion, due mainly to fragmentation reactions, is of a great interest for biological applications. (author)

  1. Modeling emissions for three-dimensional atmospheric chemistry transport models.

    Science.gov (United States)

    Matthias, Volker; Arndt, Jan A; Aulinger, Armin; Bieser, Johannes; Denier Van Der Gon, Hugo; Kranenburg, Richard; Kuenen, Jeroen; Neumann, Daniel; Pouliot, George; Quante, Markus

    2018-01-24

    Poor air quality is still a threat for human health in many parts of the world. In order to assess measures for emission reductions and improved air quality, three-dimensional atmospheric chemistry transport modeling systems are used in numerous research institutions and public authorities. These models need accurate emission data in appropriate spatial and temporal resolution as input. This paper reviews the most widely used emission inventories on global and regional scale and looks into the methods used to make the inventory data model ready. Shortcomings of using standard temporal profiles for each emission sector are discussed and new methods to improve the spatio-temporal distribution of the emissions are presented. These methods are often neither top-down nor bottom-up approaches but can be seen as hybrid methods that use detailed information about the emission process to derive spatially varying temporal emission profiles. These profiles are subsequently used to distribute bulk emissions like national totals on appropriate grids. The wide area of natural emissions is also summarized and the calculation methods are described. Almost all types of natural emissions depend on meteorological information, which is why they are highly variable in time and space and frequently calculated within the chemistry transport models themselves. The paper closes with an outlook for new ways to improve model ready emission data, for example by using external databases about road traffic flow or satellite data to determine actual land use or leaf area. In a world where emission patterns change rapidly, it seems appropriate to use new types of statistical and observational data to create detailed emission data sets and keep emission inventories up-to-date. Emission data is probably the most important input for chemistry transport model (CTM) systems. It needs to be provided in high temporal and spatial resolution and on a grid that is in agreement with the CTM grid. Simple

  2. Mathematical models in biology bringing mathematics to life

    CERN Document Server

    Ferraro, Maria; Guarracino, Mario

    2015-01-01

    This book presents an exciting collection of contributions based on the workshop “Bringing Maths to Life” held October 27-29, 2014 in Naples, Italy.  The state-of-the art research in biology and the statistical and analytical challenges facing huge masses of data collection are treated in this Work. Specific topics explored in depth surround the sessions and special invited sessions of the workshop and include genetic variability via differential expression, molecular dynamics and modeling, complex biological systems viewed from quantitative models, and microscopy images processing, to name several. In depth discussions of the mathematical analysis required to extract insights from complex bodies of biological datasets, to aid development in the field novel algorithms, methods and software tools for genetic variability, molecular dynamics, and complex biological systems are presented in this book. Researchers and graduate students in biology, life science, and mathematics/statistics will find the content...

  3. Systematic integration of experimental data and models in systems biology.

    Science.gov (United States)

    Li, Peter; Dada, Joseph O; Jameson, Daniel; Spasic, Irena; Swainston, Neil; Carroll, Kathleen; Dunn, Warwick; Khan, Farid; Malys, Naglis; Messiha, Hanan L; Simeonidis, Evangelos; Weichart, Dieter; Winder, Catherine; Wishart, Jill; Broomhead, David S; Goble, Carole A; Gaskell, Simon J; Kell, Douglas B; Westerhoff, Hans V; Mendes, Pedro; Paton, Norman W

    2010-11-29

    The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.

  4. Computer supported estimation of input data for transportation models

    OpenAIRE

    Cenek, Petr; Tarábek, Peter; Kopf, Marija

    2010-01-01

    Control and management of transportation systems frequently rely on optimization or simulation methods based on a suitable model. Such a model uses optimization or simulation procedures and correct input data. The input data define transportation infrastructure and transportation flows. Data acquisition is a costly process and so an efficient approach is highly desirable. The infrastructure can be recognized from drawn maps using segmentation, thinning and vectorization. The accurate definiti...

  5. Mesos-scale modeling of irradiation in pressurized water reactor concrete biological shields

    Energy Technology Data Exchange (ETDEWEB)

    Le Pape, Yann [ORNL; Huang, Hai [Idaho National Laboratory (INL)

    2016-01-01

    Neutron irradiation exposure causes aggregate expansion, namely radiation-induced volumetric expansion (RIVE). The structural significance of RIVE on a portion of a prototypical pressurized water reactor (PWR) concrete biological shield (CBS) is investigated by using a meso- scale nonlinear concrete model with inputs from an irradiation transport code and a coupled moisture transport-heat transfer code. RIVE-induced severe cracking onset appears to be triggered by the ini- tial shrinkage-induced cracking and propagates to a depth of > 10 cm at extended operation of 80 years. Relaxation of the cement paste stresses results in delaying the crack propagation by about 10 years.

  6. Transportation of Dangerous Goods: Turkey Model

    Directory of Open Access Journals (Sweden)

    Murat Şencan

    2017-12-01

    Full Text Available The shortcomings in the implementation of hazardous substances transport in the world and in our country lead to very serious hazards. These problems lead to life, property and very serious environmental disasters. This is not only a matter of transportation, but also of the chemistry, textile and fuel industries. This study provides information on the legislation on dangerous goods transport in Turkey. It also contains technical information on hazardous substances, following the search of the relevant literature for the province of hazardous goods.

  7. Systems modelling and the development of coherent cell biological knowledge

    NARCIS (Netherlands)

    Verhoeff, R.; Waarlo, A.J.; Boersma, K.T.

    2008-01-01

    This article reports on educational design research concerning a learning and teaching strategy for cell biology in upper-secondary education introducing systems modelling as a key competence. The strategy consists of four modelling phases in which students subsequently develop models of freeliving

  8. Some Issues of Biological Shape Modelling with Applications

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Hilger, Klaus Baggesen; Skoglund, Karl

    2003-01-01

    This paper illustrates current research at Informatics and Mathematical Modelling at the Technical University of Denmark within biological shape modelling. We illustrate a series of generalizations to, modifications to, and applications of the elements of constructing models of shape or appearanc...

  9. Contaminant transport at a waste residue deposit: 1. Inverse flow and non-reactive transport modelling

    DEFF Research Database (Denmark)

    Sonnenborg, Torben Obel; Engesgaard, Peter Knudegaard; Rosbjerg, Dan

    1996-01-01

    An application of an inverse flow and transport model to a contaminated aquifer is presented. The objective of the study is to identify physical and nonreactive flow and transport parameters through an optimization approach. The approach can be classified as a statistical procedure, where a flow ...... is the first in a two-paper series describing contaminant transport at a waste residue site. III the second paper, reactive transport at the site is investigated.......An application of an inverse flow and transport model to a contaminated aquifer is presented. The objective of the study is to identify physical and nonreactive flow and transport parameters through an optimization approach. The approach can be classified as a statistical procedure, where a flow...

  10. Modeling of capacitated transportation systems for integral scheduling

    NARCIS (Netherlands)

    Ebben, Mark; van der Heijden, Matthijs C.; Hurink, Johann L.; Schutten, Johannes M.J.

    2003-01-01

    Motivated by a planned automated cargo transportation network, we consider transportation problems in which the finite capacity of resources has to be taken into account. We present a flexible modeling methodology which allows to construct, evaluate, and improve feasible solutions. The modeling is

  11. Modeling of capacitated transportation systems for integral scheduling

    NARCIS (Netherlands)

    Ebben, Mark; van der Heijden, Matthijs C.; Hurink, Johann L.; Schutten, Johannes M.J.

    2003-01-01

    Motivated by a planned automated cargo transportation network, we consider transportation problems in which the finite capacity of resources has to be taken nto account. We present a flexible modeling methodology which allows to construct, evaluate, and improve feasible solutions. The modeling is

  12. Transport models for relativistic heavy-ion collisions at Relativistic ...

    Indian Academy of Sciences (India)

    transport model analysis of two important and complementary observables, the anisotropic flow of bulk hadrons and suppression of hadron yields at high transverse momentum, provide exciting new information on the properties of the plasma formed. Keywords. Quark-gluon plasma; transport models; flow; jet quenching.

  13. Transport models for relativistic heavy-ion collisions at Relativistic ...

    Indian Academy of Sciences (India)

    2015-04-29

    Apr 29, 2015 ... We review the transport models that are widely used to study the properties of the quark-gluon plasma formed in relativistic heavy-ion collisions at RHIC and LHC. We show that transport model analysis of two important and complementary observables, the anisotropic flow of bulk hadrons and suppression ...

  14. A Coupled Chemical and Mass Transport Model for Concrete Durability

    DEFF Research Database (Denmark)

    Jensen, Mads Mønster; Johannesson, Björn; Geiker, Mette Rica

    2012-01-01

    In this paper a general continuum theory is used to evaluate the service life of cement based materials, in terms of mass transport processes and chemical degradation of the solid matrix. The model established is a reactive mass transport model, based on an extended version of the Poisson-Nernst-...

  15. A quantum energy transport model for semiconductor device simulation

    Energy Technology Data Exchange (ETDEWEB)

    Sho, Shohiro, E-mail: shoshohiro@gmail.com [Graduate School of Information Science and Technology, Osaka University, Osaka (Japan); Odanaka, Shinji [Computer Assisted Science Division, Cybermedia Center, Osaka University, Osaka (Japan)

    2013-02-15

    This paper describes numerical methods for a quantum energy transport (QET) model in semiconductors, which is derived by using a diffusion scaling in the quantum hydrodynamic (QHD) model. We newly drive a four-moments QET model similar with a classical ET model. Space discretization is performed by a new set of unknown variables. Numerical stability and convergence are obtained by developing numerical schemes and an iterative solution method with a relaxation method. Numerical simulations of electron transport in a scaled MOSFET device are discussed. The QET model allows simulations of quantum confinement transport, and nonlocal and hot-carrier effects in scaled MOSFETs.

  16. Biocellion: accelerating computer simulation of multicellular biological system models.

    Science.gov (United States)

    Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

    2014-11-01

    Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. European initiatives for modeling emissions from transport

    DEFF Research Database (Denmark)

    Joumard, Robert; Hickman, A. John; Samaras, Zissis

    1998-01-01

    In Europe there have been many cooperative studies into transport emission inventories since the late 80s. These cover the scope of CORINAIR program involving experts from seven European Community laboratories addressing only road transport emissions at national level. These also include the latest...... COST 319 action bringing together about 80 active scientists from the whole of Europe and considering all modes of transport and all inventory levels. The paper briefly presents the history of the various multilateral and EC initiatives and discusses the latest in more detail, from the collection...... of the raw data to the design of the inventory tools. The paper also considers the structures and the main assumptions of the current inventory methods for the various transport modes and various areas of application, including reference to work currently in progress or planned for the near future. Topics...

  18. Symmetrization of mathematical model of charge transport in semiconductors

    Directory of Open Access Journals (Sweden)

    Alexander M. Blokhin

    2002-11-01

    Full Text Available A mathematical model of charge transport in semiconductors is considered. The model is a quasilinear system of differential equations. A problem of finding an additional entropy conservation law and system symmetrization are solved.

  19. Advances in dynamic network modeling in complex transportation systems

    CERN Document Server

    Ukkusuri, Satish V

    2013-01-01

    This book focuses on the latest in dynamic network modeling, including route guidance and traffic control in transportation systems and other complex infrastructure networks. Covers dynamic traffic assignment, flow modeling, mobile sensor deployment and more.

  20. A mesoscale chemical transport model (MEDIUM) nested in a global chemical transport model (MEDIANTE)

    Energy Technology Data Exchange (ETDEWEB)

    Claveau, J.; Ramaroson, R. [Office National d`Etudes et de Recherches Aerospatiales (ONERA), 92 - Chatillon (France)

    1997-12-31

    The lower stratosphere and upper troposphere (UT-LS) are frequently subject to mesoscale or local scale exchange of air masses occurring along discontinuities. This exchange (e.g. downward) can constitute one of the most important source of ozone from the stratosphere down to the middle troposphere where strong mixing dilutes the air mass and competing the non-linear chemistry. The distribution of the chemical species in the troposphere and the lower stratosphere depends upon various source emissions, e.g. from polluted boundary layer or from aircraft emissions. Global models, as well as chemical transport models describe the climatological state of the atmosphere and are not able to describe correctly the stratosphere and troposphere exchange. Mesoscale models go further in the description of smaller scales and can reasonably include a rather detailed chemistry. They can be used to assess the budget of NO{sub x} from aircraft emissions in a mesoscale domain. (author) 4 refs.

  1. Application of rrm as behavior mode choice on modelling transportation

    Science.gov (United States)

    Surbakti, M. S.; Sadullah, A. F.

    2018-03-01

    Transportation mode selection, the first step in transportation planning process, is probably one of the most important planning elements. The development of models that can explain the preference of passengers regarding their chosen mode of public transport option will contribute to the improvement and development of existing public transport. Logit models have been widely used to determine the mode choice models in which the alternative are different transport modes. Random Regret Minimization (RRM) theory is a theory developed from the behavior to choose (choice behavior) in a state of uncertainty. During its development, the theory was used in various disciplines, such as marketing, micro economy, psychology, management, and transportation. This article aims to show the use of RRM in various modes of selection, from the results of various studies that have been conducted both in north sumatera and western Java.

  2. Sediment Transport Model for a Surface Irrigation System

    OpenAIRE

    Mailapalli, Damodhara R.; Raghuwanshi, Narendra S.; Singh, Rajendra

    2013-01-01

    Controlling irrigation-induced soil erosion is one of the important issues of irrigation management and surface water impairment. Irrigation models are useful in managing the irrigation and the associated ill effects on agricultural environment. In this paper, a physically based surface irrigation model was developed to predict sediment transport in irrigated furrows by integrating an irrigation hydraulic model with a quasi-steady state sediment transport model to predict sediment load in fur...

  3. One-Dimensional Transport with Equilibrium Chemistry (OTEQ) - A Reactive Transport Model for Streams and Rivers

    Science.gov (United States)

    Runkel, Robert L.

    2010-01-01

    OTEQ is a mathematical simulation model used to characterize the fate and transport of waterborne solutes in streams and rivers. The model is formed by coupling a solute transport model with a chemical equilibrium submodel. The solute transport model is based on OTIS, a model that considers the physical processes of advection, dispersion, lateral inflow, and transient storage. The equilibrium submodel is based on MINTEQ, a model that considers the speciation and complexation of aqueous species, acid-base reactions, precipitation/dissolution, and sorption. Within OTEQ, reactions in the water column may result in the formation of solid phases (precipitates and sorbed species) that are subject to downstream transport and settling processes. Solid phases on the streambed may also interact with the water column through dissolution and sorption/desorption reactions. Consideration of both mobile (waterborne) and immobile (streambed) solid phases requires a unique set of governing differential equations and solution techniques that are developed herein. The partial differential equations describing physical transport and the algebraic equations describing chemical equilibria are coupled using the sequential iteration approach. The model's ability to simulate pH, precipitation/dissolution, and pH-dependent sorption provides a means of evaluating the complex interactions between instream chemistry and hydrologic transport at the field scale. This report details the development and application of OTEQ. Sections of the report describe model theory, input/output specifications, model applications, and installation instructions. OTEQ may be obtained over the Internet at http://water.usgs.gov/software/OTEQ.

  4. A dynamic model for functional mapping of biological rhythms.

    Science.gov (United States)

    Fu, Guifang; Luo, Jiangtao; Berg, Arthur; Wang, Zhong; Li, Jiahan; Das, Kiranmoy; Li, Runze; Wu, Rongling

    2011-01-01

    Functional mapping is a statistical method for mapping quantitative trait loci (QTLs) that regulate the dynamic pattern of a biological trait. This method integrates mathematical aspects of biological complexity into a mixture model for genetic mapping and tests the genetic effects of QTLs by comparing genotype-specific curve parameters. As a way of quantitatively specifying the dynamic behavior of a system, differential equations have proven to be powerful for modeling and unraveling the biochemical, molecular, and cellular mechanisms of a biological process, such as biological rhythms. The equipment of functional mapping with biologically meaningful differential equations provides new insights into the genetic control of any dynamic processes. We formulate a new functional mapping framework for a dynamic biological rhythm by incorporating a group of ordinary differential equations (ODE). The Runge-Kutta fourth order algorithm was implemented to estimate the parameters that define the system of ODE. The new model will find its implications for understanding the interplay between gene interactions and developmental pathways in complex biological rhythms.

  5. Review of petroleum transport network models and their applicability to a national refinery model

    Energy Technology Data Exchange (ETDEWEB)

    Hooker, J. N.

    1982-04-01

    This report examines four petroleum transport network models to determine whether parts of them can be incorporated into the transportation component of a national refinery model. Two questions in particular are addressed. (a) How do the models under examination represent the oil transport network, estimate link capacities, and calculate transport costs. (b) Are any of these network representations, capacity estimates, or cost functions suitable for inclusion in a linear programming model of oil refinery and primary distribution in the US. Only pipeline and waterway transport is discussed. The models examined are the Department of Energy's OILNET model, the Department of Transportation's Freight Energy Model, the Federal Energy Administration Petroleum Transportation Network Model, and an Oak Ridge National Laboratory oil pipeline energy model. Link capacity and cost functions are recommended for each transport mode. The coefficients of the recommended pipeline cost functions remain to be estimated.

  6. Modeling the coupled mechanics, transport, and growth processes in collagen tissues.

    Energy Technology Data Exchange (ETDEWEB)

    Holdych, David J.; Nguyen, Thao D.; Klein, Patrick A.; in' t Veld, Pieter J.; Stevens, Mark Jackson

    2006-11-01

    The purpose of this project is to develop tools to model and simulate the processes of self-assembly and growth in biological systems from the molecular to the continuum length scales. The model biological system chosen for the study is the tendon fiber which is composed mainly of Type I collagen fibrils. The macroscopic processes of self-assembly and growth at the fiber scale arise from microscopic processes at the fibrillar and molecular length scales. At these nano-scopic length scales, we employed molecular modeling and simulation method to characterize the mechanical behavior and stability of the collagen triple helix and the collagen fibril. To obtain the physical parameters governing mass transport in the tendon fiber we performed direct numerical simulations of fluid flow and solute transport through an idealized fibrillar microstructure. At the continuum scale, we developed a mixture theory approach for modeling the coupled processes of mechanical deformation, transport, and species inter-conversion involved in growth. In the mixture theory approach, the microstructure of the tissue is represented by the species concentration and transport and material parameters, obtained from fibril and molecular scale calculations, while the mechanical deformation, transport, and growth processes are governed by balance laws and constitutive relations developed within a thermodynamically consistent framework.

  7. Transport Routes Optimization Model Through Application of Fuzzy Logic

    Directory of Open Access Journals (Sweden)

    Ivan Bortas

    2018-03-01

    Full Text Available The transport policy of the European Union is based on the mission of restructuring road traffic into other and energy-favourable transport modes which have not been sufficiently represented yet. Therefore, the development of the inland waterway and rail transport, and connectivity in the intermodal transport network are development planning priorities of the European transport strategy. The aim of this research study was to apply the scientific methodology and thus analyse the factors that affect the distribution of the goods flows and by using the fuzzy logic to make an optimization model, according to the criteria of minimizing the costs and negative impact on the environment, for the selection of the optimal transport route. Testing of the model by simulation, was performed on the basis of evaluating the criteria of the influential parameters with unprecise and indefinite input parameters. The testing results show that by the distribution of the goods flow from road transport network to inland waterways or rail transport, can be predicted in advance and determine the transport route with optimal characteristics. The results of the performed research study will be used to improve the process of planning the transport service, with the aim of reducing the transport costs and environmental pollution.

  8. Two-dimensional finite elements model for selenium transport in saturated and unsaturated zones.

    Science.gov (United States)

    Tayfur, Gokmen; Tanji, Kenneth K; Baba, Alper

    2010-10-01

    A two-dimensional finite element model was developed to simulate species of selenium transport in two dimensions in both saturated and unsaturated soil zones. The model considers water, selenate, selenite, and selenomethionine uptake by plants. It also considers adsorption and desorption, oxidation and reduction, volatilization, and chemical and biological transformations of selenate, selenite, and selenomethionine. In addition to simulating water flow, selenate, selenite, and selenomethionine transport, the model also simulates organic and gaseous selenium transport. The developed model was applied to simulate two different observed field data. The simulation of the observed data was satisfactory, with mean absolute error of 48.5 microg/l and mean relative error of 8.9%.

  9. Sensitizing curium luminescence through an antenna protein to investigate biological actinide transport mechanisms.

    Science.gov (United States)

    Sturzbecher-Hoehne, Manuel; Goujon, Christophe; Deblonde, Gauthier J-P; Mason, Anne B; Abergel, Rebecca J

    2013-02-20

    Worldwide stocks of actinides and lanthanide fission products produced through conventional nuclear spent fuel are increasing continuously, resulting in a growing risk of environmental and human exposure to these toxic radioactive metal ions. Understanding the biomolecular pathways involved in mammalian uptake, transport and storage of these f-elements is crucial to the development of new decontamination strategies and could also be beneficial to the design of new containment and separation processes. To start unraveling these pathways, our approach takes advantage of the unique spectroscopic properties of trivalent curium. We clearly show that the human iron transporter transferrin acts as an antenna that sensitizes curium luminescence through intramolecular energy transfer. This behavior has been used to describe the coordination of curium within the two binding sites of the protein and to investigate the recognition of curium-transferrin complexes by the cognate transferrin receptor. In addition to providing the first protein-curium spectroscopic characterization, these studies prove that transferrin receptor-mediated endocytosis is a viable mechanism of intracellular entry for trivalent actinides such as curium and provide a new tool utilizing the specific luminescence of curium for the determination of other biological actinide transport mechanisms.

  10. A finite element model for protein transport in vivo

    Directory of Open Access Journals (Sweden)

    Montas Hubert J

    2007-06-01

    Full Text Available Abstract Background Biological mass transport processes determine the behavior and function of cells, regulate interactions between synthetic agents and recipient targets, and are key elements in the design and use of biosensors. Accurately predicting the outcomes of such processes is crucial to both enhancing our understanding of how these systems function, enabling the design of effective strategies to control their function, and verifying that engineered solutions perform according to plan. Methods A Galerkin-based finite element model was developed and implemented to solve a system of two coupled partial differential equations governing biomolecule transport and reaction in live cells. The simulator was coupled, in the framework of an inverse modeling strategy, with an optimization algorithm and an experimental time series, obtained by the Fluorescence Recovery after Photobleaching (FRAP technique, to estimate biomolecule mass transport and reaction rate parameters. In the inverse algorithm, an adaptive method was implemented to calculate sensitivity matrix. A multi-criteria termination rule was developed to stop the inverse code at the solution. The applicability of the model was illustrated by simulating the mobility and binding of GFP-tagged glucocorticoid receptor in the nucleoplasm of mouse adenocarcinoma. Results The numerical simulator shows excellent agreement with the analytic solutions and experimental FRAP data. Detailed residual analysis indicates that residuals have zero mean and constant variance and are normally distributed and uncorrelated. Therefore, the necessary and sufficient criteria for least square parameter optimization, which was used in this study, were met. Conclusion The developed strategy is an efficient approach to extract as much physiochemical information from the FRAP protocol as possible. Well-posedness analysis of the inverse problem, however, indicates that the FRAP protocol provides insufficient

  11. Particle Tracking Model and Abstraction of Transport Processes

    International Nuclear Information System (INIS)

    Robinson, B.

    2000-01-01

    The purpose of the transport methodology and component analysis is to provide the numerical methods for simulating radionuclide transport and model setup for transport in the unsaturated zone (UZ) site-scale model. The particle-tracking method of simulating radionuclide transport is incorporated into the FEHM computer code and the resulting changes in the FEHM code are to be submitted to the software configuration management system. This Analysis and Model Report (AMR) outlines the assumptions, design, and testing of a model for calculating radionuclide transport in the unsaturated zone at Yucca Mountain. In addition, methods for determining colloid-facilitated transport parameters are outlined for use in the Total System Performance Assessment (TSPA) analyses. Concurrently, process-level flow model calculations are being carrier out in a PMR for the unsaturated zone. The computer code TOUGH2 is being used to generate three-dimensional, dual-permeability flow fields, that are supplied to the Performance Assessment group for subsequent transport simulations. These flow fields are converted to input files compatible with the FEHM code, which for this application simulates radionuclide transport using the particle-tracking algorithm outlined in this AMR. Therefore, this AMR establishes the numerical method and demonstrates the use of the model, but the specific breakthrough curves presented do not necessarily represent the behavior of the Yucca Mountain unsaturated zone

  12. Limitations of sorption isotherms on modeling groundwater contaminant transport

    International Nuclear Information System (INIS)

    Silva, Eduardo Figueira da

    2007-01-01

    Design and safety assessment of radioactive waste repositories, as well as remediation of radionuclide contaminated groundwater require the development of models capable of accurately predicting trace element fate and transport. Adsorption of trace radionuclides onto soils and groundwater is an important mechanism controlling near- and far- field transport. Although surface complexation models (SCMs) can better describe the adsorption mechanisms of most radionuclides onto mineral surfaces by directly accounting for variability of system properties and mineral surface properties, isotherms are still used to model contaminant transport in groundwater, despite the much higher system dependence. The present work investigates differences between transport model results based on these two approaches for adsorption modeling. A finite element transport model is used for the isotherm model, whereas the computer program PHREEQC is used for the SCM approach. Both models are calibrated for a batch experiment, and one-dimensional transport is simulated using the calibrated parameters. At the lower injected concentrations there are large discrepancies between SCM and isotherm transport predictions, with the SCM presenting much longer tails on the breakthrough curves. Isotherms may also provide non-conservative results for time to breakthrough and for maximum concentration in a contamination plume. Isotherm models are shown not to be robust enough to predict transport behavior of some trace elements, thus discouraging their use. The results also illustrate the promise of the SCM modeling approach in safety assessment and environmental remediation applications, also suggesting that independent batch sorption measurements can be used, within the framework of the SCM, to produce a more versatile and realistic groundwater transport model for radionuclides which is capable of accounting more accurately for temporal and spatial variations in geochemical conditions. (author)

  13. Transport services quality measurment using SERVQUAL model

    Directory of Open Access Journals (Sweden)

    Maksimović Mlađan V.

    2017-01-01

    Full Text Available Quality in the world is considered to be the most important phenomenon of our age, with a permanent and irreversible growing trend of its emphasis. Many companies have come to the conclusion that high quality of services can provide them with a potential competitive advantage, leading to superior sales results and profit making. The aim of this paper is to test the applicability of service SERVQUAL dimensions and measure the quality of services in the public transport of passengers. Based on the data obtained by researching the views of public transport users in Kragujevac using the SERVQUAL methodology and statistical analysis based on defined service quality dimensions, this research will show the level of quality of urban transport services in Kragujevac and based on this, make recommendations for improving the quality of service.

  14. Modeling radon transport in multistory residential buildings

    International Nuclear Information System (INIS)

    Persily, A.K.

    1993-01-01

    Radon concentrations have been studied extensively in single-family residential buildings, but relatively little work has been done in large buildings, including multistory residential buildings. The phenomena of radon transport in multistory residential buildings is made more complicated by the multizone nature of the airflow system and the numerous interzone airflow paths that must be characterized in such a system. This paper presents the results of a computer simulation of airflow and radon transport in a twelve-story residential building. Interzone airflow rates and radon concentrations were predicted using the multizone airflow and contaminant dispersal program (CON-TAM88). Limited simulations were conducted to study the influence of two different radon source terms, indoor-outdoor temperature difference and exterior wall leakage values on radon transport and radon concentration distributions

  15. Bionic models for identification of biological systems

    Science.gov (United States)

    Gerget, O. M.

    2017-01-01

    This article proposes a clinical decision support system that processes biomedical data. For this purpose a bionic model has been designed based on neural networks, genetic algorithms and immune systems. The developed system has been tested on data from pregnant women. The paper focuses on the approach to enable selection of control actions that can minimize the risk of adverse outcome. The control actions (hyperparameters of a new type) are further used as an additional input signal. Its values are defined by a hyperparameter optimization method. A software developed with Python is briefly described.

  16. Modeling the Biological Diversity of Pig Carcasses

    DEFF Research Database (Denmark)

    Erbou, Søren Gylling Hemmingsen

    for extracting and modeling meaningful information from the vast amount of information available from non-invasive imaging data. The lean meat percentage (LMP) is a common standard for measuring the quality of pig carcasses. Measuring the LMP using CT and using this as a reference for calibration of online...... more spatially localized modes of variation that are easier interpretable and the latter enables the use of PDM’s without the need for full point correspondence of new data. There is great potential in applying CT as non-invasive modality in the meat industry, e.g. in population based studies...

  17. Advanced transport systems analysis, modeling, and evaluation of performances

    CERN Document Server

    Janić, Milan

    2014-01-01

    This book provides a systematic analysis, modeling and evaluation of the performance of advanced transport systems. It offers an innovative approach by presenting a multidimensional examination of the performance of advanced transport systems and transport modes, useful for both theoretical and practical purposes. Advanced transport systems for the twenty-first century are characterized by the superiority of one or several of their infrastructural, technical/technological, operational, economic, environmental, social, and policy performances as compared to their conventional counterparts. The advanced transport systems considered include: Bus Rapid Transit (BRT) and Personal Rapid Transit (PRT) systems in urban area(s), electric and fuel cell passenger cars, high speed tilting trains, High Speed Rail (HSR), Trans Rapid Maglev (TRM), Evacuated Tube Transport system (ETT), advanced commercial subsonic and Supersonic Transport Aircraft (STA), conventionally- and Liquid Hydrogen (LH2)-fuelled commercial air trans...

  18. Assessment of applications of transport models on regional scale solute transport

    Science.gov (United States)

    Guo, Z.; Fogg, G. E.; Henri, C.; Pauloo, R.

    2017-12-01

    Regional scale transport models are needed to support the long-term evaluation of groundwater quality and to develop management strategies aiming to prevent serious groundwater degradation. The purpose of this study is to evaluate the capacity of previously-developed upscaling approaches to accurately describe main solute transport processes including the capture of late-time tails under changing boundary conditions. Advective-dispersive contaminant transport in a 3D heterogeneous domain was simulated and used as a reference solution. Equivalent transport under homogeneous flow conditions were then evaluated applying the Multi-Rate Mass Transfer (MRMT) model. The random walk particle tracking method was used for both heterogeneous and homogeneous-MRMT scenarios under steady state and transient conditions. The results indicate that the MRMT model can capture the tails satisfactorily for plume transported with ambient steady-state flow field. However, when boundary conditions change, the mass transfer model calibrated for transport under steady-state conditions cannot accurately reproduce the tailing effect observed for the heterogeneous scenario. The deteriorating impact of transient boundary conditions on the upscaled model is more significant for regions where flow fields are dramatically affected, highlighting the poor applicability of the MRMT approach for complex field settings. Accurately simulating mass in both mobile and immobile zones is critical to represent the transport process under transient flow conditions and will be the future focus of our study.

  19. Neutron transport model for standard calculation experiment

    International Nuclear Information System (INIS)

    Lukhminskij, B.E.; Lyutostanskij, Yu.S.; Lyashchuk, V.I.; Panov, I.V.

    1989-01-01

    The neutron transport calculation algorithms in complex composition media with a predetermined geometry are realized by the multigroups representations within Monte Carlo methods in the MAMONT code. The code grade was evaluated with benchmark experiments comparison. The neutron leakage spectra calculations in the spherical-symmetric geometry were carried out for iron and polyethylene. The MAMONT code utilization for metrological furnishes of the geophysics tasks is proposed. The code is orientated towards neutron transport and secondary nuclides accumulation calculations in blankets and geophysics media. 7 refs.; 2 figs

  20. Exploring morphological indicators for improved model parameterization in transport modeling

    Science.gov (United States)

    Kumahor, Samuel K.; Vogel, Hans-Jörg

    2017-04-01

    Two phenomena that control transport of colloidal materials, including nanoparticles, are interaction at the air-water and solid-water interfaces for unsaturated flow. Current approaches for multiphase inverse modeling to quantify the associated processes utilize empirical parameters and/or assumptions to characterise these interactions. This introduces uncertainty in model outcomes. Two classical examples are: (i) application of the Young-Laplace Equation, assuming spherical air-water interfaces, to quantify interactions at the air-water interface and (ii) the choice of parameters that define the nature and shape of retention profiles for modeling straining at the solid-water interface. In this contribution, an alternate approach using some morphological indicators derived from X-ray micro-computed tomography (µ-CT) to quantify interaction at both the air-water interface and solid-water interface is presented. These indicators, related to air-water and solid-water interface densities, are thought to alleviate the deficiencies associated with modeling interaction at both the solid-water and air-water interfaces.

  1. Modeling and simulation of biological systems using SPICE language

    Science.gov (United States)

    Lallement, Christophe; Haiech, Jacques

    2017-01-01

    The article deals with BB-SPICE (SPICE for Biochemical and Biological Systems), an extension of the famous Simulation Program with Integrated Circuit Emphasis (SPICE). BB-SPICE environment is composed of three modules: a new textual and compact description formalism for biological systems, a converter that handles this description and generates the SPICE netlist of the equivalent electronic circuit and NGSPICE which is an open-source SPICE simulator. In addition, the environment provides back and forth interfaces with SBML (System Biology Markup Language), a very common description language used in systems biology. BB-SPICE has been developed in order to bridge the gap between the simulation of biological systems on the one hand and electronics circuits on the other hand. Thus, it is suitable for applications at the interface between both domains, such as development of design tools for synthetic biology and for the virtual prototyping of biosensors and lab-on-chip. Simulation results obtained with BB-SPICE and COPASI (an open-source software used for the simulation of biochemical systems) have been compared on a benchmark of models commonly used in systems biology. Results are in accordance from a quantitative viewpoint but BB-SPICE outclasses COPASI by 1 to 3 orders of magnitude regarding the computation time. Moreover, as our software is based on NGSPICE, it could take profit of incoming updates such as the GPU implementation, of the coupling with powerful analysis and verification tools or of the integration in design automation tools (synthetic biology). PMID:28787027

  2. A Transformative Model for Undergraduate Quantitative Biology Education

    Science.gov (United States)

    Driscoll, Tobin A.; Dhurjati, Prasad; Pelesko, John A.; Rossi, Louis F.; Schleiniger, Gilberto; Pusecker, Kathleen; White, Harold B.

    2010-01-01

    The BIO2010 report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3) creating a new interdisciplinary major, quantitative biology, designed for students interested in solving complex biological problems using advanced mathematical approaches. To develop the bio-calculus sections, the Department of Mathematical Sciences revised its three-semester calculus sequence to include differential equations in the first semester and, rather than using examples traditionally drawn from application domains that are most relevant to engineers, drew models and examples heavily from the life sciences. The curriculum of the B.S. degree in Quantitative Biology was designed to provide students with a solid foundation in biology, chemistry, and mathematics, with an emphasis on preparation for research careers in life sciences. Students in the program take core courses from biology, chemistry, and physics, though mathematics, as the cornerstone of all quantitative sciences, is given particular prominence. Seminars and a capstone course stress how the interplay of mathematics and biology can be used to explain complex biological systems. To initiate these academic changes required the identification of barriers and the implementation of solutions. PMID:20810949

  3. A transformative model for undergraduate quantitative biology education.

    Science.gov (United States)

    Usher, David C; Driscoll, Tobin A; Dhurjati, Prasad; Pelesko, John A; Rossi, Louis F; Schleiniger, Gilberto; Pusecker, Kathleen; White, Harold B

    2010-01-01

    The BIO2010 report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3) creating a new interdisciplinary major, quantitative biology, designed for students interested in solving complex biological problems using advanced mathematical approaches. To develop the bio-calculus sections, the Department of Mathematical Sciences revised its three-semester calculus sequence to include differential equations in the first semester and, rather than using examples traditionally drawn from application domains that are most relevant to engineers, drew models and examples heavily from the life sciences. The curriculum of the B.S. degree in Quantitative Biology was designed to provide students with a solid foundation in biology, chemistry, and mathematics, with an emphasis on preparation for research careers in life sciences. Students in the program take core courses from biology, chemistry, and physics, though mathematics, as the cornerstone of all quantitative sciences, is given particular prominence. Seminars and a capstone course stress how the interplay of mathematics and biology can be used to explain complex biological systems. To initiate these academic changes required the identification of barriers and the implementation of solutions.

  4. A Two-Layer Mathematical Modelling of Drug Delivery to Biological Tissues

    Science.gov (United States)

    Chakravarty, Koyel; Dalal, D. C.

    2016-10-01

    Local drug delivery has received much recognition in recent years, yet it is still unpredictable how drug efficacy depends on physicochemical properties and delivery kinetics. The purpose of the current study is to provide a useful mathematical model for drug release from a drug delivery device and consecutive drug transport in biological tissue, thereby aiding the development of new therapeutic drug by a systemic approach. In order to study the complete process, a two-layer spatio-temporal model depicting drug transport between the coupled media is presented. Drug release is described by considering solubilisation dynamics of drug particle, diffusion of the solubilised drug through porous matrix and also some other processes like reversible dissociation / recrystallization, drug particle-receptor binding and internalization phenomena. The model has led to a system of partial differential equations describing the important properties of drug kinetics. This model contributes towards the perception of the roles played by diffusion, mass-transfer, particle binding and internalization parameters.

  5. Contemporary Phage Biology: From Classic Models to New Insights.

    Science.gov (United States)

    Ofir, Gal; Sorek, Rotem

    2018-03-08

    Bacteriophages, discovered about a century ago, have been pivotal as models for understanding the fundamental principles of molecular biology. While interest in phage biology declined after the phage "golden era," key recent developments, including advances in phage genomics, microscopy, and the discovery of the CRISPR-Cas anti-phage defense system, have sparked a renaissance in phage research in the past decade. This review highlights recently discovered unexpected complexities in phage biology, describes a new arsenal of phage genes that help them overcome bacterial defenses, and discusses advances toward documentation of the phage biodiversity on a global scale. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. An optimization model for transportation of hazardous materials

    International Nuclear Information System (INIS)

    Seyed-Hosseini, M.; Kheirkhah, A. S.

    2005-01-01

    In this paper, the optimal routing problem for transportation of hazardous materials is studied. Routing for the purpose of reducing the risk of transportation of hazardous materials has been studied and formulated by many researcher and several routing models have been presented up to now. These models can be classified into the categories: the models for routing a single movement and the models for routing multiple movements. In this paper, according to the current rules and regulations of road transportations of hazardous materials in Iran, a routing problem is designed. In this problem, the routs for several independent movements are simultaneously determined. To examine the model, the problem the transportations of two different dangerous materials in the road network of Mazandaran province in the north of Iran is formulated and solved by applying Integer programming model

  7. Particle Tracking Model and Abstraction of Transport Processes

    International Nuclear Information System (INIS)

    Robinson, B.

    2004-01-01

    The purpose of this report is to document the abstraction model being used in total system performance assessment (TSPA) model calculations for radionuclide transport in the unsaturated zone (UZ). The UZ transport abstraction model uses the particle-tracking method that is incorporated into the finite element heat and mass model (FEHM) computer code (Zyvoloski et al. 1997 [DIRS 100615]) to simulate radionuclide transport in the UZ. This report outlines the assumptions, design, and testing of a model for calculating radionuclide transport in the UZ at Yucca Mountain. In addition, methods for determining and inputting transport parameters are outlined for use in the TSPA for license application (LA) analyses. Process-level transport model calculations are documented in another report for the UZ (BSC 2004 [DIRS 164500]). Three-dimensional, dual-permeability flow fields generated to characterize UZ flow (documented by BSC 2004 [DIRS 169861]; DTN: LB03023DSSCP9I.001 [DIRS 163044]) are converted to make them compatible with the FEHM code for use in this abstraction model. This report establishes the numerical method and demonstrates the use of the model that is intended to represent UZ transport in the TSPA-LA. Capability of the UZ barrier for retarding the transport is demonstrated in this report, and by the underlying process model (BSC 2004 [DIRS 164500]). The technical scope, content, and management of this report are described in the planning document ''Technical Work Plan for: Unsaturated Zone Transport Model Report Integration'' (BSC 2004 [DIRS 171282]). Deviations from the technical work plan (TWP) are noted within the text of this report, as appropriate. The latest version of this document is being prepared principally to correct parameter values found to be in error due to transcription errors, changes in source data that were not captured in the report, calculation errors, and errors in interpretation of source data

  8. Composite Transport Model and Water and Solute Transport across Plant Roots: An Update

    Directory of Open Access Journals (Sweden)

    Yangmin X. Kim

    2018-02-01

    Full Text Available The present review examines recent experimental findings in root transport phenomena in terms of the composite transport model (CTM. It has been a well-accepted conceptual model to explain the complex water and solute flows across the root that has been related to the composite anatomical structure. There are three parallel pathways involved in the transport of water and solutes in roots – apoplast, symplast, and transcellular paths. The role of aquaporins (AQPs, which facilitate water flows through the transcellular path, and root apoplast is examined in terms of the CTM. The contribution of the plasma membrane bound AQPs for the overall water transport in the whole plant level was varying depending on the plant species, age of roots with varying developmental stages of apoplastic barriers, and driving forces (hydrostatic vs. osmotic. Many studies have demonstrated that the apoplastic barriers, such as Casparian bands in the primary anticlinal walls and suberin lamellae in the secondary cell walls, in the endo- and exodermis are not perfect barriers and unable to completely block the transport of water and some solute transport into the stele. Recent research on water and solute transport of roots with and without exodermis triggered the importance of the extension of conventional CTM adding resistances that arrange in series (epidermis, exodermis, mid-cortex, endodermis, and pericycle. The extension of the model may answer current questions about the applicability of CTM for composite water and solute transport of roots that contain complex anatomical structures with heterogeneous cell layers.

  9. Modeling life the mathematics of biological systems

    CERN Document Server

    Garfinkel, Alan; Guo, Yina

    2017-01-01

    From predator-prey populations in an ecosystem, to hormone regulation within the body, the natural world abounds in dynamical systems that affect us profoundly. This book develops the mathematical tools essential for students in the life sciences to describe these interacting systems and to understand and predict their behavior. Complex feedback relations and counter-intuitive responses are common in dynamical systems in nature; this book develops the quantitative skills needed to explore these interactions. Differential equations are the natural mathematical tool for quantifying change, and are the driving force throughout this book. The use of Euler’s method makes nonlinear examples tractable and accessible to a broad spectrum of early-stage undergraduates, thus providing a practical alternative to the procedural approach of a traditional Calculus curriculum. Tools are developed within numerous, relevant examples, with an emphasis on the construction, evaluation, and interpretation of mathematical models ...

  10. Mathematical Modeling and Experimental Validation of Nanoemulsion-Based Drug Transport across Cellular Barriers.

    Science.gov (United States)

    Kadakia, Ekta; Shah, Lipa; Amiji, Mansoor M

    2017-07-01

    Nanoemulsions have shown potential in delivering drug across epithelial and endothelial cell barriers, which express efflux transporters. However, their transport mechanisms are not entirely understood. Our goal was to investigate the cellular permeability of nanoemulsion-encapsulated drugs and apply mathematical modeling to elucidate transport mechanisms and sensitive nanoemulsion attributes. Transport studies were performed in Caco-2 cells, using fish oil nanoemulsions and a model substrate, rhodamine-123. Permeability data was modeled using a semi-mechanistic approach, capturing the following cellular processes: endocytotic uptake of the nanoemulsion, release of rhodamine-123 from the nanoemulsion, efflux and passive permeability of rhodamine-123 in aqueous solution. Nanoemulsions not only improved the permeability of rhodamine-123, but were also less sensitive to efflux transporters. The model captured bidirectional permeability results and identified sensitive processes, such as the release of the nanoemulsion-encapsulated drug and cellular uptake of the nanoemulsion. Mathematical description of cellular processes, improved our understanding of transport mechanisms, such as nanoemulsions don't inhibit efflux to improve drug permeability. Instead, their endocytotic uptake, results in higher intracellular drug concentrations, thereby increasing the concentration gradient and transcellular permeability across biological barriers. Modeling results indicated optimizing nanoemulsion attributes like the droplet size and intracellular drug release rate, may further improve drug permeability.

  11. Mathematical modelling on transport of petroleum hydrocarbons

    Indian Academy of Sciences (India)

    A brief theory has been included on the composition and transport of petroleum hydrocarbons following an onshore oil spill in order to demonstrate the level of complexity associated with the LNAPL dissolution mass transfer even in a classical porous medium. However, such studies in saturated fractured rocks are highly ...

  12. Strategic Network Modelling for Passenger Transport Pricing

    NARCIS (Netherlands)

    Smits, E.-S.

    2017-01-01

    In the last decade the Netherlands has experienced an economic recession. Now, in 2017, the economy is picking up again. This growth does not only come with advantages because economic growth demands more from the transport system. Congestion is increasing again, the capacity of the train system is

  13. Modelling anisotropic water transport in polymer composite ...

    Indian Academy of Sciences (India)

    Abstract. This work reports anisotropic water transport in a polymer composite consisting of an epoxy matrix reinforced with aligned triangular bars made of vinyl ester. By gravimetric experiments, water diffusion in resin and polymer composites were characterized. Parameters for Fickian diffusion and polymer relaxation ...

  14. Structural Design of Oligopeptides for Intestinal Transport Model.

    Science.gov (United States)

    Hong, Seong-Min; Tanaka, Mitsuru; Koyanagi, Riho; Shen, Weilin; Matsui, Toshiro

    2016-03-16

    Glycyl-sarcosine (Gly-Sar) is a well-known model substrate for the intestinal uptake of dipeptides through peptide transporter 1 (PepT1). However, there are no other model peptides larger than tripeptides to evaluate their intestinal transport ability. In this study, we designed new oligopeptides based on the Gly-Sar structure in terms of protease resistance. Gly-Sar-Sar was found to be an appropriate transport model for tripeptides because it does not degrade during the transport across the rat intestinal membrane, while Gly-Gly-Sar was degraded to Gly-Sar during the 60 min transport. Caco-2 cell transport experiments revealed that the designed oligopeptides based on Gly-Sar-Sar showed a significantly (p transport ability by factors of 1/10-, 1/25-, and 1/40-fold for Gly-Sar-Sar, Gly-Sar-Sar-Sar, and Gly-Sar-Sar-Sar-Sar, respectively, compared to Gly-Sar (apparent permeability coefficient: 38.6 ± 11.4 cm/s). Cell experiments also showed that the designed tripeptide and Gly-Sar were transported across Caco-2 cell via PepT1, whereas the tetra- and pentapeptides were transported through the paracellular tight-junction pathway.

  15. Modelling radionuclide transport in the geosphere: a review of the models available

    International Nuclear Information System (INIS)

    Cacas, M.C.; Cordier, E.; Coudrain-Ribstein, A.; Fargue, D.; Goblet, P.; Jamet, Ph.; Ledoux, E.; Marsily, G. de; Vinsot, A.; Brun, Ch.; Cernes, A.; Jacquier, Ph.; Lewi, J.; Priem, Th.

    1990-01-01

    Over the last twelve years, several models have been developed to simulate the transport of radionuclides in the environment of a radioactive waste repository: - continuous equivalent porous media flow and transport models using the finite element method in 1, 2 or 3 dimensions and taking into account various coupled mechanisms; - discontinuous stochastic fracture network models in 3 dimensions representing flow, transport, matrix diffusion, heat flow and mechanical stress; - geochemical models representing interactions between transported elements and a solid matrix; - transport process models coupling non dominant phenomena such as thermo-diffusion or thermo-gravitation. This paper reviews the role that each of these models can play in safety analyses. 3 refs [fr

  16. Use of artificial neural networks for transport energy demand modeling

    International Nuclear Information System (INIS)

    Murat, Yetis Sazi; Ceylan, Halim

    2006-01-01

    The paper illustrates an artificial neural network (ANN) approach based on supervised neural networks for the transport energy demand forecasting using socio-economic and transport related indicators. The ANN transport energy demand model is developed. The actual forecast is obtained using a feed forward neural network, trained with back propagation algorithm. In order to investigate the influence of socio-economic indicators on the transport energy demand, the ANN is analyzed based on gross national product (GNP), population and the total annual average veh-km along with historical energy data available from 1970 to 2001. Comparing model predictions with energy data in testing period performs the model validation. The projections are made with two scenarios. It is obtained that the ANN reflects the fluctuation in historical data for both dependent and independent variables. The results obtained bear out the suitability of the adopted methodology for the transport energy-forecasting problem

  17. Physics and modelling of scrape-off layer transport

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, R.H.; Allen, S.L.; Crotinger, J.A.; Kaiser, T.B.; Milovich, J.L.; Mattor, N.; Nevins, W.M.; Porter, G.D.; Rensink, M.E.; Rognlien, T.D. [Lawrence Livermore National Lab., CA (United States); Berk, H.L. [Texas Univ., Austin, TX (United States). Inst. for Fusion Studies; Campbell, R.B. [Sandia National Labs., Albuquerque, NM (United States); Diamond, P.H.; Rosenbluth, M.N. [California Univ., San Diego, CA (United States); Hinton, F.L.; Staebler, G.M. [General Atomics, San Diego, CA (United States); Knoll, D.A. [EG and G Idaho, Inc., Idaho Falls, ID (United States); Modi, B.; Xu, X.Q. [California Univ., Berkeley, CA (United States); Prinja, A.K. [New Mexico Univ., Albuquerque, NM (United States); Ryutov, D.D.; Tsidulko, Y.A. [Budker Institute of Nuclear Physics, Novosibirsk (Russia)

    1992-12-31

    We present studies of three schemes for reducing the peak heat flux on divertor plates, divertor biasing, impurity injection (``radiative divertor``) and neutral gas injection (``gas target divertor``). We report on theoretical analysis of a likely source of turbulent transport in the SOL and incorporation of the resultant transport coefficients into self-consistent models.

  18. Physics and modelling of scrape-off layer transport

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, R.H.; Allen, S.L.; Crotinger, J.A.; Kaiser, T.B.; Milovich, J.L.; Mattor, N.; Nevins, W.M.; Porter, G.D.; Rensink, M.E.; Rognlien, T.D. (Lawrence Livermore National Lab., CA (United States)); Berk, H.L. (Texas Univ., Austin, TX (United States). Inst. for Fusion Studies); Campbell, R.B. (Sandia National Labs., Albuquerque, NM (United States)); Diamond, P.H.; Rosenbluth, M.N. (California Univ., San Di

    1992-01-01

    We present studies of three schemes for reducing the peak heat flux on divertor plates, divertor biasing, impurity injection ( radiative divertor'') and neutral gas injection ( gas target divertor''). We report on theoretical analysis of a likely source of turbulent transport in the SOL and incorporation of the resultant transport coefficients into self-consistent models.

  19. A model for assessing the environmental impact of transport

    OpenAIRE

    Malgorzata Latuszynska; Roma Strulak-Wojcikiewicz

    2013-01-01

    Environmental effects of transport, with a particular focus on the natural environment have been discussed. The authors present methods for assessing the influence of investments in transport infrastructure on the environment, as well as the concept of a simulation model which integrates various methods and approaches used to assess the impact of such investments on the environment. (original abstract)

  20. Physics and modelling of scrape-off layer transport

    International Nuclear Information System (INIS)

    Cohen, R.H.; Allen, S.L.; Crotinger, J.A.; Kaiser, T.B.; Milovich, J.L.; Mattor, N.; Nevins, W.M.; Porter, G.D.; Rensink, M.E.; Rognlien, T.D.; Berk, H.L.; Diamond, P.H.; Rosenbluth, M.N.; Hinton, F.L.; Staebler, G.M.; Knoll, D.A.; Modi, B.; Xu, X.Q.; Prinja, A.K.; Ryutov, D.D.; Tsidulko, Y.A.

    1992-01-01

    We present studies of three schemes for reducing the peak heat flux on divertor plates, divertor biasing, impurity injection (''radiative divertor'') and neutral gas injection (''gas target divertor''). We report on theoretical analysis of a likely source of turbulent transport in the SOL and incorporation of the resultant transport coefficients into self-consistent models

  1. Using views of Systems Biology Cloud: application for model building.

    Science.gov (United States)

    Ruebenacker, Oliver; Blinov, Michael

    2011-03-01

    A large and growing network ("cloud") of interlinked terms and records of items of Systems Biology knowledge is available from the web. These items include pathways, reactions, substances, literature references, organisms, and anatomy, all described in different data sets. Here, we discuss how the knowledge from the cloud can be molded into representations (views) useful for data visualization and modeling. We discuss methods to create and use various views relevant for visualization, modeling, and model annotations, while hiding irrelevant details without unacceptable loss or distortion. We show that views are compatible with understanding substances and processes as sets of microscopic compounds and events respectively, which allows the representation of specializations and generalizations as subsets and supersets respectively. We explain how these methods can be implemented based on the bridging ontology Systems Biological Pathway Exchange (SBPAX) in the Systems Biology Linker (SyBiL) we have developed.

  2. A distributed approach for parameters estimation in System Biology models

    International Nuclear Information System (INIS)

    Mosca, E.; Merelli, I.; Alfieri, R.; Milanesi, L.

    2009-01-01

    Due to the lack of experimental measurements, biological variability and experimental errors, the value of many parameters of the systems biology mathematical models is yet unknown or uncertain. A possible computational solution is the parameter estimation, that is the identification of the parameter values that determine the best model fitting respect to experimental data. We have developed an environment to distribute each run of the parameter estimation algorithm on a different computational resource. The key feature of the implementation is a relational database that allows the user to swap the candidate solutions among the working nodes during the computations. The comparison of the distributed implementation with the parallel one showed that the presented approach enables a faster and better parameter estimation of systems biology models.

  3. An integrated physical and biological model for anaerobic lagoons.

    Science.gov (United States)

    Wu, Binxin; Chen, Zhenbin

    2011-04-01

    A computational fluid dynamics (CFD) model that integrates physical and biological processes for anaerobic lagoons is presented. In the model development, turbulence is represented using a transition k-ω model, heat conduction and solar radiation are included in the thermal model, biological oxygen demand (BOD) reduction is characterized by first-order kinetics, and methane yield rate is expressed as a linear function of temperature. A test of the model applicability is conducted in a covered lagoon digester operated under tropical climate conditions. The commercial CFD software, ANSYS-Fluent, is employed to solve the integrated model. The simulation procedures include solving fluid flow and heat transfer, predicting local resident time based on the converged flow fields, and calculating the BOD reduction and methane production. The simulated results show that monthly methane production varies insignificantly, but the time to achieve a 99% BOD reduction in January is much longer than that in July. Copyright © 2011 Elsevier Ltd. All rights reserved.

  4. Parameter estimation and model selection in computational biology.

    Directory of Open Access Journals (Sweden)

    Gabriele Lillacci

    2010-03-01

    Full Text Available A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are used to assign parameter values that minimize some measure of the error between these measurements and the corresponding model prediction. The measurements, which can come from immunoblotting assays, fluorescent markers, etc., tend to be very noisy and taken at a limited number of time points. In this work we present a new approach to the problem of parameter selection of biological models. We show how one can use a dynamic recursive estimator, known as extended Kalman filter, to arrive at estimates of the model parameters. The proposed method follows. First, we use a variation of the Kalman filter that is particularly well suited to biological applications to obtain a first guess for the unknown parameters. Secondly, we employ an a posteriori identifiability test to check the reliability of the estimates. Finally, we solve an optimization problem to refine the first guess in case it should not be accurate enough. The final estimates are guaranteed to be statistically consistent with the measurements. Furthermore, we show how the same tools can be used to discriminate among alternate models of the same biological process. We demonstrate these ideas by applying our methods to two examples, namely a model of the heat shock response in E. coli, and a model of a synthetic gene regulation system. The methods presented are quite general and may be applied to a wide class of biological systems where noisy measurements are used for parameter estimation or model selection.

  5. Olkiluoto surface hydrological modelling: Update 2012 including salt transport modelling

    International Nuclear Information System (INIS)

    Karvonen, T.

    2013-11-01

    Posiva Oy is responsible for implementing a final disposal program for spent nuclear fuel of its owners Teollisuuden Voima Oyj and Fortum Power and Heat Oy. The spent nuclear fuel is planned to be disposed at a depth of about 400-450 meters in the crystalline bedrock at the Olkiluoto site. Leakages located at or close to spent fuel repository may give rise to the upconing of deep highly saline groundwater and this is a concern with regard to the performance of the tunnel backfill material after the closure of the tunnels. Therefore a salt transport sub-model was added to the Olkiluoto surface hydrological model (SHYD). The other improvements include update of the particle tracking algorithm and possibility to estimate the influence of open drillholes in a case where overpressure in inflatable packers decreases causing a hydraulic short-circuit between hydrogeological zones HZ19 and HZ20 along the drillhole. Four new hydrogeological zones HZ056, HZ146, BFZ100 and HZ039 were added to the model. In addition, zones HZ20A and HZ20B intersect with each other in the new structure model, which influences salinity upconing caused by leakages in shafts. The aim of the modelling of long-term influence of ONKALO, shafts and repository tunnels provide computational results that can be used to suggest limits for allowed leakages. The model input data included all the existing leakages into ONKALO (35-38 l/min) and shafts in the present day conditions. The influence of shafts was computed using eight different values for total shaft leakage: 5, 11, 20, 30, 40, 50, 60 and 70 l/min. The selection of the leakage criteria for shafts was influenced by the fact that upconing of saline water increases TDS-values close to the repository areas although HZ20B does not intersect any deposition tunnels. The total limit for all leakages was suggested to be 120 l/min. The limit for HZ20 zones was proposed to be 40 l/min: about 5 l/min the present day leakages to access tunnel, 25 l/min from

  6. Monte Carlo impurity transport modeling in the DIII-D transport

    International Nuclear Information System (INIS)

    Evans, T.E.; Finkenthal, D.F.

    1998-04-01

    A description of the carbon transport and sputtering physics contained in the Monte Carlo Impurity (MCI) transport code is given. Examples of statistically significant carbon transport pathways are examined using MCI's unique tracking visualizer and a mechanism for enhanced carbon accumulation on the high field side of the divertor chamber is discussed. Comparisons between carbon emissions calculated with MCI and those measured in the DIII-D tokamak are described. Good qualitative agreement is found between 2D carbon emission patterns calculated with MCI and experimentally measured carbon patterns. While uncertainties in the sputtering physics, atomic data, and transport models have made quantitative comparisons with experiments more difficult, recent results using a physics based model for physical and chemical sputtering has yielded simulations with about 50% of the total carbon radiation measured in the divertor. These results and plans for future improvement in the physics models and atomic data are discussed

  7. A Coupled Model of Multiphase Flow, Reactive Biogeochemical Transport, Thermal Transport and Geo-Mechanics.

    Science.gov (United States)

    Tsai, C. H.; Yeh, G. T.

    2015-12-01

    In this investigation, a coupled model of multiphase flow, reactive biogeochemical transport, thermal transport and geo-mechanics in subsurface media is presented. It iteratively solves the mass conservation equation for fluid flow, thermal transport equation for temperature, reactive biogeochemical transport equations for concentration distributions, and solid momentum equation for displacement with successive linearization algorithm. With species-based equations of state, density of a phase in the system is obtained by summing up concentrations of all species. This circumvents the problem of having to use empirical functions. Moreover, reaction rates of all species are incorporated in mass conservation equation for fluid flow. Formation enthalpy of all species is included in the law of energy conservation as a source-sink term. Finite element methods are used to discretize the governing equations. Numerical experiments are presented to examine the accuracy and robustness of the proposed model. The results demonstrate the feasibility and capability of present model in subsurface media.

  8. Preservice Biology Teachers' Conceptions About the Tentative Nature of Theories and Models in Biology

    Science.gov (United States)

    Reinisch, Bianca; Krüger, Dirk

    2018-02-01

    In research on the nature of science, there is a need to investigate the role and status of different scientific knowledge forms. Theories and models are two of the most important knowledge forms within biology and are the focus of this study. During interviews, preservice biology teachers ( N = 10) were asked about their understanding of theories and models. They were requested to give reasons why they see theories and models as either tentative or certain constructs. Their conceptions were then compared to philosophers' positions (e.g., Popper, Giere). A category system was developed from the qualitative content analysis of the interviews. These categories include 16 conceptions for theories ( n tentative = 11; n certai n = 5) and 18 conceptions for models ( n tentative = 10; n certain = 8). The analysis of the interviews showed that the preservice teachers gave reasons for the tentativeness or certainty of theories and models either due to their understanding of the terms or due to their understanding of the generation or evaluation of theories and models. Therefore, a variety of different terminology, from different sources, should be used in learning-teaching situations. Additionally, an understanding of which processes lead to the generation, evaluation, and refinement or rejection of theories and models should be discussed with preservice teachers. Within philosophy of science, there has been a shift from theories to models. This should be transferred to educational contexts by firstly highlighting the role of models and also their connections to theories.

  9. Modeling Biology Spanning Different Scales: An Open Challenge

    Directory of Open Access Journals (Sweden)

    Filippo Castiglione

    2014-01-01

    Full Text Available It is coming nowadays more clear that in order to obtain a unified description of the different mechanisms governing the behavior and causality relations among the various parts of a living system, the development of comprehensive computational and mathematical models at different space and time scales is required. This is one of the most formidable challenges of modern biology characterized by the availability of huge amount of high throughput measurements. In this paper we draw attention to the importance of multiscale modeling in the framework of studies of biological systems in general and of the immune system in particular.

  10. BayesMD: flexible biological modeling for motif discovery

    DEFF Research Database (Denmark)

    Tang, Man-Hung Eric; Krogh, Anders; Winther, Ole

    2008-01-01

    We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained on trans......We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained...

  11. Transport modeling of L/H transition in Tokamaks

    International Nuclear Information System (INIS)

    Fuji, Y.; Fukuyama, A.; Itoh, K.; Itoh, S.I.

    1995-01-01

    In order to study the particle transport and the mechanism of the L/H transition in tokamaks, a one-dimensional transport code which describes the toroidal and poloidal plasma rotation as well as the radial electric field has been developed. The neoclassical transport, turbulent transport and ion orbit loss are included. Using a turbulent transport model based on the current diffusive high-n ballooning mode and a fixed temperature profile, the density profile in a steady state and the dependence on the edge temperature are studied. With high edge temperature, the density gradient near the edge becomes steep and a H-mode like density profile is obtained. The preliminary calculation including heat transport is also presented. 10 refs., 3 figs

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

    Science.gov (United States)

    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.

  13. Capabilities and requirements for modelling radionuclide transport in the geosphere

    International Nuclear Information System (INIS)

    Paige, R.W.; Piper, D.

    1989-02-01

    This report gives an overview of geosphere flow and transport models suitable for use by the Department of the Environment in the performance assessment of radioactive waste disposal sites. An outline methodology for geosphere modelling is proposed, consisting of a number of different types of model. A brief description of each of the component models is given, indicating the purpose of the model, the processes being modelled and the methodologies adopted. Areas requiring development are noted. (author)

  14. Frontiers in transport phenomena research and education: Energy systems, biological systems, security, information technology and nanotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Bergman, T.L.; Faghri, A. [Department of Mechanical Engineering, The University of Connecticut, Storrs, CT 06269-3139 (United States); Viskanta, R. [School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907-2088 (United States)

    2008-09-15

    A US National Science Foundation-sponsored workshop entitled ''Frontiers in Transport Phenomena Research and Education: Energy Systems, Biological Systems, Security, Information Technology, and Nanotechnology'' was held in May of 2007 at the University of Connecticut. The workshop provided a venue for researchers, educators and policy-makers to identify frontier challenges and associated opportunities in heat and mass transfer. Approximately 300 invited participants from academia, business and government from the US and abroad attended. Based upon the final recommendations on the topical matter of the workshop, several trends become apparent. A strong interest in sustainable energy is evident. A continued need to understand the coupling between broad length (and time) scales persists, but the emerging need to better understand transport phenomena at the macro/mega scale has evolved. The need to develop new metrology techniques to collect and archive reliable property data persists. Societal sustainability received major attention in two of the reports. Matters involving innovation, entrepreneurship, and globalization of the engineering profession have emerged, and the responsibility to improve the technical literacy of the public-at-large is discussed. Integration of research thrusts and education activities is highlighted throughout. Specific recommendations, made by the panelists with input from the international heat transfer community and directed to the National Science Foundation, are included in several reports. (author)

  15. Analysis of photon transport in biological tissue and the subsequent heating effects

    International Nuclear Information System (INIS)

    Fadhali, M.M.A.

    2015-01-01

    Analysis of laser interaction with matter revealed the possibilities of many industrial and therapeutic applications. This research article discusses the theoretical aspects of laser beam interaction with biological tissues. It introduces the numerical analysis of photon distribution and transport in the tissue and its bio-thermal heating effects. The Monte Carlo method has been applied to simulate the variation of photon distribution and photon fluence with the radial distance from the point of interaction as well as laser powers and tissue thickness. For a specific wavelength, the variation of diffuse reflectance with the absorption coefficient was depicted for different values of the anisotropy factor. It has also been used to simulate the bio-heat transfer to obtain the temperature variation with the heating depth. On the other hand, finite difference method (FDM) has been applied to simulate the heating effect resulted from the incident laser beam on the tissue based on Penne's bio-heat equation combined with the obtained photon distribution and transport parameters from the MC method. The heating effect of the laser beam and hence the occurred thermal damage in the tissue was depicted. A linear relationship between the temperature and the rate of thermal damage has been manifested. This result can be used as a threshold reference for various medical applications of lasers. (authors)

  16. An architecture model for communication of safety in public transportation

    NARCIS (Netherlands)

    Rajabalinejad, Mohammad; Horváth, Imre; Pernot, Jean-Paul; Rusák, Zoltan

    2016-01-01

    Safety in transportation is under the influence of the rising complexity, increasing demands for capacity and decreasing cost. Furthermore, the interdisciplinary environment of operation and altered safety regulations invite for a centralized (integrated) modelling/ communication approach. This

  17. Modeling and analysis of modular structure in diverse biological networks.

    Science.gov (United States)

    Al-Anzi, Bader; Gerges, Sherif; Olsman, Noah; Ormerod, Christopher; Piliouras, Georgios; Ormerod, John; Zinn, Kai

    2017-06-07

    Biological networks, like most engineered networks, are not the product of a singular design but rather are the result of a long process of refinement and optimization. Many large real-world networks are comprised of well-defined and meaningful smaller modules. While engineered networks are designed and refined by humans with particular goals in mind, biological networks are created by the selective pressures of evolution. In this paper, we seek to define aspects of network architecture that are shared among different types of evolved biological networks. First, we developed a new mathematical model, the Stochastic Block Model with Path Selection (SBM-PS) that simulates biological network formation based on the selection of edges that increase clustering. SBM-PS can produce modular networks whose properties resemble those of real networks. Second, we analyzed three real networks of very different types, and showed that all three can be fit well by the SBM-PS model. Third, we showed that modular elements within the three networks correspond to meaningful biological structures. The networks chosen for analysis were a proteomic network composed of all proteins required for mitochondrial function in budding yeast, a mesoscale anatomical network composed of axonal connections among regions of the mouse brain, and the connectome of individual neurons in the nematode C. elegans. We find that the three networks have common architectural features, and each can be divided into subnetworks with characteristic topologies that control specific phenotypic outputs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Modelling of hydrodynamics and mecury transport in lake Velenje. Part 2, Modelling and model verification

    OpenAIRE

    Kotnik, Jože; Žagar, Dušan; Rajar, Rudi; Horvat, Milena

    2004-01-01

    PCFLOW3D - a three-dimensional mathematical model that was developed at the Chair of Fluid Mechanics of the Faculty of Civil and Geodetic Engineering, University of Ljubljana, was used for hydrodynamic and Hg transport simulations in Lake Velenje. The model is fully non-linear and computes three velocity components, water elevation and pressure. Transport-dispersion equations for salinity and heat (and/or any pollutant) are further used to compute the distributions of these par...

  19. Fate and transport modelling of uranium in Port Hope Harbour

    International Nuclear Information System (INIS)

    Pinilla, C.E.; Garisto, N.; Peters, R.

    2010-01-01

    Fate and transport modelling of contaminants in Port Hope Harbour and near-shore Lake Ontario was undertaken in support of an ecological and human health risk assessment. Uranium concentrations in the Harbour and near-shore Lake Ontario due to groundwater and storm water loadings were estimated with a state-of-the-art 3D hydrodynamic and contaminant transport model (ECOMSED). The hydrodynamic model was simplified to obtain a first estimate of the flow pattern in the Harbour. The model was verified with field data using a tracer (fluoride). The modelling results generally showed good agreement with the tracer field data. (author)

  20. Transport of biologically important nutrients by wind in an eroding cold desert

    Science.gov (United States)

    Sankey, Joel B.; Germino, Matthew J.; Benner, Shawn G.; Glenn, Nancy F.; Hoover, Amber N.

    2012-01-01

    Wind erosion following fire is an important landscape process that can result in the redistribution of ecologically important soil resources. In this study we evaluated the potential for a fire patch in a desert shrubland to serve as a source of biologically important nutrients to the adjacent, downwind, unburned ecosystem. We analyzed nutrient concentrations (P, K, Ca, Mg, Cu, Fe, Mn, Al) in wind-transported sediments, and soils from burned and adjacent unburned surfaces, collected during the first to second growing seasons after a wildfire that burned in 2007 in Idaho, USA in sagebrush steppe; a type of cold desert shrubland. We also evaluated the timing of potential wind erosion events and weather conditions that might have contributed to nutrient availability in downwind shrubland. Findings indicated that post-fire wind erosion resulted in an important, but transient, addition of nutrients on the downwind shrubland. Aeolian sediments from the burned area were enriched relative to both the up- and down-wind soil and indicated the potential for a fertilization effect through the deposition of the nutrient-enriched sediment during the first, but not second, summer after wildfire. Weather conditions that could have produced nutrient transport events might have provided increased soil moisture necessary to make nutrients accessible for plants in the desert environment. Wind transport of nutrients following fire is likely important in the sagebrush steppe as it could contribute to pulses of resource availability that might, for example, affect plant species differently depending on their phenology, and nutrient- and water-use requirements.

  1. Modeling of pollutant emissions from road transport; Modelisation des emissions de polluants par le transport routier

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-07-01

    COPERT III (computer programme to calculate emissions from road transport) is the third version of an MS Windows software programme aiming at the calculation of air pollutant emissions from road transport. COPERT estimates emissions of all regulated air pollutants (CO, NO{sub x}, VOC, PM) produced by different vehicle categories as well as CO{sub 2} emissions on the basis of fuel consumption. This research seminar was organized by the French agency of environment and energy mastery (Ademe) around the following topics: the uncertainties and sensitiveness analysis of the COPERT III model, the presentation of case studies that use COPERT III for the estimation of road transport emissions, and the future of the modeling of road transport emissions: from COPERT III to ARTEMIS (assessment and reliability of transport emission models and inventory systems). This document is a compilation of 8 contributions to this seminar and dealing with: the uncertainty and sensitiveness analysis of the COPERT III model; the road mode emissions of the ESCOMPTE program: sensitivity study; the sensitivity analysis of the spatialized traffic at the time-aggregation level: application in the framework of the INTERREG project (Alsace); the road transport aspect of the regional air quality plan of Bourgogne region: exhaustive consideration of the road network; intercomparison of tools and methods for the inventory of emissions of road transport origin; evolution of the French park of vehicles by 2025: new projections; application of COPERT III to the French context: a new version of IMPACT-ADEME; the European ARTEMIS project: new structural considerations for the modeling of road transport emissions. (J.S.)

  2. Biology learning evaluation model in Senior High Schools

    Directory of Open Access Journals (Sweden)

    Sri Utari

    2017-06-01

    Full Text Available The study was to develop a Biology learning evaluation model in senior high schools that referred to the research and development model by Borg & Gall and the logic model. The evaluation model included the components of input, activities, output and outcomes. The developing procedures involved a preliminary study in the form of observation and theoretical review regarding the Biology learning evaluation in senior high schools. The product development was carried out by designing an evaluation model, designing an instrument, performing instrument experiment and performing implementation. The instrument experiment involved teachers and Students from Grade XII in senior high schools located in the City of Yogyakarta. For the data gathering technique and instrument, the researchers implemented observation sheet, questionnaire and test. The questionnaire was applied in order to attain information regarding teacher performance, learning performance, classroom atmosphere and scientific attitude; on the other hand, test was applied in order to attain information regarding Biology concept mastery. Then, for the analysis of instrument construct, the researchers performed confirmatory factor analysis by means of Lisrel 0.80 software and the results of this analysis showed that the evaluation instrument valid and reliable. The construct validity was between 0.43-0.79 while the reliability of measurement model was between 0.88-0.94. Last but not the least, the model feasibility test showed that the theoretical model had been supported by the empirical data.

  3. Modeling the fate and transport of plastic debris in freshwaters

    OpenAIRE

    Kooi, Merel; Besseling, Ellen; Kroeze, Carolien; Wenzel, van, Annemarie P.; Koelmans, Albert A.

    2018-01-01

    Contamination with plastic debris has been recognized as one of today’s major environmental quality problems. Because most of the sources are land based, concerns are increasingly focused on the freshwater and terrestrial environment. Fate and transport models for plastic debris can complement information from measurements and will play an important role in the prospective risk assessment of plastic debris. We review the present knowledge with respect to fate and transport modeling of plastic...

  4. Meridional Flow Observations: Implications for the current Flux Transport Models

    International Nuclear Information System (INIS)

    Gonzalez Hernandez, Irene; Komm, Rudolf; Kholikov, Shukur; Howe, Rachel; Hill, Frank

    2011-01-01

    Meridional circulation has become a key element in the solar dynamo flux transport models. Available helioseismic observations from several instruments, Taiwan Oscillation Network (TON), Global Oscillation Network Group (GONG) and Michelson Doppler Imager (MDI), have made possible a continuous monitoring of the solar meridional flow in the subphotospheric layers for the last solar cycle, including the recent extended minimum. Here we review some of the meridional circulation observations using local helioseismology techniques and relate them to magnetic flux transport models.

  5. Modeling of biological intelligence for SCM system optimization.

    Science.gov (United States)

    Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

    2012-01-01

    This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  6. Modeling of Biological Intelligence for SCM System Optimization

    Directory of Open Access Journals (Sweden)

    Shengyong Chen

    2012-01-01

    Full Text Available This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  7. Modeling of Biological Intelligence for SCM System Optimization

    Science.gov (United States)

    Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

    2012-01-01

    This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

  8. State-of-the-art in modeling solute and sediment transport in rivers

    International Nuclear Information System (INIS)

    Sayre, W.W.

    1980-01-01

    This overview is structured around a comprehensive general model based on the conservation of mass principle as applied to dissolved and particulate constituents in rivers, with a few restricted but more specific examples that illustrate the state-of-the-art in modeling typical physical, chemical, and biological processes undergone by selected constituents in rivers. These examples include: simplified one- and two-dimensional formulations focusing on the hydrodynamic advection and dispersion mechanisms; a two-dimensional biochemial oxygen demand-dissolved oxygen model; a one-dimensional polychlorinated biphenyl model that includes uptake and release of constituent by suspended sediment, and deposition and erosion of contaminated particles; and a one-dimensional sediment transport model that accounts for interactions between the flow and the bed, and is capable of tracking dispersing slugs of sediment through cycles of erosion, entrainment, transport in suspension and as bed load, and burial and storage in the bed

  9. Probabilistic transport models for plasma transport in the presence of critical thresholds: Beyond the diffusive paradigma)

    Science.gov (United States)

    Sánchez, R.; van Milligen, B. Ph.; Carreras, B. A.

    2005-05-01

    It is argued that the modeling of plasma transport in tokamaks may benefit greatly from extending the usual local paradigm to accommodate scale-free transport mechanisms. This can be done by combining Lévy distributions and a nonlinear threshold condition within the continuous time random walk concept. The advantages of this nonlocal, nonlinear extension are illustrated by constructing a simple particle density transport model that, as a result of these ideas, spontaneously exhibits much of nondiffusive phenomenology routinely observed in tokamaks. The fluid limit of the system shows that the kind of equations that are appropriate to capture these dynamics are based on fractional differential operators. In them, effective diffusivities and pinch velocities are found that are dynamically set by the system in response to the specific characteristics of the fueling source and external perturbations. This fact suggests some dramatic consequences for the extrapolation of these transport properties to larger size systems.

  10. Probabilistic transport models for plasma transport in the presence of critical thresholds: Beyond the diffusive paradigm

    International Nuclear Information System (INIS)

    Sanchez, R.; Milligen, B.Ph. van; Carreras, B.A.

    2005-01-01

    It is argued that the modeling of plasma transport in tokamaks may benefit greatly from extending the usual local paradigm to accommodate scale-free transport mechanisms. This can be done by combining Levy distributions and a nonlinear threshold condition within the continuous time random walk concept. The advantages of this nonlocal, nonlinear extension are illustrated by constructing a simple particle density transport model that, as a result of these ideas, spontaneously exhibits much of nondiffusive phenomenology routinely observed in tokamaks. The fluid limit of the system shows that the kind of equations that are appropriate to capture these dynamics are based on fractional differential operators. In them, effective diffusivities and pinch velocities are found that are dynamically set by the system in response to the specific characteristics of the fueling source and external perturbations. This fact suggests some dramatic consequences for the extrapolation of these transport properties to larger size systems

  11. Biological restoration of major transportation facilities domestic demonstration and application project (DDAP): technology development at Sandia National Laboratories.

    Energy Technology Data Exchange (ETDEWEB)

    Ramsey, James L., Jr. (.,; .); Melton, Brad; Finley, Patrick; Brockman, John; Peyton, Chad E.; Tucker, Mark David; Einfeld, Wayne; Griffith, Richard O.; Brown, Gary Stephen; Lucero, Daniel A.; Betty, Rita G.; McKenna, Sean Andrew; Knowlton, Robert G.; Ho, Pauline

    2006-06-01

    The Bio-Restoration of Major Transportation Facilities Domestic Demonstration and Application Program (DDAP) is a designed to accelerate the restoration of transportation nodes following an attack with a biological warfare agent. This report documents the technology development work done at SNL for this DDAP, which include development of the BROOM tool, an investigation of surface sample collection efficiency, and a flow cytometry study of chlorine dioxide effects on Bacillus anthracis spore viability.

  12. Transport modelling in coastal waters using stochastic differential equations

    NARCIS (Netherlands)

    Charles, W.M.

    2007-01-01

    In this thesis, the particle model that takes into account the short term correlation behaviour of pollutants dispersion has been developed. An efficient particle model for sediment transport has been developed. We have modified the existing particle model by adding extra equations for the

  13. Boolean Models of Biological Processes Explain Cascade-Like Behavior

    Science.gov (United States)

    Chen, Hao; Wang, Guanyu; Simha, Rahul; Du, Chenghang; Zeng, Chen

    2016-01-01

    Biological networks play a key role in determining biological function and therefore, an understanding of their structure and dynamics is of central interest in systems biology. In Boolean models of such networks, the status of each molecule is either “on” or “off” and along with the molecules interact with each other, their individual status changes from “on” to “off” or vice-versa and the system of molecules in the network collectively go through a sequence of changes in state. This sequence of changes is termed a biological process. In this paper, we examine the common perception that events in biomolecular networks occur sequentially, in a cascade-like manner, and ask whether this is likely to be an inherent property. In further investigations of the budding and fission yeast cell-cycle, we identify two generic dynamical rules. A Boolean system that complies with these rules will automatically have a certain robustness. By considering the biological requirements in robustness and designability, we show that those Boolean dynamical systems, compared to an arbitrary dynamical system, statistically present the characteristics of cascadeness and sequentiality, as observed in the budding and fission yeast cell- cycle. These results suggest that cascade-like behavior might be an intrinsic property of biological processes. PMID:26821940

  14. Economic model of pipeline transportation systems

    Energy Technology Data Exchange (ETDEWEB)

    Banks, W. F.

    1977-07-29

    The objective of the work reported here was to develop a model which could be used to assess the economic effects of energy-conservative technological innovations upon the pipeline industry. The model is a dynamic simulator which accepts inputs of two classes: the physical description (design parameters, fluid properties, and financial structures) of the system to be studied, and the postulated market (throughput and price) projection. The model consists of time-independent submodels: the fluidics model which simulates the physical behavior of the system, and the financial model which operates upon the output of the fluidics model to calculate the economics outputs. Any of a number of existing fluidics models can be used in addition to that developed as a part of this study. The financial model, known as the Systems, Science and Software (S/sup 3/) Financial Projection Model, contains user options whereby pipeline-peculiar characteristics can be removed and/or modified, so that the model can be applied to virtually any kind of business enterprise. The several dozen outputs are of two classes: the energetics and the economics. The energetics outputs of primary interest are the energy intensity, also called unit energy consumption, and the total energy consumed. The primary economics outputs are the long-run average cost, profit, cash flow, and return on investment.

  15. ATTILA - Atmospheric Tracer Transport In a Langrangian Model

    Energy Technology Data Exchange (ETDEWEB)

    Reithmeier, C.; Sausen, R.

    2000-07-01

    The Lagrangian model ATTILA (atmospheric tracer transport in a Lagrangian model) has been developed to treat the global-scale transport of passive trace species in the atmosphere within the framework of a general circulation model (GCM). ATTILA runs online within the GCM ECHAM4 and uses the GCM produced wind field to advect the centrois of 80.000 to 180.000 constant mass air parcels into which the model atmosphere is divided. Each trace constituent is thereby represented by a mass mixing ratio in each parcel. ATTILA contains state-of-the-art parameterizations of convection, turbulent boundary layer mixing, and interparcel transport and provides an algorithm to map the tracer concentrations from the trajectories to the ECHAM model grid. We use two experiments to evaluate the transport characteristics of ATTILA against observations and the standard semiLagrangian transport scheme of ECHAM. In the first experiment we simulate the distribution of the short-lived tracer Radon ({sup 222}Rn) in order to examine fast vertical transport over continents, and long-range transport from the continents to remote areas. In the second experiment, we simulate the distribution of radiocarbon ({sup 14}C) that was injected into the northern stratosphere during the nuclear weapon tests in the early 60ties, in order to examine upper tropospheric and stratospheric transport characteristics. ATTILA compares well to the observations and in many respects to the semiLagrangian scheme. However, contrary to the semiLagrangian scheme, ATTILA shows a greatly reduced meridional transport in the upper troposphere and lower stratosphere, and a reduced downward flux from the stratosphere to the troposphere, especially in midlatitudes. Since both transport schemes use the same model meteorology, we conclude that the often cited enhanced meridional transport and overestimated downward flux in ECHAM as described above is rather due to the numerical properties of the semiLagrangian scheme than due to an

  16. Natural crayfish clone as emerging model for various biological ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Biosciences; Volume 36; Issue 2. Marmorkrebs: Natural crayfish clone as emerging model for various biological disciplines. Günter Vogt. Mini-review Volume 36 Issue 2 June 2011 pp 377-382. Fulltext. Click here to view fulltext PDF. Permanent link:

  17. Coarse-graining intermittent intracellular transport: Two- and three-dimensional models

    Science.gov (United States)

    Lawley, Sean D.; Tuft, Marie; Brooks, Heather A.

    2015-10-01

    Viruses and other cellular cargo that lack locomotion must rely on diffusion and cellular transport systems to navigate through a biological cell. Indeed, advances in single particle tracking have revealed that viral motion alternates between (a) diffusion in the cytoplasm and (b) active transport along microtubules. This intermittency makes quantitative analysis of trajectories difficult. Therefore, the purpose of this paper is to construct mathematical methods to approximate intermittent dynamics by effective stochastic differential equations. The coarse-graining method that we develop is more accurate than existing techniques and applicable to a wide range of intermittent transport models. In particular, we apply our method to two- and three-dimensional cell geometries (disk, sphere, and cylinder) and demonstrate its accuracy. In addition to these specific applications, we also explain our method in full generality for use on future intermittent models.

  18. Systems Biology in Immunology – A Computational Modeling Perspective

    Science.gov (United States)

    Germain, Ronald N.; Meier-Schellersheim, Martin; Nita-Lazar, Aleksandra; Fraser, Iain D. C.

    2011-01-01

    Systems biology is an emerging discipline that combines high-content, multiplexed measurements with informatic and computational modeling methods to better understand biological function at various scales. Here we present a detailed review of the methods used to create computational models and conduct simulations of immune function, We provide descriptions of the key data gathering techniques employed to generate the quantitative and qualitative data required for such modeling and simulation and summarize the progress to date in applying these tools and techniques to questions of immunological interest, including infectious disease. We include comments on what insights modeling can provide that complement information obtained from the more familiar experimental discovery methods used by most investigators and why quantitative methods are needed to eventually produce a better understanding of immune system operation in health and disease. PMID:21219182

  19. Modeling and simulation of biological systems using SPICE language.

    Directory of Open Access Journals (Sweden)

    Morgan Madec

    Full Text Available The article deals with BB-SPICE (SPICE for Biochemical and Biological Systems, an extension of the famous Simulation Program with Integrated Circuit Emphasis (SPICE. BB-SPICE environment is composed of three modules: a new textual and compact description formalism for biological systems, a converter that handles this description and generates the SPICE netlist of the equivalent electronic circuit and NGSPICE which is an open-source SPICE simulator. In addition, the environment provides back and forth interfaces with SBML (System Biology Markup Language, a very common description language used in systems biology. BB-SPICE has been developed in order to bridge the gap between the simulation of biological systems on the one hand and electronics circuits on the other hand. Thus, it is suitable for applications at the interface between both domains, such as development of design tools for synthetic biology and for the virtual prototyping of biosensors and lab-on-chip. Simulation results obtained with BB-SPICE and COPASI (an open-source software used for the simulation of biochemical systems have been compared on a benchmark of models commonly used in systems biology. Results are in accordance from a quantitative viewpoint but BB-SPICE outclasses COPASI by 1 to 3 orders of magnitude regarding the computation time. Moreover, as our software is based on NGSPICE, it could take profit of incoming updates such as the GPU implementation, of the coupling with powerful analysis and verification tools or of the integration in design automation tools (synthetic biology.

  20. Transport lattice models of heat transport in skin with spatially heterogeneous, temperature-dependent perfusion

    Directory of Open Access Journals (Sweden)

    Martin Gregory T

    2004-11-01

    Full Text Available Abstract Background Investigation of bioheat transfer problems requires the evaluation of temporal and spatial distributions of temperature. This class of problems has been traditionally addressed using the Pennes bioheat equation. Transport of heat by conduction, and by temperature-dependent, spatially heterogeneous blood perfusion is modeled here using a transport lattice approach. Methods We represent heat transport processes by using a lattice that represents the Pennes bioheat equation in perfused tissues, and diffusion in nonperfused regions. The three layer skin model has a nonperfused viable epidermis, and deeper regions of dermis and subcutaneous tissue with perfusion that is constant or temperature-dependent. Two cases are considered: (1 surface contact heating and (2 spatially distributed heating. The model is relevant to the prediction of the transient and steady state temperature rise for different methods of power deposition within the skin. Accumulated thermal damage is estimated by using an Arrhenius type rate equation at locations where viable tissue temperature exceeds 42°C. Prediction of spatial temperature distributions is also illustrated with a two-dimensional model of skin created from a histological image. Results The transport lattice approach was validated by comparison with an analytical solution for a slab with homogeneous thermal properties and spatially distributed uniform sink held at constant temperatures at the ends. For typical transcutaneous blood gas sensing conditions the estimated damage is small, even with prolonged skin contact to a 45°C surface. Spatial heterogeneity in skin thermal properties leads to a non-uniform temperature distribution during a 10 GHz electromagnetic field exposure. A realistic two-dimensional model of the skin shows that tissue heterogeneity does not lead to a significant local temperature increase when heated by a hot wire tip. Conclusions The heat transport system model of the

  1. Radiative Transport Modelling of Thermal Barrier Coatings

    Science.gov (United States)

    2017-03-24

    derived by Thrane et al from Fresnel-Huygens diffraction theory .5 The Thrane model defines the normalized signal current as a function of integrated...problem is in part application-driven, namely based on the need to be able to extract the radiative properties from the shape the LCI signal . On the...walk model to test model approaches 75 June 2017 4 Apply the theory to experimental data on TBCs 20 June 2017 5 Report on results and future

  2. Interfacial and Wall Transport Models for SPACE-CAP Code

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Soon Joon; Choo, Yeon Joon; Han, Tae Young; Hwang, Su Hyun; Lee, Byung Chul [FNC Tech., Seoul (Korea, Republic of); Choi, Hoon; Ha, Sang Jun [Korea Electric Power Research Institute, Daejeon (Korea, Republic of)

    2009-10-15

    The development project for the domestic design code was launched to be used for the safety and performance analysis of pressurized light water reactors. And CAP (Containment Analysis Package) code has been also developed for the containment safety and performance analysis side by side with SPACE. The CAP code treats three fields (gas, continuous liquid, and dispersed drop) for the assessment of containment specific phenomena, and is featured by its multidimensional assessment capabilities. Thermal hydraulics solver was already developed and now under testing of its stability and soundness. As a next step, interfacial and wall transport models was setup. In order to develop the best model and correlation package for the CAP code, various models currently used in major containment analysis codes, which are GOTHIC, CONTAIN2.0, and CONTEMPT-LT, have been reviewed. The origins of the selected models used in these codes have also been examined to find out if the models have not conflict with a proprietary right. In addition, a literature survey of the recent studies has been performed in order to incorporate the better models for the CAP code. The models and correlations of SPACE were also reviewed. CAP models and correlations are composed of interfacial heat/mass, and momentum transport models, and wall heat/mass, and momentum transport models. This paper discusses on those transport models in the CAP code.

  3. Transport modeling and advanced computer techniques

    International Nuclear Information System (INIS)

    Wiley, J.C.; Ross, D.W.; Miner, W.H. Jr.

    1988-11-01

    A workshop was held at the University of Texas in June 1988 to consider the current state of transport codes and whether improved user interfaces would make the codes more usable and accessible to the fusion community. Also considered was the possibility that a software standard could be devised to ease the exchange of routines between groups. It was noted that two of the major obstacles to exchanging routines now are the variety of geometrical representation and choices of units. While the workshop formulated no standards, it was generally agreed that good software engineering would aid in the exchange of routines, and that a continued exchange of ideas between groups would be worthwhile. It seems that before we begin to discuss software standards we should review the current state of computer technology --- both hardware and software to see what influence recent advances might have on our software goals. This is done in this paper

  4. Evaluation of radiobiological effects in 3 distinct biological models

    International Nuclear Information System (INIS)

    Lemos, J.; Costa, P.; Cunha, L.; Metello, L.F.; Carvalho, A.P.; Vasconcelos, V.; Genesio, P.; Ponte, F.; Costa, P.S.; Crespo, P.

    2015-01-01

    Full text of publication follows. The present work aims at sharing the process of development of advanced biological models to study radiobiological effects. Recognizing several known limitations and difficulties of the current monolayer cellular models, as well as the increasing difficulties to use advanced biological models, our group has been developing advanced biological alternative models, namely three-dimensional cell cultures and a less explored animal model (the Zebra fish - Danio rerio - which allows the access to inter-generational data, while characterized by a great genetic homology towards the humans). These 3 models (monolayer cellular model, three-dimensional cell cultures and zebra fish) were externally irradiated with 100 mGy, 500 mGy or 1 Gy. The consequences of that irradiation were studied using cellular and molecular tests. Our previous experimental studies with 100 mGy external gamma irradiation of HepG2 monolayer cells showed a slight increase in the proliferation rate 24 h, 48 h and 72 h post irradiation. These results also pointed into the presence of certain bystander effects 72 h post irradiation, constituting the starting point for the need of a more accurate analysis realized with this work. At this stage, we continue focused on the acute biological effects. Obtained results, namely MTT and clonogenic assays for evaluating cellular metabolic activity and proliferation in the in vitro models, as well as proteomics for the evaluation of in vivo effects will be presented, discussed and explained. Several hypotheses will be presented and defended based on the facts previously demonstrated. This work aims at sharing the actual state and the results already available from this medium-term project, building the proof of the added value on applying these advanced models, while demonstrating the strongest and weakest points from all of them (so allowing the comparison between them and to base the subsequent choice for research groups starting

  5. Mathematical Model of Ion Transport in Electrodialysis Process

    Directory of Open Access Journals (Sweden)

    F.S. Rohman

    2010-10-01

    Full Text Available Mathematical models of ion transport in electrodialysis process is reviewed and their basics concept is discussed. Three scales of ion transport reviewed are: 1 ion transport in the membrane, where two approaches are used, the irreversible thermodynamics and modeling of the membrane material; 2 ion transport in a three-layer system composed of a membrane with two adjoining diffusion layers; and 3 coupling with hydraulic flow system in an electrodialysis 2D and 3D cell, where the differential equation of convectivediffusion is used. Most of the work carried out in the past implemented NP equations since relatively easily coupled with other equations describing hydrodynamic conditions and ion transport in the surrounding solutions, chemical reactions in the solutions and the membrane, boundary and other conditions. However, it is limited to point ionic transport in homogenous and uniformly - grainy phases of structure. © 2008 BCREC UNDIP. All rights reserved.[Received: 21 January 2008, Accepted: 10 March 2008][How to Cite: F.S. Rohman, N. Aziz (2008. Mathematical Model of Ion Transport in Electrodialysis Process. Bulletin of Chemical Reaction Engineering and Catalysis, 3(1-3: 3-8. doi:10.9767/bcrec.3.1-3.7122.3-8][How to Link/DOI: http://dx.doi.org/10.9767/bcrec.3.1-3.7122.3-8 || or local: http://ejournal.undip.ac.id/index.php/bcrec/article/view/7122 ] 

  6. Methods and models in mathematical biology deterministic and stochastic approaches

    CERN Document Server

    Müller, Johannes

    2015-01-01

    This book developed from classes in mathematical biology taught by the authors over several years at the Technische Universität München. The main themes are modeling principles, mathematical principles for the analysis of these models, and model-based analysis of data. The key topics of modern biomathematics are covered: ecology, epidemiology, biochemistry, regulatory networks, neuronal networks, and population genetics. A variety of mathematical methods are introduced, ranging from ordinary and partial differential equations to stochastic graph theory and  branching processes. A special emphasis is placed on the interplay between stochastic and deterministic models.

  7. Probabilistic Model Checking of Biological Systems with Uncertain Kinetic Rates

    Science.gov (United States)

    Barbuti, Roberto; Levi, Francesca; Milazzo, Paolo; Scatena, Guido

    We present an abstraction of the probabilistic semantics of Multiset Rewriting to formally express systems of reactions with uncertain kinetic rates. This allows biological systems modelling when the exact rates are not known, but are supposed to lie in some intervals. On these (abstract) models we perform probabilistic model checking obtaining lower and upper bounds for the probabilities of reaching states satisfying given properties. These bounds are under- and over-approximations, respectively, of the probabilities one would obtain by verifying the models with exact kinetic rates belonging to the intervals.

  8. Transportation Sector Model of the National Energy Modeling System. Volume 2 -- Appendices: Part 1

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-01-01

    This volume contains input data and parameters used in the model of the transportation sector of the National Energy Modeling System. The list of Transportation Sector Model variables includes parameters for the following: Light duty vehicle modules (fuel economy, regional sales, alternative fuel vehicles); Light duty vehicle stock modules; Light duty vehicle fleet module; Air travel module (demand model and fleet efficiency model); Freight transport module; Miscellaneous energy demand module; and Transportation emissions module. Also included in these appendices are: Light duty vehicle market classes; Maximum light duty vehicle market penetration parameters; Aircraft fleet efficiency model adjustment factors; and List of expected aircraft technology improvements.

  9. Modeling the atmospheric transport of radioactive contamination using the ETA model

    International Nuclear Information System (INIS)

    Telenta, B.; Antic, D.

    1996-01-01

    The atmosphere is the main medium that transports and disperses the radioactive and/or chemical contaminants in operational use and in accidents. Atmospheric models can be used to simulate the transport of contaminants in typical accidents and for realistic meteorological conditions. This paper describes an approach to simulating the Chernobyl accident and similar hypothetical cases. The study is based on an atmospheric model extended by an additional equation that models the transport of a certain radioactive concentration. A step mountain synoptic model, called the ETA model (well-known model for weather forecasting), is used to investigate the transport and deposition of radioactive material in the Chernobyl accident zone

  10. Modelling anisotropic water transport in polymer composite ...

    Indian Academy of Sciences (India)

    and polymer composites were characterized. Parameters for Fickian diffusion and polymer relaxation models were determined by least-square curve fitting to the experimental data. Diffusion parameters of epoxy and vinyl ester resin were used as input during development of finite element (FE) model of polymer composite.

  11. Modeling and Simulation Tools: From Systems Biology to Systems Medicine.

    Science.gov (United States)

    Olivier, Brett G; Swat, Maciej J; Moné, Martijn J

    2016-01-01

    Modeling is an integral component of modern biology. In this chapter we look into the role of the model, as it pertains to Systems Medicine, and the software that is required to instantiate and run it. We do this by comparing the development, implementation, and characteristics of tools that have been developed to work with two divergent methodologies: Systems Biology and Pharmacometrics. From the Systems Biology perspective we consider the concept of "Software as a Medical Device" and what this may imply for the migration of research-oriented, simulation software into the domain of human health.In our second perspective, we see how in practice hundreds of computational tools already accompany drug discovery and development at every stage of the process. Standardized exchange formats are required to streamline the model exchange between tools, which would minimize translation errors and reduce the required time. With the emergence, almost 15 years ago, of the SBML standard, a large part of the domain of interest is already covered and models can be shared and passed from software to software without recoding them. Until recently the last stage of the process, the pharmacometric analysis used in clinical studies carried out on subject populations, lacked such an exchange medium. We describe a new emerging exchange format in Pharmacometrics which covers the non-linear mixed effects models, the standard statistical model type used in this area. By interfacing these two formats the entire domain can be covered by complementary standards and subsequently the according tools.

  12. UNCERTAINTY SUPPLY CHAIN MODEL AND TRANSPORT IN ITS DEPLOYMENTS

    Directory of Open Access Journals (Sweden)

    Fabiana Lucena Oliveira

    2014-05-01

    Full Text Available This article discusses the Model Uncertainty of Supply Chain, and proposes a matrix with their transportation modes best suited to their chains. From the detailed analysis of the matrix of uncertainty, it is suggested transportation modes best suited to the management of these chains, so that transport is the most appropriate optimization of the gains previously proposed by the original model, particularly when supply chains are distant from suppliers of raw materials and / or supplies.Here we analyze in detail Agile Supply Chains, which is a result of Uncertainty Supply Chain Model, with special attention to Manaus Industrial Center. This research was done at Manaus Industrial Pole, which is a model of industrial agglomerations, based in Manaus, State of Amazonas (Brazil, which contemplates different supply chains and strategies sharing same infrastructure of transport, handling and storage and clearance process and uses inbound for suppliers of raw material.  The state of art contemplates supply chain management, uncertainty supply chain model, agile supply chains, Manaus Industrial Center (MIC and Brazilian legislation, as a business case, and presents concepts and features, of each one. The main goal is to present and discuss how transport is able to support Uncertainty Supply Chain Model, in order to complete management model. The results obtained confirms the hypothesis of integrated logistics processes are able to guarantee attractivity for industrial agglomerations, and open discussions when the suppliers are far from the manufacturer center, in a logistics management.

  13. Ising models of strongly coupled biological networks with multivariate interactions

    Science.gov (United States)

    Merchan, Lina; Nemenman, Ilya

    2013-03-01

    Biological networks consist of a large number of variables that can be coupled by complex multivariate interactions. However, several neuroscience and cell biology experiments have reported that observed statistics of network states can be approximated surprisingly well by maximum entropy models that constrain correlations only within pairs of variables. We would like to verify if this reduction in complexity results from intricacies of biological organization, or if it is a more general attribute of these networks. We generate random networks with p-spin (p > 2) interactions, with N spins and M interaction terms. The probability distribution of the network states is then calculated and approximated with a maximum entropy model based on constraining pairwise spin correlations. Depending on the M/N ratio and the strength of the interaction terms, we observe a transition where the pairwise approximation is very good to a region where it fails. This resembles the sat-unsat transition in constraint satisfaction problems. We argue that the pairwise model works when the number of highly probable states is small. We argue that many biological systems must operate in a strongly constrained regime, and hence we expect the pairwise approximation to be accurate for a wide class of problems. This research has been partially supported by the James S McDonnell Foundation grant No.220020321.

  14. Models of transport processes in concrete

    International Nuclear Information System (INIS)

    Pommersheim, J.M.; Clifton, J.R.

    1991-01-01

    An approach being considered by the US Nuclear Regulatory Commission for disposal of low-level radioactive waste is to place the waste forms in concrete vaults buried underground. The vaults would need a service life of 500 years. Approaches for predicting the service life of concrete of such vaults include the use of mathematical models. Mathematical models are presented in this report for the major degradation processes anticipated for the concrete vaults, which are corrosion of steel reinforcement, sulfate attack, acid attack, and leaching. The models mathematically represent rate controlling processes including diffusion, convection, and reaction and sorption of chemical species. These models can form the basis for predicting the life of concrete under in-service conditions. 33 refs., 6 figs., 7 tabs

  15. Tokamak transport based on the Braginskii model

    International Nuclear Information System (INIS)

    Weitzner, H.

    1987-01-01

    The two-fluid model of Braginskii is applied to the case of a moderately large tokamak. By estimation of the order of magnitude of the various effects and omission of small terms a somewhat simpler reduced two-fluid Braginskii model is obtained. The model applies on a time scale of order τ e m i /m e , where τ e is the electron-electron collision time, and energy confinement time is of this order. With electron and ion flow velocities no larger than is necessary to obtain the correct equilibrium currents, classical parallel viscosity becomes a dominant dissipative mechanism. The model allows for the slow evolution of equilibrium states. The equilibria, which include static, ideal magnetohydrodynamic equilibria as a special case, are described. Generally the number density, electrostatic potential, and flows are not constant on a flux surface. The procedure for determination of the slow evolution of the equilibrium is sketched. (orig.)

  16. Programming biological models in Python using PySB.

    Science.gov (United States)

    Lopez, Carlos F; Muhlich, Jeremy L; Bachman, John A; Sorger, Peter K

    2013-01-01

    Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis.

  17. Cosmic-Ray Transport in Heliospheric Magnetic Structures. II. Modeling Particle Transport through Corotating Interaction Regions

    Energy Technology Data Exchange (ETDEWEB)

    Kopp, Andreas [Université Libre de Bruxelles, Service de Physique Statistique et des Plasmas, CP 231, B-1050 Brussels (Belgium); Wiengarten, Tobias; Fichtner, Horst [Institut für Theoretische Physik IV, Ruhr-Universität Bochum, D-44780 Bochum (Germany); Effenberger, Frederic [Department of Physics and KIPAC, Stanford University, Stanford, CA 94305 (United States); Kühl, Patrick; Heber, Bernd [Institut für Experimentelle und Angewandte Physik, Christian-Albrecht-Universität zu Kiel, D-24098 Kiel (Germany); Raath, Jan-Louis; Potgieter, Marius S. [Centre for Space Research, North-West University, 2520 Potchefstroom (South Africa)

    2017-03-01

    The transport of cosmic rays (CRs) in the heliosphere is determined by the properties of the solar wind plasma. The heliospheric plasma environment has been probed by spacecraft for decades and provides a unique opportunity for testing transport theories. Of particular interest for the three-dimensional (3D) heliospheric CR transport are structures such as corotating interaction regions (CIRs), which, due to the enhancement of the magnetic field strength and magnetic fluctuations within and due to the associated shocks as well as stream interfaces, do influence the CR diffusion and drift. In a three-fold series of papers, we investigate these effects by modeling inner-heliospheric solar wind conditions with the numerical magnetohydrodynamic (MHD) framework Cronos (Wiengarten et al., referred as Paper I), and the results serve as input to a transport code employing a stochastic differential equation approach (this paper). While, in Paper I, we presented results from 3D simulations with Cronos, the MHD output is now taken as an input to the CR transport modeling. We discuss the diffusion and drift behavior of Galactic cosmic rays using the example of different theories, and study the effects of CIRs on these transport processes. In particular, we point out the wide range of possible particle fluxes at a given point in space resulting from these different theories. The restriction of this variety by fitting the numerical results to spacecraft data will be the subject of the third paper of this series.

  18. Analyzing Students' Understanding of Models and Modeling Referring to the Disciplines Biology, Chemistry, and Physics

    Science.gov (United States)

    Krell, Moritz; Reinisch, Bianca; Krüger, Dirk

    2015-01-01

    In this study, secondary school students' (N?=?617; grades 7 to 10) understanding of models and modeling was assessed using tasks which explicitly refer to the scientific disciplines of biology, chemistry, and physics and, as a control, to no scientific discipline. The students' responses are interpreted as their biology-, chemistry-, and…

  19. Stencil method: a Markov model for transport in porous media

    Science.gov (United States)

    Delgoshaie, A. H.; Tchelepi, H.; Jenny, P.

    2016-12-01

    In porous media the transport of fluid is dominated by flow-field heterogeneity resulting from the underlying transmissibility field. Since the transmissibility is highly uncertain, many realizations of a geological model are used to describe the statistics of the transport phenomena in a Monte Carlo framework. One possible way to avoid the high computational cost of physics-based Monte Carlo simulations is to model the velocity field as a Markov process and use Markov Chain Monte Carlo. In previous works multiple Markov models for discrete velocity processes have been proposed. These models can be divided into two general classes of Markov models in time and Markov models in space. Both of these choices have been shown to be effective to some extent. However some studies have suggested that the Markov property cannot be confirmed for a temporal Markov process; Therefore there is not a consensus about the validity and value of Markov models in time. Moreover, previous spacial Markov models have only been used for modeling transport on structured networks and can not be readily applied to model transport in unstructured networks. In this work we propose a novel approach for constructing a Markov model in time (stencil method) for a discrete velocity process. The results form the stencil method are compared to previously proposed spacial Markov models for structured networks. The stencil method is also applied to unstructured networks and can successfully describe the dispersion of particles in this setting. Our conclusion is that both temporal Markov models and spacial Markov models for discrete velocity processes can be valid for a range of model parameters. Moreover, we show that the stencil model can be more efficient in many practical settings and is suited to model dispersion both on structured and unstructured networks.

  20. Dynamics of mathematical models in biology bringing mathematics to life

    CERN Document Server

    Zazzu, Valeria; Guarracino, Mario

    2016-01-01

    This volume focuses on contributions from both the mathematics and life science community surrounding the concepts of time and dynamicity of nature, two significant elements which are often overlooked in modeling process to avoid exponential computations. The book is divided into three distinct parts: dynamics of genomes and genetic variation, dynamics of motifs, and dynamics of biological networks. Chapters included in dynamics of genomes and genetic variation analyze the molecular mechanisms and evolutionary processes that shape the structure and function of genomes and those that govern genome dynamics. The dynamics of motifs portion of the volume provides an overview of current methods for motif searching in DNA, RNA and proteins, a key process to discover emergent properties of cells, tissues, and organisms. The part devoted to the dynamics of biological networks covers networks aptly discusses networks in complex biological functions and activities that interpret processes in cells. Moreover, chapters i...

  1. A colloid-facilitated transport model with variable colloid transport properties

    Science.gov (United States)

    Robinson, Bruce A.; Wolfsberg, Andrew V.; Viswanathan, Hari S.; Reimus, Paul W.

    2007-05-01

    Anomalous contaminant transport velocities in groundwater for species generally considered to be immobile are often attributed to the mechanism of colloid-facilitated transport. In some of the field observations attributed to colloid facilitation, an extremely small fraction of the total contaminant mass introduced to the groundwater is detected downstream. In this study, a new model of colloid-facilitated contaminant transport is proposed that explains this phenomenon as the variability of mobility of individual colloids in the population. The process of retardation via attachment and detachment of colloids on immobile surfaces is often modeled with time and space invariant parameters; here it is modeled assuming a diverse population of transport properties that account for the inherent variability of colloid size, surface charge and chemical properties, mineralogy, and the concomitant impact on colloid mobility. When the contaminant is assumed to irreversibly attach to or form colloids, the migration of the contaminant plume exhibits extremely non-Fickian behavior. The plume's center of mass travels with a velocity governed by the groundwater velocity divided by the mean colloid retardation factor. However, small quantities of contaminant attached to a few highly mobile colloids travel at velocities up to the groundwater velocity, far exceeding the velocity of the centroid of the plume. This paper introduces the colloid diversity model, presents some sensitivity calculations for an idealized case, and discusses the implications of such a model on data needs, simulation of field observations, and model scaling.

  2. A multimodal location and routing model for hazardous materials transportation.

    Science.gov (United States)

    Xie, Yuanchang; Lu, Wei; Wang, Wen; Quadrifoglio, Luca

    2012-08-15

    The recent US Commodity Flow Survey data suggest that transporting hazardous materials (HAZMAT) often involves multiple modes, especially for long-distance transportation. However, not much research has been conducted on HAZMAT location and routing on a multimodal transportation network. Most existing HAZMAT location and routing studies focus exclusively on single mode (either highways or railways). Motivated by the lack of research on multimodal HAZMAT location and routing and the fact that there is an increasing demand for it, this research proposes a multimodal HAZMAT model that simultaneously optimizes the locations of transfer yards and transportation routes. The developed model is applied to two case studies of different network sizes to demonstrate its applicability. The results are analyzed and suggestions for future research are provided. Published by Elsevier B.V.

  3. Sustainable logistics and transportation optimization models and algorithms

    CERN Document Server

    Gakis, Konstantinos; Pardalos, Panos

    2017-01-01

    Focused on the logistics and transportation operations within a supply chain, this book brings together the latest models, algorithms, and optimization possibilities. Logistics and transportation problems are examined within a sustainability perspective to offer a comprehensive assessment of environmental, social, ethical, and economic performance measures. Featured models, techniques, and algorithms may be used to construct policies on alternative transportation modes and technologies, green logistics, and incentives by the incorporation of environmental, economic, and social measures. Researchers, professionals, and graduate students in urban regional planning, logistics, transport systems, optimization, supply chain management, business administration, information science, mathematics, and industrial and systems engineering will find the real life and interdisciplinary issues presented in this book informative and useful.

  4. A mobile-mobile transport model for simulating reactive transport in connected heterogeneous fields

    Science.gov (United States)

    Lu, Chunhui; Wang, Zhiyuan; Zhao, Yue; Rathore, Saubhagya Singh; Huo, Jinge; Tang, Yuening; Liu, Ming; Gong, Rulan; Cirpka, Olaf A.; Luo, Jian

    2018-05-01

    Mobile-immobile transport models can be effective in reproducing heavily tailed breakthrough curves of concentration. However, such models may not adequately describe transport along multiple flow paths with intermediate velocity contrasts in connected fields. We propose using the mobile-mobile model for simulating subsurface flow and associated mixing-controlled reactive transport in connected fields. This model includes two local concentrations, one in the fast- and the other in the slow-flow domain, which predict both the concentration mean and variance. The normalized total concentration variance within the flux is found to be a non-monotonic function of the discharge ratio with a maximum concentration variance at intermediate values of the discharge ratio. We test the mobile-mobile model for mixing-controlled reactive transport with an instantaneous, irreversible bimolecular reaction in structured and connected random heterogeneous domains, and compare the performance of the mobile-mobile to the mobile-immobile model. The results indicate that the mobile-mobile model generally predicts the concentration breakthrough curves (BTCs) of the reactive compound better. Particularly, for cases of an elliptical inclusion with intermediate hydraulic-conductivity contrasts, where the travel-time distribution shows bimodal behavior, the prediction of both the BTCs and maximum product concentration is significantly improved. Our results exemplify that the conceptual model of two mobile domains with diffusive mass transfer in between is in general good for predicting mixing-controlled reactive transport, and particularly so in cases where the transfer in the low-conductivity zones is by slow advection rather than diffusion.

  5. Mathematical models for volume rendering and neutron transport

    International Nuclear Information System (INIS)

    Max, N.

    1994-09-01

    This paper reviews several different models for light interaction with volume densities of absorbing, glowing, reflecting, or scattering material. They include absorption only, glow only, glow and absorption combined, single scattering of external illumination, and multiple scattering. The models are derived from differential equations, and illustrated on a data set representing a cloud. They are related to corresponding models in neutron transport. The multiple scattering model uses an efficient method to propagate the radiation which does not suffer from the ray effect

  6. Routing and Scheduling Optimization Model of Sea Transportation

    Science.gov (United States)

    barus, Mika debora br; asyrafy, Habib; nababan, Esther; mawengkang, Herman

    2018-01-01

    This paper examines the routing and scheduling optimization model of sea transportation. One of the issues discussed is about the transportation of ships carrying crude oil (tankers) which is distributed to many islands. The consideration is the cost of transportation which consists of travel costs and the cost of layover at the port. Crude oil to be distributed consists of several types. This paper develops routing and scheduling model taking into consideration some objective functions and constraints. The formulation of the mathematical model analyzed is to minimize costs based on the total distance visited by the tanker and minimize the cost of the ports. In order for the model of the problem to be more realistic and the cost calculated to be more appropriate then added a parameter that states the multiplier factor of cost increases as the charge of crude oil is filled.

  7. Transport modeling of sorbing tracers in artificial fractures

    Energy Technology Data Exchange (ETDEWEB)

    Keum, Dong Kwon; Baik, Min Hoon; Park, Chung Kyun; Cho, Young Hwan; Hahn, Phil Soo

    1998-02-01

    This study was performed as part of a fifty-man year attachment program between AECL (Atomic Energy Canada Limited) and KAERI. Three kinds of computer code, HDD, POMKAP and VAMKAP, were developed to predict transport of contaminants in fractured rock. MDDM was to calculate the mass transport of contaminants in a single fracture using a simple hydrodynamic dispersion diffusion model. POMKAP was to predict the mass transport of contaminants by a two-dimensional variable aperture model. In parallel with modeling, the validation of models was also performed through the analysis of the migration experimental data obtained in acrylic plastic and granite artificial fracture system at the Whiteshell laboratories, AECL, Canada. (author). 34 refs., 11 tabs., 76 figs.

  8. Modeling and simulation of emergent behavior in transportation infrastructure restoration

    Science.gov (United States)

    Ojha, Akhilesh; Corns, Steven; Shoberg, Thomas G.; Qin, Ruwen; Long, Suzanna K.

    2018-01-01

    The objective of this chapter is to create a methodology to model the emergent behavior during a disruption in the transportation system and that calculates economic losses due to such a disruption, and to understand how an extreme event affects the road transportation network. The chapter discusses a system dynamics approach which is used to model the transportation road infrastructure system to evaluate the different factors that render road segments inoperable and calculate economic consequences of such inoperability. System dynamics models have been integrated with business process simulation model to evaluate, design, and optimize the business process. The chapter also explains how different factors affect the road capacity. After identifying the various factors affecting the available road capacity, a causal loop diagram (CLD) is created to visually represent the causes leading to a change in the available road capacity and the effects on travel costs when the available road capacity changes.

  9. Evaluation of cloud convection and tracer transport in a three-dimensional chemical transport model

    Directory of Open Access Journals (Sweden)

    W. Feng

    2011-06-01

    Full Text Available We investigate the performance of cloud convection and tracer transport in a global off-line 3-D chemical transport model. Various model simulations are performed using different meteorological (reanalyses (ERA-40, ECMWF operational and ECMWF Interim to diagnose the updraft mass flux, convective precipitation and cloud top height.

    The diagnosed upward mass flux distribution from TOMCAT agrees quite well with the ECMWF reanalysis data (ERA-40 and ERA-Interim below 200 hPa. Inclusion of midlevel convection improves the agreement at mid-high latitudes. However, the reanalyses show strong convective transport up to 100 hPa, well into the tropical tropopause layer (TTL, which is not captured by TOMCAT. Similarly, the model captures the spatial and seasonal variation of convective cloud top height although the mean modelled value is about 2 km lower than observed.

    The ERA-Interim reanalyses have smaller archived upward convective mass fluxes than ERA-40, and smaller convective precipitation, which is in better agreement with satellite-based data. TOMCAT captures these relative differences when diagnosing convection from the large-scale fields. The model also shows differences in diagnosed convection with the version of the operational analyses used, which cautions against using results of the model from one specific time period as a general evaluation.

    We have tested the effect of resolution on the diagnosed modelled convection with simulations ranging from 5.6° × 5.6° to 1° × 1°. Overall, in the off-line model, the higher model resolution gives stronger vertical tracer transport, however, it does not make a large change to the diagnosed convective updraft mass flux (i.e., the model results using the convection scheme fail to capture the strong convection transport up to 100 hPa as seen in the archived convective mass fluxes. Similarly, the resolution of the forcing winds in the higher resolution CTM does not make a

  10. Complex Behavior in Simple Models of Biological Coevolution

    Science.gov (United States)

    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.

  11. Solvable Model for Dynamic Mass Transport in Disordered Geophysical Media

    KAUST Repository

    Marder, M.

    2018-03-29

    We present an analytically solvable model for transport in geophysical materials on large length and time scales. It describes the flow of gas to a complicated absorbing boundary over long periods of time. We find a solution to this model using Green\\'s function techniques, and apply the solution to three absorbing networks of increasing complexity.

  12. A transport model for prediction of wildfire behavior

    Energy Technology Data Exchange (ETDEWEB)

    Linn, R.R.

    1997-07-01

    Wildfires are a threat to human life and property, yet they are an unavoidable part of nature. In the past people have tried to predict wildfire behavior through the use of point functional models but have been unsuccessful at adequately predicting the gross behavior of the broad spectrum of fires that occur in nature. The majority of previous models do not have self-determining propagation rates. The author uses a transport approach to represent this complicated problem and produce a model that utilizes a self-determining propagation rate. The transport approach allows one to represent a large number of environments including transition regions such as those with nonhomogeneous vegetation and terrain. Some of the most difficult features to treat are the imperfectly known boundary conditions and the fine scale structure that is unresolvable, such as the specific location of the fuel or the precise incoming winds. The author accounts for the microscopic details of a fire with macroscopic resolution by dividing quantities into mean and fluctuating parts similar to what is done in traditional turbulence modelling. The author develops a complicated model that includes the transport of multiple gas species, such as oxygen and volatile hydrocarbons, and tracks the depletion of various fuels and other stationary solids and liquids. From this model the author also forms a simplified local burning model with which he performs a number of simulations for the purpose of demonstrating the properties of a self-determining transport-based wildfire model.

  13. Modelling of transport phenomena and defects in crystal growth ...

    Indian Academy of Sciences (India)

    A brief review of single crystal growth techniques and the associated problems is presented. Emphasis is placed on models for various transport and defect phenomena involoved in the growth process with the ultimate aim of integrating them into a comprehensive numerical model. The sources of dislocation nucleation in ...

  14. Sediment Transport Model for a Surface Irrigation System

    Directory of Open Access Journals (Sweden)

    Damodhara R. Mailapalli

    2013-01-01

    Full Text Available Controlling irrigation-induced soil erosion is one of the important issues of irrigation management and surface water impairment. Irrigation models are useful in managing the irrigation and the associated ill effects on agricultural environment. In this paper, a physically based surface irrigation model was developed to predict sediment transport in irrigated furrows by integrating an irrigation hydraulic model with a quasi-steady state sediment transport model to predict sediment load in furrow irrigation. The irrigation hydraulic model simulates flow in a furrow irrigation system using the analytically solved zero-inertial overland flow equations and 1D-Green-Ampt, 2D-Fok, and Kostiakov-Lewis infiltration equations. Performance of the sediment transport model was evaluated for bare and cropped furrow fields. The results indicated that the sediment transport model can predict the initial sediment rate adequately, but the simulated sediment rate was less accurate for the later part of the irrigation event. Sensitivity analysis of the parameters of the sediment module showed that the soil erodibility coefficient was the most influential parameter for determining sediment load in furrow irrigation. The developed modeling tool can be used as a water management tool for mitigating sediment loss from the surface irrigated fields.

  15. Spatial Economics Model Predicting Transport Volume

    Directory of Open Access Journals (Sweden)

    Lu Bo

    2016-10-01

    Full Text Available It is extremely important to predict the logistics requirements in a scientific and rational way. However, in recent years, the improvement effect on the prediction method is not very significant and the traditional statistical prediction method has the defects of low precision and poor interpretation of the prediction model, which cannot only guarantee the generalization ability of the prediction model theoretically, but also cannot explain the models effectively. Therefore, in combination with the theories of the spatial economics, industrial economics, and neo-classical economics, taking city of Zhuanghe as the research object, the study identifies the leading industry that can produce a large number of cargoes, and further predicts the static logistics generation of the Zhuanghe and hinterlands. By integrating various factors that can affect the regional logistics requirements, this study established a logistics requirements potential model from the aspect of spatial economic principles, and expanded the way of logistics requirements prediction from the single statistical principles to an new area of special and regional economics.

  16. Modelling radon transport in Dutch dwellings

    NARCIS (Netherlands)

    Janssen MPM; Vries L de; Phaff JC; Graaf ER van der; Blaauboer RO; Stoop P; Lembrechts J; TNO-Bouw; KVI; LSO

    1998-01-01

    Radon concentrations and external exposure by nuclides of the U-238 decay chain were quantified for a typical Dutch townhouse using a series of interconnected computer models. The effect is studied of changes in parameter values which have simulated changes in building practices over the past

  17. Evolving Transport Networks With Cellular Automata Models Inspired by Slime Mould.

    Science.gov (United States)

    Tsompanas, Michail-Antisthenis I; Sirakoulis, Georgios Ch; Adamatzky, Andrew I

    2015-09-01

    Man-made transport networks and their design are closely related to the shortest path problem and considered amongst the most debated problems of computational intelligence. Apart from using conventional or bio-inspired computer algorithms, many researchers tried to solve this kind of problem using biological computing substrates, gas-discharge solvers, prototypes of a mobile droplet, and hot ice computers. In this aspect, another example of biological computer is the plasmodium of acellular slime mould Physarum polycephalum (P. polycephalum), which is a large single cell visible by an unaided eye and has been proven as a reliable living substrate for implementing biological computing devices for computational geometry, graph-theoretical problems, and optimization and imitation of transport networks. Although P. polycephalum is easy to experiment with, computing devices built with the living slime mould are extremely slow; it takes slime mould days to execute a computation. Consequently, mapping key computing mechanisms of the slime mould onto silicon would allow us to produce efficient bio-inspired computing devices to tackle with hard to solve computational intelligence problems like the aforementioned. Toward this direction, a cellular automaton (CA)-based, Physarum-inspired, network designing model is proposed. This novel CA-based model is inspired by the propagating strategy, the formation of tubular networks, and the computing abilities of the plasmodium of P. polycephalum. The results delivered by the CA model demonstrate a good match with several previously published results of experimental laboratory studies on imitation of man-made transport networks with P. polycephalum. Consequently, the proposed CA model can be used as a virtual, easy-to-access, and biomimicking laboratory emulator that will economize large time periods needed for biological experiments while producing networks almost identical to the tubular networks of the real-slime mould.

  18. Models to study gravitational biology of Mammalian reproduction

    Science.gov (United States)

    Tou, Janet; Ronca, April; Grindeland, Richard; Wade, Charles

    2002-01-01

    Mammalian reproduction evolved within Earth's 1-g gravitational field. As we move closer to the reality of space habitation, there is growing scientific interest in how different gravitational states influence reproduction in mammals. Habitation of space and extended spaceflight missions require prolonged exposure to decreased gravity (hypogravity, i.e., weightlessness). Lift-off and re-entry of the spacecraft are associated with exposure to increased gravity (hypergravity). Existing data suggest that spaceflight is associated with a constellation of changes in reproductive physiology and function. However, limited spaceflight opportunities and confounding effects of various nongravitational factors associated with spaceflight (i.e., radiation, stress) have led to the development of ground-based models for studying the effects of altered gravity on biological systems. Human bed rest and rodent hindlimb unloading paradigms are used to study exposure to hypogravity. Centrifugation is used to study hypergravity. Here, we review the results of spaceflight and ground-based models of altered gravity on reproductive physiology. Studies utilizing ground-based models that simulate hyper- and hypogravity have produced reproductive results similar to those obtained from spaceflight and are contributing new information on biological responses across the gravity continuum, thereby confirming the appropriateness of these models for studying reproductive responses to altered gravity and the underlying mechanisms of these responses. Together, these unique tools are yielding new insights into the gravitational biology of reproduction in mammals.

  19. An Abstraction Theory for Qualitative Models of Biological Systems

    Directory of Open Access Journals (Sweden)

    Richard Banks

    2010-10-01

    Full Text Available Multi-valued network models are an important qualitative modelling approach used widely by the biological community. In this paper we consider developing an abstraction theory for multi-valued network models that allows the state space of a model to be reduced while preserving key properties of the model. This is important as it aids the analysis and comparison of multi-valued networks and in particular, helps address the well-known problem of state space explosion associated with such analysis. We also consider developing techniques for efficiently identifying abstractions and so provide a basis for the automation of this task. We illustrate the theory and techniques developed by investigating the identification of abstractions for two published MVN models of the lysis-lysogeny switch in the bacteriophage lambda.

  20. Contaminant transport modeling studies of Russian sites

    International Nuclear Information System (INIS)

    Tsang, Chin-Fu

    1993-01-01

    Lawrence Berkeley Laboratory (LBL) established mechanisms that promoted cooperation between U.S. and Russian scientists in scientific research as well as environmental technology transfer. Using Russian experience and U.S technology, LBL developed approaches for field investigations, site evaluation, waste disposal, and remediation at Russian contaminated sites. LBL assessed a comprehensive database as well as an actual, large-scale contaminated site to evaluate existing knowledge of and test mathematical models used for the assessment of U.S. contaminated sites

  1. Assessment of parametric uncertainty for groundwater reactive transport modeling,

    Science.gov (United States)

    Shi, Xiaoqing; Ye, Ming; Curtis, Gary P.; Miller, Geoffery L.; Meyer, Philip D.; Kohler, Matthias; Yabusaki, Steve; Wu, Jichun

    2014-01-01

    The validity of using Gaussian assumptions for model residuals in uncertainty quantification of a groundwater reactive transport model was evaluated in this study. Least squares regression methods explicitly assume Gaussian residuals, and the assumption leads to Gaussian likelihood functions, model parameters, and model predictions. While the Bayesian methods do not explicitly require the Gaussian assumption, Gaussian residuals are widely used. This paper shows that the residuals of the reactive transport model are non-Gaussian, heteroscedastic, and correlated in time; characterizing them requires using a generalized likelihood function such as the formal generalized likelihood function developed by Schoups and Vrugt (2010). For the surface complexation model considered in this study for simulating uranium reactive transport in groundwater, parametric uncertainty is quantified using the least squares regression methods and Bayesian methods with both Gaussian and formal generalized likelihood functions. While the least squares methods and Bayesian methods with Gaussian likelihood function produce similar Gaussian parameter distributions, the parameter distributions of Bayesian uncertainty quantification using the formal generalized likelihood function are non-Gaussian. In addition, predictive performance of formal generalized likelihood function is superior to that of least squares regression and Bayesian methods with Gaussian likelihood function. The Bayesian uncertainty quantification is conducted using the differential evolution adaptive metropolis (DREAM(zs)) algorithm; as a Markov chain Monte Carlo (MCMC) method, it is a robust tool for quantifying uncertainty in groundwater reactive transport models. For the surface complexation model, the regression-based local sensitivity analysis and Morris- and DREAM(ZS)-based global sensitivity analysis yield almost identical ranking of parameter importance. The uncertainty analysis may help select appropriate likelihood

  2. Modeling tracer transport in randomly heterogeneous porous media by nonlocal moment equations: Anomalous transport

    Science.gov (United States)

    Morales-Casique, E.; Lezama-Campos, J. L.; Guadagnini, A.; Neuman, S. P.

    2013-05-01

    Modeling tracer transport in geologic porous media suffers from the corrupt characterization of the spatial distribution of hydrogeologic properties of the system and the incomplete knowledge of processes governing transport at multiple scales. Representations of transport dynamics based on a Fickian model of the kind considered in the advection-dispersion equation (ADE) fail to capture (a) the temporal variation associated with the rate of spreading of a tracer, and (b) the distribution of early and late arrival times which are often observed in field and/or laboratory scenarios and are considered as the signature of anomalous transport. Elsewhere we have presented exact stochastic moment equations to model tracer transport in randomly heterogeneous aquifers. We have also developed a closure scheme which enables one to provide numerical solutions of such moment equations at different orders of approximations. The resulting (ensemble) average and variance of concentration fields were found to display a good agreement against Monte Carlo - based simulation results for mildly heterogeneous (or well-conditioned strongly heterogeneous) media. Here we explore the ability of the moment equations approach to describe the distribution of early arrival times and late time tailing effects which can be observed in Monte-Carlo based breakthrough curves (BTCs) of the (ensemble) mean concentration. We show that BTCs of mean resident concentration calculated at a fixed space location through higher-order approximations of moment equations display long tailing features of the kind which is typically associated with anomalous transport behavior and are not represented by an ADE model with constant dispersive parameter, such as the zero-order approximation.

  3. High resolution model studies of transport of sedimentary material in the south-western Baltic

    Science.gov (United States)

    Seifert, Torsten; Fennel, Wolfgang; Kuhrts, Christiane

    2009-02-01

    The paper presents high resolution model simulations of transport, deposition and resuspension of sedimentary material in the south-western Baltic, based on an upgrade of the sediment transport model described in the work of Kuhrts et al. [Kuhrts, C., Fennel, W., Seifert, T., 2004. Model studies of transport of sedimentary material in the Western Baltic. Journal of Marine Systems 52, 167.]. In the western Baltic, a grid spacing of at least 1 nautical mile is required to resolve the shallow and narrow bathymetry and the associated current patterns. A series of experimental model simulations is carried out with forcing data for the year 1993, which include a sequence of storms in January. Compared to earlier model versions, a more detailed description of potential deposition areas can be provided. The study quantifies the influence of enhanced bottom roughness caused by biological structures, like mussels and worm holes, provides estimates of the regional erosion risks for fine grained sediments, and analyses scenarios of the settling and spreading of material at dumping sites. Although the effects of changed bottom roughness, as derived from more detailed, re-classified sea floor data, are relatively small, the sediment transport and deposition patterns are clearly affected by the variation of the sea bed properties.

  4. Computer-Supported Modelling of Multi modal Transportation Networks Rationalization

    Directory of Open Access Journals (Sweden)

    Ratko Zelenika

    2007-09-01

    Full Text Available This paper deals with issues of shaping and functioning ofcomputer programs in the modelling and solving of multimoda Itransportation network problems. A methodology of an integrateduse of a programming language for mathematical modellingis defined, as well as spreadsheets for the solving of complexmultimodal transportation network problems. The papercontains a comparison of the partial and integral methods ofsolving multimodal transportation networks. The basic hypothesisset forth in this paper is that the integral method results inbetter multimodal transportation network rationalization effects,whereas a multimodal transportation network modelbased on the integral method, once built, can be used as the basisfor all kinds of transportation problems within multimodaltransport. As opposed to linear transport problems, multimodaltransport network can assume very complex shapes. This papercontains a comparison of the partial and integral approach totransp01tation network solving. In the partial approach, astraightforward model of a transp01tation network, which canbe solved through the use of the Solver computer tool within theExcel spreadsheet inteiface, is quite sufficient. In the solving ofa multimodal transportation problem through the integralmethod, it is necessmy to apply sophisticated mathematicalmodelling programming languages which supp01t the use ofcomplex matrix functions and the processing of a vast amountof variables and limitations. The LINGO programming languageis more abstract than the Excel spreadsheet, and it requiresa certain programming knowledge. The definition andpresentation of a problem logic within Excel, in a manner whichis acceptable to computer software, is an ideal basis for modellingin the LINGO programming language, as well as a fasterand more effective implementation of the mathematical model.This paper provides proof for the fact that it is more rational tosolve the problem of multimodal transportation networks by

  5. Bifurcations of a class of singular biological economic models

    International Nuclear Information System (INIS)

    Zhang Xue; Zhang Qingling; Zhang Yue

    2009-01-01

    This paper studies systematically a prey-predator singular biological economic model with time delay. It shows that this model exhibits two bifurcation phenomena when the economic profit is zero. One is transcritical bifurcation which changes the stability of the system, and the other is singular induced bifurcation which indicates that zero economic profit brings impulse, i.e., rapid expansion of the population in biological explanation. On the other hand, if the economic profit is positive, at a critical value of bifurcation parameter, the system undergoes a Hopf bifurcation, i.e., the increase of delay destabilizes the system and bifurcates into small amplitude periodic solution. Finally, by using Matlab software, numerical simulations illustrate the effectiveness of the results obtained here. In addition, we study numerically that the system undergoes a saddle-node bifurcation when the bifurcation parameter goes through critical value of positive economic profit.

  6. Enterococcus infection biology: lessons from invertebrate host models.

    Science.gov (United States)

    Yuen, Grace J; Ausubel, Frederick M

    2014-03-01

    The enterococci are commensals of the gastrointestinal tract of many metazoans, from insects to humans. While they normally do not cause disease in the intestine, they can become pathogenic when they infect sites outside of the gut. Recently, the enterococci have become important nosocomial pathogens, with the majority of human enterococcal infections caused by two species, Enterococcus faecalis and Enterococcus faecium. Studies using invertebrate infection models have revealed insights into the biology of enterococcal infections, as well as general principles underlying host innate immune defense. This review highlights recent findings on Enterococcus infection biology from two invertebrate infection models, the greater wax moth Galleria mellonella and the free-living bacteriovorous nematode Caenorhabditis elegans.

  7. Combining Inverse and Transport Modeling to Estimate Bacterial Loading and Transport in a Tidal Embayment

    Directory of Open Access Journals (Sweden)

    Mac Sisson

    2016-11-01

    Full Text Available Poquoson River is a tidal coastal embayment located along the Western Shore of the Chesapeake Bay about 4 km south of the York River mouth in the City of Poquoson and in York County, Virginia. Its drainage area has diversified land uses, including high densities of residence, agricultural, salt marsh land uses, as well as a National Wildlife Refuge. This embayment experiences elevated bacterial concentration due to excess bacterial inputs from storm water runoff, nonpoint sources, and wash off from marshes due to tide and wind-induced set-up and set-down. Bacteria can also grow in the marsh and small tributaries. It is difficult to use a traditional watershed model to simulate bacterial loading, especially in this low-lying marsh area with abundant wildlife, while runoff is not solely driven by precipitation. An inverse approach is introduced to estimate loading from unknown sources based on observations in the embayment. The estimated loadings were combined with loadings estimated from different sources (human, wildlife, agriculture, pets, etc. and input to the watershed model. The watershed model simulated long-term flow and bacterial loading and discharged to a three-dimensional transport model driven by tide, wind, and freshwater discharge. The transport model efficiently simulates the transport and fate of the bacterial concentration in the embayment and is capable of determining the loading reduction needed to improve the water quality condition of the embayment. Combining inverse, watershed, and transport models is a sound approach for simulating bacterial transport correctly in the coastal embayment with complex unknown bacterial sources, which are not solely driven by precipitation.

  8. Toward a community coastal sediment transport modeling system: the second workshop

    Science.gov (United States)

    Sherwood, Christopher R.; Harris, Courtney K.; Geyer, W. Rockwell; Butman, Bradford

    2002-01-01

    Models for transport and the long-term fate of particles in coastal waters are essential for a variety of applications related to commerce, defense, public health, and the quality of the marine environment. Examples include: analysis of waste disposal and transport and the fate of contaminated materials; evaluation of burial rates for naval mines or archaeological artifacts; prediction of water-column optical properties; analysis of transport and the fate of biological particles; prediction of coastal flooding and coastal erosion; evaluation of impacts of sea-level or wave-climate changes and coastal development; planning for construction and maintenance of navigable waterways; evaluation of habitat for commercial fisheries; evaluation of impacts of natural or anthropogenic changes in coastal conditions on recreational activities; and design of intakes and outfalls for sewage treatment, cooling systems, and desalination plants.

  9. Model development for transport studies in negative shear modes

    Energy Technology Data Exchange (ETDEWEB)

    Spang, M.C.; Casper, T.B.; Thomassen, K.I.

    1997-05-01

    This study develops a simple transport model which can be used predictively for tokamak negative central shear (NCS) modes, with the assistance of Lawrence Livermore National Laboratory`s core plasma simulation code, CORSICA. The results show that the the Rebut-Lallia-Watkins Critical Electron Temperature Gradient Model, coupled with an NCS transport model and TRANSP data, renders a reasonably close match to experimental temperature profiles. Additionally, this research offers the first benchmark calculation indicating that the CORSICA code itself, when given transport coefficients from the analysis of experimental data, replicates the experimental profiles, indicating that both TRANSP and CORSICA together are consistent in their analysis of the plasma evolution. This means CORSICA is working properly and has no known major internal flaws. 14 refs., 12 figs.

  10. Model development for transport studies in negative shear modes

    International Nuclear Information System (INIS)

    Spang, M.C.; Casper, T.B.; Thomassen, K.I.

    1997-05-01

    This study develops a simple transport model which can be used predictively for tokamak negative central shear (NCS) modes, with the assistance of Lawrence Livermore National Laboratory's core plasma simulation code, CORSICA. The results show that the the Rebut-Lallia-Watkins Critical Electron Temperature Gradient Model, coupled with an NCS transport model and TRANSP data, renders a reasonably close match to experimental temperature profiles. Additionally, this research offers the first benchmark calculation indicating that the CORSICA code itself, when given transport coefficients from the analysis of experimental data, replicates the experimental profiles, indicating that both TRANSP and CORSICA together are consistent in their analysis of the plasma evolution. This means CORSICA is working properly and has no known major internal flaws. 14 refs., 12 figs

  11. Modeling transport and deposition of the Mekong River sediment

    Science.gov (United States)

    Xue, Zuo; He, Ruoying; Liu, J. Paul; Warner, John C.

    2012-01-01

    A Coupled Wave–Ocean–SedimentTransport Model was used to hindcast coastal circulation and fine sedimenttransport on the Mekong shelf in southeastern Asian in 2005. Comparisons with limited observations showed that the model simulation captured the regional patterns and temporal variability of surface wave, sea level, and suspended sediment concentration reasonably well. Significant seasonality in sedimenttransport was revealed. In summer, a large amount of fluvial sediments was delivered and deposited near the MekongRiver mouth. In the following winter, strong ocean mixing, and coastal current lead to resuspension and southwestward dispersal of a small fraction of previously deposited sediments. Model sensitivity experiments (with reduced physics) were performed to investigate the impact of tides, waves, and remotely forced ambient currents on the transport and dispersal of the fluvial sediment. Strong wave mixing and downwelling-favorable coastal current associated with the more energetic northeast monsoon in the winter season are the main factors controlling the southwestward along-shelf transport.

  12. GIS-Based Analytical Tools for Transport Planning: Spatial Regression Models for Transportation Demand Forecast

    Directory of Open Access Journals (Sweden)

    Simone Becker Lopes

    2014-04-01

    Full Text Available Considering the importance of spatial issues in transport planning, the main objective of this study was to analyze the results obtained from different approaches of spatial regression models. In the case of spatial autocorrelation, spatial dependence patterns should be incorporated in the models, since that dependence may affect the predictive power of these models. The results obtained with the spatial regression models were also compared with the results of a multiple linear regression model that is typically used in trips generation estimations. The findings support the hypothesis that the inclusion of spatial effects in regression models is important, since the best results were obtained with alternative models (spatial regression models or the ones with spatial variables included. This was observed in a case study carried out in the city of Porto Alegre, in the state of Rio Grande do Sul, Brazil, in the stages of specification and calibration of the models, with two distinct datasets.

  13. Dual-porosity model of solute diffusion in biological tissue modified by electroporation.

    Science.gov (United States)

    Mahnič-Kalamiza, Samo; Miklavčič, Damijan; Vorobiev, Eugène

    2014-07-01

    In many electroporation applications mass transport in biological tissue is of primary concern. This paper presents a theoretical advancement in the field and gives some examples of model use in electroporation applications. The study focuses on post-treatment solute diffusion. We use a dual-porosity approach to describe solute diffusion in electroporated biological tissue. The cellular membrane presents a hindrance to solute transport into the extracellular space and is modeled as electroporation-dependent porosity, assigned to the intracellular space (the finite rate of mass transfer within an individual cell is not accounted for, for reasons that we elaborate on). The second porosity is that of the extracellular space, through which solute vacates a block of tissue. The model can be used to study extraction out of or introduction of solutes into tissue, and we give three examples of application, a full account of model construction, validation with experiments, and a parametrical analysis. To facilitate easy implementation and experimentation by the reader, the complete derivation of the analytical solution for a simplified example is presented. Validation is done by comparing model results to experimentally-obtained data; we modeled kinetics of sucrose extraction by diffusion from sugar beet tissue in laboratory-scale experiments. The parametrical analysis demonstrates the importance of selected physicochemical and geometrical properties of the system, illustrating possible outcomes of applying the model to different electroporation applications. The proposed model is a new platform that supports rapid extension by state-of-the-art models of electroporation phenomena, developed as latest achievements in the field of electroporation. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Physics models in the toroidal transport code PROCTR

    Energy Technology Data Exchange (ETDEWEB)

    Howe, H.C.

    1990-08-01

    The physics models that are contained in the toroidal transport code PROCTR are described in detail. Time- and space-dependent models are included for the plasma hydrogenic-ion, helium, and impurity densities, the electron and ion temperatures, the toroidal rotation velocity, and the toroidal current profile. Time- and depth-dependent models for the trapped and mobile hydrogenic particle concentrations in the wall and a time-dependent point model for the number of particles in the limiter are also included. Time-dependent models for neutral particle transport, neutral beam deposition and thermalization, fusion heating, impurity radiation, pellet injection, and the radial electric potential are included and recalculated periodically as the time-dependent models evolve. The plasma solution is obtained either in simple flux coordinates, where the radial shift of each elliptical, toroidal flux surface is included to maintain an approximate pressure equilibrium, or in general three-dimensional torsatron coordinates represented by series of helical harmonics. The detailed coupling of the plasma, scrape-off layer, limiter, and wall models through the neutral transport model makes PROCTR especially suited for modeling of recycling and particle control in toroidal plasmas. The model may also be used in a steady-state profile analysis mode for studying energy and particle balances starting with measured plasma profiles.

  15. Multiscale modeling for fluid transport in nanosystems.

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jonathan W.; Jones, Reese E.; Mandadapu, Kranthi Kiran; Templeton, Jeremy Alan; Zimmerman, Jonathan A.

    2013-09-01

    Atomistic-scale behavior drives performance in many micro- and nano-fluidic systems, such as mircrofludic mixers and electrical energy storage devices. Bringing this information into the traditionally continuum models used for engineering analysis has proved challenging. This work describes one such approach to address this issue by developing atomistic-to-continuum multi scale and multi physics methods to enable molecular dynamics (MD) representations of atoms to incorporated into continuum simulations. Coupling is achieved by imposing constraints based on fluxes of conserved quantities between the two regions described by one of these models. The impact of electric fields and surface charges are also critical, hence, methodologies to extend finite-element (FE) MD electric field solvers have been derived to account for these effects. Finally, the continuum description can have inconsistencies with the coarse-grained MD dynamics, so FE equations based on MD statistics were derived to facilitate the multi scale coupling. Examples are shown relevant to nanofluidic systems, such as pore flow, Couette flow, and electric double layer.

  16. A self-organized criticality model for plasma transport

    International Nuclear Information System (INIS)

    Carreras, B.A.; Newman, D.; Lynch, V.E.

    1996-01-01

    Many models of natural phenomena manifest the basic hypothesis of self-organized criticality (SOC). The SOC concept brings together the self-similarity on space and time scales that is common to many of these phenomena. The application of the SOC modelling concept to the plasma dynamics near marginal stability opens new possibilities of understanding issues such as Bohm scaling, profile consistency, broad band fluctuation spectra with universal characteristics and fast time scales. A model realization of self-organized criticality for plasma transport in a magnetic confinement device is presented. The model is based on subcritical resistive pressure-gradient-driven turbulence. Three-dimensional nonlinear calculations based on this model show the existence of transport under subcritical conditions. This model that includes fluctuation dynamics leads to results very similar to the running sandpile paradigm

  17. The Global Modeling Initiative Assessment Model: Model Description, Integration and Testing of the Transport Shell

    Energy Technology Data Exchange (ETDEWEB)

    Rotman, D.A.; Tannahill, J.R.; Kinnison, D.E.; Connell, P.S.; Bergmann, D.; Proctor, D.; Rodriquez, J.M.; Lin, S.J.; Rood, R.B.; Prather, M.J.; Rasch, P.J.; Considine, D.B.; Ramaroson, R.; Kawa, S.R.

    2000-04-25

    We describe the three dimensional global stratospheric chemistry model developed under the NASA Global Modeling Initiative (GMI) to assess the possible environmental consequences from the emissions of a fleet of proposed high speed civil transport aircraft. This model was developed through a unique collaboration of the members of the GMI team. Team members provided computational modules representing various physical and chemical processes, and analysis of simulation results through extensive comparison to observation. The team members' modules were integrated within a computational framework that allowed transportability and simulations on massively parallel computers. A unique aspect of this model framework is the ability to interchange and intercompare different submodules to assess the sensitivity of numerical algorithms and model assumptions to simulation results. In this paper, we discuss the important attributes of the GMI effort, describe the GMI model computational framework and the numerical modules representing physical and chemical processes. As an application of the concept, we illustrate an analysis of the impact of advection algorithms on the dispersion of a NO{sub y}-like source in the stratosphere which mimics that of a fleet of commercial supersonic transports (High-Speed Civil Transport (HSCT)) flying between 17 and 20 kilometers.

  18. Modelling of JET hybrid scenarios with GLF23 transport model: E × B shear stabilization of anomalous transport

    NARCIS (Netherlands)

    Voitsekhovitch, I.; Belo, da Silva Ares; Citrin, J.; Fable, E.; Ferreira, J.; Garcia, J.; Garzotti, L.; Hobirk, J.; Hogeweij, G. M. D.; Joffrin, E.; Kochl, F.; Litaudon, X.; Moradi, S.; Nabais, F.; JET-EFDA Contributors,; EU-ITM ITER Scenario Modelling group,

    2014-01-01

    The E × B shear stabilization of anomalous transport in JET hybrid discharges is studied via self-consistent predictive modelling of electron and ion temperature, ion density and toroidal rotation velocity performed with the GLF23 model. The E × B shear

  19. The Extended Generalized Cost Concept and its Application in Freight Transport and General Equilibrium Modeling

    NARCIS (Netherlands)

    Tavasszy, L.; Davydenko, I.; Ruijgrok, K.

    2009-01-01

    The integration of Spatial Equilibrium models and Freight transport network models is important to produce consistent scenarios for future freight transport demand. At various spatial scales, we see the changes in production, trade, logistics networking and transportation, being driven by

  20. Co-transport and co-combustion. An alternative to separate collecting of biological waste?; Co-Transport und Co-Verwertung. Eine Alternative zur getrennten Bioabfallsammlung?

    Energy Technology Data Exchange (ETDEWEB)

    Kegebein, J.; Hoffmann, E.; Hahn, H.H. [Karlsruhe Univ. (T.H.) (Germany). Inst. fuer Siedlungswasserwirtschaft

    2001-06-01

    As an alternative or supplementary to the separate bio-waste collection system the transport of ground organic kitchen waste along with wastewater in sewer systems has been investigated and reuse processes are discussed. Organic kitchen waste has been ground with a commercial food-waste-grinder, the suspensions were characterized with respect to transport, particle size and settling velocity distribution. Approximately 1/3 of the solids were solbilized due to the grinding-process. Residual non-solubilized solids have been transported evenly as bed load and as suspended solids within a half-scale flow channel at low flow velocities. Organic food waste may be utilized as carbon-source for enhanced biological nutrient removal or as substrate for anaerobic digestion and bio-gas production or as a combination of both reuse path-ways. (orig.)

  1. Flavonoid metabolites transport across a human BBB model.

    Science.gov (United States)

    Faria, Ana; Meireles, Manuela; Fernandes, Iva; Santos-Buelga, Celestino; Gonzalez-Manzano, Susana; Dueñas, Montserrat; de Freitas, Victor; Mateus, Nuno; Calhau, Conceição

    2014-04-15

    This study aimed to evaluate the transmembrane transport of different flavonoids (flavan-3-ols, anthocyanins and flavonols) and some of their metabolites (methylated and conjugated with glucuronic acid) across hCMEC/D3 cells (a blood-brain barrier (BBB) model). Further metabolism of the tested compounds was assayed and their transport modulated in an attempt to elucidate the mechanisms behind this process. The transport across hCMEC/D3 cells was monitored in basolateral media at 1, 3 and 18 h by HPLC-DAD/MS. All the flavonoids and their metabolites were transported across hCMEC/D3 cells in a time-dependent manner. In general, the metabolites showed higher transport efficiency than the native flavonoid. No further biotransformation of the metabolites was found as consequence of cellular metabolism. Anthocyanins and their metabolites crossed this BBB cell model in a lipophilicity-dependent way. Quercetin transport was influenced by phosphatase modulators, suggesting a phosphorylation/dephosphorylation regulation mechanism. Overall, this work suggests that flavonoids are capable of crossing the BBB and reaching the central nervous system. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Radon transport in fractured soil. Laboratory experiments and modelling

    International Nuclear Information System (INIS)

    Hoff, A.

    1997-10-01

    Radon (Rn-222) transport in fractured soil has been investigated by laboratory experiments and by modelling. Radon transport experiments have been performed with two sand columns (homogeneous and inhomogeneous) and one undisturbed clayey till column containing a net of preferential flow paths (root holes). A numerical model (the finite-element model FRACTRAN) and an analytic model (a pinhole model) have been applied in simulations if soil gas and radon transport in fractured soil. Experiments and model calculations are included in a discussion of radon entry rates into houses placed on fractured soil. The main conclusion is, that fractures does not in general alter transport of internally generated radon out of soil, when the pressure and flow conditions in the soil is comparable to the conditions prevailing under a house. This indicates the important result, that fractures in soil have no impact on radon entry into a house beyond that of an increased gas permeability, but a more thorough investigation of this subject is needed. Only in the case where the soil is exposed to large pressure gradients, relative to gradients induced by a house, may it be possible to observe effects of radon exchange between fractures and matrix. (au) 52 tabs., 60 ill., 5 refs

  3. Coupled models in porous media: reactive transport and fractures

    International Nuclear Information System (INIS)

    Amir, L.

    2008-12-01

    This thesis deals with numerical simulation of coupled models for flow and transport in porous media. We present a new method for coupling chemical reactions and transport by using a Newton-Krylov method, and we also present a model of flow in fractured media, based on a domain decomposition method that takes into account the case of intersecting fractures. This study is composed of three parts: the first part contains an analysis, and implementation, of various numerical methods for discretizing advection-diffusion problems, in particular by using operator splitting methods. The second part is concerned with a fully coupled method for modeling transport and chemistry problems. The coupled transport-chemistry model is described, after discretization in time, by a system of nonlinear equations. The size of the system, namely the number of grid points times the number a chemical species, precludes a direct solution of the linear system. To alleviate this difficulty, we solve the system by a Newton-Krylov method, so as to avoid forming and factoring the Jacobian matrix. In the last part, we present a model of flow in 3D for intersecting fractures, by using a domain decomposition method. The fractures are treated as interfaces between sub-domains. We show existence and uniqueness of the solution, and we validate the model by numerical tests. (author)

  4. Consistency between 2D-3D Sediment Transport models

    Science.gov (United States)

    Villaret, Catherine; Jodeau, Magali

    2017-04-01

    Sediment transport models have been developed and applied by the engineering community to estimate transport rates and morphodynamic bed evolutions in river flows, coastal and estuarine conditions. Environmental modelling systems like the open-source Telemac modelling system include a hierarchy of models from 1D (Mascaret), 2D (Telemac-2D/Sisyphe) and 3D (Telemac-3D/Sedi-3D) and include a wide range of processes to represent sediment flow interactions under more and more complex situations (cohesive, non-cohesive and mixed sediment). Despite some tremendous progresses in the numerical techniques and computing resources, the quality/accuracy of model results mainly depend on the numerous choices and skills of the modeler. In complex situations involving stratification effects, complex geometry, recirculating flows… 2D model assumptions are no longer valid. A full 3D turbulent flow model is then required in order to capture the vertical mixing processes and to represent accurately the coupled flow/sediment distribution. However a number of theoretical and numerical difficulties arise when dealing with sediment transport modelling in 3D which will be high-lighted : (1) Dependency of model results to the vertical grid refinement and choice of boundary conditions and numerical scheme (2) The choice of turbulence model determines also the sediment vertical distribution which is governed by a balance between the downward settling term and upward turbulent diffusion. (3) The use of different numerical schemes for both hydrodynamics (mean and turbulent flow) and sediment transport modelling can lead to some inconsistency including a mismatch in the definition of numerical cells and definition of boundary conditions. We discuss here those present issues and present some detailed comparison between 2D and 3D simulations on a set of validation test cases which are available in the Telemac 7.2 release using both cohesive and non-cohesive sediments.

  5. Modelling and simulation of soot generation and transport

    OpenAIRE

    Hu, Xiaoqin

    2016-01-01

    Soot released from fires not only causes danger to lives and property damage, but also effects fire spread by altering the radiation characteristics of fire effluents. In many situations, it is the soot concentration that controls the fire development. Therefore, soot modelling is of great importance in fire safety science. This necessitates the development of a global and general soot model within fire field models that can simulate the amount of soot generated and transported in large-scale...

  6. Computer-based modelling and optimization in transportation

    CERN Document Server

    Rossi, Riccardo

    2014-01-01

    This volume brings together works resulting from research carried out by members of the EURO Working Group on Transportation (EWGT) and presented during meetings and workshops organized by the Group under the patronage of the Association of European Operational Research Societies in 2012 and 2013. The main targets of the EWGT include providing a forum to share research information and experience, encouraging joint research and the development of both theoretical methods and applications, and promoting cooperation among the many institutions and organizations which are leaders at national level in the field of transportation and logistics. The primary fields of interest concern operational research methods, mathematical models and computation algorithms, to solve and sustain solutions to problems mainly faced by public administrations, city authorities, public transport companies, service providers and logistic operators. Related areas of interest are: land use and transportation planning, traffic control and ...

  7. Boolean Networks in Inference and Dynamic Modeling of Biological Systems at the Molecular and Physiological Level

    Science.gov (United States)

    Thakar, Juilee; Albert, Réka

    The following sections are included: * Introduction * Boolean Network Concepts and History * Extensions of the Classical Boolean Framework * Boolean Inference Methods and Examples in Biology * Dynamic Boolean Models: Examples in Plant Biology, Developmental Biology and Immunology * Conclusions * References

  8. Cuttings Transport Models and Experimental Visualization of Underbalanced Horizontal Drilling

    Directory of Open Access Journals (Sweden)

    Na Wei

    2013-01-01

    Full Text Available Aerated underbalanced horizontal drilling technology has become the focus of the drilling industry at home and abroad, and one of the engineering core issues is the horizontal borehole cleaning. Therefore, calculating the minimum injection volume of gas and liquid accurately is essential for the construction in aerated underbalanced horizontal drilling. This paper establishes a physical model of carrying cuttings and borehole cleaning in wellbore of horizontal well and a critical transport mathematical model according to gas-liquid-solid flow mechanism and large plane dunes particle transport theory.

  9. Visualization and Modeling of Nanoparticle Transport in Porous Media

    Science.gov (United States)

    Berkowitz, B.; Naftaly, A.; Dror, I.

    2015-12-01

    We examine transport of nanoparticles (NPs) in a refraction index-matched, three-dimensional, water-saturated porous medium, consisting of polyacrylamide beads which carry a negative surface charge. Flow cell experiments involved use of synthesized, negatively-charged gold and silver nanoparticles (AuNPs, AgNPs) and positively-charged AgNPs, to determine the effect of surface charge on NP transport behavior. From sequential imaging of the flow cell and detailed image analysis, we obtained measurements of the temporally evolving spatial NP concentration distribution. The current experiments focused on point source, pulse injection of AuNPs and AgNPs into a uniform flow field. Parallel experiments employing a conservative (Congo red) tracer demonstrated the transport to be mildly non-Fickian. A continuous time random walk (CTRW) particle tracking (PT) model was then used to quantify the spatial and temporal migration of both the conservative and reactive tracer plumes; model parameters related to the non-Fickian transport were determined from conservative (column and flow cell) tracer experiments. The results show that the negatively-charged NPs behaved similarly to the conservative tracer. These results are in accord with previous measurements of transport of negatively-charged AgNPs in sand columns. The positively-charged AgNPs, in contrast, displayed a decreasing tendency over distance to attach to the negatively-charged porous medium. Further analysis showed that the decreasing tendency of these NPs to attach to the porous medium may be correlated to the particle residence time. This transport behavior is understood by DLS and ζ potential measurements, which showed that aggregation processes and inversion in particle surface charge occurred during the transport of the positively-charged NPs. Modeling results indicated the transport to be more non-Fickian for the positively-charged AgNPs, highlighting a coupling between attachment and transport processes. We

  10. Modelling the Influence of Shielding on Physical and Biological Organ Doses

    CERN Document Server

    Ballarini, Francesca; Ferrari, Alfredo; Ottolenghi, Andrea; Pelliccioni, Maurizio; Scannicchio, Domenico

    2002-01-01

    Distributions of "physical" and "biological" dose in different organs were calculated by coupling the FLUKA MC transport code with a geometrical human phantom inserted into a shielding box of variable shape, thickness and material. While the expression "physical dose" refers to the amount of deposited energy per unit mass (in Gy), "biological dose" was modelled with "Complex Lesions" (CL), clustered DNA strand breaks calculated in a previous work based on "event-by-event" track-structure simulations. The yields of complex lesions per cell and per unit dose were calculated for different radiation types and energies, and integrated into a version of FLUKA modified for this purpose, allowing us to estimate the effects of mixed fields. As an initial test simulation, the phantom was inserted into an aluminium parallelepiped and was isotropically irradiated with 500 MeV protons. Dose distributions were calculated for different values of the shielding thickness. The results were found to be organ-dependent. In most ...

  11. Modelling radon transport in Dutch dwellings

    Energy Technology Data Exchange (ETDEWEB)

    Janssen, M.P.M.; De Vries, L.; Phaff, J.C.; Van der Graaf, E.R.; Blaauboer, R.O.; Stoop, P.; Lembrechts, J

    1998-07-01

    Radon concentrations and external exposure by nuclides of the U-238 decay chain were quantified for a typical Dutch townhouse using a series of interconnected computer models. The effect is studied of changes in parameter values which have simulated changes in building practices over the past decades. Three groups of parameters were distinguished: (1) the air-tightness of the building shell and the distribution of leaks over outer walls and ground floor, (2) the radon-relevant characteristics of the building materials, and 3) those characterising 'habits of the occupant', such as changing mechanical ventilation rate and opening of air inlets or doors. The relative importance of increased air-tightness and of substitution of concrete by other building materials in new dwellings is illustrated. On average changes in building practices clearly enhanced the radon concentration in the living room without affecting external exposure. In new, airtight dwellings the relative effect of occupant behaviour is demonstrated as considerably larger than in old ones.

  12. Green Transport Balanced Scorecard Model with Analytic Network Process Support

    Directory of Open Access Journals (Sweden)

    David Staš

    2015-11-01

    Full Text Available In recent decades, the performance of economic and non-economic activities has required them to be friendly with the environment. Transport is one of the areas having considerable potential within the scope. The main assumption to achieve ambitious green goals is an effective green transport evaluation system. However, these systems are researched from the industrial company and supply chain perspective only sporadically. The aim of the paper is to design a conceptual framework for creating the Green Transport (GT Balanced Scorecard (BSC models from the viewpoint of industrial companies and supply chains using an appropriate multi-criteria decision making method. The models should allow green transport performance evaluation and support of an effective implementation of green transport strategies. Since performance measures used in Balanced Scorecard models are interdependent, the Analytic Network Process (ANP was used as the appropriate multi-criteria decision making method. The verification of the designed conceptual framework was performed on a real supply chain of the European automotive industry.

  13. A ballistic transport model for electronic excitation following particle impact

    Science.gov (United States)

    Hanke, S.; Heuser, C.; Weidtmann, B.; Wucher, A.

    2018-01-01

    We present a ballistic model for the transport of electronic excitation energy induced by keV particle bombardment onto a solid surface. Starting from a free electron gas model, the Boltzmann transport equation (BTE) is employed to follow the evolution of the temporal and spatial distribution function f (r → , k → , t) describing the occupation probability of an electronic state k → at position r → and time t. Three different initializations of the distribution function are considered: i) a thermal distribution function with a locally and temporally elevated electron temperature, ii) a peak excitation at a specific energy above the Fermi level with a quasi-isotropic distribution in k-space and iii) an anisotropic peak excitation with k-vectors oriented in a specific transport direction. While the first initialization resembles a distribution function which may, for instance, result from electronic friction of moving atoms within an ion induced collision cascade, the peak excitation can in principle result from an autoionization process after excitation in close binary collisions. By numerically solving the BTE, we study the electronic energy exchange along a one dimensional transport direction to obtain a time and space resolved excitation energy distribution function, which is then analyzed in view of general transport characteristics of the chosen model system.

  14. Biological profiling and dose-response modeling tools ...

    Science.gov (United States)

    Through its ToxCast project, the U.S. EPA has developed a battery of in vitro high throughput screening (HTS) assays designed to assess the potential toxicity of environmental chemicals. At present, over 1800 chemicals have been tested in up to 600 assays, yielding a large number of concentration-response data sets. Standard processing of these data sets involves finding a best fitting mathematical model and set of model parameters that specify this model. The model parameters include quantities such as the half-maximal activity concentration (or “AC50”) that have biological significance and can be used to inform the efficacy or potency of a given chemical with respect to a given assay. All of this data is processed and stored in an online-accessible database and website: http://actor.epa.gov/dashboard2. Results from these in vitro assays are used in a multitude of ways. New pathways and targets can be identified and incorporated into new or existing adverse outcome pathways (AOPs). Pharmacokinetic models such as those implemented EPA’s HTTK R package can be used to translate an in vitro concentration into an in vivo dose; i.e., one can predict the oral equivalent dose that might be expected to activate a specific biological pathway. Such predicted values can then be compared with estimated actual human exposures prioritize chemicals for further testing.Any quantitative examination should be accompanied by estimation of uncertainty. We are developing met

  15. Ground-water transport model selection and evaluation guidelines

    International Nuclear Information System (INIS)

    Simmons, C.S.; Cole, C.R.

    1983-01-01

    Guidelines are being developed to assist potential users with selecting appropriate computer codes for ground-water contaminant transport modeling. The guidelines are meant to assist managers with selecting appropriate predictive models for evaluating either arid or humid low-level radioactive waste burial sites. Evaluation test cases in the form of analytical solutions to fundamental equations and experimental data sets have been identified and recommended to ensure adequate code selection, based on accurate simulation of relevant physical processes. The recommended evaluation procedures will consider certain technical issues related to the present limitations in transport modeling capabilities. A code-selection plan will depend on identifying problem objectives, determining the extent of collectible site-specific data, and developing a site-specific conceptual model for the involved hydrology. Code selection will be predicated on steps for developing an appropriate systems model. This paper will review the progress in developing those guidelines. 12 references

  16. Analysing Models as a Knowledge Technology in Transport Planning

    DEFF Research Database (Denmark)

    Gudmundsson, Henrik

    2011-01-01

    critical analytic literature on knowledge utilization and policy influence. A simple scheme based in this literature is drawn up to provide a framework for discussing the interface between urban transport planning and model use. A successful example of model use in Stockholm, Sweden is used as a heuristic......Models belong to a wider family of knowledge technologies, applied in the transport area. Models sometimes share with other such technologies the fate of not being used as intended, or not at all. The result may be ill-conceived plans as well as wasted resources. Frequently, the blame...... device to illuminate how such an analytic scheme may allow patterns of insight about the use, influence and role of models in planning to emerge. The main contribution of the paper is to demonstrate that concepts and terminologies from knowledge use literature can provide interpretations of significance...

  17. System convergence in transport models: algorithms efficiency and output uncertainty

    DEFF Research Database (Denmark)

    Rich, Jeppe; Nielsen, Otto Anker

    2015-01-01

    of this paper is to analyse convergence performance for the external loop and to illustrate how an improper linkage between the converging parts can lead to substantial uncertainty in the final output. Although this loop is crucial for the performance of large-scale transport models it has not been analysed......-scale in the Danish National Transport Model (DNTM). It is revealed that system convergence requires that either demand or supply is without random noise but not both. In that case, if MSA is applied to the model output with random noise, it will converge effectively as the random effects are gradually dampened...... in the MSA process. In connection to DNTM it is shown that MSA works well when applied to travel-time averaging, whereas trip averaging is generally infected by random noise resulting from the assignment model. The latter implies that the minimum uncertainty in the final model output is dictated...

  18. Intelligent Transportation and Evacuation Planning A Modeling-Based Approach

    CERN Document Server

    Naser, Arab

    2012-01-01

    Intelligent Transportation and Evacuation Planning: A Modeling-Based Approach provides a new paradigm for evacuation planning strategies and techniques. Recently, evacuation planning and modeling have increasingly attracted interest among researchers as well as government officials. This interest stems from the recent catastrophic hurricanes and weather-related events that occurred in the southeastern United States (Hurricane Katrina and Rita). The evacuation methods that were in place before and during the hurricanes did not work well and resulted in thousands of deaths. This book offers insights into the methods and techniques that allow for implementing mathematical-based, simulation-based, and integrated optimization and simulation-based engineering approaches for evacuation planning. This book also: Comprehensively discusses the application of mathematical models for evacuation and intelligent transportation modeling Covers advanced methodologies in evacuation modeling and planning Discusses principles a...

  19. Model for cadmium transport and distribution in CHO cells

    Energy Technology Data Exchange (ETDEWEB)

    Hayden, T.L.; Turner, J.E.; Williams, M.W.; Cook, J.S.; Hsie, A.W.

    1982-01-01

    A compartmental model is developed to study the transport and distribution of cadmium in Chinese hamster ovary (CHO) cells. Of central importance to the model is the role played by sequestering components which bind free Cd/sup 2 +/ ions. The most important of these is a low-molecular-weight protein, metallothionein, which is produced by the cells in response to an increase in the cellular concentration of Cd/sup 2 +/. Monte Carlo techniques are used to generate a stochastic model based on existing experimental data describing the intracellular transport of cadmium between different compartments. This approach provides an alternative to the usual numerical solution of differential-delay equations that arise in deterministic models. Our model suggests subcellular structures which may be responsible for the accumulation of cadmium and, hence, could account for cadmium detoxification. 4 figures, 1 table.

  20. Analytical modelling of hydrogen transport in reactor containments

    International Nuclear Information System (INIS)

    Manno, V.P.

    1983-09-01

    A versatile computational model of hydrogen transport in nuclear plant containment buildings is developed. The background and significance of hydrogen-related nuclear safety issues are discussed. A computer program is constructed that embodies the analytical models. The thermofluid dynamic formulation spans a wide applicability range from rapid two-phase blowdown transients to slow incompressible hydrogen injection. Detailed ancillary models of molecular and turbulent diffusion, mixture transport properties, multi-phase multicomponent thermodynamics and heat sink modelling are addressed. The numerical solution of the continuum equations emphasizes both accuracy and efficiency in the employment of relatively coarse discretization and long time steps. Reducing undesirable numerical diffusion is addressed. Problem geometry options include lumped parameter zones, one dimensional meshs, two dimensional Cartesian or axisymmetric coordinate systems and three dimensional Cartesian or cylindrical regions. An efficient lumped nodal model is included for simulation of events in which spatial resolution is not significant. Several validation calculations are reported

  1. Analytical model of reactive transport processes with spatially variable coefficients.

    Science.gov (United States)

    Simpson, Matthew J; Morrow, Liam C

    2015-05-01

    Analytical solutions of partial differential equation (PDE) models describing reactive transport phenomena in saturated porous media are often used as screening tools to provide insight into contaminant fate and transport processes. While many practical modelling scenarios involve spatially variable coefficients, such as spatially variable flow velocity, v(x), or spatially variable decay rate, k(x), most analytical models deal with constant coefficients. Here we present a framework for constructing exact solutions of PDE models of reactive transport. Our approach is relevant for advection-dominant problems, and is based on a regular perturbation technique. We present a description of the solution technique for a range of one-dimensional scenarios involving constant and variable coefficients, and we show that the solutions compare well with numerical approximations. Our general approach applies to a range of initial conditions and various forms of v(x) and k(x). Instead of simply documenting specific solutions for particular cases, we present a symbolic worksheet, as supplementary material, which enables the solution to be evaluated for different choices of the initial condition, v(x) and k(x). We also discuss how the technique generalizes to apply to models of coupled multispecies reactive transport as well as higher dimensional problems.

  2. Conceptual Site Model for Newark Bay—Hydrodynamics and Sediment Transport

    Directory of Open Access Journals (Sweden)

    Parmeshwar L. Shrestha

    2014-02-01

    Full Text Available A conceptual site model (CSM has been developed for the Newark Bay Study Area (NBSA as part of the Remedial Investigation/Feasibility Study (RI/FS for this New Jersey site. The CSM is an evolving document that describes the influence of physical, chemical and biological processes on contaminant fate and transport. The CSM is initiated at the start of a project, updated during site activities, and used to inform sampling and remediation planning. This paper describes the hydrodynamic and sediment transport components of the CSM for the NBSA. Hydrodynamic processes are influenced by freshwater inflows, astronomical forcing through two tidal straits, meteorological conditions, and anthropogenic activities such as navigational dredging. Sediment dynamics are driven by hydrodynamics, waves, sediment loading from freshwater sources and the tidal straits, sediment size gradation, sediment bed properties, and particle-to-particle interactions. Cohesive sediment transport is governed by advection, dispersion, aggregation, settling, consolidation, and erosion. Noncohesive sediment transport is governed by advection, dispersion, settling, armoring, and transport in suspension and along the bed. The CSM will inform the development and application of a numerical model that accounts for all key variables to adequately describe the NBSA’s historical, current, and future physical conditions.

  3. Models for transport and fate of carbon, nutrients and point source released radionuclides to an aquatic ecosystem

    Energy Technology Data Exchange (ETDEWEB)

    Kumblad, Linda [Stockholm Univ. (Sweden). Dept. of Systems Ecology; Kautsky, Ulrik [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden)

    2004-09-01

    In this report three ecosystem models are described in terms of structure, initial data, and results. All models are dynamic, mass-balanced and describe the transport and fate of elements in an open aquatic ecosystem. The models are based on ecologically sound principles, provide model results with high resolution and transparency, and are constrained by the nutrient dynamics of the ecosystem itself. The processes driving the transport in all the models are both the biological processes such as primary production, consumption, respiration and excretion, and abiotic e.g. water exchange and air-sea exchange. The first model, the CNP-model, describes the distribution and fluxes of carbon and nutrients for the coastal ecosystem off Forsmark. The second model, the C-14 model, is an extension of the CNP-model and describes the transport and distribution of hypothetically released C-14 from the underground repository SFR-1 to the ecosystem above. The third model, the RN-model, is a generic radionuclide flow model that models the transport and distribution of radionuclides other than C-14 hypothetically discharged to the ecosystem. The model also analyses the importance of some radionuclide specific mechanisms for the radionuclide flow. The generic radionuclide model is also based on the CNP-model, but has radionuclide specific mechanisms connected to each compartment.

  4. Models for transport and fate of carbon, nutrients and point source released radionuclides to an aquatic ecosystem

    International Nuclear Information System (INIS)

    Kumblad, Linda

    2004-09-01

    In this report three ecosystem models are described in terms of structure, initial data, and results. All models are dynamic, mass-balanced and describe the transport and fate of elements in an open aquatic ecosystem. The models are based on ecologically sound principles, provide model results with high resolution and transparency, and are constrained by the nutrient dynamics of the ecosystem itself. The processes driving the transport in all the models are both the biological processes such as primary production, consumption, respiration and excretion, and abiotic e.g. water exchange and air-sea exchange. The first model, the CNP-model, describes the distribution and fluxes of carbon and nutrients for the coastal ecosystem off Forsmark. The second model, the C-14 model, is an extension of the CNP-model and describes the transport and distribution of hypothetically released C-14 from the underground repository SFR-1 to the ecosystem above. The third model, the RN-model, is a generic radionuclide flow model that models the transport and distribution of radionuclides other than C-14 hypothetically discharged to the ecosystem. The model also analyses the importance of some radionuclide specific mechanisms for the radionuclide flow. The generic radionuclide model is also based on the CNP-model, but has radionuclide specific mechanisms connected to each compartment

  5. A deterministic model of electron transport for electron probe microanalysis

    Science.gov (United States)

    Bünger, J.; Richter, S.; Torrilhon, M.

    2018-01-01

    Within the last decades significant improvements in the spatial resolution of electron probe microanalysis (EPMA) were obtained by instrumental enhancements. In contrast, the quantification procedures essentially remained unchanged. As the classical procedures assume either homogeneity or a multi-layered structure of the material, they limit the spatial resolution of EPMA. The possibilities of improving the spatial resolution through more sophisticated quantification procedures are therefore almost untouched. We investigate a new analytical model (M 1-model) for the quantification procedure based on fast and accurate modelling of electron-X-ray-matter interactions in complex materials using a deterministic approach to solve the electron transport equations. We outline the derivation of the model from the Boltzmann equation for electron transport using the method of moments with a minimum entropy closure and present first numerical results for three different test cases (homogeneous, thin film and interface). Taking Monte Carlo as a reference, the results for the three test cases show that the M 1-model is able to reproduce the electron dynamics in EPMA applications very well. Compared to classical analytical models like XPP and PAP, the M 1-model is more accurate and far more flexible, which indicates the potential of deterministic models of electron transport to further increase the spatial resolution of EPMA.

  6. Inverse modelling for flow and transport in porous media

    International Nuclear Information System (INIS)

    Giudici, M.

    2004-01-01

    The problem of parameter identification for flow and transport model in porous media is discussed in this communication. First, a general framework for the development and application of environmental models is discussed. Then the forward and inverse problems for discrete models are described in detail, introducing fundamental concepts (uniqueness, identifiability, stability, conditioning). The importance of model scales is reviewed and is shown its link with the stability and conditioning issues. Finally some remarks are given to the use of several independent sets of data in inverse modelling

  7. Modeling of impurity transport in the core plasma

    International Nuclear Information System (INIS)

    Hulse, R.A.

    1992-01-01

    This paper presents a brief overview of computer modeling of impurity transport in the core region of controlled thermonuclear fusion plasmas. The atomic processes of importance in these high temperature plasmas and the numerical formulation of the model are described. Selected modeling examples are then used to highlight some features of the physics of impurity behavior in large tokamak fusion devices, with an emphasis on demonstrating the sensitivity of such modeling to uncertainties in the rate coefficients used for the atomic processes. This leads to a discussion of current requirements and opportunities for generating the improved sets of comprehensive atomic data needed to support present and future fusion impurity modeling studies

  8. Modeling biogechemical reactive transport in a fracture zone

    Energy Technology Data Exchange (ETDEWEB)

    Molinero, Jorge; Samper, Javier; Yang, Chan Bing, and Zhang, Guoxiang; Guoxiang, Zhang

    2005-01-14

    A coupled model of groundwater flow, reactive solute transport and microbial processes for a fracture zone of the Aspo site at Sweden is presented. This is the model of the so-called Redox Zone Experiment aimed at evaluating the effects of tunnel construction on the geochemical conditions prevailing in a fracture granite. It is found that a model accounting for microbially-mediated geochemical processes is able to reproduce the unexpected measured increasing trends of dissolved sulfate and bicarbonate. The model is also useful for testing hypotheses regarding the role of microbial processes and evaluating the sensitivity of model results to changes in biochemical parameters.

  9. Modeling biogeochemical reactive transport in a fracture zone

    International Nuclear Information System (INIS)

    Molinero, Jorge; Samper, Javier; Yang, Chan Bing; Zhang, Guoxiang; Guoxiang, Zhang

    2005-01-01

    A coupled model of groundwater flow, reactive solute transport and microbial processes for a fracture zone of the Aspo site at Sweden is presented. This is the model of the so-called Redox Zone Experiment aimed at evaluating the effects of tunnel construction on the geochemical conditions prevailing in a fracture granite. It is found that a model accounting for microbially-mediated geochemical processes is able to reproduce the unexpected measured increasing trends of dissolved sulfate and bicarbonate. The model is also useful for testing hypotheses regarding the role of microbial processes and evaluating the sensitivity of model results to changes in biochemical parameters

  10. The model of drugs distribution dynamics in biological tissue

    Science.gov (United States)

    Ginevskij, D. A.; Izhevskij, P. V.; Sheino, I. N.

    2017-09-01

    The dose distribution by Neutron Capture Therapy follows the distribution of 10B in the tissue. The modern models of pharmacokinetics of drugs describe the processes occurring in conditioned "chambers" (blood-organ-tumor), but fail to describe the spatial distribution of the drug in the tumor and in normal tissue. The mathematical model of the spatial distribution dynamics of drugs in the tissue, depending on the concentration of the drug in the blood, was developed. The modeling method is the representation of the biological structure in the form of a randomly inhomogeneous medium in which the 10B distribution occurs. The parameters of the model, which cannot be determined rigorously in the experiment, are taken as the quantities subject to the laws of the unconnected random processes. The estimates of 10B distribution preparations in the tumor and healthy tissue, inside/outside the cells, are obtained.

  11. Modelling of Human Transplacental Transport as Performed in Copenhagen, Denmark

    DEFF Research Database (Denmark)

    Mathiesen, L.; Morck, T. A.; Zuri, G.

    2014-01-01

    classes of chemicals and nanoparticles for comparisons across chemical structures as well as different test systems. Our test systems are based on human material to bypass the extrapolation from animal data. By combining data from our two test systems, we are able to rank and compare the transport...... the relationships between maternal and foetal exposures to various compounds including pollutants such as polychlorinated biphenyls, polybrominated flame retardants, nanoparticles as well as recombinant human antibodies. The compounds have been studied in the human placenta perfusion model and to some extent...... in vitro with an established human monolayer trophoblast cell culture model. Results from our studies distinguish placental transport of substances by physicochemical properties, adsorption to placental tissue, binding to transport and receptor proteins and metabolism. We have collected data from different...

  12. Review of modeling and control during transport airdrop process

    Directory of Open Access Journals (Sweden)

    Bin Xu

    2016-12-01

    Full Text Available This article presents the review of modeling and control during the airdrop process of transport aircraft. According to the airdrop height, technology can be classified into high and low altitude airdrop and in this article, the research is reviewed based on the two scenarios. While high altitude airdrop is mainly focusing on the precise landing control of cargo, the low altitude flight airdrop is on the control of transport aircraft dynamics to ensure flight safety. The history of high precision airdrop system is introduced first, and then the modeling and control problem of the ultra low altitude airdrop in transport aircraft is presented. Finally, the potential problems and future direction of low altitude airdrop are discussed.

  13. Mouse models for gastric cancer: Matching models to biological questions.

    Science.gov (United States)

    Poh, Ashleigh R; O'Donoghue, Robert J J; Ernst, Matthias; Putoczki, Tracy L

    2016-07-01

    Gastric cancer is the third leading cause of cancer-related mortality worldwide. This is in part due to the asymptomatic nature of the disease, which often results in late-stage diagnosis, at which point there are limited treatment options. Even when treated successfully, gastric cancer patients have a high risk of tumor recurrence and acquired drug resistance. It is vital to gain a better understanding of the molecular mechanisms underlying gastric cancer pathogenesis to facilitate the design of new-targeted therapies that may improve patient survival. A number of chemically and genetically engineered mouse models of gastric cancer have provided significant insight into the contribution of genetic and environmental factors to disease onset and progression. This review outlines the strengths and limitations of current mouse models of gastric cancer and their relevance to the pre-clinical development of new therapeutics. © 2016 The Authors Journal of Gastroenterology and Hepatology published by Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

  14. Distribution of biologic, anthropogenic, and volcanic constituents as a proxy for sediment transport in the San Francisco Bay Coastal System

    Science.gov (United States)

    McGann, Mary; Erikson, Li H.; Wan, Elmira; Powell, Charles; Maddocks, Rosalie F.; Barnard, P.L.; Jaffee, B.E.; Schoellhamer, D.H.

    2013-01-01

    Although conventional sediment parameters (mean grain size, sorting, and skewness) and provenance have typically been used to infer sediment transport pathways, most freshwater, brackish, and marine environments are also characterized by abundant sediment constituents of biological, and possibly anthropogenic and volcanic, origin that can provide additional insight into local sedimentary processes. The biota will be spatially distributed according to its response to environmental parameters such as water temperature, salinity, dissolved oxygen, organic carbon content, grain size, and intensity of currents and tidal flow, whereas the presence of anthropogenic and volcanic constituents will reflect proximity to source areas and whether they are fluvially- or aerially-transported. Because each of these constituents have a unique environmental signature, they are a more precise proxy for that source area than the conventional sedimentary process indicators. This San Francisco Bay Coastal System study demonstrates that by applying a multi-proxy approach, the primary sites of sediment transport can be identified. Many of these sites are far from where the constituents originated, showing that sediment transport is widespread in the region. Although not often used, identifying and interpreting the distribution of naturally-occurring and allochthonous biologic, anthropogenic, and volcanic sediment constituents is a powerful tool to aid in the investigation of sediment transport pathways in other coastal systems.

  15. Cerebrospinal and interstitial fluid transport via the glymphatic pathway modeled by optimal mass transport.

    Science.gov (United States)

    Ratner, Vadim; Gao, Yi; Lee, Hedok; Elkin, Rena; Nedergaard, Maiken; Benveniste, Helene; Tannenbaum, Allen

    2017-05-15

    The glymphatic pathway is a system which facilitates continuous cerebrospinal fluid (CSF) and interstitial fluid (ISF) exchange and plays a key role in removing waste products from the rodent brain. Dysfunction of the glymphatic pathway may be implicated in the pathophysiology of Alzheimer's disease. Intriguingly, the glymphatic system is most active during deep wave sleep general anesthesia. By using paramagnetic tracers administered into CSF of rodents, we previously showed the utility of MRI in characterizing a macroscopic whole brain view of glymphatic transport but we have yet to define and visualize the specific flow patterns. Here we have applied an alternative mathematical analysis approach to a dynamic time series of MRI images acquired every 4min over ∼3h in anesthetized rats, following administration of a small molecular weight paramagnetic tracer into the CSF reservoir of the cisterna magna. We use Optimal Mass Transport (OMT) to model the glymphatic flow vector field, and then analyze the flow to find the network of CSF-ISF flow channels. We use 3D visualization computational tools to visualize the OMT defined network of CSF-ISF flow channels in relation to anatomical and vascular key landmarks from the live rodent brain. The resulting OMT model of the glymphatic transport network agrees largely with the current understanding of the glymphatic transport patterns defined by dynamic contrast-enhanced MRI revealing key CSF transport pathways along the ventral surface of the brain with a trajectory towards the pineal gland, cerebellum, hypothalamus and olfactory bulb. In addition, the OMT analysis also revealed some interesting previously unnoticed behaviors regarding CSF transport involving parenchymal streamlines moving from ventral reservoirs towards the surface of the brain, olfactory bulb and large central veins. Copyright © 2017. Published by Elsevier Inc.

  16. A new turbulence-based model for sand transport

    Science.gov (United States)

    Mayaud, Jerome; Wiggs, Giles; Bailey, Richard

    2016-04-01

    Knowledge of the changing rate of sediment flux in space and time is essential for quantifying surface erosion and deposition in desert landscapes. While many aeolian studies have relied on time-averaged parameters such as wind velocity (U) and wind shear velocity (u*) to determine sediment flux, there is increasing evidence that high-frequency turbulence is an important driving force behind the entrainment and transport of sand. However, turbulence has yet to be incorporated into a functional sand transport model that can be used for predictive purposes. In this study we present a new transport model (the 'turbulence model') that accounts for high-frequency variations in the horizontal (u) and vertical (w) components of wind flow. The turbulence model is fitted to wind velocity and sediment transport data from a field experiment undertaken in Namibia's Skeleton Coast National Park, and its performance at three temporal resolutions (10 Hz, 1 Hz, 1 min) is compared to two existing models that rely on time-averaged wind velocity data (Radok, 1977; Dong et al., 2003). The validity of the three models is analysed under a variety of saltation conditions, using a 2-hour (1 Hz measurement resolution) dataset from the Skeleton Coast and a 5-hour (1 min measurement resolution) dataset from the southwestern Kalahari Desert. The turbulence model is shown to outperform the Radok and Dong models when predicting total saltation count over the three experimental periods. For all temporal resolutions presented in this study (10 Hz-10 min), the turbulence model predicted total saltation count to within at least 0.34%, whereas the Radok and Dong models over- or underestimated total count by up to 5.50% and 20.53% respectively. The strong performance of the turbulence model can be attributed to a lag in mass flux response built into its formulation, which can be adapted depending on the temporal resolution of investigation. This accounts for the inherent lag within the physical

  17. Wave basin model tests of technical-biological bank protection

    Science.gov (United States)

    Eisenmann, J.

    2012-04-01

    Sloped embankments of inland waterways are usually protected from erosion and other negative im-pacts of ship-induced hydraulic loads by technical revetments consisting of riprap. Concerning the dimensioning of such bank protection there are several design rules available, e.g. the "Principles for the Design of Bank and Bottom Protection for Inland Waterways" or the Code of Practice "Use of Standard Construction Methods for Bank and Bottom Protection on Waterways" issued by the BAW (Federal Waterways Engineering and Research Institute). Since the European Water Framework Directive has been put into action special emphasis was put on natural banks. Therefore the application of technical-biological bank protection is favoured. Currently design principles for technical-biological bank protection on inland waterways are missing. The existing experiences mainly refer to flowing waters with no or low ship-induced hydraulic loads on the banks. Since 2004 the Federal Waterways Engineering and Research Institute has been tracking the re-search and development project "Alternative Technical-Biological Bank Protection on Inland Water-ways" in company with the Federal Institute of Hydrology. The investigation to date includes the ex-amination of waterway sections where technical- biological bank protection is applied locally. For the development of design rules for technical-biological bank protection investigations shall be carried out in a next step, considering the mechanics and resilience of technical-biological bank protection with special attention to ship-induced hydraulic loads. The presentation gives a short introduction into hydraulic loads at inland waterways and their bank protection. More in detail model tests of a willow brush mattress as a technical-biological bank protec-tion in a wave basin are explained. Within the scope of these tests the brush mattresses were ex-posed to wave impacts to determine their resilience towards hydraulic loads. Since the

  18. Indoor Air Nuclear, Biological, and Chemical Health Modeling and Assessment System

    Energy Technology Data Exchange (ETDEWEB)

    Stenner, Robert D.; Hadley, Donald L.; Armstrong, Peter R.; Buck, John W.; Hoopes, Bonnie L.; Janus, Michael C.

    2001-03-01

    Indoor air quality effects on human health are of increasing concern to public health agencies and building owners. The prevention and treatment of 'sick building' syndrome and the spread of air-borne diseases in hospitals, for example, are well known priorities. However, increasing attention is being directed to the vulnerability of our public buildings/places, public security and national defense facilities to terrorist attack or the accidental release of air-borne biological pathogens, harmful chemicals, or radioactive contaminants. The Indoor Air Nuclear, Biological, and Chemical Health Modeling and Assessment System (IA-NBC-HMAS) was developed to serve as a health impact analysis tool for use in addressing these concerns. The overall goal was to develop a user-friendly fully functional prototype Health Modeling and Assessment system, which will operate under the PNNL FRAMES system for ease of use and to maximize its integration with other modeling and assessment capabilities accessible within the FRAMES system (e.g., ambient air fate and transport models, water borne fate and transport models, Physiologically Based Pharmacokinetic models, etc.). The prototype IA-NBC-HMAS is designed to serve as a functional Health Modeling and Assessment system that can be easily tailored to meet specific building analysis needs of a customer. The prototype system was developed and tested using an actual building (i.e., the Churchville Building located at the Aberdeen Proving Ground) and release scenario (i.e., the release and measurement of tracer materials within the building) to ensure realism and practicality in the design and development of the prototype system. A user-friendly "demo" accompanies this report to allow the reader the opportunity for a "hands on" review of the prototype system's capability.

  19. Comparison of mechanistic transport cycle models of ABC exporters.

    Science.gov (United States)

    Szöllősi, Dániel; Rose-Sperling, Dania; Hellmich, Ute A; Stockner, Thomas

    2018-04-01

    ABC (ATP binding cassette) transporters, ubiquitous in all kingdoms of life, carry out essential substrate transport reactions across cell membranes. Their transmembrane domains bind and translocate substrates and are connected to a pair of nucleotide binding domains, which bind and hydrolyze ATP to energize import or export of substrates. Over four decades of investigations into ABC transporters have revealed numerous details from atomic-level structural insights to their functional and physiological roles. Despite all these advances, a comprehensive understanding of the mechanistic principles of ABC transporter function remains elusive. The human multidrug resistance transporter ABCB1, also referred to as P-glycoprotein (P-gp), is one of the most intensively studied ABC exporters. Using ABCB1 as the reference point, we aim to compare the dominating mechanistic models of substrate transport and ATP hydrolysis for ABC exporters and to highlight the experimental and computational evidence in their support. In particular, we point out in silico studies that enhance and complement available biochemical data. "This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain." Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  20. A quasilinear model for solute transport under unsaturated flow

    International Nuclear Information System (INIS)

    Houseworth, J.E.; Leem, J.

    2009-01-01

    We developed an analytical solution for solute transport under steady-state, two-dimensional, unsaturated flow and transport conditions for the investigation of high-level radioactive waste disposal. The two-dimensional, unsaturated flow problem is treated using the quasilinear flow method for a system with homogeneous material properties. Dispersion is modeled as isotropic and is proportional to the effective hydraulic conductivity. This leads to a quasilinear form for the transport problem in terms of a scalar potential that is analogous to the Kirchhoff potential for quasilinear flow. The solutions for both flow and transport scalar potentials take the form of Fourier series. The particular solution given here is for two sources of flow, with one source containing a dissolved solute. The solution method may easily be extended, however, for any combination of flow and solute sources under steady-state conditions. The analytical results for multidimensional solute transport problems, which previously could only be solved numerically, also offer an additional way to benchmark numerical solutions. An analytical solution for two-dimensional, steady-state solute transport under unsaturated flow conditions is presented. A specific case with two sources is solved but may be generalized to any combination of sources. The analytical results complement numerical solutions, which were previously required to solve this class of problems.

  1. Solute transport modelling with the variable temporally dependent ...

    Indian Academy of Sciences (India)

    Pintu Das

    2018-02-07

    Feb 7, 2018 ... In this present study, analytical and numerical solutions are obtained for solute transport modelling in homogeneous ..... Clay (0.40). Analytical solution. Numerical solution. Figure 3. Comparison of concentration distribution for sinu- soidal velocity pattern for boundary condition c0. 2 1 ю sec wt р. Ю.

  2. Modelling two-phase transport of 3H/3He

    NARCIS (Netherlands)

    Visser, A.; Schaap, J.D.; Leijnse, T.; Broers, H.P.; Bierkens, M.F.P.

    2008-01-01

    Degassing of groundwater by excess denitrification of agricultural pollution complicates the interpretation of 3H/3He data and hinders the estimation of travel times in nitrate pollution studies. In this study we used a two-phase flow and transport model (STOMP) to evaluate the method presented by

  3. Modeling the fate and transport of plastic debris in freshwaters

    NARCIS (Netherlands)

    Kooi, Merel; Besseling, Ellen; Kroeze, Carolien; Wenzel, van Annemarie P.; Koelmans, Albert A.

    2018-01-01

    Contamination with plastic debris has been recognized as one of today’s major environmental quality problems. Because most of the sources are land based, concerns are increasingly focused on the freshwater and terrestrial environment. Fate and transport models for plastic debris can complement

  4. Development of a transport model for the microbial degradation of ...

    African Journals Online (AJOL)

    A mathematical model for first order reaction rate under isothermal condition was developed for predicting the diffusivity and transport rate of anthracene and pyrene during biodegradation using two microbial strains (corynebacteria spp and pseudomonas putida) in a heterogeneous porous medium. The formulation ...

  5. Transport of Pathogen Surrogates in Soil Treatment Units: Numerical Modeling

    Directory of Open Access Journals (Sweden)

    Ivan Morales

    2014-04-01

    Full Text Available Segmented mesocosms (n = 3 packed with sand, sandy loam or clay loam soil were used to determine the effect of soil texture and depth on transport of two septic tank effluent (STE-borne microbial pathogen surrogates—green fluorescent protein-labeled E. coli (GFPE and MS-2 coliphage—in soil treatment units. HYDRUS 2D/3D software was used to model the transport of these microbes from the infiltrative surface. Mesocosms were spiked with GFPE and MS-2 coliphage at 105 cfu/mL STE and 105–106 pfu/mL STE, respectively. In all soils, removal rates were >99.99% at 25 cm. The transport simulation compared (1 optimization; and (2 trial-and-error modeling approaches. Only slight differences between the transport parameters were observed between these approaches. Treating both the die-off rates and attachment/detachment rates as variables resulted in an overall better model fit, particularly for the tailing phase of the experiments. Independent of the fitting procedure, attachment rates computed by the model were higher in sandy and sandy loam soils than clay, which was attributed to unsaturated flow conditions at lower water content in the coarser-textured soils. Early breakthrough of the bacteria and virus indicated the presence of preferential flow in the system in the structured clay loam soil, resulting in faster movement of water and microbes through the soil relative to a conservative tracer (bromide.

  6. Mathematical modelling on transport of petroleum hydrocarbons in ...

    Indian Academy of Sciences (India)

    However, such studies in saturated fractured rocks are highly complex and limited, and hence, deserve a special attention as the fate and transport of the petroleum hydrocarbons are not uncommon in saturated fractured rocks. In this context, an improved mathematical model has been proposed that will better describe the ...

  7. Modeling marine surface microplastic transport to assess optimal removal locations

    NARCIS (Netherlands)

    Sherman, Peter; Van Sebille, Erik

    2016-01-01

    Marine plastic pollution is an ever-increasing problem that demands immediate mitigation and reduction plans. Here, a model based on satellite-tracked buoy observations and scaled to a large data set of observations on microplastic from surface trawls was used to simulate the transport of plastics

  8. Solute transport modelling with the variable temporally dependent ...

    Indian Academy of Sciences (India)

    Pintu Das

    2018-02-07

    Feb 7, 2018 ... Abstract. In this present study, analytical and numerical solutions are obtained for solute transport modelling in homogeneous semi-infinite porous medium. The dispersion coefficient is assumed to be initial dispersion and velocity is assumed to be temporally dependent with initial seepage velocity. Also ...

  9. Solving vertical transport and chemistry in air pollution models

    NARCIS (Netherlands)

    P.J.F. Berkvens (Patrick); M.A. Botchev; J.G. Verwer (Jan); M.C. Krol; W. Peters

    2000-01-01

    textabstractFor the time integration of stiff transport-chemistry problems from air pollution modelling, standard ODE solvers are not feasible due to the large number of species and the 3D nature. The popular alternative, standard operator splitting, introduces artificial transients for short-lived

  10. Solving Vertical Transport and Chemistry in Air Pollution Models.

    NARCIS (Netherlands)

    Berkvens, P.J.F.; Bochev, Mikhail A.; Verwer, J.G.; Krol, M.C.; Peters, W.

    For the time integration of stiff transport-chemistry problems from air pollution modelling, standard ODE solvers are not feasible due to the large number of species and the 3D nature. The popular alternative, standard operator splitting, introduces artificial transients for short-lived species.

  11. Solving vertical transport and chemistry in air pollution models

    NARCIS (Netherlands)

    Berkvens, P.J.F.; Bochev, M.A.; Krol, M.C.; Peters, W.; Verwer, J.G.; Chock, David P.; Carmichael, Gregory R.; Brick, Patricia

    2002-01-01

    For the time integration of stiff transport-chemistry problems from air pollution modelling, standard ODE solvers are not feasible due to the large number of species and the 3D nature. The popular alternative, standard operator splitting, introduces artificial transients for short-lived species.

  12. Sample selection and taste correlation in discrete choice transport modelling

    DEFF Research Database (Denmark)

    Mabit, Stefan Lindhard

    2008-01-01

    of taste correlation in willingness-to-pay estimation are presented. The first contribution addresses how to incorporate taste correlation in the estimation of the value of travel time for public transport. Given a limited dataset the approach taken is to use theory on the value of travel time as guidance...... many issues that deserve attention. This thesis investigates how sample selection can affect estimation of discrete choice models and how taste correlation should be incorporated into applied mixed logit estimation. Sampling in transport modelling is often based on an observed trip. This may cause...... a sample to be choice-based or governed by a self-selection mechanism. In both cases, there is a possibility that sampling affects the estimation of a population model. It was established in the seventies how choice-based sampling affects the estimation of multinomial logit models. The thesis examines...

  13. Multiphysical modelling of fluid transport through osteo-articular media.

    Science.gov (United States)

    Lemaire, Thibault; Naili, Salah; Sansalone, Vittorio

    2010-03-01

    In this study, a multiphysical description of fluid transport through osteo-articular porous media is presented. Adapted from the model of Moyne and Murad, which is intended to describe clayey materials behaviour, this multiscale modelling allows for the derivation of the macroscopic response of the tissue from microscopical information. First the model is described. At the pore scale, electrohydrodynamics equations governing the electrolyte movement are coupled with local electrostatics (Gauss-Poisson equation), and ionic transport equations. Using a change of variables and an asymptotic expansion method, the macroscopic description is carried out. Results of this model are used to show the importance of couplings effects on the mechanotransduction of compact bone remodelling.

  14. Development of Numerical Grids for UZ Flow and Transport Modeling

    International Nuclear Information System (INIS)

    Hinds, J.

    2001-01-01

    This Analysis/Model Report (AMR) describes the methods used to develop numerical grids of the unsaturated hydrogeologic system beneath Yucca Mountain. Numerical grid generation is an integral part of the development of a complex, three-dimensional (3-D) model, such as the Unsaturated-Zone Flow and Transport Model (UZ Model) of Yucca Mountain. The resulting numerical grids, developed using current geologic, hydrogeologic, and mineralogic data, provide the necessary framework to: (1) develop calibrated hydrogeologic property sets and flow fields, (2) test conceptual hypotheses of flow and transport, and (3) predict flow and transport behavior under a variety of climatic and thermal loading conditions. Revision 00 of the work described herein follows the planning and work direction outlined in the ''Development of Numerical Grids for UZ Flow and Transport Modeling'' (CRWMS M and O 1999c). The technical scope, content, and management of ICN 01 of this AMR is currently controlled by the planning document, ''Technical Work Plan for Unsaturated Zone (UZ) Flow and Transport Process Model Report'' (BSC 2001a). The scope for the TBV resolution actions in this ICN is described in the ''Technical Work Plan for: Integrated Management of Technical Product Input Department'' (BSC 2001 b, Addendum B, Section 4.1). The steps involved in numerical grid development include: (1) defining the location of important calibration features, (2) determining model grid layers and fault geometry based on the Geologic Framework Model (GFM), the Integrated Site Model (ISM), and definition of hydrogeologic units (HGUs), (3) analyzing and extracting GFM and ISM data pertaining to layer contacts and property distributions, (4) discretizing and refining the two-dimensional (2-D), plan-view numerical grid, (5) generating the 3-D grid with finer resolution at the repository horizon and within the Calico Hills nonwelded (CHn) hydrogeologic unit, and (6) formulating the dual-permeability mesh. The

  15. Revision history aware repositories of computational models of biological systems.

    Science.gov (United States)

    Miller, Andrew K; Yu, Tommy; Britten, Randall; Cooling, Mike T; Lawson, James; Cowan, Dougal; Garny, Alan; Halstead, Matt D B; Hunter, Peter J; Nickerson, David P; Nunns, Geo; Wimalaratne, Sarala M; Nielsen, Poul M F

    2011-01-14

    Building repositories of computational models of biological systems ensures that published models are available for both education and further research, and can provide a source of smaller, previously verified models to integrate into a larger model. One problem with earlier repositories has been the limitations in facilities to record the revision history of models. Often, these facilities are limited to a linear series of versions which were deposited in the repository. This is problematic for several reasons. Firstly, there are many instances in the history of biological systems modelling where an 'ancestral' model is modified by different groups to create many different models. With a linear series of versions, if the changes made to one model are merged into another model, the merge appears as a single item in the history. This hides useful revision history information, and also makes further merges much more difficult, as there is no record of which changes have or have not already been merged. In addition, a long series of individual changes made outside of the repository are also all merged into a single revision when they are put back into the repository, making it difficult to separate out individual changes. Furthermore, many earlier repositories only retain the revision history of individual files, rather than of a group of files. This is an important limitation to overcome, because some types of models, such as CellML 1.1 models, can be developed as a collection of modules, each in a separate file. The need for revision history is widely recognised for computer software, and a lot of work has gone into developing version control systems and distributed version control systems (DVCSs) for tracking the revision history. However, to date, there has been no published research on how DVCSs can be applied to repositories of computational models of biological systems. We have extended the Physiome Model Repository software to be fully revision history aware

  16. Revision history aware repositories of computational models of biological systems

    Directory of Open Access Journals (Sweden)

    Nickerson David P

    2011-01-01

    Full Text Available Abstract Background Building repositories of computational models of biological systems ensures that published models are available for both education and further research, and can provide a source of smaller, previously verified models to integrate into a larger model. One problem with earlier repositories has been the limitations in facilities to record the revision history of models. Often, these facilities are limited to a linear series of versions which were deposited in the repository. This is problematic for several reasons. Firstly, there are many instances in the history of biological systems modelling where an 'ancestral' model is modified by different groups to create many different models. With a linear series of versions, if the changes made to one model are merged into another model, the merge appears as a single item in the history. This hides useful revision history information, and also makes further merges much more difficult, as there is no record of which changes have or have not already been merged. In addition, a long series of individual changes made outside of the repository are also all merged into a single revision when they are put back into the repository, making it difficult to separate out individual changes. Furthermore, many earlier repositories only retain the revision history of individual files, rather than of a group of files. This is an important limitation to overcome, because some types of models, such as CellML 1.1 models, can be developed as a collection of modules, each in a separate file. The need for revision history is widely recognised for computer software, and a lot of work has gone into developing version control systems and distributed version control systems (DVCSs for tracking the revision history. However, to date, there has been no published research on how DVCSs can be applied to repositories of computational models of biological systems. Results We have extended the Physiome Model

  17. Model documentation report: Transportation sector model of the National Energy Modeling System

    Energy Technology Data Exchange (ETDEWEB)

    1994-03-01

    This report documents the objectives, analytical approach and development of the National Energy Modeling System (NEMS) Transportation Model (TRAN). The report catalogues and describes the model assumptions, computational methodology, parameter estimation techniques, model source code, and forecast results generated by the model. This document serves three purposes. First, it is a reference document providing a detailed description of TRAN for model analysts, users, and the public. Second, this report meets the legal requirements of the Energy Information Administration (EIA) to provide adequate documentation in support of its statistical and forecast reports (Public Law 93-275, 57(b)(1)). Third, it permits continuity in model development by providing documentation from which energy analysts can undertake model enhancements, data updates, and parameter refinements.

  18. Experimental, statistical, and biological models of radon carcinogenesis

    International Nuclear Information System (INIS)

    Cross, F.T.

    1991-09-01

    Risk models developed for underground miners have not been consistently validated in studies of populations exposed to indoor radon. Imprecision in risk estimates results principally from differences between exposures in mines as compared to domestic environments and from uncertainties about the interaction between cigarette-smoking and exposure to radon decay products. Uncertainties in extrapolating miner data to domestic exposures can be reduced by means of a broad-based health effects research program that addresses the interrelated issues of exposure, respiratory tract dose, carcinogenesis (molecular/cellular and animal studies, plus developing biological and statistical models), and the relationship of radon to smoking and other copollutant exposures. This article reviews experimental animal data on radon carcinogenesis observed primarily in rats at Pacific Northwest Laboratory. Recent experimental and mechanistic carcinogenesis models of exposures to radon, uranium ore dust, and cigarette smoke are presented with statistical analyses of animal data. 20 refs., 1 fig

  19. Human pluripotent stem cells: an emerging model in developmental biology.

    Science.gov (United States)

    Zhu, Zengrong; Huangfu, Danwei

    2013-02-01

    Developmental biology has long benefited from studies of classic model organisms. Recently, human pluripotent stem cells (hPSCs), including human embryonic stem cells and human induced pluripotent stem cells, have emerged as a new model system that offers unique advantages for developmental studies. Here, we discuss how studies of hPSCs can complement classic approaches using model organisms, and how hPSCs can be used to recapitulate aspects of human embryonic development 'in a dish'. We also summarize some of the recently developed genetic tools that greatly facilitate the interrogation of gene function during hPSC differentiation. With the development of high-throughput screening technologies, hPSCs have the potential to revolutionize gene discovery in mammalian development.

  20. Experimental, statistical and biological models of radon carcinogenesis

    International Nuclear Information System (INIS)

    Cross, F.T.

    1992-01-01

    Risk models developed for underground miners have not been consistently validated in studies of populations exposed to indoor radon. Imprecision in risk estimates results principally from differences between exposures in mines as compared with domestic environments and from uncertainties about the interaction between cigarette smoking and exposure to radon decay products. Uncertainties in extrapolating miner data to domestic exposures can be reduced by means of a broad-based health effects research programme that addresses the interrelated issues of exposure, respiratory tract dose, carcinogenesis (molecular/cellular and animal studies, plus developing biological and statistical models) and the relationship of radon to smoking and other co-pollutant exposures. This article reviews experimental animal data on radon carcinogenesis observed primarily in rats at Pacific Northwest Laboratory. Recent experimental and mechanistic carcinogenesis models of exposures to radon, uranium ore dust, and cigarette smoke are presented with statistical analyses of animal data. (author)

  1. Modeling of Species Transport and Macrosegregation in Heavy Steel Ingots

    Science.gov (United States)

    Li, Wensheng; Shen, Houfa; Zhang, Xiong; Liu, Baicheng

    2014-04-01

    In the current study, two significant phenomena involved in heavy steel ingot casting, i.e., species transport and macrosegregation, were numerically simulated. First, a ladle-tundish-mold species transport model describing the entire multiple pouring process of heavy steel ingots was proposed. Carbon distribution and variation in both the tundish and the mold of a 292-ton steel ingot were predicted. Results indicate high carbon concentration in the bottom of the mold while low concentration carbon at the top of mold after the pouring process. Such concentration distribution helps in reducing both negative segregation in the bottom of the solidified ingot and positive segregation at the top. Second, a two-phase multiscale macrosegregation model was used to simulate the solidification process of industrial steel ingots. This model takes into account heat transfer, fluid flow, solute transport, and equiaxed grain motion on a system scale, as well as grain nucleation and growth on a microscopic scale. The model was first used to analyze a three-dimensional industry-scale steel ingot as a benchmark. Then, it was applied to study macrosegregation formation in a 53-ton steel ingot. Macrosegregation predicted by the numerical model was presented and compared with experimental measurements. Typical macrosegregation patterns in heavy steel ingots are found to be well reproduced with the two-phase model.

  2. Advective transport in heterogeneous aquifers: Are proxy models predictive?

    Science.gov (United States)

    Fiori, A.; Zarlenga, A.; Gotovac, H.; Jankovic, I.; Volpi, E.; Cvetkovic, V.; Dagan, G.

    2015-12-01

    We examine the prediction capability of two approximate models (Multi-Rate Mass Transfer (MRMT) and Continuous Time Random Walk (CTRW)) of non-Fickian transport, by comparison with accurate 2-D and 3-D numerical simulations. Both nonlocal in time approaches circumvent the need to solve the flow and transport equations by using proxy models to advection, providing the breakthrough curves (BTC) at control planes at any x, depending on a vector of five unknown parameters. Although underlain by different mechanisms, the two models have an identical structure in the Laplace Transform domain and have the Markovian property of independent transitions. We show that also the numerical BTCs enjoy the Markovian property. Following the procedure recommended in the literature, along a practitioner perspective, we first calibrate the parameters values by a best fit with the numerical BTC at a control plane at x1, close to the injection plane, and subsequently use it for prediction at further control planes for a few values of σY2≤8. Due to a similar structure and Markovian property, the two methods perform equally well in matching the numerical BTC. The identified parameters are generally not unique, making their identification somewhat arbitrary. The inverse Gaussian model and the recently developed Multi-Indicator Model (MIM), which does not require any fitting as it relates the BTC to the permeability structure, are also discussed. The application of the proxy models for prediction requires carrying out transport field tests of large plumes for a long duration.

  3. Combining Deterministic structures and stochastic heterogeneity for transport modeling

    Science.gov (United States)

    Zech, Alraune; Attinger, Sabine; Dietrich, Peter; Teutsch, Georg

    2017-04-01

    Contaminant transport in highly heterogeneous aquifers is extremely challenging and subject of current scientific debate. Tracer plumes often show non-symmetric but highly skewed plume shapes. Predicting such transport behavior using the classical advection-dispersion-equation (ADE) in combination with a stochastic description of aquifer properties requires a dense measurement network. This is in contrast to the available information for most aquifers. A new conceptual aquifer structure model is presented which combines large-scale deterministic information and the stochastic approach for incorporating sub-scale heterogeneity. The conceptual model is designed to allow for a goal-oriented, site specific transport analysis making use of as few data as possible. Thereby the basic idea is to reproduce highly skewed tracer plumes in heterogeneous media by incorporating deterministic contrasts and effects of connectivity instead of using unimodal heterogeneous models with high variances. The conceptual model consists of deterministic blocks of mean hydraulic conductivity which might be measured by pumping tests indicating values differing in orders of magnitudes. A sub-scale heterogeneity is introduced within every block. This heterogeneity can be modeled as bimodal or log-normal distributed. The impact of input parameters, structure and conductivity contrasts is investigated in a systematic manor. Furthermore, some first successful implementation of the model was achieved for the well known MADE site.

  4. Towards a transport model for epistemic UQ in RANS closures

    Science.gov (United States)

    Edeling, Wouter; Iaccarino, Gianluca

    2016-11-01

    Due to their computational efficiency, Reynold-Averaged Navier-Stokes (RANS) turbulence models remain a vital tool for modeling turbulent flows. However, it is well known that RANS predictions are locally corrupted by epistemic model-form uncertainty. Whereas some Uncertainty Quantification (UQ) approaches attempt to quantify this uncertainty by considering the model coefficients as random variables, we directly perturb the Reynold-stress tensor at locations in the flow domain where the modeling assumptions are likely to be invalid. Inferring the perturbations on a point-by-point basis would lead to a high-dimensional problem. To reduce the dimensionality, we propose separate model equations based on the transport of linear invariants of the anisotropy tensor. This provides us with a low-dimensional UQ framework where the invariant transport model decides on the magnitude and direction of the perturbations. Where the perturbations are small, the RANS result is recovered. Using traditional turbulence modeling practices we derive weak realizability constraints, and we will rely on Bayesian inference to calibrate the model on high-fidelity data. We will demonstrate our framework on a number of canonical flow problems where RANS models are prone to failure.

  5. Plutonium air transportable package Model PAT-1. Safety analysis report

    International Nuclear Information System (INIS)

    1978-02-01

    The document is a Safety Analysis Report for the Plutonium Air Transportable Package, Model PAT-1, which was developed by Sandia Laboratories under contract to the Nuclear Regulatory Commission (NRC). The document describes the engineering tests and evaluations that the NRC staff used as a basis to determine that the package design meets the requirements specified in the NRC ''Qualification Criteria to Certify a Package for Air Transport of Plutonium'' (NUREG-0360). By virtue of its ability to meet the NRC Qualification Criteria, the package design is capable of safely withstanding severe aircraft accidents. The document also includes engineering drawings and specifications for the package. 92 figs, 29 tables

  6. Invertebrates as model organisms for research on aging biology.

    Science.gov (United States)

    Murthy, Mahadev; Ram, Jeffrey L

    2015-01-30

    Invertebrate model systems, such as nematodes and fruit flies, have provided valuable information about the genetics and cellular biology involved in aging. However, limitations of these simple, genetically tractable organisms suggest the need for other model systems, some of them invertebrate, to facilitate further advances in the understanding of mechanisms of aging and longevity in mammals, including humans. This paper introduces 10 review articles about the use of invertebrate model systems for the study of aging by authors who participated in an 'NIA-NIH symposium on aging in invertebrate model systems' at the 2013 International Congress for Invertebrate Reproduction and Development. In contrast to the highly derived characteristics of nematodes and fruit flies as members of the superphylum Ecdysozoa, cnidarians, such as Hydra, are more 'basal' organisms that have a greater number of genetic orthologs in common with humans. Moreover, some other new model systems, such as the urochordate Botryllus schlosseri , the tunicate Ciona , and the sea urchins (Echinodermata) are members of the Deuterostomia, the same superphylum that includes all vertebrates, and thus have mechanisms that are likely to be more closely related to those occurring in humans. Additional characteristics of these new model systems, such as the recent development of new molecular and genetic tools and a more similar pattern to humans of regeneration and stem cell function suggest that these new model systems may have unique advantages for the study of mechanisms of aging and longevity.

  7. Sediment and radionuclide transport in rivers: radionuclide transport modeling for Cattaraugus and Buttermilk Creeks, New York

    International Nuclear Information System (INIS)

    Onishi, Y.; Yabusaki, S.B.; Kincaid, C.T.; Skaggs, R.L.; Walters, W.H.

    1982-12-01

    SERATRA, a transient, two-dimensional (laterally-averaged) computer model of sediment-contaminant transport in rivers, satisfactorily resolved the distribution of sediment and radionuclide concentrations in the Cattaraugus Creek stream system in New York. By modeling the physical processes of advection, diffusion, erosion, deposition, and bed armoring, SERATRA routed three sediment size fractions, including cohesive soils, to simulate three dynamic flow events. In conjunction with the sediment transport, SERATRA computed radionuclide levels in dissolved, suspended sediment, and bed sediment forms for four radionuclides ( 137 Cs, 90 Sr, 239 240 Pu, and 3 H). By accounting for time-dependent sediment-radionuclide interaction in the water column and bed, SERATA is a physically explicit model of radionuclide fate and migration. Sediment and radionuclide concentrations calculated by SERATA in the Cattaraugus Creek stream system are in reasonable agreement with measured values. SERATRA is in the field performance phase of an extensive testing program designed to establish the utility of the model as a site assessment tool. The model handles not only radionuclides but other contaminants such as pesticides, heavy metals and other toxic chemicals. Now that the model has been applied to four field sites, including the latest study of the Cattaraugus Creek stream system, it is recommended that a final model be validated through comparison of predicted results with field data from a carefully controlled tracer test at a field site. It is also recommended that a detailed laboratory flume be tested to study cohesive sediment transport, deposition, and erosion characteristics. The lack of current understanding of these characteristics is one of the weakest areas hindering the accurate assessment of the migration of radionuclides sorbed by fine sediments of silt and clay

  8. Modelling animal waste pathogen transport from agricultural land to streams

    International Nuclear Information System (INIS)

    Pandey, Pramod K; Soupir, Michelle L; Ikenberry, Charles

    2014-01-01

    The transport of animal waste pathogens from crop land to streams can potentially elevate pathogen levels in stream water. Applying animal manure into crop land as fertilizers is a common practice in developing as well as in developed countries. Manure application into the crop land, however, can cause potential human health. To control pathogen levels in ambient water bodies such as streams, improving our understanding of pathogen transport at farm scale as well as at watershed scale is required. To understand the impacts of crop land receiving animal waste as fertilizers on stream's pathogen levels, here we investigate pathogen indicator transport at watershed scale. We exploited watershed scale hydrological model to estimate the transport of pathogens from the crop land to streams. Pathogen indicator levels (i.e., E. coli levels) in the stream water were predicted. With certain assumptions, model results are reasonable. This study can be used as guidelines for developing the models for calculating the impacts of crop land's animal manure on stream water

  9. Integrating wildfire plume rises within atmospheric transport models

    Science.gov (United States)

    Mallia, D. V.; Kochanski, A.; Wu, D.; Urbanski, S. P.; Krueger, S. K.; Lin, J. C.

    2016-12-01

    Wildfires can generate significant pyro-convection that is responsible for releasing pollutants, greenhouse gases, and trace species into the free troposphere, which are then transported a significant distance downwind from the fire. Oftentimes, atmospheric transport and chemistry models have a difficult time resolving the transport of smoke from these wildfires, primarily due to deficiencies in estimating the plume injection height, which has been highlighted in previous work as the most important aspect of simulating wildfire plume transport. As a result of the uncertainties associated with modeled wildfire plume rise, researchers face difficulties modeling the impacts of wildfire smoke on air quality and constraining fire emissions using inverse modeling techniques. Currently, several plume rise parameterizations exist that are able to determine the injection height of fire emissions; however, the success of these parameterizations has been mixed. With the advent of WRF-SFIRE, the wildfire plume rise and injection height can now be explicitly calculated using a fire spread model (SFIRE) that is dynamically linked with the atmosphere simulated by WRF. However, this model has only been tested on a limited basis due to computational costs. Here, we will test the performance of WRF-SFIRE in addition to several commonly adopted plume parameterizations (Freitas, Sofiev, and Briggs) for the 2013 Patch Springs (Utah) and 2012 Baker Canyon (Washington) fires, for both of which observations of plume rise heights are available. These plume rise techniques will then be incorporated within a Lagrangian atmospheric transport model (STILT) in order to simulate CO and CO2 concentrations during NASA's CARVE Earth Science Airborne Program over Alaska during the summer of 2012. Initial model results showed that STILT model simulations were unable to reproduce enhanced CO concentrations produced by Alaskan fires observed during 2012. Near-surface concentrations were drastically

  10. Colloid transport in saturated porous media: Elimination of attachment efficiency in a new colloid transport model

    Science.gov (United States)

    Landkamer, Lee L.; Harvey, Ronald W.; Scheibe, Timothy D.; Ryan, Joseph N.

    2013-01-01

    A colloid transport model is introduced that is conceptually simple yet captures the essential features of colloid transport and retention in saturated porous media when colloid retention is dominated by the secondary minimum because an electrostatic barrier inhibits substantial deposition in the primary minimum. This model is based on conventional colloid filtration theory (CFT) but eliminates the empirical concept of attachment efficiency. The colloid deposition rate is computed directly from CFT by assuming all predicted interceptions of colloids by collectors result in at least temporary deposition in the secondary minimum. Also, a new paradigm for colloid re-entrainment based on colloid population heterogeneity is introduced. To accomplish this, the initial colloid population is divided into two fractions. One fraction, by virtue of physiochemical characteristics (e.g., size and charge), will always be re-entrained after capture in a secondary minimum. The remaining fraction of colloids, again as a result of physiochemical characteristics, will be retained “irreversibly” when captured by a secondary minimum. Assuming the dispersion coefficient can be estimated from tracer behavior, this model has only two fitting parameters: (1) the fraction of the initial colloid population that will be retained “irreversibly” upon interception by a secondary minimum, and (2) the rate at which reversibly retained colloids leave the secondary minimum. These two parameters were correlated to the depth of the Derjaguin-Landau-Verwey-Overbeek (DLVO) secondary energy minimum and pore-water velocity, two physical forces that influence colloid transport. Given this correlation, the model serves as a heuristic tool for exploring the influence of physical parameters such as surface potential and fluid velocity on colloid transport.

  11. Estimates of direct biological transport of radioactive waste in the deep sea with special reference to organic carbon budgets

    International Nuclear Information System (INIS)

    Rowe, G.T.; Shepherd, J.; Needler, G.; Hargrave, B.; Marietta, M.

    1986-01-01

    Calculations can be made for the maximum theoretical transport of pollutants such as radionuclides by movement of organisms out of a deep-sea benthic boundary layer dump site based on a presumption of a steady state organic carbon budget and estimated biological concentration factors. A calculated flux rate depends on the difference between a limiting input of organic matter and that carbon used by the biota or accumulating in the sediment. On average, the potential biological mass transport is low compared to physical transport. Exceptions to this generalization are possible in the far field after spatial gradients are obliterated or if natural mass migrations or periodic spawning concentrations occur in the near field. Biologically mediated fluxes of contaminants due to mixing of sediments by bioturbation or vertical flux due to scavenging by sinking particles are significant for movements of pollutants to and from sediments. These pathways contribute to the direct input of contaminants into food webs which may contain harvestable species. These fluxes are unimportant for mass transfers in the ocean but they determine the exposure of critical groups to contaminants

  12. Interactive 4D Visualization of Sediment Transport Models

    Science.gov (United States)

    Butkiewicz, T.; Englert, C. M.

    2013-12-01

    Coastal sediment transport models simulate the effects that waves, currents, and tides have on near-shore bathymetry and features such as beaches and barrier islands. Understanding these dynamic processes is integral to the study of coastline stability, beach erosion, and environmental contamination. Furthermore, analyzing the results of these simulations is a critical task in the design, placement, and engineering of coastal structures such as seawalls, jetties, support pilings for wind turbines, etc. Despite the importance of these models, there is a lack of available visualization software that allows users to explore and perform analysis on these datasets in an intuitive and effective manner. Existing visualization interfaces for these datasets often present only one variable at a time, using two dimensional plan or cross-sectional views. These visual restrictions limit the ability to observe the contents in the proper overall context, both in spatial and multi-dimensional terms. To improve upon these limitations, we use 3D rendering and particle system based illustration techniques to show water column/flow data across all depths simultaneously. We can also encode multiple variables across different perceptual channels (color, texture, motion, etc.) to enrich surfaces with multi-dimensional information. Interactive tools are provided, which can be used to explore the dataset and find regions-of-interest for further investigation. Our visualization package provides an intuitive 4D (3D, time-varying) visualization of sediment transport model output. In addition, we are also integrating real world observations with the simulated data to support analysis of the impact from major sediment transport events. In particular, we have been focusing on the effects of Superstorm Sandy on the Redbird Artificial Reef Site, offshore of Delaware Bay. Based on our pre- and post-storm high-resolution sonar surveys, there has significant scour and bedform migration around the

  13. Modeling and simulation of transport phenomena in ionic gels

    Science.gov (United States)

    Leichsenring, Peter; Wallmersperger, Thomas

    2015-04-01

    Ionic hydrogels belong to the class of polyelectrolyte gels or ionic gels. Their ability to swell or shrink under different environmental conditions such as change of pH, ion concentration or temperature make them promising materials, e.g. for microsensoric or microactuatoric devices. The hydrogel swelling exhibits nonlinear effects due to the occurrence of different interacting transport phenomena. Numerical simulations are an essential part in the ongoing development of microsensors and microactuators. In order to determine transport effects due to diffusion, migration and convection a multiphase mesoscale model based on the Theory of Porous Media is applied. The governing field equations are solved in the transient regime by applying the Finite Element Method. By means of the derived numerical framework a detailed investigation of the different transport phenomena is carried out. Numerical experiments are performed to characterize the dominating transfer phenomena for ionic gels under chemical stimulation.

  14. Suitability of Commercial Transport Media for Biological Pathogens under Nonideal Conditions

    Science.gov (United States)

    2011-01-01

    water and was made in-house. For the liquid transport media, one milliliter of each was added to sterile transport tubes containing a sponge (kindly...for microorganisms capable of sporulation in nutrient-poor transport media. Unfortunately, if a sample slowly converts from the vegetative to the...Efficient methods for large-area surface sampling of sites contaminated with pathogenic microorgan - isms and other hazardous agents: current state, needs

  15. Coupling of Groundwater Transport and Plant Uptake Models

    DEFF Research Database (Denmark)

    Rein, Arno; Bauer-Gottwein, Peter; Trapp, Stefan

    2010-01-01

    Plants significantly influence contaminant transport and fate. Important processes are uptake of soil and groundwater contaminants, as well as biodegradation in plants and their root zones. Models for the prediction of chemical uptake into plants are required for the setup of mass balances...... in environmental systems at different scale. Feedback mechanisms between plants and hydrological systems can play an important role, however having received little attention to date. Here, a new model concept for dynamic plant uptake models applying analytical matrix solutions is presented, which can be coupled...... to groundwater transport simulation tools. Exemplary simulations of plant uptake were carried out, in order to estimate concentrations in the soilplant- air system and the influence of plants on contaminant mass fluxes from soil to groundwater....

  16. Optimal Filtering in Mass Transport Modeling From Satellite Gravimetry Data

    Science.gov (United States)

    Ditmar, P.; Hashemi Farahani, H.; Klees, R.

    2011-12-01

    Monitoring natural mass transport in the Earth's system, which has marked a new era in Earth observation, is largely based on the data collected by the GRACE satellite mission. Unfortunately, this mission is not free from certain limitations, two of which are especially critical. Firstly, its sensitivity is strongly anisotropic: it senses the north-south component of the mass re-distribution gradient much better than the east-west component. Secondly, it suffers from a trade-off between temporal and spatial resolution: a high (e.g., daily) temporal resolution is only possible if the spatial resolution is sacrificed. To make things even worse, the GRACE satellites enter occasionally a phase when their orbit is characterized by a short repeat period, which makes it impossible to reach a high spatial resolution at all. A way to mitigate limitations of GRACE measurements is to design optimal data processing procedures, so that all available information is fully exploited when modeling mass transport. This implies, in particular, that an unconstrained model directly derived from satellite gravimetry data needs to be optimally filtered. In principle, this can be realized with a Wiener filter, which is built on the basis of covariance matrices of noise and signal. In practice, however, a compilation of both matrices (and, therefore, of the filter itself) is not a trivial task. To build the covariance matrix of noise in a mass transport model, it is necessary to start from a realistic model of noise in the level-1B data. Furthermore, a routine satellite gravimetry data processing includes, in particular, the subtraction of nuisance signals (for instance, associated with atmosphere and ocean), for which appropriate background models are used. Such models are not error-free, which has to be taken into account when the noise covariance matrix is constructed. In addition, both signal and noise covariance matrices depend on the type of mass transport processes under

  17. Cellular automaton model of coupled mass transport and chemical reactions

    International Nuclear Information System (INIS)

    Karapiperis, T.

    1994-01-01

    Mass transport, coupled with chemical reactions, is modelled as a cellular automaton in which solute molecules perform a random walk on a lattice and react according to a local probabilistic rule. Assuming molecular chaos and a smooth density function, we obtain the standard reaction-transport equations in the continuum limit. The model is applied to the reactions a + b ↔c and a + b →c, where we observe interesting macroscopic effects resulting from microscopic fluctuations and spatial correlations between molecules. We also simulate autocatalytic reaction schemes displaying spontaneous formation of spatial concentration patterns. Finally, we propose and discuss the limitations of a simple model for mineral-solute interaction. (author) 5 figs., 20 refs

  18. CFD modelling of insulation debris transport phenomena in water flow

    Energy Technology Data Exchange (ETDEWEB)

    Krepper, Eeckhard; Cartland-Glover, Gregory; Grahn, Alexander [Forschungszentrum Rossendorf e.V., Dresden (Germany). Inst. fuer Sicherheitsforschung

    2009-11-15

    The investigation of insulation debris generation, transport and sedimentation becomes important with regard to reactor safety research for PWR and BWR, when considering the long-term behaviour of emergency core cooling systems during all types of loss of coolant accidents. A joint research project on such questions is being performed in cooperation between the University of Applied Sciences Zittau/Goerlitz and the Forschungszentrum Dresden-Rossendorf. The project deals with the experimental investigation of particle transport phenomena in coolant flow and the development of CFD models for its description. While the experiments are performed at the University at Zittau/Goerlitz, the theoretical modelling efforts are concentrated at Forschungszentrum Dresden-Rossendorf. In the current paper the basic concepts for CFD modelling are described and feasibility studies are presented. (orig.)

  19. Simplified analytical model for radionuclide transport simulation in the geosphere

    International Nuclear Information System (INIS)

    Hiromoto, G.

    1996-01-01

    In order to evaluate postclosure off-site doses from a low-level radioactive waste disposal facilities, an integrated safety assessment methodology has being developed at Instituto de Pesquisas Energeticas e Nucleares. The source-term modelling approach adopted in this system is described and the results obtained in the IAEA NSARS 'The Safety Assessment of Near-Surface Radioactive Waste Disposal Facilities' programme for model intercomparison studies are presented. The radionuclides released from the waste are calculated using a simple first order kinetics model, and the transport, through porous media below the waste is determined by using an analytical solution of the mass transport equation. The methodology and the results obtained in this work are compared with those reported by others participants of the NSARS programme. (author). 4 refs., 4 figs

  20. Using data from colloid transport experiments to parameterize filtration model parameters for favorable conditions

    Science.gov (United States)

    Kamai, Tamir; Nassar, Mohamed K.; Nelson, Kirk E.; Ginn, Timothy R.

    2017-04-01

    Colloid filtration in porous media spans across many disciplines and includes scenarios such as in-situ bioremediation, colloid-facilitated transport, water treatment of suspended particles and pathogenic bacteria, and transport of natural and engineered nanoparticles in the environment. Transport and deposition of colloid particles in porous media are determined by a combination of complex processes and forces. Given the convoluted physical, chemical, and biological processes involved, and the complexity of porous media in natural settings, it should not come as surprise that colloid filtration theory does not always sufficiently predict colloidal transport, and that there is still a pressing need for improved predictive capabilities. Here, instead of developing the macroscopic equation from pore-scale models, we parametrize the different terms in the macroscopic collection equation through fitting it to experimental data, by optimizing the parameters in the different terms of the equation. This way we combine a mechanistically-based filtration-equation with empirical evidence. The impact of different properties of colloids and porous media are studied by comparing experimental properties with different terms of the correlation equation. This comparison enables insight about different processes that occur during colloid transport and retention under in porous media under favorable conditions, and provides directions for future theoretical developments.