WorldWideScience

Sample records for applied biological simulations

  1. A Strategic Initiative in Applied Biological Simulations 01-SI-012 Final Report for FY01 - FY03

    Energy Technology Data Exchange (ETDEWEB)

    Lau, E Y; Venclovas, C; Schwegler, E; Gygi, F; Colvin, M E; Bennion, B J; Barsky, D; Mundy, C; Lightstone, F C; Galli, G; Sawicka, D

    2004-02-16

    The goal of this Strategic Initiative in Applied Computational Biology has been to apply LLNL's expertise in computational simulation to forge a new laboratory core competency in biological simulation. By every measure, this SI has been very successful in this goal. Based on a strong publication record and large number of conference presentations and invited talks, we have built a recognized niche for LLNL in the burgeoning field of computational biology. Further, many of the projects that were previously part of this LDRD are now externally funded based on the research results and expertise developed under this SI. We have created successful collaborations with a number of outside research groups including several joint projects with the new UC Davis/LLNL Comprehensive Cancer Center. In addition to these scientific collaborations, the staff developed on this SI is involved in computational biology program development and advisory roles with other DOE laboratories and DOE Headquarters. Moreover, a number of capabilities and expertise created by this SI are finding use in LLNL programmatic applications. Finally, and most importantly, this SI project has brought to LLNL the human talent on who will be the ensuring the further success of computational biology at this laboratory.

  2. Biology of Applied Digital Ecosystems

    CERN Document Server

    Briscoe, G; Paperin, G

    2007-01-01

    A primary motivation for research in digital ecosystems is the desire to exploit the self-organising properties of natural ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex, dynamic problems. However, the biological processes that contribute to these properties have not been made explicit in digital ecosystem research. Here, we discuss how biological properties contribute to the self-organising features of natural ecosystems. These properties include populations of evolving agents, a complex dynamic environment, and spatial distributions which generate local interactions. The potential for exploiting these properties in artificial systems is then considered. An example architecture, the Digital Business Ecosystem (DBE), is considered in detail. Simulation results imply that the DBE performs better at large scales than a comparable service-oriented architecture. These results suggest that incorporating ideas from theoretical ecology can contribute to u...

  3. Applied large eddy simulation.

    Science.gov (United States)

    Tucker, Paul G; Lardeau, Sylvain

    2009-07-28

    Large eddy simulation (LES) is now seen more and more as a viable alternative to current industrial practice, usually based on problem-specific Reynolds-averaged Navier-Stokes (RANS) methods. Access to detailed flow physics is attractive to industry, especially in an environment in which computer modelling is bound to play an ever increasing role. However, the improvement in accuracy and flow detail has substantial cost. This has so far prevented wider industrial use of LES. The purpose of the applied LES discussion meeting was to address questions regarding what is achievable and what is not, given the current technology and knowledge, for an industrial practitioner who is interested in using LES. The use of LES was explored in an application-centred context between diverse fields. The general flow-governing equation form was explored along with various LES models. The errors occurring in LES were analysed. Also, the hybridization of RANS and LES was considered. The importance of modelling relative to boundary conditions, problem definition and other more mundane aspects were examined. It was to an extent concluded that for LES to make most rapid industrial impact, pragmatic hybrid use of LES, implicit LES and RANS elements will probably be needed. Added to this further, highly industrial sector model parametrizations will be required with clear thought on the key target design parameter(s). The combination of good numerical modelling expertise, a sound understanding of turbulence, along with artistry, pragmatism and the use of recent developments in computer science should dramatically add impetus to the industrial uptake of LES. In the light of the numerous technical challenges that remain it appears that for some time to come LES will have echoes of the high levels of technical knowledge required for safe use of RANS but with much greater fidelity. PMID:19531503

  4. Biology of Applied Digital Ecosystems

    OpenAIRE

    Briscoe, G.; Sadedin, S.; Paperin, G.

    2007-01-01

    A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex, dynamic problems. However, the biological processes that contribute to these properties have not been made explicit in Digital Ecosystems research. Here, we discuss how biological properties contribute to the self-organising features of biological ecosystem...

  5. Simulating Biological and Non-Biological Motion

    Science.gov (United States)

    Bruzzo, Angela; Gesierich, Benno; Wohlschlager, Andreas

    2008-01-01

    It is widely accepted that the brain processes biological and non-biological movements in distinct neural circuits. Biological motion, in contrast to non-biological motion, refers to active movements of living beings. Aim of our experiment was to investigate the mechanisms underlying mental simulation of these two movement types. Subjects had to…

  6. A study of the speed and the accuracy of the Boundary Element Method as applied to the computational simulation of biological organs

    CERN Document Server

    P, Kirana Kumara

    2013-01-01

    In this work, first a Fortran code is developed for three dimensional linear elastostatics using constant boundary elements; the code is based on a MATLAB code developed by the author earlier. Next, the code is parallelized using BLACS, MPI, and ScaLAPACK. Later, the parallelized code is used to demonstrate the usefulness of the Boundary Element Method (BEM) as applied to the realtime computational simulation of biological organs, while focusing on the speed and accuracy offered by BEM. A computer cluster is used in this part of the work. The commercial software package ANSYS is used to obtain the `exact' solution against which the solution from BEM is compared; analytical solutions, wherever available, are also used to establish the accuracy of BEM. A pig liver is the biological organ considered. Next, instead of the computer cluster, a Graphics Processing Unit (GPU) is used as the parallel hardware. Results indicate that BEM is an interesting choice for the simulation of biological organs. Although the use ...

  7. Modeling and simulation of three dimensional manipulations of biological micro/nanoparticles by applying cylindrical contact mechanics models by means of AFM

    Energy Technology Data Exchange (ETDEWEB)

    Korayem, M. H., E-mail: hkorayem@iust.ac.ir [Iran University of Science and Technology, Robotic Research Laboratory, School of Mechanical Engineering, Center of Excellence in Experimental Solid Mechanics and Dynamics (Iran, Islamic Republic of); Saraee, M. B. [Islamic Azad University, Department of Mechanical and Aerospace Engineering, Science and Research Branch (Iran, Islamic Republic of); Mahmoodi, Z.; Dehghani, S. [Iran University of Science and Technology, Robotic Research Laboratory, School of Mechanical Engineering, Center of Excellence in Experimental Solid Mechanics and Dynamics (Iran, Islamic Republic of)

    2015-11-15

    This paper has attempted to investigate the effective forces in 3D manipulation of biological micro/nano particles. Most of the recent researches have only examined 2D spherical geometries but in this paper, the cylindrical geometries, which are much closer to the real geometries, were considered. For achieving a more accurate modeling, manipulation dynamics was also considered to be three dimensional which have been done for the first time. Because of the sensibility to the amount of endurable applied forces, manipulation process of biological micro/nano particles has some restrictions. Therefore, applied forces exerted on the particles in all different directions were simulated in order to restrict all those possible damages cause by operator of the AFM. Those data from simulated forces will bring a more accurate and sensible understanding for the operator to operate. For the validation of results, the proposed model was compared with the model presented for manipulation of gold nanoparticle and then, by reducing the effective parameters in the 3D manipulation, the results were compared with those obtained for the 2D cylindrical model and with the experimental results of spherical nanoparticle in the 2D manipulation.

  8. Modeling and simulation of three dimensional manipulations of biological micro/nanoparticles by applying cylindrical contact mechanics models by means of AFM

    International Nuclear Information System (INIS)

    This paper has attempted to investigate the effective forces in 3D manipulation of biological micro/nano particles. Most of the recent researches have only examined 2D spherical geometries but in this paper, the cylindrical geometries, which are much closer to the real geometries, were considered. For achieving a more accurate modeling, manipulation dynamics was also considered to be three dimensional which have been done for the first time. Because of the sensibility to the amount of endurable applied forces, manipulation process of biological micro/nano particles has some restrictions. Therefore, applied forces exerted on the particles in all different directions were simulated in order to restrict all those possible damages cause by operator of the AFM. Those data from simulated forces will bring a more accurate and sensible understanding for the operator to operate. For the validation of results, the proposed model was compared with the model presented for manipulation of gold nanoparticle and then, by reducing the effective parameters in the 3D manipulation, the results were compared with those obtained for the 2D cylindrical model and with the experimental results of spherical nanoparticle in the 2D manipulation

  9. Computer simulations applied in materials

    International Nuclear Information System (INIS)

    This workshop takes stock of the simulation methods applied to nuclear materials and discusses the conditions in which these methods can predict physical results when no experimental data are available. The main topic concerns the radiation effects in oxides and includes also the behaviour of fission products in ceramics, the diffusion and segregation phenomena and the thermodynamical properties under irradiation. This document brings together a report of the previous 2002 workshop and the transparencies of 12 presentations among the 15 given at the workshop: accommodation of uranium and plutonium in pyrochlores; radiation effects in La2Zr2O7 pyrochlores; first principle calculations of defects formation energies in the Y2(Ti,Sn,Zr)2O7 pyrochlore system; an approximate approach to predicting radiation tolerant materials; molecular dynamics study of the structural effects of displacement cascades in UO2; composition defect maps for A3+B3+O3 perovskites; NMR characterization of radiation damaged materials: using simulation to interpret the data; local structure in damaged zircon: a first principle study; simulation studies on SiC; insertion and diffusion of He in 3C-SiC; a review of helium in silica; self-trapped holes in amorphous silicon dioxide: their short-range structure revealed from electron spin resonance and optical measurements and opportunities for inferring intermediate range structure by theoretical modelling. (J.S.)

  10. Computer simulations applied in materials

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-07-01

    This workshop takes stock of the simulation methods applied to nuclear materials and discusses the conditions in which these methods can predict physical results when no experimental data are available. The main topic concerns the radiation effects in oxides and includes also the behaviour of fission products in ceramics, the diffusion and segregation phenomena and the thermodynamical properties under irradiation. This document brings together a report of the previous 2002 workshop and the transparencies of 12 presentations among the 15 given at the workshop: accommodation of uranium and plutonium in pyrochlores; radiation effects in La{sub 2}Zr{sub 2}O{sub 7} pyrochlores; first principle calculations of defects formation energies in the Y{sub 2}(Ti,Sn,Zr){sub 2}O{sub 7} pyrochlore system; an approximate approach to predicting radiation tolerant materials; molecular dynamics study of the structural effects of displacement cascades in UO{sub 2}; composition defect maps for A{sup 3+}B{sup 3+}O{sub 3} perovskites; NMR characterization of radiation damaged materials: using simulation to interpret the data; local structure in damaged zircon: a first principle study; simulation studies on SiC; insertion and diffusion of He in 3C-SiC; a review of helium in silica; self-trapped holes in amorphous silicon dioxide: their short-range structure revealed from electron spin resonance and optical measurements and opportunities for inferring intermediate range structure by theoretical modelling. (J.S.)

  11. Integrative Systems Biology Applied to Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning

    that were in concordance with their effects in experimental animals. In project II, I profiled the effects on rat liver gene expression levels following exposure to a 14-chemical mixture ± the presence of an endocrine disrupting chemical. This project helped us shed light on the mechanism of action of......Humans are exposed to various chemical agents through food, cosmetics, pharmaceuticals and other sources. Exposure to chemicals is suspected of playing a main role in the development of some adverse health effects in humans. Additionally, European regulatory authorities have recognized the risk...... associated with combined exposure to multiple chemicals. Testing all possible combinations of the tens of thousands environmental chemicals is impractical. This PhD project was launched to apply existing computational systems biology methods to toxicological research. In this thesis, I present in three...

  12. microlith : Image Simulation for Biological Phase Microscopy

    CERN Document Server

    Mehta, Shalin B

    2013-01-01

    Accurate simulation of image formation remains under-exploited for biological phase microscopy methods that employ partially coherent illumination, despite being important for the design of imaging systems and the reconstruction algorithms. We present an open-source MATLAB toolbox, microlith (https://code.google.com/p/microlith), that provides accurate simulation of the 3D image of a thin specimen under any partially coherent imaging system, including coherent or incoherent systems. We demonstrate the accuracy of the microlith toolbox by comparing simulated images and experimental images of a phase-only Siemens star test target using dark field and differential interference contrast microscopes. The comparison leads to intriguing insights about the sensitivity of the dark-field microscope to sub-resolution features and effects of specimen birefringence on differential interference contrast.

  13. Stochastic Simulation of Process Calculi for Biology

    Directory of Open Access Journals (Sweden)

    Andrew Phillips

    2010-10-01

    Full Text Available Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed, many of which are expressive enough to generate unbounded numbers of molecular species and reactions. As a result of this expressiveness, such calculi cannot rely on standard reaction-based simulation methods, which require fixed numbers of species and reactions. Rather than implementing custom stochastic simulation algorithms for each process calculus, we propose to use a generic abstract machine that can be instantiated to a range of process calculi and a range of reaction-based simulation algorithms. The abstract machine functions as a just-in-time compiler, which dynamically updates the set of possible reactions and chooses the next reaction in an iterative cycle. In this short paper we give a brief summary of the generic abstract machine, and show how it can be instantiated with the stochastic simulation algorithm known as Gillespie's Direct Method. We also discuss the wider implications of such an abstract machine, and outline how it can be used to simulate multiple calculi simultaneously within a common framework.

  14. Multidimensional Simulation Applied to Water Resources Management

    Science.gov (United States)

    Camara, A. S.; Ferreira, F. C.; Loucks, D. P.; Seixas, M. J.

    1990-09-01

    A framework for an integrated decision aiding simulation (IDEAS) methodology using numerical, linguistic, and pictorial entities and operations is introduced. IDEAS relies upon traditional numerical formulations, logical rules to handle linguistic entities with linguistic values, and a set of pictorial operations. Pictorial entities are defined by their shape, size, color, and position. Pictorial operators include reproduction (copy of a pictorial entity), mutation (expansion, rotation, translation, change in color), fertile encounters (intersection, reunion), and sterile encounters (absorption). Interaction between numerical, linguistic, and pictorial entities is handled through logical rules or a simplified vector calculus operation. This approach is shown to be applicable to various environmental and water resources management analyses using a model to assess the impacts of an oil spill. Future developments, including IDEAS implementation on parallel processing machines, are also discussed.

  15. Simulation applied to innovative waste management options

    International Nuclear Information System (INIS)

    The aim of this workshop is to share experience and methods in the domains of neutronics, spallation, thermo-hydraulics, corrosion, materials, mechanics; to define the needs for the other domains in order to improve the evaluation of concepts: ADS, MSR, Gas cooled reactors; and to determine the necessity or not to couple codes and tools for the concepts studied in the frame of GEDEON activities. This document groups together the transparencies of 6 presentations given at this workshop: design and performances of CEA spallation targets; simulation of spallation; the neutronic benchmark on the Megapie spallation target; the core physics of fast spectrum gas cooled reactors; the study and modeling of the thermal-mechanical behaviour of composite fuel in reactor. (J.S.)

  16. Controlling seepage in discrete particle simulations of biological systems.

    Science.gov (United States)

    Gardiner, Bruce S; Joldes, Grand R; Wong, Kelvin K L; Tan, Chin Wee; Smith, David W

    2016-08-01

    It is now commonplace to represent materials in a simulation using assemblies of discrete particles. Sometimes, one wishes to maintain the integrity of boundaries between particle types, for example, when modelling multiple tissue layers. However, as the particle assembly evolves during a simulation, particles may pass across interfaces. This behaviour is referred to as 'seepage'. The aims of this study were (i) to examine the conditions for seepage through a confining particle membrane and (ii) to define some simple rules that can be employed to control seepage. Based on the force-deformation response of spheres with various sizes and stiffness, we develop analytic expressions for the force required to move a 'probe particle' between confining 'membrane particles'. We analyse the influence that particle's size and stiffness have on the maximum force that can act on the probe particle before the onset of seepage. The theoretical results are applied in the simulation of a biological cell under unconfined compression. PMID:26629728

  17. Results of activated sludge plants applying enhanced biological phosphorus removal

    Energy Technology Data Exchange (ETDEWEB)

    Machado, A.; Pinto, M.; Neder, K.; Hoffmann, H.

    1989-02-01

    To stop the eutrophication in lakes and rivers, the input of nutrient and phosphorus compounds must be limited. The biological elimination of phosphorus describes a possibility, to reduce phosphorus in the biological stage of a treatment plant to a considerable extent. In this paper the process-system and the operation-results of a pilot plant and two municipal treatment plants are presented, where biological phosphorus reduction about 80% takes place without any constructional modifications.

  18. Monte Carlo simulation in systems biology

    OpenAIRE

    Schellenberger, Jan

    2010-01-01

    Constraint Based Reconstruction and Analysis (COBRA) is a framework within the field of Systems Biology which aims to understand cellular metabolism through the analysis of large scale metabolic models. These models are based on meticulously curated reconstructions of all chemical reactions in an organism. Instead of attempting to predict the exact state of the biological system, COBRA describes the physiological constraints that the system must satisfy and studies the range of solutions sati...

  19. Terminology of pollination biology applied to fruit culture.

    Directory of Open Access Journals (Sweden)

    Douglas de Almeida Pereira

    2009-03-01

    Full Text Available The aim of this work was to familiarize a target audience with the terminology of scientific communication in reproductive biology with emphasis on pollination in fruit trees. This is fundamental to the professional who aims to develop and publish technical and scientific writings in this important area of research. To this end, a glossary of the usual terms employed in scientific journals and research institutes is presented.

  20. A unified biological modeling and simulation system for analyzing biological reaction networks

    Science.gov (United States)

    Yu, Seok Jong; Tung, Thai Quang; Park, Junho; Lim, Jongtae; Yoo, Jaesoo

    2013-12-01

    In order to understand the biological response in a cell, a researcher has to create a biological network and design an experiment to prove it. Although biological knowledge has been accumulated, we still don't have enough biological models to explain complex biological phenomena. If a new biological network is to be created, integrated modeling software supporting various biological models is required. In this research, we design and implement a unified biological modeling and simulation system, called ezBioNet, for analyzing biological reaction networks. ezBioNet designs kinetic and Boolean network models and simulates the biological networks using a server-side simulation system with Object Oriented Parallel Accelerator Library framework. The main advantage of ezBioNet is that a user can create a biological network by using unified modeling canvas of kinetic and Boolean models and perform massive simulations, including Ordinary Differential Equation analyses, sensitivity analyses, parameter estimates and Boolean network analysis. ezBioNet integrates useful biological databases, including the BioModels database, by connecting European Bioinformatics Institute servers through Web services Application Programming Interfaces. In addition, we employ Eclipse Rich Client Platform, which is a powerful modularity framework to allow various functional expansions. ezBioNet is intended to be an easy-to-use modeling tool and a simulation system for understanding the control mechanism by monitoring the change of each component in a biological network. The simulation result can be managed and visualized on ezBioNet, which is available free of charge at http://ezbionet.sourceforge.net or http://ezbionet.cbnu.ac.kr.

  1. Systems biology applied to vaccine and immunotherapy development

    Directory of Open Access Journals (Sweden)

    Marincola Francesco M

    2011-09-01

    Full Text Available Abstract Immunotherapies, including vaccines, represent a potent tool to prevent or contain disease with high morbidity or mortality such as infections and cancer. However, despite their widespread use, we still have a limited understanding of the mechanisms underlying the induction of protective immune responses. Immunity is made of a multifaceted set of integrated responses involving a dynamic interaction of thousands of molecules; among those is a growing appreciation for the role the innate immunity (i.e. pathogen recognition receptors - PRRs plays in determining the nature and duration (immune memory of adaptive T and B cell immunity. The complex network of interactions between immune manipulation of the host (immunotherapy on one side and innate and adaptive responses on the other might be fully understood only employing the global level of investigation provided by systems biology. In this framework, the advancement of high-throughput technologies, together with the extensive identification of new genes, proteins and other biomolecules in the "omics" era, facilitate large-scale biological measurements. Moreover, recent development of new computational tools enables the comprehensive and quantitative analysis of the interactions between all of the components of immunity over time. Here, we review recent progress in using systems biology to study and evaluate immunotherapy and vaccine strategies for infectious and neoplastic diseases. Multi-parametric data provide novel and often unsuspected mechanistic insights while enabling the identification of common immune signatures relevant to human investigation such as the prediction of immune responsiveness that could lead to the improvement of the design of future immunotherapy trials. Thus, the paradigm switch from "empirical" to "knowledge-based" conduct of medicine and immunotherapy in particular, leading to patient-tailored treatment.

  2. New methodologies of biological dosimetry applied to human protection

    International Nuclear Information System (INIS)

    Biological dosimetry is a diagnostic methodology for the measurement of the individual dose absorbed in the case of accidental overexposition to ionizing radiation. It is demonstrated how in vitro radiobiological and chemobiological studies using cytogenetic methods (count of chromosomal aberrations and micronuclei) on human lymphocytes from healthy subjects and individuals undergoing radiotherapy or chemotherapy, as well as on lymphocytes of mammals other than man (comparative cytogenetics), can help to increase the basic radiobiological and chemobiological scientific information. Such information gives a valid contribution to understanding of the action of ionizing radiation or of pharmaceuticals on cells and, in return, can be of value to human radioprotection and chemoprotection. Cytogenetic studies can be summerized as follows: a) biodosimetry (estimate of dose received after accidental events); b) individual radiosensitivity (level of individual response); c) clinical radiobiology and chemobiology (individual response to radiopharmaceuticals, to radiotherapy and to chemopharmaceuticals); d) comparative radiobiology (cytogenetic studies on species other than man); e) animal model in the environmental surveillance

  3. Applied Bayesian statistical studies in biology and medicine

    CERN Document Server

    D’Amore, G; Scalfari, F

    2004-01-01

    It was written on another occasion· that "It is apparent that the scientific culture, if one means production of scientific papers, is growing exponentially, and chaotically, in almost every field of investigation". The biomedical sciences sensu lato and mathematical statistics are no exceptions. One might say then, and with good reason, that another collection of bio­ statistical papers would only add to the overflow and cause even more confusion. Nevertheless, this book may be greeted with some interest if we state that most of the papers in it are the result of a collaboration between biologists and statisticians, and partly the product of the Summer School th "Statistical Inference in Human Biology" which reaches its 10 edition in 2003 (information about the School can be obtained at the Web site http://www2. stat. unibo. itleventilSito%20scuolalindex. htm). is common experience - and not only This is rather important. Indeed, it in Italy - that encounters between statisticians and researchers are spora...

  4. Coating-substrate-simulations applied to HFQ® forming tools

    Directory of Open Access Journals (Sweden)

    Leopold Jürgen

    2015-01-01

    Full Text Available In this paper a comparative analysis of coating-substrate simulations applied to HFQTM forming tools is presented. When using the solution heat treatment cold die forming and quenching process, known as HFQTM, for forming of hardened aluminium alloy of automotive panel parts, coating-substrate-systems have to satisfy unique requirements. Numerical experiments, based on the Advanced Adaptive FE method, will finally present.

  5. Hygrothermal Numerical Simulation Tools Applied to Building Physics

    CERN Document Server

    Delgado, João M P Q; Ramos, Nuno M M; Freitas, Vasco Peixoto

    2013-01-01

    This book presents a critical review on the development and application of hygrothermal analysis methods to simulate the coupled transport processes of Heat, Air, and Moisture (HAM) transfer for one or multidimensional cases. During the past few decades there has been relevant development in this field of study and an increase in the professional use of tools that simulate some of the physical phenomena that are involved in Heat, Air and Moisture conditions in building components or elements. Although there is a significant amount of hygrothermal models referred in the literature, the vast majority of them are not easily available to the public outside the institutions where they were developed, which restricts the analysis of this book to only 14 hygrothermal modelling tools. The special features of this book are (a) a state-of-the-art of numerical simulation tools applied to building physics, (b) the boundary conditions importance, (c) the material properties, namely, experimental methods for the measuremen...

  6. BioNSi: A Discrete Biological Network Simulator Tool.

    Science.gov (United States)

    Rubinstein, Amir; Bracha, Noga; Rudner, Liat; Zucker, Noga; Sloin, Hadas E; Chor, Benny

    2016-08-01

    Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions. To construct a network instance in BioNSi, only partial, qualitative biological data suffices. The tool is aimed for use by experimental biologists and requires no prior computational or mathematical expertise. BioNSi is freely available at http://bionsi.wix.com/bionsi , where a complete user guide and a step-by-step manual can also be found. PMID:27354160

  7. Unit testing, model validation, and biological simulation

    Science.gov (United States)

    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.

  8. Simulations in Medicine and Biology: Insights and perspectives

    Science.gov (United States)

    Spyrou, George M.

    2015-01-01

    Modern medicine and biology have been transformed into quantitative sciences of high complexity, with challenging objectives. The aims of medicine are related to early diagnosis, effective therapy, accurate intervention, real time monitoring, procedures/systems/instruments optimization, error reduction, and knowledge extraction. Concurrently, following the explosive production of biological data concerning DNA, RNA, and protein biomolecules, a plethora of questions has been raised in relation to their structure and function, the interactions between them, their relationships and dependencies, their regulation and expression, their location, and their thermodynamic characteristics. Furthermore, the interplay between medicine and biology gives rise to fields like molecular medicine and systems biology which are further interconnected with physics, mathematics, informatics, and engineering. Modelling and simulation is a powerful tool in the fields of Medicine and Biology. Simulating the phenomena hidden inside a diagnostic or therapeutic medical procedure, we are able to obtain control on the whole system and perform multilevel optimization. Furthermore, modelling and simulation gives insights in the various scales of biological representation, facilitating the understanding of the huge amounts of derived data and the related mechanisms behind them. Several examples, as well as the insights and the perspectives of simulations in biomedicine will be presented.

  9. Simulations in Medicine and Biology: Insights and perspectives

    International Nuclear Information System (INIS)

    Modern medicine and biology have been transformed into quantitative sciences of high complexity, with challenging objectives. The aims of medicine are related to early diagnosis, effective therapy, accurate intervention, real time monitoring, procedures/systems/instruments optimization, error reduction, and knowledge extraction. Concurrently, following the explosive production of biological data concerning DNA, RNA, and protein biomolecules, a plethora of questions has been raised in relation to their structure and function, the interactions between them, their relationships and dependencies, their regulation and expression, their location, and their thermodynamic characteristics. Furthermore, the interplay between medicine and biology gives rise to fields like molecular medicine and systems biology which are further interconnected with physics, mathematics, informatics, and engineering. Modelling and simulation is a powerful tool in the fields of Medicine and Biology. Simulating the phenomena hidden inside a diagnostic or therapeutic medical procedure, we are able to obtain control on the whole system and perform multilevel optimization. Furthermore, modelling and simulation gives insights in the various scales of biological representation, facilitating the understanding of the huge amounts of derived data and the related mechanisms behind them. Several examples, as well as the insights and the perspectives of simulations in biomedicine will be presented

  10. Applying systems biology methods to the study of human physiology in extreme environments

    OpenAIRE

    Edwards, Lindsay; Thiele, Ines

    2013-01-01

    Systems biology is defined in this review as ‘an iterative process of computational model building and experimental model revision with the aim of understanding or simulating complex biological systems’. We propose that, in practice, systems biology rests on three pillars: computation, the omics disciplines and repeated experimental perturbation of the system of interest. The number of ethical and physiologically relevant perturbations that can be used in experiments on healthy humans is extr...

  11. Numerical simulations and modeling for stochastic biological systems with jumps

    Science.gov (United States)

    Zou, Xiaoling; Wang, Ke

    2014-05-01

    This paper gives a numerical method to simulate sample paths for stochastic differential equations (SDEs) driven by Poisson random measures. It provides us a new approach to simulate systems with jumps from a different angle. The driving Poisson random measures are assumed to be generated by stationary Poisson point processes instead of Lévy processes. Methods provided in this paper can be used to simulate SDEs with Lévy noise approximately. The simulation is divided into two parts: the part of jumping integration is based on definition without approximation while the continuous part is based on some classical approaches. Biological explanations for stochastic integrations with jumps are motivated by several numerical simulations. How to model biological systems with jumps is showed in this paper. Moreover, method of choosing integrands and stationary Poisson point processes in jumping integrations for biological models are obtained. In addition, results are illustrated through some examples and numerical simulations. For some examples, earthquake is chose as a jumping source which causes jumps on the size of biological population.

  12. The Introduction of Biological Mensuration Techniques Through Simulation.

    Science.gov (United States)

    Spain, James D.

    New simulations for teaching quantitative biological techniques are now used at Michigan Technological University. Traditionally, such techniques work within a particular system and have the student assume certain initial conditions and employ appropriate constants. The computer generates time dependent data which are plotted. The student then…

  13. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Ihekwaba, Adoha

    2007-01-01

    A. Ihekwaba, R. Mardare. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems. Case study: NFkB system. In Proc. of International Conference of Computational Methods in Sciences and Engineering (ICCMSE), American Institute of Physics, AIP Proceedings, N 2...

  14. Biology Students Building Computer Simulations Using StarLogo TNG

    Science.gov (United States)

    Smith, V. Anne; Duncan, Ishbel

    2011-01-01

    Confidence is an important issue for biology students in handling computational concepts. This paper describes a practical in which honours-level bioscience students simulate complex animal behaviour using StarLogo TNG, a freely-available graphical programming environment. The practical consists of two sessions, the first of which guides students…

  15. Quantum mechanical simulation methods for studying biological systems

    International Nuclear Information System (INIS)

    Most known biological mechanisms can be explained using fundamental laws of physics and chemistry and a full understanding of biological processes requires a multidisciplinary approach in which all the tools of biology, chemistry and physics are employed. An area of research becoming increasingly important is the theoretical study of biological macromolecules where numerical experimentation plays a double role of establishing a link between theoretical models and predictions and allowing a quantitative comparison between experiments and models. This workshop brought researchers working on different aspects of the development and application of quantum mechanical simulation together, assessed the state-of-the-art in the field and highlighted directions for future research. Fourteen lectures (theoretical courses and specialized seminars) deal with following themes: 1) quantum mechanical calculations of large systems, 2) ab initio molecular dynamics where the calculation of the wavefunction and hence the energy and forces on the atoms for a system at a single nuclear configuration are combined with classical molecular dynamics algorithms in order to perform simulations which use a quantum mechanical potential energy surface, 3) quantum dynamical simulations, electron and proton transfer processes in proteins and in solutions and finally, 4) free seminars that helped to enlarge the scope of the workshop. (N.T.)

  16. A decontamination study of simulated chemical and biological agents

    International Nuclear Information System (INIS)

    A comprehensive decontamination scheme of the chemical and biological agents, including airborne agents and surface contaminating agents, is presented. When a chemical and biological attack occurs, it is critical to decontaminate facilities or equipments to an acceptable level in a very short time. The plasma flame presented here may provide a rapid and effective elimination of toxic substances in the interior air in isolated spaces. As an example, a reaction chamber, with the dimensions of a 22 cm diameter and 30 cm length, purifies air with an airflow rate of 5000 l/min contaminated with toluene, the simulated chemical agent, and soot from a diesel engine, the simulated aerosol for biological agents. Although the airborne agents in an isolated space are eliminated to an acceptable level by the plasma flame, the decontamination of the chemical and biological agents cannot be completed without cleaning surfaces of the facilities. A simulated sterilization study of micro-organisms was carried out using the electrolyzed ozone water. The electrolyzed ozone water very effectively kills endospores of Bacillus atrophaeus (ATCC 9372) within 3 min. The electrolyzed ozone water also kills the vegetative micro-organisms, fungi, and virus. The electrolyzed ozone water, after the decontamination process, disintegrates into ordinary water and oxygen without any trace of harmful materials to the environment

  17. Sender-receiver systems and applying information theory for quantitative synthetic biology.

    Science.gov (United States)

    Barcena Menendez, Diego; Senthivel, Vivek Raj; Isalan, Mark

    2015-02-01

    Sender-receiver (S-R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S-R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning. PMID:25282688

  18. A scenario simulation methodology applied to near field performance

    International Nuclear Information System (INIS)

    Methods of performance assessment employed within radioactive waste management must deal with numerous types of uncertainty. At the outset, the specification of those features, events and processes (FEPs) controlling the future evolution of the environment and the performance of possible pathways for radionuclide migration is contentious, and may radically bias all subsequent quantitative estimates subsequently made by whatever means. The difficulty arises from three major areas: the time and spatial scales under consideration (the consequent unavailability of practical experiments and experience); the limit in conceptual understanding, and mathematical representation of relevant processes; and the subjective nature of the selection process applied by experts in specifying scenarios, models, and input data. Recognizing this fact, there have been numerous attempts to put the subjective process of scenario and model specification within a well-defined framework. However, the complex nature of the system may be such that the key FEPs or couplings cannot be identified a-priori. Within scenario simulation the authors take an open approach and ask ''What can happen; how can the future evolve?'' In answering this question it is fundamental that they define and utilize models which incorporate the widest practical variety of processes and couplings and focus upon repeated simulation of the future as parameters and events are varied or permuted. In this way the authors test the sensitivity of results to model assumptions as well as model parameter variations at an executive level. In this paper they present an application of this approach to the performance assessment of an engineered barrier system designed for deep geological disposal

  19. A computational framework for particle and whole cell tracking applied to a real biological dataset.

    Science.gov (United States)

    Yang, Feng Wei; Venkataraman, Chandrasekhar; Styles, Vanessa; Kuttenberger, Verena; Horn, Elias; von Guttenberg, Zeno; Madzvamuse, Anotida

    2016-05-24

    Cell tracking is becoming increasingly important in cell biology as it provides a valuable tool for analysing experimental data and hence furthering our understanding of dynamic cellular phenomena. The advent of high-throughput, high-resolution microscopy and imaging techniques means that a wealth of large data is routinely generated in many laboratories. Due to the sheer magnitude of the data involved manual tracking is often cumbersome and the development of computer algorithms for automated cell tracking is thus highly desirable. In this work, we describe two approaches for automated cell tracking. Firstly, we consider particle tracking. We propose a few segmentation techniques for the detection of cells migrating in a non-uniform background, centroids of the segmented cells are then calculated and linked from frame to frame via a nearest-neighbour approach. Secondly, we consider the problem of whole cell tracking in which one wishes to reconstruct in time whole cell morphologies. Our approach is based on fitting a mathematical model to the experimental imaging data with the goal being that the physics encoded in the model is reflected in the reconstructed data. The resulting mathematical problem involves the optimal control of a phase-field formulation of a geometric evolution law. Efficient approximation of this challenging optimal control problem is achieved via advanced numerical methods for the solution of semilinear parabolic partial differential equations (PDEs) coupled with parallelisation and adaptive resolution techniques. Along with a detailed description of our algorithms, a number of simulation results are reported on. We focus on illustrating the effectivity of our approaches by applying the algorithms to the tracking of migrating cells in a dataset which reflects many of the challenges typically encountered in microscopy data. PMID:26948574

  20. Proceedings of the 4th workshop on ion-beam-applied biology

    International Nuclear Information System (INIS)

    In order to promote research on biological application using ion beam at TIARA, we have annually hold the Workshop on Ion-beam-applied Biology at JAERI Takasaki since 2002. The 4th workshop entitled 'New Frontiers of Biological Research using microbeam - Application to Radio-microsurgery and Cellular Response to Radiations -' was held on June 22nd, 2005, aimed to overview the recent progress in microbeam-applied researches, and discuss the future direction of application of microbeam not to researches in life science and biotechnology, but also to clinical medicine. This workshop was hosted by JAERI Takasaki, with the cooperation of The Ion Beam Breeding Society, The Japan Radiation Research Society, The Japanese Society for Biological Sciences in Space, The Kanto-Kohetsu Branch of The Atomic Energy Society of Japan, and The Japan Radioisotope Association. There were 104 participants including clinicians attended from universities, public research institutions, and private companies. The papers presented in the workshop were about the ion-beam-applied biological researches at JAERI, the present status of microbeam facilities in Japan and foreign countries, and the microbeam-based analyses of damage repair machinery in insects and radiation-induced bystander effects. It was realized again that microbeam is quite useful for functional analyses by targeted disruption of specific tissues in bio-organisms, and is of critical importance in investigating biological influences of low-dose radiations as well as in its radiological application. These researches using microbeam are expected to further march on. The 13 of the presented papers are indexed individually. (J.P.N.)

  1. [Numerical simulation and operation optimization of biological filter].

    Science.gov (United States)

    Zou, Zong-Sen; Shi, Han-Chang; Chen, Xiang-Qiang; Xie, Xiao-Qing

    2014-12-01

    BioWin software and two sensitivity analysis methods were used to simulate the Denitrification Biological Filter (DNBF) + Biological Aerated Filter (BAF) process in Yuandang Wastewater Treatment Plant. Based on the BioWin model of DNBF + BAF process, the operation data of September 2013 were used for sensitivity analysis and model calibration, and the operation data of October 2013 were used for model validation. The results indicated that the calibrated model could accurately simulate practical DNBF + BAF processes, and the most sensitive parameters were the parameters related to biofilm, OHOs and aeration. After the validation and calibration of model, it was used for process optimization with simulating operation results under different conditions. The results showed that, the best operation condition for discharge standard B was: reflux ratio = 50%, ceasing methanol addition, influent C/N = 4.43; while the best operation condition for discharge standard A was: reflux ratio = 50%, influent COD = 155 mg x L(-1) after methanol addition, influent C/N = 5.10. PMID:25826934

  2. Evanescent planar waveguide detection of biological warfare simulants

    Science.gov (United States)

    Sipe, David M.; Schoonmaker, Kenneth P.; Herron, James N.; Mostert, Michael J.

    2000-04-01

    An evanescent planar waveguide Mark 1.5 instrument was used to detect simulants of biological warfare agents; ovalbumin (OV), MS2 bacteriophage, BG, and Erwinia herbicola (EH). Polyclonal tracer antibodies were labeled with the fluorescent dye, Cy5. Discrete bands of polyclonal capture antibodies were immobilized to a polystyrene planar waveguide with molded integral lenses. An ST-6 CCD camera was used for detection. OV. MS2 and BG were detected in a simultaneous 3 by 3 array; with a total of nine measurements within 6 minutes. EH was analyzed in a separate array. Results were evaluate dat the US Army Joint Field Trials V, at the Dugway Proving Grounds. Over a 10 day period, 32 unknown samples were analyzed daily for each simulant. Detection limits: OV 10 ng/ml, MS2 107 pfu/ml, BG 105 cfu/ml. EH was detectable at 5 X 105 cfu/ml. Overall false positives were 3.0 percent. Therefore, the Mark 1.5 instrument, with a parallel array of detectors, evanescent flourescent excitation, and CCD imaging provides for rapid, sensitive, and specific detection of biological warfare agent simulants.

  3. Dissipative particle dynamics simulations for biological tissues: rheology and competition

    International Nuclear Information System (INIS)

    In this work, we model biological tissues using a simple, mechanistic simulation based on dissipative particle dynamics. We investigate the continuum behavior of the simulated tissue and determine its dependence on the properties of the individual cell. Cells in our simulation adhere to each other, expand in volume, divide after reaching a specific size checkpoint and undergo apoptosis at a constant rate, leading to a steady-state homeostatic pressure in the tissue. We measure the dependence of the homeostatic state on the microscopic parameters of our model and show that homeostatic pressure, rather than the unconfined rate of cell division, determines the outcome of tissue competitions. Simulated cell aggregates are cohesive and round up due to the effect of tissue surface tension, which we measure for different tissues. Furthermore, mixtures of different cells unmix according to their adhesive properties. Using a variety of shear and creep simulations, we study tissue rheology by measuring yield stresses, shear viscosities, complex viscosities as well as the loss tangents as a function of model parameters. We find that cell division and apoptosis lead to a vanishing yield stress and fluid-like tissues. The effects of different adhesion strengths and levels of noise on the rheology of the tissue are also measured. In addition, we find that the level of cell division and apoptosis drives the diffusion of cells in the tissue. Finally, we present a method for measuring the compressibility of the tissue and its response to external stress via cell division and apoptosis

  4. Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

    Directory of Open Access Journals (Sweden)

    Waltemath Dagmar

    2011-12-01

    Full Text Available Abstract Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML. SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s used

  5. NEPTUNIX, a general program of simulation applied to nuclear reactors

    International Nuclear Information System (INIS)

    Most simulation languages admit an incremental description and involve explicit integration algorithms. NEPTUNIX is a simulation language directly admitting algebraic differential equations under an implicit form, and it involves a very efficient implicit integration method with variable step and order. NEPTUNIX is a tool used for building large systems models in the field of nuclear reactors

  6. Modular Modelling and Simulation Approach - Applied to Refrigeration Systems

    DEFF Research Database (Denmark)

    Sørensen, Kresten Kjær; Stoustrup, Jakob

    2008-01-01

    This paper presents an approach to modelling and simulation of the thermal dynamics of a refrigeration system, specifically a reefer container. A modular approach is used and the objective is to increase the speed and flexibility of the developed simulation environment. The refrigeration system is...

  7. Terahertz signatures of biological-warfare-agent simulants

    Science.gov (United States)

    Globus, Tatiana; Woolard, Dwight L.; Khromova, Tatyana; Partasarathy, Ramakrishnan; Majewski, Alexander; Abreu, Rene; Hesler, Jeffrey L.; Pan, Shing-Kuo; Ediss, Geoff

    2004-09-01

    This work presents spectroscopic characterization results for biological simulant materials measured in the terahertz gap. Signature data have been collected between 3 cm-1 and 10 cm-1 for toxin Ovalbumin, bacteria Erwinia herbicola, Bacillus Subtilis lyophilized cells and RNA MS2 phage, BioGene. Measurements were conducted on a modified Bruker FTIR spectrometer equipped with the noise source developed in the NRAL. The noise source provides two orders of magnitude higher power in comparison with a conventional mercury lamp. Photometric characterization of the instrument performance demonstrates that the expected error for sample characterization inside the interval from 3 to 9.5 cm-1 is less then 1%.

  8. Applying virtual environments to training and simulation (abstract)

    OpenAIRE

    Jense, G.J.; Kuijper, F.

    1993-01-01

    Virtual environment (VE) technology is expected to make a big impact on future training and simulation systems. Direct stimulation of human-senses (eyesight, auditory, tactile) and new paradigms for user input will improve the realism of simulations and thereby the effectiveness of training systems. A virtual environment can be defined as a multi-dimensional experience which is totally or partially computer generated and can be accepted as cognitively valid. Based upon this definition, a dass...

  9. Reduction of overestimation in interval arithmetic simulation of biological wastewater treatment processes

    Science.gov (United States)

    Rauh, Andreas; Kletting, Marco; Aschemann, Harald; Hofer, Eberhard P.

    2007-02-01

    A novel interval arithmetic simulation approach is introduced in order to evaluate the performance of biological wastewater treatment processes. Such processes are typically modeled as dynamical systems where the reaction kinetics appears as additive nonlinearity in state. In the calculation of guaranteed bounds of state variables uncertain parameters and uncertain initial conditions are considered. The recursive evaluation of such systems of nonlinear state equations yields overestimation of the state variables that is accumulating over the simulation time. To cope with this wrapping effect, innovative splitting and merging criteria based on a recursive uncertain linear transformation of the state variables are discussed. Additionally, re-approximation strategies for regions in the state space calculated by interval arithmetic techniques using disjoint subintervals improve the simulation quality significantly if these regions are described by several overlapping subintervals. This simulation approach is used to find a practical compromise between computational effort and simulation quality. It is pointed out how these splitting and merging algorithms can be combined with other methods that aim at the reduction of overestimation by applying consistency techniques. Simulation results are presented for a simplified reduced-order model of the reduction of organic matter in the activated sludge process of biological wastewater treatment.

  10. Summary of the 2nd workshop on ion beam-applied biology

    International Nuclear Information System (INIS)

    Induction of novel plant resources by ion beam-irradiation has been investigated in JAERI. To share the knowledge of the present status of the field, and to find out future plants, 1st Workshop on ion beam-applied biology was held last year titled as ''Development of breeding technique for ion beams''. To further improve the research cooperation and to exchange useful information in the field, researchers inside JAERI and also with researchers outside, such as those from agricultural experiment stations, companies, and Universities met each other at the 2nd workshop on ion beam-applied biology titled as ''Future development of breeding technique for ion beams''. People from RIKEN, Institute of Radiation Breeding, Wakasa wan Energy Research Center, National Institute of Radiological Science also participated in this workshop. The 12 of the presented papers are indexed individually. (J.P.N.)

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

    Science.gov (United States)

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

    2016-01-01

    Modeling is an integral component of modern biology. In this chapter we look into the role of the model, as it pertains to Systems Medicine, and the software that is required to instantiate and run it. We do this by comparing the development, implementation, and characteristics of tools that have been developed to work with two divergent methodologies: Systems Biology and Pharmacometrics. From the Systems Biology perspective we consider the concept of "Software as a Medical Device" and what this may imply for the migration of research-oriented, simulation software into the domain of human health.In our second perspective, we see how in practice hundreds of computational tools already accompany drug discovery and development at every stage of the process. Standardized exchange formats are required to streamline the model exchange between tools, which would minimize translation errors and reduce the required time. With the emergence, almost 15 years ago, of the SBML standard, a large part of the domain of interest is already covered and models can be shared and passed from software to software without recoding them. Until recently the last stage of the process, the pharmacometric analysis used in clinical studies carried out on subject populations, lacked such an exchange medium. We describe a new emerging exchange format in Pharmacometrics which covers the non-linear mixed effects models, the standard statistical model type used in this area. By interfacing these two formats the entire domain can be covered by complementary standards and subsequently the according tools. PMID:26677194

  12. Applying Monte Carlo Simulation to Biomedical Literature to Approximate Genetic Network.

    Science.gov (United States)

    Al-Dalky, Rami; Taha, Kamal; Al Homouz, Dirar; Qasaimeh, Murad

    2016-01-01

    Biologists often need to know the set of genes associated with a given set of genes or a given disease. We propose in this paper a classifier system called Monte Carlo for Genetic Network (MCforGN) that can construct genetic networks, identify functionally related genes, and predict gene-disease associations. MCforGN identifies functionally related genes based on their co-occurrences in the abstracts of biomedical literature. For a given gene g , the system first extracts the set of genes found within the abstracts of biomedical literature associated with g. It then ranks these genes to determine the ones with high co-occurrences with g . It overcomes the limitations of current approaches that employ analytical deterministic algorithms by applying Monte Carlo Simulation to approximate genetic networks. It does so by conducting repeated random sampling to obtain numerical results and to optimize these results. Moreover, it analyzes results to obtain the probabilities of different genes' co-occurrences using series of statistical tests. MCforGN can detect gene-disease associations by employing a combination of centrality measures (to identify the central genes in disease-specific genetic networks) and Monte Carlo Simulation. MCforGN aims at enhancing state-of-the-art biological text mining by applying novel extraction techniques. We evaluated MCforGN by comparing it experimentally with nine approaches. Results showed marked improvement. PMID:26415184

  13. STSE: Spatio-Temporal Simulation Environment Dedicated to Biology

    Directory of Open Access Journals (Sweden)

    Gerber Susanne

    2011-04-01

    Full Text Available Abstract Background Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. Results The Spatio-Temporal Simulation Environment (STSE is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images. STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts

  14. Simulation Applied to the Storage Capacity and Stockpiles

    Directory of Open Access Journals (Sweden)

    Andrea Alejandra Giubergia

    2016-05-01

    Full Text Available This investigation is focused on process based simulations. The simulation is carried out (using the FlexSim 7.3.0 software to a mining process including storage hoppers and haulage equipment in order to estimate the desirable truck fleet size and the capacity of the trucks and the hoppers as well as assessing whether the design of the access roads is acceptable for the success of the operations. It is concluded that the dimensions of the loading system has been overestimated compared to the existing equipment fleet size. Therefore, it is required to increase the number of trucks or the truck haulage capacity to improve the mine productivity.

  15. Business Simulations Applied in Support of ERP Training

    Science.gov (United States)

    Conroy, George

    2012-01-01

    This quantitative, quasi-experimental study examined the application of a business simulation against training in support of an Enterprise Resource Planning (ERP) system. Defining more effective training strategies is a critical concern for organizational leaders and stakeholders concerned by today's economic challenges. The scope of this…

  16. Applying a behavioural simulation for the collection of data

    DEFF Research Database (Denmark)

    Jespersen, Kristina Risom

    2005-01-01

    To collect real-time data as opposed to retrospective data requires new methodological traits. One possibility is the use of behavioral simulations that synthesize the self-administered questionnaire, experimental designs, role-playing and scenarios. Supported by Web technology this new data...... collection methodology proves itself valid and with high appeal to respondents....

  17. Software Development Processes Applied to Computational Icing Simulation

    Science.gov (United States)

    Levinson, Laurie H.; Potapezuk, Mark G.; Mellor, Pamela A.

    1999-01-01

    The development of computational icing simulation methods is making the transition form the research to common place use in design and certification efforts. As such, standards of code management, design validation, and documentation must be adjusted to accommodate the increased expectations of the user community with respect to accuracy, reliability, capability, and usability. This paper discusses these concepts with regard to current and future icing simulation code development efforts as implemented by the Icing Branch of the NASA Lewis Research Center in collaboration with the NASA Lewis Engineering Design and Analysis Division. With the application of the techniques outlined in this paper, the LEWICE ice accretion code has become a more stable and reliable software product.

  18. Applied simulation and optimization in logistics, industrial and aeronautical practice

    CERN Document Server

    Mota, Idalia; Serrano, Daniel

    2015-01-01

    Presenting techniques, case-studies and methodologies that combine the use of simulation approaches with optimization techniques for facing problems in manufacturing, logistics, or aeronautical problems, this book provides solutions to common industrial problems in several fields, which range from manufacturing to aviation problems, where the common denominator is the combination of simulation’s flexibility with optimization techniques’ robustness. Providing readers with a comprehensive guide to tackle similar issues in industrial environments, this text explores novel ways to face industrial problems through hybrid approaches (simulation-optimization) that benefit from the advantages of both paradigms, in order to give solutions to important problems in service industry, production processes, or supply chains, such as scheduling, routing problems and resource allocations, among others.

  19. Simulation of Cognitive Radio System Applying Different Wireless Channel Models

    Directory of Open Access Journals (Sweden)

    Mohamed Shalaby

    2013-04-01

    Full Text Available Cognitive radio is an emerging technology, which aims to upgrade the spectrum utilization by allowing thesecondary users to operate at the spectrum bands vacated by the primary users. A cognitive radio systemmodel was simulated and the performance of the energy detector was evaluated by using different wirelesschannel models. These models include Additive White Gaussian Noise (AWGN model, Rayleigh fadingmodel, and Rician fading model. The simulation results show that by increasing the signal to noise ratio,the detection capability of the energy detector can be improved and the false alarm probability and themissed detection probability can be reduced. Moreover, the line of sight path strength of the Rician fadinghas a great effect on the energy detector performance. It was observed that, the line of sight path strength(k of 20 can save the signal power by 40 dB over a single path transmission and 25 dB over a multipathtransmission.

  20. Nonlinear punctual dynamic applied to simulation of PWR type reactors

    International Nuclear Information System (INIS)

    In order to study some kinds of nuclear reactor accidents, a simulation is made using the punctual kinetics model to the reactor core. The following integration methods are used: Hansen's method in which a linearization is made and C S M P using a variable interval fourth-order Runge Kutta method. The results were good and were compared with those obtained by the code Dinamica I which uses a finite difference integration method of backward kind. (author)

  1. Non-linear punctual kinetics applied to PWR reactors simulation

    International Nuclear Information System (INIS)

    In order to study some kinds of nuclear reactor accidents, a simulation is made using the punctual kinetics model for the reactor core. The following integration methods are used: Hansen's method in which a linearization is made and CSMP using a variable interval fourth-order Runge Kutta method. The results were good and were compared with those obtained by the code Dinamica I which uses a finite difference integration method of backward kind. (Author)

  2. Microcanonical ensemble simulation method applied to discrete potential fluids.

    Science.gov (United States)

    Sastre, Francisco; Benavides, Ana Laura; Torres-Arenas, José; Gil-Villegas, Alejandro

    2015-09-01

    In this work we extend the applicability of the microcanonical ensemble simulation method, originally proposed to study the Ising model [A. Hüller and M. Pleimling, Int. J. Mod. Phys. C 13, 947 (2002)0129-183110.1142/S0129183102003693], to the case of simple fluids. An algorithm is developed by measuring the transition rates probabilities between macroscopic states, that has as advantage with respect to conventional Monte Carlo NVT (MC-NVT) simulations that a continuous range of temperatures are covered in a single run. For a given density, this new algorithm provides the inverse temperature, that can be parametrized as a function of the internal energy, and the isochoric heat capacity is then evaluated through a numerical derivative. As an illustrative example we consider a fluid composed of particles interacting via a square-well (SW) pair potential of variable range. Equilibrium internal energies and isochoric heat capacities are obtained with very high accuracy compared with data obtained from MC-NVT simulations. These results are important in the context of the application of the Hüller-Pleimling method to discrete-potential systems, that are based on a generalization of the SW and square-shoulder fluids properties. PMID:26465582

  3. Simulation of Road Traffic Applying Model-Driven Engineering

    Directory of Open Access Journals (Sweden)

    Alberto FERNÁNDEZ-ISABEL

    2016-05-01

    Full Text Available Road traffic is an important phenomenon in modern societies. The study of its different aspects in the multiple scenarios where it happens is relevant for a huge number of problems. At the same time, its scale and complexity make it hard to study. Traffic simulations can alleviate these difficulties, simplifying the scenarios to consider and controlling their variables. However, their development also presents difficulties. The main ones come from the need to integrate the way of working of researchers and developers from multiple fields. Model-Driven Engineering (MDE addresses these problems using Modelling Languages (MLs and semi-automatic transformations to organise and describe the development, from requirements to code. This paper presents a domain-specific MDE framework for simulations of road traffic. It comprises an extensible ML, support tools, and development guidelines. The ML adopts an agent-based approach, which is focused on the roles of individuals in road traffic and their decision-making. A case study shows the process to model a traffic theory with the ML, and how to specialise that specification for an existing target platform and its simulations. The results are the basis for comparison with related work.

  4. Green Technology Applying Heat Pump Drying, Modelling and Simulation

    OpenAIRE

    Mukhatov, Kirill

    2014-01-01

    This work has focused on the development of atmospheric freeze and non-freeze drying applying a heat pump system as an environmental friendly and economically preferable technology compare to vacuum freeze drying. The main reason of the research is a lack of knowledge and information in the literature about the atmospheric heat pump drying, while the more common vacuum freeze drying process is widely covered.The main objective for developing atmospheric heat pump drying as a new drying techno...

  5. Monitoring Biological Modes in a Bioreactor Process by Computer Simulation

    Directory of Open Access Journals (Sweden)

    Samia Semcheddine

    2015-12-01

    Full Text Available This paper deals with the general framework of fermentation system modeling and monitoring, focusing on the fermentation of Escherichia coli. Our main objective is to develop an algorithm for the online detection of acetate production during the culture of recombinant proteins. The analysis the fermentation process shows that it behaves like a hybrid dynamic system with commutation (since it can be represented by 5 nonlinear models. We present a strategy of fault detection based on residual generation for detecting the different actual biological modes. The residual generation is based on nonlinear analytical redundancy relations. The simulation results show that the several modes that are occulted during the bacteria cultivation can be detected by residuals using a nonlinear dynamic model and a reduced instrumentation.

  6. Introduction to mathematical biology modeling, analysis, and simulations

    CERN Document Server

    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...

  7. Applying SLEUTH for simulating urban expansion of Hangzhou

    Science.gov (United States)

    Liu, Yong; Liu, Xiuhua

    2009-06-01

    Urbanization is found to be closely associated with land use/land cover change which has an important influence in our environment and ecosystems, such as urban heat island effect, biodiversity loss, soil erosion, and pollutions. Studies on accurately simulating urban expansion have been inspired by increasing concerns of the sustainability of urban development. This paper reports our research aiming to simulate the expansion of Hangzhou city using SLEUTH (slope, landuse, exclusion, urban extent, transportation and hillshade) urban growth model. In this research, we investigates the urban spatial growth patterns based on Landsat Thematic Mapper (TM)/Enhanced Thematic Mapper Plus (ETM+) images and creates four land cover change scenarios in 2020 with different socio-economic conditions. The results show that the SLEUTH model is less effective for depicting wave-like urban growth. From the four projected scenarios, urban area in this city will increase linearly and the shape of the city continues to be multi-nuclei in 2020. The hotspot area featured by intensive urban growth would, however, shift from urban center to sub-centers.

  8. Nature preservation acceptance model applied to tanker oil spill simulations

    DEFF Research Database (Denmark)

    Friis-Hansen, Peter; Ditlevsen, Ove Dalager

    2003-01-01

    This paper emphazises the adverse event categorization principle in risk acceptance analysis, and suggests the use of a standard type risk profile of lognormal type for each category of adverse events. The risk profile for a specified category of adverse events and corresponding to a given...... of the single oil spill, a risk profile for the costs is obtained that is indistinguishable from the standard lognormal risk profile.Finally the question of formulating a public risk acceptance criterion is addressed following Ditlevsen, and it is argued that a Nature Preservation Willingness Index...... risk acceptance criterion for the pollution of the environment. This NPWI acceptance criterion is applied to the oil spill example....

  9. Phosphorus recycling potential assessment by a biological test applied to wastewater sludge.

    Science.gov (United States)

    Braak, Etienne; Auby, Sarah; Piveteau, Simon; Guilayn, Felipe; Daumer, Marie-Line

    2016-01-01

    Phosphorus (P) recycling as mineral fertilizer from wastewater activated sludge (WAS) depends on the amount that can be dissolved and separated from the organic matter before the final crystallization step. The aim of the biological phosphorus dissolution potential (BPDP) test developed here was to assess the maximum amount of P that could be biologically released from WAS prior that the liquid phase enters the recovery process. It was first developed for sludge combining enhanced biological phosphorus removal and iron chloride. Because carbohydrates are known to induce acidification during the first stage of anaerobic digestion, sucrose was used as a co-substrate. Best results were obtained after 24-48 h, without inoculum, with a sugar/sludge ratio of 0.5 gCOD/gVS and under strict anaerobic conditions. Up to 75% of the total phosphorus in sludge from a wastewater treatment plant combining enhanced biological phosphorus removal and iron chloride phosphorus removal could be dissolved. Finally, the test was applied to assess BPDP from different sludge using alum compounds for P removal. No dissolution was observed when alum polychloride was used and less than 20% when alum sulphate was used. In all the cases, comparison to chemical acidification showed that the biological process was a major contributor to P dissolution. The possibility to crystallize struvite was discussed from the composition of the liquids obtained. The BPDP will be used not only to assess the potential for phosphorus recycling from sludge, but also to study the influence of the co-substrates available for anaerobic digestion of sludge. PMID:26786893

  10. The Effects of 3D Computer Simulation on Biology Students' Achievement and Memory Retention

    Science.gov (United States)

    Elangovan, Tavasuria; Ismail, Zurida

    2014-01-01

    A quasi experimental study was conducted for six weeks to determine the effectiveness of two different 3D computer simulation based teaching methods, that is, realistic simulation and non-realistic simulation on Form Four Biology students' achievement and memory retention in Perak, Malaysia. A sample of 136 Form Four Biology students in Perak,…

  11. The BioDynaMo Project: a platform for computer simulations of biological dynamics

    OpenAIRE

    Johard, Leonard; Breitwieser, Lukas; Di Meglio, Alberto; Manca, Marco; Mazzara, Manuel; Talanov, Max

    2016-01-01

    This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as well as its numerous applications to the computational biology and nanoscience communities.

  12. Teaching Fluid Mechanics for Undergraduate Students in Applied Industrial Biology: from Theory to Atypical Experiments

    CERN Document Server

    Absi, Rafik; Dufour, Florence; Huet, Denis; Bennacer, Rachid; Absi, Tahar

    2011-01-01

    EBI is a further education establishment which provides education in applied industrial biology at level of MSc engineering degree. Fluid mechanics at EBI was considered by students as difficult who seemed somewhat unmotivated. In order to motivate them, we applied a new play-based pedagogy. Students were asked to draw inspiration from everyday life situations to find applications of fluid mechanics and to do experiments to verify and validate some theoretical results obtained in course. In this paper, we present an innovative teaching/learning pedagogy which includes the concept of learning through play and its implications in fluid mechanics for engineering. Examples of atypical experiments in fluid mechanics made by students are presented. Based on teaching evaluation by students, it is possible to know how students feel the course. The effectiveness of this approach to motivate students is presented through an analysis of students' teaching assessment. Learning through play proved a great success in fluid...

  13. Biological stimulation of the Human skin applying health promoting light and plasma sources

    Energy Technology Data Exchange (ETDEWEB)

    Awakowicz, P.; Bibinov, N. [Center for Plasma Science and Technology, Ruhr-University, Bochum (Germany); Born, M.; Niemann, U. [Philips Research, Aachen (Germany); Busse, B. [Zell-Kontakt GmbH, Noerten-Hardenberg (Germany); Gesche, R.; Kuehn, S.; Porteanu, H.E. [Ferdinand-Braun-Institut fuer Hoechstfrequenztechnik, Berlin (Germany); Helmke, A. [University of Applied Sciences and Arts, Goettingen (Germany); Kaemling, A.; Wandke, D. [CINOGY GmbH, Duderstadt (Germany); Kolb-Bachofen, V.; Liebmann, J. [Institute for Immunobiology, Heinrich-Heine University, Duesseldorf (Germany); Kovacs, R.; Mertens, N.; Scherer, J. [Aurion Anlagentechnik GmbH, Seligenstadt (Germany); Oplaender, C.; Suschek, C. [Clinic for Plastic Surgery, University Clinic, Aachen (Germany); Vioel, W. [Laser-Laboratorium, Goettingen (Germany); University of Applied Sciences and Arts, Goettingen (Germany)

    2009-10-15

    In the frame of BMBF project ''BioLiP'', new physical treatment techniques aiming at medical treatment of the human skin have been developed. The acronym BioLiP stands for ''Desinfektion, Entkeimung und biologische Stimulation der Haut durch gesundheitsfoerdernde Licht- und Plasmaquellen'' (Disinfection, germ reduction and biological stimulation of the human skin by health promoting light and plasma sources). A source applying a low-temperature dielectric barrier discharge plasma (DBD) has been investigated on its effectiveness for skin disinfection and stimulation of biological material. Alternatively an atmospheric plasma source consisting of a microwave resonator combined with a solid state power oscillator has been examined. This concept which allows for a compact and efficient design avoiding external microwave power supply and matching units has been optimized with respect to nitrogen monoxide (NO) production in high yields. In both cases various application possibilities in the medical and biological domain are opened up. Light sources in the visible spectral range have been investigated with respect to the proliferation of human cell types. Intensive highly selective blue light sources based on LED technology can slow down proliferation rates without inducing toxic effects which offers new opportunities for treatments of so-called hyperproliferative skin conditions (e.g. with psoriasis or in wound healing) using UV-free light. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  14. Computer Simulation and Data Analysis in Molecular Biology and Biophysics An Introduction Using R

    CERN Document Server

    Bloomfield, Victor

    2009-01-01

    This book provides an introduction, suitable for advanced undergraduates and beginning graduate students, to two important aspects of molecular biology and biophysics: computer simulation and data analysis. It introduces tools to enable readers to learn and use fundamental methods for constructing quantitative models of biological mechanisms, both deterministic and with some elements of randomness, including complex reaction equilibria and kinetics, population models, and regulation of metabolism and development; to understand how concepts of probability can help in explaining important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data from spectroscopic, genomic, and proteomic sources. These quantitative tools are implemented using the free, open source software program R. R provides an excellent environment for general numerical and statistical computing and graphics, with capabilities similar to Matlab®. Since R is increasingly used in bioinformat...

  15. Enhancing combined biological nitrogen and phosphorus removal from wastewater by applying mechanically disintegrated excess sludge.

    Science.gov (United States)

    Zubrowska-Sudol, Monika; Walczak, Justyna

    2015-06-01

    The goal of the study was to evaluate the possibility of applying disintegrated excess sludge as a source of organic carbon to enhance biological nitrogen and phosphorus removal. The experiment, performed in a sequencing batch reactor, consisted of two two-month series, without and with applying mechanically disintegrated excess sludge, respectively. The effects on carbon, nitrogen and phosphorus removal were observed. It was shown that the method allows enhancement of combined nitrogen and phosphorus removal. After using disintegrated sludge, denitrification effectiveness increased from 49.2 ± 6.8% to 76.2 ± 2.3%, which resulted in a decline in the NOx-N concentration in the effluent from the SBR by an average of 21.4 mg NOx-N/L. Effectiveness of biological phosphorus removal increased from 28.1 ± 11.3% to 96.2 ± 2.5%, thus resulting in a drop in the [Formula: see text] concentration in the effluent by, on average, 6.05 mg PO4(3-)-P/L. The application of disintegrated sludge did not deteriorate effluent quality in terms of COD and NH4(+)-N. The concentration of NH4(+)-N in both series averaged 0.16 ± 0.11 mg NH4(+)-N/L, and the concentration of COD was 15.36 ± 3.54 mg O2/L. PMID:25776916

  16. Finite element simulation for the mechanical characterization of soft biological materials by atomic force microscopy.

    Science.gov (United States)

    Valero, C; Navarro, B; Navajas, D; García-Aznar, J M

    2016-09-01

    The characterization of the mechanical properties of soft materials has been traditionally performed through uniaxial tensile tests. Nevertheless, this method cannot be applied to certain extremely soft materials, such as biological tissues or cells that cannot be properly subjected to these tests. Alternative non-destructive tests have been designed in recent years to determine the mechanical properties of soft biological tissues. One of these techniques is based on the use of atomic force microscopy (AFM) to perform nanoindentation tests. In this work, we investigated the mechanical response of soft biological materials to nanoindentation with spherical indenters using finite element simulations. We studied the responses of three different material constitutive laws (elastic, isotropic hyperelastic and anisotropic hyperelastic) under the same process and analyzed the differences thereof. Whereas linear elastic and isotropic hyperelastic materials can be studied using an axisymmetric simplification, anisotropic hyperelastic materials require three-dimensional analyses. Moreover, we established the limiting sample size required to determine the mechanical properties of soft materials while avoiding boundary effects. Finally, we compared the results obtained by simulation with an estimate obtained from Hertz theory. Hertz theory does not distinguish between the different material constitutive laws, and thus, we proposed corrections to improve the quantitative measurement of specific material properties by nanoindentation experiments. PMID:27214690

  17. Process efficiency simulation for key process parameters in biological methanogenesis

    Directory of Open Access Journals (Sweden)

    Sébastien Bernacchi

    2014-09-01

    Full Text Available New generation biofuels are a suitable approach to produce energy carriers in an almost CO2 neutral way. A promising reaction is the conversion of CO2 and H2 to CH4. This contribution aims at elucidating a bioprocess comprised of a core reaction unit using microorganisms from the Archaea life domain, which metabolize CO2 and H2 to CH4, followed by a gas purification step. The process is simulated and analyzed thermodynamically using the Aspen Plus process simulation environment. The goal of the study was to quantify effects of process parameters on overall process efficiency using a kinetic model derived from previously published experimental results. The used empirical model links the production rate of CH4 and biomass to limiting reactant concentrations. In addition, Aspen Plus was used to improve bioprocess quantification. Impacts of pressure as well as dilution of reactant gas with up to 70% non-reactive gas on overall process efficiency was evaluated. Pressure in the reactor unit of 11 bar at 65℃ with a pressure of 21 bar for gas purification led to an overall process efficiency comprised between 66% and 70% for gaseous product and between 73% and 76% if heat of compression is considered a valuable product. The combination of 2 bar pressure in the reactor and 21 bar for purification was the most efficient combination of parameters. This result shows Aspen Plus potential for similar bioprocess development as it accounts for the energetic aspect of the entire process. In fact, the optimum for the overall process efficiency was found to differ from the optimum of the reaction unit. High efficiency of over 70% demonstrates that biological methanogenesis is a promising alternative for a chemical methanation reaction.

  18. Vertical accelerator device to apply loads simulating blast environments in the military to human surrogates.

    Science.gov (United States)

    Yoganandan, Narayan; Pintar, Frank A; Schlick, Michael; Humm, John R; Voo, Liming; Merkle, Andrew; Kleinberger, Michael

    2015-09-18

    The objective of the study was to develop a simple device, Vertical accelerator (Vertac), to apply vertical impact loads to Post Mortem Human Subject (PMHS) or dummy surrogates because injuries sustained in military conflicts are associated with this vector; example, under-body blasts from explosive devices/events. The two-part mechanically controlled device consisted of load-application and load-receiving sections connected by a lever arm. The former section incorporated a falling weight to impact one end of the lever arm inducing a reaction at the other/load-receiving end. The "launch-plate" on this end of the arm applied the vertical impact load/acceleration pulse under different initial conditions to biological/physical surrogates, attached to second section. It is possible to induce different acceleration pulses by using varying energy absorbing materials and controlling drop height and weight. The second section of Vertac had the flexibility to accommodate different body regions for vertical loading experiments. The device is simple and inexpensive. It has the ability to control pulses and flexibility to accommodate different sub-systems/components of human surrogates. It has the capability to incorporate preloads and military personal protective equipment (e.g., combat helmet). It can simulate vehicle roofs. The device allows for intermittent specimen evaluations (x-ray and palpation, without changing specimen alignment). The two free but interconnected sections can be used to advance safety to military personnel. Examples demonstrating feasibilities of the Vertac device to apply vertical impact accelerations using PMHS head-neck preparations with helmet and booted Hybrid III dummy lower leg preparations under in-contact and launch-type impact experiments are presented. PMID:26159057

  19. Computer simulations for biological aging and sexual reproduction

    Directory of Open Access Journals (Sweden)

    DIETRICH STAUFFER

    2001-03-01

    Full Text Available The sexual version of the Penna model of biological aging, simulated since 1996, is compared here with alternative forms of reproduction as well as with models not involving aging. In particular we want to check how sexual forms of life could have evolved and won over earlier asexual forms hundreds of million years ago. This computer model is based on the mutation-accumulation theory of aging, using bits-strings to represent the genome. Its population dynamics is studied by Monte Carlo methods.A versão sexual do modelo de envelhecimento biológico de Penna, simulada desde 1996, é comparada aqui com formas alternativas de reprodução bem como com modelos que não envolvem envelhecimento. Em particular, queremos verificar como formas sexuais de vida poderiam ter evoluído e predominado sobre formas assexuais há centenas de milhões de anos. Este modelo computacional baseia-se na teoria do envelhecimento por acumulação de mutações, usando 'bits-strings' para representar o genoma. Sua dinâmica de populações é estudada por métodos de Monte Carlo.

  20. Applying complex models to poultry production in the future--economics and biology.

    Science.gov (United States)

    Talpaz, H; Cohen, M; Fancher, B; Halley, J

    2013-09-01

    The ability to determine the optimal broiler feed nutrient density that maximizes margin over feeding cost (MOFC) has obvious economic value. To determine optimal feed nutrient density, one must consider ingredient prices, meat values, the product mix being marketed, and the projected biological performance. A series of 8 feeding trials was conducted to estimate biological responses to changes in ME and amino acid (AA) density. Eight different genotypes of sex-separate reared broilers were fed diets varying in ME (2,723-3,386 kcal of ME/kg) and AA (0.89-1.65% digestible lysine with all essential AA acids being indexed to lysine) levels. Broilers were processed to determine carcass component yield at many different BW (1.09-4.70 kg). Trial data generated were used in model constructed to discover the dietary levels of ME and AA that maximize MOFC on a per broiler or per broiler annualized basis (bird × number of cycles/year). The model was designed to estimate the effects of dietary nutrient concentration on broiler live weight, feed conversion, mortality, and carcass component yield. Estimated coefficients from the step-wise regression process are subsequently used to predict the optimal ME and AA concentrations that maximize MOFC. The effects of changing feed or meat prices across a wide spectrum on optimal ME and AA levels can be evaluated via parametric analysis. The model can rapidly compare both biological and economic implications of changing from current practice to the simulated optimal solution. The model can be exploited to enhance decision making under volatile market conditions. PMID:23960140

  1. Proceedings of the 3rd workshop on ion-beam-applied biology

    International Nuclear Information System (INIS)

    In order to encourage research on biological application using ion beam at TIARA, we have had the workshop on ion beam applied biology at JAERI Takasaki every year since 2002. The 3rd workshop titled 'Future development of plant research using the positron imaging method - Understanding the plant functions through visualization images-' is held this year. The main topics of this workshop are introduction of the latest studies on the assimilation and transportation of nutrients by plant using positron imaging method. Further, related technologies of the positron imaging and prospect of positron imaging for is discussed. We hope this workshop popularizes positron imaging technology for plants, accelerates cooperation between industries, universities and governmental institutes and contributes future projects of understanding of the physiological functions of plants using the positron imaging method. This workshop was held on September 29th 2004, hosted by JAERI Takasaki and cooperated by The Japan Radioisotope Association, Japanese Society of Soil Science and Plant Nutrition. The Japanese Society of Plant Physiologists, Atomic Energy Society of Japan, The Japanese Society of Nuclear and Radiochemical Science and The Ion Beam Breeding Society. There were 85 participants from not only universities and laboratories but also private company developing the environment conservation technology, so on. Highly qualified presentations were given on biological studies with ion beam, on analysis of plant functions using the positron imaging method and on supporting technology for the positron imaging monitoring. Progress in the elucidation of plant functions is expected to develop the technologies for production of safe provisions and conservation of environment with plant. The 14 of the presented papers are indexed individually. (J.P.N.)

  2. Reduction of Biological Sludge Production Applying an Alternating Oxic/anoxic Process in Water Line.

    Science.gov (United States)

    Eusebi, Anna Laura; Panigutti, Maximiliano; Battistoni, Paolo

    2016-06-01

    Alternating oxic/anoxic process, applied for the main objective of the improvement of nitrogen performances, was studied in terms of secondary effect of biomass reduction. The process was carried out in one real water resource recovery facility and the data were compared with the previous conventional period when a conventional process was adopted. The main mechanism of the process for the sludge minimization is recognized in the metabolic uncoupling. In fact, an increase of the specific oxygen uptake rate in the biological reactor was recorded stimulated by the change of the oxidation reduction potential environment. Moreover, the heterotrophic growth yield was measured equal to 0.385 kgVSS/kgCOD. The global percentage of reduction was tested with the mass balance of solids. The process is able to decrease the observed sludge yield up to 20%. The specific energy consumption was evaluated. PMID:27225780

  3. Biological and intelligent manufacturing: human life-skills applied to technological development

    Directory of Open Access Journals (Sweden)

    Claudia Nelcy Jiménez Hernández

    2010-07-01

    Full Text Available Highly competitive settings, characterised by development being promoting by the predominance of knowledge, means that mul- tidisciplinary approaches must be adopted for dealing with specific problems. Indeed, techniques and tools have been created by imitating human beings’ behaviour and applying them to productive and technological contexts to increase efficiency and enable a quick response. This paper deals with this topic and presents the results of scientometric- and technological surveillance-based research for revealing life sciences’ impact on technological development and its management. It was found that such impact has been mainly reflected in producing concepts and applications for topics such as intelligent manufacturing, biological manu- facturing systems and holonic and bionic manufacturing, thereby providing manufacturing and information management with hu- man attributes such as adaptation, self-learning, flexibility and the ability to evolve. It may thus be concluded that technological factor management has been strengthened, based on fields such as biology, thereby leading to direct outcomes regarding pro- duction.

  4. How can we improve problem-solving in undergraduate biology? Applying lessons from 30 years of physics education research

    CERN Document Server

    Hoskinson, Anne-Marie; Knight, Jennifer K

    2012-01-01

    Modern biological problems are complex. If students are to successfully grapple with such problems as scientists and citizens, they need to have practiced solving authentic, complex problems during their undergraduate years. Physics education researchers have investigated student problem-solving for the last three decades. Although the surface features and content of biology problems differ from physics problems, teachers of both sciences want students to learn to explain patterns and processes in the natural world and to make predictions about system behaviors. After surveying literature on problem-solving in physics and biology, we propose how biology education researchers could apply research-supported pedagogical techniques from physics to enhance biology students' problem-solving. First, we characterize the problems that biology students are typically asked to solve. We then describe the development of research-validated physics problem-solving curricula. Finally, we propose how biology scholars can appl...

  5. STOCHSIMGPU Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

    OpenAIRE

    Klingbeil, G.; Erban, R; Giles, M; Maini, P.K.

    2010-01-01

    Motivation: The importance of stochasticity in biological systems is becoming increasingly recognised and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU which exploits graphics processing units (GPUs)for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works wi...

  6. Applying optical forces and elastic light scattering for manipulation and analysis of biological objects

    Science.gov (United States)

    Shao, Bing

    Non-invasive manipulation and analysis of biological objects with high resolution and efficiency have become extremely important. This dissertation presents three novel techniques based on light scattering and optical forces, which could bring high resolution and speed to submicron cell characterization, improve the throughput and functionality of self-propelled cell analysis and enhance the parallelism, portability and flexibility of cell manipulation instruments. Elastic light scattering is used for submicron cell characterization. An important problem in oceanic microbial ecology is characterizing the constituents of the sea. To pursue this goal, the application of angularly-dependent light scattering on oceanic microbe differentiation has been explored. Good overall agreement is found between scattering patterns simulated with developed models and those experimentally measured. The distinct scattering patterns of different species provide fingerprint information that will allow for routine identification of marine picoplankton. Optical tweezers have been used not only for manipulating cells, viruses and organelles within cells, but also measuring biological forces on the order of picoNewtons. In the second part of this dissertation, a three-dimensional resizable annular laser trap is developed for self-propelled cell manipulation and analysis. This system offers high power efficiency and is potentially useful for high-throughput multi-level sperm sorting based on motility and chemotaxis. With only tens of milliwatts devoted to each sperm, this new type of laser trap offers a gentle way to study the effect of optical force, laser radiation and external obstacles on sperm swimming patterns and membrane potential in detail. Applications could be extended to motility and biotropism studies on other self-propelled cells, such as algae and bacteria, etc. The third part of this dissertation involves manipulation of multiple biological cells both synchronously and

  7. Response of an invasive liana to simulated herbivory: implications for its biological control

    Science.gov (United States)

    Raghu, S.; Dhileepan, K.; Treviño, M.

    2006-05-01

    Pre-release evaluation of the efficacy of biological control agents is often not possible in the case of many invasive species targeted for biocontrol. In such circumstances simulating herbivory could yield significant insights into plant response to damage, thereby improving the efficiency of agent prioritisation, increasing the chances of regulating the performance of invasive plants through herbivory and minimising potential risks posed by release of multiple herbivores. We adopted this approach to understand the weaknesses herbivores could exploit, to manage the invasive liana, Macfadyena unguis-cati. We simulated herbivory by damaging the leaves, stem, root and tuber of the plant, in isolation and in combination. We also applied these treatments at multiple frequencies. Plant response in terms of biomass allocation showed that at least two severe defoliation treatments were required to diminish this liana's climbing habit and reduce its allocation to belowground tuber reserves. Belowground damage appears to have negligible effect on the plant's biomass production and tuber damage appears to trigger a compensatory response. Plant response to combinations of different types of damage did not differ significantly to that from leaf damage. This suggests that specialist herbivores in the leaf-feeding guild capable of removing over 50% of the leaf tissue may be desirable in the biological control of this invasive species.

  8. A Friendly-Biological Reactor SIMulator (BioReSIM for studying biological processes in wastewater treatment processes

    Directory of Open Access Journals (Sweden)

    Raul Molina

    2014-12-01

    Full Text Available Biological processes for wastewater treatments are inherently dynamic systems because of the large variations in the influent wastewater flow rate, concentration composition and the adaptive behavior of the involved microorganisms. Moreover, the sludge retention time (SRT is a critical factor to understand the bioreactor performances when changes in the influent or in the operation conditions take place. Since SRT are usually in the range of 10-30 days, the performance of biological reactors needs a long time to be monitored in a regular laboratory demonstration, limiting the knowledge that can be obtained in the experimental lab practice. In order to overcome this lack, mathematical models and computer simulations are useful tools to describe biochemical processes and predict the overall performance of bioreactors under different working operation conditions and variations of the inlet wastewater composition. The mathematical solution of the model could be difficult as numerous biochemical processes can be considered. Additionally, biological reactors description (mass balance, etc. needs models represented by partial or/and ordinary differential equations associated to algebraic expressions, that require complex computational codes to obtain the numerical solutions. Different kind of software for mathematical modeling can be used, from large degree of freedom simulators capable of free models definition (as AQUASIM, to closed predefined model structure programs (as BIOWIN. The first ones usually require long learning curves, whereas the second ones could be excessively rigid for specific wastewater treatment systems. As alternative, we present Biological Reactor SIMulator (BioReSIM, a MATLAB code for the simulation of sequencing batch reactors (SBR and rotating biological contactors (RBC as biological systems of suspended and attached biomass for wastewater treatment, respectively. This BioReSIM allows the evaluation of simple and complex

  9. New derivation method and simulation of skin effect in biological tissue.

    Science.gov (United States)

    Fan, Xiaoli; Zhou, Qianxiang; Liu, Zhongqi; Xie, Fang

    2015-01-01

    Based on the electrical properties of biological tissues, bioimpedance measurement technology can be employed to collect physiologic and pathologic information by measuring changes in human bioimpedance. When an alternating current (AC) is applied as a detection signal to a tissue, the current field distribution, which is affected by skin effect, is related to both the bioimpedance of the tissue and the AC frequency. These relations would possibly reduce the accuracy and reliability of the measurement. In this study, an electromagnetic theory-based method, in which cylindrical conductor were divided into layers, was used to obtain current field distribution models of human limbs. Model simulations were conducted in MATLAB. The skin effect phenomenon and its characteristics in human tissues at different frequencies were observed, thus providing essential data on skin effect, which are useful in the development of bioimpedance measurement technology. PMID:26406033

  10. Two kinds of biological dosimeters applied to 131I-treated thyroid cancer patients

    International Nuclear Information System (INIS)

    We investigated 10 thyroid cancer patients after 131I oral medication at the range of (3.7-27.5 GBq) total activity with dicentric chromosome aberration analysis and the T-cell antigen receptor (TCR) mutation assay. We compared and evaluated both methods on their accuracy and applicability. The 10 thyroid cancer patients are at 30-50 years old, and we got 5 ml peripheral blood individually for the investigations. We worked the dicentric aberration analysis with the conventional giemsa method. The first division cells were observed, and 100 or 200 metaphase cells of each patient were investigated. The background level of dicentric analysis is 1 in 500 metaphase cells. For the TCR mutation assay, we applied the FACS caliber flow cytometer manufactured by Becton Dickinson Co. to measure the CD3-CD4+ mutant frequency. Only 0.1 ml blood were needed and stained with fluorescein-labeled anti-leu3a(CD4) and phycoerythrin-labeled anti-leu4(CD3) antibodies as specified by the supplier (BD Co.). The Mf values were calculated as the number of CD3-CD4+ in the mutant cell windows divided by the total number of CD3-CD4+ T cells in the flow distribution. The average coefficient of variation(CV) on the mutant CD3-CD4+ T cell frequency (x10-4) in 10 normal donors aged 27-50 is 34%. The background rate of CD3-CD4+ mutant cells is 1.16x10-4 on 13 healthy unexposed persons. In general, the results or dicentric analysis and TCR mutation assay with total activity 3.7-27.5 GBq or 131I oral administration on 10 thyroid cancer patients are in coincidence, but the 131I treated the affects the results. The earlier 131I exposure (around 6 years), No. 6, 7, 9 patients showed obviously a decrease in data of TCR mutant. No.7, 8, 9, 10 patients also showed a decrease in TCR rate and no. of dicentric per cell because of the early and long period (on more than 5 years) 131I treatment. But nevertheless the No.10 patient was taken 131I 27.5 GBq total activity still has the highest TCR rates and

  11. Two kinds of biological dosimeters applied to {sup 131}I-treated thyroid cancer patients

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Ming-Shia; Chen, Li-Hsiang [Health Physics Division, Institute of Nuclear Energy Research, Taiwan (China)

    2000-05-01

    We investigated 10 thyroid cancer patients after {sup 131}I oral medication at the range of (3.7-27.5 GBq) total activity with dicentric chromosome aberration analysis and the T-cell antigen receptor (TCR) mutation assay. We compared and evaluated both methods on their accuracy and applicability. The 10 thyroid cancer patients are at 30-50 years old, and we got 5 ml peripheral blood individually for the investigations. We worked the dicentric aberration analysis with the conventional giemsa method. The first division cells were observed, and 100 or 200 metaphase cells of each patient were investigated. The background level of dicentric analysis is 1 in 500 metaphase cells. For the TCR mutation assay, we applied the FACS caliber flow cytometer manufactured by Becton Dickinson Co. to measure the CD{sub 3}{sup -}CD{sub 4}{sup +} mutant frequency. Only 0.1 ml blood were needed and stained with fluorescein-labeled anti-leu3a(CD{sub 4}) and phycoerythrin-labeled anti-leu4(CD{sub 3}) antibodies as specified by the supplier (BD Co.). The Mf values were calculated as the number of CD{sub 3}{sup -}CD{sub 4}{sup +} in the mutant cell windows divided by the total number of CD{sub 3}{sup -}CD{sub 4}{sup +} T cells in the flow distribution. The average coefficient of variation(CV) on the mutant CD{sub 3}{sup -}CD{sub 4}{sup +} T cell frequency (x10{sup -4}) in 10 normal donors aged 27-50 is 34%. The background rate of CD{sub 3}{sup -}CD{sub 4}{sup +} mutant cells is 1.16x10{sup -4} on 13 healthy unexposed persons. In general, the results or dicentric analysis and TCR mutation assay with total activity 3.7-27.5 GBq or {sup 131}I oral administration on 10 thyroid cancer patients are in coincidence, but the {sup 131}I treated the affects the results. The earlier {sup 131}I exposure (around 6 years), No. 6, 7, 9 patients showed obviously a decrease in data of TCR mutant. No.7, 8, 9, 10 patients also showed a decrease in TCR rate and no. of dicentric per cell because of the early and

  12. Combinatorial Feature Optimization using Multi-objective Evolutionary Algorithms applied to a Biological Warfare Classification Problem.

    OpenAIRE

    2010-01-01

    Biological weapons is the aggressive use of organisms or toxins, also known as biological warfare agents. These weapons are invisible, odorless, tasteless and can be spread without a sound, making it difficult to detect an attack. Early warning systems based on environmental standoff detection of biological warfare agents using lidar technology require real-time signal processing, challenging the systems efficiency in terms of both computational complexity and classification accuracy. Hence, ...

  13. Program package FLUX for the simulation of fundamental and applied problems of fluid dynamics

    Science.gov (United States)

    Babakov, A. V.

    2016-06-01

    Based on parallel algorithms of a conservative numerical method, a software package for simulating fundamental and applied fluid dynamics problems in a wide range of parameters is developed. The software is implemented on a cluster computer system. Examples of the numerical simulation of three-dimensional problems in various fields of fluid dynamics are discussed, including problems of external flow around bodies, investigation of aerodynamic characteristics of flying vehicles, flows around a set of objects, flows in nozzles, and flows around underwater constructs.

  14. Demonstrating Biological Classification Using a Simulation of Natural Taxa.

    Science.gov (United States)

    Vogt, Kenneth D.

    1995-01-01

    A review of introductory college level and high school biology texts reveals that concepts and theories behind classification are usually poorly discussed. Suggests ways in which card games can be used to teach differences between the phenetic and phylogenetic approaches. (LZ)

  15. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

    KAUST Repository

    Klingbeil, G.

    2011-02-25

    Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user\\'s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. © The Author 2011. Published by Oxford University Press. All rights reserved.

  16. DSC: software tool for simulation-based design of control strategies applied to wastewater treatment plants.

    Science.gov (United States)

    Ruano, M V; Ribes, J; Seco, A; Ferrer, J

    2011-01-01

    This paper presents a computer tool called DSC (Simulation based Controllers Design) that enables an easy design of control systems and strategies applied to wastewater treatment plants. Although the control systems are developed and evaluated by simulation, this tool aims to facilitate the direct implementation of the designed control system to the PC of the full-scale WWTP (wastewater treatment plants). The designed control system can be programmed in a dedicated control application and can be connected to either the simulation software or the SCADA of the plant. To this end, the developed DSC incorporates an OPC server (OLE for process control) which facilitates an open-standard communication protocol for different industrial process applications. The potential capabilities of the DSC tool are illustrated through the example of a full-scale application. An aeration control system applied to a nutrient removing WWTP was designed, tuned and evaluated with the DSC tool before its implementation in the full scale plant. The control parameters obtained by simulation were suitable for the full scale plant with only few modifications to improve the control performance. With the DSC tool, the control systems performance can be easily evaluated by simulation. Once developed and tuned by simulation, the control systems can be directly applied to the full-scale WWTP. PMID:21330730

  17. Accurate Simulation of MPPT Methods Performance When Applied to Commercial Photovoltaic Panels

    OpenAIRE

    2015-01-01

    A new, simple, and quick-calculation methodology to obtain a solar panel model, based on the manufacturers' datasheet, to perform MPPT simulations, is described. The method takes into account variations on the ambient conditions (sun irradiation and solar cells temperature) and allows fast MPPT methods comparison or their performance prediction when applied to a particular solar panel. The feasibility of the described methodology is checked with four different MPPT methods applied to a commer...

  18. ezBioNet: A modeling and simulation system for analyzing biological reaction networks

    Science.gov (United States)

    Yu, Seok Jong; Tung, Thai Quang; Park, Junho; Lim, Jongtae; Yoo, Jaesoo

    2012-10-01

    To achieve robustness against living environments, a living organism is composed of complicated regulatory mechanisms ranging from gene regulations to signal transduction. If such life phenomena are to be understand, an integrated analysis tool that should have modeling and simulation functions for biological reactions, as well as new experimental methods for measuring biological phenomena, is fundamentally required. We have designed and implemented modeling and simulation software (ezBioNet) for analyzing biological reaction networks. The software can simultaneously perform an integrated modeling of various responses occurring in cells, ranging from gene expressions to signaling processes. To support massive analysis of biological networks, we have constructed a server-side simulation system (VCellSim) that can perform ordinary differential equations (ODE) analysis, sensitivity analysis, and parameter estimates. ezBioNet integrates the BioModel database by connecting the european bioinformatics institute (EBI) servers through Web services APIs and supports the handling of systems biology markup language (SBML) files. In addition, we employed eclipse RCP (rich client platform) which is a powerful modularity framework allowing various functional expansions. ezBioNet is intended to be an easy-to-use modeling tool, as well as a simulation system, to understand the control mechanism by monitoring the change of each component in a biological network. A researcher may perform the kinetic modeling and execute the simulation. The simulation result can be managed and visualized on ezBioNet, which is freely available at http://ezbionet.cbnu.ac.kr.

  19. Process efficiency simulation for key process parameters in biological methanogenesis

    OpenAIRE

    Sébastien Bernacchi; Michaela Weissgram; Walter Wukovits; Christoph Herwig

    2014-01-01

    New generation biofuels are a suitable approach to produce energy carriers in an almost CO2 neutral way. A promising reaction is the conversion of CO2 and H2 to CH4. This contribution aims at elucidating a bioprocess comprised of a core reaction unit using microorganisms from the Archaea life domain, which metabolize CO2 and H2 to CH4, followed by a gas purification step. The process is simulated and analyzed thermodynamically using the Aspen Plus process simulation environment. The goal of t...

  20. ADVANCES OF BASIC MOLECULAR BIOLOGY TECHNIQUES: POTENTIAL TO APPLY IN PLANT VIROID DETECTION IN SRI LANKA

    OpenAIRE

    Yapa M.A.M. Wijerathna

    2012-01-01

    Viroids are the smallest pathogens of plants. They are the cause of serious diseases on economic plants worldwide. Prevention and detection of the pathogens are the best method to reduce the economic loss from viroid infection. During last decade, genetics and molecular biology techniques have gained an increasing presence in plant pathology research. The purpose of this review is to highlight the most upgrade molecular biology techniques that have been used and studied recently. Most relevan...

  1. Diversity-Oriented Synthetic Strategies Applied to Cancer Chemical Biology and Drug Discovery

    OpenAIRE

    Ian Collins; Jones, Alan M.

    2014-01-01

    How can diversity-oriented strategies for chemical synthesis provide chemical tools to help shape our understanding of complex cancer pathways and progress anti-cancer drug discovery efforts? This review (surveying the literature from 2003 to the present) considers the applications of diversity-oriented synthesis (DOS), biology-oriented synthesis (BIOS) and associated strategies to cancer biology and drug discovery, summarising the syntheses of novel and often highly complex scaffolds from p...

  2. Characterization of dielectric barrier discharge in air applying current measurement, numerical simulation and emission spectroscopy

    CERN Document Server

    Rajasekaran, Priyadarshini; Awakowicz, Peter

    2012-01-01

    Dielectric barrier discharge (DBD) in air is characterized applying current measurement, numerical simulation and optical emission spectroscopy (OES). For OES, a non-calibrated spectrometer is used. This diagnostic method is applicable when cross-sectional area of the active plasma volume and current density can be determined. The nitrogen emission in the spectral range of 380 nm- 406 nm is used for OES diagnostics. Electric field in the active plasma volume is determined applying the measured spectrum, well-known Frank-Condon factors for nitrogen transitions and numerically- simulated electron distribution functions. The measured electric current density is used for determination of electron density in plasma. Using the determined plasma parameters, the dissociation rate of nitrogen and oxygen in active plasma volume are calculated, which can be used by simulation of the chemical kinetics.

  3. Preparation of Biological Samples Containing Metoprolol and Bisoprolol for Applying Methods for Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Corina Mahu Ştefania

    2015-12-01

    Full Text Available Arterial hypertension is a complex disease with many serious complications, representing a leading cause of mortality. Selective beta-blockers such as metoprolol and bisoprolol are frequently used in the management of hypertension. Numerous analytical methods have been developed for the determination of these substances in biological fluids, such as liquid chromatography coupled with mass spectrometry, gas chromatography coupled with mass spectrometry, high performance liquid chromatography. Due to the complex composition of biological fluids a biological sample pre-treatment before the use of the method for quantitative determination is required in order to remove proteins and potential interferences. The most commonly used methods for processing biological samples containing metoprolol and bisoprolol were identified through a thorough literature search using PubMed, ScienceDirect, and Willey Journals databases. Articles published between years 2005-2015 were reviewed. Protein precipitation, liquid-liquid extraction and solid phase extraction are the main techniques for the extraction of these drugs from plasma, serum, whole blood and urine samples. In addition, numerous other techniques have been developed for the preparation of biological samples, such as dispersive liquid-liquid microextraction, carrier-mediated liquid phase microextraction, hollow fiber-protected liquid phase microextraction, on-line molecularly imprinted solid phase extraction. The analysis of metoprolol and bisoprolol in human plasma, urine and other biological fluids provides important information in clinical and toxicological trials, thus requiring the application of appropriate extraction techniques for the detection of these antihypertensive substances at nanogram and picogram levels.

  4. CRITTERS! A Realistic Simulation for Teaching Evolutionary Biology

    Science.gov (United States)

    Latham, Luke G., II; Scully, Erik P.

    2008-01-01

    Evolutionary processes can be studied in nature and in the laboratory, but time and financial constraints result in few opportunities for undergraduate and high school students to explore the agents of genetic change in populations. One alternative to time consuming and expensive teaching laboratories is the use of computer simulations. We…

  5. Molecular dynamics simulation of a charged biological membrane

    NARCIS (Netherlands)

    López Cascales, J.J.; García de la Torre, J.; Marrink, S.J.; Berendsen, H.J.C.

    1996-01-01

    A molecular dynamics simulation of a membrane with net charge in its liquid-crystalline state was carried out. It was modeled by dipalmitoylphosphatidylserine lipids with net charge, sodium ions as counterions and water molecules. The behavior of this membrane differs from that was shown by other me

  6. Fluid models and simulations of biological cell phenomena

    Science.gov (United States)

    Greenspan, H. P.

    1982-01-01

    The dynamics of coated droplets are examined within the context of biofluids. Of specific interest is the manner in which the shape of a droplet, the motion within it as well as that of aggregates of droplets can be controlled by the modulation of surface properties and the extent to which such fluid phenomena are an intrinsic part of cellular processes. From the standpoint of biology, an objective is to elucidate some of the general dynamical features that affect the disposition of an entire cell, cell colonies and tissues. Conventionally averaged field variables of continuum mechanics are used to describe the overall global effects which result from the myriad of small scale molecular interactions. An attempt is made to establish cause and effect relationships from correct dynamical laws of motion rather than by what may have been unnecessary invocation of metabolic or life processes. Several topics are discussed where there are strong analogies droplets and cells including: encapsulated droplets/cell membranes; droplet shape/cell shape; adhesion and spread of a droplet/cell motility and adhesion; and oams and multiphase flows/cell aggregates and tissues. Evidence is presented to show that certain concepts of continuum theory such as suface tension, surface free energy, contact angle, bending moments, etc. are relevant and applicable to the study of cell biology.

  7. Simulation and visualization of coupled hydrodynamical, chemical and biological models

    Directory of Open Access Journals (Sweden)

    Dag Slagstad

    1997-04-01

    Full Text Available This paper briefly describes the principles of hydrodynamical and ecological modelling of marine systems and how model results are presented by use of MATLAB. Two application examples are shown. One refers to modelling and simulation of the carbon vertical transport in the Greenland Sea and the other is a study on the effect of wind pattern for the invasion success of zooplankton from the Norwegian Sea into the North Sea by use of particle tracking.

  8. Biological Visualization, Imaging and Simulation(Bio-VIS) at NASA Ames Research Center: Developing New Software and Technology for Astronaut Training and Biology Research in Space

    Science.gov (United States)

    Smith, Jeffrey

    2003-01-01

    The Bio- Visualization, Imaging and Simulation (BioVIS) Technology Center at NASA's Ames Research Center is dedicated to developing and applying advanced visualization, computation and simulation technologies to support NASA Space Life Sciences research and the objectives of the Fundamental Biology Program. Research ranges from high resolution 3D cell imaging and structure analysis, virtual environment simulation of fine sensory-motor tasks, computational neuroscience and biophysics to biomedical/clinical applications. Computer simulation research focuses on the development of advanced computational tools for astronaut training and education. Virtual Reality (VR) and Virtual Environment (VE) simulation systems have become important training tools in many fields from flight simulation to, more recently, surgical simulation. The type and quality of training provided by these computer-based tools ranges widely, but the value of real-time VE computer simulation as a method of preparing individuals for real-world tasks is well established. Astronauts routinely use VE systems for various training tasks, including Space Shuttle landings, robot arm manipulations and extravehicular activities (space walks). Currently, there are no VE systems to train astronauts for basic and applied research experiments which are an important part of many missions. The Virtual Glovebox (VGX) is a prototype VE system for real-time physically-based simulation of the Life Sciences Glovebox where astronauts will perform many complex tasks supporting research experiments aboard the International Space Station. The VGX consists of a physical display system utilizing duel LCD projectors and circular polarization to produce a desktop-sized 3D virtual workspace. Physically-based modeling tools (Arachi Inc.) provide real-time collision detection, rigid body dynamics, physical properties and force-based controls for objects. The human-computer interface consists of two magnetic tracking devices

  9. A Biologic Behavior Simulation:Living Migration Algorithm (LMA)

    Institute of Scientific and Technical Information of China (English)

    LI Dou-dou; SHAO Shi-huang; QI Jin-peng

    2008-01-01

    Biologic behaviors are the principal source for proposing new intelligent algorithms.Based on the mechanism of the bio-subsistence and the bio-migration,this paper proposes a novel algorithm-Living Migration Algorithm (LMA).The original contributions of LMA are three essential attributes of each individual:the minimal life-needs which ale the necessaries for survival,the migrating which is a basal action for searching new living space,and the judging which is an important ability of deciding whether to migrate or not.When living space of all individuals can satisfy the minimal life-needs at some generation,they are considered as the optimal living places where objective functions will obtain the optima.LMA may be employed in large-scale computation and engineering field.The paper mostly operates LMA to deal with four nonlinear and heterogeneous optimizations,and experiments prove LMA has better performances than Free Search algorithm.

  10. ADVANCES OF BASIC MOLECULAR BIOLOGY TECHNIQUES: POTENTIAL TO APPLY IN PLANT VIROID DETECTION IN SRI LANKA

    Directory of Open Access Journals (Sweden)

    Yapa M.A.M. Wijerathna

    2012-12-01

    Full Text Available Viroids are the smallest pathogens of plants. They are the cause of serious diseases on economic plants worldwide. Prevention and detection of the pathogens are the best method to reduce the economic loss from viroid infection. During last decade, genetics and molecular biology techniques have gained an increasing presence in plant pathology research. The purpose of this review is to highlight the most upgrade molecular biology techniques that have been used and studied recently. Most relevant published reports and hand skilled techniques have presented here with emphasis on suitable Viroid detection technique should be used for Sri Lanka.

  11. Virtual Transgenics: Using a Molecular Biology Simulation to Impact Student Academic Achievement and Attitudes

    Science.gov (United States)

    Shegog, Ross; Lazarus, Melanie M.; Murray, Nancy G.; Diamond, Pamela M.; Sessions, Nathalie; Zsigmond, Eva

    2012-10-01

    The transgenic mouse model is useful for studying the causes and potential cures for human genetic diseases. Exposing high school biology students to laboratory experience in developing transgenic animal models is logistically prohibitive. Computer-based simulation, however, offers this potential in addition to advantages of fidelity and reach. This study describes and evaluates a computer-based simulation to train advanced placement high school science students in laboratory protocols, a transgenic mouse model was produced. A simulation module on preparing a gene construct in the molecular biology lab was evaluated using a randomized clinical control design with advanced placement high school biology students in Mercedes, Texas ( n = 44). Pre-post tests assessed procedural and declarative knowledge, time on task, attitudes toward computers for learning and towards science careers. Students who used the simulation increased their procedural and declarative knowledge regarding molecular biology compared to those in the control condition (both p < 0.005). Significant increases continued to occur with additional use of the simulation ( p < 0.001). Students in the treatment group became more positive toward using computers for learning ( p < 0.001). The simulation did not significantly affect attitudes toward science in general. Computer simulation of complex transgenic protocols have potential to provide a "virtual" laboratory experience as an adjunct to conventional educational approaches.

  12. General meeting. Technical reunion: the numerical and experimental simulation applied to the Reactor Physics

    International Nuclear Information System (INIS)

    The SFEN (French Society on Nuclear Energy), organized the 18 october 2001 at Paris, a technical day on the numerical and experimental simulation, applied to the reactor Physics. Nine aspects were discussed, giving a state of the art in the domain:the french nuclear park; the future technology; the controlled thermonuclear fusion; the new organizations and their implications on the research and development programs; Framatome-ANP markets and industrial code packages; reactor core simulation at high temperature; software architecture; SALOME; DESCARTES. (A.L.B.)

  13. Friction characteristics of a new type of continuous rotary electro-hydraulic servomotor applied to simulator

    Institute of Scientific and Technical Information of China (English)

    CAO Jian; XU Hong-guang

    2008-01-01

    The principle of a new type of no-pulsation continuous rotary electro-hydraulic servomotor applied to simulators is introduced. LuGre friction model was analyzed. The identification method of LuGre parameters was proposed, and the measures to compensate the effect of friction forces were given. A friction torque model for the new rotary motor was proposed. The low-speed response and step response of the motor were studied experi-mentally. Experimental results proved that using friction compensation could eliminate stick-slip motion at the low speed, which makes the servomotor applicable to simulators.

  14. Recent advances in particle-induced X-ray emission analysis applied to biological samples

    International Nuclear Information System (INIS)

    Papers reporting the application of particle induced X-ray emission (PIXE) analysis to biological samples continue to appear regularly in the literature. The majority of these papers deal with blood, hair, and other common body organs while a few deal with biological samples from the environnment. A variety of sample preparation methods have been demonstrated, a number of which are improvements, refinements and extensions of the thick- and thin-sample preparation methods reported in the early development of PIXE. While many papers describe the development of PIXE techniques some papers are now describing applications of the methods to serious biological problems. The following two factors may help to stimulate more consistant use of the PIXE method. First, each PIXE facility should be organized to give rapid sample processing and should have available several sample preparation and handling methods. Second, those with the skill to use PIXE methods need to become closely associated with researches knowledge able in medical and biological sciences and they also need to become more involved in project planning and sample handling. (orig.)

  15. Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks

    Directory of Open Access Journals (Sweden)

    Martin Florian

    2012-05-01

    Full Text Available Abstract Background High-throughput measurement technologies produce data sets that have the potential to elucidate the biological impact of disease, drug treatment, and environmental agents on humans. The scientific community faces an ongoing challenge in the analysis of these rich data sources to more accurately characterize biological processes that have been perturbed at the mechanistic level. Here, a new approach is built on previous methodologies in which high-throughput data was interpreted using prior biological knowledge of cause and effect relationships. These relationships are structured into network models that describe specific biological processes, such as inflammatory signaling or cell cycle progression. This enables quantitative assessment of network perturbation in response to a given stimulus. Results Four complementary methods were devised to quantify treatment-induced activity changes in processes described by network models. In addition, companion statistics were developed to qualify significance and specificity of the results. This approach is called Network Perturbation Amplitude (NPA scoring because the amplitudes of treatment-induced perturbations are computed for biological network models. The NPA methods were tested on two transcriptomic data sets: normal human bronchial epithelial (NHBE cells treated with the pro-inflammatory signaling mediator TNFα, and HCT116 colon cancer cells treated with the CDK cell cycle inhibitor R547. Each data set was scored against network models representing different aspects of inflammatory signaling and cell cycle progression, and these scores were compared with independent measures of pathway activity in NHBE cells to verify the approach. The NPA scoring method successfully quantified the amplitude of TNFα-induced perturbation for each network model when compared against NF-κB nuclear localization and cell number. In addition, the degree and specificity to which CDK

  16. [New methods in training of paediatric emergencies: medical simulation applied to paediatrics].

    Science.gov (United States)

    González Gómez, J M; Chaves Vinagre, J; Ocete Hita, E; Calvo Macías, C

    2008-06-01

    Patient safety constitutes one of the main objectives in health care. Among other recommendations, such as the creation of training centres and the development of patient safety programmes, of great importance is the creation of training programmes for work teams using medical simulation. Medical simulation is defined as "a situation or environment created to allow persons to experience a representation of a real event for the purpose of practice, learning, evaluation or to understand systems or human actions". In this way, abilities can be acquired in serious and uncommon situations with no risk of harm to the patient. This study revises the origins of medical simulation and the different types of simulation are classified. The main simulators currently used in Pediatrics are presented, and the design of a simulation course applied to the training of pediatric emergencies is described, detailing all its different phases. In the first non face-to-face stage, a new concept in medical training known as e-learning is applied. In the second phase, clinical cases are carried out using robotic simulation; this is followed by a debriefing session, which is a key element for acquiring abilities and skills. Lastly, the follow-up phase allows the student to connect with the teachers to consolidate the concepts acquired during the in-person phase. In this model, the aim is to improve scientific-technical abilities in addition to a series of related abilities such as controlling crisis situations, correct leadership of work teams, distribution of tasks, communication among the team members, etc., all of these within the present concept of excellence in care and medical professionalism. PMID:18559203

  17. Antiferromagnetic TiFe{sub 2} in applied fields: experiment and simulation

    Energy Technology Data Exchange (ETDEWEB)

    Martins, T. B.; Rechenberg, H. R., E-mail: hercilio@macbeth.if.usp.br [Universidade de Sao Paulo, Instituto de Fisica (Brazil)

    2006-04-15

    Moessbauer spectra of a powdered TiFe{sub 2} sample were measured under different applied fields and the results were compared to simulated spectra obtained by minimizing the total energy of a two-sublattice antiferromagnet. In order to reproduce experimental results a highly textured distribution had to be assumed, the local anisotropy axis lying mostly perpendicular to the applied field. Thus, magnetic alignment of AF grains by an external field was demonstrated. In addition, exchange and anisotropy fields for TiFe{sub 2} at T {approx} 0 K have been determined.

  18. Accurate Simulation of MPPT Methods Performance When Applied to Commercial Photovoltaic Panels

    Directory of Open Access Journals (Sweden)

    Javier Cubas

    2015-01-01

    Full Text Available A new, simple, and quick-calculation methodology to obtain a solar panel model, based on the manufacturers’ datasheet, to perform MPPT simulations, is described. The method takes into account variations on the ambient conditions (sun irradiation and solar cells temperature and allows fast MPPT methods comparison or their performance prediction when applied to a particular solar panel. The feasibility of the described methodology is checked with four different MPPT methods applied to a commercial solar panel, within a day, and under realistic ambient conditions.

  19. 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.

  20. Simulating open quantum systems by applying SU(4) to quantum master equations

    OpenAIRE

    Xu, Minghui; Tieri, D. A.; Holland, M J

    2013-01-01

    We show that open quantum systems of two-level atoms symmetrically coupled to a single-mode photon field can be efficiently simulated by applying a SU(4) group theory to quantum master equations. This is important since many foundational examples in quantum optics fall into this class. We demonstrate the method by finding exact solutions for many-atom open quantum systems such as lasing and steady state superradiance.

  1. Editorial: Advances in Health Education Applying E-Learning, Simulations and Distance Technologies

    OpenAIRE

    Andre W. Kushniruk (ACMI Fellow; CAHS Fellow)

    2011-01-01

    This special issue of the KM&EL international journal is dedicated to coverage of novel advances in health professional education applying e-Learning, simulations and distance education technologies. Modern healthcare is beginning to be transformed through the emergence of new information technologies and rapid advances in health informatics. Advances such as electronic health record systems (EHRs), clinical decision support systems and other advanced information systems such as public health...

  2. Numerical simulation in Applied Geophysics : From the mesoscale to the macroscale

    OpenAIRE

    Santos, Juan E.; Gauzellino, Patricia M.; Savioli, Gabriela B.; Martínez Corredor, Robiel

    2013-01-01

    This paper presents a collection of finite element procedures to model seismic wave propagation at the macroscale taking into account the effects caused by heterogeneities occuring at the mesoscale. For this purpose we first apply a set of compressibility and shear experiments to representative samples of the heterogeneous fluid saturated material. In turn these experiments yield the effective coefficients of an anisotropic macroscopic medium employed for numerical simulations at the macrosca...

  3. Simulations of modal active control applied to the self-sustained oscillations of the clarinet

    OpenAIRE

    Meurisse, Thibaut; MAMOU-MANI, Adrien; Caussé, René; SHARP, David

    2013-01-01

    Modal active control enables modifications of the damping and the frequencies of the different resonances of a system. A self-sustained oscillating wind instrument is modelled as a disturbance coupled to a resonator through a non-linear coupling. The aim of this study is to present simulations of modal active control applied to a modeled simplified self-sustained oscillating wind instrument (e.g. a cylindrical tube coupled to a reed, which is considered to approximate a simplified clarinet), ...

  4. MODELLING AND SIMULATING RISKS IN THE TRAINING OF THE HUMAN RESOURCES BY APPLYING THE CHAOS THEORY

    OpenAIRE

    Eugen ROTARESCU

    2012-01-01

    The article approaches the modelling and simulation of risks in the training of the human resources, as well as the forecast of the degree of human resources training impacted by risks by applying the mathematical tools offered by the Chaos Theory and mathematical statistics. We will highlight that the level of knowledge, skills and abilities of the human resources from an organization are autocorrelated in time and they depend on the level of a previous moment of the training, as well as on ...

  5. Smart DNA Fabrication Using Sound Waves: Applying Acoustic Dispensing Technologies to Synthetic Biology.

    Science.gov (United States)

    Kanigowska, Paulina; Shen, Yue; Zheng, Yijing; Rosser, Susan; Cai, Yizhi

    2016-02-01

    Acoustic droplet ejection (ADE) technology uses focused acoustic energy to transfer nanoliter-scale liquid droplets with high precision and accuracy. This noncontact, tipless, low-volume dispensing technology minimizes the possibility of cross-contamination and potentially reduces the costs of reagents and consumables. To date, acoustic dispensers have mainly been used in screening libraries of compounds. In this paper, we describe the first application of this powerful technology to the rapidly developing field of synthetic biology, for DNA synthesis and assembly at the nanoliter scale using a Labcyte Echo 550 acoustic dispenser. We were able to successfully downscale PCRs and the popular one-pot DNA assembly methods, Golden Gate and Gibson assemblies, from the microliter to the nanoliter scale with high assembly efficiency, which effectively cut the reagent cost by 20- to 100-fold. We envision that acoustic dispensing will become an instrumental technology in synthetic biology, in particular in the era of DNA foundries. PMID:26163567

  6. Parallelizing Genetic Linkage Analysis: A Case Study for Applying Parallel Computation in Molecular Biology

    OpenAIRE

    Nadkarni, Prakash; Gelernter, Joel E.; Carriero, Nicholas; Pakstis, Andrew J.; Kidd, Kenneth K.; Miller, Perry L.

    1990-01-01

    Parallel computers offer a solution to improve the lengthy computation time of many conventional, sequential programs used in molecular biology. On a parallel computer, different pieces of the computation are performed simultaneously on different processors. LINKMAP is a sequential program widely used by scientists to perform genetic linkage analysis. We have converted LINKMAP to run on a parallel computer, using the machine-independent parallel programming language, Linda. Using the parallel...

  7. Preparation of Biological Samples Containing Metoprolol and Bisoprolol for Applying Methods for Quantitative Analysis

    OpenAIRE

    Corina Mahu Ştefania; Monica Hăncianu; Luminiţa Agoroaei; Anda Cristina Coman Băbuşanu; Elena Butnaru

    2015-01-01

    Arterial hypertension is a complex disease with many serious complications, representing a leading cause of mortality. Selective beta-blockers such as metoprolol and bisoprolol are frequently used in the management of hypertension. Numerous analytical methods have been developed for the determination of these substances in biological fluids, such as liquid chromatography coupled with mass spectrometry, gas chromatography coupled with mass spectrometry, high performance liquid chromatography. ...

  8. Multiphase Simulated Annealing Based on Boltzmann and Bose-Einstein Distribution Applied to Protein Folding Problem.

    Science.gov (United States)

    Frausto-Solis, Juan; Liñán-García, Ernesto; Sánchez-Hernández, Juan Paulo; González-Barbosa, J Javier; González-Flores, Carlos; Castilla-Valdez, Guadalupe

    2016-01-01

    A new hybrid Multiphase Simulated Annealing Algorithm using Boltzmann and Bose-Einstein distributions (MPSABBE) is proposed. MPSABBE was designed for solving the Protein Folding Problem (PFP) instances. This new approach has four phases: (i) Multiquenching Phase (MQP), (ii) Boltzmann Annealing Phase (BAP), (iii) Bose-Einstein Annealing Phase (BEAP), and (iv) Dynamical Equilibrium Phase (DEP). BAP and BEAP are simulated annealing searching procedures based on Boltzmann and Bose-Einstein distributions, respectively. DEP is also a simulated annealing search procedure, which is applied at the final temperature of the fourth phase, which can be seen as a second Bose-Einstein phase. MQP is a search process that ranges from extremely high to high temperatures, applying a very fast cooling process, and is not very restrictive to accept new solutions. However, BAP and BEAP range from high to low and from low to very low temperatures, respectively. They are more restrictive for accepting new solutions. DEP uses a particular heuristic to detect the stochastic equilibrium by applying a least squares method during its execution. MPSABBE parameters are tuned with an analytical method, which considers the maximal and minimal deterioration of problem instances. MPSABBE was tested with several instances of PFP, showing that the use of both distributions is better than using only the Boltzmann distribution on the classical SA. PMID:27413369

  9. Multiphase Simulated Annealing Based on Boltzmann and Bose-Einstein Distribution Applied to Protein Folding Problem

    Science.gov (United States)

    Liñán-García, Ernesto; Sánchez-Hernández, Juan Paulo; González-Barbosa, J. Javier; González-Flores, Carlos

    2016-01-01

    A new hybrid Multiphase Simulated Annealing Algorithm using Boltzmann and Bose-Einstein distributions (MPSABBE) is proposed. MPSABBE was designed for solving the Protein Folding Problem (PFP) instances. This new approach has four phases: (i) Multiquenching Phase (MQP), (ii) Boltzmann Annealing Phase (BAP), (iii) Bose-Einstein Annealing Phase (BEAP), and (iv) Dynamical Equilibrium Phase (DEP). BAP and BEAP are simulated annealing searching procedures based on Boltzmann and Bose-Einstein distributions, respectively. DEP is also a simulated annealing search procedure, which is applied at the final temperature of the fourth phase, which can be seen as a second Bose-Einstein phase. MQP is a search process that ranges from extremely high to high temperatures, applying a very fast cooling process, and is not very restrictive to accept new solutions. However, BAP and BEAP range from high to low and from low to very low temperatures, respectively. They are more restrictive for accepting new solutions. DEP uses a particular heuristic to detect the stochastic equilibrium by applying a least squares method during its execution. MPSABBE parameters are tuned with an analytical method, which considers the maximal and minimal deterioration of problem instances. MPSABBE was tested with several instances of PFP, showing that the use of both distributions is better than using only the Boltzmann distribution on the classical SA. PMID:27413369

  10. Diversity-Oriented Synthetic Strategies Applied to Cancer Chemical Biology and Drug Discovery

    Directory of Open Access Journals (Sweden)

    Ian Collins

    2014-10-01

    Full Text Available How can diversity-oriented strategies for chemical synthesis provide chemical tools to help shape our understanding of complex cancer pathways and progress anti-cancer drug discovery efforts? This review (surveying the literature from 2003 to the present considers the applications of diversity-oriented synthesis (DOS, biology-oriented synthesis (BIOS and associated strategies to cancer biology and drug discovery, summarising the syntheses of novel and often highly complex scaffolds from pluripotent or synthetically versatile building blocks. We highlight the role of diversity-oriented synthetic strategies in producing new chemical tools to interrogate cancer biology pathways through the assembly of relevant libraries and their application to phenotypic and biochemical screens. The use of diversity-oriented strategies to explore structure-activity relationships in more advanced drug discovery projects is discussed. We show how considering appropriate and variable focus in library design has provided a spectrum of DOS approaches relevant at all stages in anti-cancer drug discovery.

  11. Agent-based Models in Synthetic Biology: Tools for Simulation and Prospects

    Directory of Open Access Journals (Sweden)

    E.V.Krishnamurthy

    2012-03-01

    Full Text Available We describe a multiset of agents based modeling and simulation paradigm for synthetic biology. The multiset of agents –based programming paradigm, can be interpreted as the outcome arising out of deterministic, nondeterministic or stochastic interaction among elements in a multiset object space, that includes the environment. These interactions are like chemical reactions and the evolution of the multiset can emulate the system biological functions. Since the reaction rules are inherently parallel, any number of actions can be performed cooperatively or competitively among the subsets of elements, so that the elements evolve toward equilibrium or emergent state. Practical realization of this paradigm for system biological simulation is achieved through the concept of transactional style programming with agents, as well as soft computing (neural- network principles. Also we briefly describe currently available tools for agent-based-modeling, simulation and animation.

  12. BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations

    OpenAIRE

    Ghaffarizadeh, Ahmadreza; Friedman, Samuel H.; Macklin, Paul

    2015-01-01

    Motivation: Computational models of multicellular systems require solving systems of PDEs for release, uptake, decay and diffusion of multiple substrates in 3D, particularly when incorporating the impact of drugs, growth substrates and signaling factors on cell receptors and subcellular systems biology. Results: We introduce BioFVM, a diffusive transport solver tailored to biological problems. BioFVM can simulate release and uptake of many substrates by cell and bulk sources, diffusion and de...

  13. River basin soil-vegetation condition assessment applying mathematic simulation methods

    Science.gov (United States)

    Mishchenko, Natalia; Trifonova, Tatiana; Shirkin, Leonid

    2013-04-01

    Meticulous attention paid nowadays to the problem of vegetation cover productivity changes is connected also to climate global transformation. At the same time ecosystems anthropogenic transformation, basically connected to the changes of land use structure and human impact on soil fertility, is developing to a great extent independently from climatic processes and can seriously influence vegetation cover productivity not only at the local and regional levels but also globally. Analysis results of land use structure and soil cover condition influence on river basin ecosystems productive potential is presented in the research. The analysis is carried out applying integrated characteristics of ecosystems functioning, space images processing results and mathematic simulation methods. The possibility of making permanent functional simulator defining connection between macroparameters of "phytocenosis-soil" system condition on the basis of basin approach is shown. Ecosystems of river catchment basins of various degrees located in European part of Russia were chosen as research objects. For the integrated assessment of ecosystems soil and vegetation conditions the following characteristics have been applied: 1. Soil-productional potential, characterizing the ability of natural and natural-anthropogenic ecosystem in certain soil-bioclimatic conditions for long term reproduction. This indicator allows for specific phytomass characteristics and ecosystem produce, humus content in soil and bioclimatic parameters. 2. Normalized difference vegetation index (NDVI) has been applied as an efficient, remotely defined, monitoring indicator characterizing spatio-temporal unsteadiness of soil-productional potential. To design mathematic simulator functional simulation methods and principles on the basis of regression, correlation and factor analysis have been applied in the research. Coefficients values defining in the designed static model of phytoproductivity distribution has been

  14. Simulation Techniques and Prosthetic Approach Towards Biologically Efficient Artificial Sense Organs- An Overview

    CERN Document Server

    Neogi, Biswarup; Mukherjee, Soumyajit; Das, Achintya; Tibarewala, D N

    2011-01-01

    An overview of the applications of control theory to prosthetic sense organs including the senses of vision, taste and odor is being presented in this paper. Simulation aspect nowadays has been the centre of research in the field of prosthesis. There have been various successful applications of prosthetic organs, in case of natural biological organs dis-functioning patients. Simulation aspects and control modeling are indispensible for knowing system performance, and to generate an original approach of artificial organs. This overview focuses mainly on control techniques, by far a theoretical overview and fusion of artificial sense organs trying to mimic the efficacies of biologically active sensory organs. Keywords: virtual reality, prosthetic vision, artificial

  15. Applying Intelligent Computing Techniques to Modeling Biological Networks from Expression Data

    Institute of Scientific and Technical Information of China (English)

    Wei-Po Lee; Kung-Cheng Yang

    2008-01-01

    Constructing biological networks is one of the most important issues in system sbiology. However, constructing a network from data manually takes a considerable large amount of time, therefore an automated procedure is advocated. To automate the procedure of network construction, in this work we use two intelligent computing techniques, genetic programming and neural computation, to infer two kinds of network models that use continuous variables. To verify the presented approaches, experiments have been conducted and the preliminary results show that both approaches can be used to infer networks successfully.

  16. A comparison of quantitative reconstruction techniques for PIXE-tomography analysis applied to biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Beasley, D.G., E-mail: dgbeasley@ctn.ist.utl.pt [IST/C2TN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Alves, L.C. [IST/C2TN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Barberet, Ph.; Bourret, S.; Devès, G.; Gordillo, N.; Michelet, C. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Le Trequesser, Q. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB, UPR9048) CNRS, Université de Bordeaux, 87 avenue du Dr. A. Schweitzer, Pessac F-33608 (France); Marques, A.C. [IST/IPFN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Seznec, H. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Silva, R.C. da [IST/IPFN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal)

    2014-07-15

    The tomographic reconstruction of biological specimens requires robust algorithms, able to deal with low density contrast and low element concentrations. At the IST/ITN microprobe facility new GPU-accelerated reconstruction software, JPIXET, has been developed, which can significantly increase the speed of quantitative reconstruction of Proton Induced X-ray Emission Tomography (PIXE-T) data. It has a user-friendly graphical user interface for pre-processing, data analysis and reconstruction of PIXE-T and Scanning Transmission Ion Microscopy Tomography (STIM-T). The reconstruction of PIXE-T data is performed using either an algorithm based on a GPU-accelerated version of the Maximum Likelihood Expectation Maximisation (MLEM) method or a GPU-accelerated version of the Discrete Image Space Reconstruction Algorithm (DISRA) (Sakellariou (2001) [2]). The original DISRA, its accelerated version, and the MLEM algorithm, were compared for the reconstruction of a biological sample of Caenorhabditis elegans – a small worm. This sample was analysed at the microbeam line of the AIFIRA facility of CENBG, Bordeaux. A qualitative PIXE-T reconstruction was obtained using the CENBG software package TomoRebuild (Habchi et al. (2013) [6]). The effects of pre-processing and experimental conditions on the elemental concentrations are discussed.

  17. A comparison of quantitative reconstruction techniques for PIXE-tomography analysis applied to biological samples

    International Nuclear Information System (INIS)

    The tomographic reconstruction of biological specimens requires robust algorithms, able to deal with low density contrast and low element concentrations. At the IST/ITN microprobe facility new GPU-accelerated reconstruction software, JPIXET, has been developed, which can significantly increase the speed of quantitative reconstruction of Proton Induced X-ray Emission Tomography (PIXE-T) data. It has a user-friendly graphical user interface for pre-processing, data analysis and reconstruction of PIXE-T and Scanning Transmission Ion Microscopy Tomography (STIM-T). The reconstruction of PIXE-T data is performed using either an algorithm based on a GPU-accelerated version of the Maximum Likelihood Expectation Maximisation (MLEM) method or a GPU-accelerated version of the Discrete Image Space Reconstruction Algorithm (DISRA) (Sakellariou (2001) [2]). The original DISRA, its accelerated version, and the MLEM algorithm, were compared for the reconstruction of a biological sample of Caenorhabditis elegans – a small worm. This sample was analysed at the microbeam line of the AIFIRA facility of CENBG, Bordeaux. A qualitative PIXE-T reconstruction was obtained using the CENBG software package TomoRebuild (Habchi et al. (2013) [6]). The effects of pre-processing and experimental conditions on the elemental concentrations are discussed

  18. Biologic therapies in the metastatic colorectal cancer treatment continuum--applying current evidence to clinical practice.

    Science.gov (United States)

    Peeters, Marc; Price, Timothy

    2012-08-01

    More therapeutic options are now available than ever before for patients with metastatic colorectal cancer (mCRC) and, as such, treatment decisions have become more complex. A multidisciplinary approach is, therefore, required to effectively manage these patients. In the past few years, many trials have reported on the value of combining biological agents, such as those targeting vascular endothelial growth factor A and epidermal growth factor receptors, with chemotherapy. However, despite the plethora of information now available, the optimal treatment strategy for patients with mCRC remains unclear. Indeed, the propensity of investigators to conduct clinical trials utilising a variety of chemotherapy backbones combined with the increased complexity of retrospectively incorporating analyses of genetic mutation status (e.g. KRAS and BRAF) have led to conflicting results for seemingly similar endpoints, particularly overall survival. As a result, guidelines that have been developed, whilst having some similarities, have distinct differences in terms of suggested therapeutic combinations. Therefore, here, we review and distil the currently available data reported from phase III trials of biologic agents in the first-, second- and third-line mCRC settings. PMID:21899955

  19. Amplification without instability: applying fluid dynamical insights in chemistry and biology

    International Nuclear Information System (INIS)

    While amplification of small perturbations often arises from instability, transient amplification is possible locally even in asymptotically stable systems. That is, knowledge of a system's stability properties can mislead one's intuition for its transient behaviors. This insight, which has an interesting history in fluid dynamics, has more recently been rediscovered in ecology. Surprisingly, many nonlinear fluid dynamical and ecological systems share linear features associated with transient amplification of noise. This paper aims to establish that these features are widespread in many other disciplines concerned with noisy systems, especially chemistry, cell biology and molecular biology. Here, using classic nonlinear systems and the graphical language of network science, we explore how the noise amplification problem can be reframed in terms of activatory and inhibitory interactions between dynamical variables. The interaction patterns considered here are found in a great variety of systems, ranging from autocatalytic reactions and activator–inhibitor systems to influential models of nerve conduction, glycolysis, cell signaling and circadian rhythms. (paper)

  20. On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations.

    Science.gov (United States)

    Feller, S E; Pastor, R W

    1996-01-01

    As sketched in Fig. 1, a current molecular dynamics computer simulation of a lipid bilayer fails to capture significant features of the macroscopic system, including long wavelength undulations. Such fluctuations are intrinsically connected to the value of the macroscopic (or thermodynamic) surface tension (cf. Eqs. 1 and 9; for a related treatment, see Brochard et al., 1975, 1976). Consequently, the surface tension that might be evaluated in an MD simulation should not be expected to equal the surface tension obtained from macroscopic measurements. Put another way, the largest of the three simulations presented here contained over 16,000 atoms and required substantial computer time to complete, but modeled a system of only 36 lipids per side. From this perspective it is not surprising that the system is not at the thermodynamic limit. An important practical consequence of this effect is that simulations with fluctuating area should be carried out with a nonzero applied surface tension (gamma 0 of Fig. 2) even when the macroscopic tension is zero, or close to zero. Computer simulations at fixed surface area, which can explicitly determine pressure anisotropy at the molecular level, should ultimately lend insight into the value of gamma 0, including its dependence on lipid composition and other membrane components. As we have noted and will describe further in separate publications (Feller et al., 1996; Feller et al., manuscript in preparation), surface tensions obtained from simulations can be distorted by inadequate initial conditions and convergence, and are sensitive to potential energy functions, force truncation methods, and system size; it is not difficult, in fact, to tune terms in the potential energy function so as to yield surface tensions close to zero. This is why parameters should be tested extensively on simpler systems, for example, monolayers. The estimates of gamma 0 that we have presented here should be regarded as qualitative, and primarily

  1. Numerical simulation and experimental validation of the microindentation test applied to bulk elastoplastic materials

    International Nuclear Information System (INIS)

    The main objective of this work is to compare numerically simulated load–indentation depth curves together with deformation and stress fields underneath a sharp indenter for a set of mystical materials. Firstly, a numerical simulation and experimental validation of the microindentation test applied to three different bulk elastoplastic materials (copper, stainless steel and pure aluminium) using two indenters (Berkovich and spherical) are presented. The simulation of these microindentation tests is carried out using the finite element large strain elastoplastic and contact models. The corresponding results are particularly aimed at addressing the following aspects: the influence of the indenter geometry on both the load–indentation depth curve and range of plastic strains involved in the test, the comparison of the 3D results for the sharp indenter with those of the 2D approximation, the capabilities of the modelling through experimental validation of the numerical predictions and, in addition, an assessment of the indentation size effect. Secondly, the numerical results of Berkovich indentation applied to a set of mystical materials are exhaustively discussed. Although it is effectively shown that these mystical materials exhibit indistinguishable load–penetration depth curves during the loading phase, an important aspect that has not been previously addressed is that some clear differences in their responses are obtained for the unloading stage. Finally, the deformation and stress contours at the maximum indentation force and after unloading are particularly analysed. (paper)

  2. Biological dosimetry applied to treatment with 131 radio-iodine in thyroid cancers

    International Nuclear Information System (INIS)

    This study had 2 objectives: Firstly to compare the number of unstable chromosomal anomalies (dicentrics, rings and fragments) obtained by the method of conventional cytogenetics with the number of translocations revealed by in situ hybridization (FISH) and secondly to estimate the mean whole body dose after treatment with 3.7 GBq (100 mCi) of 131I. The estimated mean total body dose is 2 to 4 times higher than that based on MIRD calculations (0.13 Gy). In fact, MIRD calculations were derived from individuals with normal thyroid function and normal metabolic activity. Thyroid cancer patients are hypothyroid at the time of 131I administration. The hypothyroid status decreases the renal clearance of radioiodine and thus increases the whole body dose which can explain the discrepancy between the MIRD estimation and the values found by biological dosimetry. (author)

  3. Bridging the gap between basic and applied biology: towards preclinical translation

    OpenAIRE

    Cagan, Ross L; Justice, Monica J.; George F. Tidmarsh

    2013-01-01

    Summary To better translate basic research findings into the clinic, we are moving away from the traditional one-gene–one-phenotype model towards the discovery of complex mechanisms. In this Editorial, the new Editor-in-Chief and Senior Editors of Disease Models & Mechanisms (DMM) discuss the role that the journal will play in this transition. DMM will continue to provide a platform for studies that bridge basic and applied science, and, by demanding the rigorous assessment of animal model...

  4. Biological and intelligent manufacturing: human life-skills applied to technological development

    OpenAIRE

    Claudia Nelcy Jiménez Hernández; Óscar Fernando Castellanos Domínguez; Luz Alexandra Montoya Restrepo

    2010-01-01

    Highly competitive settings, characterised by development being promoting by the predominance of knowledge, means that mul- tidisciplinary approaches must be adopted for dealing with specific problems. Indeed, techniques and tools have been created by imitating human beings’ behaviour and applying them to productive and technological contexts to increase efficiency and enable a quick response. This paper deals with this topic and presents the results of scientometric- and technological su...

  5. Massively parallel conjugate heat transfer methods relying on large eddy simulation applied to an aeronautical combustor

    International Nuclear Information System (INIS)

    Optimizing gas turbines is a complex multi-physical and multi-component problem that has long been based on expensive experiments. Today, computer simulation can reduce design process costs and is acknowledged as a promising path for optimization. However, performing such computations using high-fidelity methods such as a large eddy simulation (LES) on gas turbines is challenging. Nevertheless, such simulations become accessible for specific components of gas turbines. These stand-alone simulations face a new challenge: to improve the quality of the results, new physics must be introduced. Therefore, an efficient massively parallel coupling methodology is investigated. The flow solver modeling relies on the LES code AVBP which has already been ported on massively parallel architectures. The conduction solver is based on the same data structure and thus shares its scalability. Accurately coupling these solvers while maintaining their scalability is challenging and is the actual objective of this work. To obtain such goals, a methodology is proposed and different key issues to code the coupling are addressed: convergence, stability, parallel geometry mapping, transfers and interpolation. This methodology is then applied to a real burner configuration, hence demonstrating the possibilities and limitations of the solution. (paper)

  6. Virtual Transgenics: Using a Molecular Biology Simulation to Impact Student Academic Achievement and Attitudes

    Science.gov (United States)

    Shegog, Ross; Lazarus, Melanie M.; Murray, Nancy G.; Diamond, Pamela M.; Sessions, Nathalie; Zsigmond, Eva

    2012-01-01

    The transgenic mouse model is useful for studying the causes and potential cures for human genetic diseases. Exposing high school biology students to laboratory experience in developing transgenic animal models is logistically prohibitive. Computer-based simulation, however, offers this potential in addition to advantages of fidelity and reach.…

  7. Bridging the gap between basic and applied biology: towards preclinical translation

    Directory of Open Access Journals (Sweden)

    Ross L. Cagan

    2013-05-01

    To better translate basic research findings into the clinic, we are moving away from the traditional one-gene–one-phenotype model towards the discovery of complex mechanisms. In this Editorial, the new Editor-in-Chief and Senior Editors of Disease Models & Mechanisms (DMM discuss the role that the journal will play in this transition. DMM will continue to provide a platform for studies that bridge basic and applied science, and, by demanding the rigorous assessment of animal models of disease, will help drive the establishment of robust standards of preclinical testing for drug development.

  8. Bridging the gap between basic and applied biology: towards preclinical translation.

    Science.gov (United States)

    Cagan, Ross L; Justice, Monica J; Tidmarsh, George F

    2013-05-01

    To better translate basic research findings into the clinic, we are moving away from the traditional one-gene-one-phenotype model towards the discovery of complex mechanisms. In this Editorial, the new Editor-in-Chief and Senior Editors of Disease Models & Mechanisms (DMM) discuss the role that the journal will play in this transition. DMM will continue to provide a platform for studies that bridge basic and applied science, and, by demanding the rigorous assessment of animal models of disease, will help drive the establishment of robust standards of preclinical testing for drug development. PMID:23616075

  9. Numerical simulation and experimental verification of silicone oil flow over magnetic fluid under applied magnetic field

    Institute of Scientific and Technical Information of China (English)

    Ruoyu; Hong; Zhiqiang; Ren; Shizhong; Zhang; Jianmin; Ding; Hongzhong; Li

    2007-01-01

    Two-layer flow of magnetic fluid and non-magnetic silicone oil was simulated numerically. The continuity equation, momentum equations,kinematic equation, and magnetic potential equation were solved in two-dimensional Cartesian coordinate. PLIC (piecewise linear integration calculation) VOF (volume of fluid) scheme was employed to track the free interface. Surface tension was treated via a continuous surface force(CSF) model that ensures robustness and accuracy. The influences of applied magnetic field, inlet velocity profile, initial surface disturbance of interface and surface tension were analyzed. The computed interface shapes at different conditions were compared with experimental observation.

  10. Simulated Annealing Approach Applied to the Energy Resource Management Considering Demand Response for Electric Vehicles

    DEFF Research Database (Denmark)

    Sousa, Tiago; Vale, Zita; Morais, Hugo

    2013-01-01

    The aggregation and management of Distributed Energy Resources (DERs) by an Virtual Power Players (VPP) is an important task in a smart grid context. The Energy Resource Management (ERM) of theses DERs can become a hard and complex optimization problem. The large integration of several DERs...... Simulated Annealing (SA) approach to determine the ERM considering an intensive use of DERs, mainly EVs. In this paper, the possibility to apply Demand Response (DR) programs to the EVs is considered. Moreover, a trip reduce DR program is implemented. The SA methodology is tested on a 32-bus distribution...

  11. Simulation of narrow-band longitudinal noise applied to J-PARC main ring

    International Nuclear Information System (INIS)

    In MR extraction studies in the beginning of 2010, the application of narrow band longitudinal noise to the MR-beam at 30 GeV in flat-top to increase the duty factor of the extracted spill was tested. The longitudinal spectrum with noise became wider than expected from the bandwidth of the band-limited noise. Here we show longitudinal beam simulations, using the same digital noise that was applied to the beam, to understand the measured spectra. This also allows to estimate, which would be good combinations of harmonic number, bandwidth and amplitude of the noise to obtain a desired beam shaping. (author)

  12. Simulations of modal active control applied to the self-sustained oscillations of the clarinet

    OpenAIRE

    Meurisse, Thibaut; MAMOU-MANI, Adrien; Causse, René; Chomette, Baptiste; SHARP, David

    2014-01-01

    This paper reports a new approach to modifying the sound produced by a wind instrument. The approach is based on modal active control, which enables adjustment of the damping and the frequencies of the different resonances of a system. A self-sustained oscillating wind instrument can be modeled as an excitation source coupled to a resonator via a non-linear coupling. The aim of this study is to present simulations of modal active control applied to a modeled self-sustained oscillating wind in...

  13. Applying fluid dynamics simulations to improve processing and remediation of nuclear waste - 59172

    International Nuclear Information System (INIS)

    Transport and processing of nuclear waste for treatment and storage can involve unique and complex thermal and fluid dynamic conditions that pose potential for safety risk and/or design uncertainty and also are likely to be subjected to more precise performance requirements than in other industries. From an engineering analysis perspective, certainty of outcome is essential. Advanced robust methods for engineering analysis and simulation of critical processes can help reduce risk of design uncertainty and help mitigate or reduce the amount of expensive full-scale demonstration testing. This paper will discuss experience gained in applying computational fluid dynamics models to key processes for mixing, transporting, and thermal treatment of nuclear waste as part of designing a massive vitrification process plant that will convert high and low level nuclear waste into glass for permanent storage. Examples from industrial scale simulations will be presented. The computational models have shown promise in replicating several complex physical processes such as solid-liquid flows in suspension, blending of slurries, and cooling of materials at extremely high temperature. Knowledge gained from applying simulation has provided detailed insight into determining the most critical aspects of these complex processes that can ultimately be used to help guide the optimum design of waste handling equipment based on credible calculations while ensuring risk of design uncertainty is minimized. The WTP Project is faced with complex technical challenges that must have solutions that enable the successful operation of the plant for its 30+ year operating life. The Project chose to reduce those risks by employing an experienced team that applied CFD in a disciplined manner and adhered to an established guideline with the following benefits: - Gained an improvement in accuracy of predictions for complex physical situations; - Gained an improvement of the quality of experimental

  14. Simulated annealing applied to two-dimensional low-beta reduced magnetohydrodynamics

    International Nuclear Information System (INIS)

    The simulated annealing (SA) method is applied to two-dimensional (2D) low-beta reduced magnetohydrodynamics (R-MHD). We have successfully obtained stationary states of the system numerically by the SA method with Casimir invariants preserved. Since the 2D low-beta R-MHD has two fields, the relaxation process becomes complex compared to a single field system such as 2D Euler flow. The obtained stationary state can have fine structure. We have found that the fine structure appears because the relaxation processes are different between kinetic energy and magnetic energy

  15. A SIMULATION OF THE PENICILLIN G PRODUCTION BIOPROCESS APPLYING NEURAL NETWORKS

    Directory of Open Access Journals (Sweden)

    A.J.G. da Cruz

    1997-12-01

    Full Text Available The production of penicillin G by Penicillium chrysogenum IFO 8644 was simulated employing a feedforward neural network with three layers. The neural network training procedure used an algorithm combining two procedures: random search and backpropagation. The results of this approach were very promising, and it was observed that the neural network was able to accurately describe the nonlinear behavior of the process. Besides, the results showed that this technique can be successfully applied to control process algorithms due to its long processing time and its flexibility in the incorporation of new data

  16. Power-feedwater temperature operating domain for Sbwr applying Monte Carlo simulation

    Energy Technology Data Exchange (ETDEWEB)

    Aguilar M, L. A.; Quezada G, S.; Espinosa M, E. G.; Vazquez R, A.; Varela H, J. R.; Cazares R, R. I.; Espinosa P, G., E-mail: sequega@gmail.com [Universidad Autonoma Metropolitana, Unidad Iztapalapa, San Rafael Atlixco No. 186, Col. Vicentina, 09340 Mexico D. F. (Mexico)

    2014-10-15

    In this work the analyses of the feedwater temperature effects on reactor power in a simplified boiling water reactor (Sbwr) applying a methodology based on Monte Carlo simulation is presented. The Monte Carlo methodology was applied systematically to establish operating domain, due that the Sbwr are not yet in operation, the analysis of the nuclear and thermal-hydraulic processes must rely on numerical modeling, with the purpose of developing or confirming the design basis and qualifying the existing or new computer codes to enable reliable analyses. The results show that the reactor power is inversely proportional to the temperature of the feedwater, reactor power changes at 8% when the feed water temperature changes in 8%. (Author)

  17. Power-feedwater temperature operating domain for Sbwr applying Monte Carlo simulation

    International Nuclear Information System (INIS)

    In this work the analyses of the feedwater temperature effects on reactor power in a simplified boiling water reactor (Sbwr) applying a methodology based on Monte Carlo simulation is presented. The Monte Carlo methodology was applied systematically to establish operating domain, due that the Sbwr are not yet in operation, the analysis of the nuclear and thermal-hydraulic processes must rely on numerical modeling, with the purpose of developing or confirming the design basis and qualifying the existing or new computer codes to enable reliable analyses. The results show that the reactor power is inversely proportional to the temperature of the feedwater, reactor power changes at 8% when the feed water temperature changes in 8%. (Author)

  18. Applying insights from biofilm biology to drug development - can a new approach be developed?

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas; Ciofu, Oana; Molin, Søren;

    2013-01-01

    Most of the research on bacterial pathogenesis has focused on acute infections, but much less is known about the pathogenesis of infections caused by bacteria that grow as aggregates in biofilms. These infections tend to be chronic as they resist innate and adaptive immune defence mechanisms as w...... pathology, and discuss how a deep insight into the physical and biological characteristics of biofilms can inform therapeutic strategies and molecular targets for the development of anti-biofilm drugs.......Most of the research on bacterial pathogenesis has focused on acute infections, but much less is known about the pathogenesis of infections caused by bacteria that grow as aggregates in biofilms. These infections tend to be chronic as they resist innate and adaptive immune defence mechanisms as...... well as antibiotics, and the treatment of biofilm infections presents a considerable unmet clinical need. To date, there are no drugs that specifically target bacteria in biofilms; however, several approaches are in early-stage development. Here, we review current insights into biofilm physiology and...

  19. Enrichment and immobilization of sulfide removal microbiota applied for environmental biological remediation of aquaculture area.

    Science.gov (United States)

    Zhao, Yang-Guo; Zheng, Yu; Tian, Weijun; Bai, Jie; Feng, Gong; Guo, Liang; Gao, Mengchun

    2016-07-01

    To remove sulfide in the deteriorating aquaculture sediment and water, sulfide-oxidizing microbiota was enriched from Jiaozhou Bay, China, by using sulfide-rich medium. Composition and structure of microbial communities in the enrichments were investigated by 16S rDNA molecular biotechniques. Results showed that microbial community structure continuously shifted and the abundance of sulfate reducing bacteria, i.e., Desulfobacterium, Desulfococcus and Desulfobacca apparently declined. Several halophile genera, Vibrio, Marinobacter, Pseudomonas, Prochlorococcus, Pediococcus and Thiobacillus predominated finally in the microbiota. The enriched microbiota was capable of removing a maximum of 1000 mg/L sulfide within 12 h with 10% inoculum at pH 7.0, 20-30 °C. After immobilized, the microbiota presented excellent resistance to impact and could completely remove 600 mg/L sulfide in 12 h. Moreover, the immobilized microbiota recovered well even recycled for five times. In conclusion, the immobilized sulfide-removing microbiota showed a quite promising application for biological restoring of sulfide-rich aquaculture environment. PMID:27105167

  20. StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes.

    Directory of Open Access Journals (Sweden)

    Timo R Maarleveld

    Full Text Available Single-cell and single-molecule measurements indicate the importance of stochastic phenomena in cell biology. Stochasticity creates spontaneous differences in the copy numbers of key macromolecules and the timing of reaction events between genetically-identical cells. Mathematical models are indispensable for the study of phenotypic stochasticity in cellular decision-making and cell survival. There is a demand for versatile, stochastic modeling environments with extensive, preprogrammed statistics functions and plotting capabilities that hide the mathematics from the novice users and offers low-level programming access to the experienced user. Here we present StochPy (Stochastic modeling in Python, which is a flexible software tool for stochastic simulation in cell biology. It provides various stochastic simulation algorithms, SBML support, analyses of the probability distributions of molecule copy numbers and event waiting times, analyses of stochastic time series, and a range of additional statistical functions and plotting facilities for stochastic simulations. We illustrate the functionality of StochPy with stochastic models of gene expression, cell division, and single-molecule enzyme kinetics. StochPy has been successfully tested against the SBML stochastic test suite, passing all tests. StochPy is a comprehensive software package for stochastic simulation of the molecular control networks of living cells. It allows novice and experienced users to study stochastic phenomena in cell biology. The integration with other Python software makes StochPy both a user-friendly and easily extendible simulation tool.

  1. Uncertainty analysis in comparative NAA applied to geological and biological matrices

    International Nuclear Information System (INIS)

    Comparative nuclear activation analysis is a multielemental primary analytical technique that may be used in a rather broad spectrum of matrices with minimal-to-none sample preprocessing. Although the total activation of a chemical element in a sample depends on a rather large set of parameters, when the sample is irradiated together with a well-known comparator, most of these parameters are crossed out and the concentration of that element can be determined simply by using the activities and masses of the comparator and the sample, the concentration of this chemical element in the sample, the half-life of the formed radionuclide and the time between counting the sample and the comparator. This simplification greatly reduces not only the calculations required, but also the uncertainty associated with the measurement; nevertheless, a cautious analysis must be carried out in order to make sure all relevant uncertainties are properly treated, so that the final result can be as representative of the measurement as possible. In this work, this analysis was performed for geological matrices, where concentrations of the interest nuclides are rather high, but so is the density and average atomic number of the sample, as well as for a biological matrix, in order to allow for a comparison. The results show that the largest part of the uncertainty comes from the activity measurements and from the concentration of the comparator, and that while the influence of time-related terms in the final uncertainty can be safely neglected, the uncertainty in the masses may be relevant under specific circumstances. (author)

  2. A simulation method for determining the optical response of highly complex photonic structures of biological origin

    CERN Document Server

    Dolinko, Andrés E

    2013-01-01

    We present a method based on a time domain simulation of wave propagation that allows studying the optical response of a broad range of dielectric photonic structures. This method is particularly suitable for dealing with complex biological structures. One of the main features of the proposed approach is the simple and intuitive way of defining the setup and the photonic structure to be simulated, which can be done by feeding the simulation with a digital image of the structure. We also develop a set of techniques to process the behavior of the evolving waves within the simulation. These techniques include a direction filter, that permits decoupling of waves travelling simultaneously in different directions, a dynamic differential absorber, to cancel the waves reflected at the edges of the simulation space, a multi-frequency excitation scheme based on a filter that allows decoupling waves of different wavelengths travelling simultaneously, and a near-to-far-field approach to evaluate the resulting wavefield o...

  3. A data integration approach for cell cycle analysis oriented to model simulation in systems biology

    Directory of Open Access Journals (Sweden)

    Mosca Ettore

    2007-08-01

    Full Text Available Abstract Background The cell cycle is one of the biological processes most frequently investigated in systems biology studies and it involves the knowledge of a large number of genes and networks of protein interactions. A deep knowledge of the molecular aspect of this biological process can contribute to making cancer research more accurate and innovative. In this context the mathematical modelling of the cell cycle has a relevant role to quantify the behaviour of each component of the systems. The mathematical modelling of a biological process such as the cell cycle allows a systemic description that helps to highlight some features such as emergent properties which could be hidden when the analysis is performed only from a reductionism point of view. Moreover, in modelling complex systems, a complete annotation of all the components is equally important to understand the interaction mechanism inside the network: for this reason data integration of the model components has high relevance in systems biology studies. Description In this work, we present a resource, the Cell Cycle Database, intended to support systems biology analysis on the Cell Cycle process, based on two organisms, yeast and mammalian. The database integrates information about genes and proteins involved in the cell cycle process, stores complete models of the interaction networks and allows the mathematical simulation over time of the quantitative behaviour of each component. To accomplish this task, we developed, a web interface for browsing information related to cell cycle genes, proteins and mathematical models. In this framework, we have implemented a pipeline which allows users to deal with the mathematical part of the models, in order to solve, using different variables, the ordinary differential equation systems that describe the biological process. Conclusion This integrated system is freely available in order to support systems biology research on the cell cycle and

  4. Using Macrocystis pyrifera (L. C. Agardh from southern Chile as a source of applied biological compounds

    Directory of Open Access Journals (Sweden)

    Andrés Mansilla

    2011-04-01

    Full Text Available The exploitation of seaweeds in Chile has been carried out for more than 60 years. More recently, seaweeds have been used for the production of alginate, agar and carrageenan, agricultural fertilizers and industrial aquaculture (feed for abalone and sea urchins, increasing the added value of this natural resource. In the Magellan Region (56ºS, the giant kelp Macrocystis pyrifera (L. C. Agardh presents the most extensive kelp forest, reaching a biomass of approximately 12 kg.m-2. Recent studies have shown potential benefits from adding M. pyrifera- derived flour to salmonid feed. Research is currently underway to evaluate the useof brown algae-derived products for marine aquaculture feed of Oncorhynchus mykiss in tanks. There was no apparent adverse effect on the evaluated parameters that can be attributed to the incorporation of M. pyrifera meal in the diets fed to salmonids. Even when the control diet had numerically the best performance in zootechnical terms, the analysis of variance of all parameters evaluated showed no significant differences with regard to diets containing M. pyrifera meal. These results demonstrated that seaweed meal has important benefits for animal health and nutrition that could be applied or tested in other marine organisms of commercial importance.

  5. Applying computer-based simulation to energy auditing: A case study

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Y. [Department of Construction Management, College of Engineering and Computing, Engineering Centre, Florida International University, Miami, FL (United States)

    2006-07-01

    Through a case study, this research explores an approach, which uses computer simulation technology, to evaluate different energy conservation alternatives and to assist facility managers to select reliable and feasible solutions. The subject facility is located in the Southeast region of the United States. One of the major challenges and operation goals of the General Services Administration, who manages the facility, is for that facility to achieve the Energy Star designation. However, due to the complexity of the facility, the requirements from building occupants, as well as other difficulties, finding a path for optimizing the operation of the facility in order to achieve the Energy Star designation is not always easy. This project uses eQuest, a simulation software tool, to create a 'virtual environment', in which the operations of the HVAC (heating ventilation air-conditioning) system and the lighting of the facility are studied. Subsequently, recommendations initially made by experts through traditional energy audit approaches are evaluated in the 'virtual environment' in order to determine the best solution to achieve the goal of the facility managers. This paper discusses major aspects of the project, including the challenges, the values and the limitations of applying computer simulation techniques in such a facility with complicated structural, occupancy and operation features. (author)

  6. Applying computer-based simulation to energy auditing: a case study

    Energy Technology Data Exchange (ETDEWEB)

    Yimin Zhu [Florida International University, Miami, FL (United States). Dept. of Construction Management

    2006-05-15

    Through a case study, this research explores an approach, which uses computer simulation technology, to evaluate different energy conservation alternatives and to assist facility managers to select reliable and feasible solutions. The subject facility is located in the Southeast region of the United States. One of the major challenges and operation goals of the General Services Administration, who manages the facility, is for that facility to achieve the Energy Star designation. However, due to the complexity of the facility, the requirements from building occupants, as well as other difficulties, finding a path for optimizing the operation of the facility in order to achieve the Energy Star designation is not always easy. This project uses eQuest, a simulation software tool, to create a ''virtual environment'', in which the operations of the HVAC (heating ventilation air-conditioning) system and the lighting of the facility are studied. Subsequently, recommendations initially made by experts through traditional energy audit approaches are evaluated in the ''virtual environment'' in order to determine the best solution to achieve the goal of the facility managers. This paper discusses major aspects of the project, including the challenges, the values and the limitations of applying computer simulation techniques in such a facility with complicated structural, occupancy and operation features. (author)

  7. Applying Monte Carlo Simulation to Launch Vehicle Design and Requirements Analysis

    Science.gov (United States)

    Hanson, J. M.; Beard, B. B.

    2010-01-01

    This Technical Publication (TP) is meant to address a number of topics related to the application of Monte Carlo simulation to launch vehicle design and requirements analysis. Although the focus is on a launch vehicle application, the methods may be applied to other complex systems as well. The TP is organized so that all the important topics are covered in the main text, and detailed derivations are in the appendices. The TP first introduces Monte Carlo simulation and the major topics to be discussed, including discussion of the input distributions for Monte Carlo runs, testing the simulation, how many runs are necessary for verification of requirements, what to do if results are desired for events that happen only rarely, and postprocessing, including analyzing any failed runs, examples of useful output products, and statistical information for generating desired results from the output data. Topics in the appendices include some tables for requirements verification, derivation of the number of runs required and generation of output probabilistic data with consumer risk included, derivation of launch vehicle models to include possible variations of assembled vehicles, minimization of a consumable to achieve a two-dimensional statistical result, recontact probability during staging, ensuring duplicated Monte Carlo random variations, and importance sampling.

  8. A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in R. sphaeroides

    Directory of Open Access Journals (Sweden)

    Hamadeh Abdullah

    2009-10-01

    Full Text Available Abstract Background Developing methods for understanding the connectivity of signalling pathways is a major challenge in biological research. For this purpose, mathematical models are routinely developed based on experimental observations, which also allow the prediction of the system behaviour under different experimental conditions. Often, however, the same experimental data can be represented by several competing network models. Results In this paper, we developed a novel mathematical model/experiment design cycle to help determine the probable network connectivity by iteratively invalidating models corresponding to competing signalling pathways. To do this, we systematically design experiments in silico that discriminate best between models of the competing signalling pathways. The method determines the inputs and parameter perturbations that will differentiate best between model outputs, corresponding to what can be measured/observed experimentally. We applied our method to the unknown connectivities in the chemotaxis pathway of the bacterium Rhodobacter sphaeroides. We first developed several models of R. sphaeroides chemotaxis corresponding to different signalling networks, all of which are biologically plausible. Parameters in these models were fitted so that they all represented wild type data equally well. The models were then compared to current mutant data and some were invalidated. To discriminate between the remaining models we used ideas from control systems theory to determine efficiently in silico an input profile that would result in the biggest difference in model outputs. However, when we applied this input to the models, we found it to be insufficient for discrimination in silico. Thus, to achieve better discrimination, we determined the best change in initial conditions (total protein concentrations as well as the best change in the input profile. The designed experiments were then performed on live cells and the resulting

  9. Stochastic simulation of biological reactions, and its applications for studying actin polymerization

    International Nuclear Information System (INIS)

    Molecular events in biological cells occur in local subregions, where the molecules tend to be small in number. The cytoskeleton, which is important for both the structural changes of cells and their functions, is also a countable entity because of its long fibrous shape. To simulate the local environment using a computer, stochastic simulations should be run. We herein report a new method of stochastic simulation based on random walk and reaction by the collision of all molecules. The microscopic reaction rate Pr is calculated from the macroscopic rate constant k. The formula involves only local parameters embedded for each molecule. The results of the stochastic simulations of simple second-order, polymerization, Michaelis–Menten-type and other reactions agreed quite well with those of deterministic simulations when the number of molecules was sufficiently large. An analysis of the theory indicated a relationship between variance and the number of molecules in the system, and results of multiple stochastic simulation runs confirmed this relationship. We simulated Ca2+ dynamics in a cell by inward flow from a point on the cell surface and the polymerization of G-actin forming F-actin. Our results showed that this theory and method can be used to simulate spatially inhomogeneous events

  10. Simulating Nationwide Pandemics: Applying the Multi-scale Epidemiologic Simulation and Analysis System to Human Infectious Diseases

    Energy Technology Data Exchange (ETDEWEB)

    Dombroski, M; Melius, C; Edmunds, T; Banks, L E; Bates, T; Wheeler, R

    2008-09-24

    This study uses the Multi-scale Epidemiologic Simulation and Analysis (MESA) system developed for foreign animal diseases to assess consequences of nationwide human infectious disease outbreaks. A literature review identified the state of the art in both small-scale regional models and large-scale nationwide models and characterized key aspects of a nationwide epidemiological model. The MESA system offers computational advantages over existing epidemiological models and enables a broader array of stochastic analyses of model runs to be conducted because of those computational advantages. However, it has only been demonstrated on foreign animal diseases. This paper applied the MESA modeling methodology to human epidemiology. The methodology divided 2000 US Census data at the census tract level into school-bound children, work-bound workers, elderly, and stay at home individuals. The model simulated mixing among these groups by incorporating schools, workplaces, households, and long-distance travel via airports. A baseline scenario with fixed input parameters was run for a nationwide influenza outbreak using relatively simple social distancing countermeasures. Analysis from the baseline scenario showed one of three possible results: (1) the outbreak burned itself out before it had a chance to spread regionally, (2) the outbreak spread regionally and lasted a relatively long time, although constrained geography enabled it to eventually be contained without affecting a disproportionately large number of people, or (3) the outbreak spread through air travel and lasted a long time with unconstrained geography, becoming a nationwide pandemic. These results are consistent with empirical influenza outbreak data. The results showed that simply scaling up a regional small-scale model is unlikely to account for all the complex variables and their interactions involved in a nationwide outbreak. There are several limitations of the methodology that should be explored in future

  11. Simulated weightlessness alters biological characteristics of human breast cancer cell line MCF-7

    Science.gov (United States)

    Qian, Airong; Zhang, Wei; Xie, Li; Weng, Yuanyuan; Yang, Pengfei; Wang, Zhe; Hu, Lifang; Xu, Huiyun; Tian, Zongcheng; Shang, Peng

    The aim of this study is to investigate the effects of the clinostat-simulated microgravity on MCF-7 cells (a breast cancer cell line) biological characteristics. MCF-7 cells were incubated for 24 h in an incubator and then rotated in a clinostat as a model of simulated microgravity for 24, 48 and 72 h, respectively. The effects of the clinostat-simulated microgravity on MCF-7 cells proliferation, invasion, migration, gelatinase production, adhesion, cell cycle, apoptosis and vinculin expression were detected. The results showed that the clinostat-simulated microgravity affected breast cancer cell invasion, migration, adhesion, cell cycle, cell apoptosis and vinculin expression. These results may explore a new field of vision to study tumor metastasis in future.

  12. System Identification Applied to Dynamic CFD Simulation and Wind Tunnel Data

    Science.gov (United States)

    Murphy, Patrick C.; Klein, Vladislav; Frink, Neal T.; Vicroy, Dan D.

    2011-01-01

    Demanding aerodynamic modeling requirements for military and civilian aircraft have provided impetus for researchers to improve computational and experimental techniques. Model validation is a key component for these research endeavors so this study is an initial effort to extend conventional time history comparisons by comparing model parameter estimates and their standard errors using system identification methods. An aerodynamic model of an aircraft performing one-degree-of-freedom roll oscillatory motion about its body axes is developed. The model includes linear aerodynamics and deficiency function parameters characterizing an unsteady effect. For estimation of unknown parameters two techniques, harmonic analysis and two-step linear regression, were applied to roll-oscillatory wind tunnel data and to computational fluid dynamics (CFD) simulated data. The model used for this study is a highly swept wing unmanned aerial combat vehicle. Differences in response prediction, parameters estimates, and standard errors are compared and discussed

  13. Mechanical biological treatment of organic fraction of MSW affected dissolved organic matter evolution in simulated landfill.

    Science.gov (United States)

    Salati, Silvia; Scaglia, Barbara; di Gregorio, Alessandra; Carrera, Alberto; Adani, Fabrizio

    2013-08-01

    The aim of this paper was to study the evolution of DOM during 1 year of observation in simulated landfill, of aerobically treated vs. untreated organic fraction of MSW. Results obtained indicated that aerobic treatment of organic fraction of MSW permitted getting good biological stability so that, successive incubation under anaerobic condition in landfill allowed biological process to continue getting a strong reduction of soluble organic matter (DOM) that showed, also, an aromatic character. Incubation of untreated waste gave similar trend, but in this case DOM decreasing was only apparent as inhibition of biological process in landfill did not allow replacing degraded/leached DOM with new material coming from hydrolysis of fresh OM. PMID:23743423

  14. Editorial: Advances in Health Education Applying E-Learning, Simulations and Distance Technologies

    Directory of Open Access Journals (Sweden)

    Andre W. Kushniruk

    2011-03-01

    Full Text Available This special issue of the KM&EL international journal is dedicated to coverage of novel advances in health professional education applying e-Learning, simulations and distance education technologies. Modern healthcare is beginning to be transformed through the emergence of new information technologies and rapid advances in health informatics. Advances such as electronic health record systems (EHRs, clinical decision support systems and other advanced information systems such as public health surveillance systems are rapidly being deployed worldwide. The education of health professionals such as medical, nursing and allied health professionals will require an improved understanding of these technologies and how they will transform their healthcare practice. However, currently there is a lack of integration of knowledge and skills related to such technology in health professional education. In this issue of the journal we present articles that describe a set of novel approaches to integrating essential health information technology into the education of health professionals, as well as the use of advanced information technologies and e-Learning approaches for improving health professional education. The approaches range from use of simulations to development of novel Web-based platforms for allowing students to interact with the technologies and healthcare practices that are rapidly changing healthcare.

  15. Examples of New Models Applied in Selected Simulation Systems with Respect to Database

    Directory of Open Access Journals (Sweden)

    Z. Ignaszak

    2013-01-01

    Full Text Available The tolerance of damage rule progressively meets the approval in the design casting parts procedures. Therefore, there were appeared thenew challenges and expectations for permanent development of process virtualization in the mechanical engineering industry.Virtualization is increasingly developed on the stage of product design and materials technologies optimization. Increasing expectations of design and process engineers regarding the practical effectiveness of applied simulation systems with new proposed up-grades modules is observed. The purpose is to obtain simulation tools allowing the most possible realistic prognosis of the casting structure, including indication, with the highest possible probability, places in the casting that are endangered with the possibility of shrinkage– and gas porosity formation. This 3D map of discontinuities and structure transformed in local mechanical characteristics are used to calculate the local stresses and safety factors. The needs of tolerance of damage and new approach to evaluate the quality of such prognosis must be defined. These problems of validation of new models/modules used to predict the shrinkage– and gas porosity including the chosen structure parameters in the example of AlSi7 alloy are discussed in the paper.

  16. Diffusion processes in biological membranes studied by molecular dynamics simulations and analytical models

    OpenAIRE

    Stachura, Slawomir,

    2014-01-01

    Various recent experimental and simulation studies show that the lateral diffusion of molecules in biological membranes exhibits anomalies, in the sense that the molecular mean square displacements increase sub-linearily instead of linearly with time. Mathematically, such diffusion processes can be modeled by generalized diffusion equations which involve an additional fractional time derivative compared to the corresponding normal counterpart. The aim of this thesis is to gain some more physi...

  17. Parameter discovery in stochastic biological models using simulated annealing and statistical model checking

    OpenAIRE

    Hussain, Faraz; Jha, Sumit K.; Jha, Susmit; Langmead, Christopher J.

    2014-01-01

    Stochastic models are increasingly used to study the behaviour of biochemical systems. While the structure of such models is often readily available from first principles, unknown quantitative features of the model are incorporated into the model as parameters. Algorithmic discovery of parameter values from experimentally observed facts remains a challenge for the computational systems biology community. We present a new parameter discovery algorithm that uses simulated annealing, sequential ...

  18. Stability and biological activity of wild blueberry (Vaccinium angustifolium) polyphenols during simulated in vitro gastrointestinal digestion.

    Science.gov (United States)

    Correa-Betanzo, J; Allen-Vercoe, E; McDonald, J; Schroeter, K; Corredig, M; Paliyath, G

    2014-12-15

    Wild blueberries are rich in polyphenols and have several potential health benefits. Understanding the factors that affect the bioaccessibility and bioavailability of polyphenols is important for evaluating their biological significance and efficacy as functional food ingredients. Since the bioavailability of polyphenols such as anthocyanins is generally low, it has been proposed that metabolites resulting during colonic fermentation may be the components that exert health benefits. In this study, an in vitro gastrointestinal model comprising sequential chemostat fermentation steps that simulate digestive conditions in the stomach, small intestine and colon was used to investigate the breakdown of blueberry polyphenols. The catabolic products were isolated and biological effects tested using a normal human colonic epithelial cell line (CRL 1790) and a human colorectal cancer cell line (HT 29). The results showed a high stability of total polyphenols and anthocyanins during simulated gastric digestion step with approximately 93% and 99% of recovery, respectively. Intestinal digestion decreased polyphenol- and anthocyanin- contents by 49% and 15%, respectively, by comparison to the non-digested samples. During chemostat fermentation that simulates colonic digestion, the complex polyphenol mixture was degraded to a limited number of phenolic compounds such as syringic, cinnamic, caffeic, and protocatechuic acids. Only acetylated anthocyanins were detected in low amounts after chemostat fermentation. The catabolites showed lowered antioxidant activity and cell growth inhibition potential. Results suggest that colonic fermentation may alter the biological activity of blueberry polyphenols. PMID:25038707

  19. Applying Monte Carlo Simulation to Launch Vehicle Design and Requirements Verification

    Science.gov (United States)

    Hanson, John M.; Beard, Bernard B.

    2010-01-01

    This paper is focused on applying Monte Carlo simulation to probabilistic launch vehicle design and requirements verification. The approaches developed in this paper can be applied to other complex design efforts as well. Typically the verification must show that requirement "x" is met for at least "y" % of cases, with, say, 10% consumer risk or 90% confidence. Two particular aspects of making these runs for requirements verification will be explored in this paper. First, there are several types of uncertainties that should be handled in different ways, depending on when they become known (or not). The paper describes how to handle different types of uncertainties and how to develop vehicle models that can be used to examine their characteristics. This includes items that are not known exactly during the design phase but that will be known for each assembled vehicle (can be used to determine the payload capability and overall behavior of that vehicle), other items that become known before or on flight day (can be used for flight day trajectory design and go/no go decision), and items that remain unknown on flight day. Second, this paper explains a method (order statistics) for determining whether certain probabilistic requirements are met or not and enables the user to determine how many Monte Carlo samples are required. Order statistics is not new, but may not be known in general to the GN&C community. The methods also apply to determining the design values of parameters of interest in driving the vehicle design. The paper briefly discusses when it is desirable to fit a distribution to the experimental Monte Carlo results rather than using order statistics.

  20. Biases in simulation of the rice phenology models when applied in warmer climates

    Science.gov (United States)

    Zhang, T.; Li, T.; Yang, X.; Simelton, E.

    2015-12-01

    The current model inter-comparison studies highlight the difference in projections between crop models when they are applied to warmer climates, but these studies do not provide results on how the accuracy of the models would change in these projections because the adequate observations under largely diverse growing season temperature (GST) are often unavailable. Here, we investigate the potential changes in the accuracy of rice phenology models when these models were applied to a significantly warmer climate. We collected phenology data from 775 trials with 19 cultivars in 5 Asian countries (China, India, Philippines, Bangladesh and Thailand). Each cultivar encompasses the phenology observations under diverse GST regimes. For a given rice cultivar in different trials, the GST difference reaches 2.2 to 8.2°C, which allows us to calibrate the models under lower GST and validate under higher GST (i.e., warmer climates). Four common phenology models representing major algorithms on simulations of rice phenology, and three model calibration experiments were conducted. The results suggest that the bilinear and beta models resulted in gradually increasing phenology bias (Figure) and double yield bias per percent increase in phenology bias, whereas the growing-degree-day (GDD) and exponential models maintained a comparatively constant bias when applied in warmer climates (Figure). Moreover, the bias of phenology estimated by the bilinear and beta models did not reduce with increase in GST when all data were used to calibrate models. These suggest that variations in phenology bias are primarily attributed to intrinsic properties of the respective phenology model rather than on the calibration dataset. Therefore we conclude that using the GDD and exponential models has more chances of predicting rice phenology correctly and thus, production under warmer climates, and result in effective agricultural strategic adaptation to and mitigation of climate change.

  1. Validity of the Cauchy-Born rule applied to discrete cellular-scale models of biological tissues

    KAUST Repository

    Davit, Y.

    2013-04-30

    The development of new models of biological tissues that consider cells in a discrete manner is becoming increasingly popular as an alternative to continuum methods based on partial differential equations, although formal relationships between the discrete and continuum frameworks remain to be established. For crystal mechanics, the discrete-to-continuum bridge is often made by assuming that local atom displacements can be mapped homogeneously from the mesoscale deformation gradient, an assumption known as the Cauchy-Born rule (CBR). Although the CBR does not hold exactly for noncrystalline materials, it may still be used as a first-order approximation for analytic calculations of effective stresses or strain energies. In this work, our goal is to investigate numerically the applicability of the CBR to two-dimensional cellular-scale models by assessing the mechanical behavior of model biological tissues, including crystalline (honeycomb) and noncrystalline reference states. The numerical procedure involves applying an affine deformation to the boundary cells and computing the quasistatic position of internal cells. The position of internal cells is then compared with the prediction of the CBR and an average deviation is calculated in the strain domain. For center-based cell models, we show that the CBR holds exactly when the deformation gradient is relatively small and the reference stress-free configuration is defined by a honeycomb lattice. We show further that the CBR may be used approximately when the reference state is perturbed from the honeycomb configuration. By contrast, for vertex-based cell models, a similar analysis reveals that the CBR does not provide a good representation of the tissue mechanics, even when the reference configuration is defined by a honeycomb lattice. The paper concludes with a discussion of the implications of these results for concurrent discrete and continuous modeling, adaptation of atom-to-continuum techniques to biological

  2. Functionalized gold nanoparticle supported sensory mechanisms applied in detection of chemical and biological threat agents: A review

    International Nuclear Information System (INIS)

    Highlights: ► Smart sensors are needed for detection of chemical and biological threat agents. ► Smart sensors detect analytes with rapid speed, high sensitivity and selectivity. ► Functionalized gold nanoparticles (GNPs) can potentially smart sense threat agents. ► Functionalized GNPs support multiple analytical methods for sensing threat agents. ► Threat agents of all types can be detected using functionalized GNPs. - Abstract: There is a great necessity for development of novel sensory concepts supportive of smart sensing capabilities in defense and homeland security applications for detection of chemical and biological threat agents. A smart sensor is a detection device that can exhibit important features such as speed, sensitivity, selectivity, portability, and more importantly, simplicity in identifying a target analyte. Emerging nanomaterial based sensors, particularly those developed by utilizing functionalized gold nanoparticles (GNPs) as a sensing component potentially offer many desirable features needed for threat agent detection. The sensitiveness of physical properties expressed by GNPs, e.g. color, surface plasmon resonance, electrical conductivity and binding affinity are significantly enhanced when they are subjected to functionalization with an appropriate metal, organic or biomolecular functional groups. This sensitive nature of functionalized GNPs can be potentially exploited in the design of threat agent detection devices with smart sensing capabilities. In the presence of a target analyte (i.e., a chemical or biological threat agent) a change proportional to concentration of the analyte is observed, which can be measured either by colorimetric, fluorimetric, electrochemical or spectroscopic means. This article provides a review of how functionally modified gold colloids are applied in the detection of a broad range of threat agents, including radioactive substances, explosive compounds, chemical warfare agents, biotoxins, and

  3. Functionalized gold nanoparticle supported sensory mechanisms applied in detection of chemical and biological threat agents: A review

    Energy Technology Data Exchange (ETDEWEB)

    Upadhyayula, Venkata K.K., E-mail: Upadhyayula.Venkata@epa.gov [Oak Ridge Institute of Science and Education (ORISE), MC-100-44, PO Box 117, Oak Ridge, TN 37831 (United States)

    2012-02-17

    Highlights: Black-Right-Pointing-Pointer Smart sensors are needed for detection of chemical and biological threat agents. Black-Right-Pointing-Pointer Smart sensors detect analytes with rapid speed, high sensitivity and selectivity. Black-Right-Pointing-Pointer Functionalized gold nanoparticles (GNPs) can potentially smart sense threat agents. Black-Right-Pointing-Pointer Functionalized GNPs support multiple analytical methods for sensing threat agents. Black-Right-Pointing-Pointer Threat agents of all types can be detected using functionalized GNPs. - Abstract: There is a great necessity for development of novel sensory concepts supportive of smart sensing capabilities in defense and homeland security applications for detection of chemical and biological threat agents. A smart sensor is a detection device that can exhibit important features such as speed, sensitivity, selectivity, portability, and more importantly, simplicity in identifying a target analyte. Emerging nanomaterial based sensors, particularly those developed by utilizing functionalized gold nanoparticles (GNPs) as a sensing component potentially offer many desirable features needed for threat agent detection. The sensitiveness of physical properties expressed by GNPs, e.g. color, surface plasmon resonance, electrical conductivity and binding affinity are significantly enhanced when they are subjected to functionalization with an appropriate metal, organic or biomolecular functional groups. This sensitive nature of functionalized GNPs can be potentially exploited in the design of threat agent detection devices with smart sensing capabilities. In the presence of a target analyte (i.e., a chemical or biological threat agent) a change proportional to concentration of the analyte is observed, which can be measured either by colorimetric, fluorimetric, electrochemical or spectroscopic means. This article provides a review of how functionally modified gold colloids are applied in the detection of a broad

  4. Respirometry applied for biological nitrogen removal process; Aplicacion de la respirometria al tratamiento biologico para la eliminacion del nitrogeno

    Energy Technology Data Exchange (ETDEWEB)

    Serrano, E.

    2004-07-01

    In waste water treatment plants, the Biological Nitrogen Removal (BNR) has acquired a fundamental importance. The BNR processes are Nitrification ( aerobic) and Denitrification (anoxic). Since both processes are carried on living microorganisms, a lack of their bioactivity information might cause serious confusion about their control criteria and following up purposes. For this reason, the Re spirometry applied to those processes has reached an important role by getting an essential information in a timely manner through respiration rate measurements in static and dynamic modes and applications such as AUR (Ammonium Uptake Rate), Nitrification Capacity. RBCOD (Readily Biodegradable COD) as well as AUR related to SRT (Sludge age), RBCOD related to NUR (Specific Nitrate Uptake Rate) and others. By other side in this article we have introduced a not very well known applications related to denitrification, about the methanol acclimatization and generated bioactivity. (Author) 6 refs.

  5. Functionalized gold nanoparticle supported sensory mechanisms applied in detection of chemical and biological threat agents: a review.

    Science.gov (United States)

    Upadhyayula, Venkata K K

    2012-02-17

    There is a great necessity for development of novel sensory concepts supportive of smart sensing capabilities in defense and homeland security applications for detection of chemical and biological threat agents. A smart sensor is a detection device that can exhibit important features such as speed, sensitivity, selectivity, portability, and more importantly, simplicity in identifying a target analyte. Emerging nanomaterial based sensors, particularly those developed by utilizing functionalized gold nanoparticles (GNPs) as a sensing component potentially offer many desirable features needed for threat agent detection. The sensitiveness of physical properties expressed by GNPs, e.g. color, surface plasmon resonance, electrical conductivity and binding affinity are significantly enhanced when they are subjected to functionalization with an appropriate metal, organic or biomolecular functional groups. This sensitive nature of functionalized GNPs can be potentially exploited in the design of threat agent detection devices with smart sensing capabilities. In the presence of a target analyte (i.e., a chemical or biological threat agent) a change proportional to concentration of the analyte is observed, which can be measured either by colorimetric, fluorimetric, electrochemical or spectroscopic means. This article provides a review of how functionally modified gold colloids are applied in the detection of a broad range of threat agents, including radioactive substances, explosive compounds, chemical warfare agents, biotoxins, and biothreat pathogens through any of the four sensory means mentioned previously. PMID:22244163

  6. Computational simulation of a new system modelling ions electromigration through biological membranes

    Science.gov (United States)

    2013-01-01

    Background The interest in cell membrane has grown drastically for their important role as controllers of biological functions in health and illness. In fact most important physiological processes are intimately related to the transport ability of the membrane, such as cell adhesion, cell signaling and immune defense. Furthermore, ion migration is connected with life-threatening pathologies such as metastases and atherosclerosis. Consequently, a large amount of research is consecrated to this topic. To better understand cell membranes, more accurate models of ionic flux are required and also their computational simulations. Results This paper is presenting the numerical simulation of a more general system modelling ion migration through biological membranes. The model includes both the effects of biochemical reaction between ions and fixed charges. The model is a nonlinear coupled system. In the first we describe the mathematical model. To realize the numerical simulation of our model, we proceed by a finite element discretisation and then by choosing an appropriate resolution algorithm to the nonlinearities. Conclusions We give numerical simulations obtained for different popular models of enzymatic reaction which were compared to those obtained in literature on systems of ordinary differential equations. The results obtained show a complete agreement between the two modellings. Furthermore, various numerical experiments are presented to confirm the accuracy, efficiency and stability of the proposed method. In particular, we show that the scheme is unconditionally stable and second-order accurate in space. PMID:24010551

  7. Report on the meeting of the working groups on neutron scattering applied to studying condensed matter, and neutron scattering and complementary methods applied in chemistry and biology

    International Nuclear Information System (INIS)

    The present volume consists of 55 lectures. The subjects are: 1) Elastic neutron diffraction, 2) Lattice dynamics, 3) Diffusion, 4) Polymers, 5) Biology, 6) Methods and tools, 7) Magnetism. For distinct papers see hints under relevant topics. (BHO)

  8. Design and simulation of high-voltage Applied-B ion diodes for inertial confinement fusion

    International Nuclear Information System (INIS)

    We present the design of the high-voltage (30 MV) Applied-B ion diode that is now being tested on the PBFA-II accelerator at Sandia National Laboratories. This diode design is the first application of a new set of numerical design tools that have been developed over the past several years. Furthermore, this design represents significant departures from previous designs due to much higher voltage and the use of a nonprotonic ion, Li+. The higher voltage increases the magnetic field strength required to insulate the diode from 1 to 2 T of previous diodes to 3--7 T. This represents a very large increase in the magnetic field energy and the magnetic forces exerted on the field-coil structures. Our new design incorporates changes in the field-coil locations to significantly reduce the field energy and the forces on the field-coil structures. The use of nonprotonic ions introduces a new complication in that these ions will be stripped when they penetrate material, i.e., the gas cell membrane. The importance of current neutralization, charge-exchange reactions, and the conservation of canonical angular momentum are discussed in the context of designing light ion diodes suitable as drivers for inertial confinement fusion. We have simulated the performance of this diode design using the electromagnetic particle-in-cell code, magIc. We find that the most sensitive point in the power flow is the transition from the self-magnetically insulated transmission line to the applied field region of the diode

  9. California Simulation of Evapotranspiration of Applied Water and Agricultural Energy Use in California

    Institute of Scientific and Technical Information of China (English)

    Morteza N Orang; Richard L Snyder; Shu Geng; Quinn J Hart; Sara Sarreshteh; Matthias Falk; Dylan Beaudette; Scott Hayes; Simon Eching

    2013-01-01

    The California Simulation of Evapotranspiration of Applied Water (Cal-SIMETAW) model is a new tool developed by the California Department of Water Resources and the University of California, Davis to perform daily soil water balance and determine crop evapotranspiration (ETc), evapotranspiration of applied water (ETaw), and applied water (AW) for use in California water resources planning. ETaw is a seasonal estimate of the water needed to irrigate a crop assuming 100%irrigation efficiency. The model accounts for soils, crop coefficients, rooting depths, seepage, etc. that influence crop water balance. It provides spatial soil and climate information and it uses historical crop and land-use category information to provide seasonal water balance estimates by combinations of detailed analysis unit and county (DAU/County) over California. The result is a large data base of ETc and ETaw that will be used to update information in the new California Water Plan (CWP). The application uses the daily climate data, i.e., maximum (Tx) and minimum (Tn) temperature and precipitation (Pcp), which were derived from monthly USDA-NRCS PRISM data (PRISM Group 2011) and daily US National Climate Data Center (NCDC) climate station data to cover California on a 4 km×4 km change grid spacing. The application uses daily weather data to determine reference evapotranspiration (ETo), using the Hargreaves-Samani (HS) equation (Hargreaves and Samani 1982, 1985). Because the HS equation is based on temperature only, ETo from the HS equation were compared with CIMIS ETo at the same locations using available CIMIS data to determine correction factors to estimate CIMIS ETo from the HS ETo to account for spatial climate differences. Cal-SIMETAW also employs near real-time reference evapotranspiration (ETo) information from Spatial CIMIS, which is a model that combines weather station data and remote sensing to provide a grid of ETo information. A second database containing the available soil

  10. Simulation study of magnetically insulated power coupling to the applied-B ion diode

    International Nuclear Information System (INIS)

    Power coupling to the applied-B ion diode from magnetically insulated transmission lines is simply described in terms of the voltage-current characteristics of both the diode and the transmission line. The accelerator load line intersects the composite characteristic at the operating voltage and current. Using 2-D PIC simulation, the authors have investigated how modification of either the ion diode or the magnetically insulated transmission line characteristic influences power coupling. Plasma prefill can modify the ion diode characteristic; a partially opened POS in the transmission line upstream of the ion diode is a possible cause of modification of the magnetically insulated transmission line characteristic. It can be useful to consider these two aspects of power coupling separately, but they are actually not independent. A good parameter to characterize the situation is the flow impedance, given by V/(Ia2 Ic2)1/2. V is the line voltage; Ia and Ic are the conduction currents flowing through the anode and cathode, respectively. The flow impedance covers a range from one half the vacuum impedance, for saturated magnetically insulated flow, to just below the vacuum impedance, for highly unsaturated flow. As the term ''flow impedance'' implies, low flow impedance coincides with greater electron flow while high flow impedance coincides with less electron flow. The flow impedance is sensitive to both the transmission line and the diode impedance. They show how the two are related, using the flow impedance as a parameter

  11. SIGMA: A Knowledge-Based Simulation Tool Applied to Ecosystem Modeling

    Science.gov (United States)

    Dungan, Jennifer L.; Keller, Richard; Lawless, James G. (Technical Monitor)

    1994-01-01

    The need for better technology to facilitate building, sharing and reusing models is generally recognized within the ecosystem modeling community. The Scientists' Intelligent Graphical Modelling Assistant (SIGMA) creates an environment for model building, sharing and reuse which provides an alternative to more conventional approaches which too often yield poorly documented, awkwardly structured model code. The SIGMA interface presents the user a list of model quantities which can be selected for computation. Equations to calculate the model quantities may be chosen from an existing library of ecosystem modeling equations, or built using a specialized equation editor. Inputs for dim equations may be supplied by data or by calculation from other equations. Each variable and equation is expressed using ecological terminology and scientific units, and is documented with explanatory descriptions and optional literature citations. Automatic scientific unit conversion is supported and only physically-consistent equations are accepted by the system. The system uses knowledge-based semantic conditions to decide which equations in its library make sense to apply in a given situation, and supplies these to the user for selection. "Me equations and variables are graphically represented as a flow diagram which provides a complete summary of the model. Forest-BGC, a stand-level model that simulates photosynthesis and evapo-transpiration for conifer canopies, was originally implemented in Fortran and subsequenty re-implemented using SIGMA. The SIGMA version reproduces daily results and also provides a knowledge base which greatly facilitates inspection, modification and extension of Forest-BGC.

  12. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  13. 3D printing method for freeform fabrication of optical phantoms simulating heterogeneous biological tissue

    Science.gov (United States)

    Wang, Minjie; Shen, Shuwei; Yang, Jie; Dong, Erbao; Xu, Ronald

    2014-03-01

    The performance of biomedical optical imaging devices heavily relies on appropriate calibration. However, many of existing calibration phantoms for biomedical optical devices are based on homogenous materials without considering the multi-layer heterogeneous structures observed in biological tissue. Using such a phantom for optical calibration may result in measurement bias. To overcome this problem, we propose a 3D printing method for freeform fabrication of tissue simulating phantoms with multilayer heterogeneous structure. The phantom simulates not only the morphologic characteristics of biological tissue but also absorption and scattering properties. The printing system is based on a 3D motion platform with coordinated control of the DC motors. A special jet nozzle is designed to mix base, scattering, and absorption materials at different ratios. 3D tissue structures are fabricated through layer-by-layer printing with selective deposition of phantom materials of different ingredients. Different mixed ratios of base, scattering and absorption materials have been tested in order to optimize the printing outcome. A spectrometer and a tissue spectrophotometer are used for characterizing phantom absorption and scattering properties. The goal of this project is to fabricate skin tissue simulating phantoms as a traceable standard for the calibration of biomedical optical spectral devices.

  14. A framework for stochastic simulations and visualization of biological electron-transfer dynamics

    Science.gov (United States)

    Nakano, C. Masato; Byun, Hye Suk; Ma, Heng; Wei, Tao; El-Naggar, Mohamed Y.

    2015-08-01

    Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr-Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr-Omc complex due to electron-electron interactions.

  15. Biological consequences of environmental changes related to coastal upwelling: a simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Howe, S.O.

    1979-05-01

    Two simulation models of marine ecosystem dynamics are formulated and applied to field data. The first is a time-dependent model of phytoplankton growth in nutrient-enriched batch cultures where spatial gradients of dependent variables and the effects of higher tropic level processes are not included. Rates of photosynthesis, nutrient uptake, chlorophyll synthesis and cell division for a single phytoplankton functional group are simulated as functions of photosynthetically active solar radiation, dissolved nutrient concentrations and cell quotas of carbon, nitrogen and silica. The second model combines the phytoplankton growth model with a time dependent, two-dimensional model of coastal upwelling off northwest Africa.

  16. STUDY ON SIMULATION EXPERIMENT OF EQUIVALENT MATERIAL APPLIED IN COAL MINE

    Institute of Scientific and Technical Information of China (English)

    柴敬; 苏普正; 刘晋安

    1998-01-01

    Based on simulation experiments of a number of scientific research items, the latestprogress of experiment method and test technique about equivalent material simulation areintroduced. The development of experiment technique makes analogy simulation evolve intoquantitative research about support-surrounding rock relationship from qualitative experiment.From this, large scale stereoscopic simulation experiment is developed, which has neverappeared in underground pressure research in China. The present mold specification is 3.6 m ×2,0 m×l.5 m.

  17. Applying Educational Theory to Simulation-Based Training and Assessment in Surgery.

    Science.gov (United States)

    Chauvin, Sheila W

    2015-08-01

    Considerable progress has been made regarding the range of simulator technologies and simulation formats. Similarly, results from research in human learning and behavior have facilitated the development of best practices in simulation-based training (SBT) and surgical education. Today, SBT is a common curriculum component in surgical education that can significantly complement clinical learning, performance, and patient care experiences. Beginning with important considerations for selecting appropriate forms of simulation, several relevant educational theories of learning are described. PMID:26210964

  18. Simulating the use of products: applying the nucleus paradigm to resource-integrated virtual interaction models

    NARCIS (Netherlands)

    Van der Vegte, W.F.; Horváth, I.; Rusák, Z.

    2009-01-01

    We introduce a methodology for modelling and simulating fully virtual human-artefact systems, aiming to resolve two issues in virtual prototyping: (i) integration of distinct modelling and simulation approaches, and (ii) extending the deployability of simulations towards conceptual design. We are go

  19. A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

    OpenAIRE

    ThomasEissing

    2011-01-01

    Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multi-scale by nature, project work and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform co...

  20. Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes

    Science.gov (United States)

    Pineda De Castro, Luis Felipe; Dopson, Mark

    2016-01-01

    In contrast to the majority of organisms that have cells bound by di-ester phospholipids, archaeal membranes consist of di- and tetraether phospholipids. Originating from organisms that withstand harsh conditions (e.g., low pH and a wide range of temperatures) such membranes have physical properties that make them attractive materials for biological research and biotechnological applications. We developed force-field parameters based on the widely used Generalized Amber Force Field (GAFF) to enable the study of anionic tetraether membranes of the model archaean Sulfolobus acidocaldarius by computer simulations. The simulations reveal that the physical properties of these unique membranes depend on the number of cyclopentane rings included in each lipid unit, and on the size of cations that are used to ensure charge neutrality. This suggests that the biophysical properties of Sulfolobus acidocaldarius cells depend not only on the compositions of their membranes but also on the media in which they grow. PMID:27167213

  1. Biological Membranes in Extreme Conditions: Simulations of Anionic Archaeal Tetraether Lipid Membranes.

    Directory of Open Access Journals (Sweden)

    Luis Felipe Pineda De Castro

    Full Text Available In contrast to the majority of organisms that have cells bound by di-ester phospholipids, archaeal membranes consist of di- and tetraether phospholipids. Originating from organisms that withstand harsh conditions (e.g., low pH and a wide range of temperatures such membranes have physical properties that make them attractive materials for biological research and biotechnological applications. We developed force-field parameters based on the widely used Generalized Amber Force Field (GAFF to enable the study of anionic tetraether membranes of the model archaean Sulfolobus acidocaldarius by computer simulations. The simulations reveal that the physical properties of these unique membranes depend on the number of cyclopentane rings included in each lipid unit, and on the size of cations that are used to ensure charge neutrality. This suggests that the biophysical properties of Sulfolobus acidocaldarius cells depend not only on the compositions of their membranes but also on the media in which they grow.

  2. Finite element simulation of welding based deposition process as applied to layered manufacturing: thermal model

    International Nuclear Information System (INIS)

    In Layered Manufacturing (LM), the CAD model of a part is sliced into layers using the conventional STL file format. This Layer wise data is fed into a deposition system, which then builds up the part, depositing the required material, layer by layer. The manufacturing of form-fit-function component rather then form-fit component is a major issue in Layered Manufacturing based Rapid Proto typing systems. As the deposition method, Gas Metal Arc welding (GMAW) has shown potential, for LM of metallic components, due to its inherent feature of high inter-layer and metallurgical bonding. Residual Stress induced warping is a major concern in a variety of LM processes, particularly those seeking to build parts directly without post processing steps. Welding is one of those processes where high heat input results in large thermal gradients; these thermal gradients along with the mechanical constraints cause the build up of residual stresses. In order to reduce the residual stresses and deformation, the first step is to correctly model the thermal cycle associated with the deposition process. More over important deposition parameters like re-melting depth, heat affected zone can also be predicted from the thermal model This paper presents a 3D finite element based thermal model of a novel welding based deposition process as applied to layered manufacturing. A Commercial finite element software ANSYS is coupled with a user programmed subroutine to implement the main welding features like Goldak Double Ellipsoidal Heat source, material addition, temperature dependent material properties along with the deposition features like deposition patterns and dimensions. Simulations have been carried out with various patterns and inter pass time and it has been found that different deposition patterns cause change in Remelting depth and thermal gradients. (author)

  3. Intelligent simulated annealing algorithm applied to the optimization of the main magnet for magnetic resonance imaging machine

    International Nuclear Information System (INIS)

    This work describes an alternative algorithm of Simulated Annealing applied to the design of the main magnet for a Magnetic Resonance Imaging machine. The algorithm uses a probabilistic radial base neuronal network to classify the possible solutions, before the objective function evaluation. This procedure allows reducing up to 50% the number of iterations required by simulated annealing to achieve the global maximum, when compared with the SA algorithm. The algorithm was applied to design a 0.1050 Tesla four coil resistive magnet, which produces a magnetic field 2.13 times more uniform than the solution given by SA. (author)

  4. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

    Science.gov (United States)

    Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

    2016-07-01

    This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. PMID:26766517

  5. Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.

    Science.gov (United States)

    Schulz, Roland; Lindner, Benjamin; Petridis, Loukas; Smith, Jeremy C

    2009-10-13

    A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors, other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million-atom biological systems scale well up to ∼30k cores, producing ∼30 ns/day. Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach. PMID:26631792

  6. Particle-based model to simulate the micromechanics of biological cells

    Science.gov (United States)

    van Liedekerke, P.; Tijskens, E.; Ramon, H.; Ghysels, P.; Samaey, G.; Roose, D.

    2010-06-01

    This paper is concerned with addressing how biological cells react to mechanical impulse. We propose a particle based model to numerically study the mechanical response of these cells with subcellular detail. The model focuses on a plant cell in which two important features are present: (1) the cell’s interior liquidlike phase inducing hydrodynamic phenomena, and (2) the cell wall, a viscoelastic solid membrane that encloses the protoplast. In this particle modeling framework, the cell fluid is modeled by a standard smoothed particle hydrodynamics (SPH) technique. For the viscoelastic solid phase (cell wall), a discrete element method (DEM) is proposed. The cell wall hydraulic conductivity (permeability) is built in through a constitutive relation in the SPH formulation. Simulations show that the SPH-DEM model is in reasonable agreement with compression experiments on an in vitro cell and with analytical models for the basic dynamical modes of a spherical liquid filled shell. We have performed simulations to explore more complex situations such as relaxation and impact, thereby considering two cell types: a stiff plant type and a soft animal-like type. Their particular behavior (force transmission) as a function of protoplasm and cell wall viscosity is discussed. We also show that the mechanics during and after cell failure can be modeled adequately. This methodology has large flexibility and opens possibilities to quantify problems dealing with the response of biological cells to mechanical impulses, e.g., impact, and the prediction of damage on a (sub)cellular scale.

  7. Simulation of a Congress at the Chair of Biology II in Bioengineering

    International Nuclear Information System (INIS)

    This work has been developed in the Chair of Biology II, the curricular contents of which correspond to Human Anatomy. This subject is taught in the second semester of the second year of studies in Bioengineering. Our main objective is that the students attending the course may integrate the syllabus contents of Anatomy with those of other subjects in the career. Ever since 1998 we have organized a congress named Congreso Intracatedra de BiologIa II (Intra Chair Congress on Biology II). This is the last assignment in the semester and is compulsory for regular students of the subject. It consists in simulating a scientific congress with international characteristics. The guidelines for the congress are made known to the students at the beginning of the semester. In groups of up to three members, the students must undertake a work that relates aspects of Anatomy with Bioengineering. Students are expected to investigate on diagnostic and/or therapeutic technology in order to write a paper that must be accepted in advance of the event. The presentation of the work must be made through PowerPoint. The originality of the research work done and the wide range of topics selected are surprising. Problems are tackled from the standpoints both of the various medical fields and of bioengineering despite the fact that they are just students of the second year in Bioengineering

  8. Simulation of a Congress at the Chair of Biology II in Bioengineering

    Science.gov (United States)

    Naranjo, A. V.; Reznichenco, V.; López, N.; Hernández, R.; Bajinay, S.

    2007-11-01

    This work has been developed in the Chair of Biology II, the curricular contents of which correspond to Human Anatomy. This subject is taught in the second semester of the second year of studies in Bioengineering. Our main objective is that the students attending the course may integrate the syllabus contents of Anatomy with those of other subjects in the career. Ever since 1998 we have organized a congress named Congreso Intracátedra de Biología II (Intra Chair Congress on Biology II). This is the last assignment in the semester and is compulsory for regular students of the subject. It consists in simulating a scientific congress with international characteristics. The guidelines for the congress are made known to the students at the beginning of the semester. In groups of up to three members, the students must undertake a work that relates aspects of Anatomy with Bioengineering. Students are expected to investigate on diagnostic and/or therapeutic technology in order to write a paper that must be accepted in advance of the event. The presentation of the work must be made through PowerPoint. The originality of the research work done and the wide range of topics selected are surprising. Problems are tackled from the standpoints both of the various medical fields and of bioengineering despite the fact that they are just students of the second year in Bioengineering.

  9. A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

    Science.gov (United States)

    Eissing, Thomas; Kuepfer, Lars; Becker, Corina; Block, Michael; Coboeken, Katrin; Gaub, Thomas; Goerlitz, Linus; Jaeger, Juergen; Loosen, Roland; Ludewig, Bernd; Meyer, Michaela; Niederalt, Christoph; Sevestre, Michael; Siegmund, Hans-Ulrich; Solodenko, Juri; Thelen, Kirstin; Telle, Ulrich; Weiss, Wolfgang; Wendl, Thomas; Willmann, Stefan; Lippert, Joerg

    2011-01-01

    Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multiscale by nature, project work, and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug–drug, or drug–metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach. PMID:21483730

  10. A computational systems biology software platform for multiscale modeling and simulation: Integrating whole-body physiology, disease biology, and molecular reaction networks

    Directory of Open Access Journals (Sweden)

    Thomas eEissing

    2011-02-01

    Full Text Available Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multi-scale by nature, project work and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug-drug or drug-metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach.

  11. Simulation models applied to practical learning and skill enhancement in direct and indirect ophthalmoscopy: a review

    Directory of Open Access Journals (Sweden)

    Lucas Holderegger Ricci

    2014-10-01

    Full Text Available The purpose of this review was to analyze and describe simulation methods for practical learning and training of the ophthalmoscopy exam and to organize them into specific topics relative to each principle of operation, while evaluating their preliminary results. A critical review of articles that described and evaluated simulated models for ophthalmoscopy published in the last ten years (2004-2014 was performed. One hundred articles about ophthalmology and simulation were found in national and international periodicals, but only a few discussed the examination of the posterior pole of the eye. For this study, 25 articles were considered; those articles described simulation methods, general concepts, and its actual use in ophthalmoscopy. There were many different simulation methods described, but only few articles proved their efficacy or performed a comparison between models. Review of this topic may give information for the critical analysis of the simulation devices and ideas for the development of new ones.

  12. The Umbra Simulation and Integration Framework Applied to Emergency Response Training

    Science.gov (United States)

    Hamilton, Paul Lawrence; Britain, Robert

    2010-01-01

    The Mine Emergency Response Interactive Training Simulation (MERITS) is intended to prepare personnel to manage an emergency in an underground coal mine. The creation of an effective training environment required realistic emergent behavior in response to simulation events and trainee interventions, exploratory modification of miner behavior rules, realistic physics, and incorporation of legacy code. It also required the ability to add rich media to the simulation without conflicting with normal desktop security settings. Our Umbra Simulation and Integration Framework facilitated agent-based modeling of miners and rescuers and made it possible to work with subject matter experts to quickly adjust behavior through script editing, rather than through lengthy programming and recompilation. Integration of Umbra code with the WebKit browser engine allowed the use of JavaScript-enabled local web pages for media support. This project greatly extended the capabilities of Umbra in support of training simulations and has implications for simulations that combine human behavior, physics, and rich media.

  13. Applying a Web and Simulation-Based System for Adaptive Competence Assessment of Spinal Anaesthesia

    Science.gov (United States)

    Hockemeyer, Cord; Nussbaumer, Alexander; Lövquist, Erik; Aboulafia, Annette; Breen, Dorothy; Shorten, George; Albert, Dietrich

    The authors present an approach for implementing a system for the assessment of medical competences using a haptic simulation device. Based on Competence based Knowledge Space Theory (CbKST), information on the learners’ competences is gathered from different sources (test questions, data from the simulator, and supervising experts’ assessments).

  14. 3-d Brownian dynamics simulations of the smallest units of an active biological material

    Science.gov (United States)

    Luettmer-Strathmann, Jutta; Paudyal, Nabina; Adeli Koudehi, Maral

    Motor proteins generate stress in a cytoskeletal network by walking on one strand of the network while being attached to another one. A protein walker in contact with two elements of the network may be considered the smallest unit of an active biological material. In vitro experiments, mathematical modeling and computer simulations have provided important insights into active matter on large and on very small length and time scales. However, it is still difficult to model the effects of local environment and interactions at intermediate scales. Recently, we developed a coarse-grained, three-dimensional model for a motor protein transporting cargo by walking on a substrate. In this work, we simulate a tethered motor protein pulling a substrate with elastic response. As the walker progresses, the retarding force due to the substrate tension increases until contact fails. We present simulation results for the effect of motor-protein activity on the tension in the substrate and the effect of the retarding force on the processivity of the molecular motor.

  15. Applying the DSNP modular modeling system to transient and accident simulations of lead cooled reactors

    International Nuclear Information System (INIS)

    The modeling and simulation of the Encapsulated Nuclear Heat Source (ENHS) is presented in this study. The purpose of the simulations was to evaluate the safety characteristics of the proposed modular liquid metal cooled reactor. The DSNP simulation package was modified to accept LBE (Lead Bismuth Eutectic) and lead as a reactor coolant and as heat transfer medium in the primary and secondary loops. Appropriate equations of state, heat transfer and flow correlations were also introduced to permit a full range of simulations of the ENHS and other lead and LBE cooled systems. Models of different levels of complexity were developed to study various events and their consequences. Due to the very large heat capacity of the ENHS reactor, unusually long simulation times ranging from hours up to days were needed to follow some of the transients. This in turn required modifications to various elements of the DSNP simulation system to permit these long execution times. It is concluded that the ENHS has an inherently safe response to all initiating events, and that the DSNP system is capable to simulate most of the accidents of interest to the safety evaluation of the plant. (author)

  16. Human dynamic orientation model applied to motion simulation. M.S. Thesis

    Science.gov (United States)

    Borah, J. D.

    1976-01-01

    The Ormsby model of dynamic orientation, in the form of a discrete time computer program was used to predict non-visually induced sensations during an idealized coordinated aircraft turn. To predict simulation fidelity, the Ormsby model was used to assign penalties for incorrect attitude and angular rate perceptions. It was determined that a three rotational degree of freedom simulation should remain faithful to attitude perception even at the expense of incorrect angular rate sensations. Implementing this strategy, a simulation profile for the idealized turn was designed for a Link GAT-1 trainer. A simple optokinetic display was added to improve the fidelity of roll rate sensations.

  17. A history of developing and applying simulators at Research and Development Technology Institute

    International Nuclear Information System (INIS)

    Research simulators providing for studying into the potentially dangerous modes during NPP testing, verification of new control algorithms and principles, as well as for personnel training and having higher accuracy as compared with educational simulators are discussed. The common computering system joining different computers into local network is used as the basis for research simulators of different NPPs. The computering system commumication with consoles is realized via fast-response unified data transmission system. The information-searching systems for teacher and students, the subsystem for operator action control and estimation, the database of initial and emergency states and the subsystem for operator action registration are developed

  18. How to apply importance-sampling techniques to simulations of optical systems

    OpenAIRE

    McKinstrie, C. J.; Winzer, P. J.

    2003-01-01

    This report contains a tutorial introduction to the method of importance sampling. The use of this method is illustrated for simulations of the noise-induced energy jitter of return-to-zero pulses in optical communication systems.

  19. Evaluation of alternative irrigation technologies based upon applied water and simulated yields

    OpenAIRE

    Santos, Francisco Lúcio

    1998-01-01

    Abstract Adequate estimates of yields under comparable amounts of infiltrated water of different irrigation systems are essential for evaluation and adoption of irrigation decisions. A simulation model, crop evapotranspiration and Young's criteria for subjective probability estimates from objective data were used to simulate water management regimes for pressurized and surface-irrigation systems. Historical climatic data, representative soil series and irrigation technologies for CentralAr...

  20. On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations.

    OpenAIRE

    Feller, S E; Pastor, R W

    1996-01-01

    As sketched in Fig. 1, a current molecular dynamics computer simulation of a lipid bilayer fails to capture significant features of the macroscopic system, including long wavelength undulations. Such fluctuations are intrinsically connected to the value of the macroscopic (or thermodynamic) surface tension (cf. Eqs. 1 and 9; for a related treatment, see Brochard et al., 1975, 1976). Consequently, the surface tension that might be evaluated in an MD simulation should not be expected to equal t...

  1. MONTE CARLO SIMULATION APPLIED TO ECONOMIC AND FINANCIAL ANALYSIS OF AN AGRIBUSINESS PROJECT

    OpenAIRE

    Danilo Simões; Lucas Raul Scherrer

    2014-01-01

    In practice, all management decisions involving an organization, regardless of size, have uncertainties which lead to different levels of risk. Monte Carlo simulation allows risk analysis by designing probabilistic models. From a deterministic model of economic viability indicators, commonly used for decision investment projects, it was developed a probabilistic model with Monte Carlo method simulations in order to carry out economic and financial analysis of an agroindustrial ...

  2. Development of a Procedure to Apply Detailed Chemical Kinetic Mechanisms to CFD Simulations as Post Processing

    DEFF Research Database (Denmark)

    Skjøth-Rasmussen, Martin Skov; Glarborg, Peter; Jensen, Anker;

    2003-01-01

    It is desired to make detailed chemical kinetic mechanisms applicable to the complex geometries of practical combustion devices simulated with computational fluid dynamics tools. This work presents a novel general approach to combining computational fluid dynamics and a detailed chemical kinetic...... mechanism. It involves post-processing of data extracted from computational fluid dynamics simulations. Application of this approach successfully describes combustion chemistry in a standard swirl burner, the so-called Harwell furnace. Nevertheless, it needs validation against more complex combustion models...

  3. BOAST-VHS. 3D 3-Phase Black Oil Applied Simulator

    Energy Technology Data Exchange (ETDEWEB)

    Chang, M.; Sarathi, P.; Heemstra, R.J.; Cheng, A.M.; Pautz, J.F. [National Institute for Petroleum and Energy Research, Bartlesville, OK (United States)

    1992-01-01

    BOAST-VHS is a three-dimensional, three-phase, finite-difference black oil simulator developed for use on a personal computer. It simulates isothermal, Darcy flow in three dimensions. The simulator assumes that the reservoir fluids can be described by three fluid phases (oil, gas, and water) of constant composition whose properties are functions of pressure only. BOAST-VHS can simulate oil and/or gas recovery by fluid expansion, displacement, gravity drainage, and imbibition mechanisms. BOAST-VHS is recommended as a cost-effective reservoir simulation tool for the study of such problems as primary depletion, pressure maintenance (by water and/or gas injection) and basic secondary recovery operations (such as waterflooding) in a black oil reservoir using slanted or horizontal wells, in addition to conventional vertical wells. The well model in BOAST-VHS permits specification of rate or pressure constraints on well performance. The model also allows the user to add or recomplete wells during the period represented by the simulation. BOAST-VHS has flexible initialization capabilities, a bubble point tracking scheme, an automatic time-step control method, a zero transmissibility option (inactive grid blocks), and a material balance check on solution stability.

  4. Polarizable Mean-Field Model of Water for Biological Simulations with Amber and Charmm force fields

    CERN Document Server

    Leontyev, Igor

    2015-01-01

    Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified since then. The reason is that the non-polarizable force fields that are mostly used to describe proteins and other biological molecules are incompatible with more sophisticated modern polarizable models of water. The issue is electronic polarizability: in liquid state, in protein, and in vacuum the water molecule is polarized differently, and therefore has different properties; thus the only way to describe all these different media with the same model is to use a polarizable water model. However, to be compatible with the force field of the rest of the system, e.g. a protein, the latter should be polarizable as well. Here we describe a novel model of water that is in effect polarizable, and yet compatible with the standard non-polarizable force fields such as AMBER, CHARMM,...

  5. How Can We Improve Problem Solving in Undergraduate Biology? Applying Lessons from 30 Years of Physics Education Research

    OpenAIRE

    Hoskinson, A.-M.; Caballero, M.D. (M.D.); Knight, J.K.

    2013-01-01

    If students are to successfully grapple with authentic, complex biological problems as scientists and citizens, they need practice solving such problems during their undergraduate years. Physics education researchers have investigated student problem solving for the last three decades. Although physics and biology problems differ in structure and content, the instructional purposes align closely: explaining patterns and processes in the natural world and making predictions about physical and ...

  6. Preconditioner methods applied to simulations of two-phase flow in porous media

    International Nuclear Information System (INIS)

    Simulations of two-phase flow in porous media require solving a set of linear equations which can be both large and sparse, and doing so repeatedly, to obtain local pressures under conditions of viscous flow. A variation of the incomplete cholesky preconditioned conjugate gradient solver has recently been developed for this purpose, and is presented here. It is found to be both stable and efficient. The variation consists of determining the sparsity structure of the preconditioner from a neighborhood search. Also, if the viscosities of the two fluids are different, the preconditioner should be updated during the course of the simulation. How often this should be done depends on the magnitude of the viscosity ratio, on the cost of updating the preconditioner and on how quickly the simulation configuration changes. To address this, a dynamic preconditioner update criterion is formulated.

  7. Simulating Dynamic Stall Effects for Vertical Axis Wind Turbines Applying a Double Multiple Streamtube Model

    Directory of Open Access Journals (Sweden)

    Eduard Dyachuk

    2015-02-01

    Full Text Available The complex unsteady aerodynamics of vertical axis wind turbines (VAWT poses significant challenges to the simulation tools. Dynamic stall is one of the phenomena associated with the unsteady conditions for VAWTs, and it is in the focus of the study. Two dynamic stall models are compared: the widely-used Gormont model and a Leishman–Beddoes-type model. The models are included in a double multiple streamtube model. The effects of flow curvature and flow expansion are also considered. The model results are assessed against the measured data on a Darrieus turbine with curved blades. To study the dynamic stall effects, the comparison of force coefficients between the simulations and experiments is done at low tip speed ratios. Simulations show that the Leishman–Beddoes model outperforms the Gormont model for all tested conditions.

  8. ESR and NMR spectra simulation applied to molecular dynamics in anisotropic medium

    International Nuclear Information System (INIS)

    We describe two conversational programs written in APL for the purpose of ESR and NMR spectra simulations as well as relaxation times and line width calculations. These programs are particularly convenient for the studies of the molecular order and dynamics in liquid crystals. Several examples of their applications are reported

  9. MAGMAsoft simulation applied in verification of technology to produce new range of alloy steel castings

    Directory of Open Access Journals (Sweden)

    A. Gwiżdż

    2010-07-01

    Full Text Available The article presents the results of MAGMAsoft application in simulation of the pouring and solidfication of castings made fromGS20Mn5 steel, basing on some principles adopted in the starting technology. The results of simulation were disclosed in the form of 3Ddrawings, showing the technology of pouring, selected stages of solidification, and porosity in castings made by the examined technology. Using simulation results, some modifications were introduced to the pouring technology, the simulation was repeated, and the results obtained for the technology before and after the modification were compared. Based on the guidelines provided in new technology, the pattern tooling was made. The process of mould preparation was described, along with the process of steel melting and pouring. Castings made by the new technology were X-rayed and subjected to heat treatment according to the newly developed cycle. Together with the main casting, test wedges were poured. Mechanical tests and structure examinations were performed. The results of the tests and investigations were evaluated.

  10. Virtual reality applied to a full simulator of electrical sub-stations

    Energy Technology Data Exchange (ETDEWEB)

    Romero, G.; Maroto, J.; Felez, J.; Cabanellas, J.M.; Martinez, M.L.; Carretero, A. [E.T.S. de Ingenieros Industriales, Universidad Politecnica de Madrid, c/ Jose Gutierrez Abascal 2, 28006 Madrid (Spain)

    2008-03-15

    This paper presents an application designed to train electrical sub-station operators by means of a virtual reality environment. The application allows full viewing of any of the sub-stations in the power supply network. With the appropriate hardware (HMD, 3D mouse and tracking systems) it is possible to navigate into the virtual world and interact with the elements. Each of the sub-station components has been reproduced in the simulation model, including the behavior laws associated with it, so the complete functionality of the sub-station can be simulated. This module is built into a larger and more complex computer system composed of the actual sub-station control system, the Geographical Information System which defines the topology of the network, and the functional system which simulates the electrical behavior of the sub-station. The application automatically updates in the virtual environment any changes to the sub-station's design and allows access, from this environment, to information on every component. The virtual reality application has been implemented in a hardware configuration and has the same interface as that used in the control system of the real sub-station. In this way, the system developed can be integrated into a replica of the complete power supply network control system emulating a real sub-station, it being able to fully interact with the global system, and allow totally real situations to be simulated. (author)

  11. Parallel simulation of particle transport in an advection field applied to volcanic explosive eruptions

    Science.gov (United States)

    Künzli, Pierre; Tsunematsu, Kae; Albuquerque, Paul; Falcone, Jean-Luc; Chopard, Bastien; Bonadonna, Costanza

    2016-04-01

    Volcanic ash transport and dispersal models typically describe particle motion via a turbulent velocity field. Particles are advected inside this field from the moment they leave the vent of the volcano until they deposit on the ground. Several techniques exist to simulate particles in an advection field such as finite difference Eulerian, Lagrangian-puff or pure Lagrangian techniques. In this paper, we present a new flexible simulation tool called TETRAS (TEphra TRAnsport Simulator) based on a hybrid Eulerian-Lagrangian model. This scheme offers the advantages of being numerically stable with no numerical diffusion and easily parallelizable. It also allows us to output particle atmospheric concentration or ground mass load at any given time. The model is validated using the advection-diffusion analytical equation. We also obtained a good agreement with field observations of the tephra deposit associated with the 2450 BP Pululagua (Ecuador) and the 1996 Ruapehu (New Zealand) eruptions. As this kind of model can lead to computationally intensive simulations, a parallelization on a distributed memory architecture was developed. A related performance model, taking into account load imbalance, is proposed and its accuracy tested.

  12. At-Risk Students and Virtual Enterprise: Tourism and Hospitality Simulations in Applied and Academic Learning.

    Science.gov (United States)

    Borgese, Anthony

    This paper discusses Virtual Enterprise (VE), a technology-driven business simulation program in which students conceive, create, and operate enterprises that utilize Web-based and other technologies to trade products and services around the world. The study examined the effects of VE on a learning community of at-risk students, defined as those…

  13. Rupther: a simulation approach applied to a PWR vessel failure during a severe accident

    International Nuclear Information System (INIS)

    The Rupther program (Rupture Under Thermal Conditions) is a part of the international researches on severe accidents in the PWR type reactors. The aim of the program is the definition of failure simulation validated by experimental data on vessel steel 16MND5 mechanical properties. The paper presents the program and the first results. (A.L.B.)

  14. Quasistatic field simulations based on finite elements and spectral methods applied to superconducting magnets

    International Nuclear Information System (INIS)

    This thesis is concerned with the numerical simulation of electromagnetic fields in the quasi-static approximation which is applicable in many practical cases. Main emphasis is put on higher-order finite element methods. Quasi-static applications can be found, e.g., in accelerator physics in terms of the design of magnets required for beam guidance, in power engineering as well as in high-voltage engineering. Especially during the first design and optimization phase of respective devices, numerical models offer a cheap alternative to the often costly assembly of prototypes. However, large differences in the magnitude of the material parameters and the geometric dimensions as well as in the time-scales of the electromagnetic phenomena involved lead to an unacceptably long simulation time or to an inadequately large memory requirement. Under certain circumstances, the simulation itself and, in turn, the desired design improvement becomes even impossible. In the context of this thesis, two strategies aiming at the extension of the range of application for numerical simulations based on the finite element method are pursued. The first strategy consists in parallelizing existing methods such that the computation can be distributed over several computers or cores of a processor. As a consequence, it becomes feasible to simulate a larger range of devices featuring more degrees of freedom in the numerical model than before. This is illustrated for the calculation of the electromagnetic fields, in particular of the eddy-current losses, inside a superconducting dipole magnet developed at the GSI Helmholtzzentrum fuer Schwerionenforschung as a part of the FAIR project. As the second strategy to improve the efficiency of numerical simulations, a hybrid discretization scheme exploiting certain geometrical symmetries is established. Using this method, a significant reduction of the numerical effort in terms of required degrees of freedom for a given accuracy is achieved. The

  15. Analysis, Modelling, and Simulation of Droop Control with Virtual Impedance Loop Applied to Parallel UPS Systems

    DEFF Research Database (Denmark)

    Lima, Francisco Kleber A.; Branco, Carlos Gustavo C.; Guerrero, Josep M.;

    2013-01-01

    This paper explores a control strategy for parallel uninterruptible power systems (UPS). The control technique used in that work was based on the droop control method. This method is usually applied to achieve good active and reactive power sharing when communication between the inverters is diff...

  16. Adaptive Finite Elements for Monolithic Fluid-StructureInteraction on a Prolongated Domain: Applied to an Heart Valve Simulation

    OpenAIRE

    Wick, Thomas

    2011-01-01

    In this work, we apply a fluid-structure interaction method to a long axis heart valve simulation. Our method of choice is based on a monolithic coupling scheme for fluid-structure interaction, where the fluid equations are rewritten in the arbitrary Lagrangian Eulerian' framework. To prevent back-flow of waves in the structure due to its hyperbolic nature, a damped structure equation is solved on an artificial layer that prolongates the computational domain. This coupling is stable on th...

  17. Modification of PRETOR Code to Be Applied to Transport Simulation in Stellarators

    International Nuclear Information System (INIS)

    The 1.5 D transport code PRETOR, that has been previously used to simulate tokamak plasmas, has been modified to perform transport analysis in stellarator geometry. The main modifications that have been introduced in the code are related with the magnetic equilibrium and with the modelling of energy and particle transport. Therefore, PRETOR- Stellarator version has been achieved and the code is suitable to perform simulations on stellarator plasmas. As an example, PRETOR- Stellarator has been used in the transport analysis of several Heliac Flexible TJ-II shots, and the results are compared with those obtained using PROCTR code. These results are also compared with the obtained using the tokamak version of PRETOR to show the importance of the introduced changes. (Author) 18 refs

  18. Simulation of low rigidity part machining applied to thin-walled structures

    OpenAIRE

    Arnaud, Lionel; Gonzalo, Oscar; Seguy, Sébastien; Jauregi, Haritz; Peigné, Grégoire

    2011-01-01

    The aim of this study is to evaluate the modelling of machining vibrations of thin-walled aluminium work- pieces at high productivity rate. The use of numerical simulation is generally aimed at giving optimal cutting conditions for the precision and the surface finish needed. The proposed modelling includes all the ingredients needed for real productive machining of thin-walled parts. It has been tested with a specially designed machining test with high cutting engagement and taking into acco...

  19. Multiagent simulation of evolutive plate tectonics applied to the thermal evolution of the Earth

    OpenAIRE

    Combes, M. (M.); Grigné, C.; HUSSON, Laurent; Conrad, C. P.; Le Yaouanq, Sébastien; Parenthoën, M.; Tisseau, C.; Tisseau, Jacques

    2012-01-01

    International audience [1] The feedback between plate tectonics and mantle convection controls the Earth's thermal evolution via the seafloor age distribution. We therefore designed the MACMA model to simulate time-dependent plate tectonics in a 2D cylindrical geometry with evolutive plate boundaries, based on multiagent systems that express thermal and mechanical interactions. We compute plate velocities using a local force balance and use explicit parameterizations to treat tectonic proc...

  20. Monte Carlo simulation of a digital coincidence system applied to 60Co standardization

    International Nuclear Information System (INIS)

    The Laboratorio de Metrologia Nuclear (LMN) at the Instituto de Pesquisas Energeticas e Nucleares (IPEN) is developing a Digital Coincidence System (DCS), including the design of the proper acquisition electronics and analysis software. A brief discussion about the measurement methodology and the electronics operation is presented. This work is focused on the results of the designed software (the Monte Carlo simulation of 60Co decay data and the Coincidence Data Analysis), which are in good agreement with the experimental data. (author)

  1. Risk analysis and Monte Carlo simulation applied to the generation of drilling AFE estimates

    International Nuclear Information System (INIS)

    This paper presents a method for developing an authorization-for-expenditure (AFE)-generating model and illustrates the technique with a specific offshore field development case study. The model combines Monte Carlo simulation and statistical analysis of historical drilling data to generate more accurate, risked, AFE estimates. In addition to the general method, two examples of making AFE time estimates for North Sea wells with the presented techniques are given

  2. Simulation of forest growth, applied to Douglas fir stands in The Netherlands.

    OpenAIRE

    Mohren, G.M.J.

    1987-01-01

    Forest growth in relation to weather and soils is studied using a physiological simulation model. Growth potential depends on physiological characteristics of the plant species in combination with ambient weather conditions (mainly temperature and incoming radiation). For a given site, growth may be lower because of incomplete canopy closure, shortage of water and nutrients, and the occurrence of growth-disturbing factors such as pests, diseases, and damage to the plants, e.g. by windthrow or...

  3. A Fast Parallel Poisson Solver on Irregular Domains Applied to Beam Dynamic Simulations

    OpenAIRE

    Adelmann, A.; P. Arbenz; Ineichen, Y.

    2009-01-01

    We discuss the scalable parallel solution of the Poisson equation within a Particle-In-Cell (PIC) code for the simulation of electron beams in particle accelerators of irregular shape. The problem is discretized by Finite Differences. Depending on the treatment of the Dirichlet boundary the resulting system of equations is symmetric or `mildly' nonsymmetric positive definite. In all cases, the system is solved by the preconditioned conjugate gradient algorithm with smoothed aggregation (SA) b...

  4. Quantitative characterization of a dielectric barrier discharge in air applying non-calibrated spectrometer, current measurement and numerical simulation

    International Nuclear Information System (INIS)

    A non-calibrated spectrometer is used for quantitative characterization of a dielectric barrier discharge (DBD) in air wherein optical emission spectroscopy (OES) is completed by current measurement and numerical simulation. This diagnostic method is applicable when the cross-sectional area of the active plasma volume and the current density can be determined. The nitrogen emission in the spectral range of 330–406 nm is used for OES diagnostics. The electric field in the active plasma volume is determined by applying the measured spectrum, well-known Franck–Condon factors for nitrogen transitions and numerically simulated electron distribution functions. The measured electric current density is used for the determination of electron density in plasma. Using the determined plasma parameters, the dissociation rates of nitrogen and oxygen in active plasma volume are calculated, which can be used for the simulation of chemical kinetics. (paper)

  5. The element-based finite volume method applied to petroleum reservoir simulation

    Energy Technology Data Exchange (ETDEWEB)

    Cordazzo, Jonas; Maliska, Clovis R.; Silva, Antonio F.C. da; Hurtado, Fernando S.V. [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil). Dept. de Engenharia Mecanica

    2004-07-01

    In this work a numerical model for simulating petroleum reservoirs using the Element-based Finite Volume Method (EbFVM) is presented. The method employs unstructured grids using triangular and/or quadrilateral elements, such that complex reservoir geometries can be easily represented. Due to the control-volume approach, local mass conservation is enforced, permitting a direct physical interpretation of the resulting discrete equations. It is demonstrated that this method can deal with the permeability maps without averaging procedures, since this scheme assumes uniform properties inside elements, instead inside of control volumes, avoiding the need of weighting the permeability values at the control volumes interfaces. Moreover, it is easy to include the full permeability tensor in this method, which is an important issue in simulating heterogeneous and anisotropic reservoirs. Finally, a comparison among the results obtained using the scheme proposed in this work in the EbFVM framework with those obtained employing the scheme commonly used in petroleum reservoir simulation is presented. It is also shown that the scheme proposed is less susceptible to the grid orientation effect with the increasing of the mobility ratio. (author)

  6. On applied state estimation and observation theory to simulation modelling of Prespa-Ohrid Lakes system

    International Nuclear Information System (INIS)

    In the south-west of the Republic of Macedonia, on the cross boundary area with Republic of Albania and Republic of Greece, Prespa-Ohrid hydrologic region is located. To this region belong Prespa and Ohrid valleys, on the bottom of which the lakes of Prespa and Ohrid reside. Due to the fact that there is no surface hydrologic link and that they are separated by high mountain Galichica, both valleys and lakes constitute almost mutually autonomous hydrologic entities. This paper presents a study on the hydrologic cycle of Prespa Lake basin for the purpose of developing and identifying a simulation model for the long term dynamics of the water level. The actual simulation modelling technique makes use of available apriori knowledge and available recorder or observed data on phenomena involving the whole cycle from precipitation to evaporation and evapotranspiration in Prespa basin. Also, a modelling account for the functional impact due to strong interaction with Ohrid basin, is included. The resulting simulation model is a set of discrete-time state equation, derived on the grounds of the conceptual model of interconnected multiple tanks and of discrete-time observation (output) equation. The dynamic structure of Kalman filter for both linear and non-linear modelling case is derived and a discussion on applicability and further research is given. (author)

  7. Numerical simulation methods applied to injection and storage of CO2 in saline aquifers

    International Nuclear Information System (INIS)

    One of the Climate Change mitigation proposals suggested by the IPCC (Intergovernmental Panel on Climate Change) in its Synthesis Report 2007 involves the launch of applications for capturing and storing carbon dioxide, existing three different geological structures suitable for gas storage: oil and gas depleted reservoirs, useless coal layers and deep saline structures. In case of deep saline structures, the main problem to prepare a study of CO2 storage is the difficulty of obtaining geological data for some selected structure with characteristics that could be suitable for injection and gas storage. According to this situation, the solution to analyze the feasibility of a storage project in a geological structure will need numerical simulation from a 3D terrain model. Numerical methods allow the simulation of the carbon dioxide filling in saline structures from a well, used to inject gas with a particular flow. This paper presents a methodology to address the modeling and simulation process of CO2 injection into deep saline aquifers. (Author)

  8. Simulation based efficiency prediction of a Brushless DC drive applied in ventricular assist devices.

    Science.gov (United States)

    Pohlmann, André; Hameyer, Kay

    2012-01-01

    Ventricular Assist Devices (VADs) are mechanical blood pumps that support the human heart in order to maintain a sufficient perfusion of the human body and its organs. During VAD operation blood damage caused by hemolysis, thrombogenecity and denaturation has to be avoided. One key parameter causing the blood's denaturation is its temperature which must not exceed 42 °C. As a temperature rise can be directly linked to the losses occuring in the drive system, this paper introduces an efficiency prediction chain for Brushless DC (BLDC) drives which are applied in various VAD systems. The presented chain is applied to various core materials and operation ranges, providing a general overview on the loss dependencies. PMID:23367198

  9. Analysis, Modelling, and Simulation of Droop Control with Virtual Impedance Loop Applied to Parallel UPS Systems

    OpenAIRE

    Lima, Francisco Kleber A.; Branco, Carlos Gustavo C.; Josep M. Guerrero; Neto, Luis Juarez C.; Carvalho, Samuel S.; Torrico-Bascope, Rene P.

    2013-01-01

    This paper explores a control strategy for parallel uninterruptible power systems (UPS). The control technique used in that work was based on the droop control method. This method is usually applied to achieve good active and reactive power sharing when communication between the inverters is difficult due to its physical location. This paper has considered that the UPS systems there were no comunication between their controls. A detailed mathematical model about the explored system is shown i...

  10. Rapid MCNP simulation of DNA double strand break (DSB) relative biological effectiveness (RBE) for photons, neutrons, and light ions

    International Nuclear Information System (INIS)

    To account for particle interactions in the extracellular (physical) environment, information from the cell-level Monte Carlo damage simulation (MCDS) for DNA double strand break (DSB) induction has been integrated into the general purpose Monte Carlo N-particle (MCNP) radiation transport code system. The effort to integrate these models is motivated by the need for a computationally efficient model to accurately predict particle relative biological effectiveness (RBE) in cell cultures and in vivo. To illustrate the approach and highlight the impact of the larger scale physical environment (e.g. establishing charged particle equilibrium), we examined the RBE for DSB induction (RBEDSB) of x-rays, 137Cs γ-rays, neutrons and light ions relative to γ-rays from 60Co in monolayer cell cultures at various depths in water. Under normoxic conditions, we found that 137Cs γ-rays are about 1.7% more effective at creating DSB than γ-rays from 60Co (RBEDSB  =  1.017) whereas 60–250 kV x-rays are 1.1 to 1.25 times more efficient at creating DSB than 60Co. Under anoxic conditions, kV x-rays may have an RBEDSB up to 1.51 times as large as 60Co γ-rays. Fission neutrons passing through monolayer cell cultures have an RBEDSB that ranges from 2.6 to 3.0 in normoxic cells, but may be as large as 9.93 for anoxic cells. For proton pencil beams, Monte Carlo simulations suggest an RBEDSB of about 1.2 at the tip of the Bragg peak and up to 1.6 a few mm beyond the Bragg peak. Bragg peak RBEDSB increases with decreasing oxygen concentration, which may create opportunities to apply proton dose painting to help address tumor hypoxia. Modeling of the particle RBE for DSB induction across multiple physical and biological scales has the potential to aid in the interpretation of laboratory experiments and provide useful information to advance the safety and effectiveness of hadron therapy in the treatment of cancer. (paper)

  11. Rapid MCNP simulation of DNA double strand break (DSB) relative biological effectiveness (RBE) for photons, neutrons, and light ions

    Science.gov (United States)

    Stewart, Robert D.; Streitmatter, Seth W.; Argento, David C.; Kirkby, Charles; Goorley, John T.; Moffitt, Greg; Jevremovic, Tatjana; Sandison, George A.

    2015-11-01

    To account for particle interactions in the extracellular (physical) environment, information from the cell-level Monte Carlo damage simulation (MCDS) for DNA double strand break (DSB) induction has been integrated into the general purpose Monte Carlo N-particle (MCNP) radiation transport code system. The effort to integrate these models is motivated by the need for a computationally efficient model to accurately predict particle relative biological effectiveness (RBE) in cell cultures and in vivo. To illustrate the approach and highlight the impact of the larger scale physical environment (e.g. establishing charged particle equilibrium), we examined the RBE for DSB induction (RBEDSB) of x-rays, 137Cs γ-rays, neutrons and light ions relative to γ-rays from 60Co in monolayer cell cultures at various depths in water. Under normoxic conditions, we found that 137Cs γ-rays are about 1.7% more effective at creating DSB than γ-rays from 60Co (RBEDSB  =  1.017) whereas 60-250 kV x-rays are 1.1 to 1.25 times more efficient at creating DSB than 60Co. Under anoxic conditions, kV x-rays may have an RBEDSB up to 1.51 times as large as 60Co γ-rays. Fission neutrons passing through monolayer cell cultures have an RBEDSB that ranges from 2.6 to 3.0 in normoxic cells, but may be as large as 9.93 for anoxic cells. For proton pencil beams, Monte Carlo simulations suggest an RBEDSB of about 1.2 at the tip of the Bragg peak and up to 1.6 a few mm beyond the Bragg peak. Bragg peak RBEDSB increases with decreasing oxygen concentration, which may create opportunities to apply proton dose painting to help address tumor hypoxia. Modeling of the particle RBE for DSB induction across multiple physical and biological scales has the potential to aid in the interpretation of laboratory experiments and provide useful information to advance the safety and effectiveness of hadron therapy in the treatment of cancer.

  12. Rapid MCNP simulation of DNA double strand break (DSB) relative biological effectiveness (RBE) for photons, neutrons, and light ions.

    Science.gov (United States)

    Stewart, Robert D; Streitmatter, Seth W; Argento, David C; Kirkby, Charles; Goorley, John T; Moffitt, Greg; Jevremovic, Tatjana; Sandison, George A

    2015-11-01

    To account for particle interactions in the extracellular (physical) environment, information from the cell-level Monte Carlo damage simulation (MCDS) for DNA double strand break (DSB) induction has been integrated into the general purpose Monte Carlo N-particle (MCNP) radiation transport code system. The effort to integrate these models is motivated by the need for a computationally efficient model to accurately predict particle relative biological effectiveness (RBE) in cell cultures and in vivo. To illustrate the approach and highlight the impact of the larger scale physical environment (e.g. establishing charged particle equilibrium), we examined the RBE for DSB induction (RBEDSB) of x-rays, (137)Cs γ-rays, neutrons and light ions relative to γ-rays from (60)Co in monolayer cell cultures at various depths in water. Under normoxic conditions, we found that (137)Cs γ-rays are about 1.7% more effective at creating DSB than γ-rays from (60)Co (RBEDSB  =  1.017) whereas 60-250 kV x-rays are 1.1 to 1.25 times more efficient at creating DSB than (60)Co. Under anoxic conditions, kV x-rays may have an RBEDSB up to 1.51 times as large as (60)Co γ-rays. Fission neutrons passing through monolayer cell cultures have an RBEDSB that ranges from 2.6 to 3.0 in normoxic cells, but may be as large as 9.93 for anoxic cells. For proton pencil beams, Monte Carlo simulations suggest an RBEDSB of about 1.2 at the tip of the Bragg peak and up to 1.6 a few mm beyond the Bragg peak. Bragg peak RBEDSB increases with decreasing oxygen concentration, which may create opportunities to apply proton dose painting to help address tumor hypoxia. Modeling of the particle RBE for DSB induction across multiple physical and biological scales has the potential to aid in the interpretation of laboratory experiments and provide useful information to advance the safety and effectiveness of hadron therapy in the treatment of cancer. PMID:26449929

  13. Comparative analysis of three simulation models applied on a motored internal combustion engine

    International Nuclear Information System (INIS)

    Highlights: ► Three simulation models of increasing complexity have been comparatively evaluated. ► All models adequately predict the cylinder pressure diagram at all engine speeds. ► For engine simulation, 1D, Q-D and CFD models need 1 s, 6 min and 20 h respectively. ► Q-D model predicts qualitatively correctly the in-cylinder temperature and velocity field. ► Q-D model offers a compromise between the detailed CFD models and the multi-zone ones. - Abstract: The motivation of the present work is to comparatively evaluate the computational time and the results obtained using three computational models of increasing complexity, for the simulation of the closed part of the cycle of an internal combustion engine with a bowl-in-piston design, running under motoring conditions in the range of 1200–3000 rpm. The first model is a single-zone thermodynamic model, the second one is a hybrid quasi-dimensional model, and the third one is a computational fluid dynamics (CFD) model. From the analysis conducted it is concluded that the single-zone model calculates with reasonable accuracy the in-cylinder pressure, while it rather underestimates the peak in-cylinder mean gas temperature near the top dead center (TDC). Its main advantageous feature is the very low computational time (1 s) compared to the 6 min and 20 h required by the quasi-dimensional and CFD models, respectively. On the other hand, the quasi-dimensional model provides information concerning the local in-cylinder temperature distribution, and describes qualitatively correctly the way the cylinder design affects the in-cylinder flow and temperature fields, as revealed by comparing its results with the corresponding ones obtained with the more accurate and time consuming CFD model.

  14. A Mental Simulation-Based Decision-Making Architecture Applied to Ground Combat

    OpenAIRE

    Kunde, Dietmar; Darken, Christian J.

    2006-01-01

    At last year's BRIMS conference, we described a model of mental simulation based on statistical event prediction (Kunde and Darken, 2005). In this paper, we describe a new decision making architecture based on our mental simualtion model. We have developed and tested the model using a scenario built in COMBAT XXI, where the model is used to make fire/hold fire decisions. While the choice of what it to be predicted and the basis for the predictions are chosen by a human modeler, the details...

  15. Estimating the Mass of the Local Group using Machine Learning Applied to Numerical Simulations

    OpenAIRE

    McLeod, Michael; Libeskind, Noam; Lahav, Ofer; Hoffman, Yehuda

    2016-01-01

    We revisit the estimation of the combined mass of the Milky Way and Andromeda (M31), which dominate the mass of the Local Group. We make use of an ensemble of 30,190 halo pairs from the Small MultiDark simulation, assuming a $\\Lambda$CDM (Cosmological Constant with Cold Dark Matter) cosmology, to investigate the relationship between the bound mass and parameters characterising the orbit of the binary and their local environment with the aid of machine learning methods (artificial neural netwo...

  16. The fast simulated annealing algorithm applied to the search problem in LEED

    Science.gov (United States)

    Nascimento, V. B.; de Carvalho, V. E.; de Castilho, C. M. C.; Costa, B. V.; Soares, E. A.

    2001-07-01

    In this work we present new results obtained from the application of the fast simulated algorithm (FSA) to the surface structure determination of the Ag(1 1 0) and CdTe(1 1 0) systems. The influence of a control parameter, the "initial temperature", on the FSA search process was investigated. A scaling behaviour, that measures the efficiency of a search method as a function of the number of parameters to be varied, was obtained for the FSA algorithm, and indicated a favourable linear scaling ( N1).

  17. Neighbourhood generation mechanism applied in simulated annealing to job shop scheduling problems

    Science.gov (United States)

    Cruz-Chávez, Marco Antonio

    2015-11-01

    This paper presents a neighbourhood generation mechanism for the job shop scheduling problems (JSSPs). In order to obtain a feasible neighbour with the generation mechanism, it is only necessary to generate a permutation of an adjacent pair of operations in a scheduling of the JSSP. If there is no slack time between the adjacent pair of operations that is permuted, then it is proven, through theory and experimentation, that the new neighbour (schedule) generated is feasible. It is demonstrated that the neighbourhood generation mechanism is very efficient and effective in a simulated annealing.

  18. Numerical simulation of nanopulse penetration of biological matter using the ADI-FDTD method

    Science.gov (United States)

    Zhu, Fei

    Nanopulses are ultra-wide-band (UWB) electromagnetic pulses with pulse duration of only a few nanoseconds and electric field amplitudes greater than 105 V/m. They have been widely used in the development of new technologies in the field of medicine. Therefore, the study of the nanopulse bioeffects is important to ensure the appropriate application with nanopulses in biomedical and biotechnological settings. The conventional finite-difference time-domain (FDTD) method for solving Maxwell's equations has been proven to be an effective method to solve the problems related to electromagnetism. However, its application is restricted by the Courant, Friedrichs, and Lewy (CFL) stability condition that confines the time increment and mesh size in the computation in order to prevent the solution from being divergent. This dissertation develops a new finite difference scheme coupled with the Cole-Cole expression for dielectric coefficients of biological tissues to simulate the electromagnetic fields inside biological tissues when exposed to nanopulses. The scheme is formulated based on the Yee's cell and alternating direction implicit (ADI) technique. The basic idea behind the ADI technique is to break up every time step into two half-time steps. At the first half-step, the finite difference operator on the right-hand side of the Maxwell's equation is implicit only along one coordinate axis direction. At the second half-step, the finite difference operator on the right-hand side of the Maxwell's equation is implicit only along the other coordinate axis direction. As such, only tridiagonal linear systems are solved. In this numerical method, the Cole-Cole expression is approximated by a second-order Taylor series based on the z-transform method. In addition, the perfectly matched layer is employed for the boundary condition, and the total/scattered field technique is employed to generate the plane wave in order to prevent the wave reflection. The scheme is tested by numerical

  19. Simulated influence of postweaning production system on performance of different biological types of cattle: III. Biological efficiency.

    Science.gov (United States)

    Williams, C B; Bennett, G L; Keele, J W

    1995-03-01

    Methods were developed and incorporated into a previously published computer model to predict ME intake and calculate biological efficiencies in terms of grams of empty BW (EBW) and fat-free matter (FFM) gained/megacalorie of ME consumed from weaning to slaughter. Efficiencies were calculated for steers from F1 crosses of 16 sire breeds (Hereford, Angus, Jersey, South Devon, Limousin, Simmental, Charolais, Red Poll, Brown Swiss, Gelbvieh, Maine Anjou, Chianina, Brahman, Sahiwal, Pinzgauer, and Tarentaise) mated to Hereford and Angus dams, grown under nine backgrounding systems, finished at either a low (1.0 kg) or high (1.36 kg) ADG, and slaughtered at 300 kg carcass weight, small or greater degree of marbling, and 28% carcass fat. Backgrounding systems were high ADG (.9 kg) for 111, 167, or 222 d, medium ADG (.5 kg) for 200, 300, or 400 d, and low ADG (.25 kg) for 300 or 400 d, and 0 d backgrounding. The high ADG finishing system was more biologically efficient than the low ADG finishing system, and generally backgrounding systems were less biologically efficient than direct finishing after weaning (0 d backgrounding). Large-framed breeds were more efficient at the constant carcass weight and carcass fatness end point, and breeds that achieved the marbling end point at low levels of carcass fatness were more efficient at this end point. Some small-framed breeds gained EBW more efficiently but gained FFM less efficiently than some of the large-framed breeds. Variation in efficiency between genotypes was greatest with 0 d backgrounding and decreased in the other backgrounding systems. PMID:7608001

  20. Monte Carlo techniques applied in complete simulation of conventional CT image acquisition: from projection data to effective dose

    International Nuclear Information System (INIS)

    Computed tomography has advanced very rapidly, resulting in a rapid increase in the number of examinations performed, as well as in the range of clinical applications now based on this technique. CT is a procedure generally associated with relatively high dose levels. It constitutes 5% of worldwide radiological examinations; yet contributes one third of the collective dose associated with medical imaging. Therefore, studies on the issue of dose optimization are welcome. Computer simulation uses theoretical models to predict performance of real systems. This kind of simulation is able, among other tasks, to evaluate the impact of geometric parameters of a tomograph on spatial resolution, for example: detector size; source-detector distance and source-isocentre distance. The development of new pre-process and image reconstruction algorithms and the evaluation of dose in organs and tissues of human body are tasks that have been developed by means of computer simulations. In this work, conventional CT acquisitions were completely simulated. Monte Carlo techniques were applied in radiation transport simulation to obtain projection data and to calculate conversion coefficients for doses in organs and tissues of a female anthropomorphic phantom. The computer simulation of the entire measurement and reconstruction process is a valuable and very effective means to evaluate the effects of individual parameters. A graphical reconstruction algorithm was used to obtain virtual tomographic images, the attenuation values of each projection were added to the related pixel of the reconstruction matrix. Several different geometries were simulated and the effect of geometric parameters on image quality and dose in organs and tissues was evaluated. (author)

  1. Integrating Math & Computer Skills in the Biology Classroom: An Example Using Spreadsheet Simulations to Teach Fundamental Sampling Concepts

    Science.gov (United States)

    Ray, Darrell L.

    2013-01-01

    Students often enter biology programs deficient in the math and computational skills that would enhance their attainment of a deeper understanding of the discipline. To address some of these concerns, I developed a series of spreadsheet simulation exercises that focus on some of the mathematical foundations of scientific inquiry and the benefits…

  2. 分子生物学技术在昆虫系统学上的应用%Molecular Biological Techniques Applied in Insect Systematics

    Institute of Scientific and Technical Information of China (English)

    黄帅; 胡红英

    2006-01-01

    介绍了广泛用于昆虫分类学当中的几种分子生物学技术,包括核酸序列分析技术,RFLP技术,PCR技术和DNA指纹技术等,以及这些技术在线粒体DNA和核糖体DNA等分子标记上的应用.现代生物技术应用于昆虫系统学的研究将会有很好的前景.%Molecular biology plays a very important role in entomotaxomomy, and a new area of entomological science forming as molecular biological techniques are applied in insect systematics. Since its commencement in 1980's, much important progress has been made and many excellent results have been achieved especially in recent years. This paper introduces many kinds of modern biological technology being widely used in study of entomotaxonomy, including nucleic acid sequence analysis, RFLP, PCR, DNAfp, etc. Their applications in some molecular markers, such as mitochondrial DNA (mtDNA) and ribosomal DNA (rDNA), and their combined dataset can be effective to applied in taxonomy and identification of species. This view showed that the insect molecular systematic combined with many kinds of modern biological technology will be one of the most important subjects in the near future.

  3. Parallel Sparse Matrix Solver on the GPU Applied to Simulation of Electrical Machines

    CERN Document Server

    Rodrigues, Antonio Wendell De Oliveira; Menach, Yvonnick Le; Dekeyser, Jean-Luc

    2010-01-01

    Nowadays, several industrial applications are being ported to parallel architectures. In fact, these platforms allow acquire more performance for system modelling and simulation. In the electric machines area, there are many problems which need speed-up on their solution. This paper examines the parallelism of sparse matrix solver on the graphics processors. More specifically, we implement the conjugate gradient technique with input matrix stored in CSR, and Symmetric CSR and CSC formats. This method is one of the most efficient iterative methods available for solving the finite-element basis functions of Maxwell's equations. The GPU (Graphics Processing Unit), which is used for its implementation, provides mechanisms to parallel the algorithm. Thus, it increases significantly the computation speed in relation to serial code on CPU based systems.

  4. A Fast Parallel Poisson Solver on Irregular Domains Applied to Beam Dynamic Simulations

    CERN Document Server

    Adelmann, A; Ineichen, Y

    2009-01-01

    We discuss the scalable parallel solution of the Poisson equation within a Particle-In-Cell (PIC) code for the simulation of electron beams in particle accelerators of irregular shape. The problem is discretized by Finite Differences. Depending on the treatment of the Dirichlet boundary the resulting system of equations is symmetric or `mildly' nonsymmetric positive definite. In all cases, the system is solved by the preconditioned conjugate gradient algorithm with smoothed aggregation (SA) based algebraic multigrid (AMG) preconditioning. We investigate variants of the implementation of SA-AMG that lead to considerable improvements in the execution times. We demonstrate good scalability of the solver on distributed memory parallel processor with up to 2048 processors. We also compare our SAAMG-PCG solver with an FFT-based solver that is more commonly used for applications in beam dynamics.

  5. Applying flexible molecular docking to simulate protein retention behavior in hydrophobic interaction chromatography

    Institute of Scientific and Technical Information of China (English)

    ZHOU; Peng; TIAN; FeiFei; LI; ZhiLiang

    2007-01-01

    Interaction between proteins and stationary phase in hydrophobic interaction chromatography (HIC) is differentiated into two thermodynamic processes involving direct nonbonding/conformation interaction and surface hydrophobic effect of proteins, hence quantitatively giving rise to a binary linear relation between HIC retention time (RT) at concentrated salting liquid and ligand-protein binding free energy. Then, possible binding manners for 27 proteins of known crystal structures with hydrophobic ligands are simulated and analyzed via ICM flexible molecular docking and genetic algorithm, with results greatly consistent with experimental values. By investigation, it is confirmed local hydrophobic effects of proteins and nonbinding/conformation interaction between ligand and protein both notably influence HIC chromatogram retention behaviors, mainly focusing on exposed portions on the protein surface.

  6. Simulation applied to working frequency selection in large-scale vibrating screen's design

    Institute of Scientific and Technical Information of China (English)

    PENG Chen-yu; SU Rong-hua

    2011-01-01

    The working frequency selection of the ZK30525 vibrating screen was studied using ANSYS.Integrating the dynamic performance simulation analysis of the vibrating screen structure,the variation laws of beams' vibration displacements changing with different exciting frequencies were researched.These beams include six beams,with one discharging beam and one in-material beam.Results indicate that vibration displacements in the middle of these beams increase with the augmentation of exciting frequency.When exciting frequency exceeds a certain value,there exists a flat change region for vibration displacement.According to vibrator characteristics,the vibrating screen's working frequency should be selected in the flat change region,and be far away from modal frequencies.The study provides theoretical guidance for the reasonable working frequency selection of the large-scale vibrating screen.

  7. Comparison of Three Soot Models Applied to Multi-Dimensional Diesel Combustion Simulations

    Science.gov (United States)

    Tao, Feng; Srinivas, Sukhin; Reitz, Rolf D.; Foster, David E.

    In this paper, three soot models previously proposed for diesel combustion and soot formation studies are briefly reviewed and compared. The three models are (1) two-step empirical soot model, (2) eight-step phenomenological soot model, and (3) complex-chemistry coupled phenomenological soot model. All three models have been implemented into the KIVA-3V simulation code. For comparison, a heavy-duty DI diesel engine case with fuel injection typical of standard DI diesel operating conditions was studied. Flame structures of a single diesel spray predicted using these three models were compared, and the results offer our perspective on the application of these three models to soot modeling in diesel engines.

  8. The prospect of applying chemical elicitors and plant strengtheners to enhance the biological control of crop pests

    OpenAIRE

    Sobhy, Islam S.; Erb, Matthias; Lou, Yonggen; Ted C J Turlings

    2014-01-01

    An imminent food crisis reinforces the need for novel strategies to increase crop yields worldwide. Effective control of pest insects should be part of such strategies, preferentially with reduced negative impact on the environment and optimal protection and utilization of existing biodiversity. Enhancing the presence and efficacy of native biological control agents could be one such strategy. Plant strengthener is a generic term for several commercially available compounds or mixtures of com...

  9. Acceleration of Peripheral Nerve Regeneration through Asymmetrically Porous Nerve Guide Conduit Applied with Biological/Physical Stimulation

    OpenAIRE

    Kim, Jin Rae; Oh, Se Heang; Kwon, Gu Birm; Namgung, Uk; Song, Kyu Sang; Jeon, Byeong Hwa; Lee, Jin Ho

    2013-01-01

    Sufficient functional restoration of damaged peripheral nerves is a big clinical challenge. In this study, a nerve guide conduit (NGC) with selective permeability was prepared by rolling an asymmetrically porous polycaprolactone/Pluronic F127 membrane fabricated using a novel immersion precipitation method. Dual stimulation (nerve growth factor [NGF] as a biological stimulus and low-intensity pulse ultrasound [US] as a physical stimulus) was adapted to enhance nerve regeneration through an NG...

  10. Computer simulation of induced electric currents and fields in biological bodies by 60 Hz magnetic fields

    International Nuclear Information System (INIS)

    Possible health effects of human exposure to 60 Hz magnetic fields are a subject of increasing concern. An understanding of the coupling of electromagnetic fields to human body tissues is essential for assessment of their biological effects. A method is presented for the computerized simulation of induced electric currents and fields in bodies of men and rodents from power-line frequency magnetic fields. In the impedance method, the body is represented by a 3 dimensional impedance network. The computational model consists of several tens of thousands of cubic numerical cells and thus represented a realistic shape. The modelling for humans is performed with two models, a heterogeneous model based on cross-section anatomy and a homogeneous one using an average tissue conductivity. A summary of computed results of induced electric currents and fields is presented. It is confirmed that induced currents are lower than endangerous current levels for most environmental exposures. However, the induced current density varies greatly, with the maximum being at least 10 times larger than the average. This difference is likely to be greater when more detailed anatomy and morphology are considered. 15 refs., 2 figs., 1 tab

  11. First Steps in Computational Systems Biology: A Practical Session in Metabolic Modeling and Simulation

    Science.gov (United States)

    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…

  12. Electroporation dynamics in biological cells subjected to ultrafast electrical pulses: A numerical simulation study

    Science.gov (United States)

    Joshi, R. P.; Schoenbach, K. H.

    2000-07-01

    A model analysis of electroporation dynamics in biological cells has been carried out based on the Smoluchowski equation. Results of the cellular response to short, electric pulses are presented, taking account of the growth and resealing dynamics of transient aqueous pores. It is shown that the application of large voltages alone may not be sufficient to cause irreversible breakdown, if the time duration is too short. Failure to cause irreversible damage at small pulse widths could be attributed to the time inadequacy for pores to grow and expand beyond a critical threshold radius. In agreement with earlier studies, it is shown that irreversible breakdown would lead to the formation of a few large pores, while a large number of smaller pores would appear in the case of reversible breakdown. Finally, a pulse width dependence of the applied voltage for irreversible breakdown has been obtained. It is shown that in the absence of dissipation, the associated energy input necessary reduces with decreasing pulse width to a limiting value. However, with circuit effects taken into account, a local minima in the pulse dependent energy function is predicted, in keeping with previously published experimental reports.

  13. Business-oriented modeling and Simulation: Dynamic Scorecard method Applied the Formularization of Strategies

    Directory of Open Access Journals (Sweden)

    Josué Vitor

    2007-12-01

    Full Text Available The main goal of this research was to application the “Scorecard Dinâmico” method onstrategic formulation process in a small business. This method incorporate qualitative andsimulation tools from System Dynamics in the strategic map provided by Balanced Scorecardmaking the strategic management flexible in accordance with the organizational realitycomplexity. The research method adopted was the “research-action” and it was possible,with participating observation, the construction of strategic models on interaction with thecompany directors. During this process, it could be assessed organizing points thatinterfering in formulation of strategy of a small business during the research. Through thisprocess, company members mental models were explained in strategic map and qualitativemodels resulting on a simulation tool for control the results and alternative prospection offuture strategies and a higher level of learning organizational. As a result, it could be pointedthe method difficult implantation in virtue of the absence quantitative data and a higherunderstanding by the research participants of the problem resulting from the systemicstructural behavior in the small business.

  14. Estimating the Mass of the Local Group using Machine Learning Applied to Numerical Simulations

    CERN Document Server

    McLeod, Michael; Lahav, Ofer; Hoffman, Yehuda

    2016-01-01

    We revisit the estimation of the combined mass of the Milky Way and Andromeda (M31), which dominate the mass of the Local Group. We make use of an ensemble of 30,190 halo pairs from the Small MultiDark simulation, assuming a $\\Lambda$CDM (Cosmological Constant with Cold Dark Matter) cosmology, to investigate the relationship between the bound mass and parameters characterising the orbit of the binary and their local environment with the aid of machine learning methods (artificial neural networks, ANN). Results from the ANN are most successful when information about the velocity shear is provided, which demonstrates the flexibility of machine learning to model physical phenomena and readily incorporate new information as it becomes available. The resulting estimate for the Local Group mass, when shear information is included, is $4.9 \\times 10^{12} M_\\odot$, with an error of $\\pm0.8 \\times 10^{12} M_\\odot$ from the 68% uncertainty in observables, and a 68% confidence interval of $^{+1.3}_{-1.4} \\times 10^{12}M...

  15. Statistical learning techniques applied to epidemiology: a simulated case-control comparison study with logistic regression

    Directory of Open Access Journals (Sweden)

    Land Walker H

    2011-01-01

    Full Text Available Abstract Background When investigating covariate interactions and group associations with standard regression analyses, the relationship between the response variable and exposure may be difficult to characterize. When the relationship is nonlinear, linear modeling techniques do not capture the nonlinear information content. Statistical learning (SL techniques with kernels are capable of addressing nonlinear problems without making parametric assumptions. However, these techniques do not produce findings relevant for epidemiologic interpretations. A simulated case-control study was used to contrast the information embedding characteristics and separation boundaries produced by a specific SL technique with logistic regression (LR modeling representing a parametric approach. The SL technique was comprised of a kernel mapping in combination with a perceptron neural network. Because the LR model has an important epidemiologic interpretation, the SL method was modified to produce the analogous interpretation and generate odds ratios for comparison. Results The SL approach is capable of generating odds ratios for main effects and risk factor interactions that better capture nonlinear relationships between exposure variables and outcome in comparison with LR. Conclusions The integration of SL methods in epidemiology may improve both the understanding and interpretation of complex exposure/disease relationships.

  16. Applying Cellular Automata for Simulating and Assessing Urban Growth Scenario Based in Nairobi, Kenya

    Directory of Open Access Journals (Sweden)

    Kenneth Mubea

    2014-01-01

    Full Text Available This research explores urban growth based scenarios for the city of Nairobi using a cellular automata urban growth model (UGM. African cities have experienced rapid urbanization over the last decade due to increased population growth and high economic activities. We used multi-temporal Landsat imageries for 1976, 1986, 2000 and 2010 to investigate urban land-use changes in Nairobi. Our UGM used data from urban land-use of 1986 and 2010, road data, slope data and exclusion layer. Monte-Carlo technique was used for model calibration and Multi Resolution Validation (MRV technique for validation. Simulation of urban land-use was done up to the year 2030 when Kenya plans to attain Vision 2030. Three scenarios were explored in the urban modelling process; unmanaged growth with no restriction on environmental areas, managed growth with moderate protection, and a managed growth with maximum protection on forest, agricultural areas, and urban green. Thus alternative scenario development using UGM is useful for planning purposes so as to ensure sustainable development is achieved. UGM provides quantitative, visual, spatial and temporal information which aid policy and decision makers can make informed decisions.

  17. Artificial intelligence applied to atomistic kinetic Monte Carlo simulations in Fe-Cu alloys

    International Nuclear Information System (INIS)

    Vacancy migration energies as functions of the local atomic configuration (LAC) in Fe-Cu alloys have been systematically tabulated using an appropriate interatomic potential for the alloy of interest. Subsets of these tabulations have been used to train an artificial neural network (ANN) to predict all vacancy migration energies depending on the LAC. The error in the prediction of the ANN has been evaluated by a fuzzy logic system (FLS), allowing a feedback to be introduced for further training, to improve the ANN prediction. This artificial intelligence (AI) system is used to develop a novel approach to atomistic kinetic Monte Carlo (AKMC) simulations, aimed at providing a better description of the kinetic path followed by the system through diffusion of solute atoms in the alloy via vacancy mechanism. Fe-Cu has been chosen because of the importance of Cu precipitation in Fe in connection with the embrittlement of reactor pressure vessels of existing nuclear power plants. In this paper the method is described in some detail and the first results of its application are presented and briefly discussed

  18. Motion Planning of a Novel 2-DOF Parallel Manipulator Applied as Driving Simulator of the Wheel Loader

    Directory of Open Access Journals (Sweden)

    Knapczyk J.

    2014-08-01

    Full Text Available A novel parallel manipulator with 3 legs (2 actuated by linear actuators and one supporting pillar,which is applied in a wheel loader driving simulator, is proposed in this paper. The roll angle and the pitch angle of the platform are derived in closed-form of functions of the variable lengths of two actuators. The linear velocity and acceleration of the selected point and angular velocity of the moving platform are determined and compared with measurement results obtained in the respective point and in the body of the wheel loader. The differences between the desired and actual actuator displacements are used as feedback to compute how much force to send to the actuators as some function of the servo error. A numerical example with a proposed mechanism as a driving simulator is presented

  19. Design and simulation of the space vector modulation and applied to a load RL powered by a voltage inverter

    Directory of Open Access Journals (Sweden)

    Marouane El Azzaoui

    2016-07-01

    Full Text Available The vector control performance applied to rotating machines depends largely on static and dynamic characteristics of the inverter associated with it. The development of the pulse-width modulation (PWM provided greater flexibility in the control of the converters. The objective of this work is to construct a simplified and practical space vector modulation (SVM based on the selection of the sequence and the calculation of the conduction time or extinction. We have presented the blocks of the simulation vector modulation on the Matlab / Simulink with a new method for determining conduction time and analyzed its application on a load RL supplied by a voltage inverter. The performance of the proposed method has been presented by the simulation results.

  20. Accretion disc time lag distributions: applying CREAM to simulated AGN light curves

    Science.gov (United States)

    Starkey, D. A.; Horne, Keith; Villforth, C.

    2016-02-01

    Active galactic nuclei (AGN) vary in their brightness across all wavelengths. Moreover, longer wavelength ultraviolet-optical continuum light curves appear to be delayed with respect to shorter wavelength light curves. A simple way to model these delays is by assuming thermal reprocessing of a variable point source (a lamp post) by a blackbody accretion disc. We introduce a new method, CREAM (Continuum REprocessed AGN Markov Chain Monte Carlo), that models continuum variations using this lamp post model. The disc light curves lag the lamp post emission with a time delay distribution sensitive to the disc temperature-radius profile and inclination. We test CREAM's ability to recover both inclination and product of black hole mass and accretion rate {Mdot{M}}, and show that the code is also able to infer the shape of the driving light curve. CREAM is applied to synthetic light curves expected from 1000 s exposures of a 17th magnitude AGN with a 2-m telescope in Sloan g and i bands with Signal-to-Noise Ratio (SNR) of 500-900 depending on the filter and lunar phase. We also test CREAM on poorer quality g and i light curves with SNR = 100. We find in the high-SNR case that CREAM can recover the accretion disc inclination to within an uncertainty of 5° and an {Mdot{M}} to within 0.04 dex.

  1. A basis for environmental monitoring in the gulf of Batabano applying hydrodynamic simulations

    International Nuclear Information System (INIS)

    The spreading of organic compounds and wastes in seawater depend on the space-time distribution of marine currents. Therefore, for the Environmental Monitoring of sea waters in the Cuban shelf it is necessary to include the marine current variable. A hydrodynamic model is applied in the Gulf of Batabano. The model was validated by using marine currents observed. Any organic compound or wastes in the Batabano or La Broa will moved slowly (1+- 0.0529 cm/s and 4.7 +- 0.0529 cm/s) until the center and southwestern part of the gulf and the western part of the Isla de la Juventud, affecting for a long time period the SW coast of the gulf. Any pollution in ocean waters adjacent to this shelf will go through the open boundary with a mean velocity between 15 +- 0.25 cm/s and 29.5 +- 0.25 cm/s until the northern part of the Isla de la Juventud; it affects quickly this island and the southwestern and southeastern coasts of the gulf; the pollution will go slowly (1+- 0.0529 cm/s and 3 +- 0.0529 cm/s) until the central and northeastern part of the gulf

  2. Accretion Disc Time Lag Distributions: Applying CREAM to Simulated AGN Light Curves

    CERN Document Server

    Starkey, David; Villforth, Carolin

    2015-01-01

    Active Galactic Nuclei (AGN) vary in their brightness across all wavelengths. Moreover, longer wavelength ultraviolet - optical continuum light curves appear to be delayed with respect to shorter wavelength light curves. A simple way to model these delays is by assuming thermal reprocessing of a variable point source (a lamp post) by a blackbody accretion disc. We introduce a new method, CREAM (\\textbf{C}ontinuum \\textbf{RE}processed \\textbf{A}GN \\textbf{M}arkov Chain Monte Carlo), that models continuum variations using this lamp post model. The disc light curves lag the lamp post emission with a time delay distribution sensitive to the disc temperature-radius profile and inclination. We test CREAM's ability to recover both inclination and product of black hole mass and accretion rate $\\mmdot$, and show that the code is also able to infer the shape of the driving light curve. CREAM is applied to synthetic light curves expected from 1000 second exposures of a 17th magnitude AGN with a 2m telescope in Sloan g a...

  3. Knowledge Mining Based on Environmental Simulation Applied to Wind Farm Power Forecasting

    Directory of Open Access Journals (Sweden)

    Dongxiao Niu

    2013-01-01

    Full Text Available Considering the inherent variability and uncertainty of wind power generation, in this study, a self-organizing map (SOM combined with rough set theory clustering technique (RST is proposed to extract the relative knowledge and to choose the most similar history situation and efficient data for wind power forecasting with numerical weather prediction (NWP. Through integrating the SOM and RST methods to cluster the historical data into several classes, the approach could find the similar days and excavate the hidden rules. According to the data reprocessing, the selected samples will improve the forecast accuracy echo state network (ESN trained by the class of the forecasting day that is adopted to forecast the wind power output accordingly. The developed methods are applied to a case of power forecasting in a wind farm located in northwest of China with wind power data from April 1, 2008, to May 6, 2009. In order to verify its effectiveness, the performance of the proposed method is compared with the traditional backpropagation neural network (BP. The results demonstrated that knowledge mining led to a promising improvement in the performance for wind farm power forecasting.

  4. FOREWORD: Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology and Mathematics

    Science.gov (United States)

    Kaski, K.; Salomaa, M.

    1990-01-01

    These are Proceedings of the Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology, and Mathematics, held August 25-26, 1989, at Lahti (Finland). The Symposium belongs to an annual series of Meetings, the first one of which was arranged in 1987 at Lund (Sweden) and the second one in 1988 at Kolle-Kolle near Copenhagen (Denmark). Although these Symposia have thus far been essentially Nordic events, their international character has increased significantly; the trend is vividly reflected through contributions in the present Topical Issue. The interdisciplinary nature of Computational Science is central to the activity; this fundamental aspect is also responsible, in an essential way, for its rapidly increasing impact. Crucially important to a wide spectrum of superficially disparate fields is the common need for extensive - and often quite demanding - computational modelling. For such theoretical models, no closed-form (analytical) solutions are available or they would be extremely difficult to find; hence one must rather resort to the Art of performing computational investigations. Among the unifying features in the computational research are the methods of simulation employed; methods which frequently are quite closely related with each other even for faculties of science that are quite unrelated. Computer simulation in Natural Sciences is presently apprehended as a discipline on its own right, occupying a broad region somewhere between the experimental and theoretical methods, but also partially overlapping with and complementing them. - Whichever its proper definition may be, the computational approach serves as a novel and an extremely versatile tool with which one can equally well perform "pure" experimental modelling and conduct "computational theory". Computational studies that have earlier been made possible only through supercomputers have opened unexpected, as well as exciting, novel frontiers equally in mathematics (e.g., fractals

  5. Calculation of the ac to dc resistance ratio of conductive nonmagnetic straight conductors by applying FEM simulations

    Science.gov (United States)

    Riba, Jordi-Roger

    2015-09-01

    This paper analyzes the skin and proximity effects in different conductive nonmagnetic straight conductor configurations subjected to applied alternating currents and voltages. These effects have important consequences, including a rise of the ac resistance, which in turn increases power loss, thus limiting the rating for the conductor. Alternating current (ac) resistance is important in power conductors and bus bars for line frequency applications, as well as in smaller conductors for high frequency applications. Despite the importance of this topic, it is not usually analyzed in detail in undergraduate and even in graduate studies. To address this, this paper compares the results provided by available exact formulas for simple geometries with those obtained by means of two-dimensional finite element method (FEM) simulations and experimental results. The paper also shows that FEM results are very accurate and more general than those provided by the formulas, since FEM models can be applied in a wide range of electrical frequencies and configurations.

  6. Applying dynamic simulation modeling methods in health care delivery research - the SIMULATE checklist: Report of the ISPOR simulation modeling emerging good practices task force

    OpenAIRE

    Marshall, Deborah A; Burgos-Liz, Lina; IJzerman, Maarten J; Osgood, Nathaniel D.; Padula, William V.; Higashi, Mitchell K.; Wong, Peter K.; Pasupathy, Kalyan S.; Crown, William

    2015-01-01

    Health care delivery systems are inherently complex, consisting of multiple tiers of interdependent subsystems and processes that are adaptive to changes in the environment and behave in a nonlinear fashion. Traditional health technology assessment and modeling methods often neglect the wider health system impacts that can be critical for achieving desired health system goals and are often of limited usefulness when applied to complex health systems. Researchers and health care decision maker...

  7. IDENTIFICATION OF WIND LOAD APPLIED TO THREE-DIMENSIONAL STRUCTURES BY VIRTUE OF ITS SIMULATION IN THE WIND TUNNEL

    Directory of Open Access Journals (Sweden)

    Doroshenko Sergey Aleksandrovich

    2012-10-01

    Full Text Available The authors discuss wind loads applied to a set of two buildings. The wind load is simulated with the help of the wind tunnel. In the Russian Federation, special attention is driven to the aerodynamics of high-rise buildings and structures. According to the Russian norms, identification of aerodynamic coefficients for high-rise buildings, as well as the influence of adjacent buildings and structures, is performed on the basis of models of structures exposed to wind impacts simulated in the wind tunnel. This article deals with the results of the wind tunnel test of buildings. The simulation was carried out with the involvement of a model of two twenty-three storied buildings. The experiment was held in a wind tunnel of the closed type at in the Institute of Mechanics of Moscow State University. Data were compared at the zero speed before and after the experiment. LabView software was used to process the output data. Graphs and tables were developed in the Microsoft Excel package. GoogleSketchUp software was used as a visualization tool. The three-dimensional flow formed in the wind tunnel can't be adequately described by solving the two-dimensional problem. The aerodynamic experiment technique is used to analyze the results for eighteen angles of the wind attack.

  8. Applying electrical resistivity tomography and biological methods to assess the surface-groundwater interaction in two Mediterranean rivers (central Spain)

    Science.gov (United States)

    Iepure, Sanda; Gómez Ortiz, David; Lillo Ramos, Javier; Rasines Ladero, Ruben; Persoiu, Aurel

    2014-05-01

    Delineation of the extent of hyporheic zone (HZ) in river ecosystems is problematic due to the scarcity of spatial information about the structure of riverbed sediments and the magnitude and extent of stream interactions with the parafluvial and riparian zones. The several existing methods vary in both quality and quantity of information and imply the use of hydrogeological and biological methods. In the last decades, various non-invasive geophysical techniques were developed to characterise the streambed architecture and also to provide detailed spatial information on its vertical and horizontal continuity. All classes of techniques have their strengths and limitations; therefore, in order to assess their potential in delineating the lateral and vertical spatial extents of alluvial sediments, we have combined the near-surface images obtained by electrical resistivity tomography (ERT) with biological assessment of invertebrates in two Mediterranean lowland rivers from central Spain. We performed in situ imaging of the thickness and continuity of alluvial sediments under the riverbed and parafluvial zone during base-flow conditions (summer 2013 and winter 2014) at two different sites with distinct lithology along the Tajuña and Henares Rivers. ERT was performed by installing the electrodes (1 m spacing) on a 47 m long transect normal to the river channel using a Wener-Schlumberger array, across both the riparian zones and the river bed. Invertebrates were collected in the streambed from a depth of 20-40 cm, using the Bou-Rouch method, and from boreholes drilled to a depth of 1.5 m in the riparian zone. The ERT images obtained at site 1 (medium and coarse sand dominated lithology) shows resistivity values ranging from ~20 to 80 ohm•m for the in-stream sediments, indicating a permeable zone up to ~ 0.5 m thick and extending laterally for ca. 5 m from the channel. These sediments contribute to active surface/hyporheic water exchanges and to low water retention in

  9. Periradicular Tissue Responses to Biologically Active Molecules or MTA When Applied in Furcal Perforation of Dogs' Teeth

    Directory of Open Access Journals (Sweden)

    Anna Zairi

    2012-01-01

    Full Text Available The aim of this study was the comparative evaluation of inflammatory reactions and tissue responses to four growth factors, or mineral trioxide aggregate (MTA, or a zinc-oxide-eugenol-based cement (IRM as controls, when used for the repair of furcal perforations in dogs’ teeth. Results showed significantly higher inflammatory cell response in the transforming growth factorβ1 (TGFβ1 and zinc-oxide-eugenol-based cement (IRM groups and higher rates of epithelial proliferation in the TGFβ1, basic fibroblast growth factor (bFGF, and insulin growth factor-I (IGF-I groups compared to the MTA. Significantly higher rates of bone formation were found in the control groups compared to the osteogenic protein-1 (OP-1. Significantly higher rates of cementum formation were observed in the IGF-I and bFGF groups compared to the IRM. None of the biologically active molecules can be suggested for repairing furcal perforations, despite the fact that growth factors exerted a clear stimulatory effect on cementum formation and inhibited collagen capsule formation. MTA exhibited better results than the growth factors.

  10. Sensitivity of Surface Flux Simulations to Hydrologic Parameters Based on an Uncertainty Quantification Framework Applied to the Community Land Model

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Zhangshuan; Huang, Maoyi; Leung, Lai-Yung R.; Lin, Guang; Ricciuto, Daniel M.

    2012-08-10

    Uncertainties in hydrologic parameters could have significant impacts on the simulated water and energy fluxes and land surface states, which will in turn affect atmospheric processes and the carbon cycle. Quantifying such uncertainties is an important step toward better understanding and quantification of uncertainty of integrated earth system models. In this paper, we introduce an uncertainty quantification (UQ) framework to analyze sensitivity of simulated surface fluxes to selected hydrologic parameters in the Community Land Model (CLM4) through forward modeling. Thirteen flux tower footprints spanning a wide range of climate and site conditions were selected to perform sensitivity analyses by perturbing the parameters identified. In the UQ framework, prior information about the parameters was used to quantify the input uncertainty using the Minimum-Relative-Entropy approach. The quasi-Monte Carlo approach was applied to generate samples of parameters on the basis of the prior pdfs. Simulations corresponding to sampled parameter sets were used to generate response curves and response surfaces and statistical tests were used to rank the significance of the parameters for output responses including latent (LH) and sensible heat (SH) fluxes. Overall, the CLM4 simulated LH and SH show the largest sensitivity to subsurface runoff generation parameters. However, study sites with deep root vegetation are also affected by surface runoff parameters, while sites with shallow root zones are also sensitive to the vadose zone soil water parameters. Generally, sites with finer soil texture and shallower rooting systems tend to have larger sensitivity of outputs to the parameters. Our results suggest the necessity of and possible ways for parameter inversion/calibration using available measurements of latent/sensible heat fluxes to obtain the optimal parameter set for CLM4. This study also provided guidance on reduction of parameter set dimensionality and parameter

  11. Impact of network geometry, observation schemes and telescope structure deformations on local ties: simulations applied to Sardinia Radio Telescope

    Science.gov (United States)

    Abbondanza, Claudio; Sarti, Pierguido

    2012-03-01

    The 64-m Sardinia Radio Telescope (SRT) is currently under construction in Sardinia (Italy). To ensure future surveying and monitoring operations at an utmost level of accuracy, we aim at selecting the optimal design and the most cost-effective solution for the establishment of the local ground control network (LGCN). We simulate and test 45 data sets corresponding to 5 different network configurations. We investigate the influence of 2 LGCN geometries (14 or 8 ground markers) and 3 terrestrial observation schemes (based on redundant forward intersections or side shots) on the precision and accuracy of the conventional reference point (CRP) of SRT and the simulated tie vector with a global navigation satellite system (GNSS) station. In addition, thermal and gravitational deformations of the radio telescope structure are simulated as systematic errors introduced into the observations and their effects on the CRP estimates are quantified. The state-of-the-art of CRP surveying and computation, based on terrestrial indirect methods, is applied. We show how terrestrial indirect methods can estimate the position of the radio telescope CRP to the millimeter precision level. With our simulations, we prove that limiting the LGCN to a 8-point configuration ensures the same precision on the CRP obtained with a 14-point network. Furthermore, we demonstrate that in the absence of telescope deformations, side shots, despite the lower redundancy, preserve a precision similar to that of redundant forward intersections. We show that the deformations due to gravitational flexure and thermal expansion of the radio telescope cannot be neglected in the tie vector computation, since they may bias the CRP estimate by several millimeters degrading its accuracy but not impacting on its formal precision. We highlight the dependency of the correlation matrices of the solutions on the geometry of the network and the observation schemes. Similarly, varying the extent of telescope deformations

  12. Development of simulation interfaces for evaluation task with the use of physiological data and virtual reality applied to a vehicle simulator

    Science.gov (United States)

    Miranda, Mateus R.; Costa, Henrik; Oliveira, Luiz; Bernardes, Thiago; Aguiar, Carla; Miosso, Cristiano; Oliveira, Alessandro B. S.; Diniz, Alberto C. G. C.; Domingues, Diana Maria G.

    2015-03-01

    This paper aims at describing an experimental platform used to evaluate the performance of individuals at training immersive physiological games. The platform proposed is embedded in an immersive environment in a CAVE of Virtual Reality and consists on a base frame with actuators with three degrees of freedom, sensor array interface and physiological sensors. Physiological data of breathing, galvanic skin resistance (GSR) and pressure on the hand of the user and a subjective questionnaire were collected during the experiments. The theoretical background used in a project focused on Software Engineering, Biomedical Engineering in the field of Ergonomics and Creative Technologies in order to presents this case study, related of an evaluation of a vehicular simulator located inside the CAVE. The analysis of the simulator uses physiological data of the drivers obtained in a period of rest and after the experience, with and without movements at the simulator. Also images from the screen are captured through time at the embedded experience and data collected through physiological data visualization (average frequency and RMS graphics). They are empowered by the subjective questionnaire as strong lived experience provided by the technological apparatus. The performed immersion experience inside the CAVE allows to replicate behaviors from physical spaces inside data space enhanced by physiological properties. In this context, the biocybrid condition is expanded beyond art and entertainment, as it is applied to automotive engineering and biomedical engineering. In fact, the kinesthetic sensations amplified by synesthesia replicates the sensation of displacement in the interior of an automobile, as well as the sensations of vibration and vertical movements typical of a vehicle, different speeds, collisions, etc. The contribution of this work is the possibility to tracing a stress analysis protocol for drivers while operating a vehicle getting affective behaviors coming from

  13. Report on intercomparison run SNR-1 for the determination of trace elements in synthetic resin simulating biological material

    International Nuclear Information System (INIS)

    A synthetic resin, SNR-1, simulating biological material and containing homogeneously distributed trace amounts of As, Au, Br, Cr, Cs, Hg, La, Mn, Rb, Sb, Se and Sr, was made available to 16 laboratories in the form of 50 mg - pellets. Various methods for the quantitative determination of these elements (and, in some cases, also of impurities) including neutron activation analysis, and neutron activation analysis with radio-chemical analysis were used in an interlaboratory comparative study. The results are tabulated

  14. Monte Carlo simulations of the relative biological effectiveness for DNA double strand breaks from 300 MeV u−1 carbon-ion beams

    International Nuclear Information System (INIS)

    Monte Carlo simulations are used to calculate the relative biological effectiveness (RBE) of 300 MeV u−1 carbon-ion beams at different depths in a cylindrical water phantom of 10 cm radius and 30 cm long. RBE values for the induction of DNA double strand breaks (DSB), a biological endpoint closely related to cell inactivation, are estimated for monoenergetic and energy-modulated carbon ion beams. Individual contributions to the RBE from primary ions and secondary nuclear fragments are simulated separately. These simulations are based on a multi-scale modelling approach by first applying the FLUKA (version 2011.2.17) transport code to estimate the absorbed doses and fluence energy spectra, then using the MCDS (version 3.10A) damage code for DSB yields. The approach is efficient since it separates the non-stochastic dosimetry problem from the stochastic DNA damage problem. The MCDS code predicts the major trends of the DSB yields from detailed track structure simulations. It is found that, as depth is increasing, RBE values increase slowly from the entrance depth to the plateau region and change substantially in the Bragg peak region. RBE values reach their maxima at the distal edge of the Bragg peak. Beyond this edge, contributions to RBE are entirely from nuclear fragments. Maximum RBE values at the distal edges of the Bragg peak and the spread-out Bragg peak are, respectively, 3.0 and 2.8. The present approach has the flexibility to weight RBE contributions from different DSB classes, i.e. DSB0, DSB+ and DSB++. (paper)

  15. Comparison between Monte Carlo simulation and measurement with a 3D polymer gel dosimeter for dose distributions in biological samples

    International Nuclear Information System (INIS)

    In this research, we used a 135 MeV/nucleon carbon-ion beam to irradiate a biological sample composed of fresh chicken meat and bones, which was placed in front of a PAGAT gel dosimeter, and compared the measured and simulated transverse-relaxation-rate (R2) distributions in the gel dosimeter. We experimentally measured the three-dimensional R2 distribution, which records the dose induced by particles penetrating the sample, by using magnetic resonance imaging. The obtained R2 distribution reflected the heterogeneity of the biological sample. We also conducted Monte Carlo simulations using the PHITS code by reconstructing the elemental composition of the biological sample from its computed tomography images while taking into account the dependence of the gel response on the linear energy transfer. The simulation reproduced the experimental distal edge structure of the R2 distribution with an accuracy under about 2 mm, which is approximately the same as the voxel size currently used in treatment planning. (paper)

  16. Comparison between Monte Carlo simulation and measurement with a 3D polymer gel dosimeter for dose distributions in biological samples

    Science.gov (United States)

    Furuta, T.; Maeyama, T.; Ishikawa, K. L.; Fukunishi, N.; Fukasaku, K.; Takagi, S.; Noda, S.; Himeno, R.; Hayashi, S.

    2015-08-01

    In this research, we used a 135 MeV/nucleon carbon-ion beam to irradiate a biological sample composed of fresh chicken meat and bones, which was placed in front of a PAGAT gel dosimeter, and compared the measured and simulated transverse-relaxation-rate (R2) distributions in the gel dosimeter. We experimentally measured the three-dimensional R2 distribution, which records the dose induced by particles penetrating the sample, by using magnetic resonance imaging. The obtained R2 distribution reflected the heterogeneity of the biological sample. We also conducted Monte Carlo simulations using the PHITS code by reconstructing the elemental composition of the biological sample from its computed tomography images while taking into account the dependence of the gel response on the linear energy transfer. The simulation reproduced the experimental distal edge structure of the R2 distribution with an accuracy under about 2 mm, which is approximately the same as the voxel size currently used in treatment planning.

  17. Improving biological relevancy of transcriptional biomarkers experiments by applying the MIQE guidelines to pre-clinical and clinical trials.

    Science.gov (United States)

    Dooms, M; Chango, A; Barbour, E; Pouillart, P; Abdel Nour, A M

    2013-01-01

    The "Minimum Information for the Publication of qPCR Experiments" (MIQE [3]) guidelines are very much targeted at basic research experiments and have to our knowledge not been applied to qPCR assays carried out in the context of clinical trials. This report details the use of the MIQE qPCR app for iPhone (App Store, Apple) to assess the MIQE compliance of one clinical and five pre-clinical trials. This resulted in the need to include 14 modifications that make the guidelines more relevant for the assessment of this special type of application. We also discuss the need for flexibility, since while some parameters increase experimental quality, they also require more reagents and more time, which is not always feasible in a clinical setting. PMID:22910527

  18. PIXE (Proton-Induced X-ray Emission) and ICP (Inductive Coupled Plasma) applied in biology and environment

    International Nuclear Information System (INIS)

    Proton-Induced X-ray Emission (PIXE) and Inductive Coupled Plasma (ICP) are sensitive and reliable techniques for the determination of elements with atomic number greater than 13 in biological materials in the case of PIXE and greater than 10 in the case of ICP. One of the research direction of our department is the application of those methods in biology, namely the elemental analysis of leaves from different Basella plants cultivated in Variety Testing Centre and in Green Houses of Targoviste and the microelemental analysis of blood serum samples collected from healthy and ill cows (downer cow syndrome (DCS)) hosted in animal farms in the neighbourhood of Targoviste city. Another research direction is the environment study, especially air samples from Romanian cities. The PIXE quantitative method applicable to Basella plants is described in this work along with the obtained results. The target samples were bombarded with 3 MeV proton beam produced at Tandem Accelerator of IFIN-HH (Horia Hulubei National Institute for Physics and Nuclear Engineering), Bucharest. The X-rays were detected with Ge high purity detector with 160 eV at 5.9 KeV energy resolution and the characteristic X-ray spectra were recorded using an acquisition system with a PC. The concentration obtained for the chemical elements who give a great nourishment value of Basella plants, P, Ca, Mg, K, Na, Fe, Mn, Zn, Cu, have an estimated precision of less than 12%. Another part of our research work is dedicated to the microelemental analysis of blood serum samples collected from healthy and ill cows (downer cow syndrome (DCS)). Until today the origin of DCS is uncertain. We assumed some connections among the diminution of some nutritive elements from food, the activity of some enzymes and the origin of DCS. To obtain a microelemental monitoring of the samples, we used a nuclear analysis method, PIXE (Particle Induced X-Rays Emission) and a spectrometric one, ICP (Inductive Coupled Plasma). For Ca and P

  19. Biomining of regolith simulants for biological in situ resource utilization Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of this proposed research is to advance the development of biological in situ resource utilization for NASA's space exploration programs. We plan to build...

  20. Comparative Study on Interaction of Form and Motion Processing Streams by Applying Two Different Classifiers in Mechanism for Recognition of Biological Movement

    Directory of Open Access Journals (Sweden)

    Bardia Yousefi

    2014-01-01

    Full Text Available Research on psychophysics, neurophysiology, and functional imaging shows particular representation of biological movements which contains two pathways. The visual perception of biological movements formed through the visual system called dorsal and ventral processing streams. Ventral processing stream is associated with the form information extraction; on the other hand, dorsal processing stream provides motion information. Active basic model (ABM as hierarchical representation of the human object had revealed novelty in form pathway due to applying Gabor based supervised object recognition method. It creates more biological plausibility along with similarity with original model. Fuzzy inference system is used for motion pattern information in motion pathway creating more robustness in recognition process. Besides, interaction of these paths is intriguing and many studies in various fields considered it. Here, the interaction of the pathways to get more appropriated results has been investigated. Extreme learning machine (ELM has been implied for classification unit of this model, due to having the main properties of artificial neural networks, but crosses from the difficulty of training time substantially diminished in it. Here, there will be a comparison between two different configurations, interactions using synergetic neural network and ELM, in terms of accuracy and compatibility.

  1. Applied research and development of neutron activation analysis - The study on human health and environment by neutron activation analysis of biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Seung Yeon; Yoo, Jong Ik; Lee, Jae Kwang; Lee, Sung Jun; Lee, Sang Sun; Jeon, Ki Hong; Na, Kyung Won; Kang, Sang Hun [Yonsei University, Seoul (Korea)

    2000-04-01

    With the development of the precise quantitative analytical method for the analysis of trace elements in the various biological samples such as hair and food, evaluation in view of health and environment to the trace elements in various sources which can be introduced inside human body was done. The trace elemental distribution in Korean total diet and representative food stuff was identified first. With the project the elemental distributions in supplemental healthy food and Korean and Chinese origin oriental medicine were identified. The amount of trace elements ingested with the hair analysis of oriental medicine takers were also estimated. The amounts of trace elements inhaled with the analysis of foundry air, blood and hair of foundry workers were also estimated. The basic estimation method in view of health and environment with the neutron activation analysis of biological samples such as foods and hair was established with the result. Nationwide usage system of the NAA facility in Hanaro in many different and important areas of biological area can be initiated with the results. The output of the project can support public heath, environment, and medical research area. The results can be applied for the process of micronutrients enhanced health food production and for the health safety and health status enhancement with the additional necessary data expansion and the development of various evaluation technique. 19 refs., 7 figs., 23 tabs. (Author)

  2. Accurate treatments of electrostatics for computer simulations of biological systems: A brief survey of developments and existing problems

    Science.gov (United States)

    Yi, Sha-Sha; Pan, Cong; Hu, Zhong-Han

    2015-12-01

    Modern computer simulations of biological systems often involve an explicit treatment of the complex interactions among a large number of molecules. While it is straightforward to compute the short-ranged Van der Waals interaction in classical molecular dynamics simulations, it has been a long-lasting issue to develop accurate methods for the longranged Coulomb interaction. In this short review, we discuss three types of methodologies for the accurate treatment of electrostatics in simulations of explicit molecules: truncation-type methods, Ewald-type methods, and mean-field-type methods. Throughout the discussion, we brief the formulations and developments of these methods, emphasize the intrinsic connections among the three types of methods, and focus on the existing problems which are often associated with the boundary conditions of electrostatics. This brief survey is summarized with a short perspective on future trends along the method developments and applications in the field of biological simulations. Project supported by the National Natural Science Foundation of China (Grant Nos. 91127015 and 21522304) and the Open Project from the State Key Laboratory of Theoretical Physics, and the Innovation Project from the State Key Laboratory of Supramolecular Structure and Materials.

  3. Monte Carlo simulation of the response functions of CdTe detectors to be applied in x-ray spectroscopy

    International Nuclear Information System (INIS)

    In this work, the energy response functions of a CdTe detector were obtained by Monte Carlo (MC) simulation in the energy range from 5 to 160 keV, using the PENELOPE code. In the response calculations the carrier transport features and the detector resolution were included. The computed energy response function was validated through comparison with experimental results obtained with 241Am and 152Eu sources. In order to investigate the influence of the correction by the detector response at diagnostic energy range, x-ray spectra were measured using a CdTe detector (model XR-100T, Amptek), and then corrected by the energy response of the detector using the stripping procedure. Results showed that the CdTe exhibits good energy response at low energies (below 40 keV), showing only small distortions on the measured spectra. For energies below about 80 keV, the contribution of the escape of Cd- and Te-K x-rays produce significant distortions on the measured x-ray spectra. For higher energies, the most important correction is the detector efficiency and the carrier trapping effects. The results showed that, after correction by the energy response, the measured spectra are in good agreement with those provided by a theoretical model of the literature. Finally, our results showed that the detailed knowledge of the response function and a proper correction procedure are fundamental for achieving more accurate spectra from which quality parameters (i.e., half-value layer and homogeneity coefficient) can be determined. - Highlights: • The response function of a CdTe detector was determined by Monte Carlo simulation. • The simulation takes into account all interaction process, the carrier transport and the Gaussian resolution. • The influence of different effects of spectral distortion was investigated. • CdTe detector was applied for x-ray spectroscopy. • The proper correction procedure is needed to achieve realistic x-ray spectra

  4. In-situ fluorescence hybridization applied to biological dosimetry: contribution of automation to the counting of radio-induced chromosome aberrations

    International Nuclear Information System (INIS)

    The frequency of chromosome aberrations on peripheral blood lymphocytes is a dose indicator in the case of ionizing radiations over-exposure. Stable chromosome aberrations (translocations, insertions) are visualized after labelling of some chromosomes using the fluorescence in-situ hybridization (FISH). The study of the use of the FISH technique in biological dosimetry is done with dose-effect curves. It seems that a bias is introduced during the observation of chromosome aberrations involving only 3 pairs of chromosomes. In order to avoid this bias, it would be useful to test the feasibility of using the multi-FISH technique in biological dosimetry. Moreover, this type of chromosome aberration changes with the type of irradiation. It is thus important to define the aberrations to be considered when the FISH technique is used. In order to reduce the time of image analysis, the CYTOGEN system, developed by IMSTAR company (Paris, France) has been adapted to the needs of biological dosimetry. This system allows to localize automatically the metaphases on the slide, which reduces the observation time by 2 or 4. An automatic detection protocol for chromosome aberrations has been implemented. It comprises the image capture, the contours detection and the classification of some chromosome aberrations. The different steps of this protocol have been tested in order to check that no bias is introduced by the automation. However, because radio-induced aberrations are rare events, it seems that a totally automatic system is not foreseeable. A semi-automatic analysis is more suitable. The use of the Slit-Scan technology (Laboratory of applied physics, Heidelberg, Germany) in biological dosimetry has been studied too. This technique allows to analyze rapidly a huge number of chromosomes. A good correlation has been observed between the dicentric frequency measured automatically and by manual counting. The system is under development and should be adapted to the detection of

  5. On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

    Energy Technology Data Exchange (ETDEWEB)

    Giampaolo, Alessia Di [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Mazza, Fernando [Department of Health Sciences, Univ. of L’Aquila, 67010 L’Aquila (Italy); Daidone, Isabella [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Amicosante, Gianfranco; Perilli, Mariagrazia [Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Aschi, Massimiliano, E-mail: massimiliano.aschi@univaq.it [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy)

    2013-07-12

    Highlights: •We have performed molecular dynamics simulations of TEM-1 mutants. •Mutations effects on the mechanical properties are considered. •Mutants do not significantly alter the average enzymes structure. •Mutants produce sharp alterations in enzyme conformational repertoire. •Mutants also produce changes in the active site volume. -- Abstract: Molecular Dynamics simulations have been carried out in order to provide a molecular rationalization of the biological and thermodynamic differences observed for a class of TEM β-lactamases. In particular we have considered the TEM-1(wt), the single point mutants TEM-40 and TEM-19 representative of IRT and ESBL classes respectively, and TEM-1 mutant M182T, TEM-32 and TEM-20 which differ from the first three for the additional of M182T mutation. Results indicate that most of the thermodynamic, and probably biological behaviour of these systems arise from subtle effects which, starting from the alterations of the local interactions, produce drastic modifications of the conformational space spanned by the enzymes. The present study suggests that systems showing essentially the same secondary and tertiary structure may differentiate their chemical–biological activity essentially (and probably exclusively) on the basis of the thermal fluctuations occurring in their physiological environment.

  6. Evaluation of finite-element-based simulation model of photoacoustics in biological tissues

    Science.gov (United States)

    Wang, Zhaohui; Ha, Seunghan; Kim, Kang

    2012-03-01

    A finite element (FE)-based simulation model for photoacoustic (PA) has been developed incorporating light propagation, PA signal generation, and sound wave propagation in soft tissues using a commercial FE simulation package, COMSOL Multiphysics. The developed simulation model is evaluated by comparing with other known simulation models such as Monte Carlo method and heat-pressure model. In this in silico simulation, FE model is composed of three parts of 1) homogeneous background soft tissues submerged in water, 2) target tissue inclusion (or PA contrast agents), and 3) short pulsed laser source (pulse length of 5-10 ns). The laser point source is placed right above the tissues submerged in water. This laser source light propagation through the multi-layer tissues using the diffusion equation is compared with Monte Carlo solution. Photoacoustic signal generation by the target tissue inclusion is simulated using bioheat equation for temperature change, and resultant stress and strain. With stress-strain model, the process of the PA signal generation can be simulated further in details step by step to understand and analyze the photothermal properties of the target tissues or PA contrast agents. The created wide-band acoustic pressure (band width > 150 MHz) propagates through the background tissues to the ultrasound detector located at the tissue surface, governed by sound wave equation. Acoustic scattering and absorption in soft tissues also have been considered. Accuracy and computational time of the developed FE-based simulation model of photoacoustics have been quantitatively analyzed.

  7. Applied Electromagnetics

    International Nuclear Information System (INIS)

    These proceedings contain papers relating to the 3rd Japanese-Bulgarian-Macedonian Joint Seminar on Applied Electromagnetics. Included are the following groups: Numerical Methods I; Electrical and Mechanical System Analysis and Simulations; Inverse Problems and Optimizations; Software Methodology; Numerical Methods II; Applied Electromagnetics

  8. Simulation

    CERN Document Server

    Ross, Sheldon

    2006-01-01

    Ross's Simulation, Fourth Edition introduces aspiring and practicing actuaries, engineers, computer scientists and others to the practical aspects of constructing computerized simulation studies to analyze and interpret real phenomena. Readers learn to apply results of these analyses to problems in a wide variety of fields to obtain effective, accurate solutions and make predictions about future outcomes. This text explains how a computer can be used to generate random numbers, and how to use these random numbers to generate the behavior of a stochastic model over time. It presents the statist

  9. Absorbed dose simulations in near-surface regions using high dose rate Iridium-192 sources applied for brachytherapy

    International Nuclear Information System (INIS)

    Brachytherapy treatment with Iridium-192 high dose rate (HDR) sources is widely used for various tumours and it could be developed in many anatomic regions. Iridium-192 sources are inserted inside or close to the region that will be treated. Usually, the treatment is performed in prostate, gynaecological, lung, breast and oral cavity regions for a better clinical dose coverage compared with other techniques, such as, high energy photons and Cobalt-60 machines. This work will evaluate absorbed dose distributions in near-surface regions around Ir-192 HDR sources. Near-surface dose measurements are a complex task, due to the contribution of beta particles in the near-surface regions. These dose distributions should be useful for non-tumour treatments, such as keloids, and other non-intracavitary technique. For the absorbed dose distribution simulations the Monte Carlo code PENELOPE with the general code penEasy was used. Ir-192 source geometry and a Polymethylmethacrylate (PMMA) tube, for beta particles shield were modelled to yield the percentage depth dose (PDD) on a cubic water phantom. Absorbed dose simulations were realized at the central axis to yield the Ir-192 dose fall-off along central axis. The results showed that more than 99.2% of the absorbed doses (relative to the surface) are deposited in 5 cm depth but with slower rate at higher distances. Near-surface treatments with Ir-192 HDR sources yields achievable measurements and with proper clinical technique and accessories should apply as an alternative for treatment of lesions where only beta sources were used. - Highlights: ► A PMMA (polymethylmethacrylate) tube was used to surround the HDR Ir-192 to shield the beta particles. ► 99.2% of the absorbed doses (relative to the surface) are deposited in 5 cm depth. ► Near-surface treatments with Ir-192 HDR sources yields achievable measurements

  10. A comparative study for different shielding material composition and beam geometry applied to PET facilities: simulated transmission curves

    Energy Technology Data Exchange (ETDEWEB)

    Hoff, Gabriela [Pontificia Univ. Catolica do Rio Grande do Sul (PUCRS), Porto Alegre, RS (Brazil). Grupo de Experimentacao e Simulacao Computacional em Fisica Medica; Costa, Paulo Roberto, E-mail: pcosta@if.usp.br [Universidade de Sao Paulo (IF/USP), SP (Brazil). Dept. de Fisica Nuclear. Lab. de Dosimetria das Radiacoes e Fisica Medica

    2013-03-15

    The aim of this work is to simulate transmission data for different beam geometry and material composition in order to evaluate the effect of these parameters on transmission curves. The simulations are focused on outgoing spectra for shielding barriers used in PET facilities. The behavior of the transmission was evaluated as a function of the shielding material composition and thickness using Geant4 Monte Carlo code, version 9.2 p 03.The application was benchmarked for barited mortar and compared to The American Association of Physicists in Medicine (AAPM) data for lead. Their influence on the transmission curves as well the study of the influence of the shielding material composition and beam geometry on the outgoing spectra were performed. Characteristics of transmitted spectra, such as shape, average energy and Half-Value Layer (HVL), were also evaluated. The Geant4 toolkit benchmark for the energy resulting from the positron annihilation phenomena and its application in transmission curves description shown good agreement between data published by American Association on Physicists in Medicine task group 108 and experimental data published by Brazil. The transmission properties for different material compositions were also studied and have shown low dependency with the considered thicknesses. The broad and narrow beams configuration presented significant differences on the result. The fitting parameter for determining the transmission curves equations, according to Archer model is presented for different material. As conclusion were defined that beam geometry has significant influence and the composition has low influence on transmission curves for shielding design for the range of energy applied to PET. (author)

  11. Absorbed dose simulations in near-surface regions using high dose rate Iridium-192 sources applied for brachytherapy

    Science.gov (United States)

    Moura, E. S.; Zeituni, C. A.; Sakuraba, R. K.; Gonçalves, V. D.; Cruz, J. C.; Júnior, D. K.; Souza, C. D.; Rostelato, M. E. C. M.

    2014-02-01

    Brachytherapy treatment with Iridium-192 high dose rate (HDR) sources is widely used for various tumours and it could be developed in many anatomic regions. Iridium-192 sources are inserted inside or close to the region that will be treated. Usually, the treatment is performed in prostate, gynaecological, lung, breast and oral cavity regions for a better clinical dose coverage compared with other techniques, such as, high energy photons and Cobalt-60 machines. This work will evaluate absorbed dose distributions in near-surface regions around Ir-192 HDR sources. Near-surface dose measurements are a complex task, due to the contribution of beta particles in the near-surface regions. These dose distributions should be useful for non-tumour treatments, such as keloids, and other non-intracavitary technique. For the absorbed dose distribution simulations the Monte Carlo code PENELOPE with the general code penEasy was used. Ir-192 source geometry and a Polymethylmethacrylate (PMMA) tube, for beta particles shield were modelled to yield the percentage depth dose (PDD) on a cubic water phantom. Absorbed dose simulations were realized at the central axis to yield the Ir-192 dose fall-off along central axis. The results showed that more than 99.2% of the absorbed doses (relative to the surface) are deposited in 5 cm depth but with slower rate at higher distances. Near-surface treatments with Ir-192 HDR sources yields achievable measurements and with proper clinical technique and accessories should apply as an alternative for treatment of lesions where only beta sources were used.

  12. IT - OSRA: applying ensemble simulations to estimate the oil spill hazard associated to operational and accidental oil spills

    Science.gov (United States)

    Sepp Neves, Antonio Augusto; Pinardi, Nadia; martins, Flavio

    2016-04-01

    Every year, 270,000 tonnes of oil are estimated to be spilled in the ocean by vessel operations (e.g. tank washing, leakage of lubricants) and the so called operational spills are typically associated with small volumes and high occurrence rate. Vessel-related accidental spills (e.g. collisions, explosions) seldom occur and usually involve high volumes of oil, accounting for about 100,000 tonnes/year. The occurrence of accidental spills and their impacts have been well documented in the available literature. On the other hand, occurrence rates of operational spills and the effects they have on the marine and coastal environments remain very uncertain due to insufficient sampling effort and methodological limitations. Trying to foresee when and where an oil spill will occur in a certain area, its characteristics and impacts is, at present, impossible. Oil spill risk assessments (OSRAs) have been employed in several parts of the globe in order to deal with such uncertainties and protect the marine environment. In the present work, we computed the oil spill risk applying ensemble oil spill simulations following an ISO-31000 compliant OSRA methodology (Sepp Neves et al. , 2015). The ensemble experiment was carried out for the Algarve coast (southern Portugal) generating a unique data set of 51,200 numerical oil spill simulations covering the main sources of uncertainties (i.e. where and when the spill will happen and oil spill model configuration). From the generated data set, the risk due to accidental and operational spills was mapped for the Algarve municipalities based on the frequency and magnitude (i.e. concentrations) of beaching events and the main sources of risk were identified. The socioeconomic and environmental dimensions of the risk were treated separately. Seasonal changes in the risk index proposed due to the variability of meteo-oceanographic variables (i.e. currents and waves) were also quantified.

  13. Numerical simulation of the throwing power of cathodic prevention applied to marine reinforced concrete piles by means of sacrificial anodes

    Energy Technology Data Exchange (ETDEWEB)

    Bertolini, Luca; Redaelli, Elena [Politecnico di Milano, Dipartimento di Chimica, Materiali e Ingegneria Chimica ' G. Natta' , Via Mancinelli, 7, 20131 Milan (Italy)

    2004-07-01

    The paper deals with the determination of current and potential distribution in reinforced concrete elements partially submerged in seawater aimed at predicting the throwing power of cathodic prevention applied by means of sacrificial anodes. Previous laboratory studies carried out on reinforced concrete columns 15 cm x 15 cm x 120 cm showed that the use of sacrificial anodes placed in the solution at the bottom of the column could provide protection of corroding steel bars in the emerged part of the pile up to about 60 cm from the water level. However, if sacrificial anodes were applied when the concrete was chloride free and steel bars were still passive, even the highest bar, placed at 1 m from the level of water, was protected. This is due to the higher polarizability of passive steel, that makes the throwing power of cathodic prevention higher compared to that of cathodic protection. In order to extend the results obtained on small-scale specimens to elements of higher dimensions, numerical simulations of current and potential distribution were carried out. Two-dimensional models were set up of reinforced concrete piles containing steel bars at different heights protected with sacrificial anodes placed in the water in which they were partially submerged. Boundary conditions describing the electrochemical behaviour of bars were obtained from polarisation curves measured on the previously mentioned columns. Values of concrete conductivity at different heights from the water level were also obtained from those tests. Several cases were considered, representative of conditions differing in electrochemical behaviour of steel bars, dimensions of element, position of sacrificial anodes. The paper discusses the results obtained from the models and compares them in terms of the throwing power that can be reached by using sacrificial anodes immersed in the seawater to protect reinforcing steel bars in the emerged part of a pile. (authors)

  14. Study for the Effect of Continuously Applied Load on a Compressed Ag Nanoparticle at Room Temperature by Atomic Scale Simulations

    Science.gov (United States)

    Zhang, Lin

    2016-05-01

    Molecular dynamics calculations are reported for structural transition of a compressed Ag nanoparticle containing 2123 atoms with a crystal structure during the processes of continuously applied load at room temperature. Analytical tools are used to demonstrate the effect of the load on the packing patterns in this deformed particle including internal energy per atom, pair distribution functions, coordination number, pair number as well as the cross-sectional images, and mean square displacements. The simulation results show that the deformation processes of this particle include different stages. Owing to the atom sliding in the (111) plane in different regions of this particle, some interfaces are formed between these regions, and they are barriers of atom movements. With increasing the load, the interfaces in the middle of this particle are disappeared, and the deformation is able to carry out. At larger load, new interfaces are formed in the different regions of this heavily compressed particle with several atom layers, and these interfaces again become obstacles for the further deformation.

  15. UQ and V&V techniques applied to experiments and simulations of heated pipes pressurized to failure.

    Energy Technology Data Exchange (ETDEWEB)

    Romero, Vicente Jose; Dempsey, J. Franklin; Antoun, Bonnie R.

    2014-05-01

    This report demonstrates versatile and practical model validation and uncertainty quantification techniques applied to the accuracy assessment of a computational model of heated steel pipes pressurized to failure. The Real Space validation methodology segregates aleatory and epistemic uncertainties to form straightforward model validation metrics especially suited for assessing models to be used in the analysis of performance and safety margins. The methodology handles difficulties associated with representing and propagating interval and/or probabilistic uncertainties from multiple correlated and uncorrelated sources in the experiments and simulations including: material variability characterized by non-parametric random functions (discrete temperature dependent stress-strain curves); very limited (sparse) experimental data at the coupon testing level for material characterization and at the pipe-test validation level; boundary condition reconstruction uncertainties from spatially sparse sensor data; normalization of pipe experimental responses for measured input-condition differences among tests and for random and systematic uncertainties in measurement/processing/inference of experimental inputs and outputs; numerical solution uncertainty from model discretization and solver effects.

  16. Analysis of applied forces and electromyography of back and shoulders muscles when performing a simulated hand scaling task.

    Science.gov (United States)

    Porter, William; Gallagher, Sean; Torma-Krajewski, Janet

    2010-05-01

    Hand scaling is a physically demanding task responsible for numerous overexertion injuries in underground mining. Scaling requires the miner to use a long pry bar to remove loose rock, reducing the likelihood of rock fall injuries. The experiments described in this article simulated "rib" scaling (scaling a mine wall) from an elevated bucket to examine force generation and electromyographic responses using two types of scaling bars (steel and fiberglass-reinforced aluminum) at five target heights ranging from floor level to 176 cm. Ten male and six female subjects were tested in separate experiments. Peak and average force applied at the scaling bar tip and normalized electromyography (EMG) of the left and right pairs of the deltoid and erectores spinae muscles were obtained. Work height significantly affected peak prying force during scaling activities with highest force capacity at the lower levels. Bar type did not affect force generation. However, use of the lighter fiberglass bar required significantly more muscle activity to achieve the same force. Results of these studies suggest that miners scale points on the rock face that are below their knees, and reposition the bucket as often as necessary to do so. PMID:19800050

  17. Developing an International Combined Applied Surgical Science and Wet Lab Simulation Course as an Undergraduate Teaching Model

    Directory of Open Access Journals (Sweden)

    Michail Sideris

    2015-01-01

    Full Text Available Background. Essential Skills in the Management of Surgical Cases (ESMSC is an international, animal model-based course. It combines interactive lectures with basic ex vivo stations and more advanced wet lab modules, that is, in vivo dissections and Heart Transplant Surgery on a swine model. Materials and Methods. Forty-nine medical students (male, N=27, female N=22, and mean age = 23.7 years from King’s College London (KCL and Greek Medical Schools attended the course. Participants were assessed with Direct Observation of Procedural Skills (DOPS, as well as Multiple Choice Questions (MCQs. Paired t-test associations were used to evaluate whether there was statistically significant improvement in their performance. Aim. To evaluate the effectiveness of a combined applied surgical science and wet lab simulation course as a teaching model for surgical skills at the undergraduate level. Results. The mean MCQ score was improved by 2.33/32 (P<0.005. Surgical skills competences, as defined by DOPS scores, were improved in a statically significant manner (P<0.005 for all paired t-test correlations. Conclusions. ESMSC seems to be an effective teaching model, which improves the understanding of the surgical approach and the basic surgical skills. In vivo models could be used potentially as a step further in the Undergraduate Surgical Education.

  18. IT-OSRA: applying ensemble simulations to estimate the oil spill risk associated to operational and accidental oil spills

    Science.gov (United States)

    Sepp Neves, Antonio Augusto; Pinardi, Nadia; Martins, Flavio

    2016-08-01

    Oil Spill Risk Assessments (OSRAs) are widely employed to support decision making regarding oil spill risks. This article adapts the ISO-compliant OSRA framework developed by Sepp Neves et al. (J Environ Manag 159:158-168, 2015) to estimate risks in a complex scenario where uncertainties related to the meteo-oceanographic conditions, where and how a spill could happen exist and the risk computation methodology is not yet well established (ensemble oil spill modeling). The improved method was applied to the Algarve coast, Portugal. Over 50,000 simulations were performed in 2 ensemble experiments to estimate the risks due to operational and accidental spill scenarios associated with maritime traffic. The level of risk was found to be important for both types of scenarios, with significant seasonal variations due to the the currents and waves variability. Higher frequency variability in the meteo-oceanographic variables were also found to contribute to the level of risk. The ensemble results show that the distribution of oil concentrations found on the coast is not Gaussian, opening up new fields of research on how to deal with oil spill risks and related uncertainties.

  19. IT-OSRA: applying ensemble simulations to estimate the oil spill risk associated to operational and accidental oil spills

    Science.gov (United States)

    Sepp Neves, Antonio Augusto; Pinardi, Nadia; Martins, Flavio

    2016-06-01

    Oil Spill Risk Assessments (OSRAs) are widely employed to support decision making regarding oil spill risks. This article adapts the ISO-compliant OSRA framework developed by Sepp Neves et al. (J Environ Manag 159:158-168, 2015) to estimate risks in a complex scenario where uncertainties related to the meteo-oceanographic conditions, where and how a spill could happen exist and the risk computation methodology is not yet well established (ensemble oil spill modeling). The improved method was applied to the Algarve coast, Portugal. Over 50,000 simulations were performed in 2 ensemble experiments to estimate the risks due to operational and accidental spill scenarios associated with maritime traffic. The level of risk was found to be important for both types of scenarios, with significant seasonal variations due to the the currents and waves variability. Higher frequency variability in the meteo-oceanographic variables were also found to contribute to the level of risk. The ensemble results show that the distribution of oil concentrations found on the coast is not Gaussian, opening up new fields of research on how to deal with oil spill risks and related uncertainties.

  20. Multi-level dynamic modeling in biological systems : application of hybrid Petri nets to network simulation

    OpenAIRE

    Costa, Rafael S.; Machado, C. D.; Neves, Ana Rute; Vinga, Susana

    2012-01-01

    The recent progress in the high-throughput experimental technologies allows the reconstruction of many biological networks and to evaluate changes in proteins, genes and metabolites levels in different conditions. On the other hand, computational models, when complemented with regulatory information, can be used to predict the phenotype of an organism under different genetic and environmental conditions. These computational methods can be used for example to identify molecular targets capable...

  1. morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python.

    Science.gov (United States)

    Hull, Michael J; Willshaw, David J

    2013-01-01

    The broad structure of a modeling study can often be explained over a cup of coffee, but converting this high-level conceptual idea into graphs of the final simulation results may require many weeks of sitting at a computer. Although models themselves can be complex, often many mental resources are wasted working around complexities of the software ecosystem such as fighting to manage files, interfacing between tools and data formats, finding mistakes in code or working out the units of variables. morphforge is a high-level, Python toolbox for building and managing simulations of small populations of multicompartmental biophysical model neurons. An entire in silico experiment, including the definition of neuronal morphologies, channel descriptions, stimuli, visualization and analysis of results can be written within a single short Python script using high-level objects. Multiple independent simulations can be created and run from a single script, allowing parameter spaces to be investigated. Consideration has been given to the reuse of both algorithmic and parameterizable components to allow both specific and stochastic parameter variations. Some other features of the toolbox include: the automatic generation of human-readable documentation (e.g., PDF files) about a simulation; the transparent handling of different biophysical units; a novel mechanism for plotting simulation results based on a system of tags; and an architecture that supports both the use of established formats for defining channels and synapses (e.g., MODL files), and the possibility to support other libraries and standards easily. We hope that this toolbox will allow scientists to quickly build simulations of multicompartmental model neurons for research and serve as a platform for further tool development. PMID:24478690

  2. Relative solubiolity in simulated biological fluids of PuO2 on air sampler filters

    International Nuclear Information System (INIS)

    An ultrafiltration method was developed to estimate the solubility of PuO2 on an air filter in simulated lung fluid (SLF), simulated gastric juice (SGJ), and in 1% DTPA. After a very rapid early appearance in the filtrate, both 238Pu and 239Pu showed similar rates of low ultrafilterability. The amount of 239Pu appearing during the first day of ultrafiltration was 10 times less in SLF than in SGJ or DTPA, although the amount of 238Pu was similar for the three solvents. The method used to estimate solubility requires only about 1000 dpm of plutonium alpha radiation per sample

  3. Inference, simulation, modeling, and analysis of complex networks, with special emphasis on complex networks in systems biology

    Science.gov (United States)

    Christensen, Claire Petra

    Across diverse fields ranging from physics to biology, sociology, and economics, the technological advances of the past decade have engendered an unprecedented explosion of data on highly complex systems with thousands, if not millions of interacting components. These systems exist at many scales of size and complexity, and it is becoming ever-more apparent that they are, in fact, universal, arising in every field of study. Moreover, they share fundamental properties---chief among these, that the individual interactions of their constituent parts may be well-understood, but the characteristic behaviour produced by the confluence of these interactions---by these complex networks---is unpredictable; in a nutshell, the whole is more than the sum of its parts. There is, perhaps, no better illustration of this concept than the discoveries being made regarding complex networks in the biological sciences. In particular, though the sequencing of the human genome in 2003 was a remarkable feat, scientists understand that the "cellular-level blueprints" for the human being are cellular-level parts lists, but they say nothing (explicitly) about cellular-level processes. The challenge of modern molecular biology is to understand these processes in terms of the networks of parts---in terms of the interactions among proteins, enzymes, genes, and metabolites---as it is these processes that ultimately differentiate animate from inanimate, giving rise to life! It is the goal of systems biology---an umbrella field encapsulating everything from molecular biology to epidemiology in social systems---to understand processes in terms of fundamental networks of core biological parts, be they proteins or people. By virtue of the fact that there are literally countless complex systems, not to mention tools and techniques used to infer, simulate, analyze, and model these systems, it is impossible to give a truly comprehensive account of the history and study of complex systems. The author

  4. From track structure to biological endpoints: models, codes and MC simulations to investigate radiation action and damage formation

    International Nuclear Information System (INIS)

    The investigation of the action of ionising radiation on biological structures requires a detailed analysis of the various stages underlying damage induction and evolution. In order to take into account the stochastic aspects characterising the process of interest ab initio models and MC simulation codes are required, which start from the physical track structure and follow its time evolution, taking into account the various levels of organisation of the biological targets (DNA, chromosomes etc.). Representative examples of the activities in this area of the Universities of Milan and Pavia will be presented, focusing on the development of models aimed: a) to better understand the action mechanisms of ionising radiation, in the framework of the EC project Low Dose Risk Models coordinated by the GSF Institute of munich; b) to study the induction of chromosome aberrations and their possible use as biomarkers, mainly in the framework of the INFN experiment DOSBI, developed in collaboration with the University of Naples; c) to provide basic data for applicative tools developed for hadron therapy and space radiation protection, in the framework of the INFN projects ATER.FIBI and FLUKA and the ASI (Italian Space Agency) project Influence of the shielding in the space radiation biological effectiveness

  5. An adaptive multi-level simulation algorithm for stochastic biological systems

    International Nuclear Information System (INIS)

    Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, “Multi-level Monte Carlo for continuous time Markov chains, with applications in biochemical kinetics,” SIAM Multiscale Model. Simul. 10(1), 146–179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the

  6. An adaptive multi-level simulation algorithm for stochastic biological systems

    Science.gov (United States)

    Lester, C.; Yates, C. A.; Giles, M. B.; Baker, R. E.

    2015-01-01

    Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, "Multi-level Monte Carlo for continuous time Markov chains, with applications in biochemical kinetics," SIAM Multiscale Model. Simul. 10(1), 146-179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the

  7. morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python

    Directory of Open Access Journals (Sweden)

    Michael James Hull

    2014-01-01

    Full Text Available The broad structure of a modelling study can often be explained over a cup of coffee, butconverting this high-level conceptual idea into graphs of the final simulation results may requiremany weeks of sitting at a computer. Although models themselves can be complex, oftenmany mental resources are wasted working around complexities of the software ecosystemsuch as fighting to manage files, interfacing between tools and data formats, finding mistakesin code or working out the units of variables. morphforge is a high-level, Python toolboxfor building and managing simulations of small populations of multicompartmental biophysicalmodel neurons. An entire in silico experiment, including the definition of neuronal morphologies,channel descriptions, stimuli, visualisation and analysis of results can be written within a singleshort Python script using high-level objects. Multiple independent simulations can be createdand run from a single script, allowing parameter spaces to be investigated. Consideration hasbeen given to the reuse of both algorithmic and parameterisable components to allow bothspecific and stochastic parameter variations. Some other features of the toolbox include: theautomatic generation of human-readable documentation (e. g. PDF-files about a simulation; thetransparent handling of different biophysical units; a novel mechanism for plotting simulationresults based on a system of tags; and an architecture that supports both the use of establishedformats for defining channels and synapses (e. g. MODL files, and the possibility to supportother libraries and standards easily. We hope that this toolbox will allow scientists to quicklybuild simulations of multicompartmental model neurons for research and serve as a platform forfurther tool development.

  8. Chemical and biological toxicity assessment of simulated Hanford site low-level waste grouts

    International Nuclear Information System (INIS)

    Defining the potential damage to the biosphere associated with exposure to low-level waste grouting operations at the Hanford Site near Richland, Washington, is difficult and controversial. Combined chemical and biological assessment of grout toxicity is needed to provide information on the potential risks of animal and plant exposure to the grouts. This paper will identify and predict the chemical components of the grout that will have the greatest potential of causing deleterious effects on fish and wildlife indigenous to the Hanford Site. This paper will also determine whether the current grout technology is adequate in controlling toxicant and pollutant releases for regulatory compliance

  9. From links calibration toward hydraulic network tuning applied to RCW System (BSI - 71340) of the Cernavoda U1 Full - Scope Simulator

    International Nuclear Information System (INIS)

    A new algorithm to compute the characteristic parameters of the hydraulic network in order to increase the simulation fidelity versus real plant response is presented. The new solution is compared with the classic method of the links calibration and applied to the Recirculated Cooling Water system, which is a representing system from the hydraulic network point of view. This new method was developed by the Cernavoda U1 Simulator team and is proposed to be used for upgrading and tuning the models. (authors)

  10. NFsim: A versatile rule-based simulator for complex biological systems

    Science.gov (United States)

    Sneddon, Michael; Faeder, James; Emonet, Thierry

    2010-03-01

    Traditional methods for biochemical reaction simulation require the enumeration of every possible molecular species and reaction channel, which can be tedious and often impossible for many large or complex systems. We have developed NFsim, a new software platform for exact stochastic simulation of large biochemical reaction networks. By using an agent-based representation of molecules and rules to define interactions, the performance of NFsim is independent of the size of the reaction network. Rates in NFsim can be defined as mathematical or conditional functions of the system to facilitate coarse-graining and general specification of complex models. Here we demonstrate NFsim's novel capabilities with general models of multi-site phosphorylation proteins, receptor signaling and aggregation in the immune system, actin filament assembly, and bacterial chemotaxis signaling.

  11. morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python

    OpenAIRE

    Michael James Hull

    2014-01-01

    The broad structure of a modelling study can often be explained over a cup of coffee, butconverting this high-level conceptual idea into graphs of the final simulation results may requiremany weeks of sitting at a computer. Although models themselves can be complex, oftenmany mental resources are wasted working around complexities of the software ecosystemsuch as fighting to manage files, interfacing between tools and data formats, finding mistakesin code or working out the units of variables...

  12. Quantum Simulation of Phylogenetic Trees

    OpenAIRE

    Ellinas, Demosthenes; Jarvis, Peter

    2011-01-01

    Quantum simulations constructing probability tensors of biological multi-taxa in phylogenetic trees are proposed, in terms of positive trace preserving maps, describing evolving systems of quantum walks with multiple walkers. Basic phylogenetic models applying on trees of various topologies are simulated following appropriate decoherent quantum circuits. Quantum simulations of statistical inference for aligned sequences of biological characters are provided in terms of a quantum pruning map o...

  13. Integrating biology, field logistics, and simulations to optimize parameter estimation for imperiled species

    Science.gov (United States)

    Lanier, Wendy E.; Bailey, Larissa L.; Muths, Erin L.

    2016-01-01

    Conservation of imperiled species often requires knowledge of vital rates and population dynamics. However, these can be difficult to estimate for rare species and small populations. This problem is further exacerbated when individuals are not available for detection during some surveys due to limited access, delaying surveys and creating mismatches between the breeding behavior and survey timing. Here we use simulations to explore the impacts of this issue using four hypothetical boreal toad (Anaxyrus boreas boreas) populations, representing combinations of logistical access (accessible, inaccessible) and breeding behavior (synchronous, asynchronous). We examine the bias and precision of survival and breeding probability estimates generated by survey designs that differ in effort and timing for these populations. Our findings indicate that the logistical access of a site and mismatch between the breeding behavior and survey design can greatly limit the ability to yield accurate and precise estimates of survival and breeding probabilities. Simulations similar to what we have performed can help researchers determine an optimal survey design(s) for their system before initiating sampling efforts.

  14. Applied optics

    International Nuclear Information System (INIS)

    The 1988 progress report, of the Applied Optics laboratory, of the (Polytechnic School, France), is presented. The optical fiber activities are focused on the development of an optical gyrometer, containing a resonance cavity. The following domains are included, in the research program: the infrared laser physics, the laser sources, the semiconductor physics, the multiple-photon ionization and the nonlinear optics. Investigations on the biomedical, the biological and biophysical domains are carried out. The published papers and the congress communications are listed

  15. Simulated studies on the biological effects of space radiation on quiescent human fibroblasts

    Science.gov (United States)

    Ding, Nan; Pei, Hailong; He, Jinpeng; Furusawa, Yoshiya; Hirayama, Ryoichi; Liu, Cuihua; Matsumoto, Yoshitaka; Li, He; Hu, Wentao; Li, Yinghui; Wang, Jufang; Wang, Tieshan; Zhou, Guangming

    2013-10-01

    High charge and energy (HZE) particles are severe risk to manned long-term outer space exploration. Studies on the biological effects of space HZE particles and the underlying mechanisms are essential to the accurate risk assessment and the development of efficient countermeasure. Since majority of the cells in human body stay quiescent (G0 phase), in this study, we established G0 cell and G1 cell models by releasing human normal embryonic lung fibroblast cells from contact inhibition and studied the radiation toxicity of various kinds of HZE particles. Results showed that all of the particles were dose-dependently lethal and G0 cells were more radioresistant than G1 cells. We also found that 53BP1 foci were induced in a LET- and fluence-dependent manner and fewer foci were induced in G0 cells than G1 cells, however, the decrease of foci in 24 h after irradiation was highly relevant to the type of particles. These results imply that even though health risk of space radiation is probably overestimated by the data obtained with exponentially growing cells, whose radiosensitivity is similar to G1 cells, the risk of space HZE particles is un-ignorable and accurate assessment and mechanistic studies should be deepened. The diverse abilities of G0 cells and G1 cells in repairing DNA damages induced by HZE particles emphasize the importance in studying the impact of HZE particles on DNA damage repair pathways.

  16. Wave simulation in biologic media based on the Kelvin-Voigt fractional-derivative stress-strain relation.

    Science.gov (United States)

    Caputo, Michele; Carcione, José M; Cavallini, Fabio

    2011-06-01

    The acoustic behavior of biologic media can be described more realistically using a stress-strain relation based on fractional time derivatives of the strain, since the fractional exponent is an additional fitting parameter. We consider a generalization of the Kelvin-Voigt rheology to the case of rational orders of differentiation, the so-called Kelvin-Voigt fractional-derivative (KVFD) constitutive equation, and introduce a novel modeling method to solve the wave equation by means of the Grünwald-Letnikov approximation and the staggered Fourier pseudospectral method to compute the spatial derivatives. The algorithm can handle complex geometries and general material-property variability. We verify the results by comparison with the analytical solution obtained for wave propagation in homogeneous media. Moreover, we illustrate the use of the algorithm by simulation of wave propagation in normal and cancerous breast tissue. PMID:21601139

  17. Flow field from transient bubble oscillation in a narrow gap: numerical simulations and effect on biological cells

    CERN Document Server

    Mohammadzadeh, Milad; Ohl, Claus-Dieter

    2016-01-01

    The flow driven by a rapidly expanding and collapsing cavitation bubble in a narrow cylindrical gap is studied with the volume of fluid method. The simulations reveal a developing plug flow during the early expansion followed by flow reversal at later stages. An adverse pressure gradient leads to boundary layer separation and flow reversal, causing large shear stress near the boundaries. Analytical solution to a planar pulsating flow shows qualitative agreement with the CFD results. The shear stress close to boundaries has implications to deformable objects located near the bubble: experiments reveal that thin, flat biological cells entrained in the boundary layer become stretched, while cells with a larger cross-section are mainly transported with the flow.

  18. Simulation of export production and biological pump structure in the South China Sea

    Science.gov (United States)

    Ma, Wentao; Chai, Fei; Xiu, Peng; Xue, Huijie; Tian, Jun

    2014-12-01

    The export flux of particulate organic carbon (POC) consumes upwelled dissolved inorganic carbon (DIC), which hinders surplus CO2 being released to the atmosphere. The export flux of POC is therefore crucial to the carbon and biogeochemical cycles. This study aims to model the long-term (1958-2009) variation of export flux and structure of the biological pump in the South China Sea (SCS) using a three-dimensional physical-biogeochemical coupled (ROMS-CoSiNE) model. The modeled POC export flux in the northeastern and north central SCS is high in winter and low in summer, whereas the flux in the central, southwestern and southern SCS varies following a "W" shape: two maxima in winter and summer, and two minima in spring and autumn. The pattern follows the variation of the East Asian monsoon and is consistent with observations. On the interannual scale, export flux is anti-phased with the El Niño-Southern Oscillation such that El Niño (La Niña) conditions correspond to low (high) export flux. Modeled annual mean POC export flux reaches up to 1.95 mmol m-2 day-1, which is underestimated comparing with field observations. The f-ratio is estimated to be ~0.4. The b value of the Martin equation for POC is 1.18±0.03. Remineralization rate of POC is greater than the classical Martin equation but is consistent with its subtropical counterparts. The modeled results indicate that the SCS is a weak source of atmospheric CO2 with a flux estimated at 1.0 mmol m-2 day-1. The modeled results provide an insight of the temporal and spatial variability of the carbon cycle in this monsoon-driven, semi-enclosed basin.

  19. 生物有机肥在铜薯2号上的应用肥效试验%Biological organic fertilizer applied application in copper chips 2 test

    Institute of Scientific and Technical Information of China (English)

    杨通华

    2015-01-01

    2010年进行了生物有机肥在红薯上的应用肥效试验.结果表明,参试生物有机肥和生物液肥施用后对红薯均有不同程度的增产效果,以生物有机肥+生物液肥处理增产效果最为显著.%the 2010 applied application test of biological organic fertilizer on the sweet potato.The results show that the volunteers' biological organic fertilizer and biological effects of fertilizer on sweet potatoes all have varying degrees of increase yield,to biological organic fertilizer + biological effects of dealing with the most significant effect to increase production.

  20. A computer simulation approach to quantify the true area and true area compressibility modulus of biological membranes

    Energy Technology Data Exchange (ETDEWEB)

    Chacón, Enrique, E-mail: echacon@icmm.csic.es [Instituto de Ciencia de Materiales de Madrid, CSIC, 28049 Madrid, Spain and Instituto de Ciencia de Materiales Nicolás Cabrera, Universidad Autónoma de Madrid, Madrid 28049 (Spain); Tarazona, Pedro, E-mail: pedro.tarazona@uam.es [Departamento de Física Teórica de la Materia Condensada, Condensed Matter Physics Center (IFIMAC), and Instituto de Ciencia de Materiales Nicolás Cabrera, Universidad Autónoma de Madrid, Madrid 28049 (Spain); Bresme, Fernando, E-mail: f.bresme@imperial.ac.uk [Department of Chemistry, Imperial College London, SW7 2AZ London (United Kingdom)

    2015-07-21

    We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke’s law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.

  1. A computer simulation approach to quantify the true area and true area compressibility modulus of biological membranes

    Science.gov (United States)

    Chacón, Enrique; Tarazona, Pedro; Bresme, Fernando

    2015-07-01

    We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke's law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.

  2. A computer simulation approach to quantify the true area and true area compressibility modulus of biological membranes

    International Nuclear Information System (INIS)

    We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke’s law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers

  3. Intelligent simulated annealing algorithm applied to the optimization of the main magnet for magnetic resonance imaging machine; Algoritmo simulated annealing inteligente aplicado a la optimizacion del iman principal de una maquina de resonancia magnetica de imagenes

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez Lopez, Hector [Universidad de Oriente, Santiago de Cuba (Cuba). Centro de Biofisica Medica]. E-mail: hsanchez@cbm.uo.edu.cu

    2001-08-01

    This work describes an alternative algorithm of Simulated Annealing applied to the design of the main magnet for a Magnetic Resonance Imaging machine. The algorithm uses a probabilistic radial base neuronal network to classify the possible solutions, before the objective function evaluation. This procedure allows reducing up to 50% the number of iterations required by simulated annealing to achieve the global maximum, when compared with the SA algorithm. The algorithm was applied to design a 0.1050 Tesla four coil resistive magnet, which produces a magnetic field 2.13 times more uniform than the solution given by SA. (author)

  4. Behavioral and biological effects of autonomous versus scheduled mission management in simulated space-dwelling groups

    Science.gov (United States)

    Roma, Peter G.; Hursh, Steven R.; Hienz, Robert D.; Emurian, Henry H.; Gasior, Eric D.; Brinson, Zabecca S.; Brady, Joseph V.

    2011-05-01

    Logistical constraints during long-duration space expeditions will limit the ability of Earth-based mission control personnel to manage their astronaut crews and will thus increase the prevalence of autonomous operations. Despite this inevitability, little research exists regarding crew performance and psychosocial adaptation under such autonomous conditions. To this end, a newly-initiated study on crew management systems was conducted to assess crew performance effectiveness under rigid schedule-based management of crew activities by Mission Control versus more flexible, autonomous management of activities by the crews themselves. Nine volunteers formed three long-term crews and were extensively trained in a simulated planetary geological exploration task over the course of several months. Each crew then embarked on two separate 3-4 h missions in a counterbalanced sequence: Scheduled, in which the crews were directed by Mission Control according to a strict topographic and temporal region-searching sequence, and Autonomous, in which the well-trained crews received equivalent baseline support from Mission Control but were free to explore the planetary surface as they saw fit. Under the autonomous missions, performance in all three crews improved (more high-valued geologic samples were retrieved), subjective self-reports of negative emotional states decreased, unstructured debriefing logs contained fewer references to negative emotions and greater use of socially-referent language, and salivary cortisol output across the missions was attenuated. The present study provides evidence that crew autonomy may improve performance and help sustain if not enhance psychosocial adaptation and biobehavioral health. These controlled experimental data contribute to an emerging empirical database on crew autonomy which the international astronautics community may build upon for future research and ultimately draw upon when designing and managing missions.

  5. Simulated-physiological loading conditions preserve biological and mechanical properties of caprine lumbar intervertebral discs in ex vivo culture.

    Directory of Open Access Journals (Sweden)

    Cornelis P L Paul

    Full Text Available Low-back pain (LBP is a common medical complaint and associated with high societal costs. Degeneration of the intervertebral disc (IVD is assumed to be an important causal factor of LBP. IVDs are continuously mechanically loaded and both positive and negative effects have been attributed to different loading conditions.In order to study mechanical loading effects, degeneration-associated processes and/or potential regenerative therapies in IVDs, it is imperative to maintain the IVDs' structural integrity. While in vivo models provide comprehensive insight in IVD biology, an accompanying organ culture model can focus on a single factor, such as loading and may serve as a prescreening model to reduce life animal testing. In the current study we examined the feasibility of organ culture of caprine lumbar discs, with the hypothesis that a simulated-physiological load will optimally preserve IVD properties.Lumbar caprine IVDs (n = 175 were cultured in a bioreactor up to 21 days either without load, low dynamic load (LDL, or with simulated-physiological load (SPL. IVD stiffness was calculated from measurements of IVD loading and displacement. IVD nucleus, inner- and outer annulus were assessed for cell viability, cell density and gene expression. The extracellular matrix (ECM was analyzed for water, glycosaminoglycan and total collagen content.IVD biomechanical properties did not change significantly with loading conditions. With SPL, cell viability, cell density and gene expression were preserved up to 21 days. Both unloaded and LDL resulted in decreased cell viability, cell density and significant changes in gene expression, yet no differences in ECM content were observed in any group.In conclusion, simulated-physiological loading preserved the native properties of caprine IVDs during a 21-day culture period. The characterization of caprine IVD response to culture in the LDCS under SPL conditions paves the way for controlled analysis of degeneration

  6. Response surface method applied to the thermoeconomic optimization of a complex cogeneration system modeled in a process simulator

    International Nuclear Information System (INIS)

    This work presents the application of a surrogate model – a response surface – to replace the objective function to be minimized in the thermoeconomic optimization of a complex thermal system modeled with the aid of an expert process simulator. The objective function accounts for fuel, capital, operation and maintenance costs of the thermal system, and depends on nine decision variables. The minimization task is performed through the computational integration of two professional programs, a process simulator and a mathematical platform. Five algorithms are used to perform the optimization: the pattern search and genetic algorithms, both available in the mathematical platform, plus three custom-coded algorithms, differential evolution, particle swarm and simulated annealing. A comparative analysis of the performance of all five methods is presented, together with a critical appraisal of the surrogate model effectiveness. In the course of the optimization procedure, the process simulator computes the thermodynamic properties of all flows of the thermal system and solves the mass and energy balances each time the objective function has to be evaluated. By handling a set of radial basis functions as an approximation model to the original computationally expensive objective function, it is found here that the number of function evaluations can be appreciably reduced without significant deviation of the optimal value. The present study indicates that, for a thermoeconomic system optimization problem with a large number of decision variables and/or a costly objective function, the application of the response surface surrogate may prove more efficient than the original simulation model, reducing substantially the computational time involved in the optimization. - Highlights: ► A successful response surface method was proposed. ► The surrogate model may be more efficient than the original simulation model. ► Relative differences of less than 5% were found for the

  7. From links calibration toward hydraulic network tuning applied to RCW System (BSI - 71340) of the Cernavoda U1 Full - Scope Simulator

    International Nuclear Information System (INIS)

    Full text: A new algorithm to compute the characteristic parameters of the hydraulic network in order to increase the simulation fidelity versus real plant response is presented. The new solution is compared with the classic method of the links calibration and applied to the Recirculated Cooling Water system, which is a representing system from the hydraulic network point of view. This new method was developed by the Cernavoda U1 Simulator team and is proposed to be used for upgrading and tuning the models. (authors)

  8. Discrete event simulation methods applied to advanced importance measures of repairable components in multistate network flow systems

    International Nuclear Information System (INIS)

    Discrete event models are frequently used in simulation studies to model and analyze pure jump processes. A discrete event model can be viewed as a system consisting of a collection of stochastic processes, where the states of the individual processes change as results of various kinds of events occurring at random points of time. We always assume that each event only affects one of the processes. Between these events the states of the processes are considered to be constant. In the present paper we use discrete event simulation in order to analyze a multistate network flow system of repairable components. In order to study how the different components contribute to the system, it is necessary to describe the often complicated interaction between component processes and processes at the system level. While analytical considerations may throw some light on this, a simulation study often allows the analyst to explore more details. By producing stable curve estimates for the development of the various processes, one gets a much better insight in how such systems develop over time. These methods are particulary useful in the study of advanced importancez measures of repairable components. Such measures can be very complicated, and thus impossible to calculate analytically. By using discrete event simulations, however, this can be done in a very natural and intuitive way. In particular significant differences between the Barlow–Proschan measure and the Natvig measure in multistate network flow systems can be explored

  9. Using Physical and Computer Simulations of Collective Behaviour as an Introduction to Modelling Concepts for Applied Biologists

    Science.gov (United States)

    Rands, Sean A.

    2012-01-01

    Models are an important tool in science: not only do they act as a convenient device for describing a system or problem, but they also act as a conceptual tool for framing and exploring hypotheses. Models, and in particular computer simulations, are also an important education tool for training scientists, but it is difficult to teach students the…

  10. Simulation by using model of two species of biomass on biological phosphorus removal processes. Seibutsugaku teki datsu rin katei no niso seibutsu model ni yoru simulation

    Energy Technology Data Exchange (ETDEWEB)

    Cho, H.; Suzuki, M. (Univ. of Tokyo, Tokyo (Japan). Inst. of Industrial Science)

    1990-07-10

    This study experimented with a simple model on the process of biological phosphorus removal by anaerobic/aerobic processes in order to estimate the changes in the concentration of phosphorus and biomass. In this model, assuming that an active sludge is constituted of two phases of phosphorus removability and non-phosphorus removability in microorganisms, characteristics in the change of concentrations of phosphous and biomass in a cycle period were examined. According to the study on the factors affecting the phosphorus concentration change during a cycle period, content of microorganisms capable of removing phosphorus in the chamber and the concentration of organic materials in the initial anaerobic stage greatly influence the behavior of phosphorus. In addition, the comparative study with the experimental results indicates that this model can roughly, accurately express the characteristics of concentration change. However, the future problem left is a proposal of a model which can apply to the accummulation and and decomposition of the biomass in the non-phosphorus microorganisms. 18 refs., 6 figs., 2 tabs.

  11. An applied simulation model for estimating the supply of and requirements for registered nurses based on population health needs.

    Science.gov (United States)

    Tomblin Murphy, Gail; MacKenzie, Adrian; Alder, Robert; Birch, Stephen; Kephart, George; O'Brien-Pallas, Linda

    2009-11-01

    Aging populations, limited budgets, changing public expectations, new technologies, and the emergence of new diseases create challenges for health care systems as ways to meet needs and protect, promote, and restore health are considered. Traditional planning methods for the professionals required to provide these services have given little consideration to changes in the needs of the populations they serve or to changes in the amount/types of services offered and the way they are delivered. In the absence of dynamic planning models that simulate alternative policies and test policy mixes for their relative effectiveness, planners have tended to rely on projecting prevailing or arbitrarily determined target provider-population ratios. A simulation model has been developed that addresses each of these shortcomings by simultaneously estimating the supply of and requirements for registered nurses based on the identification and interaction of the determinants. The model's use is illustrated using data for Nova Scotia, Canada. PMID:20164064

  12. Mixed-Mode Cohesive Damage Model Applied to the Simulation of the Mechanical Behaviour of Laminated Composite Adhesive Joints

    OpenAIRE

    de Moura, MFSF; Campilho, RDSG; Goncalves, JPM

    2009-01-01

    A study of the mechanical behaviour of laminated composite adhesive joints is presented in this paper. The study consists of both numerical simulations and experimental tests. It concentrates on single lap-shear joints made of carbon-epoxy laminated composites and an epoxy adhesive. The main objective is to verify the adequacy of cohesive damage models for the strength prediction of bonded joints. These models are attractive in modelling fracture problems since they do not require the definit...

  13. Monte Carlo simulation of the response functions of Cd Te detectors to be applied in X-rays spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tomal, A. [Universidade Federale de Goias, Instituto de Fisica, Campus Samambaia, 74001-970, Goiania, (Brazil); Lopez G, A. H.; Santos, J. C.; Costa, P. R., E-mail: alessandra_tomal@yahoo.com.br [Universidade de Sao Paulo, Instituto de Fisica, Rua du Matao Travessa R. 187, Cidade Universitaria, 05508-090 Sao Paulo (Brazil)

    2014-08-15

    In this work, the energy response functions of a Cd Te detector were obtained by Monte Carlo simulation in the energy range from 5 to 150 keV, using the Penelope code. The response functions simulated included the finite detector resolution and the carrier transport. The simulated energy response matrix was validated through comparison with experimental results obtained for radioactive sources. In order to investigate the influence of the correction by the detector response at diagnostic energy range, x-ray spectra were measured using a Cd Te detector (model Xr-100-T, Amptek), and then corrected by the energy response of the detector using the stripping procedure. Results showed that the Cd Te exhibit good energy response at low energies (below 40 keV), showing only small distortions on the measured spectra. For energies below about 70 keV, the contribution of the escape of Cd- and Te-K x-rays produce significant distortions on the measured x-ray spectra. For higher energies, the most important correction is the detector efficiency and the carrier trapping effects. The results showed that, after correction by the energy response, the measured spectra are in good agreement with those provided by different models from the literature. Finally, our results showed that the detailed knowledge of the response function and a proper correction procedure are fundamental for achieve more accurate spectra from which several qualities parameters (i.e. half-value layer, effective energy and mean energy) can be determined. (Author)

  14. An observation planning algorithm applied to multi-objective astronomical observations and its simulation in COSMOS field

    Science.gov (United States)

    Jin, Yi; Gu, Yonggang; Zhai, Chao

    2012-09-01

    Multi-Object Fiber Spectroscopic sky surveys are now booming, such as LAMOST already built by China, BIGBOSS project put forward by the U.S. Lawrence Berkeley National Lab and GTC (Gran Telescopio Canarias) telescope developed by the United States, Mexico and Spain. They all use or will use this approach and each fiber can be moved within a certain area for one astrology target, so observation planning is particularly important for this Sky Surveys. One observation planning algorithm used in multi-objective astronomical observations is developed. It can avoid the collision and interference between the fiber positioning units in the focal plane during the observation in one field of view, and the interested objects can be ovserved in a limited round with the maximize efficiency. Also, the observation simulation can be made for wide field of view through multi-FOV observation. After the observation planning is built ,the simulation is made in COSMOS field using GTC telescope. Interested galaxies, stars and high-redshift LBG galaxies are selected after the removal of the mask area, which may be bright stars. Then 9 FOV simulation is completed and observation efficiency and fiber utilization ratio for every round are given. Otherwise,allocating a certain number of fibers for background sky, giving different weights for different objects and how to move the FOV to improve the overall observation efficiency are discussed.

  15. An Ecosystem Model for the Simulation of Physical and Biological Oceanic Processes-IDAPAK User's Guide and Applications

    Science.gov (United States)

    McClain, Charles R.; Arrigo, Kevin; Murtugudde, Ragu; Signorini, Sergio R.; Tai, King-Sheng

    1998-01-01

    This TM describes the development, testing, and application of a 4-component (phytoplankton, zooplankton, nitrate, and ammonium) ecosystem model capable of simulating oceanic biological processes. It also reports and documents an in-house software package (Interactive Data Analysis Package - IDAPAK) for interactive data analysis of geophysical fields, including those related to the forcing, verification, and analysis of the ecosystem model. Two regions were studied in the Pacific: the Warm Pool (WP) in the Equatorial Pacific (165 deg. E at the equator) and at Ocean Weather Station P (OWS P) in the Northeast Pacific (50 deg. N, 145 deg. W). The WP results clearly indicate that the upwelling at 100 meters correlates well with surface blooms. The upwelling events in late 1987 and 1990 produced dramatic increases in the surface layer values of all 4 ecosystem components, whereas the spring-summer deep mixing events, do not seem to incur a significant response in any of the ecosystem quantities. The OWS P results show that the monthly profiles of temperature, the annual cycles of solar irradiance, and 0- to 50-m integrated nitrate accurately reproduce observed values. Annual primary production is 190 gC/m(exp 2)/yr, which is consistent with recent observations but is much greater than earlier estimates.

  16. A counterpoint between computer simulations and biological experiments to train new members of a laboratory of physiological sciences.

    Science.gov (United States)

    Ozu, Marcelo; Dorr, Ricardo A; Gutiérrez, Facundo; Politi, M Teresa; Toriano, Roxana

    2012-12-01

    When new members join a working group dedicated to scientific research, several changes occur in the group's dynamics. From a teaching point of view, a subsequent challenge is to develop innovative strategies to train new staff members in creative thinking, which is the most complex and abstract skill in the cognitive domain according to Bloom's revised taxonomy. In this sense, current technological and digital advances offer new possibilities in the field of education. Computer simulation and biological experiments can be used together as a combined tool for teaching and learning sometimes complex physiological and biophysical concepts. Moreover, creativity can be thought of as a social process that relies on interactions among staff members. In this regard, the acquisition of cognitive abilities coexists with the attainment of other skills from psychomotor and affective domains. Such dynamism in teaching and learning stimulates teamwork and encourages the integration of members of the working group. A practical example, based on the teaching of biophysical subjects such as osmosis, solute transport, and membrane permeability, which are crucial in understanding the physiological concept of homeostasis, is presented. PMID:23209017

  17. Simulated influence of postweaning production system on performance of different biological types of cattle: I. Estimation of model parameters.

    Science.gov (United States)

    Williams, C B; Bennett, G L; Keele, J W

    1995-03-01

    Breed parameters for a computer model that simulated differences in the composition of empty-body gain of beef cattle, resulting from differences in postweaning level of nutrition that are not associated with empty BW, were estimated for 17 biological types of cattle (steers from F1 crosses of 16 sire breeds [Hereford, Angus, Jersey, South Devon, Limousin, Simmental, Charolais, Red Poll, Brown Swiss, Gelbvieh, Maine Anjou, Chianina, Brahman, Sahiwal, Pinzgauer, and Tarentaise] mated to Hereford and Angus dams). One value for the maximum fractional growth rate of fat-free matter (KMAX) was estimated and used across all breed types. Mature fat-free matter (FFMmat) was estimated from data on mature cows for each of the 17 breed types. Breed type values for a fattening parameter (THETA) were estimated from growth and composition data at slaughter on steers of the 17 breed types, using the previously estimated constant KMAX and breed values for FFMmat. For each breed type, THETA values were unique for given values of KMAX, FFMmat, and composition at slaughter. The results showed that THETA was most sensitive to KMAX and had similar sensitivity to FFMmat and composition at slaughter. Values for THETA were most sensitive for breed types with large THETA values (Chianina, Charolais, and Limousin crossbred steers) and least sensitive for breed types with small THETA values (purebred Angus, crossbred Jersey, and Red Poll steers).(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7607999

  18. Transport behavior of surrogate biological warfare agents in a simulated landfill: Effect of leachate recirculation and water infiltration

    KAUST Repository

    Saikaly, Pascal

    2010-11-15

    An understanding of the transport behavior of biological warfare (BW) agents in landfills is required to evaluate the suitability of landfills for the disposal of building decontamination residue (BDR) following a bioterrorist attack on a building. Surrogate BW agents, Bacillus atrophaeus spores and Serratia marcescens, were spiked into simulated landfill reactors that were filled with synthetic building debris (SBD) and operated for 4 months with leachate recirculation or water infiltration. Quantitative polymerase chain reaction (Q-PCR) was used to monitor surrogate transport. In the leachate recirculation reactors, <10% of spiked surrogates were eluted in leachate over 4 months. In contrast, 45% and 31% of spiked S. marcescens and B. atrophaeus spores were eluted in leachate in the water infiltration reactors. At the termination of the experiment, the number of retained cells and spores in SBD was measured over the depth of the reactor. Less than 3% of the total spiked S. marcescens cells and no B. atrophaeus spores were detected in SBD. These results suggest that significant fractions of the spiked surrogates were strongly attached to SBD. © 2010 American Chemical Society.

  19. Simulations

    CERN Document Server

    Ngada, N M

    2015-01-01

    The complexity and cost of building and running high-power electrical systems make the use of simulations unavoidable. The simulations available today provide great understanding about how systems really operate. This paper helps the reader to gain an insight into simulation in the field of power converters for particle accelerators. Starting with the definition and basic principles of simulation, two simulation types, as well as their leading tools, are presented: analog and numerical simulations. Some practical applications of each simulation type are also considered. The final conclusion then summarizes the main important items to keep in mind before opting for a simulation tool or before performing a simulation.

  20. Comprehensive Approach to Verification and Validation of CFD Simulations Applied to Backward Facing Step-Application of CFD Uncertainty Analysis

    Science.gov (United States)

    Groves, Curtis E.; LLie, Marcel; Shallhorn, Paul A.

    2012-01-01

    There are inherent uncertainties and errors associated with using Computational Fluid Dynamics (CFD) to predict the flow field and there is no standard method for evaluating uncertainty in the CFD community. This paper describes an approach to -validate the . uncertainty in using CFD. The method will use the state of the art uncertainty analysis applying different turbulence niodels and draw conclusions on which models provide the least uncertainty and which models most accurately predict the flow of a backward facing step.

  1. MOBILIZATION OF ENDOCRINE DISRUPTING CHEMICALS AND ESTROGENIC ACTIVITY IN SIMULATED RAINFALL RUNOFF FROM LAND-APPLIED BIOSOLIDS

    OpenAIRE

    Giudice, Ben D.; Young, Thomas M.

    2011-01-01

    Municipal biosolids are commonly applied to land as soil amendment or fertilizer as a form of beneficial reuse of what could otherwise be viewed as waste. Balanced against this benefit are potential risks to groundwater and surface water quality from constituents that may be mobilized during storm events. The objective of the present study was to characterize the mobilization of selected endocrine disrupting compounds (EDCs), heavy metals, and total estrogenic activity in rainfall runoff from...

  2. Quantification and differentiation of nuclear tracks in solid state detectors by simulation of their diffraction pattern applying Fourier optics

    Energy Technology Data Exchange (ETDEWEB)

    Palacios, D. [Universidad Simon Bolivar, P.O. 89000, Caracas, (Venezuela); Palacios, F. [Universidad de Oriente, Santiago de Cuba (Cuba); Viloria, T. [Universidad del Zulia, Maracaibo, (Venezuela)]. e-mail: palacios@usb.ve

    2006-07-01

    The proposed method to count and differentiate nuclear tracks in Solid State Detectors is based on digital simulation and analysis of the Fraunhofer diffraction pattern, formed when coherent light passes through tracks in an etched detector. Analytical and numerical models were developed using, as transformation element, an optical system and a digital procedure of the Fourier Transform, respectively. Different components of developed software are described, and depending on the kind of detector used, variants of optical microscopy are suggested. The proposed method allows to calculate real track density and to differentiate tracks by their diameters. (Author)

  3. A new method for the determination of surface tension from molecular dynamics simulations applied to liquid droplets

    International Nuclear Information System (INIS)

    For the determination of surface tension of liquid droplets by molecular dynamics simulations, the most time-consuming part is the calculation of pressure tensor in the transition layer, which makes it difficult to enhance the precision of the computation. A new method for the calculation of surface tension of liquid droplets to reduce the calculation quantity of pressure tensor in transition layer to the minimum is proposed in this paper. Two thousand particles are taken as example to show how to carry out our scheme. (condensed matter: structural, mechanical, and thermal properties)

  4. Monte Carlo simulation of parameter confidence intervals for non-linear regression analysis of biological data using Microsoft Excel.

    Science.gov (United States)

    Lambert, Ronald J W; Mytilinaios, Ioannis; Maitland, Luke; Brown, Angus M

    2012-08-01

    This study describes a method to obtain parameter confidence intervals from the fitting of non-linear functions to experimental data, using the SOLVER and Analysis ToolPaK Add-In of the Microsoft Excel spreadsheet. Previously we have shown that Excel can fit complex multiple functions to biological data, obtaining values equivalent to those returned by more specialized statistical or mathematical software. However, a disadvantage of using the Excel method was the inability to return confidence intervals for the computed parameters or the correlations between them. Using a simple Monte-Carlo procedure within the Excel spreadsheet (without recourse to programming), SOLVER can provide parameter estimates (up to 200 at a time) for multiple 'virtual' data sets, from which the required confidence intervals and correlation coefficients can be obtained. The general utility of the method is exemplified by applying it to the analysis of the growth of Listeria monocytogenes, the growth inhibition of Pseudomonas aeruginosa by chlorhexidine and the further analysis of the electrophysiological data from the compound action potential of the rodent optic nerve. PMID:21764476

  5. Economic impact of explosive volcanic eruptions: A simulation-based assessment model applied to Campania region volcanoes

    Science.gov (United States)

    Zuccaro, Giulio; Leone, Mattia Federico; Del Cogliano, Davide; Sgroi, Angelo

    2013-10-01

    PLINIVS Study Centre of University of Naples Federico II has developed a methodology that aims to estimate, in probabilistic terms, the direct and the indirect economic impacts of a Sub-Plinian I or Strombolian type eruption of Vesuvius. The economic model has been implemented as a complementary tool of the Volcanic Impact Simulation Model, a tool developed at PLINIVS Center available to the Italian Civil Protection Department (DPC) decision makers to quantify the potential losses consequent to a possible eruption of Vesuvius or Campi Flegrei. Along the expected time history of the eruptive event all the possible "direct costs" and the "factors" (indirect costs) impacting the economic growth in the event area have been identified. Each cost factor is built up through a specific algorithm that is fed by various providers, in order to run software that will estimate the global amount of economic damage from a volcanic event. The model does not include the economic evaluation of intangibles (e.g. human casualties), while the evaluation of damage to the local cultural heritage (historical buildings, archeological sites, monuments, etc.), is linked to the economic impact on tourism, estimated into indirect costs. The architecture of the model is based on a simulation logic, which allows an evaluation of different economic impact scenarios through input changes, allowing the model to be used as a tool to support the decision making process.

  6. General meeting. Technical reunion: the numerical and experimental simulation applied to the Reactor Physics; Assemblee generale. Reunion technique: la simulation numerique et experimentale appliquee a la physique des reacteurs

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-10-01

    The SFEN (French Society on Nuclear Energy), organized the 18 october 2001 at Paris, a technical day on the numerical and experimental simulation, applied to the reactor Physics. Nine aspects were discussed, giving a state of the art in the domain:the french nuclear park; the future technology; the controlled thermonuclear fusion; the new organizations and their implications on the research and development programs; Framatome-ANP markets and industrial code packages; reactor core simulation at high temperature; software architecture; SALOME; DESCARTES. (A.L.B.)

  7. Local approach of cleavage fracture applied to a vessel with subclad flaw. A benchmark on computational simulation

    International Nuclear Information System (INIS)

    A benchmark on the computational simulation of a cladded vessel with a 6.2 mm sub-clad flaw submitted to a thermal transient has been conducted. Two-dimensional elastic and elastic-plastic finite element computations of the vessel have been performed by the different partners with respective finite element codes ASTER (EDF), CASTEM 2000 (CEA), SYSTUS (Framatome) and ABAQUS (AEA Technology). Main results have been compared: temperature field in the vessel, crack opening, opening stress at crack tips, stress intensity factor in cladding and base metal, Weibull stress σw and probability of failure in base metal, void growth rate R/R0 in cladding. This comparison shows an excellent agreement on main results, in particular on results obtained with local approach. (K.A.)

  8. Comparative study of OMA applied to experimental and simulated data from an operating Vestas V27 wind turbine

    DEFF Research Database (Denmark)

    Requeson, Oscar Ramirez; Tcherniak, Dmitri; Larsen, Gunner Chr.

    2015-01-01

    Today, design of wind turbines is extensively done by the implementation of numerical models. These models simulate the dynamic behaviour of full-scale wind turbines which helps to ensure the structural integrity of prototypes. However, these numerical models need validation from experimental...... results, and in turn, numerical and analytical modelling help improve and validate new experimental techniques. Wind turbines are complex dynamic systems that consist of mutually moving substructures under high dynamic loads. At a standstill, the system can be modelled as linear time-invariant (LTI), and...... assumptions, among which is the assumption of isotropic rotors. Since rotors are never completely isotropic in real life, this paper presents the application of operational modal analysis together with the Coleman transformation on both experimental data from a full-scale Vestas wind turbine with instrumented...

  9. Simulation of space-borne tsunami detection using GNSS-Reflectometry applied to tsunamis in the Indian Ocean

    Directory of Open Access Journals (Sweden)

    R. Stosius

    2010-06-01

    Full Text Available Within the German-Indonesian Tsunami Early Warning System project GITEWS (Rudloff et al., 2009, a feasibility study on a future tsunami detection system from space has been carried out. The Global Navigation Satellite System Reflectometry (GNSS-R is an innovative way of using reflected GNSS signals for remote sensing, e.g. sea surface altimetry. In contrast to conventional satellite radar altimetry, multiple height measurements within a wide field of view can be made simultaneously. With a dedicated Low Earth Orbit (LEO constellation of satellites equipped with GNSS-R, densely spaced sea surface height measurements could be established to detect tsunamis. This simulation study compares the Walker and the meshed comb constellation with respect to their global reflection point distribution. The detection performance of various LEO constellation scenarios with GPS, GLONASS and Galileo as signal sources is investigated. The study concentrates on the detection performance for six historic tsunami events in the Indian Ocean generated by earthquakes of different magnitudes, as well as on different constellation types and orbit parameters. The GNSS-R carrier phase is compared with the PARIS or code altimetry approach. The study shows that Walker constellations have a much better reflection point distribution compared to the meshed comb constellation. Considering simulation assumptions and assuming technical feasibility it can be demonstrated that strong tsunamis with magnitudes (M ≥8.5 can be detected with certainty from any orbit altitude within 15–25 min by a 48/8 or 81/9 Walker constellation if tsunami waves of 20 cm or higher can be detected by space-borne GNSS-R. The carrier phase approach outperforms the PARIS altimetry approach especially at low orbit altitudes and for a low number of LEO satellites.

  10. BioDMET: a physiologically based pharmacokinetic simulation tool for assessing proposed solutions to complex biological problems.

    Science.gov (United States)

    Graf, John F; Scholz, Bernhard J; Zavodszky, Maria I

    2012-02-01

    We developed a detailed, whole-body physiologically based pharmacokinetic (PBPK) modeling tool for calculating the distribution of pharmaceutical agents in the various tissues and organs of a human or animal as a function of time. Ordinary differential equations (ODEs) represent the circulation of body fluids through organs and tissues at the macroscopic level, and the biological transport mechanisms and biotransformations within cells and their organelles at the molecular scale. Each major organ in the body is modeled as composed of one or more tissues. Tissues are made up of cells and fluid spaces. The model accounts for the circulation of arterial and venous blood as well as lymph. Since its development was fueled by the need to accurately predict the pharmacokinetic properties of imaging agents, BioDMET is more complex than most PBPK models. The anatomical details of the model are important for the imaging simulation endpoints. Model complexity has also been crucial for quickly adapting the tool to different problems without the need to generate a new model for every problem. When simpler models are preferred, the non-critical compartments can be dynamically collapsed to reduce unnecessary complexity. BioDMET has been used for imaging feasibility calculations in oncology, neurology, cardiology, and diabetes. For this purpose, the time concentration data generated by the model is inputted into a physics-based image simulator to establish imageability criteria. These are then used to define agent and physiology property ranges required for successful imaging. BioDMET has lately been adapted to aid the development of antimicrobial therapeutics. Given a range of built-in features and its inherent flexibility to customization, the model can be used to study a variety of pharmacokinetic and pharmacodynamic problems such as the effects of inter-individual differences and disease-states on drug pharmacokinetics and pharmacodynamics, dosing optimization, and inter

  11. Simulation study on the efficiencies of MOET nucleus breeding schemes applying marker assisted selection in dairy cattle

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Advantages of breeding schemes using genetic marker information and/or multiple ovulation and embryo transfer(MOET) technology over the traditional approach were extensively evaluated through simulation.Milk yield was the trait of interest and QTL was the genetic marker utilized.Eight dairy cattle breeding scenarios were considered,i.e.,traditional progeny testing breeding scheme(denoted as STANPT),GASPT scheme including a pre-selection of young bulls entering progeny testing based on their own QTL information,MOETPT scheme using MOET technology to generate young bulls and a selection of young bulls limited within the full-sib family,GAMOPT scheme adopting both QTL pre-selection and MOET technology,COMBPT scheme using a mixed linear model which considered QTL genotype instead of the BLUP model in GAMOPT,and three non-progeny testing schemes,i.e.the MOET,GAMO and COMB schemes,corresponding to MOETPT,GAMOPT and COMBPT with progeny testing being part of the system.Animals were selected based on their breeding value which was estimated under an animal model framework.Sequential selection over 17 years was performed in the simulations and 30 replicates were designed for each scenario.The influences of using QTL information and MOET technology on favorable QTL allele frequency,true breeding values,polygenetic breeding values and the accumulated genetic superiority were extensively evaluated,for five different populations including active sires,lactating cows,bull dams,bull sires,and young bulls.The results showed that the combined schemes significantly outperformed other approaches wherein accumulated true breeding value progressed.The difference between schemes exclusively using QTL information or MOET technology was not significant.The STANPT scheme was the least efficient among the 8 schemes.The schemes using MOET technology had a higher polygenetic response than others in the 17th year.The increases of frequency of the favorable QTL allele varied more greatly across

  12. Simulation study on the efficiencies of MOET nucleus breeding schemes applying marker assisted selection in dairy cattle

    Institute of Scientific and Technical Information of China (English)

    LUO WeiZhen; WANG YaChun; ZHANG Yuan

    2009-01-01

    Advantages of breeding schemes using genetic marker information and/or multiple ovulation and em-bryo transfer (MOET) technology over the traditional approach were extensively evaluated through simulation. Milk yield was the trait of interest and QTL was the genetic marker utilized. Eight dairy cattle breeding scenarios were considered, i.e., traditional progeny testing breeding scheme (denoted as STANPT), GASPT scheme including a pre-selection of young bulls entering progeny testing based on their own QTL information, MOETPT scheme using MOET technology to generate young bulls and a selection of young bulls limited within the full-sib family, GAMOPT scheme adopting both QTL pre-selection and MOET technology, COMBPT scheme using a mixed linear model which considered QTL genotype instead of the BLUP model in GAMOPT, and three non-progeny testing schemes, i.e. the MOET, GAMO and COMB schemes, corresponding to MOETPT, GAMOPT and COMBPT with progeny testing being part of the system. Animals were selected based on their breeding value which was es-timated under an animal model framework. Sequential selection over 17 years was performed in the simulations and 30 replicates were designed for each scenario. The influences of using QTL informa-tion and MOET technology on favorable QTL allele frequency, true breeding values, polygenetic breeding values and the accumulated genetic superiority were extensively evaluated, for five different populations including active sires, lactating cows, bull dams, bull sires, and young bulls. The results showed that the combined schemes significantly outperformed other approaches wherein accumulated true breeding value progressed. The difference between schemes exclusively using QTL information or MOET technology was not significant. The STANPT scheme was the least efficient among the 8 schemes. The schemes using MOET technology had a higher polygenetic response than others in the 17th year. The increases of frequency of the favorable QTL

  13. Seasonal assessment of biological indices, bioaccumulation and bioavailability of heavy metals in mussels Mytilus galloprovincialis from Algerian west coast, applied to environmental monitoring

    Directory of Open Access Journals (Sweden)

    Omar Rouane-Hacene

    2015-10-01

    Full Text Available The aim of the present work is to broaden our knowledge on the variability of trace metals in mussel tissues, focusing on seasonal fluctuations in the three different sampling sites of Algerian west coast (Oran Harbor (S1, Ain Defla (S2 and Hadjaj (S3. For this purpose, the bioavailability (metal indices and bioaccumulation (metal concentrations in soft tissues of heavy metals (Zn, Cu, Pb, and Cd, and the physiological characteristics (e.g. biological indices such as condition index (CI of mussels Mytilus galloprovincialis have been assessed and related to seasons and sites. In S1, the highest levels of metal concentrations and indices were obtained in mussels sampled in winter for Zn, Cu and Cd, but in summer for Pb. The biological indices significantly decreased in winter. In S2, the levels of concentrations and indices of all metals varied whatever the seasons, excepting in summer where the values were the lowest. In summer and spring, the biological indices were lower than in autumn and winter. The low growth of organisms in spring and summer might be correlated to the reproductive period and the low trophic level known in S2. S3, considered as a “pristine” area, showed low metal concentrations and indices, and high biological indices, reflecting the favorable physiological conditions for the mussel growth. This approach might be used in the monitoring of the quality of coastal waters and the present work provided a useful data set for Mediterranean monitoring network.

  14. Analysis of possibility to apply new mathematical methods (R-function theory) in Monte Carlo simulation of complex geometry

    International Nuclear Information System (INIS)

    This analysis is part of the report on ' Implementation of geometry module of 05R code in another Monte Carlo code', chapter 6.0: establishment of future activity related to geometry in Monte Carlo method. The introduction points out some problems in solving complex three-dimensional models which induce the need for developing more efficient geometry modules in Monte Carlo calculations. Second part include formulation of the problem and geometry module. Two fundamental questions to be solved are defined: (1) for a given point, it is necessary to determine material region or boundary where it belongs, and (2) for a given direction, all cross section points with material regions should be determined. Third part deals with possible connection with Monte Carlo calculations for computer simulation of geometry objects. R-function theory enables creation of geometry module base on the same logic (complex regions are constructed by elementary regions sets operations) as well as construction geometry codes. R-functions can efficiently replace functions of three-value logic in all significant models. They are even more appropriate for application since three-value logic is not typical for digital computers which operate in two-value logic. This shows that there is a need for work in this field. It is shown that there is a possibility to develop interactive code for computer modeling of geometry objects in parallel with development of geometry module

  15. Monte Carlo simulation of the response functions of CdTe detectors to be applied in x-ray spectroscopy.

    Science.gov (United States)

    Tomal, A; Santos, J C; Costa, P R; Lopez Gonzales, A H; Poletti, M E

    2015-06-01

    In this work, the energy response functions of a CdTe detector were obtained by Monte Carlo (MC) simulation in the energy range from 5 to 160keV, using the PENELOPE code. In the response calculations the carrier transport features and the detector resolution were included. The computed energy response function was validated through comparison with experimental results obtained with (241)Am and (152)Eu sources. In order to investigate the influence of the correction by the detector response at diagnostic energy range, x-ray spectra were measured using a CdTe detector (model XR-100T, Amptek), and then corrected by the energy response of the detector using the stripping procedure. Results showed that the CdTe exhibits good energy response at low energies (below 40keV), showing only small distortions on the measured spectra. For energies below about 80keV, the contribution of the escape of Cd- and Te-K x-rays produce significant distortions on the measured x-ray spectra. For higher energies, the most important correction is the detector efficiency and the carrier trapping effects. The results showed that, after correction by the energy response, the measured spectra are in good agreement with those provided by a theoretical model of the literature. Finally, our results showed that the detailed knowledge of the response function and a proper correction procedure are fundamental for achieving more accurate spectra from which quality parameters (i.e., half-value layer and homogeneity coefficient) can be determined. PMID:25599872

  16. A GAMOS plug-in for GEANT4 based Monte Carlo simulation of radiation-induced light transport in biological media

    OpenAIRE

    Glaser, Adam K.; Kanick, Stephen C.; Zhang, Rongxiao; Arce, Pedro; Pogue, Brian W.

    2013-01-01

    We describe a tissue optics plug-in that interfaces with the GEANT4/GAMOS Monte Carlo (MC) architecture, providing a means of simulating radiation-induced light transport in biological media for the first time. Specifically, we focus on the simulation of light transport due to the Čerenkov effect (light emission from charged particle’s traveling faster than the local speed of light in a given medium), a phenomenon which requires accurate modeling of both the high energy particle and subsequen...

  17. Proceedings of the international conference on radiation biology and clinical applications: a molecular approach towards innovations in applied radiobiology and a workshop on strategies in radiation research

    International Nuclear Information System (INIS)

    Innovations in radiotherapy approaches to cancer and radiation biology research is of growing interest in radiation researchers to conduct preclinical studies at their centers and translating the results as soon as possible to clinical radiotherapy practice. Recent papers have greatly enriched the current knowledge of radiation oncology, especially radiobiology and molecular oncology, and this has radically changed the oncology practice in radiation therapy in just a few years. The conference theme highlights the molecular and cellular responses within tissue and higher levels of mammalian biological organization. New experimental radiobiology research to underpin current and future regulatory decisions setting workplace exposure limits. To develop rapid, high-precision analytical methods that assess radiation exposure doses from clinical samples and thus aid in the triage and medical management of radiological casualties. Innovative approaches to improve the accuracy, dose range, ease of use, and speed of classical biodosimetry. Papers relevant to INIS are indexed separately

  18. The Examination of the Effects of Biological Gender and Gender Identity Roles on Attitude of the Consumers to Advertisements Applied by Accomodation Operations

    OpenAIRE

    Evren Güçer; Özgür Yayla; Burcu Koç

    2013-01-01

    In this study, especially focused on the concept of psychological-based gender identity and researched if there is a differentiation characteristic of consumers’ sex and gender identity roles (masculinity, femininity, androgynous and neutral) on consumers’ attitude toward advertisements of accomodation establishments.According to the results,there is a general accordance between biological sex and gender identity roles of individuals and alsothe results of the previous studies were mad...

  19. Applying a low energy HPGe detector gamma ray spectrometric technique for the evaluation of Pu/Am ratio in biological samples

    International Nuclear Information System (INIS)

    The estimation of Pu/241Am ratio in the biological samples is an important input for the assessment of internal dose received by the workers. The radiochemical separation of Pu isotopes and 241Am in a sample followed by alpha spectrometry is a widely used technique for the determination of Pu/241Am ratio. However, this method is time consuming and many times quick estimation is required. In this work, Pu/241Am ratio in the biological sample was estimated with HPGe detector based measurements using gamma/X-rays emitted by these radionuclides. These results were compared with those obtained from alpha spectroscopy of sample after radiochemical analysis and found to be in good agreement. - Highlights: • High resolution gamma ray spectroscopy technique with low energy HPGe detector is used for the measurement of Pu isotopes and 241Am in biological samples. • Results obtained with gamma ray spectroscopy compared well with the results obtained from radiochemical analysis of sample followed by α-spectroscopy. • Results of this study will be useful for assessment and medical management of Pu/241Am embedded in tissue of workers

  20. The Effects Of Teaching Photosynthesis Unit With Computer Simulation Supported Co-Operative Learning On Retention And Student Attitude To Biology

    OpenAIRE

    Rıfat EFE; Behçet ORAL; ASLAN EFE, Hülya; Meral Önder SÜNKÜR

    2011-01-01

    In this study, student achievement in and attitude toward subject was investigated by comparing computer simulation supported Student Teams Achievement Divisions (STAD) of co-operative learning with traditional learning in biology classes. The study was carried out with the participation of 81 students in 10th grade at Diyarbakir Melik Ahmet Secondary School during autumn term of 2009- 2010 academic year. The control and experimental groups were randomly selected from equal groups. An achieve...

  1. Detection, simulation and evaluation of environmental impacts. Climate, shock, radiation, vibrations, electromagnetism, air pollution, biological influences. Proceeedings

    International Nuclear Information System (INIS)

    Environmental simulation is designed to reveal cause-and-effect mechanisms involved in ageing and weathering processes. The 24 contributions to the 22nd annual conference deal with the topics: detection of environmental influences, simulation techniques, strategies in environmental simulation, and effects and measures. (DG)

  2. gamma-ray DBSCAN: a clustering algorithm applied to Fermi-LAT gamma-ray data. I. Detection performances with real and simulated data

    CERN Document Server

    Tramacere, A

    2012-01-01

    The Density Based Spatial Clustering of Applications with Noise (DBSCAN) is a topometric algorithm used to cluster spatial data that are affected by background noise. For the first time, we propose the use of this method for the detection of sources in gamma-ray astrophysical images obtained from the Fermi-LAT data, where each point corresponds to the arrival direction of a photon. We investigate the detection performance of the gamma-ray DBSCAN in terms of detection efficiency and rejection of spurious clusters, using a parametric approach, and exploring a large volume of the gamma-ray DBSCAN parameter space. By means of simulated data we statistically characterize the gamma-ray DBSCAN, finding signatures that differentiate purely random fields, from fields with sources. We define a significance level for the detected clusters, and we successfully test this significance with our simulated data. We apply the method to real data, and we find an excellent agreement with the results obtained with simulated data....

  3. Simulation of CNT-AFM tip based on finite element analysis for targeted probe of the biological cell

    Science.gov (United States)

    Yousefi, Amin Termeh; Mahmood, Mohamad Rusop; Miyake, Mikio; Ikeda, Shoichiro

    2016-07-01

    Carbon nanotubes (CNTs) are potentially ideal tips for atomic force microscopy (AFM) due to the robust mechanical properties, nano scale diameter and also their ability to be functionalized by chemical and biological components at the tip ends. This contribution develops the idea of using CNTs as an AFM tip in computational analysis of the biological cell's. Finite element analysis employed for each section and displacement of the nodes located in the contact area was monitored by using an output database (ODB). This reliable integration of CNT-AFM tip process provides a new class of high performance nanoprobes for single biological cell analysis.

  4. Applied group theory applications in the engineering (physical, chemical, and medical), biological, social, and behavioral sciences and in the fine arts

    Science.gov (United States)

    Borg, S. F.

    1976-01-01

    A generalized applied group theory is developed, and it is shown that phenomena from a number of diverse disciplines may be included under the umbrella of a single theoretical formulation based upon the concept of a group consistent with the usual definition of this term.

  5. The Effects Of Teaching Photosynthesis Unit With Computer Simulation Supported Co-Operative Learning On Retention And Student Attitude To Biology

    Directory of Open Access Journals (Sweden)

    Rıfat EFE

    2011-06-01

    Full Text Available In this study, student achievement in and attitude toward subject was investigated by comparing computer simulation supported Student Teams Achievement Divisions (STAD of co-operative learning with traditional learning in biology classes. The study was carried out with the participation of 81 students in 10th grade at Diyarbakir Melik Ahmet Secondary School during autumn term of 2009- 2010 academic year. The control and experimental groups were randomly selected from equal groups. An achievement test consisted of 31 questions from photosynthesis unit and an attitude scale was used as the data collection instruments. The study revealed that teaching method that was supported by computer simulations had more effects on student achievement in comparison to the traditional teaching method. Differences between students’ attitude who were taught with computer simulation supported co-operative learning and students’ attitude who were instructed by traditional teaching did not emerge as statistically significant.Keywords:

  6. Regional-scale simulations of fungal spore aerosols using an emission parameterization adapted to local measurements of fluorescent biological aerosol particles

    Directory of Open Access Journals (Sweden)

    M. Hummel

    2014-04-01

    Full Text Available Fungal spores as a prominent type of primary biological aerosol particles (PBAP have been incorporated into the COSMO-ART regional atmospheric model, using and comparing three different emission parameterizations. Two literature-based emission rates derived from fungal spore colony counts and chemical tracer measurements were used as a parameterization baseline for this study. A third, new emission parameterization was adapted to field measurements of fluorescent biological aerosol particles (FBAP from four locations across Northern Europe. FBAP concentrations can be regarded as a lower estimate of total PBAP concentrations. Size distributions of FBAP often show a distinct mode at approx. 3 μm, corresponding to a diameter range characteristic for many fungal spores. Previous studies have suggested the majority of FBAP in several locations are dominated by fungal spores. Thus, we suggest that simulated fungal spore concentrations obtained from the emission parameterizations can be compared to the sum of total FBAP concentrations. A comparison reveals that parameterized estimates of fungal spore concentrations based on literature numbers underestimate measured FBAP concentrations. In agreement with measurement data, the model results show a diurnal cycle in simulated fungal spore concentrations, which may develop partially as a consequence of a varying boundary layer height between day and night. Measured FBAP and simulated fungal spore concentrations also correlate similarly with simulated temperature and humidity. These meteorological variables, together with leaf area index, were chosen to drive the new emission parameterization discussed here. Using the new emission parameterization on a model domain covering Western Europe, fungal spores in the lowest model layer comprise a fraction of 15% of the total aerosol mass over land and reach average number concentrations of 26 L−1. The results confirm that fungal spores and biological particles

  7. Particle induced X-ray emission and ion dose distribution in a biological micro-beam: Geant4 Monte Carlo simulations

    International Nuclear Information System (INIS)

    The goal of a microbeam is to deliver a highly localized and small dose to the biological medium. This can be achieved by using a set of collimators that confine the charged particle beam to a very small spatial area of the order of microns in diameter. By using a system that combines an appropriate beam detection method that signals to a beam shut-down mechanism, a predetermined and counted number of energetic particles can be delivered to targeted biological cells. Since the shutter and the collimators block a significant proportion of the beam, there is a probability of the production of low energy X-rays and secondary electrons through interactions with the beam. There is little information in the biological microbeam literature on potential X-ray production. We therefore used Monte Carlo simulations to investigate the potential production of particle-induced X-rays and secondary electrons in the collimation system (which is predominantly made of tungsten) and the subsequent possible effects on the total absorbed dose delivered to the biological medium. We found, through the simulation, no evidence of the escape of X-rays or secondary electrons from the collimation system for proton energies up to 3 MeV as we found that the thickness of the collimators is sufficient to reabsorb all of the generated low energy X-rays and secondary electrons. However, if the proton energy exceeds 3 MeV our simulations suggest that 10 keV X-rays can escape the collimator and expose the overlying layer of cells and medium. If the proton energy is further increased to 4.5 MeV or beyond, the collimator can become a significant source of 10 keV and 59 keV X-rays. These additional radiation fields could have effects on cells and these results should be verified through experimental measurement. We suggest that researchers using biological microbeams at higher energies need to be aware that cells may be exposed to a mixed LET radiation field and be careful in their interpretation of

  8. A parameterization for the radio emission of air showers as predicted by CoREAS simulations and applied to LOFAR measurements

    CERN Document Server

    Nelles, Anna; Falcke, Heino; Hörandel, Jörg; Huege, Tim; Schellart, Pim

    2014-01-01

    Measuring radio emission from air showers provides excellent opportunities to directly measure all air shower properties, including the shower development. To exploit this in large-scale experiments, a simple and analytic parameterization of the distribution of the pulse power at ground level is needed. Data taken with the Low-Frequency Array (LOFAR) show a complex two-dimensional pattern of pulse powers, which is sensitive to the shower geometry. Earlier parameterizations of the lateral signal distribution have proven insufficient to describe these data. In this article, we present a parameterization derived from air-shower simulations. We are able to fit the two-dimensional distribution with a double Gaussian, requiring five independent parameters. All parameters show strong correlations with air shower properties, such as the energy of the shower, the arrival direction, and the shower maximum. We successfully apply the parameterization to data taken with LOFAR and discuss implications for air shower experi...

  9. How to apply a turbulent transport model based on a gyrokinetic simulation for the ion temperature gradient mode in helical plasmas

    International Nuclear Information System (INIS)

    How to apply a reduced model for the turbulent ion heat diffusivity [Nunami M et al. 2013 Phys. Plasmas, 20 092307] derived from a gyrokinetic code to a transport simulation is proposed. The reduced model is given by the function of the linear growth rate of the ion temperature gradient (ITG) mode and the decay time of zonal flows. The ion temperature gradient scale length is chosen for the additional modeling to include the linear growth rate of the ITG mode from a gyrokinetic code. The formula for the zonal flow decay time is derived at the given magnetic field configuration. The calculation of an extremely low computational cost in this article reproduces the results of the reduced model for the turbulent ion heat diffusivity within allowable errors

  10. Opinion of the Scientific Panel on Biological Hazards on the Evaluation of the efficacy of peroxyacids for use as an antimicrobial substance applied on poultry carcasses

    DEFF Research Database (Denmark)

    Nørrung, Birgit

    The European Commission requested EFSA to evaluate the efficacy of peroxyacids as an antimicrobial substance applied to poultry carcasses. Particularly, the BIOHAZ panel was asked to assess the efficacy of the peroxyacids on the growth and/or prevalence of some microorganisms and pathogens on....../or prevalence of pathogenic microorganisms. However, according to the opinion of Scientific Committee on Veterinary Measure related to Public Health (SCVPH, 2003) and to the European Commission, decontamination should only be used as an additional measure to further reduce the load of pathogenic microorganisms...

  11. Simulation studies of statistical distributions of cell membrane capacities and an ellipse model to assess the frequency behaviour of biological tissues

    International Nuclear Information System (INIS)

    The frequency behaviour of biological tissues is commonly described by a Cole model reflecting a single-cell bio-impedance model extended with an exponent α. However, for this parameter α there is no physical or biological substrate, which impedes an interpretation. The present study confirms by computer simulations of tissue models that the factual frequency behaviour can be explained by assuming a distribution of the electrical impedance properties of cells and of the capacitive coupling between cells. This behaviour is modelled mathematically by an ellipse. A mathematical procedure is presented to estimate this ellipse from experimental data by a least square method. A model parameter β is introduced, representing the ratio of the axes of the ellipse. A higher value of β means a larger variation in cell properties, which makes a patho-physiological interpretation of changes possible.

  12. γ-ray DBSCAN: a clustering algorithm applied to Fermi-LAT γ-ray data. I. Detection performances with real and simulated data

    Science.gov (United States)

    Tramacere, A.; Vecchio, C.

    2013-01-01

    Context. The density based spatial clustering of applications with noise (DBSCAN) is a topometric algorithm used to cluster spatial data that are affected by background noise. For the first time, we propose this method to detect sources in γ-ray astrophysical images obtained from the Fermi-LAT data, where each point corresponds to the arrival direction of a photon. Aims: We investigate the detection performance of the γ-ray DBSCAN in terms of detection efficiency and rejection of spurious clusters. Methods: We used a parametric approach, exploring a large volume of the γ-ray DBSCAN parameter space. By means of simulated data we statistically characterized the γ-ray DBSCAN, finding signatures that distinguish purely random fields from fields with sources. We defined a significance level for the detected clusters and successfully tested this significance with our simulated data. We applied the method to real data and found an excellent agreement with the results obtained with simulated data. Results.We find that the γ-ray DBSCAN can be successfully used in detecting clusters in γ-ray data. The significance returned by our algorithm is strongly correlated with that provided by the maximum likelihood analysis with standard Fermi-LAT software, and can be used to safely remove spurious clusters. The positional accuracy of the reconstructed cluster centroid compares to that returned by standard maximum likelihood analysis, allowing one to look for astrophysical counterparts in narrow regions, which minimizes the chance probability in the counterpart association. Conclusions.We found that γ-ray DBSCAN is a powerful tool for detecting of clusters in γ-ray data. It can be used to look for both point-like sources and extended sources, and can be potentially applied to any astrophysical field related to detecting clusters in data. In a companion paper we will present the application of the γ-ray DBSCAN to the full Fermi-LAT sky, discussing the potential of the

  13. Simulating effects of environmental factors on biological control of Tetranychus urticae by Typhlodromus pyri in apple orchards

    NARCIS (Netherlands)

    Hardman, J.M.; Werf, van der W.; Blatt, S.E.; Franklin, J.L.; Karsten, R.; Teismann, H.

    2013-01-01

    Successful biological control of mites is possible under various conditions, and identifying what are the requirements for robust control poses a challenge because interacting factors are involved. Process-based modeling can help to explore these interactions and identify under which conditions biol

  14. And So It Grows: Using a Computer-Based Simulation of a Population Growth Model to Integrate Biology & Mathematics

    Science.gov (United States)

    Street, Garrett M.; Laubach, Timothy A.

    2013-01-01

    We provide a 5E structured-inquiry lesson so that students can learn more of the mathematics behind the logistic model of population biology. By using models and mathematics, students understand how population dynamics can be influenced by relatively simple changes in the environment.

  15. Simulation

    DEFF Research Database (Denmark)

    Gould, Derek A; Chalmers, Nicholas; Johnson, Sheena J;

    2012-01-01

    Recognition of the many limitations of traditional apprenticeship training is driving new approaches to learning medical procedural skills. Among simulation technologies and methods available today, computer-based systems are topical and bring the benefits of automated, repeatable, and reliable...... performance assessments. Human factors research is central to simulator model development that is relevant to real-world imaging-guided interventional tasks and to the credentialing programs in which it would be used....

  16. Computational Systems Chemical Biology

    OpenAIRE

    Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

  17. Ho{sup 3+} carbon paste sensor based on multi-walled carbon nanotubes: Applied for determination of holmium content in biological and environmental samples

    Energy Technology Data Exchange (ETDEWEB)

    Faridbod, Farnoush [Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Endocrinology and Metabolism Research Center, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Ganjali, Mohammad Reza, E-mail: ganjali@khayam.ut.ac.ir [Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Endocrinology and Metabolism Research Center, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Larijani, Bagher [Endocrinology and Metabolism Research Center, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Hosseini, Morteza [Department of Chemistry, Islamic Azad University, Savadkooh Branch, Savadkooh (Iran, Islamic Republic of); Norouzi, Parviz [Endocrinology and Metabolism Research Center, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran (Iran, Islamic Republic of)

    2010-05-10

    For the first time a novel multi-walled carbon nanotubes (MWCNTs) modified Ho{sup 3+} carbon paste sensor is introduced. The electrode with a composition containing 20% paraffin oil, 60% graphite powder, 15% N-(1-thia-2-ylmethylene)-1,3-benzothiazole-2-amine (TBA) as an ionophore, and 5% MWCNTs, exhibits a stable potential response to Ho{sup 3+} ions with a nice Nernstian behavior (19.3 {+-} 0.3 mV decade{sup -1}) in a wide dynamic linear concentration range of Ho{sup 3+} ions (1 x 10{sup -8}-1.0 x 10{sup -2} M). In the absence of MWCNTs, sensitivity of the Ho{sup 3+} sensor was relatively poor. The proposed modified Ho{sup 3+} sensor shows very low detection limit (7.0 x 10{sup -9} M) and a fast response time (13 s). It has a long life time (more than 2 months) and its response is independent of pH in the range of 3.8-7.5. In term of selectivity, Ho{sup 3+} sensor has a good selectivity over all lanthanide members and common alkali and alkaline earth metal ions. The Ho{sup 3+} sensor was applied for the determination of Ho{sup 3+} ion concentration in water, holmium alloys and synthetic human serum.

  18. Ho3+ carbon paste sensor based on multi-walled carbon nanotubes: Applied for determination of holmium content in biological and environmental samples

    International Nuclear Information System (INIS)

    For the first time a novel multi-walled carbon nanotubes (MWCNTs) modified Ho3+ carbon paste sensor is introduced. The electrode with a composition containing 20% paraffin oil, 60% graphite powder, 15% N-(1-thia-2-ylmethylene)-1,3-benzothiazole-2-amine (TBA) as an ionophore, and 5% MWCNTs, exhibits a stable potential response to Ho3+ ions with a nice Nernstian behavior (19.3 ± 0.3 mV decade-1) in a wide dynamic linear concentration range of Ho3+ ions (1 x 10-8-1.0 x 10-2 M). In the absence of MWCNTs, sensitivity of the Ho3+ sensor was relatively poor. The proposed modified Ho3+ sensor shows very low detection limit (7.0 x 10-9 M) and a fast response time (13 s). It has a long life time (more than 2 months) and its response is independent of pH in the range of 3.8-7.5. In term of selectivity, Ho3+ sensor has a good selectivity over all lanthanide members and common alkali and alkaline earth metal ions. The Ho3+ sensor was applied for the determination of Ho3+ ion concentration in water, holmium alloys and synthetic human serum.

  19. Modeling and Simulation of Physiology and Population-Dynamics of Copepods - Effects of Physical and Biological Parameters

    OpenAIRE

    Dag Slagstad

    1981-01-01

    A detailed model of the physiology and vertical migration behaviour of marine copepods of the ca/anus is developed. A two-dimensional population model calculates the size and developmental structure of the population in relation to its own dynamics and the environment. Examination of the effect on the population dynamics and production of copepods by changing the physical and biological parameters is performed.

  20. Modeling and Simulation of Physiology and Population-Dynamics of Copepods - Effects of Physical and Biological Parameters

    Directory of Open Access Journals (Sweden)

    Dag Slagstad

    1981-07-01

    Full Text Available A detailed model of the physiology and vertical migration behaviour of marine copepods of the ca/anus is developed. A two-dimensional population model calculates the size and developmental structure of the population in relation to its own dynamics and the environment. Examination of the effect on the population dynamics and production of copepods by changing the physical and biological parameters is performed.

  1. Mathematical simulation of microwave scattering in the medium with characteristic features of biological tissues and prospectives of microwave tomography

    OpenAIRE

    Sukharevsky, Oleg I.; Lesovoy, V. N.; Zamiatin, V. L.; Gorelyshev, S. A.; Podorozhnyak, A. A.

    1995-01-01

    Computer aided tomography is used today in many areas of science and technology, such as biology, medicine, geophysics, plasma physics, non-destructive introscopy and state control of heat-radiation elements at nuclear power plants, cartography, etc. Microwave imaging is one of the prospective methods of tomography. It is based on the retrieval of dielectric properties of a solid body irradiated by an electromagnetic wave of microwave band. Scanning the scientific and technical literature, in...

  2. Real-Time Agent-Based Modeling Simulation with in-situ Visualization of Complex Biological Systems

    Science.gov (United States)

    Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y. K.

    2016-01-01

    We present an efficient and scalable scheme for implementing agent-based modeling (ABM) simulation with In Situ visualization of large complex systems on heterogeneous computing platforms. The scheme is designed to make optimal use of the resources available on a heterogeneous platform consisting of a multicore CPU and a GPU, resulting in minimal to no resource idle time. Furthermore, the scheme was implemented under a client-server paradigm that enables remote users to visualize and analyze simulation data as it is being generated at each time step of the model. Performance of a simulation case study of vocal fold inflammation and wound healing with 3.8 million agents shows 35× and 7× speedup in execution time over single-core and multi-core CPU respectively. Each iteration of the model took less than 200 ms to simulate, visualize and send the results to the client. This enables users to monitor the simulation in real-time and modify its course as needed. PMID:27547508

  3. Approaches to the dimensioning of enhanced biological phosphorus elimination systems, taking dynamic simulation into account; Bemessungshinweise zur vermehrten biologischen Phosphorelimination unter Beruecksichtigung der dynamischen Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Scheer, H.

    1997-12-31

    With so many projects either planned or under construction, the question of the dimensioning of sewage treatment plants with enhanced biological phosphorus elimination (BIO-P) is becoming more and more important. A detailed search of literature established in how far dimensioning approaches or models were already available in the spring of 1994. These modelling approaches were critically examined and compared as to their practical applicability by means of parameter and sensitivity studies. For this purpose, they were programmed and the relevance of certain dimensioning parameters to biological phosphorus elimination was studied by means of a pilot plant. (orig./SR) [Deutsch] Der Auslegung von Klaeranlagen mit vermehrter biologischer Phosphorelimination (BIO-P) kommt bei der Vielzahl von Planungs- und Baumassnahmen eine immer wichtigere Bedeutung zu. Inwieweit fuer die Bemessung von Klaeranlagen mit BIO-P im Fruehjahr 1994 bereits auf vorhandene Bemessungsansaetze und -modelle zurueckgegriffen werden konnte, wurde mittels einer detaillierten Literaturstudie, untersucht. Diese Modellansaetze wurden im Hinblick auf ihre praxisorietierte Anwendbarkeit durch Parameter- und Sensitivitaetsstudien kritisch untersucht und verglichen. Hierzu wurden die verschiedenen, zum damaligen Zeitpunkt vorhandenen Ansaetze programmiert und die Auswirkungen wichtiger bemessungsrelevanter Parameter auf die BIO-P anhand einer Modellklaeranlage abgeschaetzt. (orig./SR)

  4. Predicting the effect of ionising radiation on biological populations: testing of a non-linear Leslie model applied to a small mammal population

    International Nuclear Information System (INIS)

    The present work describes the application of a non-linear Leslie model for predicting the effects of ionising radiation on wild populations. The model assumes that, for protracted chronic irradiation, the effect-dose relationship is linear. In particular, the effects of radiation are modelled by relating the increase in the mortality rates of the individuals to the dose rates through a proportionality factor C. The model was tested using independent data and information from a series of experiments that were aimed at assessing the response to radiation of wild populations of meadow voles and whose results were described in the international literature. The comparison of the model results with the data selected from the above mentioned experiments showed that the model overestimated the detrimental effects of radiation on the size of irradiated populations when the values of C were within the range derived from the median lethal dose (L50) for small mammals. The described non-linear model suggests that the non-expressed biotic potential of the species whose growth is limited by processes of environmental resistance, such as the competition among the individuals of the same or of different species for the exploitation of the available resources, can be a factor that determines a more effective response of population to the radiation effects. -- Highlights: • A model to assess the radiation effects on wild population is described. • The model is based on non-linear Leslie matrix. • The model is applied to small mammals living in an irradiated meadow. • Model output is conservative if effect-dose factor estimated from L50 is used. • Systemic response to stress of populations in competitive conditions may be more effective

  5. Medical students’ satisfaction with the Applied Basic Clinical Seminar with Scenarios for Students, a novel simulation-based learning method in Greece

    Science.gov (United States)

    2016-01-01

    Purpose: The integration of simulation-based learning (SBL) methods holds promise for improving the medical education system in Greece. The Applied Basic Clinical Seminar with Scenarios for Students (ABCS3) is a novel two-day SBL course that was designed by the Scientific Society of Hellenic Medical Students. The ABCS3 targeted undergraduate medical students and consisted of three core components: the case-based lectures, the ABCDE hands-on station, and the simulation-based clinical scenarios. The purpose of this study was to evaluate the general educational environment of the course, as well as the skills and knowledge acquired by the participants. Methods: Two sets of questions were distributed to the participants: the Dundee Ready Educational Environment Measure (DREEM) questionnaire and an internally designed feedback questionnaire (InEv). A multiple-choice examination was also distributed prior to the course and following its completion. A total of 176 participants answered the DREEM questionnaire, 56 the InEv, and 60 the MCQs. Results: The overall DREEM score was 144.61 (±28.05) out of 200. Delegates who participated in both the case-based lectures and the interactive scenarios core components scored higher than those who only completed the case-based lecture session (P=0.038). The mean overall feedback score was 4.12 (±0.56) out of 5. Students scored significantly higher on the post-test than on the pre-test (P<0.001). Conclusion: The ABCS3 was found to be an effective SBL program, as medical students reported positive opinions about their experiences and exhibited improvements in their clinical knowledge and skills. PMID:27012313

  6. Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications

    Directory of Open Access Journals (Sweden)

    Lee-Wei Yang

    2008-01-01

    Full Text Available Molecular dynamics (MD simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the a bsence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed.

  7. Determining DfT Hardware by VHDL-AMS Fault Simulation for Biological Micro-Electronic Fluidic Arrays

    NARCIS (Netherlands)

    Kerkhoff, H.G.; Zhang, X.; Liu, H.; Richardson, A.; Nouet, P.; Azais, F.

    2005-01-01

    The interest of microelectronic fluidic arrays for biomedical applications, like DNA determination, is rapidly increasing. In order to evaluate these systems in terms of required Design-for-Test structures, fault simulations in both fluidic and electronic domains are necessary. VHDL-AMS can be used

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

    International Nuclear Information System (INIS)

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

  9. Simulated Batch Production of Penicillin

    Science.gov (United States)

    Whitaker, A.; Walker, J. D.

    1973-01-01

    Describes a program in applied biology in which the simulation of the production of penicillin in a batch fermentor is used as a teaching technique to give students experience before handling a genuine industrial fermentation process. Details are given for the calculation of minimum production cost. (JR)

  10. The photon and fast neutron spectra measurement and calculation in the concrete of the simulator of WWER-1000 reactor biological shielding

    International Nuclear Information System (INIS)

    The measurements have been performed in the WWER-1000 model in experimental reactor LR-0 in N.R.I. (Nuclear Research Institute). The biological shielding simulator consists of serpentinite concrete with stainless steel cover. It is placed behind the reactor pressure vessel (R.P.V.) simulator situated in a concrete hall outside of LR-0 tank. Simulators of reactor internals as well as the driving core are in the LR-0 reactor tank. The fuel assemblies consist of 312 fuel pins (hexagon of WWER-1000 type) with 1.25 m active length. The measurements were performed before concrete shielding and in the channel in the concrete. The photon and neutron spectra have been measured simultaneously with two-parametric spectrometer with extended energy range [1], 0.5 MeV 10 MeV for both parts of radiation field. The results were by means of monitoring system normalized to other ones in the WWER-1000 model. The calculation of the measured spectra has been performed with the deterministic 3D code T.O.R.T. and cross section library B.U.G.L.E. 96. Comparison of calculated and measured results can enable evaluate reliability of calculation results for deep penetration of radiation, as well as the capability for planning of decommissioning issues. (authors)

  11. The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes.

    Science.gov (United States)

    Vianello, Robert; Domene, Carmen; Mavri, Janez

    2016-01-01

    HIGHLIGHTS Computational techniques provide accurate descriptions of the structure and dynamics of biological systems, contributing to their understanding at an atomic level.Classical MD simulations are a precious computational tool for the processes where no chemical reactions take place.QM calculations provide valuable information about the enzyme activity, being able to distinguish among several mechanistic pathways, provided a carefully selected cluster model of the enzyme is considered.Multiscale QM/MM simulation is the method of choice for the computational treatment of enzyme reactions offering quantitative agreement with experimentally determined reaction parameters.Molecular simulation provide insight into the mechanism of both the catalytic activity and inhibition of monoamine oxidases, thus aiding in the rational design of their inhibitors that are all employed and antidepressants and antiparkinsonian drugs. Aging society and therewith associated neurodegenerative and neuropsychiatric diseases, including depression, Alzheimer's disease, obsessive disorders, and Parkinson's disease, urgently require novel drug candidates. Targets include monoamine oxidases A and B (MAOs), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and various receptors and transporters. For rational drug design it is particularly important to combine experimental synthetic, kinetic, toxicological, and pharmacological information with structural and computational work. This paper describes the application of various modern computational biochemistry methods in order to improve the understanding of a relationship between the structure and function of large biological systems including ion channels, transporters, receptors, and metabolic enzymes. The methods covered stem from classical molecular dynamics simulations to understand the physical basis and the time evolution of the structures, to combined QM, and QM/MM approaches to probe the chemical mechanisms of enzymatic

  12. Eruca sativa Might Influence the Growth, Survival under Simulated Gastrointestinal Conditions and Some Biological Features of Lactobacillus acidophilus, Lactobacillus plantarum and Lactobacillus rhamnosus Strains

    Directory of Open Access Journals (Sweden)

    Florinda Fratianni

    2014-10-01

    Full Text Available The growth and viability of three Lactobacillus strains, Lactobacillus acidophilus, Lactobacillus plantarum and Lactobacillus rhamnosus, after their passage through simulated gastric and pancreatic juices were studied as a function of their presence in the growth medium of rocket salad (Eruca sativa. The presence of E. sativa affected some of the biological properties of the strains. For example, L. acidophilus and L. plantarum worked more efficiently in the presence of E. sativa, increasing not only the antioxidant activity of the medium, but also their own antioxidant power and antimicrobial activity; L. rhamnosus was not affected in the same manner. Overall, the presence of vegetables might help to boost, in specific cases, some of the characteristics of lactobacilli, including antioxidant and antimicrobial power.

  13. Prospective computerized simulation of breast cancer: comparison of computer predictions with nine sets of biological and clinical data.

    Science.gov (United States)

    Retsky, M W; Wardwell, R H; Swartzendruber, D E; Headley, D L

    1987-09-15

    A computer program which accepts clinically relevant information can be used to predict breast cancer growth, response to chemotherapy, and disease-free survival. The computer output is patient individualized because the program is highly iterative and simulates up to 2500 patients with exactly the same clinical presentation. Computer predictions have been compared to a broad spectrum of breast cancer data, and a high degree of correlation has been established. There are numerous significant clinical implications which can be derived from the computer model. Among these are the following. (a) Breast cancer tumors do not grow continuously but may have up to five growth plateaus each lasting from a small fraction of a year up to approximately 8 yr. (b) Adjuvant chemotherapy, such as 6-mo treatment with cyclophosphamide-methotrexate-5-fluorouracil, does not eradicate tumors but just reduces the number of viable cells by a factor of 10 to 100 and sets the eventual growth back by several years. This may partially explain why the age-adjusted death rate from breast cancer has not changed in the past 50 yr. (c) The computer model challenges the underlying principles in support of short-term intensive adjuvant chemotherapy, namely Gompertzian kinetics and genetically acquired tumor resistance to drugs. (d) The computer model questions the evidence opposing long-term maintenance chemotherapy protocols and suggests that maintenance protocols should be reexamined. PMID:2441859

  14. Mechanistic simulation of radiation damage to DNA and its repair: On the track towards systems radiation biology modelling

    International Nuclear Information System (INIS)

    The biophysical simulation code PARTRAC enables, by combining track structure calculations with DNA models on diverse genomic scales, prediction of DNA damage yields and patterns for various radiation qualities. To extend its applicability to later endpoints such as mutagenesis or cell killing, a continuative model for repair of radiation-induced double-strand break (DSB) via non-homologous end-joining has complemented the PARTRAC code by about 12 orders of magnitude on a temporal scale. The repair model describes step-by-step by the Monte Carlo method the attachment and dissociation of involved repair enzymes and diffusion motion of DNA ends. The complexity of initial DNA lesion patterns influences the repair kinetics and outcome via additional cleaning steps required for dirty DNA ends. Model parameters have been taken from measured attachment kinetics of repair enzymes and adaptation to DSB rejoining kinetics after gamma irradiation. Application of the DNA repair model to damage patterns following nitrogen ion irradiation and comparison with experimental results reveal the need for further model refinements. Nevertheless, already the present model represents a promising step towards systems modelling of cellular response to radiation. (authors)

  15. Monte Carlo simulation applied to order economic analysis Simulação de Monte Carlo aplicada à análise econômica de pedido

    Directory of Open Access Journals (Sweden)

    Abraão Freires Saraiva Júnior

    2011-03-01

    Full Text Available The use of mathematical and statistical methods can help managers to deal with decision-making difficulties in the business environment. Some of these decisions are related to productive capacity optimization in order to obtain greater economic gains for the company. Within this perspective, this study aims to present the establishment of metrics to support economic decisions related to process or not orders in a company whose products have great variability in variable direct costs per unit that generates accounting uncertainties. To achieve this objective, is proposed a five-step method built from the integration of Management Accounting and Operations Research techniques, emphasizing the Monte Carlo simulation. The method is applied from a didactic example which uses real data achieved through a field research carried out in a plastic products industry that employ recycled material. Finally, it is concluded that the Monte Carlo simulation is effective for treating variable direct costs per unit variability and that the proposed method is useful to support decision-making related to order acceptance.A utilização de métodos matemáticos e estatísticos pode auxiliar gestores a lidar com dificuldades do processo de tomada de decisão no ambiente de negócios. Algumas dessas decisões estão relacionadas à otimização da utilização da capacidade produtiva visando a obtenção de melhores resultados econômicos para a empresa. Dentro dessa perspectiva, o presente trabalho objetiva apresentar o estabelecimento de métricas que deem suporte à decisão econômica de atender ou não a pedidos em uma empresa cujos produtos têm grande variabilidade de custos variáveis diretos unitários que gera incertezas contábeis. Para cumprir esse objetivo, é proposto um método em cinco etapas, construído a partir da integração de técnicas provindas da contabilidade gerencial e da pesquisa operacional, com destaque à simulação de Monte Carlo. O m

  16. Theoretical approach to biological aging

    CERN Document Server

    D'Almeida, R M C; Penna, T J P

    1997-01-01

    We present a model for biological aging that considers the number of individuals whose (inherited) genetic charge determines the maximum age for death: each individual may die before that age due to some external factor, but never after that limit. The genetic charge of the offspring is inherited from the parent with some mutations, described by a transition matrix. The model can describe different strategies of reproduction and it is exactly soluble. We applied our method to the bit-string model for aging and the results are in perfect agreement with numerical simulations.

  17. Study of x-ray fluorescence : Development in Geant4 of new models of cross sections for simulation PIXE. Biological and archaeological applications

    International Nuclear Information System (INIS)

    the potassium content in reference samples of the types mineralogical and biological. We show on this occasion the utility of our simulation program like effective means of adjustment and validation. Lastly, since we will have in the next years at CNSTN the proton-induced x-ray emission (PIXE) technique, we describe in the final chapter, another application in analysis of archaeological samples (coins of medieval currencies) by PIXE technique. This study initially brings us to the experimental control of this alternative of the method of analysis by x-ray fluorescence to be able then to describe, by Monte Carlo simulation, the experimental device which it includes and the spectral answer that it produces. The extension of the capacities of our Monte Carlo simulation code for the adjustment of PIXE spectra is to us of a great utility for our next in situ tests of development of PIXE technique.

  18. Status of (137)Cs contamination in marine biota along the Pacific coast of eastern Japan derived from a dynamic biological model two years simulation following the Fukushima accident.

    Science.gov (United States)

    Tateda, Yutaka; Tsumune, Daisuke; Tsubono, Takaki; Misumi, Kazuhiro; Yamada, Masatoshi; Kanda, Jota; Ishimaru, Takashi

    2016-01-01

    Radiocesium ((134)Cs and (137)Cs) released into the Fukushima coastal environment was transferred to marine biota inhabiting the Pacific Ocean coastal waters of eastern Japan. Though the levels in most of the edible marine species decreased overtime, radiocesium concentrations in some fishes were still remained higher than the Japanese regulatory limit for seafood products. In this study, a dynamic food chain transfer model was applied to reconstruct (137)Cs levels in olive flounder by adopting the radiocesium concentrations in small demersal fish which constitute an important fraction of the diet of the olive flounder particularly inhabiting area near Fukushima. In addition, (137)Cs levels in slime flounder were also simulated using reported radiocesium concentrations in some prey organisms. The simulated results from Onahama on the southern border of the Fukushima coastline, and at Choshi the southernmost point where the contaminated water mass was transported by the Oyashio current, were assessed in order to identify what can be explained from present information, and what remains to be clarified three years after the Fukushima Dai-ichi nuclear power plant (1FNPP) accident. As a result, the observed (137)Cs concentrations in planktivorous fish and their predator fish could be explained by the theoretically-derived simulated levels. On the other hand, the slow (137)Cs depuration in slime flounder can be attributed to uptake from unknown sources for which the uptake fluxes were of a similar magnitude as the excretion fluxes. Since the reported (137)Cs concentrations in benthic invertebrates off Onahama were higher than the simulated values, radiocesium transfer from these benthic detritivorous invertebrates to slime flounder via ingestion was suggested as a cause for the observed slow depuration of (137)Cs in demersal fish off southern Fukushima. Furthermore, the slower depuration in the demersal fish likely required an additional source of (137)Cs, i

  19. Simulation and cost analysis of systems for handling of fuel straw - applied to a heating plant in Skaane; Simulering och kostnadsanalys av hanteringssystem foer braenslehalm - tillaempning foer en vaermeanlaeggning i Skaane

    Energy Technology Data Exchange (ETDEWEB)

    Nilsson, Daniel

    2010-05-15

    SEK/MWh for an equivalent harvest system with storage in machine sheds (0% storage losses, 60% of the construction costs assigned to the straw, the rest for other uses). - Increasing the bale weight from 530 kg to 700 kg (with unchanged dimensions of 1.2 m x 1.3 m x 2.4 m) produced cost savings of 15%. Having bales with an unchanged weight of 530 kg, but with a height of 1.0 m so that three bales could be stacked on top of one another during transport, resulted in similar cost savings. - In-depth studies are needed regarding the capacity of modern harvest and handling machines, stoppage frequency, etc. (i.e. time studies), the impact of various weather parameters on straw quality, the costs and storage losses for different storage methods, etc. - Dynamic event simulation is a useful method for analysing complex logistics systems where weather, plant biology, geography, soil characteristics, etc. have a major impact on the outcome

  20. Deformation and fault parameters of the 2005 Qeshm earthquake in Iran revisited: A Bayesian simulated annealing approach applied to the inversion of space geodetic data

    OpenAIRE

    M. Amighpey; B. Voosoghi; Mahdi Motagh

    2013-01-01

    The estimation of earthquake source parameters using an earth surface displacement field in an elastic half-space leads to a complex nonlinear inverse problem that classic inverse methods are unable to solve. Global optimization methods such as simulated annealing are a good replacement for such problems. Simulated annealing is analogous to thermodynamic annealing where, under certain conditions, the chaotic motions of atoms in a melt can settle to form a crystal with minimal energy. Followin...

  1. Applied superconductivity

    CERN Document Server

    Newhouse, Vernon L

    1975-01-01

    Applied Superconductivity, Volume II, is part of a two-volume series on applied superconductivity. The first volume dealt with electronic applications and radiation detection, and contains a chapter on liquid helium refrigeration. The present volume discusses magnets, electromechanical applications, accelerators, and microwave and rf devices. The book opens with a chapter on high-field superconducting magnets, covering applications and magnet design. Subsequent chapters discuss superconductive machinery such as superconductive bearings and motors; rf superconducting devices; and future prospec

  2. Biological Threats

    Science.gov (United States)

    ... Workplace Plans School Emergency Plans Main Content Biological Threats Biological agents are organisms or toxins that can ... for Disease Control and Prevention . Before a Biological Threat Unlike an explosion, a biological attack may or ...

  3. Numerical analysis of applied magnetic field dependence in Malmberg-Penning Trap for compact simulator of energy driver in heavy ion fusion

    Science.gov (United States)

    Sato, T.; Park, Y.; Soga, Y.; Takahashi, K.; Sasaki, T.; Kikuchi, T.; Harada, Nob

    2016-05-01

    To simulate a pulse compression process of space charge dominated beams in heavy ion fusion, we have demonstrated a multi-particle numerical simulation as an equivalent beam using the Malmberg-Penning trap device. The results show that both transverse and longitudinal velocities as a function of external magnetic field strength are increasing during the longitudinal compression. The influence of space-charge effect, which is related to the external magnetic field, was observed as the increase of high velocity particles at the weak external magnetic field.

  4. LabVIEW在蒸汽发生器动态仿真研究的应用%Labview Applied in Dynamic Simulation of Steam Generators

    Institute of Scientific and Technical Information of China (English)

    张琴舜; 李剑

    2001-01-01

    由于蒸汽发生器是压水堆的核心部件,而且蒸汽发生器的故障概率也比较高,因此蒸汽发生器的仿真研究是现今核电厂控制领域的重要课题之一。本文重点介绍一种新型仿真语言LabVIEW在蒸汽发生器仿真中的应用,对比以前所用到的仿真语言,这种语言带来许多的便利与强大的功能。%Steam generator, a key component of the PWR, has high malfunctionrate in operation. That is why its simulation becomes one of the most important topics in the area of nuclear power plant control. This paper introduces a new type simulation language of LabVIEW for simulation of steam generators. Compared with traditional simulation languages, LabVIEW proves more powerful and advantageous.

  5. Metoder for Modellering, Simulering og Regulering af Større Termiske Processer anvendt i Sukkerproduktion. Methods for Modelling, Simulation and Control of Large Scale Thermal Systems Applied in Sugar Production

    DEFF Research Database (Denmark)

    Nielsen, Kirsten Mølgaard; Nielsen, Jens Frederik Dalsgaard

    of a computer, a data terminal and an electric interface corresponding to the interface at the sugar plant. The simulator is operating in realtime and thus a realistic test of controllers is possible. The idiomatic control methodology has been investigated developing a control concept for the......The subject of this Ph.D. thesis is to investigate and develop methods for modelling, simulation and control applicable in large scale termal industrial plants. An ambition has been to evaluate the results in a physical process. Sugar production is well suited for the purpose. In collaboration with...... evaporator simulator has been developed. The simulator handles the normal working conditions relevant to control engineers. A non-linear dynamic model based on mass and energy balances has been developed. The model parameters have been adjusted to data measured on a Danish sugar plant. The simulator consists...

  6. Applied Stratigraphy

    Science.gov (United States)

    Lucas, Spencer G.

    Stratigraphy is a cornerstone of the Earth sciences. The study of layered rocks, especially their age determination and correlation, which are integral parts of stratigraphy, are key to fields as diverse as geoarchaeology and tectonics. In the Anglophile history of geology, in the early 1800s, the untutored English surveyor William Smith was the first practical stratigrapher, constructing a geological map of England based on his own applied stratigraphy. Smith has, thus, been seen as the first “industrial stratigrapher,” and practical applications of stratigraphy have since been essential to most of the extractive industries from mining to petroleum. Indeed, gasoline is in your automobile because of a tremendous use of applied stratigraphy in oil exploration, especially during the latter half of the twentieth century. Applied stratigraphy, thus, is a subject of broad interest to Earth scientists.

  7. Aerospace Medicine and Biology: A Continuing Bibliography. Supplement 483

    Science.gov (United States)

    1999-01-01

    Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion.

  8. Applied mathematics

    CERN Document Server

    Logan, J David

    2013-01-01

    Praise for the Third Edition"Future mathematicians, scientists, and engineers should find the book to be an excellent introductory text for coursework or self-study as well as worth its shelf space for reference." -MAA Reviews Applied Mathematics, Fourth Edition is a thoroughly updated and revised edition on the applications of modeling and analyzing natural, social, and technological processes. The book covers a wide range of key topics in mathematical methods and modeling and highlights the connections between mathematics and the applied and nat

  9. Laboratory of Biological Modeling

    Data.gov (United States)

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

  10. Applied mineralogy

    Energy Technology Data Exchange (ETDEWEB)

    Park, W.C.; Hausen, D.M.; Hagni, R.D. (eds.)

    1985-01-01

    A conference on applied mineralogy was held and figures were presented under the following headings: methodology (including image analysis); ore genesis; exploration; beneficiations (including precious metals); process mineralogy - low and high temperatures; and medical science applications. Two papers have been abstracted separately.

  11. High performance computing applied to simulation of the flow in pipes; Computacao de alto desempenho aplicada a simulacao de escoamento em dutos

    Energy Technology Data Exchange (ETDEWEB)

    Cozin, Cristiane; Lueders, Ricardo; Morales, Rigoberto E.M. [Universidade Tecnologica Federal do Parana (UTFPR), Curitiba, PR (Brazil). Dept. de Engenharia Mecanica

    2008-07-01

    In recent years, computer cluster has emerged as a real alternative to solution of problems which require high performance computing. Consequently, the development of new applications has been driven. Among them, flow simulation represents a real computational burden specially for large systems. This work presents a study of using parallel computing for numerical fluid flow simulation in pipelines. A mathematical flow model is numerically solved. In general, this procedure leads to a tridiagonal system of equations suitable to be solved by a parallel algorithm. In this work, this is accomplished by a parallel odd-oven reduction method found in the literature which is implemented on Fortran programming language. A computational platform composed by twelve processors was used. Many measures of CPU times for different tridiagonal system sizes and number of processors were obtained, highlighting the communication time between processors as an important issue to be considered when evaluating the performance of parallel applications. (author)

  12. Systems Biology of Industrial Microorganisms

    Science.gov (United States)

    Papini, Marta; Salazar, Margarita; Nielsen, Jens

    The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

  13. An H-formulation-based three-dimensional hysteresis loss modelling tool in a simulation including time varying applied field and transport current: the fundamental problem and its solution

    International Nuclear Information System (INIS)

    When analytic solutions are not available, finite-element-based tools can be used to simulate hysteresis losses in superconductors with various shapes. A widely used tool for the corresponding magnetoquasistatic problem is based on the H-formulation, where H is the magnetic field intensity, eddy current model. In this paper, we study this type of tool in a three-dimensional simulation problem. We consider a case where we simultaneously apply both a time-varying external magnetic field and a transport current to a twisted wire. We show how the modelling decisions (air has high finite resistivity and applied field determines the boundary condition) affect the current density distribution along the wire. According to the results, the wire carries the imposed net current only on the boundary of the modelling domain, but not inside it. The current diffuses to the air and back to the boundary. To fix this problem, we present another formulation where air is treated as a region with 0 conductivity. Correspondingly, we express H in the air with a scalar potential and a cohomology basis function which considers the net current condition. As shown in this paper, this formulation does not fail in these so-called AC-AC (time varying transport current and applied magnetic field) simulations. (paper)

  14. A primer on applying Monte Carlo simulation, real options analysis, knowledge value added, forecasting, and portfolio optimization / by Johnathan Mun, Thomas Housel.

    OpenAIRE

    Mun, Johnathan; Housel, Thomas

    2010-01-01

    In this quick primer, advanced quantitative risk-based concepts will be introduced--namely, the hands-on applications of Monte Carlo simulation, real options analysis, stochastic forecasting, portfolio optimization, and knowledge value added. These methodologies rely on common metrics and existing techniques (e.g., return on investment, discounted cash flow, cost-based analysis, and so forth), and complement these traditional techniques by pushing the envelope of analytics, not replacing them...

  15. Responses of Cell Renewal Systems to Long-term Low-Level Radiation Exposure: A Feasibility Study Applying Advanced Molecular Biology Techniques on Available Histological and Cytological Material of Exposed Animals and Men

    International Nuclear Information System (INIS)

    First results of this feasibility study showed that evaluation of the stored material of the chronically irradiated dogs with modern molecular biological techniques proved to be successful and extremely promising. Therefore an in deep analysis of at least part of the huge amount of remaining material is of outmost interest. The methods applied in this feasibility study were pathological evaluation with different staining methods, protein analysis by means of immunohistochemistry, strand break analysis with the TdT-assay, DNA- and RNA-analysis as well as genomic examination by gene array. Overall more than 50% of the investigated material could be used. In particular the results of an increased stimulation of the immune system within the dogs of the 3mSv group as both compared to the control and higher dose groups gives implications for the in depth study of the cellular events occurring in context with low dose radiation. Based on the findings of this study a further evaluation and statistically analysis of more material can help to identify promising biomarkers for low dose radiation. A systematic evaluation of a correlation of dose rates and strand breaks within the dog tissue might moreover help to explain mechanisms of tolerance to IR. One central problem is that most sequences for dog specific primers are not known yet. The discovery of the dog genome is still under progress. In this study the isolation of RNA within the dog tissue was successful. But up to now there are no gene arrays or gene chips commercially available, tested and adapted for canine tissue. The uncritical use of untested genomic test systems for canine tissue seems to be ineffective at the moment, time consuming and ineffective. Next steps in the investigation of genomic changes after IR within the stored dog tissue should be limited to quantitative RT-PCR of tested primer sequences for the dog. A collaboration with institutions working in the field of the discovery of the dog genome could

  16. Simulation Model Based on Non-Newtonian Fluid Mechanics Applied to the Evaluation of the Embolic Effect of Emulsions of Iodized Oil and Anticancer Drug

    International Nuclear Information System (INIS)

    Purpose: To verify the difference in embolic effect between oil-in-water (O-W) and water-in-oil (W-O) emulsions composed of iodized oil and an anticancer drug, epirubicin, using a simulation model based on non-Newtonian fluid mechanics.Methods: Flow curves of pure iodized oil and two types of O-W and W-O emulsions immediately and 1 hr after preparation were examined with a viscometer. Using the yield stress data obtained, we simulated the stagnation of each fluid with steady flow in a rigid tube.Results: The W-O emulsions were observed to stagnate in the thin tube at a low pressure gradient. However, the embolic effect of the W-O emulsions decreased 1 hr after preparation. The O-W emulsions were stable and did not stagnate under the conditions in which the W-O emulsions stagnated.Conclusion: The simulation model showed that the embolic effect of the W-O emulsions was superior to that of the O-W emulsions

  17. Full radius linear and nonlinear gyrokinetic simulations for tokamaks and stellarators: zonal flows, applied E x B flows, trapped electrons and finite beta

    International Nuclear Information System (INIS)

    The aim of this paper is to report on recent advances made in global gyrokinetic simulations of ion temperature gradient (ITG) modes and other microinstabilities. The nonlinear development and saturation of ITG modes and the role of E x B zonal flows are studied with a global nonlinear δf formulation that retains parallel nonlinearity and thus allows for a check of the energy conservation property as a means of verifying the quality of the numerical simulation. Due to an optimized loading technique, the conservation property is satisfied with an unprecedented quality well into the nonlinear stage. The zonal component of the perturbation evolves to a quasi-steady state with regions of ITG suppression, strongly reduced radial energy flux and steepened effective temperature profiles alternating with regions of higher ITG mode amplitudes, larger radial energy flux and flattened effective temperature profiles. A semi-Lagrangian approach free of statistical noise is proposed as an alternative to the nonlinear δf formulation. An ASDEX-Upgrade experiment with an internal transport barrier is analysed with a global gyrokinetic code that includes trapped electron dynamics. The weakly destabilizing effect of trapped electron dynamics on ITG modes in an axisymmetric bumpy configuration modelling W7-X is shown in global linear simulations that retain the full electron dynamics. Finite β effects on microinstabilities are investigated with a linear global spectral electromagnetic gyrokinetic formulation. The radial global structure of electromagnetic modes shows a resonant behaviour with rational q values. (author)

  18. Biological effect of dose distortion by fiducial markers in spot-scanning proton therapy with a limited number of fields: A simulation study

    International Nuclear Information System (INIS)

    Purpose: In accurate proton spot-scanning therapy, continuous target tracking by fluoroscopic x ray during irradiation is beneficial not only for respiratory moving tumors of lung and liver but also for relatively stationary tumors of prostate. Implanted gold markers have been used with great effect for positioning the target volume by a fluoroscopy, especially for the cases of liver and prostate with the targets surrounded by water-equivalent tissues. However, recent studies have revealed that gold markers can cause a significant underdose in proton therapy. This paper focuses on prostate cancer and explores the possibility that multiple-field irradiation improves the underdose effect by markers on tumor-control probability (TCP). Methods: A Monte Carlo simulation was performed to evaluate the dose distortion effect. A spherical gold marker was placed at several characteristic points in a water phantom. The markers were with two different diameters of 2 and 1.5 mm, both visible on fluoroscopy. Three beam arrangements of single-field uniform dose (SFUD) were examined: one lateral field, two opposite lateral fields, and three fields (two opposite lateral fields + anterior field). The relative biological effectiveness (RBE) was set to 1.1 and a dose of 74 Gy (RBE) was delivered to the target of a typical prostate size in 37 fractions. The ratios of TCP to that without the marker (TCPr) were compared with the parameters of the marker sizes, number of fields, and marker positions. To take into account the dependence of biological parameters in TCP model, α/β values of 1.5, 3, and 10 Gy (RBE) were considered. Results: It was found that the marker of 1.5 mm diameter does not affect the TCPs with all α/β values when two or more fields are used. On the other hand, if the marker diameter is 2 mm, more than two irradiation fields are required to suppress the decrease in TCP from TCPr by less than 3%. This is especially true when multiple (two or three) markers are used

  19. Biological effect of dose distortion by fiducial markers in spot-scanning proton therapy with a limited number of fields: A simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Matsuura, Taeko; Maeda, Kenichiro; Sutherland, Kenneth; Takayanagi, Taisuke; Shimizu, Shinichi; Takao, Seishin; Miyamoto, Naoki; Nihongi, Hideaki; Toramatsu, Chie; Nagamine, Yoshihiko; Fujimoto, Rintaro; Suzuki, Ryusuke; Ishikawa, Masayori; Umegaki, Kikuo; Shirato, Hiroki [Department of Medical Physics, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, 060-8638 (Japan); Hitachi, Ltd., Hitachi Research Laboratory, 7-2-1 Omika-cho, Hitachi-shi, Ibaraki 319-1221 (Japan); Department of Radiation Medicine, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, 060-8638 (Japan); Department of Medical Physics, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, 060-8638 (Japan); Hitachi, Ltd., Hitachi Works, 3-1-1 Saiwai-cho, Hitachi-shi, Ibaraki 317-8511 (Japan); Hitachi, Ltd., Hitachi Research Laboratory, 7-2-1 Omika-cho, Hitachi-shi, Ibaraki 319-1221 (Japan); Department of Medical Physics, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, 060-8638 (Japan); Department of Radiation Medicine, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, 060-8638 (Japan)

    2012-09-15

    Purpose: In accurate proton spot-scanning therapy, continuous target tracking by fluoroscopic x ray during irradiation is beneficial not only for respiratory moving tumors of lung and liver but also for relatively stationary tumors of prostate. Implanted gold markers have been used with great effect for positioning the target volume by a fluoroscopy, especially for the cases of liver and prostate with the targets surrounded by water-equivalent tissues. However, recent studies have revealed that gold markers can cause a significant underdose in proton therapy. This paper focuses on prostate cancer and explores the possibility that multiple-field irradiation improves the underdose effect by markers on tumor-control probability (TCP). Methods: A Monte Carlo simulation was performed to evaluate the dose distortion effect. A spherical gold marker was placed at several characteristic points in a water phantom. The markers were with two different diameters of 2 and 1.5 mm, both visible on fluoroscopy. Three beam arrangements of single-field uniform dose (SFUD) were examined: one lateral field, two opposite lateral fields, and three fields (two opposite lateral fields + anterior field). The relative biological effectiveness (RBE) was set to 1.1 and a dose of 74 Gy (RBE) was delivered to the target of a typical prostate size in 37 fractions. The ratios of TCP to that without the marker (TCP{sub r}) were compared with the parameters of the marker sizes, number of fields, and marker positions. To take into account the dependence of biological parameters in TCP model, {alpha}/{beta} values of 1.5, 3, and 10 Gy (RBE) were considered. Results: It was found that the marker of 1.5 mm diameter does not affect the TCPs with all {alpha}/{beta} values when two or more fields are used. On the other hand, if the marker diameter is 2 mm, more than two irradiation fields are required to suppress the decrease in TCP from TCP{sub r} by less than 3%. This is especially true when multiple

  20. A Simulation of Runoff Calculation and Confluence Calculation in Qingfeng Water Basin by Applying SCS Model%应用SCS模型模拟清丰水流域产汇流量

    Institute of Scientific and Technical Information of China (English)

    徐刘凯; 王全金; 向速林

    2011-01-01

    Based on demands of estimating non-point source pollution load in region of Poyang Lake, the paper briefly introduces SCS and its application status, and simulates runoff calculation and confluence calculation in Qingfeng water basin by applying SCS Model whose measurement data are used to set model parameters rate in ex-Qingfeng hydrometric station. Results show that the simulated data is consistent with measured data. Simulation accuracy of runoff and confluence process reaches more than 70%o Therefore, it is feasible and accurate to simulate runoff calculation and confluence calculation in Qingfeng water basin by applying SCS Model.%基于鄱阳湖区域农业非点源污染负荷估算的需要,简要介绍了径流曲线模型(SCS)及其应用现状,同时根据清丰水岗前水文站的实测数据进行模型参数率定,并将该模型应用于清丰水流域产、汇流量的模拟.结果表明,模拟数据与实测值具有较好的一致性,产汇流过程的模拟精度均达到70%以上.因此,应用SCS模型模拟清丰水流域降雨产、汇流量是可行的,具有较高的精度.

  1. 飞机电传刹车半实物仿真技术的研究%Research on Hardware in the Loop Simulation Technology Applied on Aircraft Electric Braking System

    Institute of Scientific and Technical Information of China (English)

    苏田青; 林辉

    2012-01-01

    A project from C code directly generated by Simulink models was built which could be applied on Texas Instruments C28335 development board and a hardware in the loop simulation platform was established which could be applied on any kind of aircraft braking system. Simulation and experiment results show that automatic generated code has high accuracy and efficiency and can greatly reduce development period. The hardware in the loop simulation platform runs stably and simulation results show no difference with the real braking process and satisfy the system demands.%实现了由Simulink框图直接生成可用于TI公司C28335控制器的C代码程序,建立了某型号的飞机电传刹车半实物仿真和实验系统.仿真和实验结果表明,自动生成的代码准确度高、效率高,大大缩短开发周期;半实物仿真系统运行稳定,仿真结果达到项目指标,一致性较好,满足系统要求.

  2. The Galaxies Hubble Sequence Through CosmicTimes: Applying Parameter Optimization And Constraints From The Abundance Matching Technique To The 'Next Generation' of Large Cosmological Simulations.

    Science.gov (United States)

    Governato, Fabio

    The physical processes shaping the galaxies 'Hubble Sequence' are still poorly understood. Are gas outflows generated by Supernovae the main mechanism responsible for regulating star formation and the establishing the stellar mass - metallicity relation? What fraction of stars now in spheroids was originated in mergers? How does the environment of groups and clusters affect the evolution of galaxy satellites? The PI will study these problems analyzing a new set of state of the art hydro simulations of uniform cosmological volumes. This project has already been awarded a computational budget of 200 million CPU hours (but has only limited seed funding for science, hence this proposal). The best simulations will match the force and spatial resolution of the current best 'zoomed in' runs, as 'Eris' and will yield the first large statistical sample (1500+) of internally resolved galaxy systems with stellar masses ranging from from 10^7 to 10^10.5 solar masses. These simulations will allow us, for the very first time on such a large statistical set, to fully map the thermodynamical history of the baryons of internally resolved galaxies and identify the relative importance of the processes that shape their evolution as a function of stellar mass and cosmic time. As a novel, significant improvement over previous works we will introduce a new, unbiased statistical approach to the exploration of parameter space to optimize the model for star formation (SF) and feedback from supernovae and super massive back holes. This approach will also be used to evaluate the effects of resolution. The simulations will be run using ChaNGa, an improved version of Gasoline. Our flagship run will model a large volume of space (15.6k cubic Mpc) using 25 billion resolution elements. ChaNGa currently scales up to 35,000 cores and include a new version of the SPH implementation that drastically improves the description of temperature/density discontinuities and Kelvin-Helmholtz instabilities (and

  3. Quantum biological information theory

    CERN Document Server

    Djordjevic, Ivan B

    2016-01-01

    This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

  4. An Analysis of Finite Difference and Galerkin Techniques Applied to the Simulation of Advection and Diffusion of Air Pollutants from a Line Source

    OpenAIRE

    Runca, E.; Melli, P.; Sardei, F.

    1981-01-01

    A finite difference and a Galerkin type scheme are compared with reference to a very accurate solution describing time dependent advection and diffusion of air pollutants from a line source in an atmosphere vertically stratified and limited by an inversion layer. The accurate solution was achieved by applying the finite difference scheme on a very refined grid with a very small time step. Grid size and time step were defined according to stability and accuracy criteria discussed in the t...

  5. Applied dynamics

    CERN Document Server

    Schiehlen, Werner

    2014-01-01

    Applied Dynamics is an important branch of engineering mechanics widely applied to mechanical and automotive engineering, aerospace and biomechanics as well as control engineering and mechatronics. The computational methods presented are based on common fundamentals. For this purpose analytical mechanics turns out to be very useful where D’Alembert’s principle in the Lagrangian formulation proves to be most efficient. The method of multibody systems, finite element systems and continuous systems are treated consistently. Thus, students get a much better understanding of dynamical phenomena, and engineers in design and development departments using computer codes may check the results more easily by choosing models of different complexity for vibration and stress analysis.

  6. Experiences applying Unicore grid middle-ware for nuclear simulation tools like the 3D reactor core model QUABOX/CUBBOX

    International Nuclear Information System (INIS)

    The progress of nuclear simulation techniques is characterized by more detailed modeling in neutronics and fluid dynamics and by multi-physics multi-scale coupling to fulfil the increased requirements on accuracy and fidelity of analysis. Therefore, advanced applications of reactor design and safety analysis need easy access to high performance computing resources. The vision of Grid computing is to provide these required computing resources at the engineer's desk. From the beginning SfR, the IT service provider of GRS, is participating in the development of Grid middle-ware like UNICORE (Uniform Interface to Computing Resources). The objective of this middle-ware is to establish a user friendly interface to the computing resources. UNICORE 5 is a production-ready and well tested Grid middle-ware. Meanwhile, the implementation is converted to internationally accepted Web Services standards in a similar way like the Globus Toolkit 4 leading to the new UNICORE 6 version. For testing the available Grid computing features and for getting early experiences for nuclear applications, the 3D reactor core model QUABOX/CUBBOX is chosen as an application case. This nuclear simulation code was fully integrated into a Grid infrastructure. The experiences obtained by installing the Grid middle-ware, by developing application clients and for job monitoring and data access services are presented and discussed. (authors)

  7. Competing Uses of Underground Systems Related to Energy Supply: Applying Single- and Multiphase Simulations for Site Characterization and Risk-Analysis

    Science.gov (United States)

    Kissinger, A.; Walter, L.; Darcis, M.; Flemisch, B.; Class, H.

    2012-04-01

    Global climate change, shortage of resources and the resulting turn towards renewable sources of energy lead to a growing demand for the utilization of subsurface systems. Among these competing uses are Carbon Capture and Storage (CCS), geothermal energy, nuclear waste disposal, "renewable" methane or hydrogen storage as well as the ongoing production of fossil resources like oil, gas, and coal. Besides competing among themselves, these technologies may also create conflicts with essential public interests like water supply. For example, the injection of CO2 into the underground causes an increase in pressure reaching far beyond the actual radius of influence of the CO2 plume, potentially leading to large amounts of displaced salt water. Finding suitable sites is a demanding task for several reasons. Natural systems as opposed to technical systems are always characterized by heterogeneity. Therefore, parameter uncertainty impedes reliable predictions towards capacity and safety of a site. State of the art numerical simulations combined with stochastic approaches need to be used to obtain a more reliable assessment of the involved risks and the radii of influence of the different processes. These simulations may include the modeling of single- and multiphase non-isothermal flow, geo-chemical and geo-mechanical processes in order to describe all relevant physical processes adequately. Stochastic approaches have the aim to estimate a bandwidth of the key output parameters based on uncertain input parameters. Risks for these different underground uses can then be made comparable with each other. Along with the importance and the urgency of the competing processes this may lead to a more profound basis for a decision. Communicating risks to stake holders and a concerned public is crucial for the success of finding a suitable site for CCS (or other subsurface utilization). We present and discuss first steps towards an approach for addressing the issue of competitive

  8. Simulation of the neutron spectrum from the 7Li(p,n) reaction with a liquid-lithium target at Soreq Applied Research Accelerator Facility

    International Nuclear Information System (INIS)

    The 7Li(p,n)7Be reaction has been used for the last 25 years to produce quasi-Maxwellian neutrons in order to measure Maxwellian-Averaged Cross-Sections in the relevant temperatures for stellar nucleosynthesis. A liquid-lithium target at the Soreq Applied Research Accelerator Facility is expected to allow us to perform such measurements at higher neutron intensities. Here we describe a Monte Carlo tool, SimLiT, developed to evaluate neutron spectra, intensities and angular distributions resulting from this reaction. We also demonstrate the feasibility to couple SimLiT with an advanced transport code, resulting in a powerful tool for planning and analysis of experiments using the 7Li(p,n) reaction as a neutron source.

  9. Applied geodesy

    International Nuclear Information System (INIS)

    This volume is based on the proceedings of the CERN Accelerator School's course on Applied Geodesy for Particle Accelerators held in April 1986. The purpose was to record and disseminate the knowledge gained in recent years on the geodesy of accelerators and other large systems. The latest methods for positioning equipment to sub-millimetric accuracy in deep underground tunnels several tens of kilometers long are described, as well as such sophisticated techniques as the Navstar Global Positioning System and the Terrameter. Automation of better known instruments such as the gyroscope and Distinvar is also treated along with the highly evolved treatment of components in a modern accelerator. Use of the methods described can be of great benefit in many areas of research and industrial geodesy such as surveying, nautical and aeronautical engineering, astronomical radio-interferometry, metrology of large components, deformation studies, etc

  10. Applied mathematics

    International Nuclear Information System (INIS)

    The 1988 progress report of the Applied Mathematics center (Polytechnic School, France), is presented. The research fields of the Center are the scientific calculus, the probabilities and statistics and the video image synthesis. The research topics developed are: the analysis of numerical methods, the mathematical analysis of the physics and mechanics fundamental models, the numerical solution of complex models related to the industrial problems, the stochastic calculus and the brownian movement, the stochastic partial differential equations, the identification of the adaptive filtering parameters, the discrete element systems, statistics, the stochastic control and the development, the image synthesis techniques for education and research programs. The published papers, the congress communications and the thesis are listed

  11. Two-dimensional Monte Carlo simulations of a colloidal dispersion composed of rod-like ferromagnetic particles in an applied magnetic field

    International Nuclear Information System (INIS)

    We investigated the influence of an external magnetic field on microstructures in a colloidal dispersion composed of rod-like ferromagnetic particles using the cluster-moving Monte Carlo method. The internal microstructures obtained by simulations have been analysed in terms of the orientational distribution and pair correlation functions. The results obtained are summarized as follows. As the magnetic field increases, the particles align in the direction of the magnetic field. In the case of a relatively strong magnetic interaction between particles, chain-like clusters are formed along the magnetic field direction. However, the aspect ratio of the particles and the magnetic interaction between them do not affect their orientational distribution. Two types of structures are observed in the chain-like clusters—a straight linear structure and a step-like structure. The chain-like clusters become shorter when the area fraction of the particles decreases, and the number of step-like structures increases when the area fraction of the particles increases. The step-like structure formation can be explained by the dependence of the potential energy curves on the shape of the spherocylinder particles

  12. Quantifying the effect of tissue deformation on diffusion-weighted MRI: a mathematical model and an efficient simulation framework applied to cardiac diffusion imaging

    Science.gov (United States)

    Mekkaoui, Imen; Moulin, Kevin; Croisille, Pierre; Pousin, Jerome; Viallon, Magalie

    2016-08-01

    Cardiac motion presents a major challenge in diffusion weighted MRI, often leading to large signal losses that necessitate repeated measurements. The diffusion process in the myocardium is difficult to investigate because of the unqualified sensitivity of diffusion measurements to cardiac motion. A rigorous mathematical formalism is introduced to quantify the effect of tissue motion in diffusion imaging. The presented mathematical model, based on the Bloch–Torrey equations, takes into account deformations according to the laws of continuum mechanics. Approximating this mathematical model by using finite elements method, numerical simulations can predict the sensitivity of the diffusion signal to cardiac motion. Different diffusion encoding schemes are considered and the diffusion weighted MR signals, computed numerically, are compared to available results in literature. Our numerical model can identify the existence of two time points in the cardiac cycle, at which the diffusion is unaffected by myocardial strain and cardiac motion. Of course, these time points depend on the type of diffusion encoding scheme. Our numerical results also show that the motion sensitivity of the diffusion sequence can be reduced by using either spin echo technique with acceleration motion compensation diffusion gradients or stimulated echo acquisition mode with unipolar and bipolar diffusion gradients.

  13. 3D Radiative Transfer in Eta Carinae: The SimpleX Radiative Transfer Algorithm Applied to 3D SPH Simulations of Eta Car's Colliding Winds

    Science.gov (United States)

    Clementel, N.; Madura, T. I.; Kruip, C. J. H.; Icke, V.; Gull, T. R.

    2014-04-01

    At the heart of the spectacular bipolar Homunculus nebula lies an extremely luminous (5*10^6 L_sun) colliding wind binary with a highly eccentric (e ~ 0.9), 5.54-year orbit and a total mass ~ 110 M_sun. Our closest (D ~ 2.3 kpc) and best example of a pre-hypernova environment, Eta Carinae is an ideal astrophysical laboratory for studying massive binary interactions, stellar wind-wind collisions, and massive star evolution. In order to improve our knowledge of the system, we need to generate synthetic observations and compare them with the already available and future HST/STIS data. We present initial results from full 3D radiative transfer post-processing of 3D SPH hydrodynamical simulations of the interacting winds of Eta Carinae. We use SimpleX algorithm to obtain the ionization fractions of hydrogen and helium, this results in ionization maps of both species that constrain the regions where these lines can form. These results will allow us to put constraints on the number of ionizing photons coming from the companion. This construction of synthetic observations allows us to obtain insight into the highly complex 3D flows in Eta, from the shape of the ionized volume and its resulting optical/spectral appearance.

  14. Applied partial differential equations

    CERN Document Server

    Logan, J David

    2015-01-01

    This text presents the standard material usually covered in a one-semester, undergraduate course on boundary value problems and PDEs.  Emphasis is placed on motivation, concepts, methods, and interpretation, rather than on formal theory. The concise treatment of the subject is maintained in this third edition covering all the major ideas: the wave equation, the diffusion equation, the Laplace equation, and the advection equation on bounded and unbounded domains. Methods include eigenfunction expansions, integral transforms, and characteristics. In this third edition, text remains intimately tied to applications in heat transfer, wave motion, biological systems, and a variety other topics in pure and applied science. The text offers flexibility to instructors who, for example, may wish to insert topics from biology or numerical methods at any time in the course. The exposition is presented in a friendly, easy-to-read, style, with mathematical ideas motivated from physical problems. Many exercises and worked e...

  15. Branching processes in biology

    CERN Document Server

    Kimmel, Marek

    2015-01-01

    This book provides a theoretical background of branching processes and discusses their biological applications. Branching processes are a well-developed and powerful set of tools in the field of applied probability. The range of applications considered includes molecular biology, cellular biology, human evolution and medicine. The branching processes discussed include Galton-Watson, Markov, Bellman-Harris, Multitype, and General Processes. As an aid to understanding specific examples, two introductory chapters, and two glossaries are included that provide background material in mathematics and in biology. The book will be of interest to scientists who work in quantitative modeling of biological systems, particularly probabilists, mathematical biologists, biostatisticians, cell biologists, molecular biologists, and bioinformaticians. The authors are a mathematician and cell biologist who have collaborated for more than a decade in the field of branching processes in biology for this new edition. This second ex...

  16. 发酵液作为EBPR碳源的动力学模拟%Kinetic Simulation of Enhanced Biological Phosphorus Removal with Fermentation Broth as Carbon Source

    Institute of Scientific and Technical Information of China (English)

    张超; 陈银广

    2013-01-01

    发酵液是一种优质的碳源,能够提高生物除磷系统(EBPR)的除磷效果.采用基于碳源代谢的修正ASM2模型,能够较好地模拟发酵液作为EBPR碳源的动力学变化规律.发酵液作为EBPR唯一碳源时,系统中的异养菌不仅不对聚磷菌(PAO)的生长构成竞争关系,反而促进PAO的生长.发酵液作为实际污水的补充碳源时,优化了污水中的碳源组成,创造了有利于聚磷菌生长的环境,使EBPR中聚磷菌达到微生物总量的40%以上,比实际污水作为碳源的EBPR中的PAO含量提高了3.3倍.%As a high-quality carbon source,fermentation broth could promote the phosphorus removal efficiency in enhanced biological phosphorus removal (EBPR).The transformation of substrates in EBPR fed with fermentation broth was well simulated using the modified activated sludge model No.2 (ASM2) based on the carbon source metabolism.When fermentation broth was used as the sole carbon source,it was found that heterotrophic bacteria acted as a promoter rather than a competitor to the phosphorus accumulating organisms (PAO).When fermentation broth was used as a supplementary carbon source of real municipal wastewater,the wastewater composition was optimized for PAO growth; and the PAO concentration,which was increased by 3.3 times compared to that in EBPR fed with solely real municipal wastewater,accounting for about 40% of the total biomass in the reactor.

  17. Applying radiation

    International Nuclear Information System (INIS)

    The invention discloses a method and apparatus for applying radiation by producing X-rays of a selected spectrum and intensity and directing them to a desired location. Radiant energy is directed from a laser onto a target to produce such X-rays at the target, which is so positioned adjacent to the desired location as to emit the X-rays toward the desired location; or such X-rays are produced in a region away from the desired location, and are channeled to the desired location. The radiant energy directing means may be shaped (as with bends; adjustable, if desired) to circumvent any obstruction between the laser and the target. Similarly, the X-ray channeling means may be shaped (as with fixed or adjustable bends) to circumvent any obstruction between the region where the X-rays are produced and the desired location. For producing a radiograph in a living organism the X-rays are provided in a short pulse to avoid any blurring of the radiograph from movement of or in the organism. For altering tissue in a living organism the selected spectrum and intensity are such as to affect substantially the tissue in a preselected volume without injuring nearby tissue. Typically, the selected spectrum comprises the range of about 0.1 to 100 keV, and the intensity is selected to provide about 100 to 1000 rads at the desired location. The X-rays may be produced by stimulated emission thereof, typically in a single direction

  18. Are cranial biomechanical simulation data linked to known diets in extant taxa? A method for applying diet-biomechanics linkage models to infer feeding capability of extinct species.

    Directory of Open Access Journals (Sweden)

    Zhijie Jack Tseng

    Full Text Available Performance of the masticatory system directly influences feeding and survival, so adaptive hypotheses often are proposed to explain craniodental evolution via functional morphology changes. However, the prevalence of "many-to-one" association of cranial forms and functions in vertebrates suggests a complex interplay of ecological and evolutionary histories, resulting in redundant morphology-diet linkages. Here we examine the link between cranial biomechanical properties for taxa with different dietary preferences in crown clade Carnivora, the most diverse clade of carnivorous mammals. We test whether hypercarnivores and generalists can be distinguished based on cranial mechanical simulation models, and how such diet-biomechanics linkages relate to morphology. Comparative finite element and geometric morphometrics analyses document that predicted bite force is positively allometric relative to skull strain energy; this is achieved in part by increased stiffness in larger skull models and shape changes that resist deformation and displacement. Size-standardized strain energy levels do not reflect feeding preferences; instead, caniform models have higher strain energy than feliform models. This caniform-feliform split is reinforced by a sensitivity analysis using published models for six additional taxa. Nevertheless, combined bite force-strain energy curves distinguish hypercarnivorous versus generalist feeders. These findings indicate that the link between cranial biomechanical properties and carnivoran feeding preference can be clearly defined and characterized, despite phylogenetic and allometric effects. Application of this diet-biomechanics linkage model to an analysis of an extinct stem carnivoramorphan and an outgroup creodont species provides biomechanical evidence for the evolution of taxa into distinct hypercarnivorous and generalist feeding styles prior to the appearance of crown carnivoran clades with similar feeding preferences.

  19. Are cranial biomechanical simulation data linked to known diets in extant taxa? A method for applying diet-biomechanics linkage models to infer feeding capability of extinct species.

    Science.gov (United States)

    Tseng, Zhijie Jack; Flynn, John J

    2015-01-01

    Performance of the masticatory system directly influences feeding and survival, so adaptive hypotheses often are proposed to explain craniodental evolution via functional morphology changes. However, the prevalence of "many-to-one" association of cranial forms and functions in vertebrates suggests a complex interplay of ecological and evolutionary histories, resulting in redundant morphology-diet linkages. Here we examine the link between cranial biomechanical properties for taxa with different dietary preferences in crown clade Carnivora, the most diverse clade of carnivorous mammals. We test whether hypercarnivores and generalists can be distinguished based on cranial mechanical simulation models, and how such diet-biomechanics linkages relate to morphology. Comparative finite element and geometric morphometrics analyses document that predicted bite force is positively allometric relative to skull strain energy; this is achieved in part by increased stiffness in larger skull models and shape changes that resist deformation and displacement. Size-standardized strain energy levels do not reflect feeding preferences; instead, caniform models have higher strain energy than feliform models. This caniform-feliform split is reinforced by a sensitivity analysis using published models for six additional taxa. Nevertheless, combined bite force-strain energy curves distinguish hypercarnivorous versus generalist feeders. These findings indicate that the link between cranial biomechanical properties and carnivoran feeding preference can be clearly defined and characterized, despite phylogenetic and allometric effects. Application of this diet-biomechanics linkage model to an analysis of an extinct stem carnivoramorphan and an outgroup creodont species provides biomechanical evidence for the evolution of taxa into distinct hypercarnivorous and generalist feeding styles prior to the appearance of crown carnivoran clades with similar feeding preferences. PMID:25923776

  20. Determination of the maximum energy loss for electron stopping power calculations and its effect on backscattering electron yield in Monte-Carlo simulations applying continuous slowing-down approximation

    International Nuclear Information System (INIS)

    The maximum energy loss for electron stopping power calculations by the full Penn algorithm within the dielectric formalism is determined with taking into account the contribution of electron and plasmon excitations. Use of these calculated electron stopping powers in Monte Carlo simulations applying continuous slowing down approximation gives the backscattering electron yields in much better agreement with experimental data than previous other theoretical results. The muffin-tin model is used to describe the electron elastic scattering by atom bound in solids with taking into account the exchange correlation and polarization effect

  1. Determination of the maximum energy loss for electron stopping power calculations and its effect on backscattering electron yield in Monte-Carlo simulations applying continuous slowing-down approximation

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen-Truong, Hieu T. [Faculty of Electronics and Computer Science, Volgograd State Technical University, 28 Lenin Avenue, Volgograd 400131 (Russian Federation)

    2013-10-28

    The maximum energy loss for electron stopping power calculations by the full Penn algorithm within the dielectric formalism is determined with taking into account the contribution of electron and plasmon excitations. Use of these calculated electron stopping powers in Monte Carlo simulations applying continuous slowing down approximation gives the backscattering electron yields in much better agreement with experimental data than previous other theoretical results. The muffin-tin model is used to describe the electron elastic scattering by atom bound in solids with taking into account the exchange correlation and polarization effect.

  2. Cardiovascular, renal, electrolyte, and hormonal changes in man during gravitational stress, weightlessness, and simulated weightlessness: Lower body positive pressure applied by the antigravity suit. Thesis - Oslo Univ.

    Science.gov (United States)

    Kravik, Stein E.

    1989-01-01

    Because of their erect posture, humans are more vulnerable to gravitational changes than any other animal. During standing or walking man must constantly use his antigravity muscles and his two columns, his legs, to balance against the force of gravity. At the same time, blood is surging downward to the dependent portions of the body, draining blood away from the brain and heart, and requiring a series of complex cardiovascular adjustments to maintain the human in a bipedal position. It was not until 12 April 1961, when Yuri Gagarin became the first human being to orbit Earth, that we could confirm man's ability to maintain vital functions in space -- at least for 90 min. Nevertheless, man's adaptation to weightlessness entails the deconditioning of various organs in the body. Muscles atrophy, and calcium loss leads to loss of bone strength as the demands on the musculoskeletal system are almost nonexistent in weightlessness. Because of the lack of hydrostatic pressures in space, blood rushes to the upper portions of the body, initiating a complex series of cardioregulatory responses. Deconditioning during spaceflight, however, first becomes a potentially serious problem in humans returning to Earth, when the cardiovascular system, muscles and bones are suddenly exposed to the demanding counterforce of gravity -- weight. One of the main purposes of our studies was to test the feasibility of using Lower Body Positive Pressure, applied with an antigravity suit, as a new and alternative technique to bed rest and water immersion for studying cardioregulatory, renal, electrolyte, and hormonal changes in humans. The results suggest that Lower Body Positive Pressure can be used as an analog of microgravity-induced physiological responses in humans.

  3. Toward synthesizing executable models in biology.

    Science.gov (United States)

    Fisher, Jasmin; Piterman, Nir; Bodik, Rastislav

    2014-01-01

    Over the last decade, executable models of biological behaviors have repeatedly provided new scientific discoveries, uncovered novel insights, and directed new experimental avenues. These models are computer programs whose execution mechanistically simulates aspects of the cell's behaviors. If the observed behavior of the program agrees with the observed biological behavior, then the program explains the phenomena. This approach has proven beneficial for gaining new biological insights and directing new experimental avenues. One advantage of this approach is that techniques for analysis of computer programs can be applied to the analysis of executable models. For example, one can confirm that a model agrees with experiments for all possible executions of the model (corresponding to all environmental conditions), even if there are a huge number of executions. Various formal methods have been adapted for this context, for example, model checking or symbolic analysis of state spaces. To avoid manual construction of executable models, one can apply synthesis, a method to produce programs automatically from high-level specifications. In the context of biological modeling, synthesis would correspond to extracting executable models from experimental data. We survey recent results about the usage of the techniques underlying synthesis of computer programs for the inference of biological models from experimental data. We describe synthesis of biological models from curated mutation experiment data, inferring network connectivity models from phosphoproteomic data, and synthesis of Boolean networks from gene expression data. While much work has been done on automated analysis of similar datasets using machine learning and artificial intelligence, using synthesis techniques provides new opportunities such as efficient computation of disambiguating experiments, as well as the ability to produce different kinds of models automatically from biological data. PMID:25566538

  4. Towards Synthesizing Executable Models in Biology

    Directory of Open Access Journals (Sweden)

    Jasmin eFisher

    2014-12-01

    Full Text Available Over the last decade, executable models of biological behaviors have repeatedly provided new scientific discoveries, uncovered novel insights, and directed new experimental avenues. These models are computer programs whose execution mechanistically simulates aspects of the cell’s behaviors. If the observed behavior of the program agrees with the observed biological behavior, then the program explains the phenomena. This approach has proven beneficial for gaining new biological insights and directing new experimental avenues. One advantage of this approach is that techniques for analysis of computer programs can be applied to the analysis of executable models. For example, one can confirm that a model agrees with experiments for all possible executions of the model (corresponding to all environmental conditions, even if there are a huge number of executions. Various formal methods have been adapted for this context, for example, model checking or symbolic analysis of state spaces. To avoid manual construction of executable models, one can apply synthesis, a method to produce programs automatically from high-level specifications. In the context of biological modelling, synthesis would correspond to extracting executable models from experimental data. We survey recent results about the usage of the techniques underlying synthesis of computer programs for the inference of biological models from experimental data. We describe synthesis of biological models from curated mutation experiment data, inferring network connectivity models from phosphoproteomic data, and synthesis of Boolean networks from gene expression data. While much work has been done on automated analysis of similar datasets using machine learning and artificial intelligence, using synthesis techniques provides new opportunities such as efficient computation of disambiguating experiments, as well as the ability to produce different kinds of models automatically from biological data.

  5. Applied impulsive mathematical models

    CERN Document Server

    Stamova, Ivanka

    2016-01-01

    Using the theory of impulsive differential equations, this book focuses on mathematical models which reflect current research in biology, population dynamics, neural networks and economics. The authors provide the basic background from the fundamental theory and give a systematic exposition of recent results related to the qualitative analysis of impulsive mathematical models. Consisting of six chapters, the book presents many applicable techniques, making them available in a single source easily accessible to researchers interested in mathematical models and their applications. Serving as a valuable reference, this text is addressed to a wide audience of professionals, including mathematicians, applied researchers and practitioners.

  6. Contribution to the electrothermal simulation in power electronics. Development of a simulation methodology applied to switching circuits under variable operating conditions; Contribution a la simulation electrothermique en electronique de puissance. Developpement d`une methode de simulation pour circuits de commutation soumis a des commandes variables

    Energy Technology Data Exchange (ETDEWEB)

    Vales, P.

    1997-03-19

    In modern hybrid or monolithic integrated power circuits, electrothermal effects can no longer be ignored. A methodology is proposed in order to simulate electrothermal effects in power circuits, with a significant reduction of the computation time while taking into account electrical and thermal time constants which are usually widely different. A supervising program, written in Fortran, uses system call sequences and manages an interactive dialog between a fast thermal simulator and a general electrical simulator. This explicit coupling process between two specific simulators requires a multi-task operating system. The developed software allows for the prediction of the electrothermal power dissipation drift in the active areas of components, and the prediction of thermally-induced coupling effects between adjacent components. An application to the study of hard switching circuits working under variable operating conditions is presented

  7. Optics of Biological Particles

    CERN Document Server

    Hoekstra, Alfons; Videen, Gorden

    2007-01-01

    This book covers the optics of single biological particles, both theory and experiment, with emphasis on Elastic Light Scattering and Fluorescence. It deals with the optics of bacteria (bio-aerosols), marine particles (selected phytoplankton communities) and red and white blood cells. Moreover, there are dedicated chapters on a general theory for scattering by a cell, and modelling and simulation of scattering by inhomogeneous biological cells. Finally, one chapter is dedicated to astro-biological signatures, discussing the possibilities for detecting non-terrestrial biological material. The volume has up-to-date discussions on new experimental and numerical techniques, and many examples of applications of these techniques in real-life systems, as used to detect and characterize e.g. biological warfare agents or human blood cells.

  8. Biological sequence analysis

    OpenAIRE

    Speed, T. P.

    2003-01-01

    This talk will review a little over a decade's research on applying certain stochastic models to biological sequence analysis. The models themselves have a longer history, going back over 30 years, although many novel variants have arisen since that time. The function of the models in biological sequence analysis is to summarize the information concerning what is known as a motif or a domain in bioinformatics, and to provide a tool for discovering instances of that motif or domain in a separa...

  9. Biological aerosol background characterization

    Science.gov (United States)

    Blatny, Janet; Fountain, Augustus W., III

    2011-05-01

    To provide useful information during military operations, or as part of other security situations, a biological aerosol detector has to respond within seconds or minutes to an attack by virulent biological agents, and with low false alarms. Within this time frame, measuring virulence of a known microorganism is extremely difficult, especially if the microorganism is of unknown antigenic or nucleic acid properties. Measuring "live" characteristics of an organism directly is not generally an option, yet only viable organisms are potentially infectious. Fluorescence based instruments have been designed to optically determine if aerosol particles have viability characteristics. Still, such commercially available biological aerosol detection equipment needs to be improved for their use in military and civil applications. Air has an endogenous population of microorganisms that may interfere with alarm software technologies. To design robust algorithms, a comprehensive knowledge of the airborne biological background content is essential. For this reason, there is a need to study ambient live bacterial populations in as many locations as possible. Doing so will permit collection of data to define diverse biological characteristics that in turn can be used to fine tune alarm algorithms. To avoid false alarms, improving software technologies for biological detectors is a crucial feature requiring considerations of various parameters that can be applied to suppress alarm triggers. This NATO Task Group will aim for developing reference methods for monitoring biological aerosol characteristics to improve alarm algorithms for biological detection. Additionally, they will focus on developing reference standard methodology for monitoring biological aerosol characteristics to reduce false alarm rates.

  10. Frontiers in mathematical biology

    CERN Document Server

    1994-01-01

    Volume 100, which is the final volume of the LNBM series serves to commemorate the acievements in two decades of this influential collection of books in mathematical biology. The contributions, by the leading mathematical biologists, survey the state of the art in the subject, and offer speculative, philosophical and critical analyses of the key issues confronting the field. The papers address fundamental issues in cell and molecular biology, organismal biology, evolutionary biology, population ecology, community and ecosystem ecology, and applied biology, plus the explicit and implicit mathematical challenges. Cross-cuttting issues involve the problem of variation among units in nonlinear systems, and the related problems of the interactions among phenomena across scales of space, time and organizational complexity.

  11. Measuring the evolutionary rewiring of biological networks.

    Science.gov (United States)

    Shou, Chong; Bhardwaj, Nitin; Lam, Hugo Y K; Yan, Koon-Kiu; Kim, Philip M; Snyder, Michael; Gerstein, Mark B

    2011-01-01

    We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or "rewire", at different rates. It is therefore important to develop a framework to quantify the differences between networks in a unified fashion. We developed such a formalism based on analogy to simple models of sequence evolution, and used it to conduct a systematic study of network rewiring on all the currently available biological networks. We found that, similar to sequences, biological networks show a decreased rate of change at large time divergences, because of saturation in potential substitutions. However, different types of biological networks consistently rewire at different rates. Using comparative genomics and proteomics data, we found a consistent ordering of the rewiring rates: transcription regulatory, phosphorylation regulatory, genetic interaction, miRNA regulatory, protein interaction, and metabolic pathway network, from fast to slow. This ordering was found in all comparisons we did of matched networks between organisms. To gain further intuition on network rewiring, we compared our observed rewirings with those obtained from simulation. We also investigated how readily our formalism could be mapped to other network contexts; in particular, we showed how it could be applied to analyze changes in a range of "commonplace" networks such as family trees, co-authorships and linux-kernel function dependencies. PMID:21253555

  12. Measuring the evolutionary rewiring of biological networks.

    Directory of Open Access Journals (Sweden)

    Chong Shou

    Full Text Available We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or "rewire", at different rates. It is therefore important to develop a framework to quantify the differences between networks in a unified fashion. We developed such a formalism based on analogy to simple models of sequence evolution, and used it to conduct a systematic study of network rewiring on all the currently available biological networks. We found that, similar to sequences, biological networks show a decreased rate of change at large time divergences, because of saturation in potential substitutions. However, different types of biological networks consistently rewire at different rates. Using comparative genomics and proteomics data, we found a consistent ordering of the rewiring rates: transcription regulatory, phosphorylation regulatory, genetic interaction, miRNA regulatory, protein interaction, and metabolic pathway network, from fast to slow. This ordering was found in all comparisons we did of matched networks between organisms. To gain further intuition on network rewiring, we compared our observed rewirings with those obtained from simulation. We also investigated how readily our formalism could be mapped to other network contexts; in particular, we showed how it could be applied to analyze changes in a range of "commonplace" networks such as family trees, co-authorships and linux-kernel function dependencies.

  13. Simulated experiments

    International Nuclear Information System (INIS)

    A cybernetic model has been developed to elucidate some of the main principles of the growth regulation system in the epidermis of the hairless mouse. A number of actual and theoretical biological experiments have been simulated on the model. These included simulating the cell kinetics as measured by pulse labelling with tritiated thymidine and by continuous labelling with tritiated thymidine. Other simulated experiments included steady state, wear and tear, painting with a carcinogen, heredity and heredity and tumour. Numerous diagrams illustrate the results of these simulated experiments. (JIW)

  14. Improvement of a manageability of biological nitrogen and phosphorus removal plant using a wastewater treatment process simulator; Gesui shori purosesu shimyureta no riyo ni yoru seibutsuteki chisso/rin jokyo puranto no kanrisei no kojo

    Energy Technology Data Exchange (ETDEWEB)

    Kurata, G. [Toyohashi Univ. of Technology, Aichi (Japan). Faculty of Engineering; Tsumura, K. [Kyoto Univ., Kyoto (Japan). Graduate School; Yamamoto, Y. [Osaka Prefectural Inst. of Public Health, Osaka (Japan)

    1997-02-10

    In this paper, a method for executing a stable management of wastewater treatment process is examined by using a wastewater treatment process simulator with the facilities adopting intermittently aerated 2-tank activated sludge process as the object. The following results are obtained from said examination. Based on a fact that the treatment efficiency is influenced greatly by the comparatively miner parts of the process in biological nitrogen and phosphorus removal, a wastewater treatment process simulator, by which the intrinsic process flow, restricting conditions and behaviors of controlling system of each facility can be dealt with, is developed by using object-directional model. As the results of this development, not only the effects approximate to those of actual process can be obtained, but also the trial error and alternation of process flow can be realized in a short time. The serious influence of disappearance of dissolvable organic substance in flow-adjusting tank upon the deterioration of biological phosphorus removal is clarified by the results of the simulation based on the investigation of flowing-in water quality. 12 refs., 13 figs., 4 tabs.

  15. Aerospace Medicine and Biology: A Continuing Bibliography. Supplement 476

    Science.gov (United States)

    1998-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-1998-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract.

  16. Aerospace Medicine and Biology: A Continuing Bibliography. Supplement 475

    Science.gov (United States)

    1998-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion.

  17. The biological system of the elements (BSE) - A brief introduction into historical and applied aspects with special reference on 'ecotoxicological identity cards' for different element species (F.E.AS and SN)

    International Nuclear Information System (INIS)

    There are different methods to estimate and predict effects of chemical elements and corresponding speciation forms in biochemistry and toxicology, including statements on essentiality and antagonisms. Two approaches are given here: a) 'identity cards' describing biologically fundamental aspects of element chemistry and b) qualitative discussions which assume the existence of (indirect ways into) chemical autocatalysis to be essential for maintaining life and permitting reproduction. The latter method, developed by the present authors, draws upon Stoichiometric Network Analysis (a safe procedure for complexity reduction in feedback networks) and provides estimates of concentration regimes for different elements suitable for survival and reproduction. The biochemical hierarchy level considered here is that of (metallo-)proteins. Thermodynamic toxicity aspects are given in correlations with DMSO solvent affinities and thiocyanate bonding modes. Effects of antagonists and of ion substitution within metalloenzyms or of metabolic simplification can be dealt with, likewise increased sensitivities within symbiotic relationships and within carcinomas are explained which are relevant for environmental monitoring and tumor therapy, respectively. Keywords: History of the Biological System of Elements; ecotoxicological identity cards; stoichiometric network analysis; stability of biological autocatalysis; effects of antagonists and metal ion substitutions; derivation of generalized toxicological statements. (author)

  18. Nutritional systems biology modeling: from molecular mechanisms to physiology.

    OpenAIRE

    de Graaf, Albert A.; Freidig, Andreas P.; Baukje De Roos; Neema Jamshidi; Matthias Heinemann; Rullmann, Johan A.C.; Hall, Kevin D.; Martin Adiels; Ben van Ommen

    2009-01-01

    The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the co...

  19. Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology

    OpenAIRE

    de Graaf, A A; Freidig, A.P.; Roos, B.; Jamshidi, N.; M. Heinemann; Rullmann, J.A.C.; Hall, K. D.; Adiels, M.; Ommen, B. van

    2009-01-01

    The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the co...

  20. Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology

    OpenAIRE

    de Graaf, Albert A.; Freidig, Andreas P.; de Roos, Baukje; Jamshidi, Neema; Heinemann, Matthias; Rullmann, Johan A.C.; Hall, Kevin D.; Adiels, Martin; van Ommen, Ben; Bourne, Philip E.

    2009-01-01

    The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today’s important nutritional research questions poses a challenge for modeling to become truly integrative in the co...

  1. Computer Simulation of Embryonic Systems: What can a virtual embryo teach us about developmental toxicity? (LA Conference on Computational Biology & Bioinformatics)

    Science.gov (United States)

    This presentation will cover work at EPA under the CSS program for: (1) Virtual Tissue Models built from the known biology of an embryological system and structured to recapitulate key cell signals and responses; (2) running the models with real (in vitro) or synthetic (in silico...

  2. FAMUS (Flow Assurance by Management of Uncertainty and Simulation): a new tool for integrating flow assurance effects in traditional RAM (Reliability, Availability and Maintainability) analysis applied on a Norwegian Offshore System

    Energy Technology Data Exchange (ETDEWEB)

    Eisinger, Siegfried; Isaksen, Stefan; Grande, Oystein [Det Norske Veritas (DNV), Oslo (Norway); Chame, Luciana [Det Norske Veritas (DNV), Rio de Janeiro, RJ (Brazil)

    2008-07-01

    Traditional RAM (Reliability, Availability and Maintainability) models fall short of taking flow assurance effects into account. In many Oil and Gas production systems, flow assurance issues like hydrate formation, wax deposition or particle erosion may cause a substantial amount of production upsets. Flow Assurance issues are complex and hard to quantify in a production forecast. However, without taking them into account the RAM model generally overestimates the predicted system production. This paper demonstrates the FAMUS concept, which is a method and a tool for integrating RAM and Flow Assurance into one model, providing a better foundation for decision support. FAMUS utilises therefore both Discrete Event and Thermo-Hydraulic Simulation. The method is currently applied as a decision support tool in an early phase of the development of an offshore oil field on the Norwegian continental shelf. (author)

  3. Controlled vocabularies and semantics in systems biology

    OpenAIRE

    Courtot, Mélanie; Juty, Nick; Knüpfer, Christian; Waltemath, Dagmar; Zhukova, Anna; Dräger, Andreas; Dumontier, Michel; Finney, Andrew; Golebiewski, Martin; Hastings, Janna; Hoops, Stefan; Keating, Sarah; Douglas B. Kell; Kerrien, Samuel; Lawson, James

    2011-01-01

    The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. This Perspective discusses the development and use of ontologies that are designed to add semantic information to computational models and simulations.

  4. Modeling formalisms in Systems Biology

    OpenAIRE

    Machado, C. D.; Costa, Rafael S.; Rocha, Miguel; Ferreira, E. C.; Tidor, Bruce; Rocha, I.

    2011-01-01

    Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological proc...

  5. A random walk in physical biology

    Science.gov (United States)

    Peterson, Eric Lee

    Biology as a scientific discipline is becoming evermore quantitative as tools become available to probe living systems on every scale from the macro to the micro and now even to the nanoscale. In quantitative biology the challenge is to understand the living world in an in vivo context, where it is often difficult for simple theoretical models to connect with the full richness and complexity of the observed data. Computational models and simulations offer a way to bridge the gap between simple theoretical models and real biological systems; towards that aspiration are presented in this thesis three case studies in applying computational models that may give insight into native biological structures.The first is concerned with soluble proteins; proteins, like DNA, are linear polymers written in a twenty-letter "language" of amino acids. Despite the astronomical number of possible proteins sequences, a great amount of similarity is observed among the folded structures of globular proteins. One useful way of discovering similar sequences is to align their sequences, as done e.g. by the popular BLAST program. By clustering together amino acids and reducing the alphabet that proteins are written in to fewer than twenty letters, we find that pairwise sequence alignments are actually more sensitive to proteins with similar structures.The second case study is concerned with the measurement of forces applied to a membrane. We demonstrate a general method for extracting the forces applied to a fluid lipid bilayer of arbitrary shape and show that the subpiconewton forces applied by optical tweezers to vesicles can be accurately measured in this way.In the third and final case study we examine the forces between proteins in a lipid bilayer membrane. Due to the bending of the membrane surrounding them, such proteins feel mutually attractive forces which can help them to self-organize and act in concert. These finding are relevant at the areal densities estimated for membrane

  6. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 492

    Science.gov (United States)

    1999-01-01

    This report lists reports, articles and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion.

  7. Aerospace Medicine and Biology: A Continuing Bibliography With Indexes. Supplement 486

    Science.gov (United States)

    1999-01-01

    In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract.

  8. Biology Notes.

    Science.gov (United States)

    School Science Review, 1982

    1982-01-01

    Presents procedures, exercises, demonstrations, and information on a variety of biology topics including labeling systems, biological indicators of stream pollution, growth of lichens, reproductive capacity of bulbous buttercups, a straw balance to measure transpiration, interaction of fungi, osmosis, and nitrogen fixation and crop production. (DC)

  9. American Institute of Biological Sciences

    Science.gov (United States)

    ... policy goals. News from Nov 20, 2014 Bring Evolution To Your School/Community For Darwin Day 2015. Apply Now for the Gordon Research Conference on Undergraduate Biology Education Research AIBS Education is dedicated to improving ...

  10. Spectrally-resolved fluorescence cross sections of aerosolized biological live agents and simulants using five excitation wavelengths in a BSL-3 laboratory.

    Science.gov (United States)

    Pan, Yong-Le; Hill, Steven C; Santarpia, Joshua L; Brinkley, Kelly; Sickler, Todd; Coleman, Mark; Williamson, Chatt; Gurton, Kris; Felton, Melvin; Pinnick, Ronald G; Baker, Neal; Eshbaugh, Jonathan; Hahn, Jerry; Smith, Emily; Alvarez, Ben; Prugh, Amber; Gardner, Warren

    2014-04-01

    A system for measuring spectrally-resolved fluorescence cross sections of single bioaerosol particles has been developed and employed in a biological safety level 3 (BSL-3) facility at Edgewood Chemical and Biological Center (ECBC). It is used to aerosolize the slurry or solution of live agents and surrogates into dried micron-size particles, and to measure the fluorescence spectra and sizes of the particles one at a time. Spectrally-resolved fluorescence cross sections were measured for (1) bacterial spores: Bacillus anthracis Ames (BaA), B. atrophaeus var. globigii (BG) (formerly known as Bacillus globigii), B. thuringiensis israelensis (Bti), B. thuringiensis kurstaki (Btk), B. anthracis Sterne (BaS); (2) vegetative bacteria: Escherichia coli (E. coli), Pantoea agglomerans (Eh) (formerly known as Erwinia herbicola), Yersinia rohdei (Yr), Yersinia pestis CO92 (Yp); and (3) virus preparations: Venezuelan equine encephalitis TC83 (VEE) and the bacteriophage MS2. The excitation wavelengths were 266 nm, 273 nm, 280 nm, 365 nm and 405 nm. PMID:24718194

  11. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

    Directory of Open Access Journals (Sweden)

    Lauren Boldon

    2015-02-01

    Full Text Available In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS experiments, molecular dynamics (MD simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

  12. 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.

  13. DNA in a Tunnel: A Comfy Spot for Recognition - or -The Structure of BsoBI Complexed with DNA. What can we Learn about Function via Structure Determination and how can this be Applied to Bone or Muscle Biology?

    Science.gov (United States)

    vanderWoerd, Mark

    2004-01-01

    The structure and function of a biologically active molecule are related. To understand its function, it is necessary (but not always sufficient) to know the structure of the molecule. There are many ways of relating the molecular function with the structure. Mutation analysis can identify pertinent amino acids of an enzyme, or alternatively structure comparison of the of two similar molecules with different function may lead to understanding which parts are responsible for a functional aspect, or a series of "structural cartoons" - enzyme structure, enzyme plus substrate, enzyme with transition state analog, and enzyme with product - may give insight in the function of a molecule. As an example we will discuss the structure and function of the restriction enzyme BsoBI from Bacillus stearothemzophilus in complex with its cognate DNA. The enzyme forms a unique complex with DNA in that it completely encircles the DNA. The structure reveals the enzyme-DNA contacts, how the DNA is distorted compared with the canonical forms, and elegantly shows how two distinct DNA sequences can be recognized with the same efficiency. Based on the structure we may also propose a hypothesis how the enzymatic mechanism works. The knowledge gained thru studies such as this one can be used to alter the function by changing the molecular structure. Usually this is done by design of inhibitors specifically active against and fitting into an active site of the enzyme of choice. In the case of BsoBI one of the objectives of the study was to alter the enzyme specificity. In bone biology there are many candidates available for molecular study in order to explain, alter, or (temporarily) suspend activity. For example, the understanding of a pathway that negatively regulates bone formation may be a good target for drug design to stimulate bone formation and have good potential as the basis for new countermeasures against bone loss. In principle the same approach may aid muscle atrophy, radiation

  14. Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems.

    Science.gov (United States)

    Isaksen, Geir Villy; Andberg, Tor Arne Heim; Åqvist, Johan; Brandsdal, Bjørn Olav

    2015-07-01

    Structural information and activity data has increased rapidly for many protein targets during the last decades. In this paper, we present a high-throughput interface (Qgui) for automated free energy and empirical valence bond (EVB) calculations that use molecular dynamics (MD) simulations for conformational sampling. Applications to ligand binding using both the linear interaction energy (LIE) method and the free energy perturbation (FEP) technique are given using the estrogen receptor (ERα) as a model system. Examples of free energy profiles obtained using the EVB method for the rate-limiting step of the enzymatic reaction catalyzed by trypsin are also shown. In addition, we present calculation of high-precision Arrhenius plots to obtain the thermodynamic activation enthalpy and entropy with Qgui from running a large number of EVB simulations. PMID:26080356

  15. Bigraphical Languages and their Simulation

    DEFF Research Database (Denmark)

    Højsgaard, Espen

    We study bigraphs as a foundation for practical formal languages and the problem of simulating such bigraphical languages. The theory of bigraphs is a foundational, graphical model of concurrent systems focusing on mobility and connectivity. It is a meta-model in the sense that it is parametrized...... for practical formal languages. However, while direct models of many process calculi have been constructed, it is unclear how suitable bigraphs are for more practical formal languages. Also, the generality of bigraphs comes at a price of complexity in the theory and simulation of bigraphical models is non......-trivial. A key problem is that of matching: deciding if and how a reaction rule applies to a bigraph. In this dissertation, we study bigraphs and their simulation for two types of practical formal languages: programming languages and languages for cell biology. First, we study programming languages and binding...

  16. ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

    CERN Document Server

    Hinkelmann, Franziska; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard

    2010-01-01

    Motivation: Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, bounded Petri nets, and agent-based models. Simulation is a common practice for analyzing discrete models, but many systems are far too large to capture all the relevant dynamical features through simulation alone. Results: We convert discrete models into algebraic models and apply tools from computational algebra to analyze their dynamics. The key feature of biological systems that is exploited by our algorithms is their sparsity: while the number of nodes in a biological network may be quite large, each node is affected only by a small number of other nodes. In our experience with models arising in systems biology and random models, this structure leads to fast computations when using algebraic models, and thus efficient analysis. Availability: All algorithms and methods are available in our package Analysis of Dynamic Algebraic Models (ADAM), a user friendly web-interf...

  17. Quantum Biology

    Directory of Open Access Journals (Sweden)

    Alessandro Sergi

    2009-06-01

    Full Text Available A critical assessment of the recent developmentsof molecular biology is presented.The thesis that they do not lead to a conceptualunderstanding of life and biological systems is defended.Maturana and Varela's concept of autopoiesis is briefly sketchedand its logical circularity avoided by postulatingthe existence of underlying living processes,entailing amplification from the microscopic to the macroscopic scale,with increasing complexity in the passage from one scale to the other.Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces,is criticized. It is suggested that the correct interpretationof quantum dispersion forces (van der Waals, hydrogen bonding, and so onas quantum coherence effects hints at the necessity of includinglong-ranged forces (or mechanisms for them incondensed matter theories of biological processes.Some quantum effects in biology are reviewedand quantum mechanics is acknowledged as conceptually important to biology since withoutit most (if not all of the biological structuresand signalling processes would not even exist. Moreover, it is suggested that long-rangequantum coherent dynamics, including electron polarization,may be invoked to explain signal amplificationprocess in biological systems in general.

  18. Quantum Biology

    CERN Document Server

    Sergi, Alessandro

    2009-01-01

    A critical assessment of the recent developments of molecular biology is presented. The thesis that they do not lead to a conceptual understanding of life and biological systems is defended. Maturana and Varela's concept of autopoiesis is briefly sketched and its logical circularity avoided by postulating the existence of underlying {\\it living processes}, entailing amplification from the microscopic to the macroscopic scale, with increasing complexity in the passage from one scale to the other. Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces, is criticized. It is suggested that the correct interpretation of quantum dispersion forces (van der Waals, hydrogen bonding, and so on) as quantum coherence effects hints at the necessity of including long-ranged forces (or mechanisms for them) in condensed matter theories of biological processes. Some quantum effects in biology are reviewed and quantum mechanics is acknowledge...

  19. Improving the biological realism in an individual-based model simulating the forest colonisation at landscape scale:application to a data set from Scots pine trees

    OpenAIRE

    Robert, A.; Coquillard, P.; Prévosto, B.

    2003-01-01

    In some mid-elevation mountain areas of center and south-east of France, Scots pine proves to be invasive species, colonising pasture abandonments and forms, within the while of few decades, monospecific natural forests. Our work deals with a simulation model, which was developed in order to rebuild the entire forest colonisation process of pine settlement. It is an individual-based model that takes into account bath space and time, and includes tree growth, seed production and dispersaI, and...

  20. Applied mechanics of solids

    CERN Document Server

    Bower, Allan F

    2009-01-01

    Modern computer simulations make stress analysis easy. As they continue to replace classical mathematical methods of analysis, these software programs require users to have a solid understanding of the fundamental principles on which they are based. Develop Intuitive Ability to Identify and Avoid Physically Meaningless Predictions Applied Mechanics of Solids is a powerful tool for understanding how to take advantage of these revolutionary computer advances in the field of solid mechanics. Beginning with a description of the physical and mathematical laws that govern deformation in solids, the text presents modern constitutive equations, as well as analytical and computational methods of stress analysis and fracture mechanics. It also addresses the nonlinear theory of deformable rods, membranes, plates, and shells, and solutions to important boundary and initial value problems in solid mechanics. The author uses the step-by-step manner of a blackboard lecture to explain problem solving methods, often providing...