Bahrami, Hadi; Gosselin, Benoit; Rusch, Leslie A
2012-01-01
Several emerging medical applications require that a miniature data acquisition device be implanted into the head to extract and wirelessly communicate brain activity to other devices. Designing a reliable communication link for such an application requires a realistic model of the surrounding biological tissues. This paper exploits a realistic model of the biological channel to design a suitable wireless ultra wideband communication link in a brain monitoring application. Two scenarios for positioning the implanted transmitting antenna are considered. The 1(st) scenario places the antenna under the skull, whereas the 2(nd) scenario places the antenna under the skin, above the skull. The propagation characteristics of the signal through the tissues of the human head have been determined with full-wave electromagnetic simulation based on Finite Element Method. The implantable antenna and the external antenna are key components to establish an electromagnetic link between an implanted transmitter and an external receiver. The average specific absorption rate (ASAR) of the implantable antennas are evaluated and compared for the two proposed scenarios. Moreover, the maximum available power from the implanted antenna is evaluated to characterize the performance of the communication link established between the implantable antenna and the external antenna, with respect to spectrum and safety regulations. We show how sensitive the receiver must be in order to implement a reliable telemetry link based on the proposed model of the channel.
International Nuclear Information System (INIS)
Riviere, Jim E; Scoglio, Caterina; Sahneh, Faryad D; Monteiro-Riviere, Nancy A
2013-01-01
The field of nanomaterial pharmacokinetics is in its infancy, with major advances largely restricted by a lack of biologically relevant metrics, fundamental differences between particles and small molecules of organic chemicals and drugs relative to biological processes involved in disposition, a scarcity of sufficiently rich and characterized in vivo data and a lack of computational approaches to integrating nanomaterial properties to biological endpoints. A central concept that links nanomaterial properties to biological disposition, in addition to their colloidal properties, is the tendency to form a biocorona which modulates biological interactions including cellular uptake and biodistribution. Pharmacokinetic models must take this crucial process into consideration to accurately predict in vivo disposition, especially when extrapolating from laboratory animals to humans since allometric principles may not be applicable. The dynamics of corona formation, which modulates biological interactions including cellular uptake and biodistribution, is thereby a crucial process involved in the rate and extent of biodisposition. The challenge will be to develop a quantitative metric that characterizes a nanoparticle's surface adsorption forces that are important for predicting biocorona dynamics. These types of integrative quantitative approaches discussed in this paper for the dynamics of corona formation must be developed before realistic engineered nanomaterial risk assessment can be accomplished. (paper)
A Novel CPU/GPU Simulation Environment for Large-Scale Biologically-Realistic Neural Modeling
Directory of Open Access Journals (Sweden)
Roger V Hoang
2013-10-01
Full Text Available Computational Neuroscience is an emerging field that provides unique opportunities to studycomplex brain structures through realistic neural simulations. However, as biological details are added tomodels, the execution time for the simulation becomes longer. Graphics Processing Units (GPUs are now being utilized to accelerate simulations due to their ability to perform computations in parallel. As such, they haveshown significant improvement in execution time compared to Central Processing Units (CPUs. Most neural simulators utilize either multiple CPUs or a single GPU for better performance, but still show limitations in execution time when biological details are not sacrificed. Therefore, we present a novel CPU/GPU simulation environment for large-scale biological networks,the NeoCortical Simulator version 6 (NCS6. NCS6 is a free, open-source, parallelizable, and scalable simula-tor, designed to run on clusters of multiple machines, potentially with high performance computing devicesin each of them. It has built-in leaky-integrate-and-fire (LIF and Izhikevich (IZH neuron models, but usersalso have the capability to design their own plug-in interface for different neuron types as desired. NCS6is currently able to simulate one million cells and 100 million synapses in quasi real time by distributing dataacross these heterogeneous clusters of CPUs and GPUs.
Realistic Material Appearance Modelling
Czech Academy of Sciences Publication Activity Database
Haindl, Michal; Filip, Jiří; Hatka, Martin
2010-01-01
Roč. 2010, č. 81 (2010), s. 13-14 ISSN 0926-4981 R&D Projects: GA ČR GA102/08/0593 Institutional research plan: CEZ:AV0Z10750506 Keywords : bidirectional texture function * texture modelling Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2010/RO/haindl-realistic material appearance modelling.pdf
Directory of Open Access Journals (Sweden)
Yoann Thomas
Full Text Available Studying the larval dispersal of bottom-dwelling species is necessary to understand their population dynamics and optimize their management. The black-lip pearl oyster (Pinctada margaritifera is cultured extensively to produce black pearls, especially in French Polynesia's atoll lagoons. This aquaculture relies on spat collection, a process that can be optimized by understanding which factors influence larval dispersal. Here, we investigate the sensitivity of P. margaritifera larval dispersal kernel to both physical and biological factors in the lagoon of Ahe atoll. Specifically, using a validated 3D larval dispersal model, the variability of lagoon-scale connectivity is investigated against wind forcing, depth and location of larval release, destination location, vertical swimming behavior and pelagic larval duration (PLD factors. The potential connectivity was spatially weighted according to both the natural and cultivated broodstock densities to provide a realistic view of connectivity. We found that the mean pattern of potential connectivity was driven by the southwest and northeast main barotropic circulation structures, with high retention levels in both. Destination locations, spawning sites and PLD were the main drivers of potential connectivity, explaining respectively 26%, 59% and 5% of the variance. Differences between potential and realistic connectivity showed the significant contribution of the pearl oyster broodstock location to its own dynamics. Realistic connectivity showed larger larval supply in the western destination locations, which are preferentially used by farmers for spat collection. In addition, larval supply in the same sectors was enhanced during summer wind conditions. These results provide new cues to understanding the dynamics of bottom-dwelling populations in atoll lagoons, and show how to take advantage of numerical models for pearl oyster management.
Realistic split fermion models
Indian Academy of Sciences (India)
wall fermions, namely, a bulk scalar field with non-trivial VEV that couples to the fermions. In addition, the ... yields the flavor hierarchy. We consider a model with two scalar fields that couple to the fermions [5]. .... model will correctly reproduce the quark flavor parameters the following relation should hold [2]:. Γ-1Щmax ~03.
National Research Council Canada - National Science Library
Goodman, Philip
2000-01-01
The purpose of this project was to better understand brain-like network dynamics by incorporated biological parameters into large-scale computer simulations using parallel distributed "Beowulf" clustering...
Realistic biological approaches for improving thermoradiotherapy
DEFF Research Database (Denmark)
Horsman, Michael R
2016-01-01
components of tumours. Strategies include targeting the radiation DNA repair processes, improving drug delivery using nanoparticles, exploiting immunotherapy mechanisms, reducing tumour pH, or modifying the tumour vascular supply. All of these approaches have been combined with either hyperthermia...... or radiation in preclinical models and clear benefits in tumour response observed. But few of these methods have actually been combined with thermoradiotherapy. Furthermore, very few combinations have been tested in relevant normal tissue studies, despite the fact that it is the normal tissue response...
Development of KAERI LBLOCA realistic evaluation model
International Nuclear Information System (INIS)
Lee, W.J.; Lee, Y.J.; Chung, B.D.; Lee, S.Y.
1994-01-01
A realistic evaluation model (REM) for LBLOCA licensing calculation is developed and proposed for application to pressurized light water reactors. The developmental aim of the KAERI-REM is to provide a systematic methodology that is simple in structure and to use and built upon sound logical reasoning, for improving the code capability to realistically describe the LBLOCA phenomena and for evaluating the associated uncertainties. The method strives to be faithful to the intention of being best-estimate, that is, the method aims to evaluate the best-estimate values and the associated uncertainties while complying to the requirements in the ECCS regulations. (author)
Mathematical modeling in realistic mathematics education
Riyanto, B.; Zulkardi; Putri, R. I. I.; Darmawijoyo
2017-12-01
The purpose of this paper is to produce Mathematical modelling in Realistics Mathematics Education of Junior High School. This study used development research consisting of 3 stages, namely analysis, design and evaluation. The success criteria of this study were obtained in the form of local instruction theory for school mathematical modelling learning which was valid and practical for students. The data were analyzed using descriptive analysis method as follows: (1) walk through, analysis based on the expert comments in the expert review to get Hypothetical Learning Trajectory for valid mathematical modelling learning; (2) analyzing the results of the review in one to one and small group to gain practicality. Based on the expert validation and students’ opinion and answers, the obtained mathematical modeling problem in Realistics Mathematics Education was valid and practical.
TMS modeling toolbox for realistic simulation.
Cho, Young Sun; Suh, Hyun Sang; Lee, Won Hee; Kim, Tae-Seong
2010-01-01
Transcranial magnetic stimulation (TMS) is a technique for brain stimulation using rapidly changing magnetic fields generated by coils. It has been established as an effective stimulation technique to treat patients suffering from damaged brain functions. Although TMS is known to be painless and noninvasive, it can also be harmful to the brain by incorrect focusing and excessive stimulation which might result in seizure. Therefore there is ongoing research effort to elucidate and better understand the effect and mechanism of TMS. Lately Boundary element method (BEM) and Finite element method (FEM) have been used to simulate the electromagnetic phenomenon of TMS. However, there is a lack of general tools to generate the models of TMS due to some difficulties in realistic modeling of the human head and TMS coils. In this study, we have developed a toolbox through which one can generate high-resolution FE TMS models. The toolbox allows creating FE models of the head with isotropic and anisotropic electrical conductivities in five different tissues of the head and the coils in 3D. The generated TMS model is importable to FE software packages such as ANSYS for further and efficient electromagnetic analysis. We present a set of demonstrative results of realistic simulation of TMS with our toolbox.
A Computational Framework for Realistic Retina Modeling.
Martínez-Cañada, Pablo; Morillas, Christian; Pino, Begoña; Ros, Eduardo; Pelayo, Francisco
2016-11-01
Computational simulations of the retina have led to valuable insights about the biophysics of its neuronal activity and processing principles. A great number of retina models have been proposed to reproduce the behavioral diversity of the different visual processing pathways. While many of these models share common computational stages, previous efforts have been more focused on fitting specific retina functions rather than generalizing them beyond a particular model. Here, we define a set of computational retinal microcircuits that can be used as basic building blocks for the modeling of different retina mechanisms. To validate the hypothesis that similar processing structures may be repeatedly found in different retina functions, we implemented a series of retina models simply by combining these computational retinal microcircuits. Accuracy of the retina models for capturing neural behavior was assessed by fitting published electrophysiological recordings that characterize some of the best-known phenomena observed in the retina: adaptation to the mean light intensity and temporal contrast, and differential motion sensitivity. The retinal microcircuits are part of a new software platform for efficient computational retina modeling from single-cell to large-scale levels. It includes an interface with spiking neural networks that allows simulation of the spiking response of ganglion cells and integration with models of higher visual areas.
Physically realistic modeling of maritime training simulation
Cieutat , Jean-Marc
2003-01-01
Maritime training simulation is an important matter of maritime teaching, which requires a lot of scientific and technical skills.In this framework, where the real time constraint has to be maintained, all physical phenomena cannot be studied; the most visual physical phenomena relating to the natural elements and the ship behaviour are reproduced only. Our swell model, based on a surface wave simulation approach, permits to simulate the shape and the propagation of a regular train of waves f...
Realistic modeling of radiation transmission inspection systems
International Nuclear Information System (INIS)
Sale, K.E.
1993-01-01
We have applied Monte Carlo particle transport methods to assess a proposed neutron transmission inspection system for checked luggage. The geometry of the system and the time, energy and angle dependence of the source have been modeled in detail. A pulsed deuteron beam incident on a thick Be target generates a neutron pulse with a very broad energy spectrum which is detected after passage through the luggage item by a plastic scintillator detector operating in current mode (as opposed to pulse counting mode). The neutron transmission as a function of time information is used to infer the densities of hydrogen, carbon, oxygen and nitrogen in the volume sampled. The measured elemental densities can be compared to signatures for explosives or other contraband. By using such computational modeling it is possible to optimize many aspects of the design of an inspection system without costly and time consuming prototyping experiments or to determine that a proposed scheme will not work. The methods applied here can be used to evaluate neutron or photon schemes based on transmission, scattering or reaction techniques
Interferometric data modelling: issues in realistic data generation
International Nuclear Information System (INIS)
Mukherjee, Soma
2004-01-01
This study describes algorithms developed for modelling interferometric noise in a realistic manner, i.e. incorporating non-stationarity that can be seen in the data from the present generation of interferometers. The noise model is based on individual component models (ICM) with the application of auto regressive moving average (ARMA) models. The data obtained from the model are vindicated by standard statistical tests, e.g. the KS test and Akaike minimum criterion. The results indicate a very good fit. The advantage of using ARMA for ICMs is that the model parameters can be controlled and hence injection and efficiency studies can be conducted in a more controlled environment. This realistic non-stationary noise generator is intended to be integrated within the data monitoring tool framework
Biophysically realistic filament bending dynamics in agent-based biological simulation.
Directory of Open Access Journals (Sweden)
Jonathan B Alberts
Full Text Available An appealing tool for study of the complex biological behaviors that can emerge from networks of simple molecular interactions is an agent-based, computational simulation that explicitly tracks small-scale local interactions--following thousands to millions of states through time. For many critical cell processes (e.g. cytokinetic furrow specification, nuclear centration, cytokinesis, the flexible nature of cytoskeletal filaments is likely to be critical. Any computer model that hopes to explain the complex emergent behaviors in these processes therefore needs to encode filament flexibility in a realistic manner. Here I present a numerically convenient and biophysically realistic method for modeling cytoskeletal filament flexibility in silico. Each cytoskeletal filament is represented by a series of rigid segments linked end-to-end in series with a variable attachment point for the translational elastic element. This connection scheme allows an empirically tuning, for a wide range of segment sizes, viscosities, and time-steps, that endows any filament species with the experimentally observed (or theoretically expected static force deflection, relaxation time-constant, and thermal writhing motions. I additionally employ a unique pair of elastic elements--one representing the axial and the other the bending rigidity- that formulate the restoring force in terms of single time-step constraint resolution. This method is highly local -adjacent rigid segments of a filament only interact with one another through constraint forces-and is thus well-suited to simulations in which arbitrary additional forces (e.g. those representing interactions of a filament with other bodies or cross-links / entanglements between filaments may be present. Implementation in code is straightforward; Java source code is available at www.celldynamics.org.
Resonance and continuum Gamow shell model with realistic nuclear forces
Sun, Z. H.; Wu, Q.; Zhao, Z. H.; Hu, B. S.; Dai, S. J.; Xu, F. R.
2017-06-01
Starting from realistic nuclear forces, we have developed a core Gamow shell model which can describe resonance and continuum properties of loosely-bound or unbound nuclear systems. To describe properly resonance and continuum, the Berggren representation has been employed, which treats bound, resonant and continuum states on equal footing in a complex-momentum (complex-k) plane. To derive the model-space effective interaction based on realistic forces, the full Q ˆ -box folded-diagram renormalization has been, for the first time, extended to the nondegenerate complex-k space. The CD-Bonn potential is softened by using the Vlow-k method. Choosing 16O as the inert core, we have calculated sd-shell neutron-rich oxygen isotopes, giving good descriptions of both bound and resonant states. The isotopes 25,26O are calculated to be resonant even in their ground states.
Building Realistic Mobility Models for Mobile Ad Hoc Networks
Directory of Open Access Journals (Sweden)
Adrian Pullin
2018-04-01
Full Text Available A mobile ad hoc network (MANET is a self-configuring wireless network in which each node could act as a router, as well as a data source or sink. Its application areas include battlefields and vehicular and disaster areas. Many techniques applied to infrastructure-based networks are less effective in MANETs, with routing being a particular challenge. This paper presents a rigorous study into simulation techniques for evaluating routing solutions for MANETs with the aim of producing more realistic simulation models and thereby, more accurate protocol evaluations. MANET simulations require models that reflect the world in which the MANET is to operate. Much of the published research uses movement models, such as the random waypoint (RWP model, with arbitrary world sizes and node counts. This paper presents a technique for developing more realistic simulation models to test and evaluate MANET protocols. The technique is animation, which is applied to a realistic scenario to produce a model that accurately reflects the size and shape of the world, node count, movement patterns, and time period over which the MANET may operate. The animation technique has been used to develop a battlefield model based on established military tactics. Trace data has been used to build a model of maritime movements in the Irish Sea. Similar world models have been built using the random waypoint movement model for comparison. All models have been built using the ns-2 simulator. These models have been used to compare the performance of three routing protocols: dynamic source routing (DSR, destination-sequenced distance-vector routing (DSDV, and ad hoc n-demand distance vector routing (AODV. The findings reveal that protocol performance is dependent on the model used. In particular, it is shown that RWP models do not reflect the performance of these protocols under realistic circumstances, and protocol selection is subject to the scenario to which it is applied. To
A scan for models with realistic fermion mass patterns
International Nuclear Information System (INIS)
Bijnens, J.; Wetterich, C.
1986-03-01
We consider models which have no small Yukawa couplings unrelated to symmetry. This situation is generic in higher dimensional unification where Yukawa couplings are predicted to have strength similar to the gauge couplings. Generations have then to be differentiated by symmetry properties and the structure of fermion mass matrices is given in terms of quantum numbers alone. We scan possible symmetries leading to realistic mass matrices. (orig.)
Realistic simplified gaugino-higgsino models in the MSSM
Fuks, Benjamin; Klasen, Michael; Schmiemann, Saskia; Sunder, Marthijn
2018-03-01
We present simplified MSSM models for light neutralinos and charginos with realistic mass spectra and realistic gaugino-higgsino mixing, that can be used in experimental searches at the LHC. The formerly used naive approach of defining mass spectra and mixing matrix elements manually and independently of each other does not yield genuine MSSM benchmarks. We suggest the use of less simplified, but realistic MSSM models, whose mass spectra and mixing matrix elements are the result of a proper matrix diagonalisation. We propose a novel strategy targeting the design of such benchmark scenarios, accounting for user-defined constraints in terms of masses and particle mixing. We apply it to the higgsino case and implement a scan in the four relevant underlying parameters {μ , tan β , M1, M2} for a given set of light neutralino and chargino masses. We define a measure for the quality of the obtained benchmarks, that also includes criteria to assess the higgsino content of the resulting charginos and neutralinos. We finally discuss the distribution of the resulting models in the MSSM parameter space as well as their implications for supersymmetric dark matter phenomenology.
Toward the classification of the realistic free fermionic models
International Nuclear Information System (INIS)
Faraggi, A.E.
1997-08-01
The realistic free fermionic models have had remarkable success in providing plausible explanations for various properties of the Standard Model which include the natural appearance of three generations, the explanation of the heavy top quark mass and the qualitative structure of the fermion mass spectrum in general, the stability of the proton and more. These intriguing achievements makes evident the need to understand the general space of these models. While the number of possibilities is large, general patterns can be extracted. In this paper the author presents a detailed discussion on the construction of the realistic free fermionic models with the aim of providing some insight into the basic structures and building blocks that enter the construction. The role of free phases in the determination of the phenomenology of the models is discussed in detail. The author discusses the connection between the free phases and mirror symmetry in (2,2) models and the corresponding symmetries in the case of (2,0) models. The importance of the free phases in determining the effective low energy phenomenology is illustrated in several examples. The classification of the models in terms of boundary condition selection rules, real world-sheet fermion pairings, exotic matter states and the hidden sector is discussed
Gauge coupling unification in realistic free-fermionic string models
International Nuclear Information System (INIS)
Dienes, K.R.; Faraggi, A.E.
1995-01-01
We discuss the unification of gauge couplings within the framework of a wide class of realistic free-fermionic string models which have appeared in the literature, including the flipped SU(5), SO(6)xSO(4), and various SU(3)xSU(2)xU(1) models. If the matter spectrum below the string scale is that of the Minimal Supersymmetric Standard Model (MSSM), then string unification is in disagreement with experiment. We therefore examine several effects that may modify the minimal string predictions. First, we develop a systematic procedure for evaluating the one-loop heavy string threshold corrections in free-fermionic string models, and we explicitly evaluate these corrections for each of the realistic models. We find that these string threshold corrections are small, and we provide general arguments explaining why such threshold corrections are suppressed in string theory. Thus heavy thresholds cannot resolve the disagreement with experiment. We also study the effect of non-standard hypercharge normalizations, light SUSY thresholds, and intermediate-scale gauge structure, and similarly conclude that these effects cannot resolve the disagreement with low-energy data. Finally, we examine the effects of additional color triplets and electroweak doublets beyond the MSSM. Although not required in ordinary grand unification scenarios, such states generically appear within the context of certain realistic free-fermionic string models. We show that if these states exist at the appropriate thresholds, then the gauge couplings will indeed unify at the string scale. Thus, within these string models, string unification can be in agreement with low-energy data. (orig.)
A conceptual ENSO model under realistic noise forcing
Directory of Open Access Journals (Sweden)
J. Saynisch
2006-01-01
Full Text Available We investigated the influence of atmospheric noise on the generation of interannual El Niño variability. Therefore, we perturbed a conceptual ENSO delay model with surrogate windstress data generated from tropical windspeed measurements. The effect of the additional stochastic forcing was studied for various parameter sets including periodic and chaotic regimes. The evaluation was based on a spectrum and amplitude-period relation comparison between model and measured sea surface temperature data. The additional forcing turned out to increase the variability of the model output in general. The noise-free model was unable to reproduce the observed spectral bandwidth for any choice of parameters. On the contrary, the stochastically forced model is capable of producing a realistic spectrum. The weakly nonlinear regimes of the model exhibit a proportional relation between amplitude and period matching the relation derived from measurement data. The chaotic regime, however, shows an inversely proportional relation. A stability analysis of the different regimes revealed that the spectra of the weakly nonlinear regimes are robust against slight parameter changes representing disregarded physical mechanisms, whereas the chaotic regime exhibits a very unstable realistic spectrum. We conclude that the model including stochastic forcing in a parameter range of moderate nonlinearity best matches the real conditions. This suggests that atmospheric noise plays an important role in the coupled tropical pacific ocean-atmosphere system.
Finite Time Blowup in a Realistic Food-Chain Model
Parshad, Rana
2013-05-19
We investigate a realistic three-species food-chain model, with generalist top predator. The model based on a modified version of the Leslie-Gower scheme incorporates mutual interference in all the three populations and generalizes several other known models in the ecological literature. We show that the model exhibits finite time blowup in certain parameter range and for large enough initial data. This result implies that finite time blowup is possible in a large class of such three-species food-chain models. We propose a modification to the model and prove that the modified model has globally existing classical solutions, as well as a global attractor. We reconstruct the attractor using nonlinear time series analysis and show that it pssesses rich dynamics, including chaos in certain parameter regime, whilst avoiding blowup in any parameter regime. We also provide estimates on its fractal dimension as well as provide numerical simulations to visualise the spatiotemporal chaos.
Plotnitsky, Arkady
2016-01-13
The project of this article is twofold. First, it aims to offer a new perspective on, and a new argument concerning, realist and non-realist mathematical models, and differences and affinities between them, using physics as a paradigmatic field of mathematical modelling in science. Most of the article is devoted to this topic. Second, the article aims to explore the implications of this argument for mathematical modelling in other fields, in particular in cognitive psychology and economics. © 2015 The Author(s).
Electron percolation in realistic models of carbon nanotube networks
Simoneau, Louis-Philippe; Villeneuve, Jérémie; Rochefort, Alain
2015-09-01
The influence of penetrable and curved carbon nanotubes (CNT) on the charge percolation in three-dimensional disordered CNT networks have been studied with Monte-Carlo simulations. By considering carbon nanotubes as solid objects but where the overlap between their electron cloud can be controlled, we observed that the structural characteristics of networks containing lower aspect ratio CNT are highly sensitive to the degree of penetration between crossed nanotubes. Following our efficient strategy to displace CNT to different positions to create more realistic statistical models, we conclude that the connectivity between objects increases with the hard-core/soft-shell radii ratio. In contrast, the presence of curved CNT in the random networks leads to an increasing percolation threshold and to a decreasing electrical conductivity at saturation. The waviness of CNT decreases the effective distance between the nanotube extremities, hence reducing their connectivity and degrading their electrical properties. We present the results of our simulation in terms of thickness of the CNT network from which simple structural parameters such as the volume fraction or the carbon nanotube density can be accurately evaluated with our more realistic models.
Supersymmetry and light quark masses in a realistic superstring model
International Nuclear Information System (INIS)
Halyo, Edi.
1993-10-01
We examine the light quark masses in a standard-like superstring model in the four dimensional free fermionic formulation. We find that the supersymmetry constraints in the observable and hidden sectors eliminate all large contributions to m u and m d and force them to be much smaller than the other quark masses. The requirement for an acceptable Higgs doublet spectrum results in m u d . In these models a realistic m d can always be obtained whereas m u is at most 10 -5 MeV. For particular choices on flat direction or vacua m u can be as small as 10 -7 MeV but cannot vanish. (author) 15 refs, 2 tabs
Experimental Study of Aerosol Deposition in a Realistic Lung Model
Directory of Open Access Journals (Sweden)
František LÍZAL
2010-12-01
Full Text Available The inhalation route for administration of medicaments is becoming more and more popular in recent years. The reason is non-invasiveness of the method and instantaneous absorption of drugs to the blood circulation. It is necessary to deliver exact amount of drug to the specific segment because of occurrence of diverse diseases in different segments of lungs. The aim of our work is to contribute to better understanding of transport and deposition of aerosolized drugs in lungs and hence to more effective treatment of respiratory diseases due to the targeted drug delivery. We provided measurements of aerosol deposition in segmented realistic model of lungs without a mouth cavity. Monodisperse particles marked with fluorescein were supplied to the model. The model was then disassembled to segments and each segment was rinsed with isopropanol, whereby fluorescent samples were created. Each sample was analysed by fluorometer and an amount of aerosol deposited in the segment was calculated. Experiences obtained by this study were used for creation of a new model with the mouth cavity. This model will be used for future studies with porous and fiber aerosols.
Realistic Matematic Approach through Numbered Head Together Learning Model
Sugihatno, A. C. M. S.; Budiyono; Slamet, I.
2017-09-01
Recently, the teaching process which is conducted based on teacher center affect the students interaction in the class. It causes students become less interest to participate. That is why teachers should be more creative in designing learning using other types of cooperative learning model. Therefore, this research is aimed to implement NHT with RMA in the teaching process. We utilize NHT since it is a variant of group discussion whose aim is giving a chance to the students to share their ideas related to the teacher’s question. By using NHT in the class, a teacher can give a better understanding about the material which is given with the help of Realistic Mathematics Approach (RMA) which known for its real problem contex. Meanwhile, the researcher assumes instead of selecting teaching model, Adversity Quotient (AQ) of student also influences students’ achievement. This research used the quasi experimental research. The samples is 60 students in junior high school, it was taken by using the stratified cluster random sampling technique. The results show NHT-RMA gives a better learning achievement of mathematics than direct teaching model and NHT-RMA teaching model with categorized as high AQ show different learning achievement from the students with categorized as moderate and low AQ.
Applying a realistic evaluation model to occupational safety interventions
DEFF Research Database (Denmark)
Pedersen, Louise Møller
2018-01-01
Background: Recent literature characterizes occupational safety interventions as complex social activities, applied in complex and dynamic social systems. Hence, the actual outcomes of an intervention will vary, depending on the intervention, the implementation process, context, personal characte......Background: Recent literature characterizes occupational safety interventions as complex social activities, applied in complex and dynamic social systems. Hence, the actual outcomes of an intervention will vary, depending on the intervention, the implementation process, context, personal...... characteristics of key actors (defined mechanisms), and the interplay between them, and can be categorized as expected or unexpected. However, little is known about ’how’ to include context and mechanisms in evaluations of intervention effectiveness. A revised realistic evaluation model has been introduced...... and qualitative methods. This revised model has, however, not been applied in a real life context. Method: The model is applied in a controlled, four-component, integrated behaviour-based and safety culture-based safety intervention study (2008-2010) in a medium-sized wood manufacturing company. The interventions...
Murphy, Kelly E.
2012-01-13
Fibroblasts and their activated phenotype, myofibroblasts, are the primary cell types involved in the contraction associated with dermal wound healing. Recent experimental evidence indicates that the transformation from fibroblasts to myofibroblasts involves two distinct processes: The cells are stimulated to change phenotype by the combined actions of transforming growth factor β (TGFβ) and mechanical tension. This observation indicates a need for a detailed exploration of the effect of the strong interactions between the mechanical changes and growth factors in dermal wound healing. We review the experimental findings in detail and develop a model of dermal wound healing that incorporates these phenomena. Our model includes the interactions between TGFβ and collagenase, providing a more biologically realistic form for the growth factor kinetics than those included in previous mechanochemical descriptions. A comparison is made between the model predictions and experimental data on human dermal wound healing and all the essential features are well matched. © 2012 Society for Mathematical Biology.
Bayesian inversion using a geologically realistic and discrete model space
Jaeggli, C.; Julien, S.; Renard, P.
2017-12-01
Since the early days of groundwater modeling, inverse methods play a crucial role. Many research and engineering groups aim to infer extensive knowledge of aquifer parameters from a sparse set of observations. Despite decades of dedicated research on this topic, there are still several major issues to be solved. In the hydrogeological framework, one is often confronted with underground structures that present very sharp contrasts of geophysical properties. In particular, subsoil structures such as karst conduits, channels, faults, or lenses, strongly influence groundwater flow and transport behavior of the underground. For this reason it can be essential to identify their location and shape very precisely. Unfortunately, when inverse methods are specially trained to consider such complex features, their computation effort often becomes unaffordably high. The following work is an attempt to solve this dilemma. We present a new method that is, in some sense, a compromise between the ergodicity of Markov chain Monte Carlo (McMC) methods and the efficient handling of data by the ensemble based Kalmann filters. The realistic and complex random fields are generated by a Multiple-Point Statistics (MPS) tool. Nonetheless, it is applicable with any conditional geostatistical simulation tool. Furthermore, the algorithm is independent of any parametrization what becomes most important when two parametric systems are equivalent (permeability and resistivity, speed and slowness, etc.). When compared to two existing McMC schemes, the computational effort was divided by a factor of 12.
Realistic modelling of observed seismic motion in complex sedimentary basins
International Nuclear Information System (INIS)
Faeh, D.; Panza, G.F.
1994-03-01
Three applications of a numerical technique are illustrated to model realistically the seismic ground motion for complex two-dimensional structures. First we consider a sedimentary basin in the Friuli region, and we model strong motion records from an aftershock of the 1976 earthquake. Then we simulate the ground motion caused in Rome by the 1915, Fucino (Italy) earthquake, and we compare our modelling with the damage distribution observed in the town. Finally we deal with the interpretation of ground motion recorded in Mexico City, as a consequence of earthquakes in the Mexican subduction zone. The synthetic signals explain the major characteristics (relative amplitudes, spectral amplification, frequency content) of the considered seismograms, and the space distribution of the available macroseismic data. For the sedimentary basin in the Friuli area, parametric studies demonstrate the relevant sensitivity of the computed ground motion to small changes in the subsurface topography of the sedimentary basin, and in the velocity and quality factor of the sediments. The total energy of ground motion, determined from our numerical simulation in Rome, is in very good agreement with the distribution of damage observed during the Fucino earthquake. For epicentral distances in the range 50km-100km, the source location and not only the local soil conditions control the local effects. For Mexico City, the observed ground motion can be explained as resonance effects and as excitation of local surface waves, and the theoretical and the observed maximum spectral amplifications are very similar. In general, our numerical simulations permit the estimate of the maximum and average spectral amplification for specific sites, i.e. are a very powerful tool for accurate micro-zonation. (author). 38 refs, 19 figs, 1 tab
A review of toxicity models for realistic atmospheric applications
Gunatilaka, Ajith; Skvortsov, Alex; Gailis, Ralph
2014-02-01
There are many applications that need to study human health effects caused by exposure to toxic chemicals. Risk analysis for industrial sites, study of population health impacts of atmospheric pollutants, and operations research for assessing the potential impacts of chemical releases in military contexts are some examples. Because of safety risks and the high cost of field trials involving hazardous chemical releases, computer simulations are widely used for such studies. Modelling of atmospheric transport and dispersion of chemicals released into the atmosphere to determine the toxic chemical concentrations to which individuals will be exposed is one main component of these simulations, and there are well established atmospheric dispersion models for this purpose. Estimating the human health effects caused by the exposure to these predicted toxic chemical concentrations is the other main component. A number of different toxicity models for assessing the health effects of toxic chemical exposure are found in the literature. Because these different models have been developed based on different assumptions about the plume characteristics, chemical properties, and physiological response, there is a need to review and compare these models to understand their applicability. This paper reviews several toxicity models described in the literature. The paper also presents results of applying different toxicity models to simulated concentration time series data. These results show that the use of ensemble mean concentrations, which are what atmospheric dispersion models typically provide, to estimate human health effects of exposure to hazardous chemical releases may underestimate their impact when toxic exponent, n, of the chemical is greater than one; the opposite phenomenon appears to hold when n biological recovery processes may predict greater toxicity than the explicitly parameterised models. Despite the wide variety of models of varying degrees of complexity that is
Realistic full wave modeling of focal plane array pixels.
Energy Technology Data Exchange (ETDEWEB)
Campione, Salvatore [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Electromagnetic Theory Dept.; Warne, Larry K. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Electromagnetic Theory Dept.; Jorgenson, Roy E. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Electromagnetic Theory Dept.; Davids, Paul [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Applied Photonic Microsystems Dept.; Peters, David W. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Applied Photonic Microsystems Dept.
2017-11-01
Here, we investigate full-wave simulations of realistic implementations of multifunctional nanoantenna enabled detectors (NEDs). We focus on a 2x2 pixelated array structure that supports two wavelengths of operation. We design each resonating structure independently using full-wave simulations with periodic boundary conditions mimicking the whole infinite array. We then construct a supercell made of a 2x2 pixelated array with periodic boundary conditions mimicking the full NED; in this case, however, each pixel comprises 10-20 antennas per side. In this way, the cross-talk between contiguous pixels is accounted for in our simulations. We observe that, even though there are finite extent effects, the pixels work as designed, each responding at the respective wavelength of operation. This allows us to stress that realistic simulations of multifunctional NEDs need to be performed to verify the design functionality by taking into account finite extent and cross-talk effects.
Nursing and the new biology: towards a realist, anti-reductionist approach to nursing knowledge.
Nairn, Stuart
2014-10-01
As a system of knowledge, nursing has utilized a range of subjects and reconstituted them to reflect the thinking and practice of health care. Often drawn to a holistic model, nursing finds it difficult to resist the reductionist tendencies in biological and medical thinking. In this paper I will propose a relational approach to knowledge that is able to address this issue. The paper argues that biology is not characterized by one stable theory but is often a contentious topic and employs philosophically diverse models in its scientific research. Biology need not be seen as a reductionist science, but reductionism is nonetheless an important current within biological thinking. These reductionist currents can undermine nursing knowledge in four main ways. Firstly, that the conclusions drawn from reductionism go far beyond their data based on an approach that prioritizes biological explanations and eliminates others. Secondly, that the methods employed by biologists are sometimes weak, and the limitations are insufficiently acknowledged. Thirdly, that the assumptions that drive the research agenda are problematic, and finally that uncritical application of these ideas can be potentially disastrous for nursing practice. These issues are explored through an examination of the problems reductionism poses for the issue of gender, mental health, and altruism. I then propose an approach based on critical realism that adopts an anti-reductionist philosophy that utilizes the conceptual tools of emergence and a relational ontology. © 2014 John Wiley & Sons Ltd.
Laboratory of Biological Modeling
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...
Realistic edge field model code REFC for designing and study of isochronous cyclotron
International Nuclear Information System (INIS)
Ismail, M.
1989-01-01
The focussing properties and the requirements for isochronism in cyclotron magnet configuration are well-known in hard edge field model. The fact that they quite often change considerably in realistic field can be attributed mainly to the influence of the edge field. A solution to this problem requires a field model which allows a simple construction of equilibrium orbit and yield simple formulae. This can be achieved by using a fitted realistic edge field (Hudson et al 1975) in the region of the pole edge and such a field model is therefore called a realistic edge field model. A code REFC based on realistic edge field model has been developed to design the cyclotron sectors and the code FIELDER has been used to study the beam properties. In this report REFC code has been described along with some relevant explaination of the FIELDER code. (author). 11 refs., 6 figs
Development of Realistic Head Models for Electromagnetic Source Imaging of the Human Brain
National Research Council Canada - National Science Library
Akalin, Z
2001-01-01
In this work, a methodology is developed to solve the forward problem of electromagnetic source imaging using realistic head models, For this purpose, first segmentation of the 3 dimensional MR head...
Realistic Avatar Eye and Head Animation Using a Neurobiological Model of Visual Attention
National Research Council Canada - National Science Library
Itti, L; Dhavale, N; Pighin, F
2003-01-01
We describe a neurobiological model of visual attention and eye/head movements in primates, and its application to the automatic animation of a realistic virtual human head watching an unconstrained...
Constructing Realistic Szekeres Models from Initial and Final Data
Walters, Anthony; Hellaby, Charles
2012-01-01
The Szekeres family of inhomogeneous solutions, which are defined by six arbitrary metric functions, offers a wide range of possibilities for modelling cosmic structure. Here we present a model construction procedure for the quasispherical case using given data at initial and final times. Of the six arbitrary metric functions, the three which are common to both Szekeres and Lema\\^itre-Tolman models are determined by the model construction procedure of Krasinski & Hellaby. For the remaining th...
Constructing realistic Szekeres models from initial and final data
Energy Technology Data Exchange (ETDEWEB)
Walters, Anthony; Hellaby, Charles, E-mail: tony.walters@uct.ac.za, E-mail: charles.hellaby@uct.ac.za [Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch, 7701 (South Africa)
2012-12-01
The Szekeres family of inhomogeneous solutions, which are defined by six arbitrary metric functions, offers a wide range of possibilities for modelling cosmic structure. Here we present a model construction procedure for the quasispherical case using given data at initial and final times. Of the six arbitrary metric functions, the three which are common to both Szekeres and Lemaître-Tolman models are determined by the model construction procedure of Krasinski and Hellaby. For the remaining three functions, which are unique to Szekeres models, we derive exact analytic expressions in terms of more physically intuitive quantities — density profiles and dipole orientation angles. Using MATLAB, we implement the model construction procedure and simulate the time evolution.
Assumptions behind size-based ecosystem models are realistic
DEFF Research Database (Denmark)
Andersen, Ken Haste; Blanchard, Julia L.; Fulton, Elizabeth A.
2016-01-01
A recent publication about balanced harvesting (Froese et al., ICES Journal of Marine Science; doi:10.1093/icesjms/fsv122) contains several erroneous statements about size-spectrum models. We refute the statements by showing that the assumptions pertaining to size-spectrum models discussed by Fro...... that there is indeed a constructive role for a wide suite of ecosystem models to evaluate fishing strategies in an ecosystem context...
More-Realistic Digital Modeling of a Human Body
Rogge, Renee
2010-01-01
A MATLAB computer program has been written to enable improved (relative to an older program) modeling of a human body for purposes of designing space suits and other hardware with which an astronaut must interact. The older program implements a kinematic model based on traditional anthropometric measurements that do provide important volume and surface information. The present program generates a three-dimensional (3D) whole-body model from 3D body-scan data. The program utilizes thin-plate spline theory to reposition the model without need for additional scans.
A Note on Realistic Dividends in Actuarial Surplus Models
Directory of Open Access Journals (Sweden)
Benjamin Avanzi
2016-10-01
Full Text Available Because of the profitable nature of risk businesses in the long term, de Finetti suggested that surplus models should allow for cash leakages, as otherwise the surplus would unrealistically grow (on average to infinity. These leakages were interpreted as ‘dividends’. Subsequent literature on actuarial surplus models with dividend distribution has mainly focussed on dividend strategies that either maximise the expected present value of dividends until ruin or lead to a probability of ruin that is less than one (see Albrecher and Thonhauser, Avanzi for reviews. An increasing number of papers are directly interested in modelling dividend policies that are consistent with actual practice in financial markets. In this short note, we review the corporate finance literature with the specific aim of fleshing out properties that dividend strategies should ideally satisfy, if one wants to model behaviour that is consistent with practice.
A Note on Realistic Dividends in Actuarial Surplus Models
Benjamin Avanzi; Vincent Tu; Bernard Wong
2016-01-01
Because of the profitable nature of risk businesses in the long term, de Finetti suggested that surplus models should allow for cash leakages, as otherwise the surplus would unrealistically grow (on average) to infinity. These leakages were interpreted as 'dividends'. Subsequent literature on actuarial surplus models with dividend distribution has mainly focussed on dividend strategies that either maximise the expected present value of dividends until ruin or lead to a probability of ruin tha...
Model of Ni-63 battery with realistic PIN structure
Munson, Charles E.; Arif, Muhammad; Streque, Jeremy; Belahsene, Sofiane; Martinez, Anthony; Ramdane, Abderrahim; El Gmili, Youssef; Salvestrini, Jean-Paul; Voss, Paul L.; Ougazzaden, Abdallah
2015-09-01
GaN, with its wide bandgap of 3.4 eV, has emerged as an efficient material for designing high-efficiency betavoltaic batteries. An important part of designing efficient betavoltaic batteries involves a good understanding of the full process, from the behavior of the nuclear material and the creation of electron-hole pairs all the way through the collection of photo-generated carriers. This paper presents a detailed model based on Monte Carlo and Silvaco for a GaN-based betavoltaic battery device, modeled after Ni-63 as an energy source. The accuracy of the model is verified by comparing it with experimental values obtained for a GaN-based p-i-n structure under scanning electron microscope illumination.
Model of Ni-63 battery with realistic PIN structure
Energy Technology Data Exchange (ETDEWEB)
Munson, Charles E.; Voss, Paul L.; Ougazzaden, Abdallah, E-mail: aougazza@georgiatech-metz.fr [Georgia Tech Lorraine, Georgia Tech-C.N.R.S., UMI2958, 2-3 rue Marconi, 57070 Metz (France); School of Electrical and Computer Engineering, Georgia Institute of Technology, 777 Atlantic Drive NW, 30332-0250 Atlanta (United States); Arif, Muhammad; Salvestrini, Jean-Paul [Georgia Tech Lorraine, Georgia Tech-C.N.R.S., UMI2958, 2-3 rue Marconi, 57070 Metz (France); Université de Lorraine, CentraleSupélec, LMOPS, EA 4423, 2 rue E. Belin, 57070 Metz (France); Streque, Jeremy; El Gmili, Youssef [Georgia Tech Lorraine, Georgia Tech-C.N.R.S., UMI2958, 2-3 rue Marconi, 57070 Metz (France); Belahsene, Sofiane; Martinez, Anthony; Ramdane, Abderrahim [Laboratory for Photonics and Nanostructures, CNRS, Route de Nozay, 91460 Marcoussis (France)
2015-09-14
GaN, with its wide bandgap of 3.4 eV, has emerged as an efficient material for designing high-efficiency betavoltaic batteries. An important part of designing efficient betavoltaic batteries involves a good understanding of the full process, from the behavior of the nuclear material and the creation of electron-hole pairs all the way through the collection of photo-generated carriers. This paper presents a detailed model based on Monte Carlo and Silvaco for a GaN-based betavoltaic battery device, modeled after Ni-63 as an energy source. The accuracy of the model is verified by comparing it with experimental values obtained for a GaN-based p-i-n structure under scanning electron microscope illumination.
Model of Ni-63 battery with realistic PIN structure
International Nuclear Information System (INIS)
Munson, Charles E.; Voss, Paul L.; Ougazzaden, Abdallah; Arif, Muhammad; Salvestrini, Jean-Paul; Streque, Jeremy; El Gmili, Youssef; Belahsene, Sofiane; Martinez, Anthony; Ramdane, Abderrahim
2015-01-01
GaN, with its wide bandgap of 3.4 eV, has emerged as an efficient material for designing high-efficiency betavoltaic batteries. An important part of designing efficient betavoltaic batteries involves a good understanding of the full process, from the behavior of the nuclear material and the creation of electron-hole pairs all the way through the collection of photo-generated carriers. This paper presents a detailed model based on Monte Carlo and Silvaco for a GaN-based betavoltaic battery device, modeled after Ni-63 as an energy source. The accuracy of the model is verified by comparing it with experimental values obtained for a GaN-based p-i-n structure under scanning electron microscope illumination
Towards a realistic composite model of quarks and leptons
International Nuclear Information System (INIS)
Li Xiaoyuan; Marshak, R.E.
1985-06-01
Within the context of the 't Hooft anomaly matching scheme, some guiding principles for the model building are discussed with an eye to low energy phenomenology. It is argued that Λsub(ch) (chiral symmetry breaking scale of the global color-flavor group Gsub(CF)) proportional Λsub(MC) (metacolor scale) and Λ sub(gsub(CF)) (unification scale of the gauge subgroup of Gsub(CF)) < or approx. Λsub(ch). As illustrations of the method, two composite models are suggested that can give rise to three or four generations of ordinary quarks and leptons without exotic fermions. (orig.)
Anisotropic, nonsingular early universe model leading to a realistic cosmology
International Nuclear Information System (INIS)
Dechant, Pierre-Philippe; Lasenby, Anthony N.; Hobson, Michael P.
2009-01-01
We present a novel cosmological model in which scalar field matter in a biaxial Bianchi IX geometry leads to a nonsingular 'pancaking' solution: the hypersurface volume goes to zero instantaneously at the 'big bang', but all physical quantities, such as curvature invariants and the matter energy density remain finite, and continue smoothly through the big bang. We demonstrate that there exist geodesics extending through the big bang, but that there are also incomplete geodesics that spiral infinitely around a topologically closed spatial dimension at the big bang, rendering it, at worst, a quasiregular singularity. The model is thus reminiscent of the Taub-NUT vacuum solution in that it has biaxial Bianchi IX geometry and its evolution exhibits a dimensionality reduction at a quasiregular singularity; the two models are, however, rather different, as we will show in a future work. Here we concentrate on the cosmological implications of our model and show how the scalar field drives both isotropization and inflation, thus raising the question of whether structure on the largest scales was laid down at a time when the universe was still oblate (as also suggested by [T. S. Pereira, C. Pitrou, and J.-P. Uzan, J. Cosmol. Astropart. Phys. 9 (2007) 6.][C. Pitrou, T. S. Pereira, and J.-P. Uzan, J. Cosmol. Astropart. Phys. 4 (2008) 4.][A. Guemruekcueoglu, C. Contaldi, and M. Peloso, J. Cosmol. Astropart. Phys. 11 (2007) 005.]). We also discuss the stability of our model to small perturbations around biaxiality and draw an analogy with cosmological perturbations. We conclude by presenting a separate, bouncing solution, which generalizes the known bouncing solution in closed FRW universes.
Kim, Ji-Woong; Phuong, Nguyen Lu; Aramaki, Shin-Ichiro; Ito, Kazuhide
2018-05-01
Studies concerning inhalation toxicology and respiratory drug-delivery systems require biological testing involving experiments performed on animals. Particle image velocimetry (PIV) is an effective in vitro technique that reveals detailed inhalation flow patterns, thereby assisting analyses of inhalation exposure to various substances. A realistic model of a rhesus-monkey upper airway was developed to investigate flow patterns in its oral and nasal cavities through PIV experiments performed under steady-state constant inhalation conditions at various flow rates-4, 10, and 20 L/min. Flow rate of the fluid passing through the inlet into the trachea was measured to obtain characteristic flow mechanisms, and flow phenomena in the model were confirmed via characterized flow fields. It was observed that increase in flow rate leads to constant velocity profiles in upper and lower trachea regions. It is expected that the results of this study would contribute to future validation of studies aimed at developing in silico models, especially those involving computational fluid dynamic (CFD) analysis. Copyright © 2018 Elsevier B.V. All rights reserved.
A realistic model for quantum theory with a locality property
International Nuclear Information System (INIS)
Eberhard, P.H.
1987-04-01
A model reproducing the predictions of relativistic quantum theory to any desired degree of accuracy is described in this paper. It involves quantities that are independent of the observer's knowledge, and therefore can be called real, and which are defined at each point in space, and therefore can be called local in a rudimentary sense. It involves faster-than-light, but not instantaneous, action at distance
Toward the M(F)--Theory Embedding of Realistic Free-Fermion Models
Berglund, P; Faraggi, A E; Nanopoulos, Dimitri V; Qiu, Z; Berglund, Per; Ellis, John; Faraggi, Alon E.; Qiu, Zongan
1998-01-01
We construct a Landau-Ginzburg model with the same data and symmetries as a $Z_2\\times Z_2$ orbifold that corresponds to a class of realistic free-fermion models. Within the class of interest, we show that this orbifolding connects between different $Z_2\\times Z_2$ orbifold models and commutes with the mirror symmetry. Our work suggests that duality symmetries previously discussed in the context of specific $M$ and $F$ theory compactifications may be extended to the special $Z_2\\times Z_2$ orbifold that characterizes realistic free-fermion models.
Realistic Mathematics Learning Using Cooperative Strategy Model in Junior High School
Dwiyana
2015-01-01
This study aims to develop a realistic mathematics learning model using cooperative strategy. This study applies research and development approach conducted at Junior High School "Laboratorium," State University of Malang. The implementation of this model is conducted through five stages: 1) previous study phase; 2) model planning phase;…
Reliable modeling of the electronic spectra of realistic uranium complexes
Tecmer, Paweł; Govind, Niranjan; Kowalski, Karol; de Jong, Wibe A.; Visscher, Lucas
2013-07-01
We present an EOMCCSD (equation of motion coupled cluster with singles and doubles) study of excited states of the small [UO2]2+ and [UO2]+ model systems as well as the larger UVIO2(saldien) complex. In addition, the triples contribution within the EOMCCSDT and CR-EOMCCSD(T) (completely renormalized EOMCCSD with non-iterative triples) approaches for the [UO2]2+ and [UO2]+ systems as well as the active-space variant of the CR-EOMCCSD(T) method—CR-EOMCCSd(t)—for the UVIO2(saldien) molecule are investigated. The coupled cluster data were employed as benchmark to choose the "best" appropriate exchange-correlation functional for subsequent time-dependent density functional (TD-DFT) studies on the transition energies for closed-shell species. Furthermore, the influence of the saldien ligands on the electronic structure and excitation energies of the [UO2]+ molecule is discussed. The electronic excitations as well as their oscillator dipole strengths modeled with TD-DFT approach using the CAM-B3LYP exchange-correlation functional for the [UVO2(saldien)]- with explicit inclusion of two dimethyl sulfoxide molecules are in good agreement with the experimental data of Takao et al. [Inorg. Chem. 49, 2349 (2010), 10.1021/ic902225f].
Realistic Modeling of Seismic Wave Ground Motion in Beijing City
Ding, Z.; Romanelli, F.; Chen, Y. T.; Panza, G. F.
Algorithms for the calculation of synthetic seismograms in laterally heterogeneous anelastic media have been applied to model the ground motion in Beijing City. The synthetic signals are compared with the few available seismic recordings (1998, Zhangbei earthquake) and with the distribution of observed macroseismic intensity (1976, Tangshan earthquake). The synthetic three-component seismograms have been computed for the Xiji area and Beijing City. The numerical results show that the thick Tertiary and Quaternary sediments are responsible for the severe amplification of the seismic ground motion. Such a result is well correlated with the abnormally high macroseismic intensity zone in the Xiji area associated with the 1976 Tangshan earthquake as well as with the ground motion recorded in Beijing city in the wake of the 1998 Zhangbei earthquake.
Realistic modeling of seismic wave ground motion in Beijing City
International Nuclear Information System (INIS)
Ding, Z.; Chen, Y.T.; Romanelli, F.; Panza, G.F.
2002-05-01
Advanced algorithms for the calculation of synthetic seismograms in laterally heterogeneous anelastic media have been applied to model the ground motion in Beijing City. The synthetic signals are compared with the few available seismic recordings (1998, Zhangbei earthquake) and with the distribution of the observed macroseismic intensity (1976, Tangshan earthquake). The synthetic 3-component seismograms have been computed in the Xiji area and in Beijing town. The numerical results show that the thick Tertiary and Quaternary sediments are responsible of the severe amplification of the seismic ground motion. Such a result is well correlated with the abnormally high macroseismic intensity zone (Xiji area) associated to the 1976 Tangshan earthquake and with the records in Beijing town, associated to the 1998 Zhangbei earthquake. (author)
Stochastic Allocation of Transmit Power for Realistic Wireless Channel Models
Directory of Open Access Journals (Sweden)
N. G. Tarhuni
2016-06-01
Full Text Available Control of transmitted power is crucial for the successful operation of multi-user wireless channels communications. There are practical situations in which the transmitted power cannot be adjusted by feedback information; hence, only forward transmit power allocation can be applied, especially in situations where a feedback channel is not available in a wireless network or when wireless nodes are only transmit types. Conventionally, transmitted power can be fixed. Higher gain may be observed if the sensors’ transmitted power is randomized. In this work, random power allocation for a Nakagami-m distributed wireless channel model was investigated, and a number of random distributions were evaluated theoretically and tested by simulations. The outage probability was evaluated theoretically and validated by Monte Carlo simulations.
Order Matters: Sequencing Scale-Realistic Versus Simplified Models to Improve Science Learning
Chen, Chen; Schneps, Matthew H.; Sonnert, Gerhard
2016-10-01
Teachers choosing between different models to facilitate students' understanding of an abstract system must decide whether to adopt a model that is simplified and striking or one that is realistic and complex. Only recently have instructional technologies enabled teachers and learners to change presentations swiftly and to provide for learning based on multiple models, thus giving rise to questions about the order of presentation. Using disjoint individual growth modeling to examine the learning of astronomical concepts using a simulation of the solar system on tablets for 152 high school students (age 15), the authors detect both a model effect and an order effect in the use of the Orrery, a simplified model that exaggerates the scale relationships, and the True-to-scale, a proportional model that more accurately represents the realistic scale relationships. Specifically, earlier exposure to the simplified model resulted in diminution of the conceptual gain from the subsequent realistic model, but the realistic model did not impede learning from the following simplified model.
Vogt, William C.; Jia, Congxian; Wear, Keith A.; Garra, Brian S.; Pfefer, T. Joshua
2017-03-01
Recent years have seen rapid development of hybrid optical-acoustic imaging modalities with broad applications in research and clinical imaging, including photoacoustic tomography (PAT), photoacoustic microscopy, and ultrasound-modulated optical tomography. Tissue-mimicking phantoms are an important tool for objectively and quantitatively simulating in vivo imaging system performance. However, no standard tissue phantoms exist for such systems. One major challenge is the development of tissue-mimicking materials (TMMs) that are both highly stable and possess biologically realistic properties. To address this need, we have explored the use of various formulations of PVC plastisol (PVCP) based on varying mixtures of several liquid plasticizers. We developed a custom PVCP formulation with optical absorption and scattering coefficients, speed of sound, and acoustic attenuation that are tunable and tissue-relevant. This TMM can simulate different tissue compositions and offers greater mechanical strength than hydrogels. Optical properties of PVCP samples with varying composition were characterized using integrating sphere spectrophotometry and the inverse adding-doubling method. Acoustic properties were determined using a broadband pulse-transmission technique. To demonstrate the utility of this bimodal TMM, we constructed an image quality phantom designed to enable quantitative evaluation of PAT spatial resolution. The phantom was imaged using a custom combined PAT-ultrasound imaging system. Results indicated that this more biologically realistic TMM produced performance trends not captured in simpler liquid phantoms. In the future, this TMM may be broadly utilized for performance evaluation of optical, acoustic, and hybrid optical-acoustic imaging systems.
On the geometric lattice approximation to a realistic model of QCD
International Nuclear Information System (INIS)
Becher, P.; Joos, H.
1982-12-01
We suggest a model of QCD with four flavour degrees of freedom on the lattice. This model has a well-defined continuum limit and no spurious quark degrees of freedom. The formulation is realistic insofar as the different quarks may have different bare masses. For Monte-Carlo calculations on finite lattices our suggestion should be superior to comparable other models. The model is formulated within the Dirac-Kaehler description of fermions which we repeat in a short glossary. (orig.)
Photocatalytic elimination of indoor air biological and chemical pollution in realistic conditions.
Sánchez, Benigno; Sánchez-Muñoz, Marta; Muñoz-Vicente, María; Cobas, Guillermo; Portela, Raquel; Suárez, Silvia; González, Aldo E; Rodríguez, Nuria; Amils, Ricardo
2012-05-01
The photocatalytic elimination of microorganisms from indoor air in realistic conditions and the feasibility of simultaneous elimination of chemical contaminants have been studied at laboratory scale. Transparent polymeric monoliths have been coated with sol-gel TiO(2) films and used as photocatalyst to treat real indoor air in a laboratory-scale single-step annular photocatalytic reactor. The analytical techniques used to characterize the air quality and analyze the results of the photocatalytic tests were: colony counting, microscopy and PCR with subsequent sequencing for microbial quantification and identification; automated thermal desorption coupled to gas chromatography with mass spectrometry detection for chemical analysis. The first experiments performed proved that photocatalysis based on UVA-irradiated TiO(2) for the reduction of the concentration of bacteria in the air could compete with the conventional photolytic treatment with UVC radiation, more expensive and hazardous. Simultaneously to the disinfection, the concentration of volatile organic compounds was greatly reduced, which adds value to this technology for real applications. The fungal colony number was not apparently modified. Copyright Â© 2012 Elsevier Ltd. All rights reserved.
Peters, J. M.; Kravtsov, S.
2011-12-01
This study quantifies the dependence of nonlinear regimes (manifested in non-gaussian probability distributions) and spreads of ensemble trajectories in a reduced phase space of a realistic three-layer quasi-geostrophic (QG3) atmospheric model on this model's climate state.To elucidate probabilistic properties of the QG3 trajectories, we compute, in phase planes of leading EOFs of the model, the coefficients of the corresponding Fokker-Planck (FP) equations. These coefficients represent drift vectors (computed from one-day phase space tendencies) and diffusion tensors (computed from one-day lagged covariance matrices of model trajectory displacements), and are based on a long QG3 simulation. We also fit two statistical trajectory models to the reduced phase-space time series spanned by the full QG3 model states. One reduced model is a standard Linear Inverse Model (LIM) fitted to a long QG3 time series. The LIM model is forced by state-independent (additive) noise and has a deterministic operator which represents non-divergent velocity field in the reduced phase space considered. The other, more advanced model (NSM), is nonlinear, divergent, and is driven by state-dependent noise. The NSM model mimics well the full QG3 model trajectory behavior in the reduced phase space; its corresponding FP model is nearly identical to that based on the full QG3 simulations. By systematic analysis of the differences between the drift vectors and diffusion tensors of the QG3-based, NSM-based, and LIM-based FP models, as well as the PDF evolution simulated by these FP models, we disentangle the contributions of the multiplicative noise and deterministic dynamics into nonlinear behavior and predictability of the atmospheric states produced by the dynamical QG3 model.
Ziegler, Erik; Chellappa, Sarah L; Gaggioni, Giulia; Ly, Julien Q M; Vandewalle, Gilles; André, Elodie; Geuzaine, Christophe; Phillips, Christophe
2014-12-01
We present a finite element modeling (FEM) implementation for solving the forward problem in electroencephalography (EEG). The solution is based on Helmholtz's principle of reciprocity which allows for dramatically reduced computational time when constructing the leadfield matrix. The approach was validated using a 4-shell spherical model and shown to perform comparably with two current state-of-the-art alternatives (OpenMEEG for boundary element modeling and SimBio for finite element modeling). We applied the method to real human brain MRI data and created a model with five tissue types: white matter, gray matter, cerebrospinal fluid, skull, and scalp. By calculating conductivity tensors from diffusion-weighted MR images, we also demonstrate one of the main benefits of FEM: the ability to include anisotropic conductivities within the head model. Root-mean square deviation between the standard leadfield and the leadfield including white-matter anisotropy showed that ignoring the directional conductivity of white matter fiber tracts leads to orientation-specific errors in the forward model. Realistic head models are necessary for precise source localization in individuals. Our approach is fast, accurate, open-source and freely available online. Copyright © 2014 Elsevier Inc. All rights reserved.
The impact of realistic age structure in simple models of tuberculosis transmission.
Brooks-Pollock, Ellen; Cohen, Ted; Murray, Megan
2010-01-07
Mathematical models of tuberculosis (TB) transmission have been used to characterize disease dynamics, investigate the potential effects of public health interventions, and prioritize control measures. While previous work has addressed the mathematical description of TB natural history, the impact of demography on the behaviour of TB models has not been assessed. A simple model of TB transmission, with alternative assumptions about survivorship, is used to explore the effect of age structure on the prevalence of infection, disease, basic reproductive ratio and the projected impact of control interventions. We focus our analytic arguments on the differences between constant and exponentially distributed lifespans and use an individual-based model to investigate the range of behaviour arising from realistic distributions of survivorship. The choice of age structure and natural (non-disease related) mortality strongly affects steady-state dynamics, parameter estimation and predictions about the effectiveness of control interventions. Since most individuals infected with TB develop an asymptomatic latent infection and never progress to active disease, we find that assuming a constant mortality rate results in a larger reproductive ratio and an overestimation of the effort required for disease control in comparison to using more realistic age-specific mortality rates. Demographic modelling assumptions should be considered in the interpretation of models of chronic infectious diseases such as TB. For simple models, we find that assuming constant lifetimes, rather than exponential lifetimes, produces dynamics more representative of models with realistic age structure.
Directory of Open Access Journals (Sweden)
Peng Wang
Full Text Available In this work we propose a biologically realistic local cortical circuit model (LCCM, based on neural masses, that incorporates important aspects of the functional organization of the brain that have not been covered by previous models: (1 activity dependent plasticity of excitatory synaptic couplings via depleting and recycling of neurotransmitters and (2 realistic inter-laminar dynamics via laminar-specific distribution of and connections between neural populations. The potential of the LCCM was demonstrated by accounting for the process of auditory habituation. The model parameters were specified using Bayesian inference. It was found that: (1 besides the major serial excitatory information pathway (layer 4 to layer 2/3 to layer 5/6, there exists a parallel "short-cut" pathway (layer 4 to layer 5/6, (2 the excitatory signal flow from the pyramidal cells to the inhibitory interneurons seems to be more intra-laminar while, in contrast, the inhibitory signal flow from inhibitory interneurons to the pyramidal cells seems to be both intra- and inter-laminar, and (3 the habituation rates of the connections are unsymmetrical: forward connections (from layer 4 to layer 2/3 are more strongly habituated than backward connections (from Layer 5/6 to layer 4. Our evaluation demonstrates that the novel features of the LCCM are of crucial importance for mechanistic explanations of brain function. The incorporation of these features into a mass model makes them applicable to modeling based on macroscopic data (like EEG or MEG, which are usually available in human experiments. Our LCCM is therefore a valuable building block for future realistic models of human cognitive function.
Realistic Gamow shell model for resonance and continuum in atomic nuclei
Xu, F. R.; Sun, Z. H.; Wu, Q.; Hu, B. S.; Dai, S. J.
2018-02-01
The Gamow shell model can describe resonance and continuum for atomic nuclei. The model is established in the complex-moment (complex-k) plane of the Berggren coordinates in which bound, resonant and continuum states are treated on equal footing self-consistently. In the present work, the realistic nuclear force, CD Bonn, has been used. We have developed the full \\hat{Q}-box folded-diagram method to derive the realistic effective interaction in the model space which is nondegenerate and contains resonance and continuum channels. The CD-Bonn potential is renormalized using the V low-k method. With choosing 16O as the inert core, we have applied the Gamow shell model to oxygen isotopes.
Rapid creation, Monte Carlo simulation, and visualization of realistic 3D cell models.
Czech, Jacob; Dittrich, Markus; Stiles, Joel R
2009-01-01
Spatially realistic diffusion-reaction simulations supplement traditional experiments and provide testable hypotheses for complex physiological systems. To date, however, the creation of realistic 3D cell models has been difficult and time-consuming, typically involving hand reconstruction from electron microscopic images. Here, we present a complementary approach that is much simpler and faster, because the cell architecture (geometry) is created directly in silico using 3D modeling software like that used for commercial film animations. We show how a freely available open source program (Blender) can be used to create the model geometry, which then can be read by our Monte Carlo simulation and visualization softwares (MCell and DReAMM, respectively). This new workflow allows rapid prototyping and development of realistic computational models, and thus should dramatically accelerate their use by a wide variety of computational and experimental investigators. Using two self-contained examples based on synaptic transmission, we illustrate the creation of 3D cellular geometry with Blender, addition of molecules, reactions, and other run-time conditions using MCell's Model Description Language (MDL), and subsequent MCell simulations and DReAMM visualizations. In the first example, we simulate calcium influx through voltage-gated channels localized on a presynaptic bouton, with subsequent intracellular calcium diffusion and binding to sites on synaptic vesicles. In the second example, we simulate neurotransmitter release from synaptic vesicles as they fuse with the presynaptic membrane, subsequent transmitter diffusion into the synaptic cleft, and binding to postsynaptic receptors on a dendritic spine.
Numerical Modeling of Plasmonic Nanoantennas with Realistic 3D Roughness and Distortion
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Vladimir P. Drachev
2011-07-01
Full Text Available Nanostructured plasmonic metamaterials, including optical nanoantenna arrays, are important for advanced optical sensing and imaging applications including surface-enhanced fluorescence, chemiluminescence, and Raman scattering. Although designs typically use ideally smooth geometries, realistic nanoantennas have nonzero roughness, which typically results in a modified enhancement factor that should be involved in their design. Herein we aim to treat roughness by introducing a realistic roughened geometry into the finite element (FE model. Even if the roughness does not result in significant loss, it does result in a spectral shift and inhomogeneous broadening of the resonance, which could be critical when fitting the FE simulations of plasmonic nanoantennas to experiments. Moreover, the proposed approach could be applied to any model, whether mechanical, acoustic, electromagnetic, thermal, etc, in order to simulate a given roughness-generated physical phenomenon.
Farquharson, C.; Long, J.; Lu, X.; Lelievre, P. G.
2017-12-01
makes the process of building a geophysical Earth model from a geological model much simpler. In this presentation we will explore the issues that arise when working with realistic Earth models and when synthesizing geophysical electromagnetic data for them. We briefly consider meshfree methods as a possible means of alleviating some of these issues.
International Nuclear Information System (INIS)
Ding Lei; Lai Yuan; He Bin
2005-01-01
It is of importance to localize neural sources from scalp recorded EEG. Low resolution brain electromagnetic tomography (LORETA) has received considerable attention for localizing brain electrical sources. However, most such efforts have used spherical head models in representing the head volume conductor. Investigation of the performance of LORETA in a realistic geometry head model, as compared with the spherical model, will provide useful information guiding interpretation of data obtained by using the spherical head model. The performance of LORETA was evaluated by means of computer simulations. The boundary element method was used to solve the forward problem. A three-shell realistic geometry (RG) head model was constructed from MRI scans of a human subject. Dipole source configurations of a single dipole located at different regions of the brain with varying depth were used to assess the performance of LORETA in different regions of the brain. A three-sphere head model was also used to approximate the RG head model, and similar simulations performed, and results compared with the RG-LORETA with reference to the locations of the simulated sources. Multi-source localizations were discussed and examples given in the RG head model. Localization errors employing the spherical LORETA, with reference to the source locations within the realistic geometry head, were about 20-30 mm, for four brain regions evaluated: frontal, parietal, temporal and occipital regions. Localization errors employing the RG head model were about 10 mm over the same four brain regions. The present simulation results suggest that the use of the RG head model reduces the localization error of LORETA, and that the RG head model based LORETA is desirable if high localization accuracy is needed
Validation of systems biology models
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
Directory of Open Access Journals (Sweden)
Gidrol Xavier
2008-02-01
Full Text Available Abstract Background Inferring gene regulatory networks from data requires the development of algorithms devoted to structure extraction. When only static data are available, gene interactions may be modelled by a Bayesian Network (BN that represents the presence of direct interactions from regulators to regulees by conditional probability distributions. We used enhanced evolutionary algorithms to stochastically evolve a set of candidate BN structures and found the model that best fits data without prior knowledge. Results We proposed various evolutionary strategies suitable for the task and tested our choices using simulated data drawn from a given bio-realistic network of 35 nodes, the so-called insulin network, which has been used in the literature for benchmarking. We assessed the inferred models against this reference to obtain statistical performance results. We then compared performances of evolutionary algorithms using two kinds of recombination operators that operate at different scales in the graphs. We introduced a niching strategy that reinforces diversity through the population and avoided trapping of the algorithm in one local minimum in the early steps of learning. We show the limited effect of the mutation operator when niching is applied. Finally, we compared our best evolutionary approach with various well known learning algorithms (MCMC, K2, greedy search, TPDA, MMHC devoted to BN structure learning. Conclusion We studied the behaviour of an evolutionary approach enhanced by niching for the learning of gene regulatory networks with BN. We show that this approach outperforms classical structure learning methods in elucidating the original model. These results were obtained for the learning of a bio-realistic network and, more importantly, on various small datasets. This is a suitable approach for learning transcriptional regulatory networks from real datasets without prior knowledge.
Data processing path from multimodal 3D measurement to realistic virtual model
Sitnik, Robert; Krzeslowski, Jakub; Mączkowski, Grzegorz
2011-03-01
A set of calculation methods has been developed and tested to provide means of creating virtual copies of three dimensional (3D) historical objects with minimal user input. We present a step by step data processing path along with algorithm description required to reconstruct a realistic 3D model of a culturally significant object. The important feature for archiving historical objects is the ability to include both information about its shape and texture, allowing visualization using arbitrary conditions of illumination. Data samples used as input for the processing method chain were collected using an integrated device consisting of shape, multispectral color and simplified BRDF measurements. To confirm the usability of presented methods, it has been tested by example of real life object - statue of an ancient Greek goddess Kybele. Additional visualization methods have also been examined to render a realistic virtual representation satisfying intrinsic surface properties of the investigated specimen.
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...
Characterization of photomultiplier tubes with a realistic model through GPU-boosted simulation
Anthony, M.; Aprile, E.; Grandi, L.; Lin, Q.; Saldanha, R.
2018-02-01
The accurate characterization of a photomultiplier tube (PMT) is crucial in a wide-variety of applications. However, current methods do not give fully accurate representations of the response of a PMT, especially at very low light levels. In this work, we present a new and more realistic model of the response of a PMT, called the cascade model, and use it to characterize two different PMTs at various voltages and light levels. The cascade model is shown to outperform the more common Gaussian model in almost all circumstances and to agree well with a newly introduced model independent approach. The technical and computational challenges of this model are also presented along with the employed solution of developing a robust GPU-based analysis framework for this and other non-analytical models.
Numerical Simulation of Air Flow in Realistic Model of Human Upper Airways
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Jakub ELCNER
2010-12-01
Full Text Available This article deals with CFD calculations of flow patterns in a realistic model of the upper respiratory tract. RANS method was used for the calculation. The flow was solved as an unsteady one due to its nature. Two breathing cycles were simulated, 15 l/min which corresponds to the idle breathing mode and 30 l/min which corresponds to light activity. The model of upper airways consists of the oral cavity, larynx and trachea, which branches up to the fourth generation. Values of the velocity field distribution calculated are the basis for future calculations of aerosol transport and deposition in the human respiratory tract.
Model-based Evaluation of Location-based Relaying Policies in a Realistic Mobile Indoor Scenario
DEFF Research Database (Denmark)
Nielsen, Jimmy Jessen; Olsen, Rasmus Løvenstein; Madsen, Tatiana Kozlova
2012-01-01
For WLAN systems in which relaying is exploited for improving throughput performance, node mobility and in- formation collection delays can have a significant impact on the performance of a relay selection scheme. This paper analyzes this influence on the decision process using a previously...... developed Markov Chain model for a realistic indoor scenario that is based on ray-tracing enriched measurements from the WHERE2 project. These results are furthermore compared to results obtained using an idealistic path loss model, and it is shown that the performance impact of node mobility...
Realistic modeling of seismic input for megacities and large urban areas
International Nuclear Information System (INIS)
Panza, Giuliano F.; Alvarez, Leonardo; Aoudia, Abdelkrim
2002-06-01
The project addressed the problem of pre-disaster orientation: hazard prediction, risk assessment, and hazard mapping, in connection with seismic activity and man-induced vibrations. The definition of realistic seismic input has been obtained from the computation of a wide set of time histories and spectral information, corresponding to possible seismotectonic scenarios for different source and structural models. The innovative modeling technique, that constitutes the common tool to the entire project, takes into account source, propagation and local site effects. This is done using first principles of physics about wave generation and propagation in complex media, and does not require to resort to convolutive approaches, that have been proven to be quite unreliable, mainly when dealing with complex geological structures, the most interesting from the practical point of view. In fact, several techniques that have been proposed to empirically estimate the site effects using observations convolved with theoretically computed signals corresponding to simplified models, supply reliable information about the site response to non-interfering seismic phases. They are not adequate in most of the real cases, when the seismic sequel is formed by several interfering waves. The availability of realistic numerical simulations enables us to reliably estimate the amplification effects even in complex geological structures, exploiting the available geotechnical, lithological, geophysical parameters, topography of the medium, tectonic, historical, palaeoseismological data, and seismotectonic models. The realistic modeling of the ground motion is a very important base of knowledge for the preparation of groundshaking scenarios that represent a valid and economic tool for the seismic microzonation. This knowledge can be very fruitfully used by civil engineers in the design of new seismo-resistant constructions and in the reinforcement of the existing built environment, and, therefore
Batmunkh, Munkhbaatar; Bugay, Alexander; Bayarchimeg, Lkhagvaa; Lkhagva, Oidov
2018-02-01
The present study is focused on the development of optimal models of neuron morphology for Monte Carlo microdosimetry simulations of initial radiation-induced events of heavy charged particles in the specific types of cells of the hippocampus, which is the most radiation-sensitive structure of the central nervous system. The neuron geometry and particles track structures were simulated by the Geant4/Geant4-DNA Monte Carlo toolkits. The calculations were made for beams of protons and heavy ions with different energies and doses corresponding to real fluxes of galactic cosmic rays. A simple compartmental model and a complex model with realistic morphology extracted from experimental data were constructed and compared. We estimated the distribution of the energy deposition events and the production of reactive chemical species within the developed models of CA3/CA1 pyramidal neurons and DG granule cells of the rat hippocampus under exposure to different particles with the same dose. Similar distributions of the energy deposition events and concentration of some oxidative radical species were obtained in both the simplified and realistic neuron models.
The ultimate signal-to-noise ratio in realistic body models.
Guérin, Bastien; Villena, Jorge F; Polimeridis, Athanasios G; Adalsteinsson, Elfar; Daniel, Luca; White, Jacob K; Wald, Lawrence L
2017-11-01
We compute the ultimate signal-to-noise ratio (uSNR) and G-factor (uGF) in a realistic head model from 0.5 to 21 Tesla. We excite the head model and a uniform sphere with a large number of electric and magnetic dipoles placed at 3 cm from the object. The resulting electromagnetic fields are computed using an ultrafast volume integral solver, which are used as basis functions for the uSNR and uGF computations. Our generalized uSNR calculation shows good convergence in the sphere and the head and is in close agreement with the dyadic Green's function approach in the uniform sphere. In both models, the uSNR versus B 0 trend was linear at shallow depths and supralinear at deeper locations. At equivalent positions, the rate of increase of the uSNR with B 0 was greater in the sphere than in the head model. The uGFs were lower in the realistic head than in the sphere for acceleration in the anterior-posterior direction, but similar for the left-right direction. The uSNR and uGFs are computable in nonuniform body models and provide fundamental performance limits for human imaging with close-fitting MRI array coils. Magn Reson Med 78:1969-1980, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.
Directory of Open Access Journals (Sweden)
Sorinel A. Oprisan
2011-09-01
Full Text Available In most species, the capability of perceiving and using the passage of time in the seconds-to-minutes range (interval timing is not only accurate but also scalar: errors in time estimation are linearly related to the estimated duration. The ubiquity of scalar timing extends over behavioral, lesion, and pharmacological manipulations. For example, in mammals, dopaminergic drugs induce an immediate, scalar change in the perceived time (clock pattern, whereas cholinergic drugs induce a gradual, scalar change in perceived time (memory pattern. How do these properties emerge from unreliable, noisy neurons firing in the milliseconds range? Neurobiological information relative to the brain circuits involved in interval timing provide support for an Striatal Beat Frequency (SBF model, in which time is coded by the coincidental activation of striatal spiny neurons by cortical neural oscillators. While biologically plausible, the impracticality of perfect oscillators, or their lack thereof, questions this mechanism in a brain with noisy neurons. We explored the computational mechanisms required for the clock and memory patterns in an SBF model with biophysically realistic and noisy Morris-Lecar neurons (SBF-ML. Under the assumption that dopaminergic drugs modulate the firing frequency of cortical oscillators, and that cholinergic drugs modulate the memory representation of the criterion time, we show that our SBF-ML model can reproduce the pharmacological clock and memory patterns observed in the literature. Numerical results also indicate that parameter variability (noise – which is ubiquitous in the form of small fluctuations in the intrinsic frequencies of neural oscillators within and between trails, and in the errors in recording/retrieving stored information related to criterion time – seems to be critical for the time-scale invariance of the clock and memory patterns.
Magnetic reconnection in the low solar chromosphere with a more realistic radiative cooling model
Ni, Lei; Lukin, Vyacheslav S.; Murphy, Nicholas A.; Lin, Jun
2018-04-01
Magnetic reconnection is the most likely mechanism responsible for the high temperature events that are observed in strongly magnetized locations around the temperature minimum in the low solar chromosphere. This work improves upon our previous work [Ni et al., Astrophys. J. 852, 95 (2018)] by using a more realistic radiative cooling model computed from the OPACITY project and the CHIANTI database. We find that the rate of ionization of the neutral component of the plasma is still faster than recombination within the current sheet region. For low β plasmas, the ionized and neutral fluid flows are well-coupled throughout the reconnection region resembling the single-fluid Sweet-Parker model dynamics. Decoupling of the ion and neutral inflows appears in the higher β case with β0=1.46 , which leads to a reconnection rate about three times faster than the rate predicted by the Sweet-Parker model. In all cases, the plasma temperature increases with time inside the current sheet, and the maximum value is above 2 ×104 K when the reconnection magnetic field strength is greater than 500 G. While the more realistic radiative cooling model does not result in qualitative changes of the characteristics of magnetic reconnection, it is necessary for studying the variations of the plasma temperature and ionization fraction inside current sheets in strongly magnetized regions of the low solar atmosphere. It is also important for studying energy conversion during the magnetic reconnection process when the hydrogen-dominated plasma approaches full ionization.
3D realistic head model simulation based on transcranial magnetic stimulation.
Yang, Shuo; Xu, Guizhi; Wang, Lei; Chen, Yong; Wu, Huanli; Li, Ying; Yang, Qingxin
2006-01-01
Transcranial magnetic stimulation (TMS) is a powerful non-invasive tool for investigating functions in the brain. The target inside the head is stimulated with eddy currents induced in the tissue by the time-varying magnetic field. Precise spatial localization of stimulation sites is the key of efficient functional magnetic stimulations. Many researchers devote to magnetic field analysis in empty free space. In this paper, a realistic head model used in Finite Element Method has been developed. The magnetic field inducted in the head bt TMS has been analysed. This three-dimensional simulation is useful for spatial localization of stimulation.
Hoshi, Koki; Irisawa, Atsushi; Shibukawa, Goro; Yamabe, Akane; Fujisawa, Mariko; Igarashi, Ryo; Yoshida, Yoshitsugu; Abe, Yoko; Imbe, Koh
2016-09-01
Trainees are required to learn EUS-FNA using a model before working with a patient. The aim of the current study was to validate a new training model developed for EUS-FNA. Several fresh chicken tenderloins were embedded as target lesions in the submucosal layer of an isolated porcine stomach. The stomach was fixed to a plate with nails, and was placed in a tub filled with water. The primary endpoint was feasibility of the newly developed model for EUS-FNA training, evaluated as follows: 1) visualization of the target lesion with blinding for lesion location; 2) penetrability of the needle; 3) sampling rate of macroscopic specimen; and 4) ROSE capability. Secondary endpoints were its durability and utility for multiple EUS-FNA procedures during EUS-FNA training, and the ease and cost of preparing the model. Six endoscopists (1 expert, 5 trainees) attempted EUS-FNA procedures using this model. The target lesion could be identified clearly, and EUS-FNA could be performed with realistic resistance felt. In addition, rapid on-site evaluation could be easily achieved. Based on 10 needlings by each endoscopist, adequate specimens for histology could be macroscopically taken with an average 85 % success rate. Visibility and maneuverability were maintained throughout all needlings. Preparation time for this model was less than 30 minutes with a total cost of $ 22. An easy-to-use and inexpensive training model with a realistic feel of needling was created. This model can potentially enable beginners to practice safe and effective EUS-FNA procedures.
Mathematical modeling of biological processes
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.
Realistic modelling of the seismic input: Site effects and parametric studies
International Nuclear Information System (INIS)
Romanelli, F.; Vaccari, F.; Panza, G.F.
2002-11-01
We illustrate the work done in the framework of a large international cooperation, showing the very recent numerical experiments carried out within the framework of the EC project 'Advanced methods for assessing the seismic vulnerability of existing motorway bridges' (VAB) to assess the importance of non-synchronous seismic excitation of long structures. The definition of the seismic input at the Warth bridge site, i.e. the determination of the seismic ground motion due to an earthquake with a given magnitude and epicentral distance from the site, has been done following a theoretical approach. In order to perform an accurate and realistic estimate of site effects and of differential motion it is necessary to make a parametric study that takes into account the complex combination of the source and propagation parameters, in realistic geological structures. The computation of a wide set of time histories and spectral information, corresponding to possible seismotectonic scenarios for different sources and structural models, allows us the construction of damage scenarios that are out of the reach of stochastic models, at a very low cost/benefit ratio. (author)
A Local-Realistic Model of Quantum Mechanics Based on a Discrete Spacetime
Sciarretta, Antonio
2018-01-01
This paper presents a realistic, stochastic, and local model that reproduces nonrelativistic quantum mechanics (QM) results without using its mathematical formulation. The proposed model only uses integer-valued quantities and operations on probabilities, in particular assuming a discrete spacetime under the form of a Euclidean lattice. Individual (spinless) particle trajectories are described as random walks. Transition probabilities are simple functions of a few quantities that are either randomly associated to the particles during their preparation, or stored in the lattice nodes they visit during the walk. QM predictions are retrieved as probability distributions of similarly-prepared ensembles of particles. The scenarios considered to assess the model comprise of free particle, constant external force, harmonic oscillator, particle in a box, the Delta potential, particle on a ring, particle on a sphere and include quantization of energy levels and angular momentum, as well as momentum entanglement.
REALISTIC NON-LINEAR MODEL AND FIELD QUALITY ANALYSIS IN RHIC INTERACTION REGIONS.
Energy Technology Data Exchange (ETDEWEB)
BEEBE-WANG,J.; JAIN, A.
2007-06-25
The existence of multipole components in the dipole and quadrupole magnets is one of the factors limiting the beam stability in the RHIC operations. So, a realistic non-linear model is crucial for understanding the beam behavior and to achieve the ultimate performance in RHIC. A procedure is developed to build a non-linear model using the available multipole component data obtained from measurements of RHIC magnets. We first discuss the measurements performed at different stages of manufacturing of the magnets in relation to their current state in RHIC. We then describe the procedure to implement these measurement data into tracking models, including the implementation of the multipole feed down effect due to the beam orbit offset from the magnet center. Finally, the field quality analysis in the RHIC interaction regions (IR) is presented.
XCAT/DRASIM: a realistic CT/human-model simulation package
Fung, George S. K.; Stierstorfer, Karl; Segars, W. Paul; Taguchi, Katsuyuki; Flohr, Thomas G.; Tsui, Benjamin M. W.
2011-03-01
The aim of this research is to develop a complete CT/human-model simulation package by integrating the 4D eXtended CArdiac-Torso (XCAT) phantom, a computer generated NURBS surface based phantom that provides a realistic model of human anatomy and respiratory and cardiac motions, and the DRASIM (Siemens Healthcare) CT-data simulation program. Unlike other CT simulation tools which are based on simple mathematical primitives or voxelized phantoms, this new simulation package has the advantages of utilizing a realistic model of human anatomy and physiological motions without voxelization and with accurate modeling of the characteristics of clinical Siemens CT systems. First, we incorporated the 4D XCAT anatomy and motion models into DRASIM by implementing a new library which consists of functions to read-in the NURBS surfaces of anatomical objects and their overlapping order and material properties in the XCAT phantom. Second, we incorporated an efficient ray-tracing algorithm for line integral calculation in DRASIM by computing the intersection points of the rays cast from the x-ray source to the detector elements through the NURBS surfaces of the multiple XCAT anatomical objects along the ray paths. Third, we evaluated the integrated simulation package by performing a number of sample simulations of multiple x-ray projections from different views followed by image reconstruction. The initial simulation results were found to be promising by qualitative evaluation. In conclusion, we have developed a unique CT/human-model simulation package which has great potential as a tool in the design and optimization of CT scanners, and the development of scanning protocols and image reconstruction methods for improving CT image quality and reducing radiation dose.
Kornelsen, Jude; McCartney, Kevin; Williams, Kim
2016-01-01
This article was developed as part of a larger realist review investigating the viability and efficacy of decentralized models of perinatal surgical services for rural women in the context of recent and ongoing service centralization witnessed in many developed nations. The larger realist review was commissioned by the British Columbia Ministry of Health and Perinatal Services of British Columbia, Canada. Findings from that review are addressed in this article specific to the sustainability of rural perinatal surgical sites and the satisfaction of providers that underpins their recruitment to and retention at such sites. A realist method was used in the selection and analysis of literature with the intention to iteratively develop a sophisticated understanding of how perinatal surgical services can best meet the needs of women who live in rural and remote environments. The goal of a realist review is to examine what works for whom under what circumstances and why. The high sensitivity search used language (English) and year (since 1990) limiters in keeping with both a realist and rapid review tradition of using reasoned contextual boundaries. No exclusions were made based on methodology or methodological approach in keeping with a realist review. Databases searched included MEDLINE, PubMed, EBSCO, CINAHL, EBM Reviews, NHS Economic Evaluation Database and PAIS International for literature in December 2013. Database searching produced 103 included academic articles. A further 59 resources were added through pearling and 13 grey literature reports were added on recommendation from the commissioner. A total of 42 of these 175 articles were included in this article as specific to provider satisfaction and service sustainability. Operative perinatal practice was found to be a lynchpin of sustainable primary and surgical services in rural communities. Rural shortages of providers, including challenges with recruitment and retention, were found to be a complex issue, with
Robust mode space approach for atomistic modeling of realistically large nanowire transistors
Huang, Jun Z.; Ilatikhameneh, Hesameddin; Povolotskyi, Michael; Klimeck, Gerhard
2018-01-01
Nanoelectronic transistors have reached 3D length scales in which the number of atoms is countable. Truly atomistic device representations are needed to capture the essential functionalities of the devices. Atomistic quantum transport simulations of realistically extended devices are, however, computationally very demanding. The widely used mode space (MS) approach can significantly reduce the numerical cost, but a good MS basis is usually very hard to obtain for atomistic full-band models. In this work, a robust and parallel algorithm is developed to optimize the MS basis for atomistic nanowires. This enables engineering-level, reliable tight binding non-equilibrium Green's function simulation of nanowire metal-oxide-semiconductor field-effect transistor (MOSFET) with a realistic cross section of 10 nm × 10 nm using a small computer cluster. This approach is applied to compare the performance of InGaAs and Si nanowire n-type MOSFETs (nMOSFETs) with various channel lengths and cross sections. Simulation results with full-band accuracy indicate that InGaAs nanowire nMOSFETs have no drive current advantage over their Si counterparts for cross sections up to about 10 nm × 10 nm.
Kim, Yong-Cheol; Fox, Peter A.; Sofia, Sabatino; Demarque, Pierre
1995-01-01
In an attempt to understand the properties of convective energy transport in the solar convective zone, a numerical model has been constructed for turbulent flows in a compressible, radiation-coupled, nonmagnetic, gravitationally stratified medium using a realistic equation of state and realistic opacities. The time-dependent, three-dimensional hydrodynamic equations are solved with minimal simplifications. The statistical information obtained from the present simulation provides an improved undserstanding of solar photospheric convection. The characteristics of solar convection in shallow regions is parameterized and compared with the results of Chan & Sofia's (1989) simulations of deep and efficient convection. We assess the importance of the zones of partial ionization in the simulation and confirm that the radiative energy transfer is negliglble throughout the region except in the uppermost scale heights of the convection zone, a region of very high superadiabaticity. When the effects of partial ionization are included, the dynamics of flows are altered significantly. However, we confirm the Chan & Sofia result that kinetic energy flux is nonnegligible and can have a negative value in the convection zone.
The non-unitary model operator approach with realistic potentials and its application to 4He
International Nuclear Information System (INIS)
Panos, C.P.
1986-01-01
The non-unitary model operator approach, which has been previously used for calculating the binding energy of closed shell nuclei for central potentials, is formulated in a way suitable to realistic potentials, such as the Hamada-Johnston and the Reid soft-core ones. The factor-cluster expansion, truncated at the two-body terms, together with a 'healing condition' is used. The Euler-Lagrange equations which result from the application of the variational principle are integrodifferential and two kinds of coupling appear: one because of the tensor potential and one because of the non-unitary model operator. By solving these equations numerically for 4 He, the binding energy of this nucleus is obtained for various values of the harmonic oscillator parameter and saturation is observed. (author)
Cellular potts models multiscale extensions and biological applications
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...
Model of a realistic InP surface quantum dot extrapolated from atomic force microscopy results
Barettin, Daniele; De Angelis, Roberta; Prosposito, Paolo; Auf der Maur, Matthias; Casalboni, Mauro; Pecchia, Alessandro
2014-05-01
We report on numerical simulations of a zincblende InP surface quantum dot (QD) on \\text{I}{{\\text{n}}_{0.48}}\\text{G}{{\\text{a}}_{0.52}}\\text{P} buffer. Our model is strictly based on experimental structures, since we extrapolated a three-dimensional dot directly by atomic force microscopy results. Continuum electromechanical, \\vec{k}\\;\\cdot \\;\\vec{p} bandstructure and optical calculations are presented for this realistic structure, together with benchmark calculations for a lens-shape QD with the same radius and height of the extrapolated dot. Interesting similarities and differences are shown by comparing the results obtained with the two different structures, leading to the conclusion that the use of a more realistic structure can provide significant improvements in the modeling of QDs fact, the remarkable splitting for the electron p-like levels of the extrapolated dot seems to prove that a realistic experimental structure can reproduce the right symmetry and a correct splitting usually given by atomistic calculations even within the multiband \\vec{k}\\;\\cdot \\;\\vec{p} approach. Moreover, the energy levels and the symmetry of the holes are strongly dependent on the shape of the dot. In particular, as far as we know, their wave function symmetries do not seem to resemble to any results previously obtained with simulations of zincblende ideal structures, such as lenses or truncated pyramids. The magnitude of the oscillator strengths is also strongly dependent on the shape of the dot, showing a lower intensity for the extrapolated dot, especially for the transition between the electrons and holes ground state, as a result of a relevant reduction of the wave functions overlap. We also compare an experimental photoluminescence spectrum measured on an homogeneous sample containing about 60 dots with a numerical ensemble average derived from single dot calculations. The broader energy range of the numerical spectrum motivated us to perform further
Model of a realistic InP surface quantum dot extrapolated from atomic force microscopy results.
Barettin, Daniele; De Angelis, Roberta; Prosposito, Paolo; Auf der Maur, Matthias; Casalboni, Mauro; Pecchia, Alessandro
2014-05-16
We report on numerical simulations of a zincblende InP surface quantum dot (QD) on In₀.₄₈Ga₀.₅₂ buffer. Our model is strictly based on experimental structures, since we extrapolated a three-dimensional dot directly by atomic force microscopy results. Continuum electromechanical, [Formula: see text] bandstructure and optical calculations are presented for this realistic structure, together with benchmark calculations for a lens-shape QD with the same radius and height of the extrapolated dot. Interesting similarities and differences are shown by comparing the results obtained with the two different structures, leading to the conclusion that the use of a more realistic structure can provide significant improvements in the modeling of QDs fact, the remarkable splitting for the electron p-like levels of the extrapolated dot seems to prove that a realistic experimental structure can reproduce the right symmetry and a correct splitting usually given by atomistic calculations even within the multiband [Formula: see text] approach. Moreover, the energy levels and the symmetry of the holes are strongly dependent on the shape of the dot. In particular, as far as we know, their wave function symmetries do not seem to resemble to any results previously obtained with simulations of zincblende ideal structures, such as lenses or truncated pyramids. The magnitude of the oscillator strengths is also strongly dependent on the shape of the dot, showing a lower intensity for the extrapolated dot, especially for the transition between the electrons and holes ground state, as a result of a relevant reduction of the wave functions overlap. We also compare an experimental photoluminescence spectrum measured on an homogeneous sample containing about 60 dots with a numerical ensemble average derived from single dot calculations. The broader energy range of the numerical spectrum motivated us to perform further verifications, which have clarified some aspects of the experimental
Realistic Modeling of Fast MHD Wave Trains in Coronal Active Regions
Ofman, Leon; Sun, Xudong
2017-08-01
Motivated by recent SDO/AIA observations we have developed realistic modeling of quasi-periodic, fast-mode propagating MHD wave trains (QFPs) using 3D MHD model initiated with potential magnetic field extrapolated from the solar coronal boundary. Localized quasi-periodic pulsations associated with C-class flares that drive the waves (as deduced from observations) are modeled with transverse periodic displacement of magnetic field at the lower coronal boundary. The modeled propagating speed and the form of the wave expansions matches the observed fast MHD waves speed >1000 km/s and topology. We study the parametric dependence of the amplitude, propagation, and damping of the waves for a range of key model parameters, such as the background temperature, density, and the location of the flaring site within the active region. We investigate the interaction of multiple QFP wave trains excited by adjacent flaring sources. We use the model results to synthesize EUV intensities in multiple AIA channels and obtain the model parameters that best reproduce the properties of observed QFPs, such as the recent DEM analysis. We discuss the implications of our modeling results for the seismological application of QFPs for the diagnostic of the active region field, flare pulsations, end estimate the energy flux carried by the waves.
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...
Law, Yuen C.; Tenbrinck, Daniel; Jiang, Xiaoyi; Kuhlen, Torsten
2014-03-01
Computer-assisted processing and interpretation of medical ultrasound images is one of the most challenging tasks within image analysis. Physical phenomena in ultrasonographic images, e.g., the characteristic speckle noise and shadowing effects, make the majority of standard methods from image analysis non optimal. Furthermore, validation of adapted computer vision methods proves to be difficult due to missing ground truth information. There is no widely accepted software phantom in the community and existing software phantoms are not exible enough to support the use of specific speckle models for different tissue types, e.g., muscle and fat tissue. In this work we propose an anatomical software phantom with a realistic speckle pattern simulation to _ll this gap and provide a exible tool for validation purposes in medical ultrasound image analysis. We discuss the generation of speckle patterns and perform statistical analysis of the simulated textures to obtain quantitative measures of the realism and accuracy regarding the resulting textures.
Dobslaw, Henryk; Forootan, Ehsan; Bergmann-Wolf, Inga; Neumayer, Karl-Hans; Mayer-Gürr, Torsten; Kusche, Jürgen; Flechtner, Frank
2015-04-01
Recently completed performance studies of future gravity mission concepts arrived at sometimes contradicting conclusions about the importance of non-tidal aliasing errors that remain in the finally retrieved gravity field time-series. In those studies, typically a fraction of the differences between two different models of atmosphere and ocean mass variability determined the magnitude of the aliasing errors. Since differences among arbitrary pairs of the numerical models available might lead to widely different aliasing errors and thus conclusions regarding limiting error contributors of a candidate mission, we present here for the first time a version of a realistically perturbed de-aliasing model that is consistent with the updated ESA Earth System Model for gravity mission simulation studies (Dobslaw et al., 2015). The error model is available over the whole 12-year period of the ESA ESM and consists of two parts: (i) a component containing signals from physical processes that are intentionally omitted from de-aliasing models, as for a example, variations in global eustatic sea-level; and (ii) a series of true errors that consist of in total five different components with realistically re-scaled variability at both small and large spatial scales for different frequency bands ranging from sub-daily to sub-monthly periods. Based on a multi-model ensemble of atmosphere and ocean mass variability available to us for the year 2006, we will demonstrate that our re-scaled true errors have plausible magnitudes and correlation characteristics in all frequency bands considered. The realism of the selected scaling coefficients for periods between 1 and 30 days is tested further by means of a variance component estimation based on the constrained daily GRACE solution series ITSG-GRACE2014. Initial full-scale simulation experiments are used to re-assess the relative importance of non-tidal de-aliasing errors for the GRACE-FO mission, which might be subsequently expanded to
Calculation of electrical potentials on the surface of a realistic head model by finite differences
International Nuclear Information System (INIS)
Lemieux, L.; McBride, A.; Hand, J.W.
1996-01-01
We present a method for the calculation of electrical potentials at the surface of realistic head models from a point dipole generator based on a 3D finite-difference algorithm. The model was validated by comparing calculated values with those obtained algebraically for a three-shell spherical model. For a 1.25 mm cubic grid size, the mean error was 4.9% for a superficial dipole (3.75 mm from the inner surface of the skull) pointing in the radial direction. The effect of generator discretization and node spacing on the accuracy of the model was studied. Three values of the node spacing were considered: 1, 1.25 and 1.5 mm. The mean relative errors were 4.2, 6.3 and 9.3%, respectively. The quality of the approximation of a point dipole by an array of nodes in a spherical neighbourhood did not depend significantly on the number of nodes used. The application of the method to a conduction model derived from MRI data is demonstrated. (author)
Directory of Open Access Journals (Sweden)
Woo Chul Jeong
2015-08-01
Full Text Available Electromagnetic fields provide fundamental data for the imaging of electrical tissue properties, such as conductivity and permittivity, in recent magnetic resonance (MR-based tissue property mapping. The induced voltage, current density, and magnetic flux density caused by externally injected current are critical factors for determining the image quality of electrical tissue conductivity. As a useful tool to identify bio-electromagnetic phenomena, precise approaches are required to understand the exact responses inside the human body subject to an injected currents. In this study, we provide the numerical simulation results of electromagnetic field mapping of brain tissues using a MR-based conductivity imaging method. First, we implemented a realistic three-dimensional human anisotropic head model using high-resolution anatomical and diffusion tensor MR images. The voltage, current density, and magnetic flux density of brain tissues were imaged by injecting 1 mA of current through pairs of electrodes on the surface of our head model. The current density map of anisotropic brain tissues was calculated from the measured magnetic flux density based on the linear relationship between the water diffusion tensor and the electrical conductivity tensor. Comparing the current density to the previous isotropic model, the anisotropic model clearly showed the differences between the brain tissues. This originates from the enhanced signals by the inherent conductivity contrast as well as the actual tissue condition resulting from the injected currents.
Compositional Modeling of Biological Systems
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 ...
Implications of introducing realistic fire response traits in a Dynamic Global Vegetation Model
Kelley, D.; Harrison, S. P.; Prentice, I. C.
2013-12-01
Bark thickness is a key trait protecting woody plants against fire damage, while the ability to resprout is a trait that confers competitive advantage over non-resprouting individuals in fire-prone landscapes. Neither trait is well represented in fire-enabled dynamic global vegetation models (DGVMs). Here we describe a version of the Land Processes and eXchanges (LPX-Mv1) DGVM that incorporates both of these traits in a realistic way. From a synthesis of a large number of field studies, we show there is considerable innate variability in bark thickness between species within a plant-functional type (PFT). Furthermore, bark thickness is an adaptive trait at ecosystem level, increasing with fire frequency. We use the data to specify the range of bark thicknesses characteristic of each model PFT. We allow this distribution to change dynamically: thinner-barked trees are killed preferentially by fire, shifting the distribution of bark thicknesses represented in a model grid cell. We use the PFT-specific bark-thickness probability range for saplings during re-establishment. Since it is rare to destroy all trees in a grid cell, this treatment results in average bark thickness increasing with fire frequency and intensity. Resprouting is a prominent adaptation of temperate and tropical trees in fire-prone areas. The ability to resprout from above-ground tissue (apical or epicormic resprouting) results in the fastest recovery of total biomass after disturbance; resprouting from basal or below-ground meristems results in slower recovery, while non-resprouting species must regenerate from seed and therefore take the longest time to recover. Our analyses show that resprouting species have thicker bark than non-resprouting species. Investment in resprouting is accompanied by reduced efficacy of regeneration from seed. We introduce resprouting PFTs in LPX-Mv1 by specifying an appropriate range of bark thickness, allowing resprouters to survive fire and regenerate vegetatively in
Smart-DS: Synthetic Models for Advanced, Realistic Testing: Distribution Systems and Scenarios
Energy Technology Data Exchange (ETDEWEB)
Krishnan, Venkat K [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Palmintier, Bryan S [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Hodge, Brian S [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Hale, Elaine T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Elgindy, Tarek [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Bugbee, Bruce [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Rossol, Michael N [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Lopez, Anthony J [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Krishnamurthy, Dheepak [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Vergara, Claudio [MIT; Domingo, Carlos Mateo [IIT Comillas; Postigo, Fernando [IIT Comillas; de Cuadra, Fernando [IIT Comillas; Gomez, Tomas [IIT Comillas; Duenas, Pablo [MIT; Luke, Max [MIT; Li, Vivian [MIT; Vinoth, Mohan [GE Grid Solutions; Kadankodu, Sree [GE Grid Solutions
2017-08-09
The National Renewable Energy Laboratory (NREL) in collaboration with Massachusetts Institute of Technology (MIT), Universidad Pontificia Comillas (Comillas-IIT, Spain) and GE Grid Solutions, is working on an ARPA-E GRID DATA project, titled Smart-DS, to create: 1) High-quality, realistic, synthetic distribution network models, and 2) Advanced tools for automated scenario generation based on high-resolution weather data and generation growth projections. Through these advancements, the Smart-DS project is envisioned to accelerate the development, testing, and adoption of advanced algorithms, approaches, and technologies for sustainable and resilient electric power systems, especially in the realm of U.S. distribution systems. This talk will present the goals and overall approach of the Smart-DS project, including the process of creating the synthetic distribution datasets using reference network model (RNM) and the comprehensive validation process to ensure network realism, feasibility, and applicability to advanced use cases. The talk will provide demonstrations of early versions of synthetic models, along with the lessons learnt from expert engagements to enhance future iterations. Finally, the scenario generation framework, its development plans, and co-ordination with GRID DATA repository teams to house these datasets for public access will also be discussed.
Explicit all-atom modeling of realistically sized ligand-capped nanocrystals
Kaushik, Ananth P.
2012-01-01
We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes. © 2012 American Institute of Physics.
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...
Jain, Vaibhav; Maiti, Prabal K; Bharatam, Prasad V
2016-09-28
Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH 2 ) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH 2 ) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH 2 ) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an
Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.
2016-09-01
Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an
PIV-measured versus CFD-predicted flow dynamics in anatomically realistic cerebral aneurysm models.
Ford, Matthew D; Nikolov, Hristo N; Milner, Jaques S; Lownie, Stephen P; Demont, Edwin M; Kalata, Wojciech; Loth, Francis; Holdsworth, David W; Steinman, David A
2008-04-01
Computational fluid dynamics (CFD) modeling of nominally patient-specific cerebral aneurysms is increasingly being used as a research tool to further understand the development, prognosis, and treatment of brain aneurysms. We have previously developed virtual angiography to indirectly validate CFD-predicted gross flow dynamics against the routinely acquired digital subtraction angiograms. Toward a more direct validation, here we compare detailed, CFD-predicted velocity fields against those measured using particle imaging velocimetry (PIV). Two anatomically realistic flow-through phantoms, one a giant internal carotid artery (ICA) aneurysm and the other a basilar artery (BA) tip aneurysm, were constructed of a clear silicone elastomer. The phantoms were placed within a computer-controlled flow loop, programed with representative flow rate waveforms. PIV images were collected on several anterior-posterior (AP) and lateral (LAT) planes. CFD simulations were then carried out using a well-validated, in-house solver, based on micro-CT reconstructions of the geometries of the flow-through phantoms and inlet/outlet boundary conditions derived from flow rates measured during the PIV experiments. PIV and CFD results from the central AP plane of the ICA aneurysm showed a large stable vortex throughout the cardiac cycle. Complex vortex dynamics, captured by PIV and CFD, persisted throughout the cardiac cycle on the central LAT plane. Velocity vector fields showed good overall agreement. For the BA, aneurysm agreement was more compelling, with both PIV and CFD similarly resolving the dynamics of counter-rotating vortices on both AP and LAT planes. Despite the imposition of periodic flow boundary conditions for the CFD simulations, cycle-to-cycle fluctuations were evident in the BA aneurysm simulations, which agreed well, in terms of both amplitudes and spatial distributions, with cycle-to-cycle fluctuations measured by PIV in the same geometry. The overall good agreement
Rapidly re-computable EEG (electroencephalography) forward models for realistic head shapes
Energy Technology Data Exchange (ETDEWEB)
Ermer, J. J. (John J.); Mosher, J. C. (John C.); Baillet, S. (Sylvain); Leahy, R. M. (Richard M.)
2001-01-01
Solution of the EEG source localization (inverse) problem utilizing model-based methods typically requires a significant number of forward model evaluations. For subspace based inverse methods like MUSIC [6], the total number of forward model evaluations can often approach an order of 10{sup 3} or 10{sup 4}. Techniques based on least-squares minimization may require significantly more evaluations. The observed set of measurements over an M-sensor array is often expressed as a linear forward spatio-temporal model of the form: F = GQ + N (1) where the observed forward field F (M-sensors x N-time samples) can be expressed in terms of the forward model G, a set of dipole moment(s) Q (3xP-dipoles x N-time samples) and additive noise N. Because of their simplicity, ease of computation, and relatively good accuracy, multi-layer spherical models [7] (or fast approximations described in [1], [7]) have traditionally been the 'forward model of choice' for approximating the human head. However, approximation of the human head via a spherical model does have several key drawbacks. By its very shape, the use of a spherical model distorts the true distribution of passive currents in the skull cavity. Spherical models also require that the sensor positions be projected onto the fitted sphere (Fig. 1), resulting in a distortion of the true sensor-dipole spatial geometry (and ultimately the computed surface potential). The use of a single 'best-fitted' sphere has the added drawback of incomplete coverage of the inner skull region, often ignoring areas such as the frontal cortex. In practice, this problem is typically countered by fitting additional sphere(s) to those region(s) not covered by the primary sphere. The use of these additional spheres results in added complication to the forward model. Using high-resolution spatial information obtained via X-ray CT or MR imaging, a realistic head model can be formed by tessellating the head into a set of contiguous
3D Realistic Radiative Hydrodynamic Modeling of a Moderate-Mass Star: Effects of Rotation
Kitiashvili, Irina; Kosovichev, Alexander G.; Mansour, Nagi N.; Wray, Alan A.
2018-01-01
Recent progress in stellar observations opens new perspectives in understanding stellar evolution and structure. However, complex interactions in the turbulent radiating plasma together with effects of magnetic fields and rotation make inferences of stellar properties uncertain. The standard 1D mixing-length-based evolutionary models are not able to capture many physical processes of stellar interior dynamics, but they provide an initial approximation of the stellar structure that can be used to initialize 3D time-dependent radiative hydrodynamics simulations, based on first physical principles, that take into account the effects of turbulence, radiation, and others. In this presentation we will show simulation results from a 3D realistic modeling of an F-type main-sequence star with mass 1.47 Msun, in which the computational domain includes the upper layers of the radiation zone, the entire convection zone, and the photosphere. The simulation results provide new insight into the formation and properties of the convective overshoot region, the dynamics of the near-surface, highly turbulent layer, the structure and dynamics of granulation, and the excitation of acoustic and gravity oscillations. We will discuss the thermodynamic structure, oscillations, and effects of rotation on the dynamics of the star across these layers.
Simulating the value of electric-vehicle-grid integration using a behaviourally realistic model
Wolinetz, Michael; Axsen, Jonn; Peters, Jotham; Crawford, Curran
2018-02-01
Vehicle-grid integration (VGI) uses the interaction between electric vehicles and the electrical grid to provide benefits that may include reducing the cost of using intermittent renwable electricity or providing a financial incentive for electric vehicle ownerhip. However, studies that estimate the value of VGI benefits have largely ignored how consumer behaviour will affect the magnitude of the impact. Here, we simulate the long-term impact of VGI using behaviourally realistic and empirically derived models of vehicle adoption and charging combined with an electricity system model. We focus on the case where a central entity manages the charging rate and timing for participating electric vehicles. VGI is found not to increase the adoption of electric vehicles, but does have a a small beneficial impact on electricity prices. By 2050, VGI reduces wholesale electricity prices by 0.6-0.7% (0.7 MWh-1, 2010 CAD) relative to an equivalent scenario without VGI. Excluding consumer behaviour from the analysis inflates the value of VGI.
Development of Realistic Head Models for Electromagnetic Source Imaging of the Human Brain
National Research Council Canada - National Science Library
Akalin, Z
2001-01-01
... images is performed Then triangular, quadratic meshes are formed for the interfaces of the tissues, Thus, realistic meshes, representing scalp, skull, CSF, brain and eye tissues, are formed, At least...
Mathematical models in biological discovery
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...
Lee, Won Hee; Lisanby, Sarah H; Laine, Andrew F; Peterchev, Angel V
2014-01-01
This study examines the characteristics of the electric field (E-field) induced in the brain by electroconvulsive therapy (ECT) and magnetic seizure therapy (MST). The electric field induced by five ECT electrode configurations (bilateral, bifrontal, right unilateral, focal electrically administered seizure therapy, and frontomedial) as well as an MST coil configuration (circular) was computed in an anatomically realistic finite element model of the human head. We computed the maps of the electric field strength relative to an estimated neural activation threshold, and used them to evaluate the stimulation strength and focality of the various ECT and MST paradigms. The results show that the median ECT stimulation strength in the brain is 3-11 times higher than that for MST, and that the stimulated brain volume is substantially higher with ECT (47-100%) than with MST (21%). Our study provides insight into the observed reduction of cognitive side effects in MST compared to ECT, and supports arguments for lowering ECT current amplitude as a means of curbing its side effects.
Improving atomic displacement and replacement calculations with physically realistic damage models.
Nordlund, Kai; Zinkle, Steven J; Sand, Andrea E; Granberg, Fredric; Averback, Robert S; Stoller, Roger; Suzudo, Tomoaki; Malerba, Lorenzo; Banhart, Florian; Weber, William J; Willaime, Francois; Dudarev, Sergei L; Simeone, David
2018-03-14
Atomic collision processes are fundamental to numerous advanced materials technologies such as electron microscopy, semiconductor processing and nuclear power generation. Extensive experimental and computer simulation studies over the past several decades provide the physical basis for understanding the atomic-scale processes occurring during primary displacement events. The current international standard for quantifying this energetic particle damage, the Norgett-Robinson-Torrens displacements per atom (NRT-dpa) model, has nowadays several well-known limitations. In particular, the number of radiation defects produced in energetic cascades in metals is only ~1/3 the NRT-dpa prediction, while the number of atoms involved in atomic mixing is about a factor of 30 larger than the dpa value. Here we propose two new complementary displacement production estimators (athermal recombination corrected dpa, arc-dpa) and atomic mixing (replacements per atom, rpa) functions that extend the NRT-dpa by providing more physically realistic descriptions of primary defect creation in materials and may become additional standard measures for radiation damage quantification.
Turbulent transport measurements in a cold model of GT-burner at realistic flow rates
Directory of Open Access Journals (Sweden)
Gobyzov Oleg
2016-01-01
Full Text Available In the present work simultaneous velocity field and passive admixture concentration field measurements at realistic flow-rates conditions in a non-reacting flow in a model of combustion chamber with an industrial mixing device are reported. In the experiments for safety reasons the real fuel (natural gas was replaced with neon gas to simulate stratification in a strongly swirling flow. Measurements were performed by means of planar laser-induced fluorescence (PLIF and particle image velocimetry technique (PIV at Reynolds number, based on the mean flow rate and nozzle diameter, ≈300 000. Details on experimental technique, features of the experimental setup, images and data preprocessing procedures and results of performed measurements are given in the paper. In addition to the raw velocity and admixture concentration data in-depth evaluation approaches aimed for estimation of turbulent kinetic energy (TKE components, assessment of turbulent Schmidt number and analysis of the gradient closure hypothesis from experimental data are presented in the paper.
Directory of Open Access Journals (Sweden)
Jozsef eHaller
2014-10-01
Full Text Available Among the multitude of factors that can transform human social interactions into violent conflicts, biological features received much attention in recent years as correlates of decision making and aggressiveness especially in critical situations. We present here a highly realistic new model of human aggression and violence, where genuine acts of aggression are readily performed and which at the same time allows the parallel recording of biological concomitants. Particularly, we studied police officers trained at the International Training Centre (Budapest, Hungary, who are prepared to perform operations under extreme conditions of stress. We found that aggressive arousal can transform a basically peaceful social encounter into a violent conflict. Autonomic recordings show that this change is accompanied by increased heart rates, which was associated earlier with reduced cognitive complexity of perceptions (attentional myopia and promotes a bias towards hostile attributions and aggression. We also observed reduced heart rate variability in violent subjects, which is believed to signal a poor functioning of prefrontal-subcortical inhibitory circuits and reduces self-control. Importantly, these autonomic particularities were observed already at the beginning of social encounters i.e. before aggressive acts were initiated, suggesting that individual characteristics of the stress-response define the way in which social pressure affects social behavior, particularly the way in which this develops into violence. Taken together, these findings suggest that cardiac autonomic functions are valuable external symptoms of internal motivational states and decision making processes, and raise the possibility that behavior under social pressure can be predicted by the individual characteristics of stress responsiveness.
Realistic modelling of observed seismic motion in compIex sedimentary basins
Directory of Open Access Journals (Sweden)
G. F. Panza
1994-06-01
Full Text Available Three applications of a numerical technique are illustrated to model realistically the seismic ground motion for complex two-dimensional structures. First we consider a sedimentary basin in the Friuli region, and we model strong motion records from an aftershock of the 1976 earthquake. Then we simulate the ground motion caused in Rome by the 1915, Fucino (Italy earthquake, and we compare our modelling with the damage distribution observed in the town. Finally we deal with the interpretation of ground motion recorded in Mexico City, as a consequence of earthquakes in the Mexican subduction zone. The synthetic signals explain the major characteristics (relative amplitudes, spectral amplification, frequency content of the considered seismograms, and the space distribution of the available macroseismic data. For the sedimentary basin in the Friuli area, parametric studies demonstrate the relevant sensitivity of the computed ground motion to small changes in the subsurface topography of the sedimentary basin, and in the velocity and quality factor of the sediments. The relative Arias Intensity, determined from our numerical simulation in Rome, is in very good agreoment with the distribution of damage observed during the Fucino earthquake. For epicentral distances in the range 50 km-100 km, the source location and not only the local soil conditions control the local effects. For Mexico City, the observed ground motion can be explained as resonance effects and as excitation of local surface waves, and the theoretical and the observed maximum spectral amplifications are very similar. In general, our numerical simulations estimate the maximum and average spectral amplification for specific sites, i.e. they are a very powerful tool for accurate micro-zonation
Accelerating Bayesian inference for evolutionary biology models.
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.
How realistic are air quality hindcasts driven by forcings from climate model simulations?
Lacressonnière, G.; Peuch, V.-H.; Arteta, J.; Josse, B.; Joly, M.; Marécal, V.; Saint Martin, D.; Déqué, M.; Watson, L.
2012-12-01
Predicting how European air quality could evolve over the next decades in the context of changing climate requires the use of climate models to produce results that can be averaged in a climatologically and statistically sound manner. This is a very different approach from the one that is generally used for air quality hindcasts for the present period; analysed meteorological fields are used to represent specifically each date and hour. Differences arise both from the fact that a climate model run results in a pure model output, with no influence from observations (which are useful to correct for a range of errors), and that in a "climate" set-up, simulations on a given day, month or even season cannot be related to any specific period of time (but can just be interpreted in a climatological sense). Hence, although an air quality model can be thoroughly validated in a "realistic" set-up using analysed meteorological fields, the question remains of how far its outputs can be interpreted in a "climate" set-up. For this purpose, we focus on Europe and on the current decade using three 5-yr simulations performed with the multiscale chemistry-transport model MOCAGE and use meteorological forcings either from operational meteorological analyses or from climate simulations. We investigate how statistical skill indicators compare in the different simulations, discriminating also the effects of meteorology on atmospheric fields (winds, temperature, humidity, pressure, etc.) and on the dependent emissions and deposition processes (volatile organic compound emissions, deposition velocities, etc.). Our results show in particular how differing boundary layer heights and deposition velocities affect horizontal and vertical distributions of species. When the model is driven by operational analyses, the simulation accurately reproduces the observed values of O3, NOx, SO2 and, with some bias that can be explained by the set-up, PM10. We study how the simulations driven by climate
Futscher, Moritz H; Ehrler, Bruno
2017-09-08
Perovskite/Si tandem solar cells have the potential to considerably out-perform conventional solar cells. Under standard test conditions, perovskite/Si tandem solar cells already outperform the Si single junction. Under realistic conditions, however, as we show, tandem solar cells made from current record cells are hardly more efficient than the Si cell alone. We model the performance of realistic perovskite/Si tandem solar cells under real-world climate conditions, by incorporating parasitic cell resistances, nonradiative recombination, and optical losses into the detailed-balance limit. We show quantitatively that when optimizing these parameters in the perovskite top cell, perovskite/Si tandem solar cells could reach efficiencies above 38% under realistic conditions, even while leaving the Si cell untouched. Despite the rapid efficiency increase of perovskite solar cells, our results emphasize the need for further material development, careful device design, and light management strategies, all necessary for highly efficient perovskite/Si tandem solar cells.
Realistic modeling of seismic input for megacities and large urban areas
Panza, G. F.; Unesco/Iugs/Igcp Project 414 Team
2003-04-01
The project addressed the problem of pre-disaster orientation: hazard prediction, risk assessment, and hazard mapping, in connection with seismic activity and man-induced vibrations. The definition of realistic seismic input has been obtained from the computation of a wide set of time histories and spectral information, corresponding to possible seismotectonic scenarios for different source and structural models. The innovative modeling technique, that constitutes the common tool to the entire project, takes into account source, propagation and local site effects. This is done using first principles of physics about wave generation and propagation in complex media, and does not require to resort to convolutive approaches, that have been proven to be quite unreliable, mainly when dealing with complex geological structures, the most interesting from the practical point of view. In fact, several techniques that have been proposed to empirically estimate the site effects using observations convolved with theoretically computed signals corresponding to simplified models, supply reliable information about the site response to non-interfering seismic phases. They are not adequate in most of the real cases, when the seismic sequel is formed by several interfering waves. The availability of realistic numerical simulations enables us to reliably estimate the amplification effects even in complex geological structures, exploiting the available geotechnical, lithological, geophysical parameters, topography of the medium, tectonic, historical, palaeoseismological data, and seismotectonic models. The realistic modeling of the ground motion is a very important base of knowledge for the preparation of groundshaking scenarios that represent a valid and economic tool for the seismic microzonation. This knowledge can be very fruitfully used by civil engineers in the design of new seismo-resistant constructions and in the reinforcement of the existing built environment, and, therefore
International Nuclear Information System (INIS)
Mailhe, P.; Barbier, B.; Garnier, C.; Landskron, H.; Sedlacek, R.; Arimescu, I.; Smith, M.; Bellanger, P.
2013-01-01
The availability of reliable tools and associated methodology able to accurately predict the LWR fuel behavior in all conditions is of great importance for safe and economic fuel usage. For that purpose, AREVA has developed its new global fuel rod performance code GALILEO along with its associated realistic thermal-mechanical analysis methodology. This realistic methodology is based on a Monte Carlo type random sampling of all relevant input variables. After having outlined the AREVA realistic methodology, this paper will be focused on the GALILEO code benchmarking process, on its extended experimental database and on the GALILEO model uncertainties assessment. The propagation of these model uncertainties through the AREVA realistic methodology is also presented. This GALILEO model uncertainties processing is of the utmost importance for accurate fuel design margin evaluation as illustrated on some application examples. With the submittal of Topical Report GALILEO to the U.S. NRC in 2013, GALILEO and its methodology are on the way to be industrially used in a wide range of irradiation conditions. (authors)
Lesperance, Marielle; Inglis-Whalen, M; Thomson, R M
2014-02-01
To investigate the effects of the composition and geometry of ocular media and tissues surrounding the eye on dose distributions for COMS eye plaque brachytherapy with(125)I, (103)Pd, or (131)Cs seeds, and to investigate doses to ocular structures. An anatomically and compositionally realistic voxelized eye model with a medial tumor is developed based on a literature review. Mass energy absorption and attenuation coefficients for ocular media are calculated. Radiation transport and dose deposition are simulated using the EGSnrc Monte Carlo user-code BrachyDose for a fully loaded COMS eye plaque within a water phantom and our full eye model for the three radionuclides. A TG-43 simulation with the same seed configuration in a water phantom neglecting the plaque and interseed effects is also performed. The impact on dose distributions of varying tumor position, as well as tumor and surrounding tissue media is investigated. Each simulation and radionuclide is compared using isodose contours, dose volume histograms for the lens and tumor, maximum, minimum, and average doses to structures of interest, and doses to voxels of interest within the eye. Mass energy absorption and attenuation coefficients of the ocular media differ from those of water by as much as 12% within the 20-30 keV photon energy range. For all radionuclides studied, average doses to the tumor and lens regions in the full eye model differ from those for the plaque in water by 8%-10% and 13%-14%, respectively; the average doses to the tumor and lens regions differ between the full eye model and the TG-43 simulation by 2%-17% and 29%-34%, respectively. Replacing the surrounding tissues in the eye model with water increases the maximum and average doses to the lens by 2% and 3%, respectively. Substituting the tumor medium in the eye model for water, soft tissue, or an alternate melanoma composition affects tumor dose compared to the default eye model simulation by up to 16%. In the full eye model
International Nuclear Information System (INIS)
Lesperance, Marielle; Inglis-Whalen, M.; Thomson, R. M.
2014-01-01
Purpose : To investigate the effects of the composition and geometry of ocular media and tissues surrounding the eye on dose distributions for COMS eye plaque brachytherapy with 125 I, 103 Pd, or 131 Cs seeds, and to investigate doses to ocular structures. Methods : An anatomically and compositionally realistic voxelized eye model with a medial tumor is developed based on a literature review. Mass energy absorption and attenuation coefficients for ocular media are calculated. Radiation transport and dose deposition are simulated using the EGSnrc Monte Carlo user-code BrachyDose for a fully loaded COMS eye plaque within a water phantom and our full eye model for the three radionuclides. A TG-43 simulation with the same seed configuration in a water phantom neglecting the plaque and interseed effects is also performed. The impact on dose distributions of varying tumor position, as well as tumor and surrounding tissue media is investigated. Each simulation and radionuclide is compared using isodose contours, dose volume histograms for the lens and tumor, maximum, minimum, and average doses to structures of interest, and doses to voxels of interest within the eye. Results : Mass energy absorption and attenuation coefficients of the ocular media differ from those of water by as much as 12% within the 20–30 keV photon energy range. For all radionuclides studied, average doses to the tumor and lens regions in the full eye model differ from those for the plaque in water by 8%–10% and 13%–14%, respectively; the average doses to the tumor and lens regions differ between the full eye model and the TG-43 simulation by 2%–17% and 29%–34%, respectively. Replacing the surrounding tissues in the eye model with water increases the maximum and average doses to the lens by 2% and 3%, respectively. Substituting the tumor medium in the eye model for water, soft tissue, or an alternate melanoma composition affects tumor dose compared to the default eye model simulation by up
Energy Technology Data Exchange (ETDEWEB)
Lesperance, Marielle; Inglis-Whalen, M.; Thomson, R. M., E-mail: rthomson@physics.carleton.ca [Carleton Laboratory for Radiotherapy Physics, Department of Physics, Carleton University, Ottawa K1S 5B6 (Canada)
2014-02-15
Purpose : To investigate the effects of the composition and geometry of ocular media and tissues surrounding the eye on dose distributions for COMS eye plaque brachytherapy with{sup 125}I, {sup 103}Pd, or {sup 131}Cs seeds, and to investigate doses to ocular structures. Methods : An anatomically and compositionally realistic voxelized eye model with a medial tumor is developed based on a literature review. Mass energy absorption and attenuation coefficients for ocular media are calculated. Radiation transport and dose deposition are simulated using the EGSnrc Monte Carlo user-code BrachyDose for a fully loaded COMS eye plaque within a water phantom and our full eye model for the three radionuclides. A TG-43 simulation with the same seed configuration in a water phantom neglecting the plaque and interseed effects is also performed. The impact on dose distributions of varying tumor position, as well as tumor and surrounding tissue media is investigated. Each simulation and radionuclide is compared using isodose contours, dose volume histograms for the lens and tumor, maximum, minimum, and average doses to structures of interest, and doses to voxels of interest within the eye. Results : Mass energy absorption and attenuation coefficients of the ocular media differ from those of water by as much as 12% within the 20–30 keV photon energy range. For all radionuclides studied, average doses to the tumor and lens regions in the full eye model differ from those for the plaque in water by 8%–10% and 13%–14%, respectively; the average doses to the tumor and lens regions differ between the full eye model and the TG-43 simulation by 2%–17% and 29%–34%, respectively. Replacing the surrounding tissues in the eye model with water increases the maximum and average doses to the lens by 2% and 3%, respectively. Substituting the tumor medium in the eye model for water, soft tissue, or an alternate melanoma composition affects tumor dose compared to the default eye model
Numerical simulation of wave propagation in a realistic model of the human external ear.
Fadaei, Mohaddeseh; Abouali, Omid; Emdad, Homayoun; Faramarzi, Mohammad; Ahmadi, Goodarz
2015-01-01
In this study, a numerical investigation is performed to evaluate the effects of high-pressure sinusoidal and blast wave's propagation around and inside of a human external ear. A series of computed tomography images are used to reconstruct a realistic three-dimensional (3D) model of a human ear canal and the auricle. The airflow field is then computed by solving the governing differential equations in the time domain using a computational fluid dynamics software. An unsteady algorithm is used to obtain the high-pressure wave propagation throughout the ear canal which is validated against the available analytical and numerical data in literature. The effects of frequency, wave shape, and the auricle on pressure distribution are then evaluated and discussed. The results clearly indicate that the frequency plays a key role on pressure distribution within the ear canal. At 4 kHz frequency, the pressure magnitude is much more amplified within the ear canal than the frequencies of 2 and 6 kHz, for the incident wave angle of 90° investigated in this study, attributable to the '4-kHz notch' in patients with noise-induced hearing loss. According to the results, the pressure distribution patterns at the ear canal are very similar for both sinusoidal pressure waveform with the frequency of 2 kHz and blast wave. The ratio of the peak pressure value at the eardrum to that at the canal entrance increases from about 8% to 30% as the peak pressure value of the blast wave increases from 5 to 100 kPa for the incident wave angle of 90° investigated in this study. Furthermore, incorporation of the auricle to the ear canal model is associated with centerline pressure magnitudes of about 50% and 7% more than those of the ear canal model without the auricle throughout the ear canal for sinusoidal and blast waves, respectively, without any significant effect on pressure distribution pattern along the ear canal for the incident wave angle of 90° investigated in this study.
Lazy Updating of hubs can enable more realistic models by speeding up stochastic simulations
Ehlert, Kurt; Loewe, Laurence
2014-11-01
To respect the nature of discrete parts in a system, stochastic simulation algorithms (SSAs) must update for each action (i) all part counts and (ii) each action's probability of occurring next and its timing. This makes it expensive to simulate biological networks with well-connected "hubs" such as ATP that affect many actions. Temperature and volume also affect many actions and may be changed significantly in small steps by the network itself during fever and cell growth, respectively. Such trends matter for evolutionary questions, as cell volume determines doubling times and fever may affect survival, both key traits for biological evolution. Yet simulations often ignore such trends and assume constant environments to avoid many costly probability updates. Such computational convenience precludes analyses of important aspects of evolution. Here we present "Lazy Updating," an add-on for SSAs designed to reduce the cost of simulating hubs. When a hub changes, Lazy Updating postpones all probability updates for reactions depending on this hub, until a threshold is crossed. Speedup is substantial if most computing time is spent on such updates. We implemented Lazy Updating for the Sorting Direct Method and it is easily integrated into other SSAs such as Gillespie's Direct Method or the Next Reaction Method. Testing on several toy models and a cellular metabolism model showed >10× faster simulations for its use-cases—with a small loss of accuracy. Thus we see Lazy Updating as a valuable tool for some special but important simulation problems that are difficult to address efficiently otherwise.
Schippers, P.
2009-01-01
The acoustic modelling in TNO’s ALMOST (=Acoustic Loss Model for Operational Studies and Tasks) uses a bubble migration model as realistic input for wake modelling. The modelled bubble cloud represents the actual ship wake. Ship hull, propeller and bow wave are the main generators of bubbles in the
Time lags in biological models
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...
Realistic modelling of the seismic input Site effects and parametric studies
Romanelli, F; Vaccari, F
2002-01-01
We illustrate the work done in the framework of a large international cooperation, showing the very recent numerical experiments carried out within the framework of the EC project 'Advanced methods for assessing the seismic vulnerability of existing motorway bridges' (VAB) to assess the importance of non-synchronous seismic excitation of long structures. The definition of the seismic input at the Warth bridge site, i.e. the determination of the seismic ground motion due to an earthquake with a given magnitude and epicentral distance from the site, has been done following a theoretical approach. In order to perform an accurate and realistic estimate of site effects and of differential motion it is necessary to make a parametric study that takes into account the complex combination of the source and propagation parameters, in realistic geological structures. The computation of a wide set of time histories and spectral information, corresponding to possible seismotectonic scenarios for different sources and stru...
Hanson, C; Wilkinson, T; Macluskey, M
2018-02-01
Teaching exodontia to novice undergraduates requires a realistic model. Thiel-embalmed cadavers retain the flexibility of the soft tissues and could be used to teach exodontia. The objective was to determine whether Thiel-embalmed cadavers were perceived to be a more realistic model by undergraduates in comparison with mannequins. Over a period of 4 years (2011-2014), students were randomly assigned into two groups: those taught exodontia on mannequins only (NT) and those who also experienced cadaveric teaching (T). This was followed by an assessment. There were 174 students in the T group and 108 in the NT group. Sixty-five per cent of the T group and 69% of the NT group provided feedback. Ninety-eight per cent (98%) felt that they had been advantaged by being included in the group compared with 95% in the NT who felt disadvantaged. The majority (98%) thought that using the cadavers was advantageous and gave a realistic feel for soft tissue management (89%) and that it was similar to managing a patient (81%). Self-reported confidence in undertaking an extraction was not different between the two groups (P=.078), and performance in the extraction assessment was not significantly different between the two groups over the 4 years (P=.8). The Thiel-embalmed cadavers were well received by the students who found it a more realistic model for exodontia than a mannequin, even though this did not impact on their performance in a following assessment. Future work on these cadavers may be expanded to include surgical procedures. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Track structure in biological models.
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.
Assessment of radiation dose in nuclear cardiovascular imaging using realistic computational models
Energy Technology Data Exchange (ETDEWEB)
Xie, Tianwu [Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva 4 CH-1211 (Switzerland); Lee, Choonsik [Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, Maryland 20852 (United States); Bolch, Wesley E. [Departments of Nuclear and Radiological and Biomedical Engineering, University of Florida, Gainesville, Florida 32611 (United States); Zaidi, Habib, E-mail: habib.zaidi@hcuge.ch [Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva 4 CH-1211 (Switzerland); Geneva Neuroscience Center, Geneva University, Geneva CH-1205 (Switzerland); Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen 9700 RB (Netherlands)
2015-06-15
Purpose: Nuclear cardiology plays an important role in clinical assessment and has enormous impact on the management of a variety of cardiovascular diseases. Pediatric patients at different age groups are exposed to a spectrum of radiation dose levels and associated cancer risks different from those of adults in diagnostic nuclear medicine procedures. Therefore, comprehensive radiation dosimetry evaluations for commonly used myocardial perfusion imaging (MPI) and viability radiotracers in target population (children and adults) at different age groups are highly desired. Methods: Using Monte Carlo calculations and biological effects of ionizing radiation VII model, we calculate the S-values for a number of radionuclides (Tl-201, Tc-99m, I-123, C-11, N-13, O-15, F-18, and Rb-82) and estimate the absorbed dose and effective dose for 12 MPI radiotracers in computational models including the newborn, 1-, 5-, 10-, 15-yr-old, and adult male and female computational phantoms. Results: For most organs, {sup 201}Tl produces the highest absorbed dose whereas {sup 82}Rb and {sup 15}O-water produce the lowest absorbed dose. For the newborn baby and adult patient, the effective dose of {sup 82}Rb is 48% and 77% lower than that of {sup 99m}Tc-tetrofosmin (rest), respectively. Conclusions: {sup 82}Rb results in lower effective dose in adults compared to {sup 99m}Tc-labeled tracers. However, this advantage is less apparent in children. The produced dosimetric databases for various radiotracers used in cardiovascular imaging, using new generation of computational models, can be used for risk-benefit assessment of a spectrum of patient population in clinical nuclear cardiology practice.
Realistic modelling of the effects of asynchronous motion at the base of bridge piers
Romanelli, F; Vaccari, F
2002-01-01
Frequently long-span bridges provide deep valley crossings, which require special consideration due to the possibility of local amplification of the ground motion as a consequence of topographical irregularities and local soil conditions. This does in fact cause locally enhanced seismic input with the possibility for the bridge piers to respond asynchronously. This introduces special design requirements so that possible out-of-phase ground displacements and the associated large relative displacements of adjacent piers can be accommodated without excessive damage. Assessment of the local variability of the ground motion due to local lateral heterogeneities and to attenuation properties is thus crucial toward the realistic definition of the asynchronous motion at the base of the bridge piers. We illustrate the work done in the framework of a large international cooperation to assess the importance of non-synchronous seismic excitation of long structures. To accomplish this task we compute complete synthetic acc...
2012-01-12
machined based on this model. The key features include the adjustable inlet tube and insertion of electrodes, which will allow for application of an...Goldberg, D.E.; Holland, J.H. Machine Learning 1988, 3, 95-99. [13] Puzyn, T.; et.al. Nature Nanotechnology 2011, 6, 175–178...Braydich- Stolle , L.K.; Maurer, E.I.; Park, K.; Maccuspie, R.I.; Afrooz, A.N.; Saleh, N.B.; Vaia, R.A.; Hussain, S.M. Does shape matter? Bioeffects
Ivannikova, E.; Kruglyakov, M.; Kuvshinov, A. V.; Rastaetter, L.; Pulkkinen, A. A.; Ngwira, C. M.
2017-12-01
During extreme space weather events electric currents in the Earth's magnetosphere and ionosphere experience large variations, which leads to dramatic intensification of the fluctuating magnetic field at the surface of the Earth. According to Faraday's law of induction, the fluctuating geomagnetic field in turn induces electric field that generates harmful currents (so-called "geomagnetically induced currents"; GICs) in grounded technological systems. Understanding (via modeling) of the spatio-temporal evolution of the geoelectric field during enhanced geomagnetic activity is a key consideration in estimating the hazard to technological systems from space weather. We present the results of ground geoelectric field modeling for the Northeast United States, which is performed with the use of our novel numerical tool based on integral equation approach. The tool exploits realistic regional three-dimensional (3-D) models of the Earth's electrical conductivity and realistic global models of the spatio-temporal evolution of the magnetospheric and ionospheric current systems responsible for geomagnetic disturbances. We also explore in detail the manifestation of the coastal effect (anomalous intensification of the geoelectric field near the coasts) in this region.
Directory of Open Access Journals (Sweden)
Lionel Roques
Full Text Available We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D landscape crossed by linear one-dimensional (1D corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid "2D/1D model", i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department and the output of the model (population densities at each point of the landscape, and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature.
Roques, Lionel; Bonnefon, Olivier
2016-01-01
We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D) landscape crossed by linear one-dimensional (1D) corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid "2D/1D model", i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department) and the output of the model (population densities at each point of the landscape), and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case) on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature.
2016-01-01
We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D) landscape crossed by linear one-dimensional (1D) corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid “2D/1D model”, i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department) and the output of the model (population densities at each point of the landscape), and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case) on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature. PMID:26986201
Credit Card Fraud Detection: A Realistic Modeling and a Novel Learning Strategy.
Dal Pozzolo, Andrea; Boracchi, Giacomo; Caelen, Olivier; Alippi, Cesare; Bontempi, Gianluca
2017-09-14
Detecting frauds in credit card transactions is perhaps one of the best testbeds for computational intelligence algorithms. In fact, this problem involves a number of relevant challenges, namely: concept drift (customers' habits evolve and fraudsters change their strategies over time), class imbalance (genuine transactions far outnumber frauds), and verification latency (only a small set of transactions are timely checked by investigators). However, the vast majority of learning algorithms that have been proposed for fraud detection rely on assumptions that hardly hold in a real-world fraud-detection system (FDS). This lack of realism concerns two main aspects: 1) the way and timing with which supervised information is provided and 2) the measures used to assess fraud-detection performance. This paper has three major contributions. First, we propose, with the help of our industrial partner, a formalization of the fraud-detection problem that realistically describes the operating conditions of FDSs that everyday analyze massive streams of credit card transactions. We also illustrate the most appropriate performance measures to be used for fraud-detection purposes. Second, we design and assess a novel learning strategy that effectively addresses class imbalance, concept drift, and verification latency. Third, in our experiments, we demonstrate the impact of class unbalance and concept drift in a real-world data stream containing more than 75 million transactions, authorized over a time window of three years.
Realistic modelling of the effects of asynchronous motion at the base of bridge piers
International Nuclear Information System (INIS)
Romanelli, F.; Panza, G.F.; Vaccari, F.
2002-11-01
Frequently long-span bridges provide deep valley crossings, which require special consideration due to the possibility of local amplification of the ground motion as a consequence of topographical irregularities and local soil conditions. This does in fact cause locally enhanced seismic input with the possibility for the bridge piers to respond asynchronously. This introduces special design requirements so that possible out-of-phase ground displacements and the associated large relative displacements of adjacent piers can be accommodated without excessive damage. Assessment of the local variability of the ground motion due to local lateral heterogeneities and to attenuation properties is thus crucial toward the realistic definition of the asynchronous motion at the base of the bridge piers. We illustrate the work done in the framework of a large international cooperation to assess the importance of non-synchronous seismic excitation of long structures. To accomplish this task we compute complete synthetic accelerograms using as input a set of parameters that describes, to the best of our knowledge, the geological structure and seismotectonic setting of the investigated area. (author)
International Nuclear Information System (INIS)
Johnsen, S.; Furuholt, E.
1995-01-01
Risk assessment of discharges from offshore oil and gas production to the marine environment features determination of potential environmental concentration (PEC) levels and no observed effect concentration (NOEC) levels. The PEC values are normally based on dilution of chemical components in the actual discharge source in the recipient, while the NOEC values are determined by applying a safety factor to acute toxic effects from laboratory tests. The DREAM concept focuses on realistic exposure doses as function of contact time and dilution, rather than fixed exposure concentrations of chemicals in long time exposure regimes. In its present state, the DREAM model is based on a number of assumptions with respect to the link between real life exposure doses and effects observed in laboratory tests. A research project has recently been initiated to develop the concept further, with special focus on chronic effects of different chemical compounds on the marine ecosystem. One of the questions that will be addressed is the link between exposure time, dose, concentration and effect. Validation of the safety factors applied for transforming acute toxic data into NOEC values will also be included. The DREAM model has been used by Statoil for risk assessment of discharges from new and existing offshore oil and gas production fields, and has been found to give a much more realistic results than conventional risk assessment tools. The presentation outlines the background for the DREAM approach, describes the model in its present state, discusses further developments and applications, and shows a number of examples on the performance of DREAM
Bates, P. D.; Quinn, N.; Sampson, C. C.; Smith, A.; Wing, O.; Neal, J. C.
2017-12-01
Remotely sensed data has transformed the field of large scale hydraulic modelling. New digital elevation, hydrography and river width data has allowed such models to be created for the first time, and remotely sensed observations of water height, slope and water extent has allowed them to be calibrated and tested. As a result, we are now able to conduct flood risk analyses at national, continental or even global scales. However, continental scale analyses have significant additional complexity compared to typical flood risk modelling approaches. Traditional flood risk assessment uses frequency curves to define the magnitude of extreme flows at gauging stations. The flow values for given design events, such as the 1 in 100 year return period flow, are then used to drive hydraulic models in order to produce maps of flood hazard. Such an approach works well for single gauge locations and local models because over relatively short river reaches (say 10-60km) one can assume that the return period of an event does not vary. At regional to national scales and across multiple river catchments this assumption breaks down, and for a given flood event the return period will be different at different gauging stations, a pattern known as the event `footprint'. Despite this, many national scale risk analyses still use `constant in space' return period hazard layers (e.g. the FEMA Special Flood Hazard Areas) in their calculations. Such an approach can estimate potential exposure, but will over-estimate risk and cannot determine likely flood losses over a whole region or country. We address this problem by using a stochastic model to simulate many realistic extreme event footprints based on observed gauged flows and the statistics of gauge to gauge correlations. We take the entire USGS gauge data catalogue for sites with > 45 years of record and use a conditional approach for multivariate extreme values to generate sets of flood events with realistic return period variation in
Directory of Open Access Journals (Sweden)
Edwin Musdi
2016-02-01
Full Text Available This research aims to develop a mathematics instructional model based realistic mathematics education (RME to promote students' problem-solving abilities. The design research used Plomp models, which consists of preliminary phase, development or proto-typing phase and assessment phase. At this study, only the first two phases conducted. The first phase, a preliminary investigation, carried out with a literature study to examine the theory-based instructional learning RME model, characteristics of learners, learning management descriptions by junior high school mathematics teacher and relevant research. The development phase is done by developing a draft model (an early prototype model that consists of the syntax, the social system, the principle of reaction, support systems, and the impact and effects of instructional support. Early prototype model contain a draft model, lesson plans, worksheets, and assessments. Tesssmer formative evaluation model used to revise the model. In this study only phase of one to one evaluation conducted. In the ppreliminary phase has produced a theory-based learning RME model, a description of the characteristics of learners in grade VIII Junior High School Padang and the description of teacher teaching in the classroom. The result showed that most students were still not be able to solve the non-routine problem. Teachers did not optimally facilitate students to develop problem-solving skills of students. It was recommended that the model can be applied in the classroom.
Seo, Hyeon; Kim, Donghyeon; Jun, Sung Chan
2016-06-01
Electrical brain stimulation (EBS) is an emerging therapy for the treatment of neurological disorders, and computational modeling studies of EBS have been used to determine the optimal parameters for highly cost-effective electrotherapy. Recent notable growth in computing capability has enabled researchers to consider an anatomically realistic head model that represents the full head and complex geometry of the brain rather than the previous simplified partial head model (extruded slab) that represents only the precentral gyrus. In this work, subdural cortical stimulation (SuCS) was found to offer a better understanding of the differential activation of cortical neurons in the anatomically realistic full-head model than in the simplified partial-head models. We observed that layer 3 pyramidal neurons had comparable stimulation thresholds in both head models, while layer 5 pyramidal neurons showed a notable discrepancy between the models; in particular, layer 5 pyramidal neurons demonstrated asymmetry in the thresholds and action potential initiation sites in the anatomically realistic full-head model. Overall, the anatomically realistic full-head model may offer a better understanding of layer 5 pyramidal neuronal responses. Accordingly, the effects of using the realistic full-head model in SuCS are compelling in computational modeling studies, even though this modeling requires substantially more effort.
Elangovan, Premkumar; Mackenzie, Alistair; Dance, David R; Young, Kenneth C; Cooke, Victoria; Wilkinson, Louise; Given-Wilson, Rosalind M; Wallis, Matthew G; Wells, Kevin
2017-04-07
A novel method has been developed for generating quasi-realistic voxel phantoms which simulate the compressed breast in mammography and digital breast tomosynthesis (DBT). The models are suitable for use in virtual clinical trials requiring realistic anatomy which use the multiple alternative forced choice (AFC) paradigm and patches from the complete breast image. The breast models are produced by extracting features of breast tissue components from DBT clinical images including skin, adipose and fibro-glandular tissue, blood vessels and Cooper's ligaments. A range of different breast models can then be generated by combining these components. Visual realism was validated using a receiver operating characteristic (ROC) study of patches from simulated images calculated using the breast models and from real patient images. Quantitative analysis was undertaken using fractal dimension and power spectrum analysis. The average areas under the ROC curves for 2D and DBT images were 0.51 ± 0.06 and 0.54 ± 0.09 demonstrating that simulated and real images were statistically indistinguishable by expert breast readers (7 observers); errors represented as one standard error of the mean. The average fractal dimensions (2D, DBT) for real and simulated images were (2.72 ± 0.01, 2.75 ± 0.01) and (2.77 ± 0.03, 2.82 ± 0.04) respectively; errors represented as one standard error of the mean. Excellent agreement was found between power spectrum curves of real and simulated images, with average β values (2D, DBT) of (3.10 ± 0.17, 3.21 ± 0.11) and (3.01 ± 0.32, 3.19 ± 0.07) respectively; errors represented as one standard error of the mean. These results demonstrate that radiological images of these breast models realistically represent the complexity of real breast structures and can be used to simulate patches from mammograms and DBT images that are indistinguishable from
Elangovan, Premkumar; Mackenzie, Alistair; Dance, David R.; Young, Kenneth C.; Cooke, Victoria; Wilkinson, Louise; Given-Wilson, Rosalind M.; Wallis, Matthew G.; Wells, Kevin
2017-04-01
A novel method has been developed for generating quasi-realistic voxel phantoms which simulate the compressed breast in mammography and digital breast tomosynthesis (DBT). The models are suitable for use in virtual clinical trials requiring realistic anatomy which use the multiple alternative forced choice (AFC) paradigm and patches from the complete breast image. The breast models are produced by extracting features of breast tissue components from DBT clinical images including skin, adipose and fibro-glandular tissue, blood vessels and Cooper’s ligaments. A range of different breast models can then be generated by combining these components. Visual realism was validated using a receiver operating characteristic (ROC) study of patches from simulated images calculated using the breast models and from real patient images. Quantitative analysis was undertaken using fractal dimension and power spectrum analysis. The average areas under the ROC curves for 2D and DBT images were 0.51 ± 0.06 and 0.54 ± 0.09 demonstrating that simulated and real images were statistically indistinguishable by expert breast readers (7 observers); errors represented as one standard error of the mean. The average fractal dimensions (2D, DBT) for real and simulated images were (2.72 ± 0.01, 2.75 ± 0.01) and (2.77 ± 0.03, 2.82 ± 0.04) respectively; errors represented as one standard error of the mean. Excellent agreement was found between power spectrum curves of real and simulated images, with average β values (2D, DBT) of (3.10 ± 0.17, 3.21 ± 0.11) and (3.01 ± 0.32, 3.19 ± 0.07) respectively; errors represented as one standard error of the mean. These results demonstrate that radiological images of these breast models realistically represent the complexity of real breast structures and can be used to simulate patches from mammograms and DBT images that are indistinguishable from
International Nuclear Information System (INIS)
De Geeter, N; Crevecoeur, G; Dupré, L; Leemans, A
2015-01-01
In transcranial magnetic stimulation (TMS), an applied alternating magnetic field induces an electric field in the brain that can interact with the neural system. It is generally assumed that this induced electric field is the crucial effect exciting a certain region of the brain. More specifically, it is the component of this field parallel to the neuron’s local orientation, the so-called effective electric field, that can initiate neuronal stimulation. Deeper insights on the stimulation mechanisms can be acquired through extensive TMS modelling. Most models study simple representations of neurons with assumed geometries, whereas we embed realistic neural trajectories computed using tractography based on diffusion tensor images. This way of modelling ensures a more accurate spatial distribution of the effective electric field that is in addition patient and case specific. The case study of this paper focuses on the single pulse stimulation of the left primary motor cortex with a standard figure-of-eight coil. Including realistic neural geometry in the model demonstrates the strong and localized variations of the effective electric field between the tracts themselves and along them due to the interplay of factors such as the tract’s position and orientation in relation to the TMS coil, the neural trajectory and its course along the white and grey matter interface. Furthermore, the influence of changes in the coil orientation is studied. Investigating the impact of tissue anisotropy confirms that its contribution is not negligible. Moreover, assuming isotropic tissues lead to errors of the same size as rotating or tilting the coil with 10 degrees. In contrast, the model proves to be less sensitive towards the not well-known tissue conductivity values. (paper)
A Biologically Realistic Cortical Model of Eye Movement Control in Reading
Heinzle, Jakob; Hepp, Klaus; Martin, Kevan A. C.
2010-01-01
Reading is a highly complex task involving a precise integration of vision, attention, saccadic eye movements, and high-level language processing. Although there is a long history of psychological research in reading, it is only recently that imaging studies have identified some neural correlates of reading. Thus, the underlying neural mechanisms…
Confirmation of a realistic reactor model for BNCT dosimetry at the TRIGA Mainz
Energy Technology Data Exchange (ETDEWEB)
Ziegner, Markus, E-mail: Markus.Ziegner.fl@ait.ac.at [AIT Austrian Institute of Technology GmbH, Vienna A-1220, Austria and Institute of Atomic and Subatomic Physics, Vienna University of Technology, Vienna A-1020 (Austria); Schmitz, Tobias; Hampel, Gabriele [Institut für Kernchemie, Johannes Gutenberg-Universität, Mainz DE-55128 (Germany); Khan, Rustam [Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad PK-44000 (Pakistan); Blaickner, Matthias [AIT Austrian Institute of Technology GmbH, Vienna A-1220 (Austria); Palmans, Hugo [Acoustics and Ionising Radiation Division, National Physical Laboratory, Teddington TW11 0LW, United Kingdom and Medical Physics Group, EBG MedAustron GmbH, Wiener Neustadt A-2700 (Austria); Sharpe, Peter [Acoustics and Ionising Radiation Division, National Physical Laboratory, Teddington TW11 0LW (United Kingdom); Böck, Helmuth [Institute of Atomic and Subatomic Physics, Vienna University of Technology, Vienna A-1020 (Austria)
2014-11-01
Purpose: In order to build up a reliable dose monitoring system for boron neutron capture therapy (BNCT) applications at the TRIGA reactor in Mainz, a computer model for the entire reactor was established, simulating the radiation field by means of the Monte Carlo method. The impact of different source definition techniques was compared and the model was validated by experimental fluence and dose determinations. Methods: The depletion calculation code ORIGEN2 was used to compute the burn-up and relevant material composition of each burned fuel element from the day of first reactor operation to its current core. The material composition of the current core was used in a MCNP5 model of the initial core developed earlier. To perform calculations for the region outside the reactor core, the model was expanded to include the thermal column and compared with the previously established ATTILA model. Subsequently, the computational model is simplified in order to reduce the calculation time. Both simulation models are validated by experiments with different setups using alanine dosimetry and gold activation measurements with two different types of phantoms. Results: The MCNP5 simulated neutron spectrum and source strength are found to be in good agreement with the previous ATTILA model whereas the photon production is much lower. Both MCNP5 simulation models predict all experimental dose values with an accuracy of about 5%. The simulations reveal that a Teflon environment favorably reduces the gamma dose component as compared to a polymethyl methacrylate phantom. Conclusions: A computer model for BNCT dosimetry was established, allowing the prediction of dosimetric quantities without further calibration and within a reasonable computation time for clinical applications. The good agreement between the MCNP5 simulations and experiments demonstrates that the ATTILA model overestimates the gamma dose contribution. The detailed model can be used for the planning of structural
Pursuing realistic hydrologic model under SUPERFLEX framework in a semi-humid catchment in China
Wei, Lingna; Savenije, Hubert H. G.; Gao, Hongkai; Chen, Xi
2016-04-01
Model realism is pursued perpetually by hydrologists for flood and drought prediction, integrated water resources management and decision support of water security. "Physical-based" distributed hydrologic models are speedily developed but they also encounter unneglectable challenges, for instance, computational time with low efficiency and parameters uncertainty. This study step-wisely tested four conceptual hydrologic models under the framework of SUPERFLEX in a small semi-humid catchment in southern Huai River basin of China. The original lumped FLEXL has hypothesized model structure of four reservoirs to represent canopy interception, unsaturated zone, subsurface flow of fast and slow components and base flow storage. Considering the uneven rainfall in space, the second model (FLEXD) is developed with same parameter set for different rain gauge controlling units. To reveal the effect of topography, terrain descriptor of height above the nearest drainage (HAND) combined with slope is applied to classify the experimental catchment into two landscapes. Then the third one (FLEXTOPO) builds different model blocks in consideration of the dominant hydrologic process corresponding to the topographical condition. The fourth one named FLEXTOPOD integrating the parallel framework of FLEXTOPO in four controlled units is designed to interpret spatial variability of rainfall patterns and topographic features. Through pairwise comparison, our results suggest that: (1) semi-distributed models (FLEXD and FLEXTOPOD) taking precipitation spatial heterogeneity into account has improved model performance with parsimonious parameter set, and (2) hydrologic model architecture with flexibility to reflect perceived dominant hydrologic processes can include the local terrain circumstances for each landscape. Hence, the modeling actions are coincided with the catchment behaviour and close to the "reality". The presented methodology is regarding hydrologic model as a tool to test our
Quasi-realistic distribution of interaction fields leading to a variant of Ising spin glass model
International Nuclear Information System (INIS)
Tanasa, Radu; Enachescu, Cristian; Stancu, Alexandru; Linares, Jorge; Varret, Francois
2004-01-01
The distribution of interaction fields of an Ising-like system, obtained by Monte Carlo entropic sampling is used for modeling the hysteretic behavior of patterned media made of magnetic particles with a common anisotropy axis; a variant of the canonical Edwards-Anderson Ising spin glass model is introduced
Towards more realistic projections of soil carbon dynamics by Earth System Models
Luo, Y.; Ahlström, A.; Allison, S.D.; Batjes, N.H.; Brovkin, V.; Carvalhais, N.; Chappell, A.; Ciais, P.; Davidson, E.A.; Finzi, A.
2016-01-01
Soil carbon (C) is a critical component of Earth system models (ESMs), and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the third to fifth assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C
Gasification of biomass in a fixed bed downdraft gasifier--a realistic model including tar.
Barman, Niladri Sekhar; Ghosh, Sudip; De, Sudipta
2012-03-01
This study presents a model for fixed bed downdraft biomass gasifiers considering tar also as one of the gasification products. A representative tar composition along with its mole fractions, as available in the literature was used as an input parameter within the model. The study used an equilibrium approach for the applicable gasification reactions and also considered possible deviations from equilibrium to further upgrade the equilibrium model to validate a range of reported experimental results. Heat balance was applied to predict the gasification temperature and the predicted values were compared with reported results in literature. A comparative study was made with some reference models available in the literature and also with experimental results reported in the literature. Finally a predicted variation of performance of the gasifier by this validated model for different air-fuel ratio and moisture content was also discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.
Developing a realistic sexual network model of chlamydia transmission in Britain
Directory of Open Access Journals (Sweden)
Mercer Catherine
2006-01-01
Full Text Available Abstract Background A national chlamydia screening programme is currently being rolled out in the UK and other countries. However, much of the epidemiology remains poorly understood. In this paper we present a stochastic, individual based, dynamic sexual network model of chlamydia transmission and its parameterisation. Mathematical models provide a theoretical framework for understanding the key epidemiological features of chlamydia: sexual behaviour, health care seeking and transmission dynamics. Results The model parameters were estimated either directly or by systematic fitting to a variety of appropriate data sources. The fitted model was representative of sexual behaviour, chlamydia epidemiology and health care use in England. We were able to recapture the observed age distribution of chlamydia prevalence. Conclusion Estimating parameters for models of sexual behaviour and transmission of chlamydia is complex. Most of the parameter values are highly correlated, highly variable and there is little empirical evidence to inform estimates. We used a novel approach to estimate the rate of active treatment seeking, by combining data sources, which improved the credibility of the model results. The model structure is flexible and is broadly applicable to other developed world settings and provides a practical tool for public health decision makers.
SMART-DS: Synthetic Models for Advanced, Realistic Testing: Distribution Systems and Scenarios
Energy Technology Data Exchange (ETDEWEB)
Palmintier, Bryan: Hodge, Bri-Mathias
2017-01-26
This presentation provides a Smart-DS project overview and status update for the ARPA-e GRID DATA program meeting 2017, including distribution systems, models, and scenarios, as well as opportunities for GRID DATA collaborations.
Air traffic management accident risk, part 1: the limits of realistic modelling
Brooker, Peter
2005-01-01
The prime goal of the Air Traffic Management (ATM) system is to control accident risk. Some key questions are posed, including: What do design safety targets really mean and imply for risk modelling? In what circumstances can future accident risk really be modelled with sufficient precision? If risk cannot be estimated with precision, then how is safety to be assured with traffic growth and operational/technical changes? This paper endeavours to answer these questions by an ...
Rodehacke, Christian; Mottram, Ruth; Langen, Peter; Madsen, Marianne; Yang, Shuting; Boberg, Fredrik; Christensen, Jens
2017-04-01
The surface mass balance (SMB) is the most import boundary conditions for the state of glaciers and ice sheets. Hence its representation in numerical model simulations is of highest interest for glacier, ice cap and ice sheet modeling efforts. While descent SMB distributions of the current climate could be interfered with the help of various observation techniques and platforms, its construction for older past and future climates relies on input from spatially coarse resolved global climate models or reconstructions. These coarse SMB estimates with a footprint in the order of 100 km could hardly resolve the marginal ablations zones where the Greenland ice sheets, for instance, loses snow and ice. We present a downscaling method that is based on the physical calculation of the surface mass and energy balance. By the consequent application of universal and computationally cheap parameterizations we get an astonishing good representation of the SMB distribution including its marginal ablation zone. However the method has its limitations; for example wrong accumulation rates due to an insufficient precipitation field leaves its imprint on the SMB distribution. Also the still not satisfactory description of the bare ice albedo, in particular, in parts of Greenland is a challenge. We inspect our Greenland SMB fields' for various forcings and compare them with some widely used reference fields in the community to highlight the weakness and strength of our approach. We use the ERA-Interim reanalyzes period starting in 1979 directly as well as dynamically downscaled by our regional climate model HIRHAM (5 km resolution). Also SMB distributions obtained from the climate model EC-Earth with a resolution of T159 (approx. 125 km resolution in Greenland) are used either directly or downscaled with our regional climate model HIRHAM. Model-based End-of-the-century SMB estimates give an outlook of the future.
Steinig, S; Harlaß, J; Park, W; Latif, M
2018-02-07
The simulation of Sahel rainfall and its onset during the West African Monsoon (WAM) remains a challenge for current state-of-the-art climate models due to their persistent biases, especially in the tropical Atlantic region. Here we show that improved representation of Atlantic Cold Tongue (ACT) development is essential for a more realistic seasonal evolution of the WAM, which is due to a further inland migration of the precipitation maximum. The observed marked relationship between ACT development and Sahel rainfall onset only can be reproduced by a climate model, the Kiel Climate Model (KCM), when sufficiently high resolution in its atmospheric component is employed, enabling enhanced equatorial Atlantic interannual sea surface temperature variability in the ACT region relative to versions with coarser atmospheric resolution. The ACT/Sahel rainfall relationship in the model critically depends on the correct seasonal phase-locking of the interannual variability rather than on its magnitude. We compare the KCM results with those obtained from climate models participating in the Coupled Model Intercomparison Project phase 5 (CMIP5).
Validation of Tilt Gain under Realistic Path Loss Model and Network Scenario
DEFF Research Database (Denmark)
Nguyen, Huan Cong; Rodriguez, Ignacio; Sørensen, Troels Bundgaard
2013-01-01
Despite being a simple and commonly-applied radio optimization technique, the impact on practical network performance from base station antenna downtilt is not well understood. Most published studies based on empirical path loss models report tilt angles and performance gains that are far higher...... than practical experience suggests. We motivate in this paper, based on a practical LTE scenario, that the discrepancy partly lies in the path loss model, and shows that a more detailed semi-deterministic model leads to both lower gains in terms of SINR, outage probability and downlink throughput...... and lower optimum tilt settings. Furthermore, we show that a simple geometrically based tilt optimization algorithm can outperform other tilt profiles, including the setting applied by the cellular operator in the specific case. In general, the network performance is not highly sensitive to the tilt...
DEFF Research Database (Denmark)
Lowes, F.J.; Olsen, Nils
2004-01-01
, led to quite inaccurate variance estimates. We estimate correction factors which range from 1/4 to 20, with the largest increases being for the zonal, m = 0, and sectorial, m = n, terms. With no correction, the OSVM variances give a mean-square vector field error of prediction over the Earth's surface......Most modern spherical harmonic geomagnetic models based on satellite data include estimates of the variances of the spherical harmonic coefficients of the model; these estimates are based on the geometry of the data and the fitting functions, and on the magnitude of the residuals. However...
Piecewise deterministic processes in biological models
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...
Interaction between π mesons and nucleons in a realistic dual model
International Nuclear Information System (INIS)
Antonov, E.N.; Kudryavtsev, V.A.
1985-01-01
The narrow-resonance model with quantized slope of the Regge trajectories proposed earlier by one of the authors is used to describe the interaction between π mesons and nucleons. The value of the coupling g 2 /sub piN/Nroughly-equal12 is found in the Born approximation
An approach to creating a more realistic working model from a protein data bank entry.
Brandon, Christopher J; Martin, Benjamin P; McGee, Kelly J; Stewart, James J P; Braun-Sand, Sonja B
2015-01-01
An accurate model of three-dimensional protein structure is important in a variety of fields such as structure-based drug design and mechanistic studies of enzymatic reactions. While the entries in the Protein Data Bank ( http://www.pdb.org ) provide valuable information about protein structures, a small fraction of the PDB structures were found to contain anomalies not reported in the PDB file. The semiempirical PM7 method in MOPAC2012 was used for identifying anomalously short hydrogen bonds, C-H⋯O/C-H⋯N interactions, non-bonding close contacts, and unrealistic covalent bond lengths in recently published Protein Data Bank files. It was also used to generate new structures with these faults removed. When the semiempirical models were compared to those of PDB_REDO (http://www.cmbi.ru.nl/pdb_redo/), the clashscores, as defined by MolProbity ( http://molprobity.biochem.duke.edu/), were better in about 50% of the structures. The semiempirical models also had a lower root-mean-square-deviation value in nearly all cases than those from PDB_REDO, indicative of a better conservation of the tertiary structure. Finally, the semiempirical models were found to have lower clashscores than the initial PDB file in all but one case. Because this approach maintains as much of the original tertiary structure as possible while improving anomalous interactions, it should be useful to theoreticians, experimentalists, and crystallographers investigating the structure and function of proteins.
Realistic D-brane models on warped throats: Fluxes, hierarchies and moduli stabilization
International Nuclear Information System (INIS)
Cascales, J.F.G.; Garcia del Moral, M.P.; Quevedo, F.; Uranga, A.
2004-01-01
We describe the construction of string theory models with semirealistic spectrum in a sector of (anti) D3-branes located at an orbifold singularity at the bottom of a highly warped throat geometry, which is a generalisation of the Klebanov-Strassler deformed conifold. These models realise the Randall-Sundrum proposal to naturally generate the Planck/electroweak hierarchy in a concrete string theory embedding, and yielding interesting chiral open string spectra. We describe examples with Standard Model gauge group (or left-right symmetric extensions) and three families of SM fermions, with correct quantum numbers including hypercharge. The dilaton and complex structure moduli of the geometry are stabilised by the 3-form fluxes required to build the throat. We describe diverse issues concerning the stabilisation of geometric Kahler moduli, like blow-up modes of the orbifold singularities, via D term potentials and gauge theory non-perturbative effects, like gaugino condensation. This local geometry, once embedded in a full compactification, could give rise to models with all moduli stabilised, and with the potential to lead to de Sitter vacua. Issues of gauge unification, proton stability, supersymmetry breaking and Yukawa couplings are also discussed. (author)
International Nuclear Information System (INIS)
Lindstrom, F.T.; Cawlfield, D.E.; Donahue, M.E.; Emer, D.F.; Shott, G.J.
1992-01-01
US DOE Order 5820.2A (1988) requires that a performance assessment of all new and existing low-level radioactive waste management sites be made. An integral part of every performance assessment is the mathematical modeling of the transport and fate of noble gas radionuclides in the gas phase. Current in depth site characterization of the high desert alluvium in Area 5 of the Nevada Test Site (NTS) is showing that the alluvium is very very dry all the way to the water table (240 meters below land surface). The potential for radioactive noble gas (e.g. Rn-220 and Rn-222) transport to the atmosphere from shallow land burial of Thorium and Uranium waste is very high. Objectives of this modeling effort include: Construct a physics based sits specific noble gas transport model; Include induced advection due to barometric pressure changes at the atmospheric boundary layer (thin) - dry desert alluvium interface; User selected option for use of NOAA barometric pressure or a ''home brewed'' barometric pressure wave made up of up to 15 sinusoids and cosinusoids; Use the model to help make engineering decisions on the design of the burial pits and associated closure caps
STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies
Directory of Open Access Journals (Sweden)
Hepburn Iain
2012-05-01
Full Text Available Abstract Background Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins, conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. Results We describe STEPS, a stochastic reaction–diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction–diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. Conclusion STEPS simulates
Directory of Open Access Journals (Sweden)
Sebastian Oeder
Full Text Available Ship engine emissions are important with regard to lung and cardiovascular diseases especially in coastal regions worldwide. Known cellular responses to combustion particles include oxidative stress and inflammatory signalling.To provide a molecular link between the chemical and physical characteristics of ship emission particles and the cellular responses they elicit and to identify potentially harmful fractions in shipping emission aerosols.Through an air-liquid interface exposure system, we exposed human lung cells under realistic in vitro conditions to exhaust fumes from a ship engine running on either common heavy fuel oil (HFO or cleaner-burning diesel fuel (DF. Advanced chemical analyses of the exhaust aerosols were combined with transcriptional, proteomic and metabolomic profiling including isotope labelling methods to characterise the lung cell responses.The HFO emissions contained high concentrations of toxic compounds such as metals and polycyclic aromatic hydrocarbon, and were higher in particle mass. These compounds were lower in DF emissions, which in turn had higher concentrations of elemental carbon ("soot". Common cellular reactions included cellular stress responses and endocytosis. Reactions to HFO emissions were dominated by oxidative stress and inflammatory responses, whereas DF emissions induced generally a broader biological response than HFO emissions and affected essential cellular pathways such as energy metabolism, protein synthesis, and chromatin modification.Despite a lower content of known toxic compounds, combustion particles from the clean shipping fuel DF influenced several essential pathways of lung cell metabolism more strongly than particles from the unrefined fuel HFO. This might be attributable to a higher soot content in DF. Thus the role of diesel soot, which is a known carcinogen in acute air pollution-induced health effects should be further investigated. For the use of HFO and DF we recommend a
Dilger, Marco; Paur, Hanns-Rudolf; Schlager, Christoph; Mülhopt, Sonja; Diabaté, Silvia; Weiss, Carsten; Stengel, Benjamin; Rabe, Rom; Harndorf, Horst; Torvela, Tiina; Jokiniemi, Jorma K.; Hirvonen, Maija-Riitta; Schmidt-Weber, Carsten; Traidl-Hoffmann, Claudia; BéruBé, Kelly A.; Wlodarczyk, Anna J.; Prytherch, Zoë; Michalke, Bernhard; Krebs, Tobias; Prévôt, André S. H.; Kelbg, Michael; Tiggesbäumker, Josef; Karg, Erwin; Jakobi, Gert; Scholtes, Sorana; Schnelle-Kreis, Jürgen; Lintelmann, Jutta; Matuschek, Georg; Sklorz, Martin; Klingbeil, Sophie; Orasche, Jürgen; Richthammer, Patrick; Müller, Laarnie; Elsasser, Michael; Reda, Ahmed; Gröger, Thomas; Weggler, Benedikt; Schwemer, Theo; Czech, Hendryk; Rüger, Christopher P.; Abbaszade, Gülcin; Radischat, Christian; Hiller, Karsten; Buters, Jeroen T. M.; Dittmar, Gunnar; Zimmermann, Ralf
2015-01-01
Background Ship engine emissions are important with regard to lung and cardiovascular diseases especially in coastal regions worldwide. Known cellular responses to combustion particles include oxidative stress and inflammatory signalling. Objectives To provide a molecular link between the chemical and physical characteristics of ship emission particles and the cellular responses they elicit and to identify potentially harmful fractions in shipping emission aerosols. Methods Through an air-liquid interface exposure system, we exposed human lung cells under realistic in vitro conditions to exhaust fumes from a ship engine running on either common heavy fuel oil (HFO) or cleaner-burning diesel fuel (DF). Advanced chemical analyses of the exhaust aerosols were combined with transcriptional, proteomic and metabolomic profiling including isotope labelling methods to characterise the lung cell responses. Results The HFO emissions contained high concentrations of toxic compounds such as metals and polycyclic aromatic hydrocarbon, and were higher in particle mass. These compounds were lower in DF emissions, which in turn had higher concentrations of elemental carbon (“soot”). Common cellular reactions included cellular stress responses and endocytosis. Reactions to HFO emissions were dominated by oxidative stress and inflammatory responses, whereas DF emissions induced generally a broader biological response than HFO emissions and affected essential cellular pathways such as energy metabolism, protein synthesis, and chromatin modification. Conclusions Despite a lower content of known toxic compounds, combustion particles from the clean shipping fuel DF influenced several essential pathways of lung cell metabolism more strongly than particles from the unrefined fuel HFO. This might be attributable to a higher soot content in DF. Thus the role of diesel soot, which is a known carcinogen in acute air pollution-induced health effects should be further investigated. For the
Stochastic modelling of dynamical systems in biology
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
Neutrino Textures in the Light of Super-Kamiokande Data and a Realistic String Model
Ellis, Jonathan Richard; Lola, S; Nanopoulos, Dimitri V
1999-01-01
Motivated by the Super-Kamiokande atmospheric neutrino data, we discuss possible textures for Majorana and Dirac neutrino masses within the see-saw framework. The main purposes of this paper are twofold: first to obtain intuition from a purely phenomenological analysis, and secondly to explore to what extent it may be realized in a specific model. We comment initially on the simplified two-generation case, emphasizing that large mixing is not incompatible with a large hierarchy of mass eigenvalues. We also emphasize that renormalization-group effects may amplify neutrino mixing, presenting semi-analytic expressions for estimating this amplification. Several examples are then given of three-family neutrino mass textures which may also accommodate the persistent solar neutrino deficit, with different assumptions for the neutrino Dirac mass matrices. We comment on a few features of neutrino mass textures arising in models with a U(1) flavour symmetry. Finally, we discuss the possible pattern of neutrino masses i...
Anderson, D. E., Jr.; Meier, R. R.; Hodges, R. R., Jr.; Tinsley, B. A.
1987-01-01
The H Balmer alpha nightglow is investigated by using Monte Carlo models of asymmetric geocoronal atomic hydrogen distributions as input to a radiative transfer model of solar Lyman-beta radiation in the thermosphere and atmosphere. It is shown that it is essential to include multiple scattering of Lyman-beta radiation in the interpretation of Balmer alpha airglow data. Observations of diurnal variation in the Balmer alpha airglow showing slightly greater intensities in the morning relative to evening are consistent with theory. No evidence is found for anything other than a single sinusoidal diurnal variation of exobase density. Dramatic changes in effective temperature derived from the observed Balmer alpha line profiles are expected on the basis of changing illumination conditions in the thermosphere and exosphere as different regions of the sky are scanned.
Design and Modeling of Turbine Airfoils with Active Flow Control in Realistic Engine Conditions
2008-07-16
for cylinders make using a simple 2d model less meaningful. The solver used for the cylinder cases was SFELES, a quasi 3D large eddy simulation that...would take into account the 3d aspects of the flow. This is appropriate because the upstream flow in the tunnel is essentially laminar and at the...H2O Druck pressure transducer to measure the local cp distribution. The cp is calculated by taking the inlet total pressure from an upstream pitot
Modeling of pulsatile flow-dependent nitric oxide regulation in a realistic microvascular network.
Wang, Ruofan; Pan, Qing; Kuebler, Wolfgang M; Li, John K-J; Pries, Axel R; Ning, Gangmin
2017-09-01
Hemodynamic pulsatility has been reported to regulate microcirculatory function. To quantitatively assess the impact of flow pulsatility on the microvasculature, a mathematical model was first developed to simulate the regulation of NO production by pulsatile flow in the microcirculation. Shear stress and pressure pulsatility were selected as regulators of endothelial NO production and NO-dependent vessel dilation as feedback to control microvascular hemodynamics. The model was then applied to a real microvascular network of the rat mesentery consisting of 546 microvessels. As compared to steady flow conditions, pulsatile flow increased the average NO concentration in arterioles from 256.8±93.1nM to 274.8±101.1nM (Pflow as compared to steady flow conditions. Network perfusion and flow heterogeneity were improved under pulsatile flow conditions, and vasodilation within the network was more sensitive to heart rate changes than pulse pressure amplitude. The proposed model simulates the role of flow pulsatility in the regulation of a complex microvascular network in terms of NO concentration and hemodynamics under varied physiological conditions. Copyright © 2017 Elsevier Inc. All rights reserved.
Vermeeren, Günter; Joseph, Wout; Martens, Luc
2013-04-01
Assessing the whole-body absorption in a human in a realistic environment requires a statistical approach covering all possible exposure situations. This article describes the development of a statistical multi-path exposure method for heterogeneous realistic human body models. The method is applied for the 6-year-old Virtual Family boy (VFB) exposed to the GSM downlink at 950 MHz. It is shown that the whole-body SAR does not differ significantly over the different environments at an operating frequency of 950 MHz. Furthermore, the whole-body SAR in the VFB for multi-path exposure exceeds the whole-body SAR for worst-case single-incident plane wave exposure by 3.6%. Moreover, the ICNIRP reference levels are not conservative with the basic restrictions in 0.3% of the exposure samples for the VFB at the GSM downlink of 950 MHz. The homogeneous spheroid with the dielectric properties of the head suggested by the IEC underestimates the absorption compared to realistic human body models. Moreover, the variation in the whole-body SAR for realistic human body models is larger than for homogeneous spheroid models. This is mainly due to the heterogeneity of the tissues and the irregular shape of the realistic human body model compared to homogeneous spheroid human body models. Copyright © 2012 Wiley Periodicals, Inc.
PHOTO REALISTIC 3D MODELING WITH UAV: GEDİK AHMET PASHA MOSQUE IN AFYONKARAHİSAR
Directory of Open Access Journals (Sweden)
M. Uysal
2013-07-01
Full Text Available Many of the cultural heritages in the world have been totally or partly destroyed by natural events and human activities such as earthquake, flood and fire until the present day. Cultural heritages are legacy for us as well; it is also a fiduciary for next generation. To deliver this fiduciary to the future generations, cultural heritages have to be protected and registered. There are different methods for applying this registry but Photogrammetry is the most accurate and rapid method. Photogrammetry enables us to registry cultural heritages and generating 3D photo-realistic models. Nowadays, 3D models are being used in various fields such as education and tourism. In registration of complex and high construction by Photogrammetry, there are some problems in data acquisition and processing. Especially for high construction's photographs, some additional equipment is required such as balloon and lifter. In recent years The Unmanned Aerial Vehicles (UAV are commonly started to be used in different fields for different goals. In Photogrammetry, The UAVs are being used for particularly data acquisition. It is not always easy to capture data due to the situation of historical places and their neighbourhood. The use of UAVs for documentation of cultural heritage will make an important contribution. The main goals of this study are to survey cultural heritages by Photogrammetry and to investigate the potential of UAVs in 3D modelling. In this purpose we surveyed Gedik Ahmet Pasha Mosque photogrammetricly by UAV and will produce photorealistic 3D model. Gedik Ahmet Pasha, The Grand Vizier of Fatih Sultan Mehmet, has been in Afyonkarahisar during the campaign to Karaman between the years of 1472–1473. He wanted Architect Ayaz Agha to build a complex of Bathhouse, Mosque and a Madrasah here, Afyon, due to admiration of this city. Gedik Ahmet Pasha Mosque is in the centre of this complex. Gedik Ahmet Pasha Mosque is popularly known as Imaret Mosque among
Photo Realistic 3d Modeling with Uav: GEDİK Ahmet Pasha Mosque in AFYONKARAHİSAR
Uysal, M.; Toprak, A. S.; Polat, N.
2013-07-01
Many of the cultural heritages in the world have been totally or partly destroyed by natural events and human activities such as earthquake, flood and fire until the present day. Cultural heritages are legacy for us as well; it is also a fiduciary for next generation. To deliver this fiduciary to the future generations, cultural heritages have to be protected and registered. There are different methods for applying this registry but Photogrammetry is the most accurate and rapid method. Photogrammetry enables us to registry cultural heritages and generating 3D photo-realistic models. Nowadays, 3D models are being used in various fields such as education and tourism. In registration of complex and high construction by Photogrammetry, there are some problems in data acquisition and processing. Especially for high construction's photographs, some additional equipment is required such as balloon and lifter. In recent years The Unmanned Aerial Vehicles (UAV) are commonly started to be used in different fields for different goals. In Photogrammetry, The UAVs are being used for particularly data acquisition. It is not always easy to capture data due to the situation of historical places and their neighbourhood. The use of UAVs for documentation of cultural heritage will make an important contribution. The main goals of this study are to survey cultural heritages by Photogrammetry and to investigate the potential of UAVs in 3D modelling. In this purpose we surveyed Gedik Ahmet Pasha Mosque photogrammetricly by UAV and will produce photorealistic 3D model. Gedik Ahmet Pasha, The Grand Vizier of Fatih Sultan Mehmet, has been in Afyonkarahisar during the campaign to Karaman between the years of 1472-1473. He wanted Architect Ayaz Agha to build a complex of Bathhouse, Mosque and a Madrasah here, Afyon, due to admiration of this city. Gedik Ahmet Pasha Mosque is in the centre of this complex. Gedik Ahmet Pasha Mosque is popularly known as Imaret Mosque among the people of Afyon
Field Distribution of Transcranial Static Magnetic Stimulation in Realistic Human Head Model.
Tharayil, Joseph J; Goetz, Stefan M; Bernabei, John M; Peterchev, Angel V
2017-10-10
The objective of this work was to characterize the magnetic field (B-field) that arises in a human brain model from the application of transcranial static magnetic field stimulation (tSMS). The spatial distribution of the B-field magnitude and gradient of a cylindrical, 5.08 cm × 2.54 cm NdFeB magnet were simulated in air and in a human head model using the finite element method and calibrated with measurements in air. The B-field was simulated for magnet placements over prefrontal, motor, sensory, and visual cortex targets. The impact of magnetic susceptibility of head tissues on the B-field was quantified. Peak B-field magnitude and gradient respectively ranged from 179-245 mT and from 13.3-19.0 T/m across the cortical targets. B-field magnitude, focality, and gradient decreased with magnet-cortex distance. The variation in B-field strength and gradient across the anatomical targets largely arose from the magnet-cortex distance. Head magnetic susceptibilities had negligible impact on the B-field characteristics. The half-maximum focality of the tSMS B-field ranged from 7-12 cm 3 . This is the first presentation and characterization of the three-dimensional (3D) spatial distribution of the B-field generated in a human brain model by tSMS. These data can provide quantitative dosing guidance for tSMS applications across various cortical targets and subjects. The finding that the B-field gradient is high near the magnet edges should be considered in studies where neural tissue is placed close to the magnet. The observation that susceptibility has negligible effects confirms assumptions in the literature. © 2017 International Neuromodulation Society.
Realistic Creativity Training for Innovation Practitioners: The Know-Recognize-React Model
DEFF Research Database (Denmark)
Valgeirsdóttir, Dagný; Onarheim, Balder
2017-01-01
As creativity becomes increasingly recognized as important raw material for innovation, the importance of identifying ways to increase practitioners’ creativity through rigorously designed creativity training programs is highlighted. Therefore we sat out to design a creativity training program...... the transdisciplinary study described in this paper. Co-creation was employed as a method to ensure the three layers of focus would be taken into consideration. The result is a program called Creative Awareness Training which is based on the new Know-Recognize-React model....
CFD modelling of abdominal aortic aneurysm on hemodynamic loads using a realistic geometry with CT.
Soudah, Eduardo; Ng, E Y K; Loong, T H; Bordone, Maurizio; Pua, Uei; Narayanan, Sriram
2013-01-01
The objective of this study is to find a correlation between the abdominal aortic aneurysm (AAA) geometric parameters, wall stress shear (WSS), abdominal flow patterns, intraluminal thrombus (ILT), and AAA arterial wall rupture using computational fluid dynamics (CFD). Real AAA 3D models were created by three-dimensional (3D) reconstruction of in vivo acquired computed tomography (CT) images from 5 patients. Based on 3D AAA models, high quality volume meshes were created using an optimal tetrahedral aspect ratio for the whole domain. In order to quantify the WSS and the recirculation inside the AAA, a 3D CFD using finite elements analysis was used. The CFD computation was performed assuming that the arterial wall is rigid and the blood is considered a homogeneous Newtonian fluid with a density of 1050 kg/m(3) and a kinematic viscosity of 4 × 10(-3) Pa·s. Parallelization procedures were used in order to increase the performance of the CFD calculations. A relation between AAA geometric parameters (asymmetry index ( β ), saccular index ( γ ), deformation diameter ratio ( χ ), and tortuosity index ( ε )) and hemodynamic loads was observed, and it could be used as a potential predictor of AAA arterial wall rupture and potential ILT formation.
CFD Modelling of Abdominal Aortic Aneurysm on Hemodynamic Loads Using a Realistic Geometry with CT
Directory of Open Access Journals (Sweden)
Eduardo Soudah
2013-01-01
Full Text Available The objective of this study is to find a correlation between the abdominal aortic aneurysm (AAA geometric parameters, wall stress shear (WSS, abdominal flow patterns, intraluminal thrombus (ILT, and AAA arterial wall rupture using computational fluid dynamics (CFD. Real AAA 3D models were created by three-dimensional (3D reconstruction of in vivo acquired computed tomography (CT images from 5 patients. Based on 3D AAA models, high quality volume meshes were created using an optimal tetrahedral aspect ratio for the whole domain. In order to quantify the WSS and the recirculation inside the AAA, a 3D CFD using finite elements analysis was used. The CFD computation was performed assuming that the arterial wall is rigid and the blood is considered a homogeneous Newtonian fluid with a density of 1050 kg/m3 and a kinematic viscosity of 4×10-3 Pa·s. Parallelization procedures were used in order to increase the performance of the CFD calculations. A relation between AAA geometric parameters (asymmetry index (β, saccular index (γ, deformation diameter ratio (χ, and tortuosity index (ε and hemodynamic loads was observed, and it could be used as a potential predictor of AAA arterial wall rupture and potential ILT formation.
Directory of Open Access Journals (Sweden)
L. Sun
2007-10-01
Full Text Available In order to study the filter effect of the background winds on the propagation of gravity waves, a three-dimensional transfer function model is developed on the basis of the complex dispersion relation of internal gravity waves in a stratified dissipative atmosphere with background winds. Our model has successfully represented the main results of the ray tracing method, e.g. the trend of the gravity waves to travel in the anti-windward direction. Furthermore, some interesting characteristics are manifest as follows: (1 The method provides the distribution characteristic of whole wave fields which propagate in the way of the distorted concentric circles at the same altitude under the control of the winds. (2 Through analyzing the frequency and wave number response curve of the transfer function, we find that the gravity waves in a wave band of about 15–30 min periods and of about 200–400 km horizontal wave lengths are most likely to propagate to the 300-km ionospheric height. Furthermore, there is an obvious frequency deviation for gravity waves propagating with winds in the frequency domain. The maximum power of the transfer function with background winds is smaller than that without background winds. (3 The atmospheric winds may act as a directional filter that will permit gravity wave packets propagating against the winds to reach the ionospheric height with minimum energy loss.
Instance-Based Generative Biological Shape Modeling.
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.
Realistic Creativity Training for Innovation Practitioners: The Know-Recognize-React Model
DEFF Research Database (Denmark)
Valgeirsdóttir, Dagný; Onarheim, Balder
2017-01-01
As creativity becomes increasingly recognized as important raw material for innovation, the importance of identifying ways to increase practitioners’ creativity through rigorously designed creativity training programs is highlighted. Therefore we sat out to design a creativity training program sp...... the transdisciplinary study described in this paper. Co-creation was employed as a method to ensure the three layers of focus would be taken into consideration. The result is a program called Creative Awareness Training which is based on the new Know-Recognize-React model.......As creativity becomes increasingly recognized as important raw material for innovation, the importance of identifying ways to increase practitioners’ creativity through rigorously designed creativity training programs is highlighted. Therefore we sat out to design a creativity training program...
Cosandier-Rimélé, D.; Ramantani, G.; Zentner, J.; Schulze-Bonhage, A.; Dümpelmann, M.
2017-10-01
Objective. Electrical source localization (ESL) deriving from scalp EEG and, in recent years, from intracranial EEG (iEEG), is an established method in epilepsy surgery workup. We aimed to validate the distributed ESL derived from scalp EEG and iEEG, particularly regarding the spatial extent of the source, using a realistic epileptic spike activity simulator. Approach. ESL was applied to the averaged scalp EEG and iEEG spikes of two patients with drug-resistant structural epilepsy. The ESL results for both patients were used to outline the location and extent of epileptic cortical patches, which served as the basis for designing a spatiotemporal source model. EEG signals for both modalities were then generated for different anatomic locations and spatial extents. ESL was subsequently performed on simulated signals with sLORETA, a commonly used distributed algorithm. ESL accuracy was quantitatively assessed for iEEG and scalp EEG. Main results. The source volume was overestimated by sLORETA at both EEG scales, with the error increasing with source size, particularly for iEEG. For larger sources, ESL accuracy drastically decreased, and reconstruction volumes shifted to the center of the head for iEEG, while remaining stable for scalp EEG. Overall, the mislocalization of the reconstructed source was more pronounced for iEEG. Significance. We present a novel multiscale framework for the evaluation of distributed ESL, based on realistic multiscale EEG simulations. Our findings support that reconstruction results for scalp EEG are often more accurate than for iEEG, owing to the superior 3D coverage of the head. Particularly the iEEG-derived reconstruction results for larger, widespread generators should be treated with caution.
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.
Integrating interactive computational modeling in biology curricula.
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.
International Nuclear Information System (INIS)
Veress, Alexander I.; Segars, W. Paul; Weiss, Jeffrey A.; Tsui, Benjamin M.W.; Gullberg, Grant T.
2006-01-01
The 4D NURBS-based Cardiac-Torso (NCAT) phantom, which provides a realistic model of the normal human anatomy and cardiac and respiratory motions, is used in medical imaging research to evaluate and improve imaging devices and techniques, especially dynamic cardiac applications. One limitation of the phantom is that it lacks the ability to accurately simulate altered functions of the heart that result from cardiac pathologies such as coronary artery disease (CAD). The goal of this work was to enhance the 4D NCAT phantom by incorporating a physiologically based, finite-element (FE) mechanical model of the left ventricle (LV) to simulate both normal and abnormal cardiac motions. The geometry of the FE mechanical model was based on gated high-resolution x-ray multi-slice computed tomography (MSCT) data of a healthy male subject. The myocardial wall was represented as transversely isotropichyperelastic material, with the fiber angle varying from -90 degrees at the epicardial surface, through 0 degrees at the mid-wall, to 90 degrees at the endocardial surface. A time varying elastance model was used to simulate fiber contraction, and physiological intraventricular systolic pressure-time curves were applied to simulate the cardiac motion over the entire cardiac cycle. To demonstrate the ability of the FE mechanical model to accurately simulate the normal cardiac motion as well abnormal motions indicative of CAD, a normal case and two pathologic cases were simulated and analyzed. In the first pathologic model, a subendocardial anterior ischemic region was defined. A second model was created with a transmural ischemic region defined in the same location. The FE based deformations were incorporated into the 4D NCAT cardiac model through the control points that define the cardiac structures in the phantom which were set to move according to the predictions of the mechanical model. A simulation study was performed using the FE-NCAT combination to investigate how the
Czech Academy of Sciences Publication Activity Database
Vlček, Lukáš; Nezbeda, Ivo
2004-01-01
Roč. 102, č. 5 (2004), s. 485-497 ISSN 0026-8976 R&D Projects: GA ČR GA203/02/0764; GA AV ČR IAA4072303; GA AV ČR IAA4072309 Institutional research plan: CEZ:AV0Z4072921 Keywords : primitive model * association fluids * ethanol Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.406, year: 2004
Akhlaghi, Parisa; Ebrahimi-Khankook, Atiyeh; Vejdani-Noghreiyan, Alireza
2017-05-01
In head computed tomography, radiation upon the eye lens (as an organ with high radiosensitivity) may cause lenticular opacity and cataracts. Therefore, quantitative dose assessment due to exposure of the eye lens and surrounding tissue is a matter of concern. For this purpose, an accurate eye model with realistic geometry and shape, in which different eye substructures are considered, is needed. To calculate the absorbed radiation dose of visual organs during head computed tomography scans, in this study, an existing sophisticated eye model was inserted at the related location in the head of the reference adult male phantom recommended by the International Commission on Radiological Protection (ICRP). Then absorbed doses and distributions of energy deposition in different parts of this eye model were calculated and compared with those based on a previous simple eye model. All calculations were done using the Monte Carlo code MCNP4C for tube voltages of 80, 100, 120 and 140 kVp. In spite of the similarity of total dose to the eye lens for both eye models, the dose delivered to the sensitive zone, which plays an important role in the induction of cataracts, was on average 3% higher for the sophisticated model as compared to the simple model. By increasing the tube voltage, differences between the total dose to the eye lens between the two phantoms decrease to 1%. Due to this level of agreement, use of the sophisticated eye model for patient dosimetry is not necessary. However, it still helps for an estimation of doses received by different eye substructures separately.
Energy Technology Data Exchange (ETDEWEB)
Veress, Alexander I.; Segars, W. Paul; Weiss, Jeffrey A.; Tsui,Benjamin M.W.; Gullberg, Grant T.
2006-08-02
The 4D NURBS-based Cardiac-Torso (NCAT) phantom, whichprovides a realistic model of the normal human anatomy and cardiac andrespiratory motions, is used in medical imaging research to evaluate andimprove imaging devices and techniques, especially dynamic cardiacapplications. One limitation of the phantom is that it lacks the abilityto accurately simulate altered functions of the heart that result fromcardiac pathologies such as coronary artery disease (CAD). The goal ofthis work was to enhance the 4D NCAT phantom by incorporating aphysiologically based, finite-element (FE) mechanical model of the leftventricle (LV) to simulate both normal and abnormal cardiac motions. Thegeometry of the FE mechanical model was based on gated high-resolutionx-ray multi-slice computed tomography (MSCT) data of a healthy malesubject. The myocardial wall was represented as transversely isotropichyperelastic material, with the fiber angle varying from -90 degrees atthe epicardial surface, through 0 degreesat the mid-wall, to 90 degreesat the endocardial surface. A time varying elastance model was used tosimulate fiber contraction, and physiological intraventricular systolicpressure-time curves were applied to simulate the cardiac motion over theentire cardiac cycle. To demonstrate the ability of the FE mechanicalmodel to accurately simulate the normal cardiac motion as well abnormalmotions indicative of CAD, a normal case and two pathologic cases weresimulated and analyzed. In the first pathologic model, a subendocardialanterior ischemic region was defined. A second model was created with atransmural ischemic region defined in the same location. The FE baseddeformations were incorporated into the 4D NCAT cardiac model through thecontrol points that define the cardiac structures in the phantom whichwere set to move according to the predictions of the mechanical model. Asimulation study was performed using the FE-NCAT combination toinvestigate how the differences in contractile function
Back to the drawing board--the need for more realistic model systems for immunotherapy.
Alexander, P
1977-07-01
In experimental animals the growth of tumors which display strong immunogenicity can be slowed by immunological maneuvers that increase the magnitude of the host response to the specific tumor antigens. Such immunogeneic tumors do not, in general, cause distant metastases and may, therefore, not be relevant to the treatment of disseminated disease in man. This may explain why the current experience with immunotherapy based on such animal models has, with very few exceptions, been disappointing. Animal tumors which are not immunogenic by standard transplantation tests frequently disseminate and it seems likely that clinically useful immunotherapy has to be based on procedures which are effective against such tumors. The lack of immunogenicity detectable by transplantation may be due to the absence of tumor-specific transplantation antigens (TSTAs), in which case if there is to be any immunotherapy it will have to be direct at boosting some innate type of host resistance. Alternatively, the lack of immunogenicity may be attributable to the intervention of "escape mechanisms" which pervert the immunologically specific host response to TSTAs. In this case, the immunological maneuvre should be directed at overcoming the escape problem and not at boosting the magnitude of the specific host reaction to the TSTAs.
International Nuclear Information System (INIS)
Lentz, Eric J.; Mezzacappa, Anthony; Hix, W. Raphael; Messer, O. E. Bronson; Liebendörfer, Matthias; Bruenn, Stephen W.
2012-01-01
We have conducted a series of numerical experiments with the spherically symmetric, general relativistic, neutrino radiation hydrodynamics code AGILE-BOLTZTRAN to examine the effects of several approximations used in multidimensional core-collapse supernova simulations. Our code permits us to examine the effects of these approximations quantitatively by removing, or substituting for, the pieces of supernova physics of interest. These approximations include: (1) using Newtonian versus general relativistic gravity, hydrodynamics, and transport; (2) using a reduced set of weak interactions, including the omission of non-isoenergetic neutrino scattering, versus the current state-of-the-art; and (3) omitting the velocity-dependent terms, or observer corrections, from the neutrino Boltzmann kinetic equation. We demonstrate that each of these changes has noticeable effects on the outcomes of our simulations. Of these, we find that the omission of observer corrections is particularly detrimental to the potential for neutrino-driven explosions and exhibits a failure to conserve lepton number. Finally, we discuss the impact of these results on our understanding of current, and the requirements for future, multidimensional models.
Modelling collagen diseases: STRUCTURAL BIOLOGY
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.
Setting Parameters for Biological Models With ANIMO
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
Currenti, Gilda; Napoli, Rosalba; Del Negro, Ciro
2011-12-01
The combination of (i) DInSAR data, capable of observing deformation pattern at a spatial resolution unachievable with other sparse geodetic measurements, (ii) continuous GPS data, able to provide temporal constraints on source evolution, and (iii) numerical modeling procedures, appropriate to consider a non-uniform opening distribution of a source embedded in a 3D heterogeneous medium, allowed us to infer a complex and realistic deformation model of the magmatic intrusion that occurred in the northern flank of Etna on 13 May 2008. Numerical modeling of ground deformation data defines a near-vertical dyke intruded for 2.5 km starting from a depth of 1400 m asl right below the summit craters and reaching shallow crust level in the northern flank. From the estimated opening distribution of the propagating magma-filled crack, which reached a maximum value of about 2 m, a volumetric expansion of crustal rocks of about 5.3 × 10 6 m 3 was obtained. Also, we clarified the temporal evolution of the northward magmatic intrusion, which lasted just over 5 h with an initial magma propagation velocity of about 1.2 km/h, and decreased to about 0.24 km/h as the driving pressure lowered due to the effusive activity started at southern vents.
Biological transportation networks: Modeling and simulation
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.
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.
Structured population models in biology and epidemiology
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.
Reinhardt, James W; Gooch, Keith J
2014-02-01
Agent-based modeling was used to model collagen fibrils, composed of a string of nodes serially connected by links that act as Hookean springs. Bending mechanics are implemented as torsional springs that act upon each set of three serially connected nodes as a linear function of angular deflection about the central node. These fibrils were evaluated under conditions that simulated axial extension, simple three-point bending and an end-loaded cantilever. The deformation of fibrils under axial loading varied <0.001% from the analytical solution for linearly elastic fibrils. For fibrils between 100 μm and 200 μm in length experiencing small deflections, differences between simulated deflections and their analytical solutions were <1% for fibrils experiencing three-point bending and <7% for fibrils experiencing cantilever bending. When these new rules for fibril mechanics were introduced into a model that allowed for cross-linking of fibrils to form a network and the application of cell traction force, the fibrous network underwent macroscopic compaction and aligned between cells. Further, fibril density increased between cells to a greater extent than that observed macroscopically and appeared similar to matrical tracks that have been observed experimentally in cell-populated collagen gels. This behavior is consistent with observations in previous versions of the model that did not allow for the physically realistic simulation of fibril mechanics. The significance of the torsional spring constant value was then explored to determine its impact on remodeling of the simulated fibrous network. Although a stronger torsional spring constant reduced the degree of quantitative remodeling that occurred, the inclusion of torsional springs in the model was not necessary for the model to reproduce key qualitative aspects of remodeling, indicating that the presence of Hookean springs is essential for this behavior. These results suggest that traction force mediated matrix
Directory of Open Access Journals (Sweden)
Yunfei eShi
2014-08-01
Full Text Available The morphogenetic process of cardiac looping transforms the straight heart tube into a curved tube that resembles the shape of the future four-chambered heart. Although great progress has been made in identifying the molecular and genetic factors involved in looping, the physical mechanisms that drive this process have remained poorly understood. Recent work, however, has shed new light on this complicated problem. After briefly reviewing the current state of knowledge, we propose a relatively comprehensive hypothesis for the mechanics of the first phase of looping, termed c-looping, as the straight heart tube deforms into a c-shaped tube. According to this hypothesis, differential hypertrophic growth in the myocardium supplies the main forces that cause the heart tube to bend ventrally, while regional growth and contraction in the omphalomesenteric veins (primitive atria and compressive loads exerted by the splanchnopleuric membrane drive rightward torsion. A computational model based on realistic embryonic heart geometry is used to test this hypothesis. The behavior of the model is in reasonable agreement with available experimental data from control and perturbed embryos, offering support for our hypothesis. The results also suggest, however, that several other mechanisms contribute secondarily to normal looping, and we speculate that these mechanisms play backup roles when looping is perturbed. Finally, some outstanding questions are discussed for future study.
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)
Bridging physics and biology teaching through modeling
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.
Wijsen, N.; Poedts, S.; Pomoell, J.
2017-12-01
Solar energetic particles (SEPs) are high energy particles originating from solar eruptive events. These particles can be energised at solar flare sites during magnetic reconnection events, or in shock waves propagating in front of coronal mass ejections (CMEs). These CME-driven shocks are in particular believed to act as powerful accelerators of charged particles throughout their propagation in the solar corona. After escaping from their acceleration site, SEPs propagate through the heliosphere and may eventually reach our planet where they can disrupt the microelectronics on satellites in orbit and endanger astronauts among other effects. Therefore it is of vital importance to understand and thereby build models capable of predicting the characteristics of SEP events. The propagation of SEPs in the heliosphere can be described by the time-dependent focused transport equation. This five-dimensional parabolic partial differential equation can be solved using e.g., a finite difference method or by integrating a set of corresponding first order stochastic differential equations. In this work we take the latter approach to model SEP events under different solar wind and scattering conditions. The background solar wind in which the energetic particles propagate is computed using a magnetohydrodynamic model. This allows us to study the influence of different realistic heliospheric configurations on SEP transport. In particular, in this study we focus on exploring the influence of high speed solar wind streams originating from coronal holes that are located close to the eruption source region on the resulting particle characteristics at Earth. Finally, we discuss our upcoming efforts towards integrating our particle propagation model with time-dependent heliospheric MHD space weather modelling.
Samoudi, Amine M; Kampusch, Stefan; Tanghe, Emmeric; Széles, Jozsef C; Martens, Luc; Kaniusas, Eugenijus; Joseph, Wout
2017-10-01
Percutaneous stimulation of the auricular branch of the vagus nerve (pVNS) by miniaturized needle electrodes in the auricle gained importance as a treatment for acute and chronic pain. The objective is to establish a realistic numerical model of pVNS and investigate the effects of stimulation waveform, electrodes' depth, and electrodes' position on nerve excitation threshold and the percentage of stimulated nerves. Simulations were performed with Sim4Life. An electrostatic solver and neural tissue models were combined for electromagnetic and neural simulation. The numerical model consisted of a realistic high-resolution model of a human ear, blood vessels, nerves, and three needle electrodes. A novel 3D ear model was established, including blood vessels and nerves. The electric field distribution was extracted and evaluated. Maximum sensitivity to needles' depth and displacement was evaluated to be 9.8 and 15.5% per 0.1 mm, respectively. Stimulation was most effective using biphasic compared to mono-phasic pulses. The established model allows easy and quantitative evaluation of various stimulation setups, enabling optimization of pVNS in experimental settings. Results suggest a high sensitivity of pVNS to the electrodes' position and depth, implying the need for precise electrode positioning. Validation of the model needs to be performed.
Use of genome-scale metabolic models in evolutionary systems biology.
Papp, Balázs; Szappanos, Balázs; Notebaart, Richard A
2011-01-01
One of the major aims of the nascent field of evolutionary systems biology is to test evolutionary hypotheses that are not only realistic from a population genetic point of view but also detailed in terms of molecular biology mechanisms. By providing a mapping between genotype and phenotype for hundreds of genes, genome-scale systems biology models of metabolic networks have already provided valuable insights into the evolution of metabolic gene contents and phenotypes of yeast and other microbial species. Here we review the recent use of these computational models to predict the fitness effect of mutations, genetic interactions, evolutionary outcomes, and to decipher the mechanisms of mutational robustness. While these studies have demonstrated that even simplified models of biochemical reaction networks can be highly informative for evolutionary analyses, they have also revealed the weakness of this modeling framework to quantitatively predict mutational effects, a challenge that needs to be addressed for future progress in evolutionary systems biology.
Laser interaction with biological material mathematical modeling
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.
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...
Notions of similarity for computational biology models
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.
Xu, Jinyu; Deng, Benqiang; Fang, Yibin; Yu, Ying; Cheng, Jiyong; Wang, Shengzhang; Wang, Kuizhong; Liu, Jian-Min; Huang, Qinghai
2013-01-01
Adjusting hemodynamics via flow diverter (FD) implantation is emerging as a novel method of treating cerebral aneurysms. However, most previous FD-related hemodynamic studies were based on virtual FD deployment, which may produce different hemodynamic outcomes than realistic (in vivo) FD deployment. We compared hemodynamics between virtual FD and realistic FD deployments in rabbit aneurysm models using computational fluid dynamics (CFD) simulations. FDs were implanted for aneurysms in 14 rabbits. Vascular models based on rabbit-specific angiograms were reconstructed for CFD studies. Real FD configurations were reconstructed based on micro-CT scans after sacrifice, while virtual FD configurations were constructed with SolidWorks software. Hemodynamic parameters before and after FD deployment were analyzed. According to the metal coverage (MC) of implanted FDs calculated based on micro-CT reconstruction, 14 rabbits were divided into two groups (A, MC >35%; B, MC FD deployment, but pressure was not (P>0.05). The normalized mean WSS in Group A after realistic FD implantation was significantly lower than that of Group B. All parameters in Group B exhibited no significant difference between realistic and virtual FDs. This study confirmed MC-correlated differences in hemodynamic parameters between realistic and virtual FD deployment.
International Nuclear Information System (INIS)
Wiegel, B.; Alevra, A.V.; Siebert, B.R.L.
1994-11-01
A realistic geometry model of a Bonner sphere system with a spherical 3 He-filled proportional counter and 12 polyethylene moderating spheres with diameters ranging from 7,62 cm (3'') to 45,72 cm (18'') is introduced. The MCNP Monte Carlo computer code is used to calculate the responses of this Bonner sphere system to monoenergetic neutrons in the energy range between 1 meV to 20 MeV. The relative uncertainties of the responses due to the Monte Carlo calculations are less than 1% for spheres up to 30,48 cm (12'') in diameter and less than 2% for the 15'' and 18'' spheres. Resonances in the carbon cross section are seen as significant structures in the response functions. Additional calculations were made to study the influence of the 3 He number density and the polyethylene mass density on the response as well as the angular dependence of the Bonner sphere system. The calculated responses can be adjusted to a large set of calibration measurements with only a single fit factor common to all sphere diameters and energies. (orig.) [de
Creation of a realistic model for removal of a metallic corneal foreign body for less than $75.
Directory of Open Access Journals (Sweden)
Sayegh, Julie Sami
2017-01-01
Full Text Available Metallic corneal foreign bodies (MCFBs are one of the most common causes of ocular injury presenting to the emergency department. Delays in removal, or forceful attempts to remove the MCFB can lead to infection, further injury to the eye, and worsening of vision. In order to prevent these underlying complications, it is imperative for the medical provider to properly master this technique. As current trends in simulation become more focused on patient safety, task-trainers can provide an invaluable learning experience for residents, medical students and physicians. Models made from bovine eyes, agar plates, gelatin, and corneas created from glass and paraffin wax have been previously been created.One study also used a rubber glove filled with water to simulate intraocular measurement with a Tonopen. However the use of corneas created from ballistics gel for MCFB removal and intraocular pressure measurement has not been studied. We propose a realistic, sustainable, cost-effective MCFB task-trainer to introduce the fundamental skills required for MCFB removal and measurement of intraocular pressure with a Tonopen. A pilot survey study performed on medical students and emergency medicine resident physicians showed an increase in comfort levels performing both MCFB removal and measurement of intraocular pressure with a Tonopen after using this task-trainer.
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.
Blash, Derek M.
The region known as Low-Earth Orbit (LEO) has become populated with artificial satellites and space debris since humanities initial venture into the region. This has turned LEO into a hazardous region. Since LEO is very valuable to many different countries, there has been a push to prevent further buildup and talk of even deorbiting spent satellites and debris already in LEO. One of the more attractive concepts available for deorbiting debris and spent satellites is a Bare Electrodynamic Tether (BET). A BET is a propellantless propulsion technique in which two objects are joined together by a thin conducting material. When these tethered objects are placed in LEO, the tether sweeps across the magnetic field lines of the Earth and induces an electromotive force (emf) along the tether. Current from the space plasma is collected on the bare tether under the action of the induced emf, and this current interacts with the Earth's magnetic field to create a drag force that can be used to deorbit spent satellites and space debris. A Plasma Contactor (PC) is used to close the electrical circuit between the BET and the ionospheric plasma. The PC requires a voltage and, depending on the device, a gas flow to emit electrons through a plasma bridge to the ionospheric plasma. The PC also can require a plasma discharge electrode and a heater to condition the PC for operation. These parameters as well as the PC performance are required to build an accurate simulation of a PC and, therefore, a BET deorbiting system. This thesis focuses on the development, validation, and implementation of a simulation tool to model the effects of a realistic hollow cathode PC system model on a BET deorbit system.
Stochastic resonance in biological nonlinear evolution models
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.
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
Modelling biological pathway dynamics with Timed Automata
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
Agent-based modelling in synthetic biology.
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).
Directory of Open Access Journals (Sweden)
Jícha Miroslav
2012-04-01
Full Text Available Transport and deposition of particles in human airways has been of research interest for many years. Various experimental methods such as constant temperature anemometry, particle image velocimetry and laser-Doppler based techniques were employed for study of aerosol transport in the past. We use Phase-Doppler Particle Analyser (P/DPA for time resolved size and velocity measurement of liquid aerosol particles in a size range 1 to 8 μm. The di-2ethylhexyl sabacate (DEHS particles were produced by condensation monodisperse aerosol generator. A thin-wall transparent model of human airways with non-symmetric bifurcations and non-planar geometry containing parts from throat to 3rd-4th generation of bronchi was fabricated for the study. Several cyclic (sinusoidal breathing regimes were simulated using pneumatic breathing mechanism. Analogous steady-flow regimes were also investigated and used for comparison. An analysis of the particle velocity data was performed with aim to gain deeper understanding of the transport phenomena in the realistic bifurcating airway system. Flows of particles of different sizes in range 1 – 10 μm was found to slightly differ for extremely high Stokes numbers. Differences in steady and cyclic turbulence intensities were documented in the paper. Systematically higher turbulence intensity was found for cyclic flows and mainly in the expiration breathing phase. Negligible differences were found for behaviour of different particle size classes in the inspected range 1 to 8 μm. Possibility of velocity spectra estimation of air flow using the P/DPA data is discussed.
Modeling nonspecific interactions at biological interfaces
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.
Modeling human risk: Cell & molecular biology in context
Energy Technology Data Exchange (ETDEWEB)
NONE
1997-06-01
It is anticipated that early in the next century manned missions into outer space will occur, with a mission to Mars scheduled between 2015 and 2020. However, before such missions can be undertaken, a realistic estimation of the potential risks to the flight crews is required. One of the uncertainties remaining in this risk estimation is that posed by the effects of exposure to the radiation environment of outer space. Although the composition of this environment is fairly well understood, the biological effects arising from exposure to it are not. The reasons for this are three-fold: (1) A small but highly significant component of the radiation spectrum in outer space consists of highly charged, high energy (HZE) particles which are not routinely experienced on earth, and for which there are insufficient data on biological effects; (2) Most studies on the biological effects of radiation to date have been high-dose, high dose-rate, whereas in space, with the exception of solar particle events, radiation exposures will be low-dose, low dose-rate; (3) Although it has been established that the virtual absence of gravity in space has a profound effect on human physiology, it is not clear whether these effects will act synergistically with those of radiation exposure. A select panel will evaluate the utilizing experiments and models to accurately predict the risks associated with exposure to HZE particles. Topics of research include cellular and tissue response, health effects associated with radiation damage, model animal systems, and critical markers of Radiation response.
Modeling human risk: Cell ampersand molecular biology in context
International Nuclear Information System (INIS)
1997-06-01
It is anticipated that early in the next century manned missions into outer space will occur, with a mission to Mars scheduled between 2015 and 2020. However, before such missions can be undertaken, a realistic estimation of the potential risks to the flight crews is required. One of the uncertainties remaining in this risk estimation is that posed by the effects of exposure to the radiation environment of outer space. Although the composition of this environment is fairly well understood, the biological effects arising from exposure to it are not. The reasons for this are three-fold: (1) A small but highly significant component of the radiation spectrum in outer space consists of highly charged, high energy (HZE) particles which are not routinely experienced on earth, and for which there are insufficient data on biological effects; (2) Most studies on the biological effects of radiation to date have been high-dose, high dose-rate, whereas in space, with the exception of solar particle events, radiation exposures will be low-dose, low dose-rate; (3) Although it has been established that the virtual absence of gravity in space has a profound effect on human physiology, it is not clear whether these effects will act synergistically with those of radiation exposure. A select panel will evaluate the utilizing experiments and models to accurately predict the risks associated with exposure to HZE particles. Topics of research include cellular and tissue response, health effects associated with radiation damage, model animal systems, and critical markers of Radiation response
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...
International Nuclear Information System (INIS)
Camus, H.
1996-08-01
This is the final report of the Working Group describing: the enhancement of the previously devised V1 scenario to produce a V2 scenario which includes more detailed source term and other site specific data; the application of models in deterministic and probabilistic mode to calculate contaminant concentrations in biosphere media, and related radiation doses, contaminant intakes and health risks, including estimates of uncertainties; the comparison and analysis of the resulting calculations. A series of scenarios was developed based on data provided by Working Group members from a range of actual tailings disposal sites, culminating in the V2.2 and V2.3 scenarios. The V2.2 and V2.3 scenarios are identical in all respects, except that the V2.2 considers radioactive (U-238 chain) contaminants, whilst the V2.3 considers stable elements (As, Ni, Pb). Since the scenarios are based on data obtained from a range of actual sites, they should be considered to be generically realistic rather than representative of a particular single site. In both scenarios, the contaminants of interest are assumed to be released in leachate from a tailings pile into an underlying aquifer. They are transported in groundwater through the aquifer to a well. Water is abstracted from the well and used for: watering beef cattle; human consumption; and irrigating leafy vegetables. The beef and leafy vegetables are consumed by humans living in the area. The same contaminants are also released into the atmosphere due to the wind erosion of the pile and then deposited upon the soil, pasture and leafy vegetables. In addition, for the V2.2 scenario, Rn-222 is assumed to be released to atmosphere from the pile. Unlike the V1 scenario, no consideration is given to surface water exposure pathways. Results show that there is exceedingly good agreement between participants' deterministic and probabilistic estimates of total dose or intake. They agree within a factor of two to three for both scenarios. Even
Energy Technology Data Exchange (ETDEWEB)
Camus, H. [CEA Centre d' Etudes Nucleaires de Fontenay-aux-Roses, 92 (France). Inst. de Protection et de Surete Nucleaire] [and others
1996-08-01
This is the final report of the Working Group describing: the enhancement of the previously devised V1 scenario to produce a V2 scenario which includes more detailed source term and other site specific data; the application of models in deterministic and probabilistic mode to calculate contaminant concentrations in biosphere media, and related radiation doses, contaminant intakes and health risks, including estimates of uncertainties; the comparison and analysis of the resulting calculations. A series of scenarios was developed based on data provided by Working Group members from a range of actual tailings disposal sites, culminating in the V2.2 and V2.3 scenarios. The V2.2 and V2.3 scenarios are identical in all respects, except that the V2.2 considers radioactive (U-238 chain) contaminants, whilst the V2.3 considers stable elements (As, Ni, Pb). Since the scenarios are based on data obtained from a range of actual sites, they should be considered to be generically realistic rather than representative of a particular single site. In both scenarios, the contaminants of interest are assumed to be released in leachate from a tailings pile into an underlying aquifer. They are transported in groundwater through the aquifer to a well. Water is abstracted from the well and used for: watering beef cattle; human consumption; and irrigating leafy vegetables. The beef and leafy vegetables are consumed by humans living in the area. The same contaminants are also released into the atmosphere due to the wind erosion of the pile and then deposited upon the soil, pasture and leafy vegetables. In addition, for the V2.2 scenario, Rn-222 is assumed to be released to atmosphere from the pile. Unlike the V1 scenario, no consideration is given to surface water exposure pathways. Results show that there is exceedingly good agreement between participants' deterministic and probabilistic estimates of total dose or intake. They agree within a factor of two to three for both scenarios
Lee, Won Hee; Deng, Zhi-De; Kim, Tae-Seong; Laine, Andrew F; Lisanby, Sarah H; Peterchev, Angel V
2012-02-01
We present the first computational study investigating the electric field (E-field) strength generated by various electroconvulsive therapy (ECT) electrode configurations in specific brain regions of interest (ROIs) that have putative roles in the therapeutic action and/or adverse side effects of ECT. This study also characterizes the impact of the white matter (WM) conductivity anisotropy on the E-field distribution. A finite element head model incorporating tissue heterogeneity and WM anisotropic conductivity was constructed based on structural magnetic resonance imaging (MRI) and diffusion tensor MRI data. We computed the spatial E-field distributions generated by three standard ECT electrode placements including bilateral (BL), bifrontal (BF), and right unilateral (RUL) and an investigational electrode configuration for focal electrically administered seizure therapy (FEAST). The key results are that (1) the median E-field strength over the whole brain is 3.9, 1.5, 2.3, and 2.6 V/cm for the BL, BF, RUL, and FEAST electrode configurations, respectively, which coupled with the broad spread of the BL E-field suggests a biophysical basis for observations of superior efficacy of BL ECT compared to BF and RUL ECT; (2) in the hippocampi, BL ECT produces a median E-field of 4.8 V/cm that is 1.5-2.8 times stronger than that for the other electrode configurations, consistent with the more pronounced amnestic effects of BL ECT; and (3) neglecting the WM conductivity anisotropy results in E-field strength error up to 18% overall and up to 39% in specific ROIs, motivating the inclusion of the WM conductivity anisotropy in accurate head models. This computational study demonstrates how the realistic finite element head model incorporating tissue conductivity anisotropy provides quantitative insight into the biophysics of ECT, which may shed light on the differential clinical outcomes seen with various forms of ECT, and may guide the development of novel stimulation paradigms
International Nuclear Information System (INIS)
Won Kim, Chang; Kim, Jong Hyo
2014-01-01
Purpose: Reducing the patient dose while maintaining the diagnostic image quality during CT exams is the subject of a growing number of studies, in which simulations of reduced-dose CT with patient data have been used as an effective technique when exploring the potential of various dose reduction techniques. Difficulties in accessing raw sinogram data, however, have restricted the use of this technique to a limited number of institutions. Here, we present a novel reduced-dose CT simulation technique which provides realistic low-dose images without the requirement of raw sinogram data. Methods: Two key characteristics of CT systems, the noise equivalent quanta (NEQ) and the algorithmic modulation transfer function (MTF), were measured for various combinations of object attenuation and tube currents by analyzing the noise power spectrum (NPS) of CT images obtained with a set of phantoms. Those measurements were used to develop a comprehensive CT noise model covering the reduced x-ray photon flux, object attenuation, system noise, and bow-tie filter, which was then employed to generate a simulated noise sinogram for the reduced-dose condition with the use of a synthetic sinogram generated from a reference CT image. The simulated noise sinogram was filtered with the algorithmic MTF and back-projected to create a noise CT image, which was then added to the reference CT image, finally providing a simulated reduced-dose CT image. The simulation performance was evaluated in terms of the degree of NPS similarity, the noise magnitude, the bow-tie filter effect, and the streak noise pattern at photon starvation sites with the set of phantom images. Results: The simulation results showed good agreement with actual low-dose CT images in terms of their visual appearance and in a quantitative evaluation test. The magnitude and shape of the NPS curves of the simulated low-dose images agreed well with those of real low-dose images, showing discrepancies of less than +/−3.2% in
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.
Structural sensitivity of biological models revisited.
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.
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.
Continuum Modeling of Biological Network Formation
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.
Unit testing, model validation, and biological simulation.
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.
Neural network models: from biology to many - body phenomenology
International Nuclear Information System (INIS)
Clark, J.W.
1993-01-01
Theoretical work in neural networks has a strange feel for most physicists. In some cases the aspect of design becomes paramount. More comfortable ground at least for many body theorists may be found in realistic biological simulation, although the complexity of most problems is so awesome that incisive results will be hard won. It has also shown the impressive capabilities of artificial networks in pattern recognition and classification may be exploited to solve management problems in experimental physics and for discovery of radically new theoretical description of physical systems. This advance represents an important step towards the ultimate goal of neuro biological paradigm. (A.B.)
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.
Spherical cancer models in tumor biology.
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.
Simple and Realistic Data Generation
DEFF Research Database (Denmark)
Pedersen, Kenneth Houkjær; Torp, Kristian; Wind, Rico
2006-01-01
This paper presents a generic, DBMS independent, and highly extensible relational data generation tool. The tool can efficiently generate realistic test data for OLTP, OLAP, and data streaming applications. The tool uses a graph model to direct the data generation. This model makes it very simple...... to generate data even for large database schemas with complex inter- and intra table relationships. The model also makes it possible to generate data with very accurate characteristics....
Multiscale mechanical modeling of soft biological tissues
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.
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
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.
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.
Logic-statistic modeling and analysis of biological sequence data
DEFF Research Database (Denmark)
Christiansen, Henning
2007-01-01
We describe here the intentions and plans of a newly started, funded research project in order to further the dialogue with the international research in the field. The purpose is to obtain experiences for realistic applications of flexible and powerful modeling tools that integrate logic and sta...... and statistics, as exemplified by the PRISM system. As part of this, we will develop systematic and automatic optimizations, and the overall goal is to see how far it is possible to promote such techniques in computational biology....
Stockmann, M; Schikora, J; Becker, D-A; Flügge, J; Noseck, U; Brendler, V
2017-11-01
One natural retardation process to be considered in risk assessment for contaminants in the environment is sorption on mineral surfaces. A realistic geochemical modeling is of high relevance in many application areas such as groundwater protection, environmental remediation, or disposal of hazardous waste. Most often concepts with constant distribution coefficients (K d -values) are applied in geochemical modeling with the advantage to be simple and computationally fast, but not reflecting changes in geochemical conditions. In this paper, we describe an innovative and efficient method, where the smart K d -concept, a mechanistic approach mainly based on surface complexation modeling, is used (and modified for complex geochemical models) to calculate and apply realistic distribution coefficients. Using the geochemical speciation code PHREEQC, multidimensional smart K d -matrices are computed as a function of varying (or uncertain) environmental conditions. On the one hand, sensitivity and uncertainty statements for the distribution coefficients can be derived. On the other hand, smart K d -matrices can be used in reactive transport (or migration) codes (not shown here). This strategy has various benefits: (1) rapid computation of K d -values for large numbers of environmental parameter combinations; (2) variable geochemistry is taken into account more realistically; (3) efficiency in computing time is ensured, and (4) uncertainty and sensitivity analysis are accessible. Results are presented exemplarily for the sorption of uranium(VI) onto a natural sandy aquifer material and are compared to results based on the conventional K d -concept. In general, the sorption behavior of U(VI) in dependence of changing geochemical conditions is described quite well. Copyright © 2017 Elsevier Ltd. All rights reserved.
Nonlinear Rheology in a Model Biological Tissue.
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.
Topological Data Analysis of Biological Aggregation Models
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
Computational Modeling of Biological Systems From Molecules to Pathways
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.
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
Rahimi-Gorji, Mohammad; Gorji, Tahereh B; Gorji-Bandpy, Mofid
2016-07-01
In the present investigation, detailed two-phase flow modeling of airflow, transport and deposition of micro-particles (1-10µm) in a realistic tracheobronchial airway geometry based on CT scan images under various breathing conditions (i.e. 10-60l/min) was considered. Lagrangian particle tracking has been used to investigate the particle deposition patterns in a model comprising mouth up to generation G6 of tracheobronchial airways. The results demonstrated that during all breathing patterns, the maximum velocity change occurred in the narrow throat region (Larynx). Due to implementing a realistic geometry for simulations, many irregularities and bending deflections exist in the airways model. Thereby, at higher inhalation rates, these areas are prone to vortical effects which tend to entrap the inhaled particles. According to the results, deposition fraction has a direct relationship with particle aerodynamic diameter (for dp=1-10µm). Enhancing inhalation flow rate and particle size will largely increase the inertial force and consequently, more particle deposition is evident suggesting that inertial impaction is the dominant deposition mechanism in tracheobronchial airways. Copyright © 2016 Elsevier Ltd. All rights reserved.
Jiao, Jialong; Ren, Huilong; Adenya, Christiaan Adika; Chen, Chaohe
2017-10-29
Wave-induced motion and load responses are important criteria for ship performance evaluation. Physical experiments have long been an indispensable tool in the predictions of ship's navigation state, speed, motions, accelerations, sectional loads and wave impact pressure. Currently, majority of the experiments are conducted in laboratory tank environment, where the wave environments are different from the realistic sea waves. In this paper, a laboratory tank testing system for ship motions and loads measurement is reviewed and reported first. Then, a novel large-scale model measurement technique is developed based on the laboratory testing foundations to obtain accurate motion and load responses of ships in realistic sea conditions. For this purpose, a suite of advanced remote control and telemetry experimental system was developed in-house to allow for the implementation of large-scale model seakeeping measurement at sea. The experimental system includes a series of technique sensors, e.g., the Global Position System/Inertial Navigation System (GPS/INS) module, course top, optical fiber sensors, strain gauges, pressure sensors and accelerometers. The developed measurement system was tested by field experiments in coastal seas, which indicates that the proposed large-scale model testing scheme is capable and feasible. Meaningful data including ocean environment parameters, ship navigation state, motions and loads were obtained through the sea trial campaign.
Directory of Open Access Journals (Sweden)
E. E. Popova
2006-01-01
Full Text Available A global general circulation model coupled to a simple six-compartment ecosystem model is used to study the extent to which global variability in primary and export production can be realistically predicted on the basis of advanced parameterizations of upper mixed layer physics, without recourse to introducing extra complexity in model biology. The "K profile parameterization" (KPP scheme employed, combined with 6-hourly external forcing, is able to capture short-term periodic and episodic events such as diurnal cycling and storm-induced deepening. The model realistically reproduces various features of global ecosystem dynamics that have been problematic in previous global modelling studies, using a single generic parameter set. The realistic simulation of deep convection in the North Atlantic, and lack of it in the North Pacific and Southern Oceans, leads to good predictions of chlorophyll and primary production in these contrasting areas. Realistic levels of primary production are predicted in the oligotrophic gyres due to high frequency external forcing of the upper mixed layer (accompanying paper Popova et al., 2006 and novel parameterizations of zooplankton excretion. Good agreement is shown between model and observations at various JGOFS time series sites: BATS, KERFIX, Papa and HOT. One exception is the northern North Atlantic where lower grazing rates are needed, perhaps related to the dominance of mesozooplankton there. The model is therefore not globally robust in the sense that additional parameterizations are needed to realistically simulate ecosystem dynamics in the North Atlantic. Nevertheless, the work emphasises the need to pay particular attention to the parameterization of mixed layer physics in global ocean ecosystem modelling as a prerequisite to increasing the complexity of ecosystem models.
Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.
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).
Modelling realistic TiO2 nanospheres: A benchmark study of SCC-DFTB against hybrid DFT
Selli, Daniele; Fazio, Gianluca; Di Valentin, Cristiana
2017-10-01
TiO2 nanoparticles (NPs) are nowadays considered fundamental building blocks for many technological applications. Morphology is found to play a key role with spherical NPs presenting higher binding properties and chemical activity. From the experimental point of view, the characterization of these nano-objects is extremely complex, opening a large room for computational investigations. In this work, TiO2 spherical NPs of different sizes (from 300 to 4000 atoms) have been studied with a two-scale computational approach. Global optimization to obtain stable and equilibrated nanospheres was performed with a self-consistent charge density functional tight-binding (SCC-DFTB) simulated annealing process, causing a considerable atomic rearrangement within the nanospheres. Those SCC-DFTB relaxed structures have been then optimized at the DFT(B3LYP) level of theory. We present a systematic and comparative SCC-DFTB vs DFT(B3LYP) study of the structural properties, with particular emphasis on the surface-to-bulk sites ratio, coordination distribution of surface sites, and surface energy. From the electronic point of view, we compare HOMO-LUMO and Kohn-Sham gaps, total and projected density of states. Overall, the comparisons between DFTB and hybrid density functional theory show that DFTB provides a rather accurate geometrical and electronic description of these nanospheres of realistic size (up to a diameter of 4.4 nm) at an extremely reduced computational cost. This opens for new challenges in simulations of very large systems and more extended molecular dynamics.
Huynh, Bao K; Traini, Daniela; Farkas, Dale R; Longest, P Worth; Hindle, Michael; Young, Paul M
2018-04-01
Current in vitro approaches to assess lung deposition, dissolution, and cellular transport behavior of orally inhaled products (OIPs) have relied on compendial impactors to collect drug particles that are likely to deposit in the airway; however, the main drawback with this approach is that these impactors do not reflect the airway and may not necessarily represent drug deposition behavior in vivo. The aim of this article is to describe the development and method validation of a novel hybrid in vitro approach to assess drug deposition and permeation behavior in a more representative airway model. The medium-sized Virginia Commonwealth University (VCU) mouth-throat (MT) and tracheal-bronchial (TB) realistic upper airway models were used in this study as representative models of the upper airway. The TB model was modified to accommodate two Snapwell ® inserts above the first TB airway bifurcation region to collect deposited nebulized ciprofloxacin-hydrochloride (CIP-HCL) droplets as a model drug aerosol system. Permeation characteristics of deposited nebulized CIP-HCL droplets were assessed across different synthetic membranes using the Snapwell test system. The Snapwell test system demonstrated reproducible and discriminatory drug permeation profiles for already dissolved and nebulized CIP-HCL droplets through a range of synthetic permeable membranes under different test conditions. The rate and extent of drug permeation depended on the permeable membrane material used, presence of a stirrer in the receptor compartment, and, most importantly, the drug collection method. This novel hybrid in vitro approach, which incorporates a modified version of a realistic upper airway model, coupled with the Snapwell test system holds great potential to evaluate postairway deposition characteristics, such as drug permeation and particle dissolution behavior of OIPs. Future studies will expand this approach using a cell culture-based setup instead of synthetic membranes, within a
Biological darkening of ice: measurements and models
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.
INTERVAL OBSERVER FOR A BIOLOGICAL REACTOR MODEL
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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.
Keyvanloo, A; Burke, B; Tadic, T; Warkentin, B; Kirkby, C; Rathee, S; Fallone, B
2012-06-01
This study quantifies the effects of the magnetic field of a longitudinal linac-MR system (B-field parallel to beam direction) on skin dose due to the confinement of contaminant electrons, using Monte Carlo calculations and realistic 3-D models of the magnetic field. The complete realistic 3-D magnetic fields generated by the bi-planar Linac-MR magnet assembly are calculated with the finite element method using Opera- 3D. EGSnrc simulations are performed in the presence of ∼0.6T and IT MRI fields that have realistic rapid fall-off of the fringe field. The simulation geometry includes a Varian 600C 6MV linac, the yoke and magnetic shields of the MRIs, and features an isocentre distance of 126 cm. Phase spaces at the surface of a water phantom are scored using BEAMnrc; DOSXYZnrc is used to score the resulting CAX percent depth-doses in the phantom and the 2D skin dose distributions in the first 70 urn layer. For comparison, skin doses are also calculated in the absence of magnetic field and using a 1-D magnetic field with an unrealistic fringe field. The effects of field size and air gap (between phantom surface and magnet pole) are also examined. Analysis of the phase-space and dose distributions reveals that significant containment of electrons occurs primarily close to the uniform magnetic field region. The increase in skin dose due to the magnetic field depends on the air gap, varying from 1% to 13% for air gaps of 5 to 31 cm, respectively. The increase is also field-size dependent, varying from 3% at 20×20 cm2 to 11% at 5×5 cm2. Calculations based on various realistic MRI 3D magnetic-field maps that appropriately account for the rapid decay of the fringe field show that the increase in the patient skin dose of a longitudinal Linac-MR system is clinically insignificant. © 2012 American Association of Physicists in Medicine.
Network-Based Models in Molecular Biology
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.
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.
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
Oscillation and stability of delay models in biology
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.
Computerised modelling for developmental biology : an exploration with case studies
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
Meads, C; Nyssen, O P; Wong, G; Steed, L; Bourke, L; Ross, C A; Hayman, S; Field, V; Lord, J; Greenhalgh, T; Taylor, S J C
2014-02-18
Long-term medical conditions (LTCs) cause reduced health-related quality of life and considerable health service expenditure. Writing therapy has potential to improve physical and mental health in people with LTCs, but its effectiveness is not established. This project aims to establish the clinical and cost-effectiveness of therapeutic writing in LTCs by systematic review and economic evaluation, and to evaluate context and mechanisms by which it might work, through realist synthesis. Included are any comparative study of therapeutic writing compared with no writing, waiting list, attention control or placebo writing in patients with any diagnosed LTCs that report at least one of the following: relevant clinical outcomes; quality of life; health service use; psychological, behavioural or social functioning; adherence or adverse events. Searches will be conducted in the main medical databases including MEDLINE, EMBASE, PsycINFO, The Cochrane Library and Science Citation Index. For the realist review, further purposive and iterative searches through snowballing techniques will be undertaken. Inclusions, data extraction and quality assessment will be in duplicate with disagreements resolved through discussion. Quality assessment will include using Grading of Recommendations Assessment, Development and Evaluation (GRADE) criteria. Data synthesis will be narrative and tabular with meta-analysis where appropriate. De novo economic modelling will be attempted in one clinical area if sufficient evidence is available and performed according to the National Institute for Health and Care Excellence (NICE) reference case.
Fournier, Marc; Mahmoudzadeh, Mahdi; Kazemi, Kamran; Kongolo, Guy; Dehaene-Lambertz, Ghislaine; Grebe, Reinhard; Wallois, Fabrice
2012-01-01
In this paper we propose an auditory stimulation and near infra-red spectroscopy (NIRS) hemodynamic changes acquisition protocol for preterm neonates. This study is designed to assess the specific characteristics of neurovascular coupling to auditory stimuli in healthy and ill neonate brains. The method could lead to clinical application in intra-ventricular hemorrhage (IVH) diagnosis along with other techniques such as EEG. We propose a realistic head model creation with all useful head structures and brain tissues including the neonate fontanel for more accurate results from NIRS signals modeling. We also design a 3D imaging tool for dynamic mapping and analysis of brain activation onto the cortex surface. Results show significant differences in oxy-hemoglobin between healthy neonates and subjects with IVH.
Morphogenesis and pattern formation in biological systems experiments and models
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.
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.
Solar system tests for realistic f(T) models with non-minimal torsion-matter coupling
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Lin, Rui-Hui; Zhai, Xiang-Hua; Li, Xin-Zhou [Shanghai Normal University, Shanghai United Center for Astrophysics (SUCA), Shanghai (China)
2017-08-15
In the previous paper, we have constructed two f(T) models with non-minimal torsion-matter coupling extension, which are successful in describing the evolution history of the Universe including the radiation-dominated era, the matter-dominated era, and the present accelerating expansion. Meantime, the significant advantage of these models is that they could avoid the cosmological constant problem of ΛCDM. However, the non-minimal coupling between matter and torsion will affect the tests of the Solar system. In this paper, we study the effects of the Solar system in these models, including the gravitation redshift, geodetic effect and perihelion precession. We find that Model I can pass all three of the Solar system tests. For Model II, the parameter is constrained by the uncertainties of the planets' estimated perihelion precessions. (orig.)
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.
Parisi, Laura
2016-02-10
The surface wave full ray theory (FRT) is an efficient tool to calculate synthetic waveforms of surface waves. It combines the concept of local modes with exact ray tracing as a function of frequency, providing a more complete description of surface wave propagation than the widely used great circle approximation (GCA). The purpose of this study is to evaluate the ability of the FRT approach to model teleseismic long-period surface waveforms (T ∼ 45–150 s) in the context of current 3-D Earth models to empirically assess its validity domain and its scope for future studies in seismic tomography. To achieve this goal, we compute vertical and horizontal component fundamental mode synthetic Rayleigh waveforms using the FRT, which are compared with calculations using the highly accurate spectral element method. We use 13 global earth models including 3-D crustal and mantle structure, which are derived by successively varying the strength and lengthscale of heterogeneity in current tomographic models. For completeness, GCA waveforms are also compared with the spectral element method. We find that the FRT accurately predicts the phase and amplitude of long-period Rayleigh waves (T ∼ 45–150 s) for almost all the models considered, with errors in the modelling of the phase (amplitude) of Rayleigh waves being smaller than 5 per cent (10 per cent) in most cases. The largest errors in phase and amplitude are observed for T ∼ 45 s and for the three roughest earth models considered that exhibit shear wave anomalies of up to ∼20 per cent, which is much larger than in current global tomographic models. In addition, we find that overall the GCA does not predict Rayleigh wave amplitudes well, except for the longest wave periods (T ∼ 150 s) and the smoothest models considered. Although the GCA accurately predicts Rayleigh wave phase for current earth models such as S20RTS and S40RTS, FRT\\'s phase errors are smaller, notably for the shortest wave periods considered (T
Energy Technology Data Exchange (ETDEWEB)
Draxl, C.; Churchfield, M.; Mirocha, J.; Lee, S.; Lundquist, J.; Michalakes, J.; Moriarty, P.; Purkayastha, A.; Sprague, M.; Vanderwende, B.
2014-06-01
Wind plant aerodynamics are influenced by a combination of microscale and mesoscale phenomena. Incorporating mesoscale atmospheric forcing (e.g., diurnal cycles and frontal passages) into wind plant simulations can lead to a more accurate representation of microscale flows, aerodynamics, and wind turbine/plant performance. Our goal is to couple a numerical weather prediction model that can represent mesoscale flow [specifically the Weather Research and Forecasting model] with a microscale LES model (OpenFOAM) that can predict microscale turbulence and wake losses.
Directory of Open Access Journals (Sweden)
Wenbin Mao
Full Text Available In this study, we present a fully-coupled fluid-structure interaction (FSI framework that combines smoothed particle hydrodynamics (SPH and nonlinear finite element (FE method to investigate the coupled aortic and mitral valves structural response and the bulk intraventricular hemodynamics in a realistic left ventricle (LV model during the entire cardiac cycle. The FSI model incorporates valve structures that consider native asymmetric leaflet geometries, anisotropic hyperelastic material models and human material properties. Comparison of FSI results with subject-specific echocardiography data demonstrates that the SPH-FE approach is able to quantitatively predict the opening and closing times of the valves, the mitral leaflet opening and closing angles, and the large-scale intraventricular flow phenomena with a reasonable agreement. Moreover, comparison of FSI results with a LV model without valves reveals substantial differences in the flow field. Peak systolic velocities obtained from the FSI model and the LV model without valves are 2.56 m/s and 1.16 m/s, respectively, compared to the Doppler echo data of 2.17 m/s. The proposed SPH-FE FSI framework represents a further step towards modeling patient-specific coupled LV-valve dynamics, and has the potential to improve our understanding of cardiovascular physiology and to support professionals in clinical decision-making.
Török, Gabriel; Goluchová, Kateřina; Urbanec, Martin; Šrámková, Eva; Adámek, Karel; Urbancová, Gabriela; Pecháček, Tomáš; Bakala, Pavel; Stuchlík, Zdeněk; Horák, Jiří; Juryšek, Jakub
2016-12-01
Twin-peak quasi-periodic oscillations (QPOs) are observed in the X-ray power-density spectra of several accreting low-mass neutron star (NS) binaries. In our previous work we have considered several QPO models. We have identified and explored mass-angular-momentum relations implied by individual QPO models for the atoll source 4U 1636-53. In this paper we extend our study and confront QPO models with various NS equations of state (EoS). We start with simplified calculations assuming Kerr background geometry and then present results of detailed calculations considering the influence of NS quadrupole moment (related to rotationally induced NS oblateness) assuming Hartle-Thorne spacetimes. We show that the application of concrete EoS together with a particular QPO model yields a specific mass-angular-momentum relation. However, we demonstrate that the degeneracy in mass and angular momentum can be removed when the NS spin frequency inferred from the X-ray burst observations is considered. We inspect a large set of EoS and discuss their compatibility with the considered QPO models. We conclude that when the NS spin frequency in 4U 1636-53 is close to 580 Hz, we can exclude 51 of the 90 considered combinations of EoS and QPO models. We also discuss additional restrictions that may exclude even more combinations. Namely, 13 EOS are compatible with the observed twin-peak QPOs and the relativistic precession model. However, when considering the low-frequency QPOs and Lense-Thirring precession, only 5 EOS are compatible with the model.
Directory of Open Access Journals (Sweden)
Michel Ghins
1998-06-01
Full Text Available Although Kuhn is much more an antirealist than a realist, the earlier and later articulations of realist and antirealist ingredients in his views merit close scrutiny. What are the constituents of the real invariant World posited by Kuhn and its relation to the mutable paradigm-related worlds? Various proposed solutions to this problem (dubbed the "new-world problem" by Ian Hacking are examined and shown to be unsatisfactory. In The Structure of Scientific Revolutions, the stable World can reasonably be taken to be made up of ordinary perceived objects, whereas in Kuhn's later works the transparadigmatic World is identified with something akin to the Kantian world-in-itself. It is argued that both proposals are beset with insuperable difficulties which render Kuhn's earlier and later versions of antirealism implausible.
Genome-scale biological models for industrial microbial systems.
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.
Energy Technology Data Exchange (ETDEWEB)
Sabchevski, S. [Bulgarian Academy of Sciences (Bulgaria). Institute of Electronics; Zhelyazkov, I. [Sofia Univ. (Bulgaria). Faculty of Physics; Illy, S.; Piosczyk, B.; Borie, E.
2008-07-15
Numerical experiments based on adequate, self-consistent physical models implemented in simulation codes are widely used for computer-aided design (CAD), analysis and optimization of the electron optical systems (EOS) of the gyrotrons. An essential part of the physical model is the emission model, i.e., the relations that govern the value of the beam current extracted from the emitter as well as its energy spectrum, spatial and angular distribution. In this paper, we present a compendium of the basic theory, the most essential formulas and discuss the most important factors responsible for the nonuniformity of the emission and velocity spread. We also review the emission models realized in various ray-tracing and Particle-In-Cell (PIC) codes and present a general formulation of a 3D emission model based on the principle of decomposition of the region near the cathode to a set of equivalent diodes. It is believed that the information summarized in this compendium will be helpful for the development of novel modules for calculation of the initial distribution in both the available 2D computer programs that are being upgraded now and in the novel 3D simulation tools development of which is in progress now. (orig.)
Psikuta, Agnes; Mert, Emel; Annaheim, Simon; Rossi, René M.
2018-02-01
To evaluate the quality of new energy-saving and performance-supporting building and urban settings, the thermal sensation and comfort models are often used. The accuracy of these models is related to accurate prediction of the human thermo-physiological response that, in turn, is highly sensitive to the local effect of clothing. This study aimed at the development of an empirical regression model of the air gap thickness and the contact area in clothing to accurately simulate human thermal and perceptual response. The statistical model predicted reliably both parameters for 14 body regions based on the clothing ease allowances. The effect of the standard error in air gap prediction on the thermo-physiological response was lower than the differences between healthy humans. It was demonstrated that currently used assumptions and methods for determination of the air gap thickness can produce a substantial error for all global, mean, and local physiological parameters, and hence, lead to false estimation of the resultant physiological state of the human body, thermal sensation, and comfort. Thus, this model may help researchers to strive for improvement of human thermal comfort, health, productivity, safety, and overall sense of well-being with simultaneous reduction of energy consumption and costs in built environment.
Realistic model for a fifth force explaining anomaly in Be8* →8Bee+e- decay
Gu, Pei-Hong; He, Xiao-Gang
2017-06-01
We propose a theoretical model to explain a 6.8 σ anomaly recently reported in the opening angle and invariant mass distributions of e+e- pairs produced in excited Be8* nuclear transition to its ground state 8B e. The anomaly is explained by a fifth force mediated by a 17 MeV X boson through the decay Be8* →8Be X followed by X →e+e-. The X boson comes from extension of the standard model with two additional U(1) gauge symmetries producing a protophobic pure vector current interaction with quarks. The model also contains axial-vector current interaction. Although the existent axial-vector current interactions are strongly constrained by the measurement of parity violation in e-quark scattering, their contributions cancel out in the iso-scalar interaction for Be8* →8Be X. It is remarkable that the model parameters need to explain the anomaly survive all known low energy experimental constraints. The model may also alleviate the long-standing (g - 2)μ anomaly problem and can be probed by the LHCb experiment.
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...
Jones, Stephanie R; Pritchett, Dominique L; Sikora, Michael A; Stufflebeam, Steven M; Hämäläinen, Matti; Moore, Christopher I
2009-12-01
Variations in cortical oscillations in the alpha (7-14 Hz) and beta (15-29 Hz) range have been correlated with attention, working memory, and stimulus detection. The mu rhythm recorded with magnetoencephalography (MEG) is a prominent oscillation generated by Rolandic cortex containing alpha and beta bands. Despite its prominence, the neural mechanisms regulating mu are unknown. We characterized the ongoing MEG mu rhythm from a localized source in the finger representation of primary somatosensory (SI) cortex. Subjects showed variation in the relative expression of mu-alpha or mu-beta, which were nonoverlapping for roughly 50% of their respective durations on single trials. To delineate the origins of this rhythm, a biophysically principled computational neural model of SI was developed, with distinct laminae, inhibitory and excitatory neurons, and feedforward (FF, representative of lemniscal thalamic drive) and feedback (FB, representative of higher-order cortical drive or input from nonlemniscal thalamic nuclei) inputs defined by the laminar location of their postsynaptic effects. The mu-alpha component was accurately modeled by rhythmic FF input at approximately 10-Hz. The mu-beta component was accurately modeled by the addition of approximately 10-Hz FB input that was nearly synchronous with the FF input. The relative dominance of these two frequencies depended on the delay between FF and FB drives, their relative input strengths, and stochastic changes in these variables. The model also reproduced key features of the impact of high prestimulus mu power on peaks in SI-evoked activity. For stimuli presented during high mu power, the model predicted enhancement in an initial evoked peak and decreased subsequent deflections. In agreement, the MEG-evoked responses showed an enhanced initial peak and a trend to smaller subsequent peaks. These data provide new information on the dynamics of the mu rhythm in humans and the model provides a novel mechanistic
Stupina, T.; Koulakov, I.; Kopp, H.
2009-04-01
We consider questions of creating structural models and resolution assessment in tomographic inversion of wide-angle active seismic profiling data. For our investigations, we use the PROFIT (Profile Forward and Inverse Tomographic modeling) algorithm which was tested earlier with different datasets. Here we consider offshore seismic profiling data from three areas (Chile, Java and Central Pacific). Two of the study areas are characterized by subduction zones whereas the third data set covers a seamount province. We have explored different algorithmic issues concerning the quality of the solution, such as (1) resolution assessment using different sizes and complexity of synthetic anomalies; (2) grid spacing effects; (3) amplitude damping and smoothing; (4) criteria for rejection of outliers; (5) quantitative criteria for comparing models. Having determined optimal algorithmic parameters for the observed seismic profiling data we have created structural synthetic models which reproduce the results of the observed data inversion. For the Chilean and Java subduction zones our results show similar patterns: a relatively thin sediment layer on the oceanic plate, thicker inhomogeneous sediments in the overlying plate and a large area of very strong low velocity anomalies in the accretionary wedge. For two seamounts in the Pacific we observe high velocity anomalies in the crust which can be interpreted as frozen channels inside the dormant volcano cones. Along both profiles we obtain considerable crustal thickening beneath the seamounts.
Tran, Thang H.; Baba, Yoshihiro; Somu, Vijaya B.; Rakov, Vladimir A.
2017-12-01
The finite difference time domain (FDTD) method in the 2-D cylindrical coordinate system was used to compute the nearly full-frequency-bandwidth vertical electric field and azimuthal magnetic field waveforms produced on the ground surface by lightning return strokes. The lightning source was represented by the modified transmission-line model with linear current decay with height, which was implemented in the FDTD computations as an appropriate vertical phased-current-source array. The conductivity of atmosphere was assumed to increase exponentially with height, with different conductivity profiles being used for daytime and nighttime conditions. The fields were computed at distances ranging from 50 to 500 km. Sky waves (reflections from the ionosphere) were identified in computed waveforms and used for estimation of apparent ionospheric reflection heights. It was found that our model reproduces reasonably well the daytime electric field waveforms measured at different distances and simulated (using a more sophisticated propagation model) by Qin et al. (2017). Sensitivity of model predictions to changes in the parameters of atmospheric conductivity profile, as well as influences of the lightning source characteristics (current waveshape parameters, return-stroke speed, and channel length) and ground conductivity were examined.
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
Digital Learning Material for Model Building in Molecular Biology
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…
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.
Sherman, Christopher Scott
Naturally occurring geologic heterogeneity is an important, but often overlooked, aspect of seismic wave propagation. This dissertation presents a strategy for modeling the effects of heterogeneity using a combination of geostatistics and Finite Difference simulation. In the first chapter, I discuss my motivations for studying geologic heterogeneity and seis- mic wave propagation. Models based upon fractal statistics are powerful tools in geophysics for modeling heterogeneity. The important features of these fractal models are illustrated using borehole log data from an oil well and geomorphological observations from a site in Death Valley, California. A large part of the computational work presented in this disserta- tion was completed using the Finite Difference Code E3D. I discuss the Python-based user interface for E3D and the computational strategies for working with heterogeneous models developed over the course of this research. The second chapter explores a phenomenon observed for wave propagation in heteroge- neous media - the generation of unexpected shear wave phases in the near-source region. In spite of their popularity amongst seismic researchers, approximate methods for modeling wave propagation in these media, such as the Born and Rytov methods or Radiative Trans- fer Theory, are incapable of explaining these shear waves. This is primarily due to these method's assumptions regarding the coupling of near-source terms with the heterogeneities and mode conversion. To determine the source of these shear waves, I generate a suite of 3D synthetic heterogeneous fractal geologic models and use E3D to simulate the wave propaga- tion for a vertical point force on the surface of the models. I also present a methodology for calculating the effective source radiation patterns from the models. The numerical results show that, due to a combination of mode conversion and coupling with near-source hetero- geneity, shear wave energy on the order of 10% of the
International Nuclear Information System (INIS)
Levkovitch, Vladislav; Svendsen, Bob
2007-01-01
Sheet metal forming involves large strains and severe strain-path changes. Large plastic strains lead in many metals to the development of persistent dislocation structures resulting in strong flow anisotropy. This induced anisotropic behavior manifests itself in the case of a strain path change through very different stress-strain responses depending on the type of the strain-path change. While many metals exhibit a drop of the yield stress (Bauschinger effect) after a load reversal, some metals show an increase of the yield stress after an orthogonal strain-path change (so-called cross hardening). To model the Bauschinger effect, kinematic hardening has been successfully used for years. However, the usage of the kinematic hardening leads automatically to a drop of the yield stress after an orthogonal strain-path change contradicting tests exhibiting the cross hardening effect. Another effect, not accounted for in the classical elasto-plasticity, is the difference between the tensile and compressive strength, exhibited e.g. by some steel materials. In this work we present a phenomenological material model whose structure is motivated by polycrystalline modeling that takes into account the evolution of polarized dislocation structures on the grain level - the main cause of the induced flow anisotropy on the macroscopic level. The model considers besides the movement of the yield surface and its proportional expansion, as it is the case in conventional plasticity, also the changes of the yield surface shape (distortional hardening) and accounts for the pressure dependence of the flow stress. All these additional attributes turn out to be essential to model the stress-strain response of dual phase high strength steels subjected to non-proportional loading
International Nuclear Information System (INIS)
Levkovitch, Vladislav; Svendsen, Bob
2007-01-01
Sheet metal forming involves large strains and severe strain-path changes. Large plastic strains lead in many metals to the development of persistent dislocation structures resulting in strong flow anisotropy. This induced anisotropic behavior manifests itself in the case of a strain path change through very different stress-strain responses depending on the type of the strain-path change. While many metals exhibit a drop of the yield stress (Bauschinger effect) after a load reversal, some metals show an increase of the yield stress after an orthogonal strain-path change (so-called cross hardening). To model the Bauschinger effect, kinematic hardening has been successfully used for years. However, the usage of the kinematic hardening leads automatically to a drop of the yield stress after an orthogonal strain-path change contradicting tests exhibiting the cross hardening effect. Another effect, not accounted for in the classical elasto-plasticity, is the difference between the tensile and compressive strength, exhibited e.g. by some steel materials. In this work we present a phenomenological material model whose structure is motivated by polycrystalline modeling that takes into account the evolution of polarized dislocation structures on the grain level - the main cause of the induced flow anisotropy on the macroscopic level. The model considers besides the movement of the yield surface and its proportional expansion, as it is the case in conventional plasticity, also the changes of the yield surface shape (distortional hardening) and accounts for the pressure dependence of the flow stress. All these additional attributes turn out to be essential to model the stress-strain response of dual phase high strength steels subjected to non-proportional loading
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…
International Nuclear Information System (INIS)
Hallez, Hans; Staelens, Steven; Lemahieu, Ignace
2009-01-01
EEG source analysis is a valuable tool for brain functionality research and for diagnosing neurological disorders, such as epilepsy. It requires a geometrical representation of the human head or a head model, which is often modeled as an isotropic conductor. However, it is known that some brain tissues, such as the skull or white matter, have an anisotropic conductivity. Many studies reported that the anisotropic conductivities have an influence on the calculated electrode potentials. However, few studies have assessed the influence of anisotropic conductivities on the dipole estimations. In this study, we want to determine the dipole estimation errors due to not taking into account the anisotropic conductivities of the skull and/or brain tissues. Therefore, head models are constructed with the same geometry, but with an anisotropically conducting skull and/or brain tissue compartment. These head models are used in simulation studies where the dipole location and orientation error is calculated due to neglecting anisotropic conductivities of the skull and brain tissue. Results show that not taking into account the anisotropic conductivities of the skull yields a dipole location error between 2 and 25 mm, with an average of 10 mm. When the anisotropic conductivities of the brain tissues are neglected, the dipole location error ranges between 0 and 5 mm. In this case, the average dipole location error was 2.3 mm. In all simulations, the dipole orientation error was smaller than 10 deg. We can conclude that the anisotropic conductivities of the skull have to be incorporated to improve the accuracy of EEG source analysis. The results of the simulation, as presented here, also suggest that incorporation of the anisotropic conductivities of brain tissues is not necessary. However, more studies are needed to confirm these suggestions.
FreeCAD visualization of realistic 3D physical optics beams within a CAD system-model
Gayer, D.; O'Sullivan, C.; Scully, S.; Burke, D.; Brossard, J.; Chapron, C.
2016-07-01
The facility to realise the shape and extent of optical beams within a telescope or beamcombiner can aid greatly in the design and layout of optical elements within the system. It can also greatly facilitate communication between the optical design team and other teams working on the mechanical design of an instrument. Beyond the realm where raytracing is applicable however, it becomes much more difficult to realise accurate 3D beams which incorporate diffraction effects. It then is another issue to incorporate this into a CAD model of the system. A novel method is proposed which has been used to aid with the design of an optical beam combiner for the QUBIC (Q and U Bolometric Interferometer for Cosmology) 1 experiment operating at 150 GHz and 220 GHz. The method combines calculation work in GRASP 2, a commercial physical optics modelling tool from TICRA, geometrical work in Mathematica, and post processing in MATLAB. Finally, the Python console of the open source package FreeCAD3 is exploited to realise the 3D beams in a complete CAD system-model of the QUBIC optical beam combiner. This paper details and explains the work carried out to reach the goal and presents some graphics of the outcome. 3D representations of beams from some back-to-back input horns of the QUBIC instrument are shown within the CAD model. Beams of the -3dB and -13dB contour envelope are shown as well as envelopes enclosing 80% and 95% of the power of the beam. The ability to see these beams in situ with all the other elements of the combiner such as mirrors, cold stop, beam splitter and cryostat widows etc. greatly simplified the design for these elements and facilitated communication of element dimension and location between different subgroups within the QUBIC group.
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...
Bertram, C D; Macaskill, C; Davis, M J; Moore, J E
2014-04-01
Our published model of a lymphatic vessel consisting of multiple actively contracting segments between non-return valves has been further developed by the incorporation of properties derived from observations and measurements of rat mesenteric vessels. These included (1) a refractory period between contractions, (2) a highly nonlinear form for the passive part of the pressure-diameter relationship, (3) hysteretic and transmural-pressure-dependent valve opening and closing pressure thresholds and (4) dependence of active tension on muscle length as reflected in local diameter. Experimentally, lymphatic valves are known to be biased to stay open. In consequence, in the improved model, vessel pumping of fluid suffers losses by regurgitation, and valve closure is dependent on backflow first causing an adverse valve pressure drop sufficient to reach the closure threshold. The assumed resistance of an open valve therefore becomes a critical parameter, and experiments to measure this quantity are reported here. However, incorporating this parameter value, along with other parameter values based on existing measurements, led to ineffective pumping. It is argued that the published measurements of valve-closing pressure threshold overestimate this quantity owing to neglect of micro-pipette resistance. An estimate is made of the extent of the possible resulting error. Correcting by this amount, the pumping performance is improved, but still very inefficient unless the open-valve resistance is also increased beyond the measured level. Arguments are given as to why this is justified, and other areas where experimental data are lacking are identified. The model is capable of future adaptation as new experimental data appear.
DEFF Research Database (Denmark)
Lukianova, R.; Christiansen, Freddy
2006-01-01
[1] A new approach for modeling the global distribution of ionospheric electric potentials utilizing high-precision maps of FACs derived from measurements by the Orsted and Champ satellites as input to a comprehensive numerical scheme is presented. The boundary conditions provide a correct...... predicts that the summer cross-polar potentials are smaller than the winter potentials. The value of the ratio depends on the combination of season/IMF B-Y sign. The ratio is found to be greater for the combination of B-Y > 0/southern summer and B-Y value is obtained...
Energy Technology Data Exchange (ETDEWEB)
Corella, J.; Narvaez, I.; Orio, A. [Complutense Univ. of Madrid (Spain). Dept. of Chemical Engineering
1996-12-31
A model for fresh tar destruction over catalysts placed downstream a biomass gasifier is presented. It includes the stoichio-metry and the calculation of the kinetic constants for the tar destruction. Catalysts studied include commercial Ni steam reforming catalysts and calcinated dolomites. Kinetic constants for tar destruction are calculated for several particle sizes, times- on-stream and temperatures of the catalyst and equivalence ratios in the gasifier. Such intrinsic kinetic constants allow a rigorous or scientific comparison of solids and conditions to be used in an advanced gasification process. (orig.) 4 refs.
Use of genome-scale metabolic models in evolutionary systems biology.
Papp, B.; Szappanos, B.; Notebaart, R.A.
2011-01-01
One of the major aims of the nascent field of evolutionary systems biology is to test evolutionary hypotheses that are not only realistic from a population genetic point of view but also detailed in terms of molecular biology mechanisms. By providing a mapping between genotype and phenotype for
International Nuclear Information System (INIS)
Nogueira, P; Vaz, P; Zankl, M; Schlattl, H
2011-01-01
The radiation-induced posterior subcapsular cataract has long been generally accepted to be a deterministic effect that does not occur at doses below a threshold of at least 2 Gy. Recent epidemiological studies indicate that the threshold for cataract induction may be much lower or that there may be no threshold at all. A thorough study of this subject requires more accurate dose estimates for the eye lens than those available in ICRP Publication 74. Eye lens absorbed dose per unit fluence conversion coefficients for electron irradiation were calculated using a geometrical model of the eye that takes into account different cell populations of the lens epithelium, together with the MCNPX Monte Carlo radiation transport code package. For the cell population most sensitive to ionizing radiation-the germinative cells-absorbed dose per unit fluence conversion coefficients were determined that are up to a factor of 4.8 higher than the mean eye lens absorbed dose conversion coefficients for electron energies below 2 MeV. Comparison of the results with previously published values for a slightly different eye model showed generally good agreement for all electron energies. Finally, the influence of individual anatomical variability was quantified by positioning the lens at various depths below the cornea. A depth difference of 2 mm between the shallowest and the deepest location of the germinative zone can lead to a difference between the resulting absorbed doses of up to nearly a factor of 5000 for electron energy of 0.7 MeV.
Pinzon-Morales, Ruben-Dario; Hirata, Yutaka
2015-01-01
The cerebellar granule cells (GCs) have been proposed to perform lossless, adaptive spatio-temporal coding of incoming sensory/motor information required by downstream cerebellar circuits to support motor learning, motor coordination, and cognition. Here we use a physio-anatomically inspired bi-hemispheric cerebellar neuronal network (biCNN) to selectively enable/disable the output of GCs and evaluate the behavioral and neural consequences during three different control scenarios. The control scenarios are a simple direct current motor (1 degree of freedom: DOF), an unstable two-wheel balancing robot (2 DOFs), and a simulation model of a quadcopter (6 DOFs). Results showed that adequate control was maintained with a relatively small number of GCs (< 200) in all the control scenarios. However, the minimum number of GCs required to successfully govern each control plant increased with their complexity (i.e., DOFs). It was also shown that increasing the number of GCs resulted in higher robustness against changes in the initialization parameters of the biCNN model (i.e., synaptic connections and synaptic weights). Therefore, we suggest that the abundant GCs in the cerebellar cortex provide the computational power during the large repertoire of motor activities and motor plants the cerebellum is involved with, and bring robustness against changes in the cerebellar microcircuit (e.g., neuronal connections).
Directory of Open Access Journals (Sweden)
Ruben Dario Pinzon Morales
2015-05-01
Full Text Available The cerebellar granule cells (GCs have been proposed to perform lossless, adaptive spatio-temporal coding of incoming sensory/motor information required by downstream cerebellar circuits to textcolor{red}{support} motor learning, motor coordination, and cognition. Here we use a physio-anatomically inspired bi-hemispheric cerebellar neuronal network (biCNN to selectively enable/disable the output of GCs and evaluate the behavioral and neural consequences during three different control scenarios. The control scenarios are a simple direct current motor (1 degree of freedom: DOF, an unstable two-wheel balancing robot (2 DOFs, and a simulation model of a quadcopter (6 DOFs. Results showed that adequate control was maintained with a relatively small number of GCs ($<$ 200 in all the control scenarios. However, the minimum number of GCs required to successfully govern each control plant increased with their complexity (i.e., DOFs. It was also shown that increasing the number of GCs resulted in higher robustness against changes in the initialization parameters of the biCNN model (i.e., synaptic connections and synaptic weights. Therefore, we suggest that the abundant GCs in the cerebellar cortex provide the computational power during the large repertoire of motor activities and motor plants the cerebellum is involved with, and bring robustness against changes in the cerebellar microcircuit (e.g., neuronal connections.
Energy Technology Data Exchange (ETDEWEB)
Nogueira, P; Vaz, P [Technological and Nuclear Institute, Estrada Nacional No 10, 2686-953 Sacavem (Portugal); Zankl, M; Schlattl, H, E-mail: pedro.nogueira@helmholtz-muenchen.de [Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Research Unit Medical Radiation Physics and Diagnostics, Ingolstaedter Landstrasse 1, D-85764 Neuherberg (Germany)
2011-11-07
The radiation-induced posterior subcapsular cataract has long been generally accepted to be a deterministic effect that does not occur at doses below a threshold of at least 2 Gy. Recent epidemiological studies indicate that the threshold for cataract induction may be much lower or that there may be no threshold at all. A thorough study of this subject requires more accurate dose estimates for the eye lens than those available in ICRP Publication 74. Eye lens absorbed dose per unit fluence conversion coefficients for electron irradiation were calculated using a geometrical model of the eye that takes into account different cell populations of the lens epithelium, together with the MCNPX Monte Carlo radiation transport code package. For the cell population most sensitive to ionizing radiation-the germinative cells-absorbed dose per unit fluence conversion coefficients were determined that are up to a factor of 4.8 higher than the mean eye lens absorbed dose conversion coefficients for electron energies below 2 MeV. Comparison of the results with previously published values for a slightly different eye model showed generally good agreement for all electron energies. Finally, the influence of individual anatomical variability was quantified by positioning the lens at various depths below the cornea. A depth difference of 2 mm between the shallowest and the deepest location of the germinative zone can lead to a difference between the resulting absorbed doses of up to nearly a factor of 5000 for electron energy of 0.7 MeV.
Nogueira, P; Zankl, M; Schlattl, H; Vaz, P
2011-11-07
The radiation-induced posterior subcapsular cataract has long been generally accepted to be a deterministic effect that does not occur at doses below a threshold of at least 2 Gy. Recent epidemiological studies indicate that the threshold for cataract induction may be much lower or that there may be no threshold at all. A thorough study of this subject requires more accurate dose estimates for the eye lens than those available in ICRP Publication 74. Eye lens absorbed dose per unit fluence conversion coefficients for electron irradiation were calculated using a geometrical model of the eye that takes into account different cell populations of the lens epithelium, together with the MCNPX Monte Carlo radiation transport code package. For the cell population most sensitive to ionizing radiation-the germinative cells-absorbed dose per unit fluence conversion coefficients were determined that are up to a factor of 4.8 higher than the mean eye lens absorbed dose conversion coefficients for electron energies below 2 MeV. Comparison of the results with previously published values for a slightly different eye model showed generally good agreement for all electron energies. Finally, the influence of individual anatomical variability was quantified by positioning the lens at various depths below the cornea. A depth difference of 2 mm between the shallowest and the deepest location of the germinative zone can lead to a difference between the resulting absorbed doses of up to nearly a factor of 5000 for electron energy of 0.7 MeV.
Directory of Open Access Journals (Sweden)
Lei Zhao
2014-01-01
Full Text Available An efficient algorithm is proposed to analyze the electromagnetic scattering problem from a high resolution head model with pixel data format. The algorithm is based on parallel technique and the conjugate gradient (CG method combined with the fast Fourier transform (FFT. Using the parallel CG-FFT method, the proposed algorithm is very efficient and can solve very electrically large-scale problems which cannot be solved using the conventional CG-FFT method in a personal computer. The accuracy of the proposed algorithm is verified by comparing numerical results with analytical Mie-series solutions for dielectric spheres. Numerical experiments have demonstrated that the proposed method has good performance on parallel efficiency.
Directory of Open Access Journals (Sweden)
Trang Minh Duong
2012-09-01
Full Text Available Tidal inlets are of great societal importance as they are often associated with ports and harbours, industry, tourism, recreation and prime waterfront real estate. Their behaviour is governed by the delicate balance of oceanic processes (tides, waves and mean sea level, and fluvial/estuarine processes (riverflow and heat fluxes, all of which can be significantly affected by climate change (CC processes. This study investigates the potential range of CC impacts on the stability (closed/open state and locational stability via the application of a sophisticated process based morphodynamic model (Delft3D to strategically selected schematized inlet morphologies and forcing conditions. Results show that, under worst case scenario conditions, the integrated effect of climate change driven increase in mean sea level, wave height and wave angle may significantly change inlet stability condition.
Energy Technology Data Exchange (ETDEWEB)
Colby, Sean M.; Kabilan, Senthil; Jacob, Richard E.; Kuprat, Andrew P.; Einstein, Daniel R.; Corley, Richard A.
2016-03-17
Abstract Context: Computational fluid dynamics (CFD) simulations of airflows coupled with physiologically based pharmacokinetic (PBPK) modeling of respiratory tissue doses of airborne materials have traditionally used either steady-state inhalation or a sinusoidal approximation of the breathing cycle for airflow simulations despite their differences from normal breathing patterns. Objective: Evaluate the impact of realistic breathing patterns, including sniffing, on predicted nasal tissue concentrations of a reactive vapor that targets the nose in rats as a case study. Materials and methods: Whole-body plethysmography measurements from a free-breathing rat were used to produce profiles of normal breathing, sniffing and combinations of both as flow inputs to CFD/PBPK simulations of acetaldehyde exposure. Results: For the normal measured ventilation profile, modest reductions in time- and tissue depth-dependent areas under the curve (AUC) acetaldehyde concentrations were predicted in the wet squamous, respiratory and transitional epithelium along the main airflow path, while corresponding increases were predicted in the olfactory epithelium, especially the most distal regions of the ethmoid turbinates, versus the idealized profile. The higher amplitude/frequency sniffing profile produced greater AUC increases over the idealized profile in the olfactory epithelium, especially in the posterior region. Conclusions: The differences in tissue AUCs at known lesion-forming regions for acetaldehyde between normal and idealized profiles were minimal, suggesting that sinusoidal profiles may be used for this chemical and exposure concentration. However, depending upon the chemical, exposure system and concentration and the time spent sniffing, the use of realistic breathing profiles, including sniffing, could become an important modulator for local tissue dose predictions.
Directory of Open Access Journals (Sweden)
Ümit Aydin
Full Text Available To increase the reliability for the non-invasive determination of the irritative zone in presurgical epilepsy diagnosis, we introduce here a new experimental and methodological source analysis pipeline that combines the complementary information in EEG and MEG, and apply it to data from a patient, suffering from refractory focal epilepsy. Skull conductivity parameters in a six compartment finite element head model with brain anisotropy, constructed from individual MRI data, are estimated in a calibration procedure using somatosensory evoked potential (SEP and field (SEF data. These data are measured in a single run before acquisition of further runs of spontaneous epileptic activity. Our results show that even for single interictal spikes, volume conduction effects dominate over noise and need to be taken into account for accurate source analysis. While cerebrospinal fluid and brain anisotropy influence both modalities, only EEG is sensitive to skull conductivity and conductivity calibration significantly reduces the difference in especially depth localization of both modalities, emphasizing its importance for combining EEG and MEG source analysis. On the other hand, localization differences which are due to the distinct sensitivity profiles of EEG and MEG persist. In case of a moderate error in skull conductivity, combined source analysis results can still profit from the different sensitivity profiles of EEG and MEG to accurately determine location, orientation and strength of the underlying sources. On the other side, significant errors in skull modeling are reflected in EEG reconstruction errors and could reduce the goodness of fit to combined datasets. For combined EEG and MEG source analysis, we therefore recommend calibrating skull conductivity using additionally acquired SEP/SEF data.
Aydin, Ümit; Vorwerk, Johannes; Küpper, Philipp; Heers, Marcel; Kugel, Harald; Galka, Andreas; Hamid, Laith; Wellmer, Jörg; Kellinghaus, Christoph; Rampp, Stefan; Wolters, Carsten Hermann
2014-01-01
To increase the reliability for the non-invasive determination of the irritative zone in presurgical epilepsy diagnosis, we introduce here a new experimental and methodological source analysis pipeline that combines the complementary information in EEG and MEG, and apply it to data from a patient, suffering from refractory focal epilepsy. Skull conductivity parameters in a six compartment finite element head model with brain anisotropy, constructed from individual MRI data, are estimated in a calibration procedure using somatosensory evoked potential (SEP) and field (SEF) data. These data are measured in a single run before acquisition of further runs of spontaneous epileptic activity. Our results show that even for single interictal spikes, volume conduction effects dominate over noise and need to be taken into account for accurate source analysis. While cerebrospinal fluid and brain anisotropy influence both modalities, only EEG is sensitive to skull conductivity and conductivity calibration significantly reduces the difference in especially depth localization of both modalities, emphasizing its importance for combining EEG and MEG source analysis. On the other hand, localization differences which are due to the distinct sensitivity profiles of EEG and MEG persist. In case of a moderate error in skull conductivity, combined source analysis results can still profit from the different sensitivity profiles of EEG and MEG to accurately determine location, orientation and strength of the underlying sources. On the other side, significant errors in skull modeling are reflected in EEG reconstruction errors and could reduce the goodness of fit to combined datasets. For combined EEG and MEG source analysis, we therefore recommend calibrating skull conductivity using additionally acquired SEP/SEF data.
Nielsen, Jesper D; Madsen, Kristoffer H; Puonti, Oula; Siebner, Hartwig R; Bauer, Christian; Madsen, Camilla Gøbel; Saturnino, Guilherme B; Thielscher, Axel
2018-03-12
Anatomically realistic volume conductor models of the human head are important for accurate forward modeling of the electric field during transcranial brain stimulation (TBS), electro- (EEG) and magnetoencephalography (MEG). In particular, the skull compartment exerts a strong influence on the field distribution due to its low conductivity, suggesting the need to represent its geometry accurately. However, automatic skull reconstruction from structural magnetic resonance (MR) images is difficult, as compact bone has a very low signal in magnetic resonance imaging (MRI). Here, we evaluate three methods for skull segmentation, namely FSL BET2, the unified segmentation routine of SPM12 with extended spatial tissue priors, and the skullfinder tool of BrainSuite. To our knowledge, this study is the first to rigorously assess the accuracy of these state-of-the-art tools by comparison with CT-based skull segmentations on a group of ten subjects. We demonstrate several key factors that improve the segmentation quality, including the use of multi-contrast MRI data, the optimization of the MR sequences and the adaptation of the parameters of the segmentation methods. We conclude that FSL and SPM12 achieve better skull segmentations than BrainSuite. The former methods obtain reasonable results for the upper part of the skull when a combination of T1- and T2-weighted images is used as input. The SPM12-based results can be improved slightly further by means of simple morphological operations to fix local defects. In contrast to FSL BET2, the SPM12-based segmentation with extended spatial tissue priors and the BrainSuite-based segmentation provide coarse reconstructions of the vertebrae, enabling the construction of volume conductor models that include the neck. We exemplarily demonstrate that the extended models enable a more accurate estimation of the electric field distribution during transcranial direct current stimulation (tDCS) for montages that involve extraencephalic
Getting realistic; Endstation Demut
Energy Technology Data Exchange (ETDEWEB)
Meyer, J.P.
2004-01-28
The fuel cell hype of the turn of the millenium has reached its end. The industry is getting realistic. If at all, fuel cell systems for private single-family and multiple dwellings will not be available until the next decade. With a Europe-wide field test, Vaillant intends to advance the PEM technology. [German] Der Brennstoffzellen-Hype der Jahrtausendwende ist verfolgen. Die Branche uebt sich in Bescheidenheit. Die Marktreife der Systeme fuer Ein- und Mehrfamilienhaeuser wird - wenn ueberhaupt - wohl erst im naechsten Jahrzehnt erreicht sein. Vaillant will durch einen europaweiten Feldtest die Entwicklung der PEM-Technologie vorantreiben. (orig.)
Sensitivity analysis approaches applied to systems biology models.
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.
Computer Models and Automata Theory in Biology and Medicine
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...
Mathematical Modeling of Complex Biological Systems
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...
Modelling and Inference Strategies for Biological Systems
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...
A guide to numerical modelling in systems biology
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...
BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.
Directory of Open Access Journals (Sweden)
Thomas E Gorochowski
Full Text Available Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.
Learning (from) the errors of a systems biology model.
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.
Directory of Open Access Journals (Sweden)
Himmatul Afthina
2017-12-01
Full Text Available The aims of this research to determine the effect of Think Talk Write (TTW and Think Pair Share (TPS model with Realistic Mathematics Education (RME approach viewed from mathematical-logical intelligence. This research employed the quasi experimental research. The population of research was all students of the eight graders of junior high school in Karangamyar Regency in academic year 2016/2017. The result of this research shows that (1 TTW with RME approach gave better mathematics achievement than TPS with RME approach, (2 Students with high mathematical-logical intelligence can reach a better mathematics achievement than those with average and low, whereas students with average mathematical-logical intelligence can reach a better achievement than those with low one, (3 In TTW model with RME approach, students with high mathematical-logical intelligence can reach a better mathematics achievement than those with average and low, whereas students with average and low mathematical-logical intelligence gave same mathematics achievement, and in TPS model with RME approach students with high mathematical-logical intelligence can reach a better mathematics achievement than those with average and low, whereas students with average mathematical-logical intelligence can reach a better achievement than those with low one (4 In each category of mathematical-logical intelligence, TTW with RME approach and TPS with RME approach gave same mathematics achievement.
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 ...
Uncertainty in biology a computational modeling approach
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...
A Modeling Approach to Teaching Evolutionary Biology in High Schools.
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.)…
Kou, Jisheng
2018-02-25
In this paper, we consider mathematical modeling and numerical simulation of non-isothermal compressible multi-component diffuse-interface two-phase flows with realistic equations of state. A general model with general reference velocity is derived rigorously through thermodynamical laws and Onsager\\'s reciprocal principle, and it is capable of characterizing compressibility and partial miscibility between multiple fluids. We prove a novel relation among the pressure, temperature and chemical potentials, which results in a new formulation of the momentum conservation equation indicating that the gradients of chemical potentials and temperature become the primary driving force of the fluid motion except for the external forces. A key challenge in numerical simulation is to develop entropy stable numerical schemes preserving the laws of thermodynamics. Based on the convex-concave splitting of Helmholtz free energy density with respect to molar densities and temperature, we propose an entropy stable numerical method, which solves the total energy balance equation directly, and thus, naturally satisfies the first law of thermodynamics. Unconditional entropy stability (the second law of thermodynamics) of the proposed method is proved by estimating the variations of Helmholtz free energy and kinetic energy with time steps. Numerical results validate the proposed method.
Spatial Modeling Tools for Cell Biology
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
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.
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.)
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...
Mathematical models in biology bringing mathematics to life
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...
Sass, Lucas R; Khani, Mohammadreza; Natividad, Gabryel Connely; Tubbs, R Shane; Baledent, Olivier; Martin, Bryn A
2017-12-19
The spinal subarachnoid space (SSS) has a complex 3D fluid-filled geometry with multiple levels of anatomic complexity, the most salient features being the spinal cord and dorsal and ventral nerve rootlets. An accurate anthropomorphic representation of these features is needed for development of in vitro and numerical models of cerebrospinal fluid (CSF) dynamics that can be used to inform and optimize CSF-based therapeutics. A subject-specific 3D model of the SSS was constructed based on high-resolution anatomic MRI. An expert operator completed manual segmentation of the CSF space with detailed consideration of the anatomy. 31 pairs of semi-idealized dorsal and ventral nerve rootlets (NR) were added to the model based on anatomic reference to the magnetic resonance (MR) imaging and cadaveric measurements in the literature. Key design criteria for each NR pair included the radicular line, descending angle, number of NR, attachment location along the spinal cord and exit through the dura mater. Model simplification and smoothing was performed to produce a final model with minimum vertices while maintaining minimum error between the original segmentation and final design. Final model geometry and hydrodynamics were characterized in terms of axial distribution of Reynolds number, Womersley number, hydraulic diameter, cross-sectional area and perimeter. The final model had a total of 139,901 vertices with a total CSF volume within the SSS of 97.3 cm 3 . Volume of the dura mater, spinal cord and NR was 123.1, 19.9 and 5.8 cm 3 . Surface area of these features was 318.52, 112.2 and 232.1 cm 2 respectively. Maximum Reynolds number was 174.9 and average Womersley number was 9.6, likely indicating presence of a laminar inertia-dominated oscillatory CSF flow field. This study details an anatomically realistic anthropomorphic 3D model of the SSS based on high-resolution MR imaging of a healthy human adult female. The model is provided for re-use under the Creative Commons
Systematic integration of experimental data and models in systems biology.
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.
Systems modelling and the development of coherent cell biological knowledge
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
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...
Biocellion: accelerating computer simulation of multicellular biological system models.
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.
Ding, Lei; He, Bin
2006-09-01
The subspace source localization approach, i.e., first principle vectors (FINE), is able to enhance the spatial resolvability and localization accuracy for closely-spaced neural sources from EEG and MEG measurements. Computer simulations were conducted to evaluate the performance of the FINE algorithm in an inhomogeneous realistic geometry head model under a variety of conditions. The source localization abilities of FINE were examined at different cortical regions and at different depths. The present computer simulation results indicate that FINE has enhanced source localization capability, as compared with MUSIC and RAP-MUSIC, when sources are closely spaced, highly noise-contaminated, or inter-correlated. The source localization accuracy of FINE is better, for closely-spaced sources, than MUSIC at various noise levels, i.e., signal-to-noise ratio (SNR) from 6 dB to 16 dB, and RAP-MUSIC at relatively low noise levels, i.e., 6 dB to 12 dB. The FINE approach has been further applied to localize brain sources of motor potentials, obtained during the finger tapping tasks in a human subject. The experimental results suggest that the detailed neural activity distribution could be revealed by FINE. The present study suggests that FINE provides enhanced performance in localizing multiple closely spaced, and inter-correlated sources under low SNR, and may become an important alternative to brain source localization from EEG or MEG.
Majumder, R.; Pandit, R.; Panfilov, A. V.
2016-12-01
Nonlinear waves of the reaction-diffusion (RD) type occur in many biophysical systems, including the heart, where they initiate cardiac contraction. Such waves can form vortices called scroll waves, which result in the onset of life-threatening cardiac arrhythmias. The dynamics of scroll waves is affected by the presence of inhomogeneities, which, in a very general way, can be of (i) ionic type; i.e., they affect the reaction part, or (ii) conduction type, i.e., they affect the diffusion part of an RD-equation. We demonstrate, for the first time, by using a state-of-the-art, anatomically realistic model of the pig heart, how differences in the geometrical and biophysical nature of such inhomogeneities can influence scroll-wave dynamics in different ways. Our study reveals that conduction-type inhomogeneities become increasingly important at small length scales, i.e., in the case of multiple, randomly distributed, obstacles in space at the cellular scale (0.2-0.4 mm). Such configurations can lead to scroll-wave break up. In contrast, ionic inhomogeneities affect scroll-wave dynamics significantly at large length scales, when these inhomogeneities are localized in space at the tissue level (5-10 mm). In such configurations, these inhomogeneities can attract scroll waves, by pinning them to the heterogeneity, or lead to scroll-wave breakup.
A dynamic model for functional mapping of biological rhythms.
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.
Modelling effective dielectric properties of materials containing diverse types of biological cells
International Nuclear Information System (INIS)
Huclova, Sonja; Froehlich, Juerg; Erni, Daniel
2010-01-01
An efficient and versatile numerical method for the generation of different realistically shaped biological cells is developed. This framework is used to calculate the dielectric spectra of materials containing specific types of biological cells. For the generation of the numerical models of the cells a flexible parametrization method based on the so-called superformula is applied including the option of obtaining non-axisymmetric shapes such as box-shaped cells and even shapes corresponding to echinocytes. The dielectric spectra of effective media containing various cell morphologies are calculated focusing on the dependence of the spectral features on the cell shape. The numerical method is validated by comparing a model of spherical inclusions at a low volume fraction with the analytical solution obtained by the Maxwell-Garnett mixing formula, resulting in good agreement. Our simulation data for different cell shapes suggest that around 1MHz the effective dielectric properties of different cell shapes at different volume fractions significantly deviate from the spherical case. The most pronounced change exhibits ε eff between 0.1 and 1 MHz with a deviation of up to 35% for a box-shaped cell and 15% for an echinocyte compared with the sphere at a volume fraction of 0.4. This hampers the unique interpretation of changes in cellular features measured by dielectric spectroscopy when simplified material models are used.
International Nuclear Information System (INIS)
Nagaoka, Tomoaki; Togashi, Toshihiro; Saito, Kazuyuki; Takahashi, Masaharu; Ito, Koichi; Watanabe, Soichi
2007-01-01
The numerical dosimetry of pregnant women is an important issue in electromagnetic-field safety. However, an anatomically realistic whole-body pregnant-woman model for electromagnetic dosimetry has not been developed. Therefore, we have developed a high-resolution whole-body model of pregnant women. A new fetus model including inherent tissues of pregnant women was constructed on the basis of abdominal magnetic resonance imaging data of a 26-week-pregnant woman. The whole-body pregnant-woman model was developed by combining the fetus model and a nonpregnant-woman model that was developed previously. The developed model consists of about 7 million cubical voxels of 2 mm size and is segmented into 56 tissues and organs. This pregnant-woman model is the first completely anatomically realistic voxel model that includes a realistic fetus model and enables a numerical simulation of electromagnetic dosimetry up to the gigahertz band. In this paper, we also present the basic specific absorption rate characteristics of the pregnant-woman model exposed to vertically and horizontally polarized electromagnetic waves from 10 MHz to 2 GHz
Lu, L.; Colas, L.; Jacquot, J.; Després, B.; Heuraux, S.; Faudot, E.; Van Eester, D.; Crombé, K.; Křivská, A.; Noterdaeme, J.-M.; Helou, W.; Hillairet, J.
2018-03-01
In order to model the sheath rectification in a realistic geometry over the size of ion cyclotron resonant heating (ICRH) antennas, the self-consistent sheaths and waves for ICH (SSWICH) code couples self-consistently the RF wave propagation and the DC SOL biasing via nonlinear RF and DC sheath boundary conditions applied at plasma/wall interfaces. A first version of SSWICH had 2D (toroidal and radial) geometry, rectangular walls either normal or parallel to the confinement magnetic field B 0 and only included the evanescent slow wave (SW) excited parasitically by the ICRH antenna. The main wave for plasma heating, the fast wave (FW) plays no role on the sheath excitation in this version. A new version of the code, 2D SSWICH-full wave, was developed based on the COMSOL software, to accommodate full RF field polarization and shaped walls tilted with respect to B 0 . SSWICH-full wave simulations have shown the mode conversion of FW into SW occurring at the sharp corners where the boundary shape varies rapidly. It has also evidenced ‘far-field’ sheath oscillations appearing at the shaped walls with a relatively long magnetic connection length to the antenna, that are only accessible to the propagating FW. Joint simulation, conducted by SSWICH-full wave within a multi-2D approach excited using the 3D wave coupling code (RAPLICASOL), has recovered the double-hump poloidal structure measured in the experimental temperature and potential maps when only the SW is modelled. The FW contribution on the potential poloidal structure seems to be affected by the 3D effects, which was ignored in the current stage. Finally, SSWICH-full wave simulation revealed the left–right asymmetry that has been observed extensively in the unbalanced strap feeding experiments, suggesting that the spatial proximity effects in RF sheath excitation, studied for SW only previously, is still important in the vicinity of the wave launcher under full wave polarizations.
Bunn, Frances; Goodman, Claire; Manthorpe, Jill; Durand, Marie-Anne; Hodkinson, Isabel; Rait, Greta; Millac, Paul; Davies, Sue L; Russell, Bridget; Wilson, Patricia
2017-02-07
Including the patient or user perspective is a central organising principle of integrated care. Moreover, there is increasing recognition of the importance of strengthening relationships among patients, carers and practitioners, particularly for individuals receiving substantial health and care support, such as those with long-term or multiple conditions. The overall aims of this synthesis are to provide a context-relevant understanding of how models to facilitate shared decision-making (SDM) might work for older people with multiple health and care needs, and how they might be applied to integrated care models. The synthesis draws on the principles of realist inquiry, to explain how, in what contexts and for whom, interventions that aim to strengthen SDM among older patients, carers and practitioners are effective. We will use an iterative, stakeholder-driven, three-phase approach. Phase 1: development of programme theory/theories that will be tested through a first scoping of the literature and consultation with key stakeholder groups; phase 2: systematic searches of the evidence to test and develop the theories identified in phase 1; phase 3: validation of programme theory/theories with a purposive sample of participants from phase 1. The synthesis will draw on prevailing theories such as candidacy, self-efficacy, personalisation and coproduction. Ethics approval for the stakeholder interviews was obtained from the University of Hertfordshire ECDA (Ethics Committee with Delegated Authority), reference number HSK/SF/UH/02387. The propositions arising from this review will be used to develop recommendations about how to tailor SDM interventions to older people with complex health and social care needs in an integrated care setting. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.
Bionic models for identification of biological systems
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.
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...
Modeling and simulation of biological systems using SPICE language
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
A Transformative Model for Undergraduate Quantitative Biology Education
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
A transformative model for undergraduate quantitative biology education.
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.
Contemporary Phage Biology: From Classic Models to New Insights.
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.
Modeling life the mathematics of biological systems
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 ...
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...
Using views of Systems Biology Cloud: application for model building.
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.
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.
An integrated physical and biological model for anaerobic lagoons.
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.
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.
Directory of Open Access Journals (Sweden)
Valladares, Fernando
2000-06-01
Full Text Available Main results from different studies of crown architecture adaptation to extreme light environments are presented. Light capture and carbon gain by plants from low (forest understory and high (open Mediterranean-type ecosystems light environments were simulated with a 3-D model (YPLANT, which was developed specifically to analyse the structural features that determine light interception and photosynthesis at the whole plant level. Distantly related taxa with contrasting architectures exhibited similar efficiencies of light interception (functional convergence. Between habitats large differences in architecture existed depending on whether light capture must be maximised or whether excess photon flux density must be avoided. These differences are realised both at the species level and within a species because of plastic adjustments of crown architecture to the external light environment. Realistic, 3-D architectural models are indispensable tools in this kind of comparative studies due to the intrinsic complexity of plant architecture. Their efficient development requires a fluid exchange of ideas between botanists, ecologists and plant modellers.Se presentan los resultados principales de varios estudios sobre las adaptaciones del follaje a ambientes lumínicos extremos. Plantas de ambientes oscuros (sotobosques de bosques templados y tropicales y de ambientes muy luminosos (ecosistemas abiertos de tipo Mediterráneo han sido estudiadas mediante un modelo (YPLANT que permite la reconstrucción tridimensional de la parte aérea de las plantas e identificar los rasgos estructurales que determinan la interceptación de luz y la fotosíntesis y transpiraci6n potencial a nivel de toda la copa. Taxones no relacionados y con arquitecturas muy diferentes mostraron una eficiencia en la interceptaci6n de luz similar (convergencia funcional. La comparación entre hábitat revelo grandes diferencias arquitecturales dependiendo de si la absorción de luz deb
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.
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.
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...
Realistic Approach for Phasor Measurement Unit Placement
DEFF Research Database (Denmark)
Rather, Zakir Hussain; Chen, Zhe; Thøgersen, Paul
2015-01-01
This paper presents a realistic cost-effectivemodel for optimal placement of phasor measurement units (PMUs) for complete observability of a power system considering practical cost implications. The proposed model considers hidden or otherwise unaccounted practical costs involved in PMU installat...
Spatial Visualization by Realistic 3D Views
Yue, Jianping
2008-01-01
In this study, the popular Purdue Spatial Visualization Test-Visualization by Rotations (PSVT-R) in isometric drawings was recreated with CAD software that allows 3D solid modeling and rendering to provide more realistic pictorial views. Both the original and the modified PSVT-R tests were given to students and their scores on the two tests were…
Realistic Simulation of Rice Plant
Directory of Open Access Journals (Sweden)
Wei-long DING
2011-09-01
Full Text Available The existing research results of virtual modeling of rice plant, however, is far from perfect compared to that of other crops due to its complex structure and growth process. Techniques to visually simulate the architecture of rice plant and its growth process are presented based on the analysis of the morphological characteristics at different stages. Firstly, the simulations of geometrical shape, the bending status and the structural distortion of rice leaves are conducted. Then, by using an improved model for bending deformation, the curved patterns of panicle axis and various types of panicle branches are generated, and the spatial shape of rice panicle is therefore created. Parametric L-system is employed to generate its topological structures, and finite-state automaton is adopted to describe the development of geometrical structures. Finally, the computer visualization of three-dimensional morphologies of rice plant at both organ and individual levels is achieved. The experimental results showed that the proposed methods of modeling the three-dimensional shapes of organs and simulating the growth of rice plant are feasible and effective, and the generated three-dimensional images are realistic.
Modeling and analysis of modular structure in diverse biological networks.
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.
A phenomenological biological dose model for proton therapy based on linear energy transfer spectra.
Rørvik, Eivind; Thörnqvist, Sara; Stokkevåg, Camilla H; Dahle, Tordis J; Fjaera, Lars Fredrik; Ytre-Hauge, Kristian S
2017-06-01
The relative biological effectiveness (RBE) of protons varies with the radiation quality, quantified by the linear energy transfer (LET). Most phenomenological models employ a linear dependency of the dose-averaged LET (LET d ) to calculate the biological dose. However, several experiments have indicated a possible non-linear trend. Our aim was to investigate if biological dose models including non-linear LET dependencies should be considered, by introducing a LET spectrum based dose model. The RBE-LET relationship was investigated by fitting of polynomials from 1st to 5th degree to a database of 85 data points from aerobic in vitro experiments. We included both unweighted and weighted regression, the latter taking into account experimental uncertainties. Statistical testing was performed to decide whether higher degree polynomials provided better fits to the data as compared to lower degrees. The newly developed models were compared to three published LET d based models for a simulated spread out Bragg peak (SOBP) scenario. The statistical analysis of the weighted regression analysis favored a non-linear RBE-LET relationship, with the quartic polynomial found to best represent the experimental data (P = 0.010). The results of the unweighted regression analysis were on the borderline of statistical significance for non-linear functions (P = 0.053), and with the current database a linear dependency could not be rejected. For the SOBP scenario, the weighted non-linear model estimated a similar mean RBE value (1.14) compared to the three established models (1.13-1.17). The unweighted model calculated a considerably higher RBE value (1.22). The analysis indicated that non-linear models could give a better representation of the RBE-LET relationship. However, this is not decisive, as inclusion of the experimental uncertainties in the regression analysis had a significant impact on the determination and ranking of the models. As differences between the models were
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.
Modeling of biological intelligence for SCM system optimization.
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.
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.
Modeling of Biological Intelligence for SCM System Optimization
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
Boolean Models of Biological Processes Explain Cascade-Like Behavior
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
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:
Biological channel modeling and implantable UWB antenna design for neural recording systems.
Bahrami, Hadi; Mirbozorgi, S Abdollah; Rusch, Leslie A; Gosselin, Benoit
2015-01-01
Ultrawideband (UWB) short-range communication systems have proved to be valuable in medical technology, particularly for implanted devices, due to their low-power consumption, low cost, small size, and high data rates. Neural activity monitoring in the brain requires high data rate (800 kb/s per neural sensor), and we target a system supporting a large number of sensors, in particular, aggregate transmission above 430 Mb/s (∼512 sensors). Knowledge of channel behavior is required to determine the maximum allowable power to 1) respect ANSI guidelines for avoiding tissue damage, and 2) respect FCC guidelines on unlicensed transmissions. We utilize a realistic model of the biological channel to inform the design of antennas for the implanted transmitter and the external receiver under these requirements. Antennas placement is examined under two scenarios having contrasting power constraints. Performance of the system within the biological tissues is examined via simulation and experiment. Our miniaturized antennas, 12 mm ×12 mm, need worst-case receiver sensitivities of -38 and -30.5 dBm for the first and second scenarios, respectively. These sensitivities allow us to successfully detect signals transmitted through tissues in the 3.1-10.6-GHz UWB band.
Systems Biology in Immunology – A Computational Modeling Perspective
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
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.
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
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.
Methods and models in mathematical biology deterministic and stochastic approaches
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.
Probabilistic Model Checking of Biological Systems with Uncertain Kinetic Rates
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.
Modeling and Simulation Tools: From Systems Biology to Systems Medicine.
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.
Mihaescu, Mihai; Murugappan, Shanmugam; Kalra, Maninder; Khosla, Sid; Gutmark, Ephraim
2008-07-19
Computational fluid dynamics techniques employing primarily steady Reynolds-Averaged Navier-Stokes (RANS) methodology have been recently used to characterize the transitional/turbulent flow field in human airways. The use of RANS implies that flow phenomena are averaged over time, the flow dynamics not being captured. Further, RANS uses two-equation turbulence models that are not adequate for predicting anisotropic flows, flows with high streamline curvature, or flows where separation occurs. A more accurate approach for such flow situations that occur in the human airway is Large Eddy Simulation (LES). The paper considers flow modeling in a pharyngeal airway model reconstructed from cross-sectional magnetic resonance scans of a patient with obstructive sleep apnea. The airway model is characterized by a maximum narrowing at the site of retropalatal pharynx. Two flow-modeling strategies are employed: steady RANS and the LES approach. In the RANS modeling framework both k-epsilon and k-omega turbulence models are used. The paper discusses the differences between the airflow characteristics obtained from the RANS and LES calculations. The largest discrepancies were found in the axial velocity distributions downstream of the minimum cross-sectional area. This region is characterized by flow separation and large radial velocity gradients across the developed shear layers. The largest difference in static pressure distributions on the airway walls was found between the LES and the k-epsilon data at the site of maximum narrowing in the retropalatal pharynx.
Ising models of strongly coupled biological networks with multivariate interactions
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.
Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology.
Das, Arya A; Ajayakumar Darsana, T; Jacob, Elizabeth
2017-03-01
Experiments in systems biology are generally supported by a computational model which quantitatively estimates the parameters of the system by finding the best fit to the experiment. Mathematical models have proved to be successful in reverse engineering the system. The data generated is interpreted to understand the dynamics of the underlying phenomena. The question we have sought to answer is that - is it possible to use an agent-based approach to re-engineer a biological process, making use of the available knowledge from experimental and modelling efforts? Can the bottom-up approach benefit from the top-down exercise so as to create an integrated modelling formalism for systems biology? We propose a modelling pipeline that learns from the data given by reverse engineering, and uses it for re-engineering the system, to carry out in-silico experiments. A mathematical model that quantitatively predicts co-expression of EGFR-HER2 receptors in activation and trafficking has been taken for this study. The pipeline architecture takes cues from the population model that gives the rates of biochemical reactions, to formulate knowledge-based rules for the particle model. Agent-based simulations using these rules, support the existing facts on EGFR-HER2 dynamics. We conclude that, re-engineering models, built using the results of reverse engineering, opens up the possibility of harnessing the power pack of data which now lies scattered in literature. Virtual experiments could then become more realistic when empowered with the findings of empirical cell biology and modelling studies. Implemented on the Agent Modelling Framework developed in-house. C ++ code templates available in Supplementary material . liz.csir@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com
Yang, Xue; Lauzon, Carolyn B; Crainiceanu, Ciprian; Caffo, Brian; Resnick, Susan M; Landman, Bennett A
2012-09-01
Massively univariate regression and inference in the form of statistical parametric mapping have transformed the way in which multi-dimensional imaging data are studied. In functional and structural neuroimaging, the de facto standard "design matrix"-based general linear regression model and its multi-level cousins have enabled investigation of the biological basis of the human brain. With modern study designs, it is possible to acquire multi-modal three-dimensional assessments of the same individuals--e.g., structural, functional and quantitative magnetic resonance imaging, alongside functional and ligand binding maps with positron emission tomography. Largely, current statistical methods in the imaging community assume that the regressors are non-random. For more realistic multi-parametric assessment (e.g., voxel-wise modeling), distributional consideration of all observations is appropriate. Herein, we discuss two unified regression and inference approaches, model II regression and regression calibration, for use in massively univariate inference with imaging data. These methods use the design matrix paradigm and account for both random and non-random imaging regressors. We characterize these methods in simulation and illustrate their use on an empirical dataset. Both methods have been made readily available as a toolbox plug-in for the SPM software. Copyright © 2012 Elsevier Inc. All rights reserved.
Recurrent Convolutional Neural Networks: A Better Model of Biological Object Recognition.
Spoerer, Courtney J; McClure, Patrick; Kriegeskorte, Nikolaus
2017-01-01
Feedforward neural networks provide the dominant model of how the brain performs visual object recognition. However, these networks lack the lateral and feedback connections, and the resulting recurrent neuronal dynamics, of the ventral visual pathway in the human and non-human primate brain. Here we investigate recurrent convolutional neural networks with bottom-up (B), lateral (L), and top-down (T) connections. Combining these types of connections yields four architectures (B, BT, BL, and BLT), which we systematically test and compare. We hypothesized that recurrent dynamics might improve recognition performance in the challenging scenario of partial occlusion. We introduce two novel occluded object recognition tasks to test the efficacy of the models, digit clutter (where multiple target digits occlude one another) and digit debris (where target digits are occluded by digit fragments). We find that recurrent neural networks outperform feedforward control models (approximately matched in parametric complexity) at recognizing objects, both in the absence of occlusion and in all occlusion conditions. Recurrent networks were also found to be more robust to the inclusion of additive Gaussian noise. Recurrent neural networks are better in two respects: (1) they are more neurobiologically realistic than their feedforward counterparts; (2) they are better in terms of their ability to recognize objects, especially under challenging conditions. This work shows that computer vision can benefit from using recurrent convolutional architectures and suggests that the ubiquitous recurrent connections in biological brains are essential for task performance.
Programming biological models in Python using PySB.
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.
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…
Dynamics of mathematical models in biology bringing mathematics to life
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...
Guevara, Lázaro; Gerstner, Beth E; Kass, Jamie M; Anderson, Robert P
2018-04-01
There is an urgent need for more ecologically realistic models for better predicting the effects of climate change on species' potential geographic distributions. Here we build ecological niche models using MAXENT and test whether selecting predictor variables based on biological knowledge and selecting ecologically realistic response curves can improve cross-time distributional predictions. We also evaluate how the method chosen for extrapolation into nonanalog conditions affects the prediction. We do so by estimating the potential distribution of a montane shrew (Mammalia, Soricidae, Cryptotis mexicanus) at present and the Last Glacial Maximum (LGM). Because it is tightly associated with cloud forests (with climatically determined upper and lower limits) whose distributional shifts are well characterized, this species provides clear expectations of plausible vs. implausible results. Response curves for the MAXENT model made using variables selected via biological justification were ecologically more realistic compared with those of the model made using many potential predictors. This strategy also led to much more plausible geographic predictions for upper and lower elevational limits of the species both for the present and during the LGM. By inspecting the modeled response curves, we also determined the most appropriate way to extrapolate into nonanalog environments, a previously overlooked factor in studies involving model transfer. This study provides intuitive context for recommendations that should promote more realistic ecological niche models for transfer across space and time. © 2017 John Wiley & Sons Ltd.
Complex Behavior in Simple Models of Biological Coevolution
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.
Papoutsi, Chrysanthi; Hargreaves, Dougal; Colligan, Grainne; Hagell, Ann; Patel, Anita; Campbell-Richards, Desirée; Viner, Russell M; Vijayaraghavan, Shanti; Marshall, Martin; Greenhalgh, Trisha; Finer, Sarah
2017-06-21
Young adults with diabetes often report dissatisfaction with care and have poor diabetes-related health outcomes. As diabetes prevalence continues to rise, group-based care could provide a sustainable alternative to traditional one-to-one consultations, by engaging young people through life stage-, context- and culturally-sensitive approaches. In this study, we will co-design and evaluate a group-based care model for young adults with diabetes and complex health and social needs in socioeconomically deprived areas. This participatory study will include three phases. In phase 1, we will carry out a realist review to synthesise the literature on group-based care for young adults with diabetes. This theory-driven understanding will provide the basis for phase 2, where we will draw on experience-based co-design methodologies to develop a new, group-based care model for young adults (aged adult diabetes services). In phase 3, we will use a researcher-in-residence approach to implement and evaluate the co-designed group clinic model and compare with traditional care. We will employ qualitative (observations in clinics, patient and staff interviews and document analysis) and quantitative methods (eg, biological markers, patient enablement instrument and diabetes distress scale), including a cost analysis. National Health Service ethics approval has been granted (reference 17/NI/0019). The project will directly inform service redesign to better meet the needs of young adults with diabetes in socioeconomically deprived areas and may guide a possible cluster-randomised trial, powered to clinical and cost-effectiveness outcomes. Findings from this study may be transferable to other long-term conditions and/or age groups. Project outputs will include briefing statements, summaries and academic papers, tailored for different audiences, including people living with diabetes, clinicians, policy makers and strategic decision makers. PROSPERO (CRD42017058726). © Article author
Models to study gravitational biology of Mammalian reproduction
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.
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.
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.
Enterococcus infection biology: lessons from invertebrate host models.
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.
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
Continuous Modeling of Calcium Transport Through Biological Membranes
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).
Should scientific realists be platonists?
DEFF Research Database (Denmark)
Busch, Jacob; Morrison, Joe
2015-01-01
Realists about are arrived at by any inferen- tial route which eschews causes (§3), and nor is there any direct pressure for Scientific Real- ists to change their inferential methods (§4). We suggest that in order to maintain inferential parity with Scientific Realism, proponents of EIA need to give......Enhanced Indispensability Arguments (EIA) claim that Scientific Realists are committed to the existence of mathematical entities due to their reliance on Inference to the Best Explana- tion (IBE). Our central question concerns this purported parity of reasoning: do people who defend the EIA make...... an appropriate use of the resources of Scientific Realism (in particular, IBE) to achieve platonism? (§2) We argue that just because a variety of different inferential strategies can be employed by Scientific Realists does not mean that ontological conclusions concerning which things we should be Scientific...
Biological profiling and dose-response modeling tools ...
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
The model of drugs distribution dynamics in biological tissue
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.
Mouse models for gastric cancer: Matching models to biological questions.
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.
Wave basin model tests of technical-biological bank protection
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
Biologically based neural circuit modelling for the study of fear learning and extinction
Nair, Satish S.; Paré, Denis; Vicentic, Aleksandra
2016-11-01
The neuronal systems that promote protective defensive behaviours have been studied extensively using Pavlovian conditioning. In this paradigm, an initially neutral-conditioned stimulus is paired with an aversive unconditioned stimulus leading the subjects to display behavioural signs of fear. Decades of research into the neural bases of this simple behavioural paradigm uncovered that the amygdala, a complex structure comprised of several interconnected nuclei, is an essential part of the neural circuits required for the acquisition, consolidation and expression of fear memory. However, emerging evidence from the confluence of electrophysiological, tract tracing, imaging, molecular, optogenetic and chemogenetic methodologies, reveals that fear learning is mediated by multiple connections between several amygdala nuclei and their distributed targets, dynamical changes in plasticity in local circuit elements as well as neuromodulatory mechanisms that promote synaptic plasticity. To uncover these complex relations and analyse multi-modal data sets acquired from these studies, we argue that biologically realistic computational modelling, in conjunction with experiments, offers an opportunity to advance our understanding of the neural circuit mechanisms of fear learning and to address how their dysfunction may lead to maladaptive fear responses in mental disorders.
Realistic Visualization of Virtual Views
DEFF Research Database (Denmark)
Livatino, Salvatore
2005-01-01
phenomena captured in the reference photographs, (i.e. the transfer of photographic-realism). An overview of most prominent approaches in realistic virtual view synthesis will be presented and briefly discussed. Applications of proposed methods to visual survey, virtual cinematography, as well as mobile...
Assessment and realistic mathematics education
Heuvel-Panhuizen, M.H.A.M. van den
1996-01-01
This book describes the consequences of Realistic Mathematics Education (RME) for assessing students’ understanding of mathematics in primary school. RME is the Dutch answer to the worldwide need to reform mathematics education. Changed ideas about mathematics as a school subject, its goals,
Revision history aware repositories of computational models of biological systems.
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
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
Regularization techniques in realistic Laplacian computation.
Bortel, Radoslav; Sovka, Pavel
2007-11-01
This paper explores regularization options for the ill-posed spline coefficient equations in the realistic Laplacian computation. We investigate the use of the Tikhonov regularization, truncated singular value decomposition, and the so-called lambda-correction with the regularization parameter chosen by the L-curve, generalized cross-validation, quasi-optimality, and the discrepancy principle criteria. The provided range of regularization techniques is much wider than in the previous works. The improvement of the realistic Laplacian is investigated by simulations on the three-shell spherical head model. The conclusion is that the best performance is provided by the combination of the Tikhonov regularization and the generalized cross-validation criterion-a combination that has never been suggested for this task before.
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
Human pluripotent stem cells: an emerging model in developmental biology.
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.
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)
Invertebrates as model organisms for research on aging biology.
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.
True-to-Life? Realistic Fiction.
Jordan, Anne Devereaux
1995-01-01
Suggests that modern realistic fiction for young readers is intensely moralistic and directive at the spoken and unspoken behest of the adults who write, select, and buy that literature. Discusses moral tales, early realistic fiction, modern realistic fiction, and choosing realistic fiction. (RS)
Indian Academy of Sciences (India)
I am particularly happy that the Academy is bringing out this document by Professor M S. Valiathan on Ayurvedic Biology. It is an effort to place before the scientific community, especially that of India, the unique scientific opportunities that arise out of viewing Ayurveda from the perspective of contemporary science, its tools ...
Bayesian Network Webserver: a comprehensive tool for biological network modeling.
Ziebarth, Jesse D; Bhattacharya, Anindya; Cui, Yan
2013-11-01
The Bayesian Network Webserver (BNW) is a platform for comprehensive network modeling of systems genetics and other biological datasets. It allows users to quickly and seamlessly upload a dataset, learn the structure of the network model that best explains the data and use the model to understand relationships between network variables. Many datasets, including those used to create genetic network models, contain both discrete (e.g. genotype) and continuous (e.g. gene expression traits) variables, and BNW allows for modeling hybrid datasets. Users of BNW can incorporate prior knowledge during structure learning through an easy-to-use structural constraint interface. After structure learning, users are immediately presented with an interactive network model, which can be used to make testable hypotheses about network relationships. BNW, including a downloadable structure learning package, is available at http://compbio.uthsc.edu/BNW. (The BNW interface for adding structural constraints uses HTML5 features that are not supported by current version of Internet Explorer. We suggest using other browsers (e.g. Google Chrome or Mozilla Firefox) when accessing BNW). ycui2@uthsc.edu. Supplementary data are available at Bioinformatics online.
Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm.
Stoll, Gautier; Viara, Eric; Barillot, Emmanuel; Calzone, Laurence
2012-01-01
Abstract Mathematical modeling is used as a Systems Biology tool to answer biological questions, and more precisely, to validate a network that describes biological observations and predict the effect of perturbations. This article presents an algorithm for modeling biological networks in a discrete framework with continuous time. Background There exist two major types of mathematical modeling approaches: (1) quantitative modeling, representing various chemical species concentrations by real...
Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles.
Directory of Open Access Journals (Sweden)
Olga Kononova
2016-01-01
Full Text Available The mechanical properties of virus capsids correlate with local conformational dynamics in the capsid structure. They also reflect the required stability needed to withstand high internal pressures generated upon genome loading and contribute to the success of important events in viral infectivity, such as capsid maturation, genome uncoating and receptor binding. The mechanical properties of biological nanoparticles are often determined from monitoring their dynamic deformations in Atomic Force Microscopy nanoindentation experiments; but a comprehensive theory describing the full range of observed deformation behaviors has not previously been described. We present a new theory for modeling dynamic deformations of biological nanoparticles, which considers the non-linear Hertzian deformation, resulting from an indenter-particle physical contact, and the bending of curved elements (beams modeling the particle structure. The beams' deformation beyond the critical point triggers a dynamic transition of the particle to the collapsed state. This extreme event is accompanied by a catastrophic force drop as observed in the experimental or simulated force (F-deformation (X spectra. The theory interprets fine features of the spectra, including the nonlinear components of the FX-curves, in terms of the Young's moduli for Hertzian and bending deformations, and the structural damage dependent beams' survival probability, in terms of the maximum strength and the cooperativity parameter. The theory is exemplified by successfully describing the deformation dynamics of natural nanoparticles through comparing theoretical curves with experimental force-deformation spectra for several virus particles. This approach provides a comprehensive description of the dynamic structural transitions in biological and artificial nanoparticles, which is essential for their optimal use in nanotechnology and nanomedicine applications.
MacLeod, Miles; Nersessian, Nancy J
2018-01-08
Modern integrative systems biology defines itself by the complexity of the problems it takes on through computational modeling and simulation. However in integrative systems biology computers do not solve problems alone. Problem solving depends as ever on human cognitive resources. Current philosophical accounts hint at their importance, but it remains to be understood what roles human cognition plays in computational modeling. In this paper we focus on practices through which modelers in systems biology use computational simulation and other tools to handle the cognitive complexity of their modeling problems so as to be able to make significant contributions to understanding, intervening in, and controlling complex biological systems. We thus show how cognition, especially processes of simulative mental modeling, is implicated centrally in processes of model-building. At the same time we suggest how the representational choices of what to model in systems biology are limited or constrained as a result. Such constraints help us both understand and rationalize the restricted form that problem solving takes in the field and why its results do not always measure up to expectations.
Naumovozyma castellii: an alternative model for budding yeast molecular biology.
Karademir Andersson, Ahu; Cohn, Marita
2017-03-01
Naumovozyma castellii (Saccharomyces castellii) is a member of the budding yeast family Saccharomycetaceae. It has been extensively used as a model organism for telomere biology research and has gained increasing interest as a budding yeast model for functional analyses owing to its amenability to genetic modifications. Owing to the suitable phylogenetic distance to S. cerevisiae, the whole genome sequence of N. castellii has provided unique data for comparative genomic studies, and it played a key role in the establishment of the timing of the whole genome duplication and the evolutionary events that took place in the subsequent genomic evolution of the Saccharomyces lineage. Here we summarize the historical background of its establishment as a laboratory yeast species, and the development of genetic and molecular tools and strains. We review the research performed on N. castellii, focusing on areas where it has significantly contributed to the discovery of new features of molecular biology and to the advancement of our understanding of molecular evolution. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.
Systemic Modeling of Biological Functions in Consideration of Physiome Project
Minamitani, Haruyuki
Emerging of the physiome project provides various influences on the medical, biological and pharmaceutical development. In this paper, as an example of physiome research, neural network model analysis providing the conduction mechanisms of pain and tactile sensations was presented, and the functional relations between neural activities of the network cells and stimulus intensity applied on the peripheral receptive fields were described. The modeling presented here is based on the various assumptions made by the results of physiological and anatomical studies reported in the literature. The functional activities of spinothalamic and thalamocortical cells show a good agreement with the physiological and psychophysical functions of somatosensory system that are very instructive for covering the gap between physiologically and psychophysically aspects of pain and tactile sensation.
Introduction to mathematical biology modeling, analysis, and simulations
Chou, Ching Shan
2016-01-01
This book is based on a one semester course that the authors have been teaching for several years, and includes two sets of case studies. The first includes chemostat models, predator-prey interaction, competition among species, the spread of infectious diseases, and oscillations arising from bifurcations. In developing these topics, readers will also be introduced to the basic theory of ordinary differential equations, and how to work with MATLAB without having any prior programming experience. The second set of case studies were adapted from recent and current research papers to the level of the students. Topics have been selected based on public health interest. This includes the risk of atherosclerosis associated with high cholesterol levels, cancer and immune interactions, cancer therapy, and tuberculosis. Readers will experience how mathematical models and their numerical simulations can provide explanations that guide biological and biomedical research. Considered to be the undergraduate companion to t...
Mass balances for a biological life support system simulation model
Volk, Tyler; Rummel, John D.
1987-01-01
Design decisions to aid the development of future space based biological life support systems (BLSS) can be made with simulation models. The biochemistry stoichiometry was developed for: (1) protein, carbohydrate, fat, fiber, and lignin production in the edible and inedible parts of plants; (2) food consumption and production of organic solids in urine, feces, and wash water by the humans; and (3) operation of the waste processor. Flux values for all components are derived for a steady state system with wheat as the sole food source. The large scale dynamics of a materially closed (BLSS) computer model is described in a companion paper. An extension of this methodology can explore multifood systems and more complex biochemical dynamics while maintaining whole system closure as a focus.
Quasi – biological model of radiogenic cancer morbidity
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A. T. Gubin
2015-01-01
Full Text Available The methods: Linear differential equations were used to formalize contemporary assumptions of self –sustaining tissue cell kinetics under the impact of adverse factors, on the formation and repairing of cell “pre-cancer” defects, on inheritance and retaining such defects in daughter cells which results in malignant neoplasms, on age-dependent impairment of human body’s function to eliminate such cells.The results: The model reproduces the well-known regularities of radiogenic cancer morbidity increase depending on instantaneous radiation exposure age and on attained age: the relative reduction at increased radiation age which the model attributes to age decrease of stem cells, relative reduction at increased time after radiation induced by “sorting out” of cells with “pre-cancer” defects, absolute increase with age proportional to natural cause mortality rate.The relevance of the developed quasi-biological model is displayed via comparison to the ICRP model for radiogenic increase of solid carcinomas’ morbidity after single radiation exposure. The latter model had been developed after Japanese cohort observations. For both genders high goodness-of-fit was achieved between the models at values of Gompertz’ law factor which had been defined for men and women in this cohort via selecting the value of the only free parameter indicating age-dependent exponential retardation of stem cells’ division.The conclusion: The proposed model suggests that the estimation of radiogenic risk inter-population transfer can be done on the basis of the data on age-dependent mortality intensity increase from all natural causes. The model also creates the premises for inter-species transfer of risk following the well-known parameters of cell populations’ kinetics in animal’s organs and tissues and Gompertz’s law parameters. This model is applicable also for analyses of age-dependent changes of background cancer morbidity.
Realist Criminology and its Discontents
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Simon Winlow
2016-09-01
Full Text Available Critical criminology must move beyond twentieth-century empiricist and idealist paradigms because the concepts and research programmes influenced by these paradigms are falling into obsolescence. Roger Matthews’ recent work firmly advocates this position and helps to set the ball rolling. Here we argue that Matthews’ attempt to use critical realist thought to move Left Realism towards an advanced position can help to put criminology on a sound new footing. However, before this becomes possible numerous philosophical and theoretical issues must be ironed out. Most importantly, critical criminology must avoid political pragmatism and adopt a more critical stance towards consumer culture’s spectacle. A searching analysis of these issues suggests that, ultimately, criminology is weighed down with obsolete thinking to such an extent that to remain intellectually relevant it must move beyond both Left Realism and Critical Realism to construct a new ultra-realist position.
Realist cinema as world cinema
Nagib, Lucia
2017-01-01
The idea that “realism” is the common denominator across the vast range of productions normally labelled as “world cinema” is widespread and seemly uncontroversial. Leaving aside oppositional binaries that define world cinema as the other of Hollywood or of classical cinema, this chapter will test the realist premise by locating it in the mode of production. It will define this mode as an ethics that engages filmmakers, at cinema’s creative peaks, with the physical and historical environment,...
Realist Criminology and its Discontents
Simon Winlow; Steve Hall
2016-01-01
Critical criminology must move beyond twentieth-century empiricist and idealist paradigms because the concepts and research programmes influenced by these paradigms are falling into obsolescence. Roger Matthews’ recent work firmly advocates this position and helps to set the ball rolling. Here we argue that Matthews’ attempt to use critical realist thought to move Left Realism towards an advanced position can help to put criminology on a sound new footing. However, before this becomes possibl...
Realistic rhetoric and legal decision
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João Maurício Adeodato
2017-06-01
Full Text Available The text aims to lay the foundations of a realistic rhetoric, from the descriptive perspective of how the legal decision actually takes place, without normative considerations. Aristotle's rhetorical idealism and its later prestige reduced rhetoric to the art of persuasion, eliminating important elements of sophistry, especially with regard to legal decision. It concludes with a rhetorical perspective of judicial activism in complex societies.
A Color-Opponency Based Biological Model for Color Constancy
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Yongjie Li
2011-05-01
Full Text Available Color constancy is the ability of the human visual system to adaptively correct color-biased scenes under different illuminants. Most of the existing color constancy models are nonphysiologically plausible. Among the limited biological models, the great majority is Retinex and its variations, and only two or three models directly simulate the feature of color-opponency, but only of the very earliest stages of visual pathway, i.e., the single-opponent mechanisms involved at the levels of retinal ganglion cells and lateral geniculate nucleus (LGN neurons. Considering the extensive physiological evidences supporting that both the single-opponent cells in retina and LGN and the double-opponent neurons in primary visual cortex (V1 are the building blocks for color constancy, in this study we construct a color-opponency based color constancy model by simulating the opponent fashions of both the single-opponent and double-opponent cells in a forward manner. As for the spatial structure of the receptive fields (RF, both the classical RF (CRF center and the nonclassical RF (nCRF surround are taken into account for all the cells. The proposed model was tested on several typical image databases commonly used for performance evaluation of color constancy methods, and exciting results were achieved.
Computational brain models: Advances from system biology and future challenges
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George E. Barreto
2015-02-01
Full Text Available Computational brain models focused on the interactions between neurons and astrocytes, modeled via metabolic reconstructions, are reviewed. The large source of experimental data provided by the -omics techniques and the advance/application of computational and data-management tools are being fundamental. For instance, in the understanding of the crosstalk between these cells, the key neuroprotective mechanisms mediated by astrocytes in specific metabolic scenarios (1 and the identification of biomarkers for neurodegenerative diseases (2,3. However, the modeling of these interactions demands a clear view of the metabolic and signaling pathways implicated, but most of them are controversial and are still under evaluation (4. Hence, to gain insight into the complexity of these interactions a current view of the main pathways implicated in the neuron-astrocyte communication processes have been made from recent experimental reports and reviews. Furthermore, target problems, limitations and main conclusions have been identified from metabolic models of the brain reported from 2010. Finally, key aspects to take into account into the development of a computational model of the brain and topics that could be approached from a systems biology perspective in future research are highlighted.
Models for integrated pest control and their biological implications.
Tang, Sanyi; Cheke, Robert A
2008-09-01
Successful integrated pest management (IPM) control programmes depend on many factors which include host-parasitoid ratios, starting densities, timings of parasitoid releases, dosages and timings of insecticide applications and levels of host-feeding and parasitism. Mathematical models can help us to clarify and predict the effects of such factors on the stability of host-parasitoid systems, which we illustrate here by extending the classical continuous and discrete host-parasitoid models to include an IPM control programme. The results indicate that one of three control methods can maintain the host level below the economic threshold (ET) in relation to different ET levels, initial densities of host and parasitoid populations and host-parasitoid ratios. The effects of host intrinsic growth rate and parasitoid searching efficiency on host mean outbreak period can be calculated numerically from the models presented. The instantaneous pest killing rate of an insecticide application is also estimated from the models. The results imply that the modelling methods described can help in the design of appropriate control strategies and assist management decision-making. The results also indicate that a high initial density of parasitoids (such as in inundative releases) and high parasitoid inter-generational survival rates will lead to more frequent host outbreaks and, therefore, greater economic damage. The biological implications of this counter intuitive result are discussed.
Respectful Modeling: Addressing Uncertainty in Dynamic System Models for Molecular Biology.
Tsigkinopoulou, Areti; Baker, Syed Murtuza; Breitling, Rainer
2017-06-01
Although there is still some skepticism in the biological community regarding the value and significance of quantitative computational modeling, important steps are continually being taken to enhance its accessibility and predictive power. We view these developments as essential components of an emerging 'respectful modeling' framework which has two key aims: (i) respecting the models themselves and facilitating the reproduction and update of modeling results by other scientists, and (ii) respecting the predictions of the models and rigorously quantifying the confidence associated with the modeling results. This respectful attitude will guide the design of higher-quality models and facilitate the use of models in modern applications such as engineering and manipulating microbial metabolism by synthetic biology. Copyright © 2016 Elsevier Ltd. All rights reserved.
Modeling biological tissue growth: discrete to continuum representations.
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.
Erythrocytes as a biological model for screening of xenobiotics toxicity.
Farag, Mayada Ragab; Alagawany, Mahmoud
2018-01-05
Erythrocytes are the main cells in circulation. They are devoid of internal membrane structures and easy to be isolated and handled providing a good model for different assays. Red blood cells (RBCs) plasma membrane is a multi-component structure that keeps the cell morphology, elasticity, flexibility and deformability. Alteration of membrane structure upon exposure to xenobiotics could induce various cellular abnormalities and releasing of intracellular components. Therefore the morphological changes and extracellular release of haemoglobin [hemolysis] and increased content of extracellular adenosine triphosphate (ATP) [as signs of membrane stability] could be used to evaluate the cytotoxic effects of various molecules. The nucleated RBCs from birds, fish and amphibians can be used to evaluate genotoxicity of different xenobiotics using comet, DNA fragmentation and micronucleus assays. The RBCs could undergo programmed cell death (eryptosis) in response to injury providing a useful model to analyze some mechanisms of toxicity that could be implicated in apoptosis of nucleated cells. Erythrocytes are vulnerable to peroxidation making it a good biological membrane model for analyzing the oxidative stress and lipid peroxidation of various xenobiotics. The RBCs contain a large number of enzymatic and non-enzymatic antioxidants. The changes of the RBCs antioxidant capacity could reflect the capability of xenobiotics to generate reactive oxygen species (ROS) resulting in oxidative damage of tissue. These criteria make RBCs a valuable in vitro model to evaluate the cytotoxicity of different natural or synthetic and organic or inorganic molecules by cellular damage measures. Copyright © 2017. Published by Elsevier B.V.
Loehr, John Francis
The issue of student preparation for college study in science has been an ongoing concern for both college-bound students and educators of various levels. This study uses a national sample of college students enrolled in introductory biology courses to address the relationship between high school biology preparation and subsequent introductory college biology performance. Multi-Level Modeling was used to investigate the relationship between students' high school science and mathematics experiences and college biology performance. This analysis controls for student demographic and educational background factors along with factors associated with the college or university attended. The results indicated that high school course-taking and science instructional experiences have the largest impact on student achievement in the first introductory college biology course. In particular, enrollment in courses, such as high school Calculus and Advanced Placement (AP) Biology, along with biology course content that focuses on developing a deep understanding of the topics is found to be positively associated with student achievement in introductory college biology. On the other hand, experiencing high numbers of laboratory activities, demonstrations, and independent projects along with higher levels of laboratory freedom are associated with negative achievement. These findings are relevant to high school biology teachers, college students, their parents, and educators looking beyond the goal of high school graduation.
Models to Study NK Cell Biology and Possible Clinical Application.
Zamora, Anthony E; Grossenbacher, Steven K; Aguilar, Ethan G; Murphy, William J
2015-08-03
Natural killer (NK) cells are large granular lymphocytes of the innate immune system, responsible for direct targeting and killing of both virally infected and transformed cells. NK cells rapidly recognize and respond to abnormal cells in the absence of prior sensitization due to their wide array of germline-encoded inhibitory and activating receptors, which differs from the receptor diversity found in B and T lymphocytes that is due to the use of recombination-activation gene (RAG) enzymes. Although NK cells have traditionally been described as natural killers that provide a first line of defense prior to the induction of adaptive immunity, a more complex view of NK cells is beginning to emerge, indicating they may also function in various immunoregulatory roles and have the capacity to shape adaptive immune responses. With the growing appreciation for the diverse functions of NK cells, and recent technological advancements that allow for a more in-depth understanding of NK cell biology, we can now begin to explore new ways to manipulate NK cells to increase their clinical utility. In this overview unit, we introduce the reader to various aspects of NK cell biology by reviewing topics ranging from NK cell diversity and function, mouse models, and the roles of NK cells in health and disease, to potential clinical applications. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.
Experimental "evolutional machines": mathematical and experimental modeling of biological evolution
Brilkov, A. V.; Loginov, I. A.; Morozova, E. V.; Shuvaev, A. N.; Pechurkin, N. S.
Experimentalists possess model systems of two major types for study of evolution continuous cultivation in the chemostat and long-term development in closed laboratory microecosystems with several trophic structure If evolutionary changes or transfer from one steady state to another in the result of changing qualitative properties of the system take place in such systems the main characteristics of these evolution steps can be measured By now this has not been realized from the point of view of methodology though a lot of data on the work of both types of evolutionary machines has been collected In our experiments with long-term continuous cultivation we used the bacterial strains containing in plasmids the cloned genes of bioluminescence and green fluorescent protein which expression level can be easily changed and controlled In spite of the apparent kinetic diversity of evolutionary transfers in two types of systems the general mechanisms characterizing the increase of used energy flow by populations of primer producent can be revealed at their study According to the energy approach at spontaneous transfer from one steady state to another e g in the process of microevolution competition or selection heat dissipation characterizing the rate of entropy growth should increase rather then decrease or maintain steady as usually believed The results of our observations of experimental evolution require further development of thermodynamic theory of open and closed biological systems and further study of general mechanisms of biological
Micrasterias as a model system in plant cell biology
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Ursula Luetz-Meindl
2016-07-01
Full Text Available The unicellular freshwater alga Micrasterias denticulata is an exceptional organism due to its extraordinary star-shaped, highly symmetric morphology and has thus attracted the interest of researchers for many decades. As a member of the Streptophyta, Micrasterias is not only genetically closely related to higher land plants but shares common features with them in many physiological and cell biological aspects. These facts, together with its considerable cell size of about 200 µm, its modest cultivation conditions and the uncomplicated accessibility particularly to any microscopic techniques, make Micrasterias a very well suited cell biological plant model system. The review focuses particularly on cell wall formation and composition, dictyosomal structure and function, cytoskeleton control of growth and morphogenesis as well as on ionic regulation and signal transduction. It has been also shown in the recent years that Micrasterias is a highly sensitive indicator for environmental stress impact such as heavy metals, high salinity, oxidative stress or starvation. Stress induced organelle degradation, autophagy, adaption and detoxification mechanisms have moved in the center of interest and have been investigated with modern microscopic techniques such as 3-D- and analytical electron microscopy as well as with biochemical, physiological and molecular approaches. This review is intended to summarize and discuss the most important results obtained in Micrasterias in the last 20 years and to compare the results to similar processes in higher plant cells.
Chemo-mechanical model of biological membranes for actuation mechanisms
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.
Phase-field theories for mathematical modeling of biological membranes.
Lázaro, Guillermo R; Pagonabarraga, Ignacio; Hernández-Machado, Aurora
2015-01-01
Biological membranes are complex structures whose mechanics are usually described at a mesoscopic level, such as the Helfrich bending theory. In this article, we present the phase-field methods, a useful tool for studying complex membrane problems which can be applied to very different phenomena. We start with an overview of the general theory of elasticity, paying special attention to its derivation from a molecular scale. We then study the particular case of membrane elasticity, explicitly obtaining the Helfrich bending energy. Within the framework of this theory, we derive a phase-field model for biological membranes and explore its physical basis and interpretation in terms of membrane elasticity. We finally explain three examples of applications of these methods to membrane related problems. First, the case of vesicle pearling and tubulation, when lipidic vesicles are exposed to the presence of hydrophobic polymers that anchor to the membrane, inducing a shape instability. Finally, we study the behavior of red blood cells while flowing in narrow microchannels, focusing on the importance of membrane elasticity to the cell flow capabilities. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
Theories and models on the Biology of Cells in Space
Todd, P.; Klaus, D. M.
A wide variety of observations on cells in space, admittedly made under constraining and unnatural conditions in many cases, have led to experimental results that were surprising or unexpected. Reproducibility, freedom from artifacts, and plausibility must be considered in all cases, even when results are not surprising. The papers in the symposium on ``Theories and Models on the Biology of Cells in Space'' are dedicated to the subject of theplausibility of cellular responses to gravity -- inertial accelerations between 0 and 9.8 m/s^2 and higher. The mechanical phenomena inside the cell, the gravitactic locomotion of single eukaryotic and prokaryotic cells, and the effects of inertial unloading on cellular physiology are addressed in theoretical and experimental studies.
Xenografted tissue models for the study of human endometrial biology.
Kuokkanen, Satu; Zhu, Liyin; Pollard, Jeffrey W
The human endometrium undergoes extensive morphological, biochemical and molecular changes under the influence of female sex steroid hormones. Besides the fact that estrogen stimulates endometrial cell proliferation and progesterone inhibits this proliferation and induces differentiation, there is limited knowledge about precise molecular mechanisms underlying human endometrial biology. The importance of paracrine signaling in endometrial physiology explains why in vitro culture of endometrial cells has been challenging. Researchers, therefore, have developed alternative experimental in vivo models for the study of endometrial biology. The objective of this review is to summarize the recent developments and work on these in vivo endometrial research models. The in vivo recombinant tissue models in which wild-type endometrial cells are combined with endometrial cells from a gene-targeted mouse strain followed by xenografting to host mice have been critical in confirming the significance of paracrine signaling between the epithelium and stroma in the growth regulation of the endometrium. Additionally, these studies have uncovered differences between the mouse and human, emphasizing the need for the development of experimental models specifically of the human endometrium. Recently, xenotransplants of human endometrial fragments into the subcutaneous space of host mice and endometrial xenografts of dissociated and recombined epithelial and stromal cells beneath the kidney capsule of immunodeficient host mice have proven to be highly promising tools for in vivo research of endometrial functions. For the first time, the latter approach provides an immense opportunity for the application of genome engineering, such as targeted ablation of endometrial genes for example by using CRISPR/CAS9 system. This research will begin to elucidate the functional role of specific genes in this complex tissue. Another advantage of xenotransplantation and xenograft models of the human
Monitoring and modeling of microbial and biological water quality
Microbial and biological water quality informs on the health of water systems and their suitability for uses in irrigation, recreation, aquaculture, and other activities. Indicators of microbial and biological water quality demonstrate high spatial and temporal variability. Therefore, monitoring str...
A model of engineering materials inspired by biological tissues
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Holeček M.
2009-12-01
Full Text Available The perfect ability of living tissues to control and adapt their mechanical properties to varying external conditions may be an inspiration for designing engineering materials. An interesting example is the smooth muscle tissue since this "material" is able to change its global mechanical properties considerably by a subtle mechanism within individual muscle cells. Multi-scale continuum models may be useful in designing essentially simpler engineering materials having similar properties. As an illustration we present the model of an incompressible material whose microscopic structure is formed by flexible, soft but incompressible balls connected mutually by linear springs. This simple model, however, shows a nontrivial nonlinear behavior caused by the incompressibility of balls and is very sensitive on some microscopic parameters. It may elucidate the way by which "small" changes in biopolymer networks within individual muscular cells may control the stiffness of the biological tissue, which outlines a way of designing similar engineering materials. The 'balls and springs' material presents also prestress-induced stiffening and allows elucidating a contribution of extracellular fluids into the tissue’s viscous properties.
Modelling biological invasions: Individual to population scales at interfaces
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.
Reyes-Palomares, Armando; Sanchez-Jimenez, Francisca; Medina, Miguel Angel
2009-01-01
A comprehensive understanding of biological functions requires new systemic perspectives, such as those provided by systems biology. Systems biology approaches are hypothesis-driven and involve iterative rounds of model building, prediction, experimentation, model refinement, and development. Developments in computer science are allowing for ever…
A biological model of tamponade gases following pneumatic retinopexy.
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.
Hansen, Kenneth; Altwegg, Kathrin; Berthelier, Jean-Jacques; Bieler, Andre; Calmonte, Ursina; Combi, Michael; De Keyser, Johan; Fiethe, Björn; Fougere, Nicolas; Fuselier, Stephen; Gombosi, Tamas; Hässig, Myrtha; Huang, Zhenguang; Le Roy, Lena; Rubin, Martin; Tenishev, Valeriy; Toth, Gabor; Tzou, Chia-Yu
2016-04-01
We have previously used results from the AMPS DSMC (Adaptive Mesh Particle Simulator Direct Simulation Monte Carlo) model to create an empirical model of the near comet coma (empirical model to the post-equinox, post-perihelion time period. In addition, we extend the coma model to significantly further from the comet (~100,000-1,000,000 km). The empirical model characterizes the neutral coma in a comet centered, sun fixed reference frame as a function of heliocentric distance, radial distance from the comet, local time and declination. Furthermore, we have generalized the model beyond application to 67P by replacing the heliocentric distance parameterizations and mapping them to production rates. Using this method, the model become significantly more general and can be applied to any comet. The model is a significant improvement over simpler empirical models, such as the Haser model. For 67P, the DSMC results are, of course, a more accurate representation of the coma at any given time, but the advantage of a mean state, empirical model is the ease and speed of use. One application of the empirical model is to de-trend the spacecraft motion from the ROSINA COPS and DFMS data (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis, Comet Pressure Sensor, Double Focusing Mass Spectrometer). The ROSINA instrument measures the neutral coma density at a single point and the measured value is influenced by the location of the spacecraft relative to the comet and the comet-sun line. Using the empirical coma model we can correct for the position of the spacecraft and compute a total production rate based on the single point measurement. In this presentation we will present the coma production rate as a function of heliocentric distance both pre- and post-equinox and perihelion.
Tuukka Kaidesoja on Critical Realist Transcendental Realism
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Groff Ruth
2015-09-01
Full Text Available I argue that critical realists think pretty much what Tukka Kaidesoja says that he himself thinks, but also that Kaidesoja’s objections to the views that he attributes to critical realists are not persuasive.
Behavior of lyophilized biological valves in a chronic animal model.
Maizato, Marina J S; Taniguchi, Fabio P; Ambar, Rafael F; Pitombo, Ronaldo N M; Leirner, Adolfo A; Cestari, Idágene A; Stolf, Noedir A G
2013-11-01
Glutaraldehyde is used in order to improve the mechanical and immunogenic properties of biological tissues, such as bovine pericardium membranes, used to manufacture heart valve bioprostheses. Lyophilization, also known as freeze-drying, preserves biological material without damage by freezing the water content and removing ice by sublimation. Through this process, dehydrated products of high quality may be obtained; also, the material may be easily handled. The lyophilization process reduces aldehyde residues in biological tissue previously treated with glutaraldehyde, thus promoting reduction of cytotoxicity, increasing resistance to inflammation, and possibly decreasing the potential for tissue calcification. The objective of this study was to chronically evaluate the calcification of bovine pericardium heart valve prostheses, previously lyophilized or not, in an animal model. Six-month-old sheep received implants of lyophilized and unlyophilized heart valve prostheses in the pulmonary position with right bypass. The study followed 16 animals for a period of 90 days. Right ventricle-pulmonary artery (RV/PA) transvalvular pressure gradient was evaluated before and immediately after implantation and before explantation, as were tissue calcium, inflammation intensity, and thrombosis and pannus formation. The t-test was used for statistical analysis. Twelve animals survived to the end of the experiment, but one of the animals in the control group had endocarditis and was excluded from the data. Four animals died early. The mean RV/PA gradient on implantation was 2.0 ± 1.6 mm Hg in the control group and 6.2 ± 4.1 mm Hg in the lyophilized group (P = 0.064). This mean gradient increased at explantation to 7.7 ± 3.9 mm Hg and 8.6 ± 5.8 mm Hg, respectively (P = 0.777). The average calcium content in the tissue leaflets after 3 months was 21.6 ± 39.1 mg Ca(2+)/g dry weight in the control group, compared with an average content of 41.2 ± 46.9 mg Ca(2+)/g dry weight
Hansen, K. C.; Fougere, N.; Bieler, A. M.; Altwegg, K.; Combi, M. R.; Gombosi, T. I.; Huang, Z.; Rubin, M.; Tenishev, V.; Toth, G.; Tzou, C. Y.
2015-12-01
We have previously published results from the AMPS DSMC (Adaptive Mesh Particle Simulator Direct Simulation Monte Carlo) model and its characterization of the neutral coma of comet 67P/Churyumov-Gerasimenko through detailed comparison with data collected by the ROSINA/COPS (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis/COmet Pressure Sensor) instrument aboard the Rosetta spacecraft [Bieler, 2015]. Results from these DSMC models have been used to create an empirical model of the near comet coma (empirical model characterizes the neutral coma in a comet centered, sun fixed reference frame as a function of heliocentric distance, radial distance from the comet, local time and declination. The model is a significant improvement over more simple empirical models, such as the Haser model. While the DSMC results are a more accurate representation of the coma at any given time, the advantage of a mean state, empirical model is the ease and speed of use. One use of such an empirical model is in the calculation of a total cometary coma production rate from the ROSINA/COPS data. The COPS data are in situ measurements of gas density and velocity along the ROSETTA spacecraft track. Converting the measured neutral density into a production rate requires knowledge of the neutral gas distribution in the coma. Our empirical model provides this information and therefore allows us to correct for the spacecraft location to calculate a production rate as a function of heliocentric distance. We will present the full empirical model as well as the calculated neutral production rate for the period of August 2014 - August 2015 (perihelion).
In vivo biological effects of stereotactic radiosurgery: A primate model
Energy Technology Data Exchange (ETDEWEB)
Lunsford, L.D.; Altschuler, E.M.; Flickinger, J.C.; Wu, A.; Martinez, A.J. (Univ. of Pittsburgh School of Medicine, PA (USA))
1990-09-01
Single-fraction, closed skull, small-volume irradiation (radiosurgery) of intact intracranial structures requires accurate knowledge of radiation tolerance. We have developed a baboon model to assess the in vivo destructive radiobiological effects of stereotactic radiosurgery. Three baboons received a single-fraction, 150-Gy lesion of the caudate nucleus, the thalamus, or the pons using the 8-mm diameter collimator of the gamma unit. Serial standard neurodiagnostic tests (neurological examination, computed tomographic scan, magnetic resonance imaging, stable xenon-enhanced computed tomographic scan of cerebral blood flow, somatosensory and brain stem evoked potentials, and myelin basic protein levels of cerebrospinal fluid) were compared with preoperative studies. Magnetic resonance imaging revealed the development of a lesion at the target site between 45 and 60 days after irradiation. Deterioration of the brain stem evoked potentials preceded imaging changes when the lesion encroached on auditory pathways. Myelin basic protein levels increased subsequent to imaging changes. Postmortem neuropathological examination confirmed a well-demarcated radionecrosis of the target volume. The baboon model appears to be an excellent method to study the in vivo biological effects of radiosurgery.
Snowden, Thomas J; van der Graaf, Piet H; Tindall, Marcus J
2018-03-26
In this paper we present a framework for the reduction and linking of physiologically based pharmacokinetic (PBPK) models with models of systems biology to describe the effects of drug administration across multiple scales. To address the issue of model complexity, we propose the reduction of each type of model separately prior to being linked. We highlight the use of balanced truncation in reducing the linear components of PBPK models, whilst proper lumping is shown to be efficient in reducing typically nonlinear systems biology type models. The overall methodology is demonstrated via two example systems; a model of bacterial chemotactic signalling in Escherichia coli and a model of extracellular regulatory kinase activation mediated via the extracellular growth factor and nerve growth factor receptor pathways. Each system is tested under the simulated administration of three hypothetical compounds; a strong base, a weak base, and an acid, mirroring the parameterisation of pindolol, midazolam, and thiopental, respectively. Our method can produce up to an 80% decrease in simulation time, allowing substantial speed-up for computationally intensive applications including parameter fitting or agent based modelling. The approach provides a straightforward means to construct simplified Quantitative Systems Pharmacology models that still provide significant insight into the mechanisms of drug action. Such a framework can potentially bridge pre-clinical and clinical modelling - providing an intermediate level of model granularity between classical, empirical approaches and mechanistic systems describing the molecular scale.
International Nuclear Information System (INIS)
Kobayashi, Tatsuo; Raby, Stuart; Zhang Renjie
2005-01-01
Motivated by orbifold grand unified theories, we construct a class of three-family Pati-Salam models in a Z6 Abelian symmetric orbifold with two discrete Wilson lines. These models have marked differences from previously-constructed three-family models in prime-order orbifolds. In the limit where one of the six compactified dimensions (which lies in a Z2 sub-orbifold) is large compared to the string length scale, our models reproduce the supersymmetry and gauge symmetry breaking pattern of 5d orbifold grand unified theories on an S1/Z2 orbicircle. We find a horizontal 2+1 splitting in the chiral matter spectra-2 families of matter are localized on the Z2 orbifold fixed points, and 1 family propagates in the 5d bulk-and identify them as the first-two and third families. Remarkably, the first two families enjoy a non-Abelian dihedral D4 family symmetry, due to the geometric setup of the compactified space. In all our models there are always some color triplets, i.e., (6,1,1) representations of the Pati-Salam group, survive orbifold projections. They could be utilized to spontaneously break the Pati-Salam symmetry to that of the Standard Model. One model, with a 5d E 6 symmetry, may give rise to interesting low energy phenomenology. We study gauge coupling unification, allowed Yukawa couplings and some of their phenomenological consequences. The E6 model has a renormalizable Yukawa coupling only for the third family. It predicts a gauge-Yukawa unification relation at the 5d compactification scale, and is capable of generating reasonable quark/lepton masses and mixings. Potential problems are also addressed, they may point to the direction for refining our models
Directory of Open Access Journals (Sweden)
K. Fennel
2011-07-01
Full Text Available The Texas-Louisiana shelf in the Northern Gulf of Mexico receives large inputs of nutrients and freshwater from the Mississippi/Atchafalaya River system. The nutrients stimulate high rates of primary production in the river plume, which contributes to the development of a large and recurring hypoxic area in summer, but the mechanistic links between hypoxia and river discharge of freshwater and nutrients are complex as the accumulation and vertical export of organic matter, the establishment and maintenance of vertical stratification, and the microbial degradation of organic matter are controlled by a non-linear interplay of factors. Unraveling these interactions will have to rely on a combination of observations and models. Here we present results from a realistic, 3-dimensional, physical-biological model with focus on a quantification of nutrient-stimulated phytoplankton growth, its variability and the fate of this organic matter. We demonstrate that the model realistically reproduces many features of observed nitrate and phytoplankton dynamics including observed property distributions and rates. We then contrast the environmental factors and phytoplankton source and sink terms characteristic of three model subregions that represent an ecological gradient from eutrophic to oligotrophic conditions. We analyze specifically the reasons behind the counterintuitive observation that primary production in the light-limited plume region near the Mississippi River delta is positively correlated with river nutrient input, and find that, while primary production and phytoplankton biomass are positively correlated with nutrient load, phytoplankton growth rate is not. This suggests that accumulation of biomass in this region is not primarily controlled bottom up by nutrient-stimulation, but top down by systematic differences in the loss processes.
Spatial succession modeling of biological communities: a multi-model approach.
Zhang, WenJun; Wei, Wu
2009-11-01
Strong spatial correlation may exist in the spatial succession of biological communities, and the spatial succession can be mathematically described. It was confirmed by our study on spatial succession of both plant and arthropod communities along a linear transect of natural grassland. Both auto-correlation and cross-correlation analyses revealed that the succession of plant and arthropod communities exhibited a significant spatial correlation, and the spatial correlation for plant community succession was stronger than arthropod community succession. Theoretically it should be reasonable to infer a site's community composition from the last site in the linear transect. An artificial neural network for state space modeling (ANNSSM) was developed in present study. An algorithm (i.e., Importance Detection Method (IDM)) for determining the relative importance of input variables was proposed. The relative importance for plant families Gramineae, Compositae and Leguminosae, and arthropod orders Homoptera, Diptera and Orthoptera, were detected and analyzed using IDM. ANNSSM performed better than multivariate linear regression and ordinary differential equation, while ordinary differential equation exhibited the worst performance in the simulation and prediction of spatial succession of biological communities. A state transition probability model (STPM) was proposed to simulate the state transition process of biological communities. STPM performed better than multinomial logistic regression in the state transition modeling. We suggested a novel multi-model framework, i.e., the joint use of ANNSSM and STPM, to predict the spatial succession of biological communities. In this framework, ANNSSM and STPM can be separately used to simulate the continuous and discrete dynamics.
A modified microdosimetric kinetic model for relative biological effectiveness calculation
Chen, Yizheng; Li, Junli; Li, Chunyan; Qiu, Rui; Wu, Zhen
2018-01-01
In the heavy ion therapy, not only the distribution of physical absorbed dose, but also the relative biological effectiveness (RBE) weighted dose needs to be taken into account. The microdosimetric kinetic model (MKM) can predict the RBE value of heavy ions with saturation-corrected dose-mean specific energy, which has been used in clinical treatment planning at the National Institute of Radiological Sciences. In the theoretical assumption of the MKM, the yield of the primary lesion is independent of the radiation quality, while the experimental data shows that DNA double strand break (DSB) yield, considered as the main primary lesion, depends on the LET of the particle. Besides, the β parameter of the MKM is constant with LET resulting from this assumption, which also differs from the experimental conclusion. In this study, a modified MKM was developed, named MMKM. Based on the experimental DSB yield of mammalian cells under the irradiation of ions with different LETs, a RBEDSB (RBE for the induction of DSB)-LET curve was fitted as the correction factor to modify the primary lesion yield in the MKM, and the variation of the primary lesion yield with LET is considered in the MMKM. Compared with the present the MKM, not only the α parameter of the MMKM for mono-energetic ions agree with the experimental data, but also the β parameter varies with LET and the variation trend of the experimental result can be reproduced on the whole. Then a spread-out Bragg peaks (SOBP) distribution of physical dose was simulated with Geant4 Monte Carlo code, and the biological and clinical dose distributions were calculated, under the irradiation of carbon ions. The results show that the distribution of clinical dose calculated with the MMKM is closed to the distribution with the MKM in the SOBP, while the discrepancy before and after the SOBP are both within 10%. Moreover, the MKM might overestimate the clinical dose at the distal end of the SOBP more than 5% because of its
A Transformative Model for Undergraduate Quantitative Biology Education
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 mathematic...
Pharmacology and toxicology of diphenyl diselenide in several biological models
Directory of Open Access Journals (Sweden)
R.M. Rosa
2007-10-01
Full Text Available The pharmacology of synthetic organoselenium compounds indicates that they can be used as antioxidants, enzyme inhibitors, neuroprotectors, anti-tumor and anti-infectious agents, and immunomodulators. In this review, we focus on the effects of diphenyl diselenide (DPDS in various biological model organisms. DPDS possesses antioxidant activity, confirmed in several in vitro and in vivo systems, and thus has a protective effect against hepatic, renal and gastric injuries, in addition to its neuroprotective activity. The activity of the compound on the central nervous system has been studied since DPDS has lipophilic characteristics, increasing adenylyl cyclase activity and inhibiting glutamate and MK-801 binding to rat synaptic membranes. Systemic administration facilitates the formation of long-term object recognition memory in mice and has a protective effect against brain ischemia and on reserpine-induced orofacial dyskinesia in rats. On the other hand, DPDS may be toxic, mainly because of its interaction with thiol groups. In the yeast Saccharomyces cerevisiae, the molecule acts as a pro-oxidant by depleting free glutathione. Administration to mice during cadmium intoxication has the opposite effect, reducing oxidative stress in various tissues. DPDS is a potent inhibitor of d-aminolevulinate dehydratase and chronic exposure to high doses of this compound has central effects on mouse brain, as well as liver and renal toxicity. Genotoxicity of this compound has been assessed in bacteria, haploid and diploid yeast and in a tumor cell line.
METABOLIC MODELLING IN THE DEVELOPMENT OF CELL FACTORIES BY SYNTHETIC BIOLOGY
Directory of Open Access Journals (Sweden)
Paula Jouhten
2012-10-01
Full Text Available Cell factories are commonly microbial organisms utilized for bioconversion of renewable resources to bulk or high value chemicals. Introduction of novel production pathways in chassis strains is the core of the development of cell factories by synthetic biology. Synthetic biology aims to create novel biological functions and systems not found in nature by combining biology with engineering. The workflow of the development of novel cell factories with synthetic biology is ideally linear which will be attainable with the quantitative engineering approach, high-quality predictive models, and libraries of well-characterized parts. Different types of metabolic models, mathematical representations of metabolism and its components, enzymes and metabolites, are useful in particular phases of the synthetic biology workflow. In this minireview, the role of metabolic modelling in synthetic biology will be discussed with a review of current status of compatible methods and models for the in silico design and quantitative evaluation of a cell factory.
Biology meets Physics: Reductionism and Multi-scale Modeling of Morphogenesis
DEFF Research Database (Denmark)
Green, Sara; Batterman, Robert
2017-01-01
from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological processes such as gene regulation and evolution. This paper takes a step back in asking whether bottom......-up modeling is feasible even when modeling simple physical systems across scales. By comparing examples of multi-scale modeling in physics and biology, we argue that the “tyranny of scales” problem present a challenge to reductive explanations in both physics and biology. The problem refers to the scale......-dependency of physical and biological behaviors that forces researchers to combine different models relying on different scale-specific mathematical strategies and boundary conditions. Analyzing the ways in which different models are combined in multi-scale modeling also has implications for the relation between physics...
Terray, P.; Sooraj, K. P.; Masson, S.; Krishna, R. P. M.; Samson, G.; Prajeesh, A. G.
2017-07-01
State-of-the-art global coupled models used in seasonal prediction systems and climate projections still have important deficiencies in representing the boreal summer tropical rainfall climatology. These errors include prominently a severe dry bias over all the Northern Hemisphere monsoon regions, excessive rainfall over the ocean and an unrealistic double inter-tropical convergence zone (ITCZ) structure in the tropical Pacific. While these systematic errors can be partly reduced by increasing the horizontal atmospheric resolution of the models, they also illustrate our incomplete understanding of the key mechanisms controlling the position of the ITCZ during boreal summer. Using a large collection of coupled models and dedicated coupled experiments, we show that these tropical rainfall errors are partly associated with insufficient surface thermal forcing and incorrect representation of the surface albedo over the Northern Hemisphere continents. Improving the parameterization of the land albedo in two global coupled models leads to a large reduction of these systematic errors and further demonstrates that the Northern Hemisphere subtropical deserts play a seminal role in these improvements through a heat low mechanism.
International Nuclear Information System (INIS)
Sakhaee, Mahmoud; Vejdani-Noghreiyan, Alireza; Ebrahimi-Khankook, Atiyeh
2015-01-01
Radiation induced cataract has been demonstrated among people who are exposed to ionizing radiation. To evaluate the deterministic effects of ionizing radiation on the eye lens, several papers dealing with the eye lens dose have been published. ICRP Publication 103 states that the lens of the eye may be more radiosensitive than previously considered. Detailed investigation of the response of the lens showed that there are strong differences in sensitivity to ionizing radiation exposure with respect to cataract induction among the tissues of the lens of the eye. This motivated several groups to look deeper into issue of the dose to a sensitive cell population within the lens, especially for radiations with low energy penetrability that have steep dose gradients inside the lens. Two sophisticated mathematical models of the eye including the inner structure have been designed for the accurate dose estimation in recent years. This study focuses on the calculations of the absorbed doses of different parts of the eye using the stylized models located in UF-ORNL phantom and comparison with the data calculated with the reference computational phantom in a broad parallel beam incident of protons with energies between 20 MeV and 10 GeV. The obtained results indicate that the total lens absorbed doses of reference phantom has good compliance with those of the more sensitive regions of stylized models. However, total eye absorbed dose of these models greatly differ with each other for lower energies. - Highlights: • The validation of reference data for the eye was studied for proton exposures. • Two real mathematical models of the eye were imported into the UF-ORNL phantom. • Fluence to dose conversion coefficients were calculated for different eye sections. • Obtained Results were compared with that of assessed by ICRP adult male phantom
Biology Based Lung Cancer Model for Chronic Low Radon Exposures
International Nuclear Information System (INIS)
Truta-Popa, Lucia-Adina; Hofmann, Werner; Fakir, Hatim; Cosma, Constantin
2008-01-01
Low dose effects of alpha particles at the tissue level are characterized by the interaction of single alpha particles, affecting only a small fraction of the cells within that tissue. Alpha particle intersections of bronchial target cells during a given exposure period were simulated by an initiation-promotion model, formulated in terms of cellular hits within the cycle time of the cell (dose-rate) and then integrated over the whole exposure period (dose). For a given average number of cellular hits during the lifetime of bronchial cells, the actual number of single and multiple hits was selected from a Poisson distribution. While oncogenic transformation is interpreted as the primary initiation step, stimulated mitosis by killing adjacent cells is assumed to be the primary radiological promotion event. Analytical initiation and promotion functions were derived from experimental in vitro data on oncogenic transformation and cellular survival.To investigate the shape of the lung cancer risk function at chronic, low level exposures in more detail, additional biological factors describing the tissue response and operating specifically at low doses were incorporated into the initiation-promotion model. These mechanisms modifying the initial response at the cellular level were: adaptive response, genomic instability, induction of apoptosis by surrounding cells, and detrimental as well as protective bystander mechanisms. To quantify the effects of these mechanisms as functions of dose, analytical functions were derived from the experimental evidence presently available. Predictions of lung cancer risk, including these mechanisms, exhibit a distinct sublinear dose-response relationship at low exposures, particularly for very low exposure rates
Sarma, Gopal P.; Faundez, Victor
2017-01-01
ABSTRACT Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems, a diverse array of biological systems have been the target of large-scale computational modeling efforts. Nonetheless, these research agendas have yet to prove decisively their value among the broader community of theoretical and experimental biolo...
Realistic Simulations of Coronagraphic Observations with WFIRST
Rizzo, Maxime; Zimmerman, Neil; Roberge, Aki; Lincowski, Andrew; Arney, Giada; Stark, Chris; Jansen, Tiffany; Turnbull, Margaret; WFIRST Science Investigation Team (Turnbull)
2018-01-01
We present a framework to simulate observing scenarios with the WFIRST Coronagraphic Instrument (CGI). The Coronagraph and Rapid Imaging Spectrograph in Python (crispy) is an open-source package that can be used to create CGI data products for analysis and development of post-processing routines. The software convolves time-varying coronagraphic PSFs with realistic astrophysical scenes which contain a planetary architecture, a consistent dust structure, and a background field composed of stars and galaxies. The focal plane can be read out by a WFIRST electron-multiplying CCD model directly, or passed through a WFIRST integral field spectrograph model first. Several elementary post-processing routines are provided as part of the package.
Realistic microscopic level densities for spherical nuclei
International Nuclear Information System (INIS)
Cerf, N.
1994-01-01
Nuclear level densities play an important role in nuclear reactions such as the formation of the compound nucleus. We develop a microscopic calculation of the level density based on a combinatorial evaluation from a realistic single-particle level scheme. This calculation makes use of a fast Monte Carlo algorithm allowing us to consider large shell model spaces which could not be treated previously in combinatorial approaches. Since our model relies on a microscopic basis, it can be applied to exotic nuclei with more confidence than the commonly used semiphenomenological formuals. An exhaustive comparison of our predicted neutron s-wave resonance spacings with experimental data for a wide range of nuclei is presented
Directory of Open Access Journals (Sweden)
W. Liu
2017-10-01
Full Text Available Solar induced chlorophyll a fluorescence (SIF has been shown to be an excellent proxy of photosynthesis at multiple scales. However, the mechanical linkages between fluorescence and photosynthesis at the leaf level cannot be directly applied at canopy or field scales, as the larger scale SIF emission depends on canopy structure. This is especially true for the forest canopies characterized by high horizontal and vertical heterogeneity. While most of the current studies on SIF radiative transfer in plant canopies are based on the assumption of a homogeneous canopy, recently codes have been developed capable of simulation of fluorescence signal in explicit 3-D forest canopies. Here we present a canopy SIF upscaling method consisting of the integration of the 3-D radiative transfer model DART and a 3-D object model BLENDER. Our aim was to better understand the effect of boreal forest canopy structure on SIF for a spatially explicit forest canopy.
Liu, W.; Atherton, J.; Mõttus, M.; MacArthur, A.; Teemu, H.; Maseyk, K.; Robinson, I.; Honkavaara, E.; Porcar-Castell, A.
2017-10-01
Solar induced chlorophyll a fluorescence (SIF) has been shown to be an excellent proxy of photosynthesis at multiple scales. However, the mechanical linkages between fluorescence and photosynthesis at the leaf level cannot be directly applied at canopy or field scales, as the larger scale SIF emission depends on canopy structure. This is especially true for the forest canopies characterized by high horizontal and vertical heterogeneity. While most of the current studies on SIF radiative transfer in plant canopies are based on the assumption of a homogeneous canopy, recently codes have been developed capable of simulation of fluorescence signal in explicit 3-D forest canopies. Here we present a canopy SIF upscaling method consisting of the integration of the 3-D radiative transfer model DART and a 3-D object model BLENDER. Our aim was to better understand the effect of boreal forest canopy structure on SIF for a spatially explicit forest canopy.
DEFF Research Database (Denmark)
Nielsen, Jesper Duemose; Madsen, Kristoffer Hougaard; Puonti, Oula
2018-01-01
three methods for skull segmentation, namely FSL BET2, the unified segmentation routine of SPM12 with extended spatial tissue priors, and the skullfinder tool of BrainSuite. To our knowledge, this study is the first to rigorously assess the accuracy of these state-of-the-art tools by comparison with CT...... models based on tetrahedral meshes, which are distributed as part of the open-source software package SimNIBS for field calculations for transcranial brain stimulation....
Martins, Ana Margarida; Vera-Licona, Paola; Laubenbacher, Reinhard
2008-01-01
This article describes a mathematical biology workshop given to secondary school teachers of the Danville area in Virginia, USA. The goal of the workshop was to enable teams of teachers with biology and mathematics expertise to incorporate lesson plans in mathematical modelling into the curriculum. The biological focus of the activities is the…
Biernath, Christian; Hauck, Julia; Klein, Christian; Thieme, Christoph; Heinlein, Florian; Priesack, Eckart
2014-05-01
Persons susceptible to allergenic pollen grains need to apply suppressive pharmacy before the occurrence of the first allergy symptoms. Patient targeted medication could be improved if forecasts of the allergenic potential of pollen (biochemical composition of the pollen grain) and the onset, duration, and end of the pollen season are precise on regional scale. In plant tissue the biochemical composition may change within hours due to the resource availability for plant growth and plant internal nutrient re-mobilization. As these processes highly depend on both, the environmental conditions and the development stage of a plant, precise simulations of the onset and duration of the flowering period are crucial to determine the allergenic potential of tissues and pollen. Here, dynamic plant models that consider the dependence of the chemical composition of tissue on the development stage of the plant embedded in process-based ecosystem models seem promising tools; however, today dynamic plant growth is widely ignored in simulations of atmospheric pollen loads. In this study we raise the question whether frequently applied temperature sum models (TSM) could precisely simulate the plant development stages in case of birches on regional scale. These TSM integrate average temperatures above a base temperature below which no further plant development is assumed. In this study, we therefore tested the ability of TSM to simulate the flowering period of birches on more than 100 sites in Bavaria, Germany over a period of three years (2010-2012). Our simulations indicate that the often applied base temperatures between 2.3°C and 3.5°C for the integration of daily or hourly average temperatures, respectively, in Europe are too high to adequately simulate the onset of birch flowering in Bavaria where a base temperature of 1°C seems more convenient. A more regional calibration of the models to sub-regions in Bavaria with comparable climatic conditions could further improve the
U.S. Environmental Protection Agency — Spreadsheets are included here to support the manuscript "Boosted Regression Tree Models to Explain Watershed Nutrient Concentrations and Biological Condition". This...
International Nuclear Information System (INIS)
Sontheimer, F.; Landskron, H.
1999-01-01
Radial matrix fission gas release (fgr) profiles of UO 2 fuel measured by electron probe micro analysis usually have the shape of a bowler hat: High release in the fuel central part, low release in the rim and a continuous transition zone in between; this holds for both steady state irradiated fuel and ramped fuel. Good fission gas release models based mainly on diffusional processes are capable of describing such radial fgr profiles with the shape of a bowler. Occasionally, the bowler becomes battered: The formerly smooth transition zone between rim and center has pronounced steps and the height of the bowler increases (continued fgr in central part) despite decreasing temperatures at high burnup. Additionally, the rim of the bowler swings up at high burnup due to the rim effect which transports gas from the matrix to the rim bubbles. Standard diffusional fgr models are unable to describe 'battered bowlers' and especially the steps in the transition zone, which also show up in the etched cross-sections of the fuel as dark double rings or even multiple rings instead of the usual single dark ring, still await theoretical explanation. For the rim, it is meanwhile well known, that saturation processes are responsible for the redistribution of the fission gas from the matrix to the rim bubbles; empirical models as for example published by Lassmann from ITU/Karlsruhe do a good job in this regard. In this paper, it is shown that saturation processes are also responsible for the steps in the. transition zone sometimes seen in radial matrix fission gas release profiles of both steady state irradiated and ramped UO 2 fuel rods. Also the steadily increasing height of the bowler at high burnups of steady state irradiated rods, where temperatures fell so low that diffusional fission gas release in the central parts of the fuel stopped long before end of irradiation, is due to such saturation processes. These saturation processes are modeled with a concept based on Lassmann
Basic science through engineering? Synthetic modeling and the idea of biology-inspired engineering.
Knuuttila, Tarja; Loettgers, Andrea
2013-06-01
Synthetic biology is often understood in terms of the pursuit for well-characterized biological parts to create synthetic wholes. Accordingly, it has typically been conceived of as an engineering dominated and application oriented field. We argue that the relationship of synthetic biology to engineering is far more nuanced than that and involves a sophisticated epistemic dimension, as shown by the recent practice of synthetic modeling. Synthetic models are engineered genetic networks that are implanted in a natural cell environment. Their construction is typically combined with experiments on model organisms as well as mathematical modeling and simulation. What is especially interesting about this combinational modeling practice is that, apart from greater integration between these different epistemic activities, it has also led to the questioning of some central assumptions and notions on which synthetic biology is based. As a result synthetic biology is in the process of becoming more "biology inspired." Copyright © 2013 Elsevier Ltd. All rights reserved.
International Nuclear Information System (INIS)
Tofts, Paul S.; Cutajar, Marica; Mendichovszky, Iosif A.; Peters, A.M.; Gordon, Isky
2012-01-01
To model the uptake phase of T 1 -weighted DCE-MRI data in normal kidneys and to demonstrate that the fitted physiological parameters correlate with published normal values. The model incorporates delay and broadening of the arterial vascular peak as it appears in the capillary bed, two distinct compartments for renal intravascular and extravascular Gd tracer, and uses a small-vessel haematocrit value of 24%. Four physiological parameters can be estimated: regional filtration K trans (ml min -1 [ml tissue ] -1 ), perfusion F (ml min -1 [100 ml tissue ] -1 ), blood volume v b (%) and mean residence time MRT (s). From these are found the filtration fraction (FF; %) and total GFR (ml min -1 ). Fifteen healthy volunteers were imaged twice using oblique coronal slices every 2.5 s to determine the reproducibility. Using parenchymal ROIs, group mean values for renal biomarkers all agreed with published values: K trans : 0.25; F: 219; v b : 34; MRT: 5.5; FF: 15; GFR: 115. Nominally cortical ROIs consistently underestimated total filtration (by ∝ 50%). Reproducibility was 7-18%. Sensitivity analysis showed that these fitted parameters are most vulnerable to errors in the fixed parameters kidney T 1 , flip angle, haematocrit and relaxivity. These renal biomarkers can potentially measure renal physiology in diagnosis and treatment. circle Dynamic contrast-enhanced magnetic resonance imaging can measure renal function. circle Filtration and perfusion values in healthy volunteers agree with published normal values. circle Precision measured in healthy volunteers is between 7 and 15%. (orig.)
Tang, H.; Sun, W.
2016-12-01
The theoretical computation of dislocation theory in a given earth model is necessary in the explanation of observations of the co- and post-seismic deformation of earthquakes. For this purpose, computation theories based on layered or pure half space [Okada, 1985; Okubo, 1992; Wang et al., 2006] and on spherically symmetric earth [Piersanti et al., 1995; Pollitz, 1997; Sabadini & Vermeersen, 1997; Wang, 1999] have been proposed. It is indicated that the compressibility, curvature and the continuous variation of the radial structure of Earth should be simultaneously taken into account for modern high precision displacement-based observations like GPS. Therefore, Tanaka et al. [2006; 2007] computed global displacement and gravity variation by combining the reciprocity theorem (RPT) [Okubo, 1993] and numerical inverse Laplace integration (NIL) instead of the normal mode method [Peltier, 1974]. Without using RPT, we follow the straightforward numerical integration of co-seismic deformation given by Sun et al. [1996] to present a straightforward numerical inverse Laplace integration method (SNIL). This method is used to compute the co- and post-seismic displacement of point dislocations buried in a spherically symmetric, self-gravitating viscoelastic and multilayered earth model and is easy to extended to the application of geoid and gravity. Comparing with pre-existing method, this method is relatively more straightforward and time-saving, mainly because we sum associated Legendre polynomials and dislocation love numbers before using Riemann-Merlin formula to implement SNIL.
International Nuclear Information System (INIS)
Robert C. Starr
2005-01-01
seven plumes at 24 DOE facilities were screened, and 14 plumes were selected for detailed examination. In the plumes selected for further study, spatial changes in the concentration of a conservative co-contaminant were used to compensate for the effects of mixing and temporal changes in TCE release from the contaminant source. Decline in TCE concentration along a flow path in excess of the co contaminant concentration decline was attributed to cometabolic degradation. This study indicated that TCE was degraded in 9 of the 14 plumes examined, with first order degradation half-lives ranging from about 1 to 12 years. TCE degradation in about two-thirds of the plumes examined suggests that cometabolism of TCE in aerobic groundwater is a common occurrence, in contrast to the conventional wisdom that TCE is recalcitrant in aerobic groundwater. The degradation half-life values calculated in this study are short enough that natural attenuation may be a viable remedy in many aerobic plumes. Computer modeling of groundwater flow and contaminant transport and degradation is frequently used to predict the evolution of groundwater plumes, and for evaluating natural attenuation and other remedial alternatives. An important aspect of a computer model is the mathematical approach for describing degradation kinetics. A common approach is to assume that degradation occurs as a first-order process. First order kinetics are easily incorporated into transport models and require only a single value (a degradation half-life) to describe reaction kinetics. The use of first order kinetics is justified in many cases because more elaborate kinetic equations often closely approximate first order kinetics under typical field conditions. A previous modeling study successfully simulated the INL TCE plume using first order degradation kinetics. TCE cometabolism is the result of TCE reacting with microbial enzymes that were produced for other purposes, such as oxidizing a growth substrate to obtain
Bellizzi, Gennaro; Bucci, Ovidio M; Chirico, Gaetano
2016-09-01
This paper presents a numerical study aiming at assessing the effectiveness of a recently proposed optimisation criterion for determining the optimal operative conditions in magnetic nanoparticle hyperthermia applied to the clinically relevant case of brain tumours. The study is carried out using the Zubal numerical phantom, and performing electromagnetic-thermal co-simulations. The Pennes model is used for thermal balance; the dissipation models for the magnetic nanoparticles are those available in the literature. The results concerning the optimal therapeutic concentration of nanoparticles, obtained through the analysis, are validated using experimental data on the specific absorption rate of iron oxide nanoparticles, available in the literature. The numerical estimates obtained by applying the criterion to the treatment of brain tumours shows that the acceptable values for the product between the magnetic field amplitude and frequency may be two to four times larger than the safety threshold of 4.85 × 10(8)A/m/s usually considered. This would allow the reduction of the dosage of nanoparticles required for an effective treatment. In particular, depending on the tumour depth, concentrations of nanoparticles smaller than 10 mg/mL of tumour may be sufficient for heating tumours smaller than 10 mm above 42 °C. Moreover, the study of the clinical scalability shows that, whatever the tumour position, lesions larger than 15 mm may be successfully treated with concentrations lower than 10 mg/mL. The criterion also allows the prediction of the temperature rise in healthy tissue, thus assuring safe treatment. The criterion can represent a helpful tool for planning and optimising an effective hyperthermia treatment.
Energy Technology Data Exchange (ETDEWEB)
Tofts, Paul S. [Brighton and Sussex Medical School, Falmer, Sussex (United Kingdom); UCL Institute of Neurology, London (United Kingdom); Cutajar, Marica [Brighton and Sussex Medical School, Falmer, Sussex (United Kingdom); UCL Institute of Child Health, London (United Kingdom); Mendichovszky, Iosif A. [University of Manchester, Imaging Science and Biomedical Engineering, Manchester (United Kingdom); Peters, A.M. [Brighton and Sussex Medical School, Falmer, Sussex (United Kingdom); Gordon, Isky [UCL Institute of Child Health, London (United Kingdom)
2012-06-15
To model the uptake phase of T{sub 1}-weighted DCE-MRI data in normal kidneys and to demonstrate that the fitted physiological parameters correlate with published normal values. The model incorporates delay and broadening of the arterial vascular peak as it appears in the capillary bed, two distinct compartments for renal intravascular and extravascular Gd tracer, and uses a small-vessel haematocrit value of 24%. Four physiological parameters can be estimated: regional filtration K{sup trans} (ml min {sup -1} [ml tissue ]{sup -1}), perfusion F (ml min {sup -1} [100 ml tissue ]{sup -1}), blood volume v{sub b} (%) and mean residence time MRT (s). From these are found the filtration fraction (FF; %) and total GFR (ml min {sup -1}). Fifteen healthy volunteers were imaged twice using oblique coronal slices every 2.5 s to determine the reproducibility. Using parenchymal ROIs, group mean values for renal biomarkers all agreed with published values: K{sup trans}: 0.25; F: 219; v{sub b}: 34; MRT: 5.5; FF: 15; GFR: 115. Nominally cortical ROIs consistently underestimated total filtration (by {proportional_to} 50%). Reproducibility was 7-18%. Sensitivity analysis showed that these fitted parameters are most vulnerable to errors in the fixed parameters kidney T{sub 1}, flip angle, haematocrit and relaxivity. These renal biomarkers can potentially measure renal physiology in diagnosis and treatment. circle Dynamic contrast-enhanced magnetic resonance imaging can measure renal function. circle Filtration and perfusion values in healthy volunteers agree with published normal values. circle Precision measured in healthy volunteers is between 7 and 15%. (orig.)
Problem Posing with Realistic Mathematics Education Approach in Geometry Learning
Mahendra, R.; Slamet, I.; Budiyono
2017-09-01
One of the difficulties of students in the learning of geometry is on the subject of plane that requires students to understand the abstract matter. The aim of this research is to determine the effect of Problem Posing learning model with Realistic Mathematics Education Approach in geometry learning. This quasi experimental research was conducted in one of the junior high schools in Karanganyar, Indonesia. The sample was taken using stratified cluster random sampling technique. The results of this research indicate that the model of Problem Posing learning with Realistic Mathematics Education Approach can improve students’ conceptual understanding significantly in geometry learning especially on plane topics. It is because students on the application of Problem Posing with Realistic Mathematics Education Approach are become to be active in constructing their knowledge, proposing, and problem solving in realistic, so it easier for students to understand concepts and solve the problems. Therefore, the model of Problem Posing learning with Realistic Mathematics Education Approach is appropriately applied in mathematics learning especially on geometry material. Furthermore, the impact can improve student achievement.
International Nuclear Information System (INIS)
Xu, X; Lin, H; Gao, Y; Caracappa, P; Wang, Y; Huo, W; Pi, Y; Feng, M; Chen, Z; Dauer, L; Thornton, R; Dauer, Z; Alvarado, K; St Germain, J; Solomon, S
2016-01-01
Purpose: To study how eyeglass design features and postures of the interventional radiologist affect the radiation dose to the lens of the eye. Methods: A mesh-based deformable phantom, consisting of an ultra-fine eye model, was used to simulate postures of a radiologist in fluoroscopically guided interventional procedure (facing the patient, 45 degree to the left, and 45 degree to the right). Various eyewear design features were studied, including the shape, lead-equivalent thickness, and separation from the face. The MCNPX Monte Carlo code was used to simulate the X-ray source used for the transcatheter arterial chemoembolization procedure (The X-ray tube is located 35 cm from the ground, emitting X-rays toward to the ceiling; Field size is 40cm X 40cm; X-ray tube voltage is 90 kVp). Experiments were also performed using dosimeter placed on a physical phantom behind eyeglasses. Results: Without protective eyewear, the radiologist’s eye lens can receive an annual dose equivalent of about 80 mSv. When wearing a pair of lead eyeglasses with lead-equivalent of 0.5-mm Pb, the annual dose equivalent of the eye lens is reduced to 31.47 mSv, but both exceed the new ICRP limit of 20 mSv. A face shield with a lead-equivalent of 0.125-mm Pb in the shape of a semi-cylinder (13cm in radius and 20-cm in height) would further reduce the exposure to the lens of the eye. Examination of postures and eyeglass features reveal surprising information, including that the glass-to-eye separation also plays an important role in the dose to the eye lens from scattered X-ray from underneath and the side. Results are in general agreement with measurements. Conclusion: There is an urgent need to further understand the relationship between the radiation environment and the radiologist’s eyewear and posture in order to provide necessary protection to the interventional radiologists under newly reduced dose limits.
International Nuclear Information System (INIS)
Amaro-Seoane, Pau; Preto, Miguel
2011-01-01
One of the most interesting sources of gravitational waves (GWs) for LISA is the inspiral of compact objects on to a massive black hole (MBH), commonly referred to as an 'extreme-mass ratio inspiral' (EMRI). The small object, typically a stellar black hole, emits significant amounts of GW along each orbit in the detector bandwidth. The slowly, adiabatic inspiral of these sources will allow us to map spacetime around MBHs in detail, as well as to test our current conception of gravitation in the strong regime. The event rate of this kind of source has been addressed many times in the literature and the numbers reported fluctuate by orders of magnitude. On the other hand, recent observations of the Galactic centre revealed a dearth of giant stars inside the inner parsec relative to the numbers theoretically expected for a fully relaxed stellar cusp. The possibility of unrelaxed nuclei (or, equivalently, with no or only a very shallow cusp, or core) adds substantial uncertainty to the estimates. Having this timely question in mind, we run a significant number of direct-summation N-body simulations with up to half a million particles to calibrate a much faster orbit-averaged Fokker-Planck code. We show that, under quite generic initial conditions, the time required for the growth of a relaxed, mass segregated stellar cusp is shorter than a Hubble time for MBHs with M . ∼ 6 M o-dot (i.e. nuclei in the range of LISA). We then investigate the regime of strong mass segregation (SMS) for models with two different stellar mass components. Given the most recent stellar mass normalization for the inner parsec of the Galactic centre, SMS has the significant impact of boosting the EMRI rates by a factor of ∼10 in comparison to what would result from a 7/4-Bahcall and Wolf cusp resulting in ∼250 events per Gyr per Milky Way type galaxy. Such an intrinsic rate should translate roughly into ∼10 2 -7 x 10 2 sbh's (EMRIs detected by LISA over a mission lifetime of 2 or 5
Energy Technology Data Exchange (ETDEWEB)
Xu, X [Rensselaer Polytechnic Inst., Troy, NY (United States); Lin, H [Rensselaer Polytechnic Institute, Troy, NY (United States); Gao, Y; Caracappa, P [RPI, Troy, NY (United States); Wang, Y; Huo, W; Pi, Y; Feng, M; Chen, Z [USTC, Hefei, Anhui (China); Dauer, L [Memorial Sloan-Kettering Cancer Ctr, New York, NY (United States); Thornton, R; Dauer, Z; Alvarado, K [Memorial Sloan Kettering Cancer Center, New York, NY (United States); St Germain, J [Mem Sloan-Kettering Cancer Ctr, New York, NY (United States); Solomon, S [Rensselaer Polytechnic Inst., Troy, NY (United States); USTC, Hefei, Anhui (China)
2016-06-15
Purpose: To study how eyeglass design features and postures of the interventional radiologist affect the radiation dose to the lens of the eye. Methods: A mesh-based deformable phantom, consisting of an ultra-fine eye model, was used to simulate postures of a radiologist in fluoroscopically guided interventional procedure (facing the patient, 45 degree to the left, and 45 degree to the right). Various eyewear design features were studied, including the shape, lead-equivalent thickness, and separation from the face. The MCNPX Monte Carlo code was used to simulate the X-ray source used for the transcatheter arterial chemoembolization procedure (The X-ray tube is located 35 cm from the ground, emitting X-rays toward to the ceiling; Field size is 40cm X 40cm; X-ray tube voltage is 90 kVp). Experiments were also performed using dosimeter placed on a physical phantom behind eyeglasses. Results: Without protective eyewear, the radiologist’s eye lens can receive an annual dose equivalent of about 80 mSv. When wearing a pair of lead eyeglasses with lead-equivalent of 0.5-mm Pb, the annual dose equivalent of the eye lens is reduced to 31.47 mSv, but both exceed the new ICRP limit of 20 mSv. A face shield with a lead-equivalent of 0.125-mm Pb in the shape of a semi-cylinder (13cm in radius and 20-cm in height) would further reduce the exposure to the lens of the eye. Examination of postures and eyeglass features reveal surprising information, including that the glass-to-eye separation also plays an important role in the dose to the eye lens from scattered X-ray from underneath and the side. Results are in general agreement with measurements. Conclusion: There is an urgent need to further understand the relationship between the radiation environment and the radiologist’s eyewear and posture in order to provide necessary protection to the interventional radiologists under newly reduced dose limits.
Helioseismology of a Realistic Magnetoconvective Sunspot Simulation
Braun, D. C.; Birch, A. C.; Rempel, M.; Duvall, T. L., Jr.
2012-01-01
We compare helioseismic travel-time shifts measured from a realistic magnetoconvective sunspot simulation using both helioseismic holography and time-distance helioseismology, and measured from real sunspots observed with the Helioseismic and Magnetic Imager instrument on board the Solar Dynamics Observatory and the Michelson Doppler Imager instrument on board the Solar and Heliospheric Observatory. We find remarkable similarities in the travel-time shifts measured between the methodologies applied and between the simulated and real sunspots. Forward modeling of the travel-time shifts using either Born or ray approximation kernels and the sound-speed perturbations present in the simulation indicates major disagreements with the measured travel-time shifts. These findings do not substantially change with the application of a correction for the reduction of wave amplitudes in the simulated and real sunspots. Overall, our findings demonstrate the need for new methods for inferring the subsurface structure of sunspots through helioseismic inversions.
A Comprehensive Web-based Platform For Domain-Specific Biological Models
Czech Academy of Sciences Publication Activity Database
Klement, M.; Šafránek, D.; Děd, J.; Pejznoch, A.; Nedbal, Ladislav; Steuer, Ralf; Červený, Jan; Müller, Stefan
2013-01-01
Roč. 299, 25 Dec (2013), s. 61-67 ISSN 1571-0661 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : biological models * model annotation * systems biology * simulation * database Subject RIV: EH - Ecology, Behaviour
Differential Equations Models in Biology, Epidemiology and Ecology
Martelli, Mario
1991-01-01
The past forty years have been the stage for the maturation of mathematical biolo~ as a scientific field. The foundations laid by the pioneers of the field during the first half of this century have been combined with advances in ap plied mathematics and the computational sciences to create a vibrant area of scientific research with established research journals, professional societies, deep subspecialty areas, and graduate education programs. Mathematical biology is by its very nature cross-disciplinary, and research papers appear in mathemat ics, biology and other scientific journals, as well as in the specialty journals devoted to mathematical and theoretical biology. Multiple author papers are common, and so are collaborations between individuals who have academic bases in different traditional departments. Those who seek to keep abreast of current trends and problems need to interact with research workers from a much broader spectrum of fields than is common in the traditional mono-culture discipline...
Bell Operator Method to Classify Local Realistic Theories
International Nuclear Information System (INIS)
Nagata, Koji
2010-01-01
We review the historical fact of multipartite Bell inequalities with an arbitrary number of settings. An explicit local realistic model for the values of a correlation function, given in a two-setting Bell experiment (two-setting model), works only for the specific set of settings in the given experiment, but cannot construct a local realistic model for the values of a correlation function, given in a continuous-infinite settings Bell experiment (infinite-setting model), even though there exist two-setting models for all directions in space. Hence, the two-setting model does not have the property that the infinite-setting model has. Here, we show that an explicit two-setting model cannot construct a local realistic model for the values of a correlation function, given in an M-setting Bell experiment (M-setting model), even though there exist two-setting models for the M measurement directions chosen in the given M-setting experiment. Hence, the two-setting model does not have the property that the M-setting model has. (general)
Development of a kinetic model for biological sulphate reduction ...
African Journals Online (AJOL)
The Rhodes BioSUREÆÊ Process is a low-cost active treatment system for acid mine drainage (AMD) waters. Central to this process is biological sulphate reduction (BSR) using primary sewage sludge (PSS) as the electron donor and organic carbon source, with the concomitant reduction of sulphate to sulphide and ...
ANIMO: a tool for modeling biological pathway dynamics
Schivo, Stefano; Scholma, Jetse; Karperien, Hermanus Bernardus Johannes; Langerak, Romanus; van de Pol, Jan Cornelis; Post, Janine Nicole
2014-01-01
Introduction Computational methods are applied with increasing success to the analysis of complex biological systems. However, their adoption is sometimes made difficult by requiring prior knowledge about the foundations of such methods, which often come from a different branch of science. The
A Transformative Model for Undergraduate Quantitative Biology Education
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)…
Atomic force microscopy on domains in biological model membranes
Rinia, H.A.
2001-01-01
This thesis describes the preparation and imaging of supported lipid bilayers, which can be regarded as biological modelmembranes, in the light of the formation of domains. The bilayers were prepared with either the Langmuir-Blodgett method, or with vesicle fusion. They were imaged with Atomic Force
Varentsov, Mikhail; Wouters, Hendrik; Trusilova, Kristina; Samsonov, Timofey; Konstantinov, Pavel
2017-04-01
, we used originally technology of GIS-based processing of realistic OpenStreetMap data, which includes size and shape of the most of the in the city (Samsonov et al., 2015). Our testbed allows to make more detailed comparison between the modelling approaches, and also reveals the importance of correct definition of the of turbulent mixing in the ABL in the atmospheric model, and the realistic specification of the building morphology parameters and anthropogenic heat fluxes. In addition, strong seasonal variation of the importance of different factors, responsible for UHI appearance, was shown. Moreover, the framework allows to identify and solve issues regarding the different model approaches: detailed analysis of spatial and temporal variations of modelled urban temperature anomalies and their vertical extent has shown that version of COSMO-CLM model with TERRA-URB scheme simulate UHI effect in more realistic way. Research was supported by Russian Foundation for Basic Research (RFBR) and Russian Geographic Society (RGS): RFBR projects № 16-35-00474, 15-35-21129 and 16-05-00704 A, RGS-RFBR project № 13-05-41306. References: 1. Lokoshchenko, M. A. (2014). Urban 'heat island' in Moscow. Urban Climate, 10, 550-562. 2. Samsonov, T. E., Konstantinov, P. I., & Varentsov, M. I. (2015). Object-oriented approach to urban canyon analysis and its applications in meteorological modeling. Urban Climate, 13, 122-139. 3. Trusilova K., Früh, B., Brienen, S., Walter, A., Masson, V., Pigeon, G., Becker, P. Implementation of an Urban Parameterization Scheme into the Regional Climate Model COSMO-CLM// Journal of Applied Meteorology and Climatology. 2013. Vol. 52. P. 2296-2311. 4. Wouters, H., Demuzere, M., Blahak, U., Fortuniak, K., Maiheu, B., Camps, J., & van Lipzig, N. P. (2016). The efficient urban canopy dependency parametrization (SURY) v1.0 for atmospheric modelling: description and application with the COSMO-CLM model for a Belgian summer. Geoscientific Model Development, 9
Realistic Modeling of Wireless Network Environments
2015-03-01
these three functions. Frequency conversion - The RF Front End (RFFE) translates radio frequency (" passband ") signals down to, and up from, complex...have to be determined empirically. The frequency synthesizer outputs go through filter banks consisting of five banks for different sections of the...frequency change may therefore require a filter switch, adding roughly 100 nanoseconds of latency. The RFFE also contains extensive filtering of the RF