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. 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 ...

  5. 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...

  6. 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.

  7. 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

  8. 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…

  9. 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.)

  10. [Applied problems of mathematical biology and bioinformatics].

    Science.gov (United States)

    Lakhno, V D

    2011-01-01

    Mathematical biology and bioinformatics represent a new and rapidly progressing line of investigations which emerged in the course of work on the project "Human genome". The main applied problems of these sciences are grug design, patient-specific medicine and nanobioelectronics. It is shown that progress in the technology of mass sequencing of the human genome has set the stage for starting the national program on patient-specific medicine.

  11. Integrative Systems Biology Applied to Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning

    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...... 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 the 14-chemical mixture and the endocrine disrupting chemical. In project III, I modeled a predictive signature for an in vivo endpoint that is sensitive to endocrine disruption. I used publicly available data generated for the purpose of modeling predictive signatures for various in vivo endpoints. From...

  12. Applying appropriates methods for teaching cell biology

    OpenAIRE

    Stavreva Veselinovska, Snezana; Koleva Gudeva, Liljana; Djokic, Milena

    2011-01-01

    Cell biology is an important basic subject of modern life sciences, consisting of fundamental life activities of the cell at the microscopic, sub microscopic and molecular levels. The cell is the basic unit of living things, with all of the activities of life taking place in the cell and with is eases also due to abnormal changes of cells. With the current framework of teaching quality reform in higher education, this paper will review the current curriculum of a cell biology course and the w...

  13. Text Mining applied to Molecular Biology

    NARCIS (Netherlands)

    R. Jelier (Rob)

    2008-01-01

    textabstractThis thesis describes the development of text-mining algorithms for molecular biology, in particular for DNA microarray data analysis. Concept profiles were introduced, which characterize the context in which a gene is mentioned in literature, to retrieve functional associations

  14. Spatial Aspects in Biological System Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Resat, Haluk; Costa, Michelle N.; Shankaran, Harish

    2011-01-30

    Mathematical models of the dynamical properties of biological systems aim to improve our understanding of the studied system with the ultimate goal of being able to predict system responses in the absence of experimentation. Despite the enormous advances that have been made in biological modeling and simulation, the inherently multiscale character of biological systems and the stochasticity of biological processes continue to present significant computational and conceptual challenges. Biological systems often consist of well-organized structural hierarchies, which inevitably lead to multiscale problems. This chapter introduces and discusses the advantages and shortcomings of several simulation methods that are being used by the scientific community to investigate the spatio-temporal properties of model biological systems. We first describe the foundations of the methods and then describe their relevance and possible application areas with illustrative examples from our own research. Possible ways to address the encountered computational difficulties are also discussed.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. Applied simulation to the project management: a review

    Directory of Open Access Journals (Sweden)

    Leonardo Rosas Leal

    2011-05-01

    Full Text Available The objective of this article is to show a literature review of Applied Simulation to the Project Management as for the last twenty years. This article reviews the main Simulation methodologies, as well as some of their properties, that have stimulated the application of Simulation in project management. Besides that, a review of historical marks is presented, since the Monte Carlo Simulation proposal as a solution to PERT/CPM methodology limitations. In addition, this work intends to outline the theme through stratifications in order to offer a holistic overview of the theme. As a result, there will be the possibility of realize some important connections and tendencies in relation to the stratifications, as the application of the Discrete Event Simulation and Monte Carlo Simulation methodologies for the schedule and cost risk management. Such applications are mainly related with high level risk projects, such as civil projects, software development, design Engineering and Oil & gas projects.

  20. Cellular systems biology profiling applied to cellular models of disease.

    Science.gov (United States)

    Giuliano, Kenneth A; Premkumar, Daniel R; Strock, Christopher J; Johnston, Patricia; Taylor, Lansing

    2009-11-01

    Building cellular models of disease based on the approach of Cellular Systems Biology (CSB) has the potential to improve the process of creating drugs as part of the continuum from early drug discovery through drug development and clinical trials and diagnostics. This paper focuses on the application of CSB to early drug discovery. We discuss the integration of protein-protein interaction biosensors with other multiplexed, functional biomarkers as an example in using CSB to optimize the identification of quality lead series compounds.

  1. 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.

  2. 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.

  3. 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.

  4. 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...

  5. ATLAS Detector Simulation in the Integrated Simulation Framework applied to the W Boson Mass Measurement

    CERN Document Server

    Ritsch, Elmar; Froidevaux, Daniel; Salzburger, Andreas

    One of the cornerstones for the success of the ATLAS experiment at the Large Hadron Collider (LHC) is a very accurate Monte Carlo detector simulation. However, a limit is being reached regarding the amount of simulated data which can be produced and stored with the computing resources available through the worldwide LHC computing grid (WLCG). The Integrated Simulation Framework (ISF) is a novel approach to detector simula- tion which enables a more efficient use of these computing resources and thus allows for the generation of more simulated data. Various simulation technologies are combined to allow for faster simulation approaches which are targeted at the specific needs of in- dividual physics studies. Costly full simulation technologies are only used where high accuracy is required by physics analyses and fast simulation technologies are applied everywhere else. As one of the first applications of the ISF, a new combined simulation approach is developed for the generation of detector calibration samples ...

  6. Metropolitan Programs in Applied Biological and Agricultural Occupations; A Need and Attitude Study. Final Report.

    Science.gov (United States)

    Thomas, Hollie B.; And Others

    To establish the feasibility of implementing applied biological and agricultural occupations programs in the metropolitan area of Chicago, four populations were surveyed by means of mailed questionnaires or interest inventories to determine: (1) the employment opportunities in the applied biological and agricultural industries, (2) the interests…

  7. 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

  8. Nuclear physics detector technology applied to plant biology research

    Energy Technology Data Exchange (ETDEWEB)

    Weisenberger, A.G., E-mail: drew@jlab.org [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Kross, B.; Lee, S.J.; McKisson, J.; McKisson, J.E.; Xi, W.; Zorn, C. [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Howell, C.R.; Crowell, A.S. [Duke University, Durham, NC (United States); Triangle Universities Nuclear Laboratory, Durham, NC (United States); Reid, C.D. [Duke University, Durham, NC (United States); Smith, M. [University of Maryland, Baltimore, MD (United States)

    2013-08-01

    The ability to detect the emissions of radioactive isotopes through radioactive decay (e.g. beta particles, x-rays and gamma-rays) has been used for over 80 years as a tracer method for studying natural phenomena. More recently a positron emitting radioisotope of carbon: {sup 11}C has been utilized as a {sup 11}CO{sub 2} tracer for plant ecophysiology research. Because of its ease of incorporation into the plant via photosynthesis, the {sup 11}CO{sub 2} radiotracer is a powerful tool for use in plant biology research. Positron emission tomography (PET) imaging has been used to study carbon transport in live plants using {sup 11}CO{sub 2}. Presently there are several groups developing and using new PET instrumentation for plant based studies. Thomas Jefferson National Accelerator Facility (Jefferson Lab) in collaboration with the Duke University Phytotron and the Triangle Universities Nuclear Laboratory (TUNL) is involved in PET detector development for plant imaging utilizing technologies developed for nuclear physics research. The latest developments of the use of a LYSO scintillator based PET detector system for {sup 11}CO{sub 2} tracer studies in plants will be briefly outlined.

  9. 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...

  10. 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

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

    Science.gov (United States)

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

    2016-01-01

    The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models. PMID:27635225

  12. 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.

  13. 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. PMID:27635225

  14. Towards Modelling and Simulation of Crowded Environments in Cell Biology

    Science.gov (United States)

    Bittig, Arne T.; Jeschke, Matthias; Uhrmacher, Adelinde M.

    2010-09-01

    In modelling and simulation of cell biological processes, spatial homogeneity in the distribution of components is a common but not always valid assumption. Spatial simulation methods differ in computational effort and accuracy, and usually rely on tool-specific input formats for model specification. A clear separation between modelling and simulation allows a declarative model specification thereby facilitating reuse of models and exploiting different simulators. We outline a modelling formalism covering both stochastic spatial simulation at the population level and simulation of individual entities moving in continuous space as well as the combination thereof. A multi-level spatial simulator is presented that combines populations of small particles simulated according to the Next Subvolume Method with individually represented large particles following Brownian motion. This approach entails several challenges that need to be overcome, but nicely balances between calculation effort and required levels of detail.

  15. Simulation of a modified neutron detector applied in CSNS

    Institute of Scientific and Technical Information of China (English)

    MA Zhong-Jian; WANG Qing-Bin; WU Qing-Biao

    2009-01-01

    We simulate the response of a modified Anderson-Braun rem counter in the energy range from thermal energy to about 10 GeV using the FLUKA code.Also,we simulate the lethargy spectrum of CSNS outside the beam dump.Traditional BFs tube is replaced by the 3He tube,a layer of 0.6 cm lead is added outside the boron doped plastic attenuator and a sphere configuration is adopted.The simulation result shows that its response is exactly fit to H*(10) in the neutron energies between 10 keV and approximately 1 GeV,although the monitor slightly underestimates H*(10) in the energy range from thermal energy to about 10 keV.According to the characteristics of the CSNS,this modified counter increases the neutron energy response by 30% compared with the traditional monitors,and it can be applied in other kinds of stray field rich of high energy neutrons.

  16. 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...

  17. Dye Degradation by Fungi: An Exercise in Applied Science for Biology Students

    Science.gov (United States)

    Lefebvre, Daniel D.; Chenaux, Peter; Edwards, Maureen

    2005-01-01

    An easily implemented practical exercise in applied science for biology students is presented that uses fungi to degrade an azo-dye. This is an example of bioremediation, the employment of living organisms to detoxify or contain pollutants. Its interdisciplinary nature widens students' perspectives of biology by exposing them to a chemical…

  18. 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…

  19. 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...

  20. Simulation of Interval Censored Data in Medical and Biological Studies

    Science.gov (United States)

    Kiani, Kaveh; Arasan, Jayanthi

    This research looks at the simulation of interval censored data when the survivor function of the survival time is known and attendance probability of the subjects for follow-ups can take any number between 0 to 1. Interval censored data often arise in the medical and biological follow-up studies where the event of interest occurs somewhere between two known times. Regardless of the methods used to analyze these types of data, simulation of interval censored data is an important and challenging step toward model building and prediction of survival time. The simulation itself is rather tedious and very computer intensive due to the interval monitoring of subjects at prescheduled times and subject's incomplete attendance to follow-ups. In this paper the simulated data by the proposed method were assessed using the bias, standard error and root mean square error (RMSE) of the parameter estimates where the survival time T is assumed to follow the Gompertz distribution function.

  1. 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.

  2. FDTD Simulation of Exposure of Biological Material to Electromagnetic Nanopulses

    CERN Document Server

    Simicevic, N; Simicevic, Neven; Haynie, Donald T

    2004-01-01

    Ultra-wideband (UWB) electromagnetic pulses of nanosecond duration, or nanopulses, are of considerable interest to the communications industry and are being explored for various applications in biotechnology and medicine. The propagation of a nanopulse through biological matter has been computed in the time domain using the finite difference-time domain method (FDTD). The approach required existing Cole-Cole model-based descriptions of dielectric properties of biological matter to be re-parametrized using the Debye model, but without loss of accuracy. The approach has been applied to several tissue types. Results show that the electromagnetic field inside a biological tissue depends on incident pulse rise time and width. Rise time dominates pulse behavior inside a tissue as conductivity increases. It has also been found that the amount of energy deposited by 20 $kV/m$ nanopulses is insufficient to change the temperature of the exposed material for the pulse repetition rates of 1 $MHz$ or less.

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

    DEFF Research Database (Denmark)

    Sørensen, Kresten Kjær; Stoustrup, Jakob

    2008-01-01

    is divided into components where the inputs and outputs are described by a set of XML files that can be combined into a composite system model that may be loaded into MATLABtrade. A set of tools that allows the user to easily load the model and run a simulation are provided. The results show a simulation......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...

  4. 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

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

    NARCIS (Netherlands)

    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.

  6. Program Applied Biology and Biotechnology. Annual report 1986. Programm Angewandte Biologie und Biotechnologie. Jahresbericht 1986

    Energy Technology Data Exchange (ETDEWEB)

    1987-01-01

    BMFT-funded research projects in 1986 on the sector 'Applied Biology and Biotechnology' are reviewed. The main fields of research were: Microbiological screening methods, waste water, refuse and soil microbiology, genetic engineering, cell cultures, development of new bioreactor systems, measurement and control, biocatalysts, plant cultivation, safety research, biosensory research, biomass utilisation.

  7. Program Applied Biology and Biotechnology. Annual report 1987. Programm Angewandte Biologie und Biotechnologie. Jahresbericht 1987

    Energy Technology Data Exchange (ETDEWEB)

    1988-01-01

    By order of the Federal Government, the Biology, Ecology, Energy Department (PBE) is responsible for the 3 sub-programs 'energy research and technologies', 'applied biology and biotechnology' and 'environmental research and technology'. This volume deals with the second-mentioned sub-program and briefly describes the projects supported by the Federal Government, specifically the objectives, working program, state of the studies, costs and share in the costs paid by the Federal Government. The following subdivision was made: 1. biological process engineering and enzyme technology, 2. cell culture and cell fusion technology, 3. genetic engineering and microbial technologies, 4. equivalent methods which can replace animal experiments, biological security, 5. plant genetics and protection, 6. promotion of focal points of activity, 7. indirect specific promotion, 8. new fields and overlapping activities in biotechnology, 9. regrowing raw materials. (RB).

  8. 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

  9. 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.

  10. [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

  11. 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

  12. Computer Science Techniques Applied to Parallel Atomistic Simulation

    Science.gov (United States)

    Nakano, Aiichiro

    1998-03-01

    Recent developments in parallel processing technology and multiresolution numerical algorithms have established large-scale molecular dynamics (MD) simulations as a new research mode for studying materials phenomena such as fracture. However, this requires large system sizes and long simulated times. We have developed: i) Space-time multiresolution schemes; ii) fuzzy-clustering approach to hierarchical dynamics; iii) wavelet-based adaptive curvilinear-coordinate load balancing; iv) multilevel preconditioned conjugate gradient method; and v) spacefilling-curve-based data compression for parallel I/O. Using these techniques, million-atom parallel MD simulations are performed for the oxidation dynamics of nanocrystalline Al. The simulations take into account the effect of dynamic charge transfer between Al and O using the electronegativity equalization scheme. The resulting long-range Coulomb interaction is calculated efficiently with the fast multipole method. Results for temperature and charge distributions, residual stresses, bond lengths and bond angles, and diffusivities of Al and O will be presented. The oxidation of nanocrystalline Al is elucidated through immersive visualization in virtual environments. A unique dual-degree education program at Louisiana State University will also be discussed in which students can obtain a Ph.D. in Physics & Astronomy and a M.S. from the Department of Computer Science in five years. This program fosters interdisciplinary research activities for interfacing High Performance Computing and Communications with large-scale atomistic simulations of advanced materials. This work was supported by NSF (CAREER Program), ARO, PRF, and Louisiana LEQSF.

  13. 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%.

  14. 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

  15. 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.

  16. 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.

  17. Uncertainty Quantification applied to flow simulations in thoracic aortic aneurysms

    Science.gov (United States)

    Boccadifuoco, Alessandro; Mariotti, Alessandro; Celi, Simona; Martini, Nicola; Salvetti, Maria Vittoria

    2015-11-01

    The thoracic aortic aneurysm is a progressive dilatation of the thoracic aorta causing a weakness in the aortic wall, which may eventually cause life-threatening events. Clinical decisions on treatment strategies are currently based on empiric criteria, like the aortic diameter value or its growth rate. Numerical simulations can give the quantification of important indexes which are impossible to be obtained through in-vivo measurements and can provide supplementary information. Hemodynamic simulations are carried out by using the open-source tool SimVascular and considering patient-specific geometries. One of the main issues in these simulations is the choice of suitable boundary conditions, modeling the organs and vessels not included in the computational domain. The current practice is to use outflow conditions based on resistance and capacitance, whose values are tuned to obtain a physiological behavior of the patient pressure. However it is not known a priori how this choice affects the results of the simulation. The impact of the uncertainties in these outflow parameters is investigated here by using the generalized Polynomial Chaos approach. This analysis also permits to calibrate the outflow-boundary parameters when patient-specific in-vivo data are available.

  18. 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...

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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...

  7. 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.

  8. 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...

  9. Applying computer simulation models as learning tools in fishery management

    Science.gov (United States)

    Johnson, B.L.

    1995-01-01

    Computer models can be powerful tools for addressing many problems in fishery management, but uncertainty about how to apply models and how they should perform can lead to a cautious approach to modeling. Within this approach, we expect models to make quantitative predictions but only after all model inputs have been estimated from empirical data and after the model has been tested for agreement with an independent data set. I review the limitations to this approach and show how models can be more useful as tools for organizing data and concepts, learning about the system to be managed, and exploring management options. Fishery management requires deciding what actions to pursue to meet management objectives. Models do not make decisions for us but can provide valuable input to the decision-making process. When empirical data are lacking, preliminary modeling with parameters derived from other sources can help determine priorities for data collection. When evaluating models for management applications, we should attempt to define the conditions under which the model is a useful, analytical tool (its domain of applicability) and should focus on the decisions made using modeling results, rather than on quantitative model predictions. I describe an example of modeling used as a learning tool for the yellow perch Perca flavescens fishery in Green Bay, Lake Michigan.

  10. 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.

  11. 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,…

  12. 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

  13. 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...

  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. 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

  16. 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.)

  17. Numerical simulations of odorant detection by biologically inspired sensor arrays.

    Science.gov (United States)

    Schuech, R; Stacey, M T; Barad, M F; Koehl, M A R

    2012-03-01

    The antennules of many marine crustaceans enable them to rapidly locate sources of odorant in turbulent environmental flows and may provide biological inspiration for engineered plume sampling systems. A substantial gap in knowledge concerns how the physical interaction between a sensing device and the chemical filaments forming a turbulent plume affects odorant detection and filters the information content of the plume. We modeled biological arrays of chemosensory hairs as infinite arrays of odorant flux-detecting cylinders and simulated the fluid flow around and odorant flux into the hair-like sensors as they intercepted a single odorant filament. As array geometry and sampling kinematics were varied, we quantified distortion of the flux time series relative to the spatial shape of the original odorant filament as well as flux metrics that may be important to both organisms and engineered systems attempting to measure plume structure and/or identify chemical composition. The most important predictor of signal distortion is the ratio of sensor diameter to odorant filament width. Achieving high peak properties (e.g. sharpness) of the flux time series and maximizing the total number of odorant molecules detected appear to be mutually exclusive design goals. Sensor arrays inspired specifically by the spiny lobster Panulirus argus and mantis shrimp Gonodactylaceus falcatus introduce little signal distortion but these species' neural systems may not be able to resolve plume structure at the level of individual filaments via temporal properties of the odorant flux. Current chemical sensors are similarly constrained. Our results suggest either that the spatial distribution of flux across the aesthetasc array is utilized by P. argus and G. falcatus, or that such high spatiotemporal resolution is unnecessary for effective plume tracking. PMID:22155966

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. Simulations in statistical physics and biology: some applications

    CERN Document Server

    Monsivais-Alonso, M P

    2006-01-01

    One of the most active areas of physics in the last decades has been that of critical phenomena, and Monte Carlo simulations have played an important role as a guide for the validation and prediction of system properties close to the critical points. The kind of phase transitions occurring for the Betts lattice (lattice constructed removing 1/7 of the sites from the triangular lattice) have been studied before with the Potts model for the values q=3, ferromagnetic and antiferromagnetic regime. Here, we add up to this research line the ferromagnetic case for q=4 and 5. In the first case, the critical exponents are estimated for the second order transition, whereas for the latter case the histogram method is applied for the occurring first order transition. Additionally, Domany's Monte Carlo based clustering technique mainly used to group genes similar in their expression levels is reviewed. Finally, a control theory tool --an adaptive observer-- is applied to estimate the exponent parameter involved in the wel...

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. Distinguishing Pattern Formation Phenotypes: Applying Minkowski Functionals to Cell Biology Systems

    Science.gov (United States)

    Rericha, Erin; Guven, Can; Parent, Carole; Losert, Wolfgang

    2011-03-01

    Spatial Clustering of proteins within cells or cells themselves frequently occur in cell biology systems. However quantifying the underlying order and determining the regulators of these cluster patterns have proved difficult due to the inherent high noise levels in the systems. For instance the patterns formed by wild type and cyclic-AMP regulatory mutant Dictyostelium cells are visually distinctive, yet the large error bars in measurements of the fractal number, area, Euler number, eccentricity, and wavelength making it difficult to quantitatively distinguish between the patterns. We apply a spatial analysis technique based on Minkowski functionals and develop metrics which clearly separate wild type and mutant cell lines into distinct categories. Having such a metric facilitated the development of a computational model for cellular aggregation and its regulators. Supported by NIH-NGHS Nanotechnology (R01GM085574) and the Burroughs Wellcome Fund.

  8. 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

  9. 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.

  10. Perspectives on low voltage transmission electron microscopy as applied to cell biology.

    Science.gov (United States)

    Bendayan, Moise; Paransky, Eugene

    2014-12-01

    Low voltage transmission electron microscopy (LVTEM) with accelerating voltages as low as 5 kV was applied to cell biology. To take advantage of the increased contrast given by LVTEM, tissue preparation was modified omitting all heavy metals such as osmium, uranium, and lead from the fixation, on block staining and counterstaining. Nonstained ultra-thin tissue sections (40 nm thick) generated highly contrasted images. While the aspect of the cells remains similar to that obtained by conventional TEM, some new substructures were revealed. The pancreatic acinar cells granules present a heterogeneous matrix with partitions corresponding to segregation of their different secretory proteins. Microvilli display their core of microfilaments anchored to the dense top membrane. Mitochondria revealed the presence of distinct particles along their cristea membranes that may correspond to the ATP synthase complexes or oxysomes. The dense nuclear chromatin displays a honey-comb appearance while distinct beads aligned along thin threads were seen in the dispersed chromatin. These new features revealed by LVTEM correlate with structures described or predicted through other approaches. Masking effects due to thickness of the tissue sections and to the presence of heavy metals must have prevented their observation by conventional TEM. Furthermore, the immunogold was adapted to LVTEM revealing nuclear lamin-A at the edge of the dense chromatin ribbons. Combining cytochemistry with LVTEM brings additional advantages to this new approach in cell biology.

  11. 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...

  12. 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...

  13. Process simulation during the design process makes the difference: process simulations applied to a traditional design

    NARCIS (Netherlands)

    Traversari, R.; Goedhart, R.; Schraagen, J.M.C.

    2013-01-01

    Objective: The objective is evaluation of a traditionally designed operating room using simulation of various surgical workflows.Background: A literature search showed that there is no evidence for an optimal operating room layout regarding the position and size of an ultraclean ventilation (UCV) ca

  14. Process simulation during the design process makes the difference : Process simulations applied to a traditional design

    NARCIS (Netherlands)

    Traversari, R.; Goedhart, R.; Schraagen, J.M.C.

    2013-01-01

    Objective: The objective is evaluation of a traditionally designed operating room using simulation of various surgical workflows. Background: A literature search showed that there is no evidence for an optimal operating room layout regarding the position and size of an ultraclean ventilation (UCV) c

  15. 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

  16. 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

  17. 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.

  18. 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.

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

    OpenAIRE

    Javier Cubas; Santiago Pindado; Ángel Sanz-Andrés

    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...

  20. Knowledge management for systems biology a general and visually driven framework applied to translational medicine

    Directory of Open Access Journals (Sweden)

    Falciani Francesco

    2011-03-01

    Full Text Available Abstract Background To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the

  1. 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.

  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. Automated multi-objective calibration of biological agent-based simulations.

    Science.gov (United States)

    Read, Mark N; Alden, Kieran; Rose, Louis M; Timmis, Jon

    2016-09-01

    Computational agent-based simulation (ABS) is increasingly used to complement laboratory techniques in advancing our understanding of biological systems. Calibration, the identification of parameter values that align simulation with biological behaviours, becomes challenging as increasingly complex biological domains are simulated. Complex domains cannot be characterized by single metrics alone, rendering simulation calibration a fundamentally multi-metric optimization problem that typical calibration techniques cannot handle. Yet calibration is an essential activity in simulation-based science; the baseline calibration forms a control for subsequent experimentation and hence is fundamental in the interpretation of results. Here, we develop and showcase a method, built around multi-objective optimization, for calibrating ABSs against complex target behaviours requiring several metrics (termed objectives) to characterize. Multi-objective calibration (MOC) delivers those sets of parameter values representing optimal trade-offs in simulation performance against each metric, in the form of a Pareto front. We use MOC to calibrate a well-understood immunological simulation against both established a priori and previously unestablished target behaviours. Furthermore, we show that simulation-borne conclusions are broadly, but not entirely, robust to adopting baseline parameter values from different extremes of the Pareto front, highlighting the importance of MOC's identification of numerous calibration solutions. We devise a method for detecting overfitting in a multi-objective context, not previously possible, used to save computational effort by terminating MOC when no improved solutions will be found. MOC can significantly impact biological simulation, adding rigour to and speeding up an otherwise time-consuming calibration process and highlighting inappropriate biological capture by simulations that cannot be well calibrated. As such, it produces more accurate

  4. Automated multi-objective calibration of biological agent-based simulations.

    Science.gov (United States)

    Read, Mark N; Alden, Kieran; Rose, Louis M; Timmis, Jon

    2016-09-01

    Computational agent-based simulation (ABS) is increasingly used to complement laboratory techniques in advancing our understanding of biological systems. Calibration, the identification of parameter values that align simulation with biological behaviours, becomes challenging as increasingly complex biological domains are simulated. Complex domains cannot be characterized by single metrics alone, rendering simulation calibration a fundamentally multi-metric optimization problem that typical calibration techniques cannot handle. Yet calibration is an essential activity in simulation-based science; the baseline calibration forms a control for subsequent experimentation and hence is fundamental in the interpretation of results. Here, we develop and showcase a method, built around multi-objective optimization, for calibrating ABSs against complex target behaviours requiring several metrics (termed objectives) to characterize. Multi-objective calibration (MOC) delivers those sets of parameter values representing optimal trade-offs in simulation performance against each metric, in the form of a Pareto front. We use MOC to calibrate a well-understood immunological simulation against both established a priori and previously unestablished target behaviours. Furthermore, we show that simulation-borne conclusions are broadly, but not entirely, robust to adopting baseline parameter values from different extremes of the Pareto front, highlighting the importance of MOC's identification of numerous calibration solutions. We devise a method for detecting overfitting in a multi-objective context, not previously possible, used to save computational effort by terminating MOC when no improved solutions will be found. MOC can significantly impact biological simulation, adding rigour to and speeding up an otherwise time-consuming calibration process and highlighting inappropriate biological capture by simulations that cannot be well calibrated. As such, it produces more accurate

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

    Science.gov (United States)

    Hoskinson, A-M; Caballero, M D; Knight, J K

    2013-06-01

    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 past 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 biological systems. In this paper, we discuss how research-supported approaches developed by physics education researchers can be adopted by biologists to enhance student problem-solving skills. First, we compare the problems that biology students are typically asked to solve with authentic, complex problems. We then describe the development of research-validated physics curricula emphasizing process skills in problem solving. We show that solving authentic, complex biology problems requires many of the same skills that practicing physicists and biologists use in representing problems, seeking relationships, making predictions, and verifying or checking solutions. We assert that acquiring these skills can help biology students become competent problem solvers. Finally, we propose how biology scholars can apply lessons from physics education in their classrooms and inspire new studies in biology education research.

  6. Mathematic simulation of soil-vegetation condition and land use structure applying basin approach

    Science.gov (United States)

    Mishchenko, Natalia; Shirkin, Leonid; Krasnoshchekov, Alexey

    2016-04-01

    Ecosystems anthropogenic transformation is basically connected to the changes of land use structure and human impact on soil fertility. The Research objective is to simulate the stationary state of river basins ecosystems. Materials and Methods. Basin approach has been applied in the research. Small rivers basins of the Klyazma river have been chosen as our research objects. They are situated in the central part of the Russian plain. The analysis is carried out applying integrated characteristics of ecosystems functioning and mathematic simulation methods. To design mathematic simulator functional simulation methods and principles on the basis of regression, correlation and factor analysis have been applied in the research. Results. Mathematic simulation resulted in defining possible permanent conditions of "phytocenosis-soil" system in coordinates of phytomass, phytoproductivity, humus percentage in soil. Ecosystem productivity is determined not only by vegetation photosynthesis activity but also by the area ratio of forest and meadow phytocenosis. Local maximums attached to certain phytomass areas and humus content in soil have been defined on the basin phytoproductivity distribution diagram. We explain the local maximum by synergetic effect. It appears with the definite ratio of forest and meadow phytocenosis. In this case, utmost values of phytomass for the whole area are higher than just a sum of utmost values of phytomass for the forest and meadow phytocenosis. Efficient correlation of natural forest and meadow phytocenosis has been defined for the Klyazma river. Conclusion. Mathematic simulation methods assist in forecasting the ecosystem conditions under various changes of land use structure. Nowadays overgrowing of the abandoned agricultural lands is very actual for the Russian Federation. Simulation results demonstrate that natural ratio of forest and meadow phytocenosis for the area will restore during agricultural overgrowing.

  7. 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.

  8. 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...

  9. 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

  10. 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…

  11. Tension moderation and fluctuation spectrum in simulated lipid membranes under an applied electric potential

    DEFF Research Database (Denmark)

    Loubet, Bastien; Lomholt, Michael Andersen; Khandelia, Himanshu

    2013-01-01

    We investigate the effect of an applied electric potential on the mechanics of a coarse grained POPC bilayer under tension. The size and duration of our simulations allow for a detailed and accurate study of the fluctuations. Effects on the fluctuation spectrum, tension, bending rigidity, and bil......We investigate the effect of an applied electric potential on the mechanics of a coarse grained POPC bilayer under tension. The size and duration of our simulations allow for a detailed and accurate study of the fluctuations. Effects on the fluctuation spectrum, tension, bending rigidity......, and bilayer thickness are investigated in detail. In particular, the least square fitting technique is used to calculate the fluctuation spectra. The simulations confirm a recently proposed theory that the effect of an applied electric potential on the membrane will be moderated by the elastic properties...... fluctuations. The effect of the applied electric potential on the bending rigidity is non-existent within error bars. However, when the membrane is stretched there is a point where the bending rigidity is lowered due to a decrease of the thickness of the membrane. All these effects should prove important...

  12. Program Applied Biology and Biotechnology. Annual report 1988. Programm Angewandte Biologie und Biotechnologie. Jahresbericht 1988

    Energy Technology Data Exchange (ETDEWEB)

    1989-01-01

    This annual report of the Biology, Ecology, Energy Department (PBE) of Juelich Nuclear Research Center contains short descriptions of the projects subsidized by the Federal Government on the following subjects: 1. Biological process and enzyme engineering; 2. Cell culture and cell fusion engineering; 3. Genetic engineering and microbial techniques; 4. Alternative methods for animal experiments, biological safety; 5. Plant breeding and plant protection; 6. Gene centres and priority projects; 7. New fields and interdisciplinary activities of biotechnology; 8. Regeneration of the raw materials. (RB).

  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. 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...

  15. Process Simulation of Complex Biological Pathways in Physical Reactive Space and Reformulated for Massively Parallel Computing Platforms.

    Science.gov (United States)

    Ganesan, Narayan; Li, Jie; Sharma, Vishakha; Jiang, Hanyu; Compagnoni, Adriana

    2016-01-01

    Biological systems encompass complexity that far surpasses many artificial systems. Modeling and simulation of large and complex biochemical pathways is a computationally intensive challenge. Traditional tools, such as ordinary differential equations, partial differential equations, stochastic master equations, and Gillespie type methods, are all limited either by their modeling fidelity or computational efficiency or both. In this work, we present a scalable computational framework based on modeling biochemical reactions in explicit 3D space, that is suitable for studying the behavior of large and complex biological pathways. The framework is designed to exploit parallelism and scalability offered by commodity massively parallel processors such as the graphics processing units (GPUs) and other parallel computing platforms. The reaction modeling in 3D space is aimed at enhancing the realism of the model compared to traditional modeling tools and framework. We introduce the Parallel Select algorithm that is key to breaking the sequential bottleneck limiting the performance of most other tools designed to study biochemical interactions. The algorithm is designed to be computationally tractable, handle hundreds of interacting chemical species and millions of independent agents by considering all-particle interactions within the system. We also present an implementation of the framework on the popular graphics processing units and apply it to the simulation study of JAK-STAT Signal Transduction Pathway. The computational framework will offer a deeper insight into various biological processes within the cell and help us observe key events as they unfold in space and time. This will advance the current state-of-the-art in simulation study of large scale biological systems and also enable the realistic simulation study of macro-biological cultures, where inter-cellular interactions are prevalent.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Accurate simulation of MPPT methods performance when applied to commercial photovoltaic panels.

    Science.gov (United States)

    Cubas, Javier; Pindado, Santiago; Sanz-Andrés, Ángel

    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 commercial solar panel, within a day, and under realistic ambient conditions. PMID:25874262

  1. 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

  2. A system simulation model applied to the production schedule of a fish processing facility

    Directory of Open Access Journals (Sweden)

    Carla Roberta Pereira

    2012-11-01

    Full Text Available The simulation seeks to import the reality to a controlled environment, where it is possible to study it behavior, under several conditions, without involving physical risks and/or high costs. Thus, the system simulation becomes a useful and powerful technique in emergence markets, as the tilapiculture sector that needs to expand its business. The main purpose of this study was the development of a simulation model to assist the decisions making of the production scheduling of a fish processing facility. It was applied, as research method, the case study and the modeling/simulation, including in this set the SimuCAD methodology and the development phases of a simulation model. The model works with several alternative scenarios, testing different working shifts, types of flows and production capacity, besides variations of the ending inventory and sales. The result of this research was a useful and differentiated model simulation to assist the decision making of the production scheduling of fish processing facility studied.

  3. 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 ...

  4. 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...

  5. 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...

  6. Human Metabolic Network: Reconstruction, Simulation, and Applications in Systems Biology

    Science.gov (United States)

    Wu, Ming; Chan, Christina

    2012-01-01

    Metabolism is crucial to cell growth and proliferation. Deficiency or alterations in metabolic functions are known to be involved in many human diseases. Therefore, understanding the human metabolic system is important for the study and treatment of complex diseases. Current reconstructions of the global human metabolic network provide a computational platform to integrate genome-scale information on metabolism. The platform enables a systematic study of the regulation and is applicable to a wide variety of cases, wherein one could rely on in silico perturbations to predict novel targets, interpret systemic effects, and identify alterations in the metabolic states to better understand the genotype-phenotype relationships. In this review, we describe the reconstruction of the human metabolic network, introduce the constraint based modeling approach to analyze metabolic networks, and discuss systems biology applications to study human physiology and pathology. We highlight the challenges and opportunities in network reconstruction and systems modeling of the human metabolic system. PMID:24957377

  7. 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.

  8. 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.

  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. 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

  11. 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.

  12. 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

  13. 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.)

  14. 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.

  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. 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

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

    Science.gov (United States)

    Feller, S E; Pastor, R W

    1996-09-01

    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

  18. 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.

  19. 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. ...

  20. 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

  1. 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)

  2. Computer simulation applied to jewellery casting: challenges, results and future possibilities

    Science.gov (United States)

    Tiberto, Dario; Klotz, Ulrich E.

    2012-07-01

    Computer simulation has been successfully applied in the past to several industrial processes (such as lost foam and die casting) by larger foundries and direct automotive suppliers, while for the jewelry sector it is a procedure which is not widespread, and which has been tested mainly in the context of research projects. On the basis of a recently concluded EU project, the authors here present the simulation of investment casting, using two different softwares: one for the filling step (Flow-3D®), the other one for the solidification (PoligonSoft®). A work on material characterization was conducted to obtain the necessary physical parameters for the investment (used for the mold) and for the gold alloys (through thermal analysis). A series of 18k and 14k gold alloys were cast in standard set-ups to have a series of benchmark trials with embedded thermocouples for temperature measurement, in order to compare and validate the software output in terms of the cooling curves for definite test parts. Results obtained with the simulation included the reduction of micro-porosity through an optimization of the feeding channels for a controlled solidification of the metal: examples of the predicted porosity in the cast parts (with metallographic comparison) will be shown. Considerations on the feasibility of applying the casting simulation in the jewelry sector will be reached, underlining the importance of the software parametrization necessary to obtain reliable results, and the discrepancies found with the experimental comparison. In addition an overview on further possibilities of application for the CFD in jewellery casting, such as the modeling of the centrifugal and tilting processes, will be presented.

  3. 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.

  4. 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)

  5. 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

  6. 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

  7. 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)

  8. 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.

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

    OpenAIRE

    Neogi, Biswarup; Ghosal, Soumya; Mukherjee, Soumyajit; Das, Achintya; D N TIBAREWALA

    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 a...

  10. Novel hybrid methods applied for the numerical simulation of three-phase biotechnological flows

    Energy Technology Data Exchange (ETDEWEB)

    Diez Robles, Lucia

    2009-07-01

    Granular Activated Sludge (GAS) is na novel biological secondary treatment of wastewater which presents multiple advantages with respect to Conventional Activated Sludge (CAS). For fluid mechanical analysis of the bioreactor in which GAS is cultivated, two strategies are adopted: numerical analysis which is carried out in the present thesis and optical in situ measurements which validate the numerical results. The Eulerian-Eulerian multi-fluid approach does not offer a satisfactory description of the three-phase flow as there is a lack of appropriate mathematical models and the solution of the equation systems is problematic. Hybrid methods are here developed in order to complement the classical numerical techniques. These improve the convergence of the numerical simulation, generate results more in accordance with the experimental results and reduce the CPU time required for the calculations. An additional momentum exchange between the dispersed phases is also proposed for the consideration of the four-way coupling case. (orig.)

  11. 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.

  12. Simulations on the Teaching of Molecular Biology: Experience’s Report

    Directory of Open Access Journals (Sweden)

    A.L.S. Silva

    2013-05-01

    Full Text Available INTRODUCTION: The comprehension of techniques used in Molecular Biology neither always is easy.Therefore, the objective of this work was to apply simulations in Molecular Biology for graduating students of a Pharmacy course froma private educational institution, to allow them to practice the apparent difficult protocols. MATERIALS AND METHODS: Three groups of students (50 each were evaluated. Two of them were submitted to different simulatory activities,such as: a visiting the virtual laboratory of Utah University (USA to understand gel electrophoresis and polymerasechain reaction (PCR techniques, b extracting DNA from oral mucosa by means of a homemade protocol, c investigating simulatory paternity tests, d proposing their own microarrays by painting them on paper and then interpreted the results according to the colors, e designing primers (small fragments of DNA to PCR with the free software Primer3 and testing them in silico PCR. The third group of students was only submitted to oral theoretical classes about all these themes. The progress of the understanding was qualitatively evaluated and compared by the analysis of questionnaires. RESULTS AND DISCUSSION: The groups submitted to the virtual classes were responsive during the development of activities and had a better performance in the examinations than the group that had only theoretical classes, showing better comprehension about the themes. Their greatest difficult was the limitation in the English language to interact with the websites (they often asked about an alternative site in Portuguese. CONCLUSION: The didactical sequence involving exercises in websites by using freeware and recreational activities in classroom with graduating students of Pharmacy proved to be an effective tool in the learning of some of the techniques in Molecular Biology, mainly when a lab and some equipment are not available to perform practical activities

  13. 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...

  14. The image simulation arithmetic of the degradating process of porous biologic ceramic in life-form

    Institute of Scientific and Technical Information of China (English)

    CHEN Zuo-bing; HUANG Jian-zhong; YAN Yu-hua; LI Shi-pu

    2001-01-01

    @@ It is a complex and difficult task to simulate the degradating process of porous biologic ceramic in life-form by computer. Because the evolvement of crystal' s structure deals with not only the mechanism of many factors, such as crystallography tropism, the reciprocity of wafer, interfacial movement, but also topology geometry mechanism of dimensional padding.

  15. 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.…

  16. 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)

  17. 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)

  18. 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.

  19. 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

  20. A Systems Biology Analysis Unfolds the Molecular Pathways and Networks of Two Proteobacteria in Spaceflight and Simulated Microgravity Conditions

    Science.gov (United States)

    Roy, Raktim; Phani Shilpa, P.; Bagh, Sangram

    2016-09-01

    Bacteria are important organisms for space missions due to their increased pathogenesis in microgravity that poses risks to the health of astronauts and for projected synthetic biology applications at the space station. We understand little about the effect, at the molecular systems level, of microgravity on bacteria, despite their significant incidence. In this study, we proposed a systems biology pipeline and performed an analysis on published gene expression data sets from multiple seminal studies on Pseudomonas aeruginosa and Salmonella enterica serovar Typhimurium under spaceflight and simulated microgravity conditions. By applying gene set enrichment analysis on the global gene expression data, we directly identified a large number of new, statistically significant cellular and metabolic pathways involved in response to microgravity. Alteration of metabolic pathways in microgravity has rarely been reported before, whereas in this analysis metabolic pathways are prevalent. Several of those pathways were found to be common across studies and species, indicating a common cellular response in microgravity. We clustered genes based on their expression patterns using consensus non-negative matrix factorization. The genes from different mathematically stable clusters showed protein-protein association networks with distinct biological functions, suggesting the plausible functional or regulatory network motifs in response to microgravity. The newly identified pathways and networks showed connection with increased survival of pathogens within macrophages, virulence, and antibiotic resistance in microgravity. Our work establishes a systems biology pipeline and provides an integrated insight into the effect of microgravity at the molecular systems level.

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. Estimating the Influence of Biological Ice Nuclei on Clouds with Regional Scale Simulations

    Science.gov (United States)

    Hummel, Matthias; Hoose, Corinna; Schaupp, Caroline; Möhler, Ottmar

    2014-05-01

    Cloud properties are largely influenced by the atmospheric formation of ice particles. Some primary biological aerosol particles (PBAP), e.g. certain bacteria, fungal spores or pollen, have been identified as effective ice nuclei (IN). The work presented here quantifies the IN concentrations originating from PBAP in order to estimate their influences on clouds with the regional scale atmospheric model COSMO-ART in a six day case study for Western Europe. The atmospheric particle distribution is calculated for three different PBAP (bacteria, fungal spores and birch pollen). The parameterizations for heterogeneous ice nucleation of PBAP are derived from AIDA cloud chamber experiments with Pseudomonas syringae bacteria and birch pollen (Schaupp, 2013) and from published data on Cladosporium spores (Iannone et al., 2011). A constant fraction of ice-active bacteria and fungal spores relative to the total bacteria and spore concentration had to be assumed. At cloud altitude, average simulated PBAP number concentrations are ~17 L-1 for bacteria and fungal spores and ~0.03 L-1 for birch pollen, including large temporal and spatial variations of more than one order of magnitude. Thus, the average, 'diagnostic' in-cloud PBAP IN concentrations, which only depend on the PBAP concentrations and temperature, without applying dynamics and cloud microphysics, lie at the lower end of the range of typically observed atmospheric IN concentrations . Average PBAP IN concentrations are between 10-6 L-1 and 10-4 L-1. Locally but not very frequently, PBAP IN concentrations can be as high as 0.2 L-1 at -10° C. Two simulations are compared to estimate the cloud impact of PBAP IN, both including mineral dust as an additional background IN with a constant concentration of 100 L-1. One of the simulations includes additional PBAP IN which can alter the cloud properties compared to the reference simulation without PBAP IN. The difference in ice particle and cloud droplet concentration between

  9. 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.

  10. Using the current Brazilian value for the biological exposure limit applied to blood lead level as a lead poisoning diagnostic criterion

    Directory of Open Access Journals (Sweden)

    Cordeiro Ricardo

    1996-01-01

    Full Text Available In general, biological exposure limits are only used for the promotion and preservation of workers' health and are not applied for diagnostic purposes. However, the issue is controversial for certain types of occupational poisoning. This paper proposes the utilization of biological exposure limits currently applied to blood lead levels in Brazil as an important criterion for diagnosing occupational lead poisoning. The author argues that contrary to the traditional clinical criterion, one should deal with the diagnostic problem of lead poisoning from an epidemiological perspective, using the current Brazilian value for the biological exposure limit applied to blood lead level as an indicator of high relative risk.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. Building a better cell trap: Applying Lagrangian modeling to the design of microfluidic devices for cell biology

    Science.gov (United States)

    Kim, Min-Cheol; Wang, Zhanhui; Lam, Raymond H. W.; Thorsen, Todd

    2008-02-01

    In this report, we show how computational fluid dynamics can be applied to the design of efficient hydrodynamic cell traps in microfluidic devices. Modeled hydrodynamic trap designs included a large, multiple-aperture "C-type" sieve for trapping hundreds of cells, flat single-aperture arrays for single cells, and "U-type" hydrodynamic structures with one or two apertures to confine small clusters of cells (˜10-15 cells per trap). Using 3T3 cells as a model system, the motion of each individual cell was calculated using a one-way coupled Lagrangian method. The cell was assumed to be a solid sphere, and interactions with other cells were only considered when a cell sedimented in the trap. The ordinary differential equations were solved along the cell trajectory for the three components of the velocity and location vector by using the Rosenbrock method based on an adaptive time-stepping technique. Validation of the predictive value of modeling, using 3T3 cells flowed through microfluidic devices containing "U-type sieves" under the simulation flow parameters, showed excellent agreement between experiment and simulation with respect to cell number per trap and the uniformity of cell distribution within individual microchambers. For applications such as on-chip cell culture or high-throughput screening of cell populations within a lab-on-a-chip environment, Lagrangian simulations have the potential to greatly simplify the design process.

  1. POD for Real-Time Simulation of Hyperelastic Soft Biological Tissue Using the Point Collocation Method of Finite Spheres

    Directory of Open Access Journals (Sweden)

    Suleiman Banihani

    2013-01-01

    Full Text Available The point collocation method of finite spheres (PCMFS is used to model the hyperelastic response of soft biological tissue in real time within the framework of virtual surgery simulation. The proper orthogonal decomposition (POD model order reduction (MOR technique was used to achieve reduced-order model of the problem, minimizing computational cost. The PCMFS is a physics-based meshfree numerical technique for real-time simulation of surgical procedures where the approximation functions are applied directly on the strong form of the boundary value problem without the need for integration, increasing computational efficiency. Since computational speed has a significant role in simulation of surgical procedures, the proposed technique was able to model realistic nonlinear behavior of organs in real time. Numerical results are shown to demonstrate the effectiveness of the new methodology through a comparison between full and reduced analyses for several nonlinear problems. It is shown that the proposed technique was able to achieve good agreement with the full model; moreover, the computational and data storage costs were significantly reduced.

  2. 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.

  3. 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)

  4. 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

  5. Optical simulation of laser beam phase-shaping focusing optimization in biological tissues

    Science.gov (United States)

    Gomes, Ricardo; Vieira, Pedro; Coelho, João. M. P.

    2013-11-01

    In this paper we report the development of an optical simulator that can be used in the development of methodologies for compensate/decrease the light scattering effect of most biological tissues through phase-shaping methods. In fact, scattering has long been a major limitation for the medical applications of lasers where in-depth tissues concerns due to the turbid nature of most biological media in the human body. In developing the simulator, two different approaches were followed: one using multiple identical beams directed to the same target area and the other using a phase-shaped beam. In the multiple identical beams approach (used mainly to illustrate the limiting effect of scattering on the beam's propagation) there was no improvement in the beam focus at 1 mm compared to a single beam layout but, in phase-shaped beam approach, a 8x improvement on the radius of the beam at the same depth was achieved. The models were created using the optical design software Zemax and numerical algorithms created in Matlab programming language to shape the beam wavefront. A dedicated toolbox allowed communication between both programs. The use of the two software's proves to be a simple and powerful solution combining the best of the two and allowing a significant potential for adapting the simulations to new systems and thus allow to assess their response and define critical engineering parameters prior to laboratorial implementation.

  6. Biocorrosion properties of antibacterial Ti-10Cu sintered alloy in several simulated biological solutions.

    Science.gov (United States)

    Liu, Cong; Zhang, Erlin

    2015-03-01

    Ti-10Cu sintered alloy has shown strong antibacterial properties against S. aureus and E. coli and good cell biocompatibility, which displays potential application in dental application. The corrosion behaviors of the alloy in five different simulated biological solutions have been investigated by electrochemical technology, surface observation, roughness measurement and immersion test. Five different simulated solutions were chosen to simulate oral condition, oral condition with F(-) ion, human body fluids with different pH values and blood system. It has been shown that Ti-10Cu alloy exhibits high corrosion rate in Saliva pH 3.5 solution and Saliva pH 6.8 + 0.2F solution but low corrosion rate in Hank's, Tyrode's and Saliva pH 6.8 solutions. The corrosion rate of Ti-10Cu alloy was in a order of Hank's, Tyrode's, Saliva pH 6.8, Saliva-pH 3.5 and Saliva pH 6.8 + 0.2F from slow to fast. All results indicated acid and F(-) containing conditions prompt the corrosion reaction of Ti-Cu alloy. It was suggested that the Cu ion release in the biological environments, especially in the acid and F(-) containing condition would lead to high antibacterial properties without any cell toxicity, displaying wide potential application of this alloy.

  7. 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.

  8. Thermo-electrical equivalents for simulating the electro-mechanical behavior of biological tissue.

    Science.gov (United States)

    Cinelli, I; Duffy, M; McHugh, P E

    2015-01-01

    Equivalence is one of most popular techniques to simulate the behavior of systems governed by the same type of differential equation. In this case, a thermo-electrical equivalence is considered as a method for modelling the inter-dependence of electrical and mechanical phenomena in biological tissue. We seek to assess this approach for multi-scale models (from micro-structure to tissue scale) of biological media, such as nerve cells and cardiac tissue, in which the electrical charge distribution is modelled as a heat distribution in an equivalent thermal system. This procedure allows for the reduction in problem complexity and it facilitates the coupling of electrical and mechanical phenomena in an efficient and practical way. Although the findings of this analysis are mainly addressed towards the electro-mechanics of tissue within the biomedical domain, the same approach could be used in other studies in which a coupled finite element analysis is required. PMID:26737163

  9. 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.

  10. 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.

  11. Numerical simulation and experiment of optothermal response of biological tissue irradiated by continuous xenon lamp

    Institute of Scientific and Technical Information of China (English)

    Meizhen Huang; Yaxing Tong

    2012-01-01

    A finite element method computation model for analyzing optothermal interaction of polychromatic light and biology tissue is proposed and proven by experiment.A continuous xenon lamp is employed as an example.First,the spectral energy distribution of the xenon lamp is measured and found to be equivalent to a series of quasi-chromatic light with different central wavelengths,different energies,and certain bandwidth.Next,according to the reported thermal and optical parameters of porcine skin and porcine liver,the temporal temperature distributions of these tissues irradiated by each quasi-chromatic light are simulated.Then,the thermal effect is superimposed to obtain the whole optothermal temporal temperature distribution.Moreover,the optothermal response experiments of fresh porcine skin and porcine liver tissues irradiated by continuous xenon lamp are carried out.The results of the simulation and experiment are analyzed and compared,and are found to be commendably matched.

  12. 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.

  13. 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...

  14. A simulation benchmark to evaluate the performance of advanced control techniques in biological wastewater treatment plants

    Directory of Open Access Journals (Sweden)

    Sotomayor O.A.Z.

    2001-01-01

    Full Text Available Wastewater treatment plants (WWTP are complex systems that incorporate a large number of biological, physicochemical and biochemical processes. They are large and nonlinear systems subject to great disturbances in incoming loads. The primary goal of a WWTP is to reduce pollutants and the second goal is disturbance rejection, in order to obtain good effluent quality. Modeling and computer simulations are key tools in the achievement of these two goals. They are essential to describe, predict and control the complicated interactions of the processes. Numerous control techniques (algorithms and control strategies (structures have been suggested to regulate WWTP; however, it is difficult to make a discerning performance evaluation due to the nonuniformity of the simulated plants used. The main objective of this paper is to present a benchmark of an entire biological wastewater treatment plant in order to evaluate, through simulations, different control techniques. This benchmark plays the role of an activated sludge process used for removal of organic matter and nitrogen from domestic effluents. The development of this simulator is based on models widely accepted by the international community and is implemented in Matlab/Simulink (The MathWorks, Inc. platform. The benchmark considers plant layout and the effects of influent characteristics. It also includes a test protocol for analyzing the open and closed-loop responses of the plant. Examples of control applications in the benchmark are implemented employing conventional PI controllers. The following common control strategies are tested: dissolved oxygen (DO concentration-based control, respirometry-based control and nitrate concentration-based control.

  15. Rings and ladders in biology - fast ab initio simulations of polypeptides and DNA.

    Science.gov (United States)

    Lewis, James P.

    1996-03-01

    Throughout the years, developments of first principles methods have allowed a theoretical investigation of a wide variety of materials from semiconductors to zeolites. However, ab initio methods have not been widespread in the area of large biological systems. Several recent advances in theoretical techniques have prompted us to examine the possibility of simulating large biological systems. Linear scaling methods have been developed to avoid the N^3 computational roadblock due to matrix diagonalization, and a hydrogen-bonding model has been developed to correctly model weak intermolecular interactions within a tight-binding like local orbital framework.(J. Ortega, J. P. Lewis, O. F. Sankey Phys. Rev. B. 50), 10516 (1994); J. P. Lewis and O. F. Sankey, Biophys. J. 69, 1068 (1995). With these developments, a simulation of a dehydrated 10 basepair poly(dG) -- poly(dC) segment of DNA will be described. Results for the electronic structure of this relaxed structure will be discussed. In addition, a simulation of this relaxed structure, involving 1932 steps, was performed to determine the dynamical matrix. The corresponding vibrational spectrum was found and trends will be compared with experimental work.(Work done in collaboration with Otto F. Sankey and Pablo Ordejón) In addition, theoretical results on the energetics, electronic, vibrational and elastic properties of cyclic peptide systems cyclo[(D-Ala-Glu-D-Ala-Gln)_m], where m=1-4, will be presented. Experimentally, these cyclic peptide nanotubes have been shown to be excellent for transporting of ions and glucose across membranes, the attempt to simulate the placement of a dopant into the nanotube structure and the effects on the electronic structure will be discussed.(Work done in collaboration with Otto F. Sankey and Norma H. Pawley)

  16. 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.

  17. SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology

    Directory of Open Access Journals (Sweden)

    Alexander Dörr

    2014-12-01

    Full Text Available The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. Parameter values from literature or experiments can often not directly be combined in complex reaction systems. Nature-inspired optimization techniques can find appropriate sets of parameters that calibrate a model to experimentally obtained time series data. We present SBMLsimulator, a tool that combines the Systems Biology Simulation Core Library for dynamic simulation of biochemical models with the heuristic optimization framework EvA2. SBMLsimulator provides an intuitive graphical user interface with various options as well as a fully-featured command-line interface for large-scale and script-based model simulation and calibration. In a parameter estimation study based on a published model and artificial data we demonstrate the capability of SBMLsimulator to identify parameters. SBMLsimulator is useful for both, the interactive simulation and exploration of the parameter space and for the large-scale model calibration and estimation of uncertain parameter values.

  18. 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.

  19. DripFume: A Visual Basic Program For Simulating Distribution And Atmospheric Volatilization Of Soil Fumigants Applied Through Drip Irrigation

    Science.gov (United States)

    A Windows-based graphical user interface program (DripFume) was developed in MS Visual Basic (VB) to utilize a two-dimensional multi-phase finite element pesticide transport model to simulate distribution and emission of volatile fumigant chemicals when applied through drip irrigation or shank injec...

  20. 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.

  1. 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

  2. Potential impacts from biological aerosols on ensembles of continental clouds simulated numerically

    Directory of Open Access Journals (Sweden)

    V. T. J. Phillips

    2009-06-01

    Full Text Available An aerosol-cloud modeling framework is described to simulate the activation of ice particles and droplets by biological aerosol particles, such as airborne ice-nucleation active (INA bacteria. It includes the empirical parameterisation of heterogeneous ice nucleation and a semi-prognostic aerosol component, which have been incorporated into a cloud-system resolving model (CSRM with double-moment bulk microphysics. The formation of cloud liquid by soluble material coated on these partially insoluble organic aerosols is represented. It determines their partial removal from deep convective clouds by accretion onto precipitation in the cloud model. This "aerosol-cloud model" is validated for diverse cases of deep convection with contrasting aerosol conditions, against satellite, ground-based and aircraft observations.

    Simulations are performed with the aerosol-cloud model for a month-long period of summertime convective activity over Oklahoma. It includes three cases of continental deep convection simulated previously by Phillips and Donner (2006. Elevated concentrations of insoluble organic aerosol, boosted by a factor of 100 beyond their usual values for this continental region, are found to influence significantly the following quantities: (1 the average numbers and sizes of ice crystals and droplets in the clouds; (2 the horizontal cloud coverage in the free troposphere; (3 precipitation at the ground; and (4 incident solar insolation at the surface. This factor of 100 is plausible for natural fluctuations of the concentration of insoluble organic aerosol, in view of variability of cell concentrations for airborne bacteria seen by Lindemann et al. (1982.

    In nature, such boosting of the insoluble organic aerosol loading could arise from enhanced emissions of biological aerosol particles from a land surface. Surface wetness and solar insolation at the ground are meteorological quantities known to influence rates of growth of

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. Implementation of a Large Eddy Simulation Method Applied to Recirculating Flow in a Ventilated Room

    DEFF Research Database (Denmark)

    Davidson, Lars

    In the present work Large Eddy Simulations are presented. The flow in a ventilated enclosure is studied. We use an explicit, two-steps time-advancement scheme where the pressure is solved from a Poisson equation....

  11. 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...

  12. 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...

  13. 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.

  14. A new simulation method for turbines in wake - Applied to extreme response during operation

    DEFF Research Database (Denmark)

    Thomsen, K.; Aagaard Madsen, H.

    2005-01-01

    The work focuses on prediction of load response for wind turbines operating in wind forms using a newly developed aeroelostic simulation method The traditionally used concept is to adjust the free flow turbulence intensity to account for increased loads in wind farms-a methodology that might...... be suitable for fatigue load simulation. For extreme response during operation the success of this simplified approach depends significantly on the physical mechanism causing the extremes. If the physical mechanism creating increased loads in wake operation is different from an increased turbulence intensity......, the resulting extremes might be erroneous. For blade loads the traditionally used simplified approach works better than for integrated rotor loads-where the instantaneous load gradient across the rotor disc is causing the extreme loads. In the article the new wake simulation approach is illustrated...

  15. A simple atmospheric boundary layer model applied to large eddy simulations of wind turbine wakes

    DEFF Research Database (Denmark)

    Troldborg, Niels; Sørensen, Jens Nørkær; Mikkelsen, Robert Flemming;

    2014-01-01

    A simple model for including the influence of the atmospheric boundary layer in connection with large eddy simulations of wind turbine wakes is presented and validated by comparing computed results with measurements as well as with direct numerical simulations. The model is based on an immersed...... boundary type technique where volume forces are used to introduce wind shear and atmospheric turbulence. The application of the model for wake studies is demonstrated by combining it with the actuator line method, and predictions are compared with field measurements. Copyright © 2013 John Wiley & Sons, Ltd....

  16. 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)

  17. 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…

  18. An interactive visualisation tool applied to the simulation of glass pressing

    NARCIS (Netherlands)

    Laevsky, K.; Telea, A.; Mattheij, R.M.M.

    2001-01-01

    An interactive numerical simulation approach to the process of glass pressing is presented. Glass is modelled as a strongly viscous Newtonian fluid whose deformation under pressure is described by a Stokes equation. Modelling the evolution of the glass free boundary in time poses a particular proble

  19. 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

    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 in that work and simulation results are presented in order to prove the theory presented....

  20. 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

    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...

  1. 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.

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

    NARCIS (Netherlands)

    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

  3. Dynamic simulation and modeling of the motion modes produced during the 3D controlled manipulation of biological micro/nanoparticles based on the AFM.

    Science.gov (United States)

    Saraee, Mahdieh B; Korayem, Moharam H

    2015-08-01

    Determining the motion modes and the exact position of a particle displaced during the manipulation process is of special importance. This issue becomes even more important when the studied particles are biological micro/nanoparticles and the goals of manipulation are the transfer of these particles within body cells, repair of cancerous cells and the delivery of medication to damaged cells. However, due to the delicate nature of biological nanoparticles and their higher vulnerability, by obtaining the necessary force of manipulation for the considered motion mode, we can prevent the sample from interlocking with or sticking to the substrate because of applying a weak force or avoid damaging the sample due to the exertion of excessive force. In this paper, the dynamic behaviors and the motion modes of biological micro/nanoparticles such as DNA, yeast, platelet and bacteria due to the 3D manipulation effect have been investigated. Since the above nanoparticles generally have a cylindrical shape, the cylindrical contact models have been employed in an attempt to more precisely model the forces exerted on the nanoparticle during the manipulation process. Also, this investigation has performed a comprehensive modeling and simulation of all the possible motion modes in 3D manipulation by taking into account the eccentricity of the applied load on the biological nanoparticle. The obtained results indicate that unlike the macroscopic scale, the sliding of nanoparticle on substrate in nano-scale takes place sooner than the other motion modes and that the spinning about the vertical and transverse axes and the rolling of nanoparticle occur later than the other motion modes. The simulation results also indicate that the applied force necessary for the onset of nanoparticle movement and the resulting motion mode depend on the size and aspect ratio of the nanoparticle.

  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. 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

  6. 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...

  7. 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...

  8. 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

  9. 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)

  10. 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)

  11. 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...

  12. 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.

  13. 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...

  14. 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...

  15. Applying measured reflection from the ground to simulations of thermal perfromance of solar collectors

    DEFF Research Database (Denmark)

    Dragsted, Janne; Furbo, Simon

    2009-01-01

    and the azimuth of the surface in question. The paper will present an analysis of simulations of the thermal performance of solar collectors using the standard description of the albedo and using the albedo determined by the measurements. It will be elucidated how important an accurate description...... of the reflection from the ground is for the thermal performance of solar collectors.......Solar radiation on tilted and vertical surfaces in the Arctic is, in large parts of the year, strongly influenced by reflection from snow. In connection with planning and optimization of energy efficient buildings and solar energy systems in the Arctic, it is important to have an accurate...

  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. Evaluation of center-cut separations applying simulated moving bed chromatography with 8 zones.

    Science.gov (United States)

    Santos da Silva, Francisco Vitor; Seidel-Morgenstern, Andreas

    2016-07-22

    Different multi-column options to perform continuous chromatographic separations of ternary mixtures have been proposed in order to overcome limitations of batch chromatography. One attractive option is given by simulated moving bed chromatography (SMB) with 8 zones, a process that offers uninterrupted production, and, potentially, improved economy. As in other established ternary separation processes, the separation sequence is crucial for the performance of the process. This problem is addressed here by computing and comparing optimal performances of the two possibilities assuming linear adsorption isotherms. The conclusions are presented in a decision tree which can be used to guide the selection of system configuration and operation. PMID:27328885

  18. 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.

  19. Electron Energy-Loss Spectroscopy Theory and Simulation Applied to Nanoparticle Plasmonics

    Science.gov (United States)

    Bigelow, Nicholas Walker

    In this dissertation, the capacity of electron energy-loss spectroscopy (EELS) to probe plasmons is examined in detail. EELS is shown to be able to detect both electric hot spots and Fano resonances in contrast to the prevailing knowledge prior to this work. The most detailed examination of magnetoplasmonic resonances in multi-ring structures to date and the utility of electron tomography to computational plasmonics is explored, and a new tomographic method for the reconstruction of a target is introduced. Since the observation of single-molecule surface-enhanced Raman scattering (SMSERS) in 1997, questions regarding the nature of the electromagnetic hot spots responsible for such observations still persist. A computational analysis of the electron- and photon-driven surface-plasmon resonances of monomer and dimer metal nanorods is presented to elucidate the differences and similarities between the two excitation mechanisms in a system with well understood optical properties. By correlating the nanostructure's simulated electron energy loss spectrum and loss-probability maps with its induced polarization and scattered electric field we discern how certain plasmon modes are selectively excited and how they funnel energy from the excitation source into the near- and far-field. Using a fully retarded electron-scattering theory capable of describing arbitrary three-dimensional nanoparticle geometries, aggregation schemes, and material compositions, we find that electron energy-loss spectroscopy (EELS) is able to indirectly probe the same electromagnetic hot spots that are generated by an optical excitation source. EELS is then employed in a scanning transmission electron microscope (STEM) to obtain maps of the localized surface plasmon modes of SMSERS-active nanostructures, which are resolved in both space and energy. Single-molecule character is confirmed by the bianalyte approach using two isotopologues of Rhodamine 6G. The origins of this observation are explored

  20. Final Technical Report for "Applied Mathematics Research: Simulation Based Optimization and Application to Electromagnetic Inverse Problems"

    Energy Technology Data Exchange (ETDEWEB)

    Haber, Eldad

    2014-03-17

    The focus of research was: Developing adaptive mesh for the solution of Maxwell's equations; Developing a parallel framework for time dependent inverse Maxwell's equations; Developing multilevel methods for optimization problems with inequal- ity constraints; A new inversion code for inverse Maxwell's equations in the 0th frequency (DC resistivity); A new inversion code for inverse Maxwell's equations in low frequency regime. Although the research concentrated on electromagnetic forward and in- verse problems the results of the research was applied to the problem of image registration.

  1. 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.

  2. 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.

  3. Simulation of Human Speech Production Applied to the Study and Synthesis of European Portuguese

    Directory of Open Access Journals (Sweden)

    Francisco A. C. Vaz

    2005-06-01

    Full Text Available A new articulatory synthesizer (SAPWindows, with a modular and flexible design, is described. A comprehensive acoustic model and a new interactive glottal source were implemented. Perceptual tests and simulations made possible by the synthesizer contributed to deepening our knowledge of one of the most important characteristics of European Portuguese, the nasal vowels. First attempts at incorporating models of frication into the articulatory synthesizer are presented, demonstrating the potential of performing fricative synthesis based on broad articulatory configurations. Synthesis of nonsense words and Portuguese words with vowels and nasal consonants is also shown. Despite not being capable of competing with mainstream concatenative speech synthesis, the anthropomorphic approach to speech synthesis, known as articulatory synthesis, proved to be a valuable tool for phonetics research and teaching. This was particularly true for the European Portuguese nasal vowels.

  4. 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.

  5. 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.

  6. 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)

  7. 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.

  8. 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

  9. Constellation of phase singularities in a speckle-like pattern for optical vortex metrology applied to biological kinematic analysis

    DEFF Research Database (Denmark)

    Wang, Wei; Qiao, Yu; Ishijima, Reika;

    2008-01-01

    A novel technique for biological kinematic analysis is proposed that makes use of the pseudophase singularities in a complex signal generated from a speckle-like pattern. In addition to the information about the locations and the anisotropic core structures of the pseudophase singularities, we al...

  10. 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.

  11. 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.

  12. 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.

  13. 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...

  14. 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

  15. 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.

  16. Numerical simulation of three-dimensional unsteady flow in a scroll expander applied in waste heat recovery

    Science.gov (United States)

    Song, P. P.; Wei, M. S.; Shi, L.; Ma, C. C.

    2013-12-01

    Three-dimensional numerical simulations of a scroll expander were performed with dynamic mesh technology. R245fa was selected as the working fluid in the simulations. The PISO algorithm was applied to solve the governing equations with RNG k-ε turbulent model. The distribution and variation of three-dimensional flow field inside the scroll expander were obtained. The research indicates that the flow field is nonuniform and asymmetrical distributions exist inside the expander. Vortex flows also exist in some working chambers. Dynamic clearance leakage flows and inlet orifice throttling have great effects on the flow field distribution. Transient output torque and the mass flux have periodic fluctuations during the working cycles.

  17. 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.

  18. 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...

  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. 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.

  1. Mobilization of endocrine-disrupting chemicals and estrogenic activity in simulated rainfall runoff from land-applied biosolids.

    Science.gov (United States)

    Giudice, Ben D; Young, Thomas M

    2011-10-01

    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, heavy metals, and total estrogenic activity in rainfall runoff from land-applied biosolids. Rainfall simulations were conducted on soil plots amended with biosolids. Surface runoff and leachate was collected and analyzed for the endocrine-disrupting compounds bisphenol A, 17α-ethynylestradiol, triclocarban, triclosan, octylphenol, and nonylphenol; a suite of 16 metals; and estrogenic activity via the estrogen receptor-mediated chemical activated luciferase gene expression (ER-CALUX) bioassay. Triclocarban (2.3-17.3 ng/L), triclosan (runoff, although unknown contributors or matrix effects were also found.

  2. 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.

  3. 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

  4. 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.

  5. 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...

  6. 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…

  7. 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

  8. 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.

  9. Mathematical modeling of cancer cell invasion of tissue: biological insight from mathematical analysis and computational simulation.

    Science.gov (United States)

    Andasari, Vivi; Gerisch, Alf; Lolas, Georgios; South, Andrew P; Chaplain, Mark A J

    2011-07-01

    The ability of cancer cells to break out of tissue compartments and invade locally gives solid tumours a defining deadly characteristic. One of the first steps of invasion is the remodelling of the surrounding tissue or extracellular matrix (ECM) and a major part of this process is the over-expression of proteolytic enzymes, such as the urokinase-type plasminogen activator (uPA) and matrix metalloproteinases (MMPs), by the cancer cells to break down ECM proteins. Degradation of the matrix enables the cancer cells to migrate through the tissue and subsequently to spread to secondary sites in the body, a process known as metastasis. In this paper we undertake an analysis of a mathematical model of cancer cell invasion of tissue, or ECM, which focuses on the role of the urokinase plasminogen activation system. The model consists of a system of five reaction-diffusion-taxis partial differential equations describing the interactions between cancer cells, uPA, uPA inhibitors, plasmin and the host tissue. Cancer cells react chemotactically and haptotactically to the spatio-temporal effects of the uPA system. The results obtained from computational simulations carried out on the model equations produce dynamic heterogeneous spatio-temporal solutions and using linear stability analysis we show that this is caused by a taxis-driven instability of a spatially homogeneous steady-state. Finally we consider the biological implications of the model results, draw parallels with clinical samples and laboratory based models of cancer cell invasion using three-dimensional invasion assay, and go on to discuss future development of the model.

  10. 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

  11. Space-resolved characterization of high frequency atmospheric-pressure plasma in nitrogen applying optical emission spectroscopy and numerical simulation

    CERN Document Server

    Rajasekaran, Priyadarshini; Bibinov, Nikita; Awakowicz, Peter

    2011-01-01

    Averaged plasma parameters such as electron distribution function and electron density are determined by characterization of high frequency (2.4 GHz) nitrogen-plasma using both experimental methods, namely optical emission spectroscopy (OES) and microphotography, and numerical simulation. Both direct and stepwise electron-impact excitation of nitrogen emissions are considered. The determination of space-resolved electron distribution function, electron density, rate constant for electron-impact dissociation of nitrogen molecule and the production of nitrogen atoms, applying the same methods, is discussed. Spatial distribution of intensities of neutral nitrogen molecule and nitrogen molecular ion from the microplasma is imaged by a CCD camera. The CCD images are calibrated using the corresponding emissions measured by absolutely-calibrated OES, and are then subjected to inverse Abel transformation to determine space-resolved intensities and other parameters. The space-resolved parameters are compared, respecti...

  12. Simulating the hydraulic stimulation of multiple fractures in an anisotropic stress field applying the discrete element method

    Science.gov (United States)

    Zeeb, Conny; Frühwirt, Thomas; Konietzky, Heinz

    2015-04-01

    Key to a successful exploitation of deep geothermal reservoirs in a petrothermal environment is the hydraulic stimulation of the host rock to increase permeability. The presented research investigates the fracture propagation and interaction during hydraulic stimulation of multiple fractures in a highly anisotropic stress field. The presented work was conducted within the framework of the OPTIRISS project, which is a cooperation of industry partners and universities in Thuringia and Saxony (Federal States of Germany) and was funded by the European Fond for Regional Development. One objective was the design optimization of the subsurface geothermal heat exchanger (SGHE) by means of numerical simulations. The presented simulations were conducted applying 3DEC (Itasca™), a software tool based on the discrete element method. The simulation results indicate that the main direction of fracture propagation is towards lower stresses and thus towards the biosphere. Therefore, barriers might be necessary to limit fracture propagation to the designated geological formation. Moreover, the hydraulic stimulation significantly alters the stresses in the vicinity of newly created fractures. Especially the change of the minimum stress component affects the hydraulic stimulation of subsequent fractures, which are deflected away from the previously stimulated fractures. This fracture deflection can render it impossible to connect all fractures with a second borehole for the later production. The results of continuative simulations indicate that a fracture deflection cannot be avoided completely. Therefore, the stage alignment was modified to minimize fracture deflection by varying (1) the pauses between stages, (2) the spacing's between adjacent stages, and (3) the angle between stimulation borehole and minimum stress component. An optimum SGHE design, which implies that all stimulated fractures are connected to the production borehole, can be achieved by aligning the stimulation

  13. 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)

  14. 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

  15. 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

  16. 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.

  17. 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)

  18. 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.

  19. Evaluation of water-soluble pouches of Bacillus sphaericus applied as prehatch treatment against Culex mosquitoes in simulated catch basins.

    Science.gov (United States)

    Su, Tianyun Steven

    2008-03-01

    An outdoor test was conducted to evaluate initial efficacy and longevity of water-soluble pouches of Bacillus sphaericus (VectoLex WSP and VBC60035 WSP), applied as prehatch treatment against Culex species in simulated catch basins. Both VectoLex WSP and VBC60035 WSP, applied at 1 pouch (10 g) per basin (single treatment), yielded significant immediate and long-term (> 90% for 203 days) control of late instars of Culex mosquitoes. Consistent and complete control of pupae (100%) as a result of larval mortality was clearly indicated for 70 days posttreatment. Control levels varied but remained high and significant on most sampling days afterwards. Exuviae counts also indicated complete control (100%) for 70 days posttreatment. Control levels indicated by exuviae counts, however, were not significant for most sampling days beyond this sampling day, because of low counts in the untreated controls. No significant differences were indicated in efficacy between VectoLex WSP and VBC 60035 WSP. The test was conducted under highly challenging conditions, such as prehatch treatment, highly polluted water, and frequent flushing. Spore counting in water and sludge samples verified the presence of B. sphaericus spores on day 196 posttreatment, after 28 flushes. The results strongly indicate that WSP formulation of B. sphaericus could be one of the best candidates for controlling larvae of Culex mosquitoes developing in catch basins, with significant initial and residual efficacy. PMID:18437815

  20. 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

  1. 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.

  2. 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

  3. 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...

  4. Distinct rhythmic locomotor patterns can be generated by a simple adaptive neural circuit: biology, simulation, and VLSI implementation.

    Science.gov (United States)

    Ryckebusch, S; Wehr, M; Laurent, G

    1994-12-01

    Rhythmic motor patterns can be induced in leg motor neurons of isolated locust thoracic ganglia by bath application of pilocarpine. We observed that the relative phases of levators and depressors differed in the three thoracic ganglia. Assuming that the central pattern generating circuits underlying these three segmental rhythms are probably very similar, we developed a simple model circuit that can produce any one of the three activity patterns and characteristic phase relationships by modifying a single synaptic weight. We show results of a computer simulation of this circuit using the neuronal simulator NeuraLOG/Spike. We built and tested an analog VLSI circuit implementation of this model circuit that exhibits the same range of "behaviors" as the computer simulation. This multidisciplinary strategy will be useful to explore the dynamics of central pattern generating networks coupled to physical actuators, and ultimately should allow the design of biologically realistic walking robots.

  5. 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

  6. 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)

  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. 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

  9. 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)

  10. 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.

  11. 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)

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  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. Response of biological uv dosimeters to the simulated extraterrestrial uv radiation

    Science.gov (United States)

    Bérces, A.; Rontó, G.; Kerékgyártó, T.; Kovács, G.; Lammer, H.

    In the Laboratory polycrystalline uracil thin layer and bacteriophage T7 detectors have been developed for UV dosimetry on the EarthSs surface. Exponential response of the uracil polycrystal has been detected both by absorption spectroscopy and measurements of the refractive index under the influence of terrestrial solar radiation or using UV-C sources. In UV biological dosimetry the UV dose scale is additive starting at a value of zero according to the definition of CIE (Technical Report TC-6-18). The biological dose can be defined by a measured end-effect. In our dosimeters (phage T7 and uracil dosimeter) exposed to natural (terrestrial) UV radiation the proportion of pyrimidin photoproducts among the total photoproducts is smaller than 0.1 and the linear correlation between the biological and physical dose is higher than 0.9. According to the experimental data this linear relationship is often not valid. We observed that UV radiation did not only induce dimerisation but shorter wavelengths caused monomerisation of pyrimidin dimers. Performing the irradiation in oxygen free environment and using a Deuterium lamp as UV source, we could increase monomerisation against dimerisation thus the DNA-based dosimetrySs additivity rule is not fulfilled in these conditions. In this study we will demonstrate those non-linear experiments which constitute the basis of our biological experiments on the International Space Station.

  1. StochPy: A Comprehensive, User-Friendly Tool for Simulating Stochastic Biological Processes

    NARCIS (Netherlands)

    Maarleveld, T.R.; Olivier, B.G.; Bruggeman, F.J.

    2013-01-01

    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 indispe

  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. 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

  5. Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation.

    Directory of Open Access Journals (Sweden)

    Justin John Finnerty

    Full Text Available Cation selective channels constitute the gate for ion currents through the cell membrane. Here we present an improved statistical mechanical model based on atomistic structural information, cation hydration state and without tuned parameters that reproduces the selectivity of biological Na+ and Ca2+ ion channels. The importance of the inclusion of step-wise cation hydration in these results confirms the essential role partial dehydration plays in the bacterial Na+ channels. The model, proven reliable against experimental data, could be straightforwardly used for designing Na+ and Ca2+ selective nanopores.

  6. 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

  7. Unit testing, model validation, and biological simulation [version 1; referees: 2 approved, 1 approved with reservations

    Directory of Open Access Journals (Sweden)

    Gopal P. Sarma

    2016-08-01

    Full Text Available 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. Modeling and simulation of equivalent circuits in description of biological systems - a fractional calculus approach

    Directory of Open Access Journals (Sweden)

    José Francisco Gómez Aguilar

    2012-07-01

    Full Text Available Using the fractional calculus approach, we present the Laplace analysis of an equivalent electrical circuit for a multilayered system, which includes distributed elements of the Cole model type. The Bode graphs are obtained from the numerical simulation of the corresponding transfer functions using arbitrary electrical parameters in order to illustrate the methodology. A numerical Laplace transform is used with respect to the simulation of the fractional differential equations. From the results shown in the analysis, we obtain the formula for the equivalent electrical circuit of a simple spectrum, such as that generated by a real sample of blood tissue, and the corresponding Nyquist diagrams. In addition to maintaining consistency in adjusted electrical parameters, the advantage of using fractional differential equations in the study of the impedance spectra is made clear in the analysis used to determine a compact formula for the equivalent electrical circuit, which includes the Cole model and a simple RC model as special cases.

  9. 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...

  10. Calculated organ doses using Monte Carlo simulations in a reference male phantom undergoing HDR brachytherapy applied to localized prostate carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Candela-Juan, Cristian [Radioprotection Department, La Fe University and Polytechnic Hospital, Valencia 46026 (Spain); Perez-Calatayud, Jose [Radiotherapy Department, La Fe University and Polytechnic Hospital, Valencia 46026 (Spain); Ballester, Facundo [Department of Atomic, Molecular and Nuclear Physics, University of Valencia, Burjassot 46100 (Spain); Rivard, Mark J. [Department of Radiation Oncology, Tufts University School of Medicine, Boston, Massachusetts 02111 (United States)

    2013-03-15

    Purpose: The aim of this study was to obtain equivalent doses in radiosensitive organs (aside from the bladder and rectum) when applying high-dose-rate (HDR) brachytherapy to a localized prostate carcinoma using {sup 60}Co or {sup 192}Ir sources. These data are compared with results in a water phantom and with expected values in an infinite water medium. A comparison with reported values from proton therapy and intensity-modulated radiation therapy (IMRT) is also provided. Methods: Monte Carlo simulations in Geant4 were performed using a voxelized phantom described in International Commission on Radiological Protection (ICRP) Publication 110, which reproduces masses and shapes from an adult reference man defined in ICRP Publication 89. Point sources of {sup 60}Co or {sup 192}Ir with photon energy spectra corresponding to those exiting their capsules were placed in the center of the prostate, and equivalent doses per clinical absorbed dose in this target organ were obtained in several radiosensitive organs. Values were corrected to account for clinical circumstances with the source located at various positions with differing dwell times throughout the prostate. This was repeated for a homogeneous water phantom. Results: For the nearest organs considered (bladder, rectum, testes, small intestine, and colon), equivalent doses given by {sup 60}Co source were smaller (8%-19%) than from {sup 192}Ir. However, as the distance increases, the more penetrating gamma rays produced by {sup 60}Co deliver higher organ equivalent doses. The overall result is that effective dose per clinical absorbed dose from a {sup 60}Co source (11.1 mSv/Gy) is lower than from a {sup 192}Ir source (13.2 mSv/Gy). On the other hand, equivalent doses were the same in the tissue and the homogeneous water phantom for those soft tissues closer to the prostate than about 30 cm. As the distance increased, the differences of photoelectric effect in water and soft tissue, and appearance of other materials

  11. Open source software for electric field Monte Carlo simulation of coherent backscattering in biological media containing birefringence.

    Science.gov (United States)

    Radosevich, Andrew J; Rogers, Jeremy D; Capoğlu, Ilker R; Mutyal, Nikhil N; Pradhan, Prabhakar; Backman, Vadim

    2012-11-01

    ABSTRACT. We present an open source electric field tracking Monte Carlo program to model backscattering in biological media containing birefringence, with computation of the coherent backscattering phenomenon as an example. These simulations enable the modeling of tissue scattering as a statistically homogeneous continuous random media under the Whittle-Matérn model, which includes the Henyey-Greenstein phase function as a special case, or as a composition of discrete spherical scatterers under Mie theory. The calculation of the amplitude scattering matrix for the above two cases as well as the implementation of birefringence using the Jones N-matrix formalism is presented. For ease of operator use and data processing, our simulation incorporates a graphical user interface written in MATLAB to interact with the underlying C code. Additionally, an increase in computational speed is achieved through implementation of message passing interface and the semi-analytical approach. Finally, we provide demonstrations of the results of our simulation for purely scattering media and scattering media containing linear birefringence.

  12. A comparative study of a stochastic and deterministic simulation of strong ground motion applied to the Kozani-Grevena (NW Greece 1995 sequence

    Directory of Open Access Journals (Sweden)

    C. Papaioannou

    2000-06-01

    Full Text Available We present the results of a comparative study of two intrinsically different methodologies, a stochastic one and a deterministic one, performed to simulate strong ground motion in the Kozani area (NW Greece. Source parameters were calculated from empirical relations in order to check their reliability, in combination with the applied methodologies, to simulate future events. Strong ground motion from the Kozani mainshock (13 May, 1995, M w = 6.5 was synthesized by using both the stochastic method for finite-fault cases and the empirical Green’s function method. The latter method was also applied to simulate a Mw = 5.1 aftershock (19 May, 1995. The results of the two simulations computed for the mainshock are quite satisfactory for both methodologies at the frequencies of engineering interest (> ~ 2 Hz. This strengthens the idea of incorporating proper empirical relations for the estimation of source parameters in a priori simulations of strong ground motion from future earthquakes. Nevertheless, the results of the simulation of the smaller earthquake point out the need for further investigation of regional or local, if possible, relations for estimating source parameters at smaller magnitude ranges

  13. Biological computation

    CERN Document Server

    Lamm, Ehud

    2011-01-01

    Introduction and Biological BackgroundBiological ComputationThe Influence of Biology on Mathematics-Historical ExamplesBiological IntroductionModels and Simulations Cellular Automata Biological BackgroundThe Game of Life General Definition of Cellular Automata One-Dimensional AutomataExamples of Cellular AutomataComparison with a Continuous Mathematical Model Computational UniversalitySelf-Replication Pseudo Code Evolutionary ComputationEvolutionary Biology and Evolutionary ComputationGenetic AlgorithmsExample ApplicationsAnalysis of the Behavior of Genetic AlgorithmsLamarckian Evolution Genet

  14. 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.

  15. 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

  16. 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)

  17. 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.

  18. 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.

  19. 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

  20. Numerical simulations of hydrodynamic instabilities: perturbation codes Pansy, Perle, and 2D code Chic applied to a realistic LIL target

    Energy Technology Data Exchange (ETDEWEB)

    Hallo, L.; Olazabal-Loume, M.; Maire, P.H.; Breil, J.; Schurtz, G. [CELIA, 33 - Talence (France); Morse, R.L. [Arizona Univ., Dept. of Nuclear Engineering, Tucson (United States)

    2006-06-15

    This paper deals with ablation front instabilities simulations in the context of direct drive inertial confinement fusion. A simplified deuterium-tritium target, representative of realistic target on LIL (laser integration line at Megajoule laser facility) is considered. We describe here two numerical approaches: the linear perturbation method using the perturbation codes Perle (planar) and Pansy (spherical) and the direct simulation method using our bi-dimensional hydrodynamic code Chic. Our work shows a good behaviour of all methods even for large wavenumbers during the acceleration phase of the ablation front. We also point out a good agreement between model and numerical predictions at ablation front during the shock wave transit.

  1. Simulation of phytoplankton distribution and variation in the Bering-Chukchi Sea using a 3-D physical-biological model

    Science.gov (United States)

    Hu, Haoguo; Wang, Jia; Liu, Hui; Goes, Joaquim

    2016-06-01

    A three-dimensional physical-biological model has been used to simulate seasonal phytoplankton variations in the Bering and Chukchi Seas with a focus on understanding the physical and biogeochemical mechanisms involved in the formation of the Bering Sea Green Belt (GB) and the Subsurface Chlorophyll Maxima (SCM). Model results suggest that the horizontal distribution of the GB is controlled by a combination of light, temperature, and nutrients. Model results indicated that the SCM, frequently seen below the thermocline, exists because of a rich supply of nutrients and sufficient light. The seasonal onset of phytoplankton blooms is controlled by different factors at different locations in the Bering-Chukchi Sea. In the off-shelf central region of the Bering Sea, phytoplankton blooms are regulated by available light. On the Bering Sea shelf, sea ice through its influence on light and temperature plays a key role in the formation of blooms, whereas in the Chukchi Sea, bloom formation is largely controlled by ambient seawater temperatures. A numerical experiment conducted as part of this study revealed that plankton sinking is important for simulating the vertical distribution of phytoplankton and the seasonal formation of the SCM. An additional numerical experiment revealed that sea ice algae account for 14.3-36.9% of total phytoplankton production during the melting season, and it cannot be ignored when evaluating primary productivity in the Arctic Ocean.

  2. 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.

  3. Reconstruction of complex passageways for simulations of transport phenomena: development of a graphical user interface for biological applications.

    Science.gov (United States)

    Godo, M N; Morgan, K T; Richardson, R B; Kimbell, J S

    1995-07-01

    Flow of fluids, such as blood, lymph and air, plays a major role in the normal physiology of all living organisms. Within individual organ systems, flow fields may significantly influence the transport of solutes, including nutrients and chemical toxicants, to and from the confining vessel walls (epithelia and endothelia). Computational fluid dynamics (CFD) provides a potentially useful tool for biologists and toxicologists investigating solute disposition in these flow fields in both normal and disease states. Application of CFD is dependent upon generation of accurate representations of the geometry of the system of interest in the form of a computational reconstruction. The present investigations, which were based on studies of the toxicology of inhaled reactive gases in the respiratory tract of rodents, provide computer programs for the generation of finite element meshes from serial tissue cross-sections. These programs, which interface with a commercial finite element fluid dynamics simulation package (FIDAP 7.05, Fluid Dynamics International, Evanston, IL), permit simulation of fluid flow in the complex geometries and local solute mass flux to the vessel walls of biological systems. The use of these programs and their application to studies of respiratory tract toxicology are described.

  4. 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.

  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. 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…

  7. 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.

  8. ERGONOMÍA Y SIMULACIÓN APLICADAS A LA INDUSTRIA / ERGONOMICS AND SIMULATION APPLIED TO THE INDUSTRY

    Directory of Open Access Journals (Sweden)

    Yordán Rodríguez-Ruíz

    2011-03-01

    Full Text Available

    La simulación permite estimar el comportamiento de sistemas estocásticos complejos, cuando su estudio por la vía analítica resulta insuficiente. En este estudio se empleó esta técnica numérica, para mostrar el impacto de los rediseños ergonómicos realizados a las estaciones de trabajo de una estera. Para simular este sistema, se realizó un análisis preliminar de las estaciones de trabajo, con el objetivo de recoger información útil para diseñar un modelo lógico. El modelo fue simulado y sometido a los cambios resultantes del rediseño ergonómico de las estaciones de trabajo. Los resultados obtenidos mostraron la utilidad de la simulación para la predicción y el análisis del impacto que tendrían las propuestas efectuadas.

    Abstract

    Simulation is used when the stochastic system is too complex to be analyzed satisfactorily through analytic-mathematical models. In this research, the simulation was used to show the impact of the ergonomic redesigns at the workstations in a conveyor. To simulate this system, a preliminary analysis of the workstations was made in the order to collect useful information to design a logic model. This model was simulated and changed according to the ergonomic redesign of the workstations. The results proved the usefulness of simulation for predicting and analyzing the impact of the implemented propositions.

  9. 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.

  10. 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)

  11. 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.

  12. 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.

  13. 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...

  14. 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.

  15. 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)

  16. 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)

  17. 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.

  18. Rainfall simulation in greenhouse microcosms to assess bacterial-associated runoff from land-applied poultry litter.

    Science.gov (United States)

    Brooks, John P; Adeli, Ardeshir; Read, John J; McLaughlin, Michael R

    2009-01-01

    Runoff water following a rain event is one possible source of environmental contamination after a manure application. This greenhouse study used a rainfall simulator to determine bacterial-associated runoff from troughs of common bermudagrass [Cynodon dactylon (L.) Pers.] that were treated with P-based, N-based, and N plus lime rates of poultry (Gallus gallus) litter, recommended inorganic fertilizer, and control. Total heterotrophic plate count (HPC) bacteria, total and thermotolerant coliforms, enterococci, staphylococci, Clostridium perfringens, Salmonella, and Campylobacter, as well as antibiotic resistance profiles for the staphylococci and enterococci isolates were all monitored in runoff waters. Analysis following five rainfall events indicated that staphylococci, enterococci, and clostridia levels were related to manure application rate. Runoff release of staphylococci, enterococci, and C. perfringens were approximately 3 to 6 log10 greater in litter vs. control treatment. In addition, traditional indicators such as thermotolerant and total coliforms performed poorly as fecal indicators. Some isolated enterococci demonstrated increased antibiotic resistance to polymixin b and/or select aminoglyocosides, while many staphylococci were susceptible to most antimicrobials tested. Results indicated poultry litter application can lead to microbial runoff following simulated rain events. Future studies should focus on the use of staphylococci, enterococci, and C. perfringens as indicators.

  19. Applying new hybrid method of analytical hierarchy process, Monte Carlo Simulation and PROMETHEE to prioritize and selecting appropriate target market

    Directory of Open Access Journals (Sweden)

    Amir Kariznoee

    2015-06-01

    Full Text Available Making decision to choose the appropriate target market is one of the key decisions in the success of firms, which has direct effect in the amount of their profits. The aim of this paper is to introduce and use of new hybrid method of AHP, Monte Carlo simulation and PROMETHEE to prioritize cities to establish retailers, considering different indices. The problem of this study is related to a factory, constructing premade pieces of buildings, that to introduce and distribute its new products is searching the new retailers in different cities. To prioritize cities, with the interview with experts and the studying of the previous works the indices have been determined and the hierarchy pattern has been made. Then using the hybrid method of AHP and Monte Carlo simulation the weights of the indices have been determined and then using PROMETHEE method the best city has been chosen and the other ones have been prioritized. From the benefits of the new introduced hybrid method with respect to other ways of selecting target markets is decreasing the risk and increasing the power of decision making.

  20. [The specific features of the damage to the non-biological and biological simulators of the human body inflicted by the shots from a 9.0 mm pneumatic rifle].

    Science.gov (United States)

    Raizberg, S A; Makarov, L Iu; Lorents, A S

    2015-01-01

    The objective of the present work was to study the specific constructional features of a 9.0 mm pneumatic rifle designed to use three types of bullets differing in the head shape. Also, the morphological signs of the injuries inflicted by such bullets that can serve as the prerequisites for objective differentiation of the damages are considered. The study revealed peculiarities of experimental damage to the non-biological (plasticine blocks) and biological (bio-mannequins) simulators of homogeneous human tissues inflicted by the shots from the pneumatic rifle from different distances. PMID:26036065

  1. 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.)

  2. Boron neutron capture therapy applied to advanced breast cancers: Engineering simulation and feasibility study of the radiation treatment protocol

    Science.gov (United States)

    Sztejnberg Goncalves-Carralves, Manuel Leonardo

    This dissertation describes a novel Boron Neutron Capture Therapy (BNCT) application for the treatment of human epidermal growth factor receptor type 2 positive (HER2+) breast cancers. The original contribution of the dissertation is the development of the engineering simulation and the feasibility study of the radiation treatment protocol for this novel combination of BNCT and HER2+ breast cancer treatment. This new concept of BNCT, representing a radiation binary targeted treatment, consists of the combination of two approaches never used in a synergism before. This combination may offer realistic hope for relapsed and/or metastasized breast cancers. This treatment assumes that the boronated anti-HER2 monoclonal antibodies (MABs) are administrated to the patient and accumulate preferentially in the tumor. Then the tumor is destroyed when is exposed to neutron irradiation. Since the use of anti-HER2 MABs yields good and promising results, the proposed concept is expected to amplify the known effect and be considered as a possible additional treatment approach to the most severe breast cancers for patients with metastasized cancer for which the current protocol is not successful and for patients refusing to have the standard treatment protocol. This dissertation makes an original contribution with an integral numerical approach and proves feasible the combination of the aforementioned therapy and disease. With these goals, the dissertation describes the theoretical analysis of the proposed concept providing an integral engineering simulation study of the treatment protocol. An extensive analysis of the potential limitations, capabilities and optimization factors are well studied using simplified models, models based on real CT patients' images, cellular models, and Monte Carlo (MCNP5/X) transport codes. One of the outcomes of the integral dosimetry assessment originally developed for the proposed treatment of advanced breast cancers is the implementation of BNCT

  3. 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.

  4. 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

  5. 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.

  6. Montecarlo Simulation Applied to Measurement of the Impact of the Smart Antenna Technology in Digital Cellular Systems

    Directory of Open Access Journals (Sweden)

    Castañeda-Camacho Josefina

    2015-03-01

    Full Text Available The smart antenna technology has received increasing interest due to its capability for improving the performance of wireless radio systems. In this work, we studied the throughput maximization in a digital cellular system when a smart antenna array is implemented. We focus, in the study of the downlink of a 3G cellular system and consider a packet data direct-sequence code division, multiple access (DS-CDMA. Our methodology is based on the Monte Carlo simulation technique, and it is used to show that it is possible to obtain a significant increment in the throughput of the system due to the switched beam smart antenna array. From our results we conclude that it is feasible to consider the application of this technology in 4G environments.

  7. 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...... is the Coleman transformation, which transforms the vibrations expressed in the blade rotating coordinates to the fixed-ground frame of reference. The application of this transformation, originally from helicopter theory, allows for the conversion of a LPTV system to a LTI system under certain assumptions, among...

  8. 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.

  9. A numerical model (MISER) for the simulation of coupled physical, chemical and biological processes in soil vapor extraction and bioventing systems

    Science.gov (United States)

    Rathfelder, Klaus M.; Lang, John R.; Abriola, Linda M.

    2000-05-01

    The efficiency and effectiveness of soil vapor extraction (SVE) and bioventing (BV) systems for remediation of unsaturated zone soils is controlled by a complex combination of physical, chemical and biological factors. The Michigan soil vapor extraction remediation (MISER) model, a two-dimensional numerical simulator, is developed to advance our ability to investigate the performance of field scale SVE and BV systems by integrating processes of multiphase flow, multicomponent compositional transport with nonequilibrium interphase mass transfer, and aerobic biodegradation. Subsequent to the model presentation, example simulations of single well SVE and BV systems are used to illustrate the interplay between physical, chemical and biological processes and their potential influence on remediation efficiency and the pathways of contaminant removal. Simulations of SVE reveal that removal efficiency is controlled primarily by the ability to engineer gas flow through regions of organic liquid contaminated soil and by interphase mass transfer limitations. Biodegradation is found to play a minor role in mass removal for the examined SVE scenarios. Simulations of BV systems suggest that the effective supply of oxygen may not be the sole criterion for efficient BV performance. The efficiency and contaminant removal pathways in these systems can be significantly influenced by interdependent dynamics involving biological growth factors, interphase mass transfer rates, and air injection rates. Simulation results emphasize the need for the continued refinement and validation of predictive interphase mass transfer models applicable under a variety of conditions and for the continued elucidation and quantification of microbial processes under unsaturated field conditions.

  10. 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.

  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. Systematic study of the effects of mass and time scaling techniques applied in numerical rock mechanics simulations

    Science.gov (United States)

    Heinze, Thomas; Jansen, Gunnar; Galvan, Boris; Miller, Stephen A.

    2016-08-01

    Numerical modeling is a well established tool in rock mechanics studies investigating a wide range of problems. Implicit methods for solving linear equations have the advantage of being unconditionally stable, while explicit methods, although limited by the time step, are often used because of their limited memory demand, their scalability in parallel computing, and simple implementation of complex boundary conditions. In numerical modeling of explicit elastoplastic dynamics where the time step is limited by the material density, mass scaling techniques can be used to overcome this limit and significantly reduce computation time. While often used, the effect of mass and time scaling and how it may influence the numerical results is rarely-mentioned in publications, and choosing the right scaling technique is typically performed by trial and error. To our knowledge, no systematic studies have addressed how mass scaling might affect the numerical results. In this paper, we present results from an extensive and systematic study of the influence of mass and time scaling on the behavior of a variety of rock-mechanical models. We employ a finite difference scheme to model uniaxial and biaxial compression experiments using different mass and time scaling factors, and with physical models of increasing complexity up to a cohesion-weakening frictional-strengthening model (CWFS). We also introduce a normalized energy ratio to assist analyzing mass scaling effects. We find the tested models to be less sensitive to time scaling than to mass scaling, so mass scaling has higher potential for decreasing computational costs. However, we also demonstrate that mass scaling may lead to quantitatively wrong results, so care must be taken in interpreting stress values when mass scaling is used in complicated rock mechanics simulations. Mass scaling significantly influences the stress-strain response of numerical rocks because mass scaling acts as an artificial hardening agent on rock

  14. 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

  15. Biological Interactions and Simulated Climate Change Modulates the Ecophysiological Performance of Colobanthus quitensis in the Antarctic Ecosystem

    Science.gov (United States)

    Torres-Díaz, Cristian; Gallardo-Cerda, Jorge; Lavin, Paris; Oses, Rómulo; Carrasco-Urra, Fernando; Atala, Cristian; Acuña-Rodríguez, Ian S.; Convey, Peter; Molina-Montenegro, Marco A.

    2016-01-01

    Most climate and environmental change models predict significant increases in temperature and precipitation by the end of the 21st Century, for which the current functional output of certain symbioses may also be altered. In this context we address the following questions: 1) How the expected changes in abiotic factors (temperature, and water) differentially affect the ecophysiological performance of the plant Colobanthus quitensis? and 2) Will this environmental change indirectly affect C. quitensis photochemical performance and biomass accumulation by modifying its association with fungal endophytes? Plants of C. quitensis from King George Island in the South Shetland archipelago (62°09′ S), and Lagotellerie Island in the Antarctic Peninsula (65°53′ S) were put under simulated abiotic conditions in growth chambers following predictive models of global climate change (GCC). The indirect effect of GCC on the interaction between C. quitensis and fungal endophytes was assessed in a field experiment carried out in the Antarctica, in which we eliminated endophytes under contemporary conditions and applied experimental watering to simulate increased precipitation input. We measured four proxies of plant performance. First, we found that warming (+W) significantly increased plant performance, however its effect tended to be less than watering (+W) and combined warming and watering (+T°+W). Second, the presence of fungal endophytes improved plant performance, and its effect was significantly decreased under experimental watering. Our results indicate that both biotic and abiotic factors affect ecophysiological performance, and the directions of these influences will change with climate change. Our findings provide valuable information that will help to predict future population spread and evolution through using ecological niche models under different climatic scenarios. PMID:27776181

  16. A Tricky Trait: Applying the Fruits of the "Function Debate" in the Philosophy of Biology to the "Venom Debate" in the Science of Toxinology.

    Science.gov (United States)

    Jackson, Timothy N W; Fry, Bryan G

    2016-01-01

    The "function debate" in the philosophy of biology and the "venom debate" in the science of toxinology are conceptually related. Venom systems are complex multifunctional traits that have evolved independently numerous times throughout the animal kingdom. No single concept of function, amongst those popularly defended, appears adequate to describe these systems in all their evolutionary contexts and extant variations. As such, a pluralistic view of function, previously defended by some philosophers of biology, is most appropriate. Venom systems, like many other functional traits, exist in nature as points on a continuum and the boundaries between "venomous" and "non-venomous" species may not always be clearly defined. This paper includes a brief overview of the concept of function, followed by in-depth discussion of its application to venom systems. A sound understanding of function may aid in moving the venom debate forward. Similarly, consideration of a complex functional trait such as venom may be of interest to philosophers of biology.

  17. Mathmatical Model Method Applied in the High School Biology Teaching%数学模型法在高中生物教学中的应用

    Institute of Scientific and Technical Information of China (English)

    钟静

    2012-01-01

    In high school biology teaching, the use of mathmatical model method to solve the mathematics of biological scences can make the abstract problem more specific, problem solving process more regular and improve the accuracy of the answer, which is an effective method to solve the mathematics in high school biology teaching.%在高中生物教学中,运用数学模型法来解决生物学科中的数学问题,可以把抽象问题具体化、解题过程规律化,能提高答题的准确性,是解决高中生物学科中的数学问题的有效方法。

  18. A Tricky Trait: Applying the Fruits of the "Function Debate" in the Philosophy of Biology to the "Venom Debate" in the Science of Toxinology.

    Science.gov (United States)

    Jackson, Timothy N W; Fry, Bryan G

    2016-01-01

    The "function debate" in the philosophy of biology and the "venom debate" in the science of toxinology are conceptually related. Venom systems are complex multifunctional traits that have evolved independently numerous times throughout the animal kingdom. No single concept of function, amongst those popularly defended, appears adequate to describe these systems in all their evolutionary contexts and extant variations. As such, a pluralistic view of function, previously defended by some philosophers of biology, is most appropriate. Venom systems, like many other functional traits, exist in nature as points on a continuum and the boundaries between "venomous" and "non-venomous" species may not always be clearly defined. This paper includes a brief overview of the concept of function, followed by in-depth discussion of its application to venom systems. A sound understanding of function may aid in moving the venom debate forward. Similarly, consideration of a complex functional trait such as venom may be of interest to philosophers of biology. PMID:27618098

  19. 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.

  20. 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...

  1. 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...

  2. 一种改进的自组织生物群体仿真模型%An Improved Self- organization Biological Swarm Simulation Model

    Institute of Scientific and Technical Information of China (English)

    王楠楠; 于航; 陈婧; 王元刚

    2012-01-01

    在Boid群体仿真规则基础上,增加了3类控制变量:环境变量、种群特征变量和性格变量构建自组织生物群体仿真系统。利用社会学习因子和自学习因子构建了个体的种群靠拢系数、速度匹配系数和自由游弋系数等参数,去除了传统模型中个体一致性假设,更为真实地反映不同生物群体的群体行为。本文在此基础上构建了相应的仿真平台。仿真实验结果表明,可以更好地对生物群体行为仿真进行建模,同时给出了鸟群、鱼群和昆虫群3种典型生物群体仿真的参数集合,同时还分析了不同群体的特征。%On the basis of Boid simulation model, in this paper three types of control variables are increased which are environment variables, population character variables and personality variables to build simulation systems of self - organization biological swarm. Traditional simula- tion model assumes that the individual parameters are identical, but the differences of individual parameters in real biological groups exist objectively. Therefore population closer coefficient, speed matching coefficient and free cruising coefficient and other parameters using social learn- ing factors and self - learning factors are constructed, and the individual consistency assumptions in traditional model are remcved, which reflects the behavior of different groups of biological swarm even more truly. Based on the above the corresponding simulation platform is builded. Simulation results show that the improved model proposed in this paper is better for the modeling of the simulation of biological groups' behaviors, and gives parameter sets of simulation of birds, fish and insects groups of the three typical biological swarms, and at the same time analy- zes the characteristics of different swarm.

  3. 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)

  4. The Examination of the Effects of Biological Gender and Gender Identity Roles on Attitude of the Consumers to Advertisements Applied by Accomodation Operations

    Directory of Open Access Journals (Sweden)

    Evren Güçer

    2013-12-01

    Full Text Available 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 made in different areas in the same subject was supported with determination ofit is possible to participants have gender identity roles different from their biological sex to some extent.Otherwise; determination of theadvertisements ofaccomodationestablishments, contain feminine messages, are more preferred by people who have feminine and androgynous identity than the others; and advertisements ofaccomodationestablishments, contain masculinemessages, are preferred by all gender identity roles are ones of the results

  5. A Tricky Trait: Applying the Fruits of the “Function Debate” in the Philosophy of Biology to the “Venom Debate” in the Science of Toxinology

    Directory of Open Access Journals (Sweden)

    Timothy N. W. Jackson

    2016-09-01

    Full Text Available The “function debate” in the philosophy of biology and the “venom debate” in the science of toxinology are conceptually related. Venom systems are complex multifunctional traits that have evolved independently numerous times throughout the animal kingdom. No single concept of function, amongst those popularly defended, appears adequate to describe these systems in all their evolutionary contexts and extant variations. As such, a pluralistic view of function, previously defended by some philosophers of biology, is most appropriate. Venom systems, like many other functional traits, exist in nature as points on a continuum and the boundaries between “venomous” and “non-venomous” species may not always be clearly defined. This paper includes a brief overview of the concept of function, followed by in-depth discussion of its application to venom systems. A sound understanding of function may aid in moving the venom debate forward. Similarly, consideration of a complex functional trait such as venom may be of interest to philosophers of biology.

  6. Is synthetic biology mechanical biology?

    Science.gov (United States)

    Holm, Sune

    2015-12-01

    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  7. 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.

  8. 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:

  9. 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.

  10. 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....

  11. 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

  12. 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 pou...... and it must not be used as a substitute for normal good hygienic practice. Moreover, the experimental evaluation of the efficacy of peroxyacids must be under conditions comparable to European industrial processing conditions and practices....

  13. 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

  14. 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

  15. 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.

  16. Applying x-ray tomography in the field of vertebrate biology: form, function, and evolution of the skull of caecilians (Lissamphibia: Gymnophiona)

    Science.gov (United States)

    Kleinteich, Thomas; Beckmann, Felix; Herzen, Julia; Summers, Adam P.; Haas, Alexander

    2008-08-01

    Evolutionary research in biology relies on the comparison of different individuals of different species in order to explore the history of today's biodiversity. Synchrotron radiation based high resolution X-ray tomography (SRμCT) rapidly generates detailed three dimensional datasets. At the beamlines W2 and BW2 of the storage ring DORIS at DESY, Hamburg, Germany, we used SRμCT to study the cranial anatomy of different species and different developmental stages of caecilians (Lissamphibia: Gymnophiona). Here we describe a work-flow for analysis of the SRμCT data that covers segmentation of tissues in Amira® (Mercury Computer Systems), photorealistic rendering and animation in MayaTM, rapid prototyping, and morphometrics. The integration of different analyses of SRμCT data in our study resulted in a comprehensive understanding of form, function, and evolution of caecilian skulls. SRμCT imaging has the potential to become a standard technique for life sciences applications in the near future.

  17. Statistical Model Checking for Biological Systems

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  18. 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)

  19. 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

  20. 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...

  1. 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.

  2. 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.

  3. 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).

  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. 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

  6. Bayes in biological anthropology.

    Science.gov (United States)

    Konigsberg, Lyle W; Frankenberg, Susan R

    2013-12-01

    In this article, we both contend and illustrate that biological anthropologists, particularly in the Americas, often think like Bayesians but act like frequentists when it comes to analyzing a wide variety of data. In other words, while our research goals and perspectives are rooted in probabilistic thinking and rest on prior knowledge, we often proceed to use statistical hypothesis tests and confidence interval methods unrelated (or tenuously related) to the research questions of interest. We advocate for applying Bayesian analyses to a number of different bioanthropological questions, especially since many of the programming and computational challenges to doing so have been overcome in the past two decades. To facilitate such applications, this article explains Bayesian principles and concepts, and provides concrete examples of Bayesian computer simulations and statistics that address questions relevant to biological anthropology, focusing particularly on bioarchaeology and forensic anthropology. It also simultaneously reviews the use of Bayesian methods and inference within the discipline to date. This article is intended to act as primer to Bayesian methods and inference in biological anthropology, explaining the relationships of various methods to likelihoods or probabilities and to classical statistical models. Our contention is not that traditional frequentist statistics should be rejected outright, but that there are many situations where biological anthropology is better served by taking a Bayesian approach. To this end it is hoped that the examples provided in this article will assist researchers in choosing from among the broad array of statistical methods currently available.

  7. 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.

  8. 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)

  9. 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)

  10. 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

  11. 海流发电用翼型的水动力学模拟%Hydrodynamic Simulation of Hydrofoil Marine Current Turbine Applies

    Institute of Scientific and Technical Information of China (English)

    张玉良; 朱祖超; 崔宝玲; 李昳; 金英子

    2011-01-01

    With the aggravation of energy crisis in world, the energy of ocean current is greatly focused. At present, the most important application is the use of marine current turbine, the performance of which depends on the hydrodynamic performance of hydrofoil mostly. In order to study the influence of ocean current's parameters on hydrodynamic performance of hydrofoil, according to the characteristic of random fluctuation in ocean current, angle of attack, Reynolds Number and turbulence intensity are selected as three factors of orthogonal experiment in this paper, and every factor selects four influence levels to carry out a L16 (43) orthogonal experiment. The hydrodynamic performance of hydrofoil NACA63440 that marine current turbine often applies is numerically simulated under steady flow condition for sixteen schemes, and the influence laws of ocean current's parameters on hydrodynamic performance of hydrofoil are analyzed in detail. The results of numerical simulation show that the influence of turbulence intensity on hydrodynamic performance of hydrofoil is maximal, the angle of attack is next, while Reynolds Number is minimal. The influence of turbulence intensity and angle of attack on lift coefficient and drag coefficient of hydrofoil is more evident. Increasing angle of attack can improve effectively lift-drag ratio, but it has a extremum. If angle of attack exceeds the critical value, the hydrofoil will appear stalling phenomenon. Increasing Reynolds Number can improve moderately lift-drag ratio. The forebody of hydrofoil is the main region that generates lift, and the top region of forebody is most vulnerable to cavitation. Above research conclusions will provide significant referrence for more hydrodynamic performance research of hydrofoil.%为研究海流各个流动参数同时对水翼水动力学性能的影响,根据海流随机波动特点,选取海流的攻角、雷诺数和湍流强度3个因素,每个因素选取4个水平,进行了L16(43)

  12. 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

  13. 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.

  14. Eruca sativa might influence the growth, survival under simulated gastrointestinal conditions and some biological features of Lactobacillus acidophilus, Lactobacillus plantarum and Lactobacillus rhamnosus strains.

    Science.gov (United States)

    Fratianni, Florinda; Pepe, Selenia; Cardinale, Federica; Granese, Tiziana; Cozzolino, Autilia; Coppola, Raffaele; Nazzaro, Filomena

    2014-10-01

    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.

  15. 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

  16. The accurate calculation of the band gap of liquid water by means of GW corrections applied to plane-wave density functional theory molecular dynamics simulations

    NARCIS (Netherlands)

    Fang, Changming; Li, Wun Fan; Koster, Rik S.; Klimeš, Jiří; Van Blaaderen, Alfons; Van Huis, Marijn A.

    2015-01-01

    Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initi

  17. 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...

  18. 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.

  19. 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

  20. 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

  1. Translational environmental biology: cell biology informing conservation.

    Science.gov (United States)

    Traylor-Knowles, Nikki; Palumbi, Stephen R

    2014-05-01

    Typically, findings from cell biology have been beneficial for preventing human disease. However, translational applications from cell biology can also be applied to conservation efforts, such as protecting coral reefs. Recent efforts to understand the cell biological mechanisms maintaining coral health such as innate immunity and acclimatization have prompted new developments in conservation. Similar to biomedicine, we urge that future efforts should focus on better frameworks for biomarker development to protect coral reefs.

  2. PSPs and ERPs: applying the dynamics of post-synaptic potentials to individual units in simulation of temporally extended Event-Related Potential reading data.

    Science.gov (United States)

    Laszlo, Sarah; Armstrong, Blair C

    2014-05-01

    The Parallel Distributed Processing (PDP) framework is built on neural-style computation, and is thus well-suited for simulating the neural implementation of cognition. However, relatively little cognitive modeling work has concerned neural measures, instead focusing on behavior. Here, we extend a PDP model of reading-related components in the Event-Related Potential (ERP) to simulation of the N400 repetition effect. We accomplish this by incorporating the dynamics of cortical post-synaptic potentials--the source of the ERP signal--into the model. Simulations demonstrate that application of these dynamics is critical for model elicitation of repetition effects in the time and frequency domains. We conclude that by advancing a neurocomputational understanding of repetition effects, we are able to posit an interpretation of their source that is both explicitly specified and mechanistically different from the well-accepted cognitive one. PMID:24686264

  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. 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

  5. (Biological dosimetry)

    Energy Technology Data Exchange (ETDEWEB)

    Preston, R.J.

    1990-12-17

    The traveler attended the 1st International Conference on Biological Dosimetry in Madrid, Spain. This conference was organized to provide information to a general audience of biologists, physicists, radiotherapists, industrial hygiene personnel and individuals from related fields on the current ability of cytogenetic analysis to provide estimates of radiation dose in cases of occupational or environmental exposure. There is a growing interest in Spain in biological dosimetry because of the increased use of radiation sources for medical and occupational uses, and with this the anticipated and actual increase in numbers of overexposure. The traveler delivered the introductory lecture on Biological Dosimetry: Mechanistic Concepts'' that was intended to provide a framework by which the more applied lectures could be interpreted in a mechanistic way. A second component of the trip was to provide advice with regard to several recent cases of overexposure that had been or were being assessed by the Radiopathology and Radiotherapy Department of the Hospital General Gregorio Maranon'' in Madrid. The traveler had provided information on several of these, and had analyzed cells from some exposed or purportedly exposed individuals. The members of the biological dosimetry group were referred to individuals at REACTS at Oak Ridge Associated Universities for advice on follow-up treatment.

  6. 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.

  7. 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

  8. Preliminary results of the ion extraction simulations applied to the MONO1000 and SUPERSHyPIE electron cyclotron resonance ion sources.

    Science.gov (United States)

    Pierret, C; Maunoury, L; Biri, S; Pacquet, J Y; Tuske, O; Delferriere, O

    2008-02-01

    The goal of this article is to present simulations on the extraction from an electron cyclotron resonance ion source (ECRIS). The aim of this work is to find out an extraction system, which allows one to reduce the emittances and to increase the current of the extracted ion beam at the focal point of the analyzing dipole. But first, we should locate the correct software which is able to reproduce the specific physics of an ion beam. To perform the simulations, the following softwares have been tested: SIMION 3D, AXCEL, CPO 3D, and especially, for the magnetic field calculation, MATHEMATICA coupled with the RADIA module. Emittance calculations have been done with two types of ECRIS: one with a hexapole and one without a hexapole, and the difference will be discussed.

  9. Preliminary results of the ion extraction simulations applied to the MONO1000 and SUPERSHyPIE electron cyclotron resonance ion sourcesa)

    Science.gov (United States)

    Pierret, C.; Maunoury, L.; Biri, S.; Pacquet, J. Y.; Tuske, O.; Delferriere, O.

    2008-02-01

    The goal of this article is to present simulations on the extraction from an electron cyclotron resonance ion source (ECRIS). The aim of this work is to find out an extraction system, which allows one to reduce the emittances and to increase the current of the extracted ion beam at the focal point of the analyzing dipole. But first, we should locate the correct software which is able to reproduce the specific physics of an ion beam. To perform the simulations, the following softwares have been tested: SIMION 3D, AXCEL, CPO 3D, and especially, for the magnetic field calculation, MATHEMATICA coupled with the RADIA module. Emittance calculations have been done with two types of ECRIS: one with a hexapole and one without a hexapole, and the difference will be discussed.

  10. 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)

  11. 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)

  12. 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...

  13. Thermal-comfort analysis and simulation for various low-energy cooling-technologies applied to an office building in a subtropical climate

    Energy Technology Data Exchange (ETDEWEB)

    Chowdhury, Ashfaque Ahmed; Rasul, M.G.; Khan, M.M.K. [College of Engineering and the Built Environment, Faculty of Sciences, Engineering and Health, Central Queensland University, Rockhampton, Qld 4702 (Australia)

    2008-06-15

    Simulation of buildings' thermal-performances is necessary to predict comfort of the occupants in buildings and to identify alternate cooling control-systems for achieving better indoor thermal environments. An analysis and prediction of thermal-comfort using DesignBuilder, based on the state-of-the-art building performance simulation software EnergyPlus, is carried out in an air-conditioned multi-storeyed building in the city of Rockhampton in Central Queensland, Australia. Rockhampton is located in a hot humid-region; therefore, indoor thermal-comfort is strongly affected by the outdoor climate. This study evaluates the actual thermal conditions of the Information Technology Division (ITD) building at Central Queensland University during winter and summer seasons and identifies the thermal comfort level of the occupants using low-energy cooling technologies namely, chilled ceiling (CC), economiser usages and pre-cooling. The Fanger comfort-model, Pierce two-node model and KSU two-node model were used to predict thermal performance of the building. A sophisticated building-analysis tool was integrated with the thermal comfort models for determining appropriate cooling-technologies for the occupants to be thermally comfortable while achieving sufficient energy savings. This study compares the predicted mean-vote (PMV) index on a seven-point thermal-sensation scale, calculated using the effective temperature and relative humidity for those cooling techniques. Simulated results show that systems using a chilled ceiling offer the best thermal comfort for the occupants during summer and winter in subtropical climates. The validity of the simulation results was checked with measured values of temperature and humidity for typical days in both summer and winter. The predicted results show a reasonable agreement with the measured data. (author)

  14. 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.

  15. 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.

  16. 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

    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 The Danish Sugar Corporation two subsystems in the production have been chosen for application - the evaporation process and the crystallization process. In order to obtain information about the static and dynamic behaviour of the subsystems, field measurements have been performed. A realtime 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...

  17. 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

  18. Systems biology in animal sciences

    NARCIS (Netherlands)

    Woelders, H.; Pas, te M.F.W.; Bannink, A.; Veerkamp, R.F.; Smits, M.A.

    2011-01-01

    Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes an

  19. Computational systems chemical biology.

    Science.gov (United States)

    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) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

  20. 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 ...

  1. 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.

  2. 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.

  3. 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

  4. 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

    Energy Technology Data Exchange (ETDEWEB)

    Fliedner Theodor M.; Feinendegen Ludwig E.; Meineke Viktor; Fritz Thomas E.

    2005-02-28

    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

  5. 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

  6. Monte Carlo electron-trajectory simulations in bright-field and dark-field STEM: Implications for tomography of thick biological sections

    Energy Technology Data Exchange (ETDEWEB)

    Sousa, A.A.; Hohmann-Marriott, M.F.; Zhang, G. [Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bldg. 13, Rm. 3N17, 13 South Drive, Bethesda, MD 20892-5766 (United States); Leapman, R.D. [Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bldg. 13, Rm. 3N17, 13 South Drive, Bethesda, MD 20892-5766 (United States)], E-mail: leapmanr@mail.nih.gov

    2009-02-15

    A Monte Carlo electron-trajectory calculation has been implemented to assess the optimal detector configuration for scanning transmission electron microscopy (STEM) tomography of thick biological sections. By modeling specimens containing 2 and 3 at% osmium in a carbon matrix, it was found that for 1-{mu}m-thick samples the bright-field (BF) and annular dark-field (ADF) signals give similar contrast and signal-to-noise ratio provided the ADF inner angle and BF outer angle are chosen optimally. Spatial resolution in STEM imaging of thick sections is compromised by multiple elastic scattering which results in a spread of scattering angles and thus a spread in lateral distances of the electrons leaving the bottom surface. However, the simulations reveal that a large fraction of these multiply scattered electrons are excluded from the BF detector, which results in higher spatial resolution in BF than in high-angle ADF images for objects situated towards the bottom of the sample. The calculations imply that STEM electron tomography of thick sections should be performed using a BF rather than an ADF detector. This advantage was verified by recording simultaneous BF and high-angle ADF STEM tomographic tilt series from a stained 600-nm-thick section of C. elegans. It was found that loss of spatial resolution occurred markedly at the bottom surface of the specimen in the ADF STEM but significantly less in the BF STEM tomographic reconstruction. Our results indicate that it might be feasible to use BF STEM tomography to determine the 3D structure of whole eukaryotic microorganisms prepared by freeze-substitution, embedding, and sectioning.

  7. 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.

  8. 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...

  9. 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.

  10. 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. PMID:27385441

  11. 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

  12. 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

  13. 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...

  14. 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.

  15. 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

  16. 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.

  17. 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...

  18. Simulation on Performance of Thermoelectric Generator Applied in Waste Heat Recovery%废热式温差发电器性能仿真

    Institute of Scientific and Technical Information of China (English)

    杨素文; 肖恒; 欧强; 苟小龙

    2012-01-01

    研究温差发电优化控制问题,温差发电技术是用回收废热转化为电能的转换器,使得温差发电运行稳定,产生大功率效能.温差发电技术涉及三大基本效应,导致其温度分布模型不清,难以实现上述目的.为了探究温差发电器的运行规律,指导温差发电器处于较大输出功率下运行,采用温差发电原理以及传热学理论,建立了一种用以求解温差发电器内部温度分布的数学模型.并以输出功率为目标函数,通过仿真计算得到温差发电器在不同工作条件下的性能特性.仿真比较发现,增强冷端散热能力是提高温差发电器输出功率的有效途径,且水冷效果相比空冷效果优势明显.实验结果可为优化温差发电器工作条件和提高其输出功率提供有价值的理论指导.%Thermoelectric generator technology, due to its several kinds of advantages, especially its promising applications to recover waste heat, has become a noticeable researcher direction. Thermoelectric technology involves three basic effects, which lead to the temperature distribution being difficult to solve. In order to explore operation law which makes thermoelectric generator have a bigger output power, a mathematical model based on thermoelectric principle and heat transfer theory has been built and was used to solve the temperature distribution of thermoelectric generator. The performance characteristics of thermoelectric generator in different operation conditions have been gained in the objective function of output power by simulating. By the comparison, it is found that reinforcing the heat transfer capability is an effective approach and the water is superior to the air for the cooling effect. The results can provide meaningful guidelines for optimizing operation conditions and improving output power of thermoelectric generator.

  19. 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

  20. 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.

  1. 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.

  2. 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...

  3. 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)

  4. Systems biology, emergence and antireductionism.

    Science.gov (United States)

    Kesić, Srdjan

    2016-09-01

    This study explores the conceptual history of systems biology and its impact on philosophical and scientific conceptions of reductionism, antireductionism and emergence. Development of systems biology at the beginning of 21st century transformed biological science. Systems biology is a new holistic approach or strategy how to research biological organisms, developed through three phases. The first phase was completed when molecular biology transformed into systems molecular biology. Prior to the second phase, convergence between applied general systems theory and nonlinear dynamics took place, hence allowing the formation of systems mathematical biology. The second phase happened when systems molecular biology and systems mathematical biology, together, were applied for analysis of biological data. Finally, after successful application in science, medicine and biotechnology, the process of the formation of modern systems biology was completed. Systems and molecular reductionist views on organisms were completely opposed to each other. Implications of systems and molecular biology on reductionist-antireductionist debate were quite different. The analysis of reductionism, antireductionism and emergence issues, in the era of systems biology, revealed the hierarchy between methodological, epistemological and ontological antireductionism. Primarily, methodological antireductionism followed from the systems biology. Only after, epistemological and ontological antireductionism could be supported.

  5. 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

  6. 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.

  7. The Impact of a Web-Based Research Simulation in Bioinformatics on Students' Understanding of Genetics

    Science.gov (United States)

    Gelbart, Hadas; Brill, Gilat; Yarden, Anat

    2009-01-01

    Providing learners with opportunities to engage in activities similar to those carried out by scientists was addressed in a web-based research simulation in genetics developed for high school biology students. The research simulation enables learners to apply their genetics knowledge while giving them an opportunity to participate in an authentic…

  8. MEMBRANE COMPUTING AS THE PARADIGM FOR MODELING SYSTEMS BIOLOGY

    Directory of Open Access Journals (Sweden)

    Ravie Chandren Muniyandi

    2013-01-01

    Full Text Available Membrane computing is a field in computer science that is inspired from the structure and the processes of living cells and is being considered as an alternative in solving the limitations in conventional mathematical approaches by taking into consideration its essential features that are of interest for research in systems biology. Advancements in computability make it feasible to handle huge volumes of data in biology and propose a new and better approach using a discreet computer science model, such as membrane computing. In this respect, membrane-computing abilities, to enhance the understanding of the system level of biological systems, have been explored. This study discusses experiences in applying membrane computing in modeling biological systems as well as possibilities of incorporating membrane computing into other computer science paradigms to enhance the use of membrane computing in systems biology. Experiences in modeling aspects of systems biology with membrane computing demonstrate additional advantages and possibilities compared with conventional methods. However, they are not yet used widely to model or simulate biological processes or systems. A general framework of modeling and verifying biological systems using membrane computing is essential as a guideline for biologists in their research in systems biology.

  9. 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)

  10. 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.

  11. 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.

  12. 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...

  13. The effect of exposure misclassification in spontaneous ADR reports on the time to detection of product-specific risks for biologicals : A simulation study

    NARCIS (Netherlands)

    Vermeer, Niels S.; Ebbers, Hans C.; Straus, Sabine M J M; Leufkens, Hubert G M; Egberts, Toine C G; De Bruin, Marie L.

    2016-01-01

    Background and Objective: The availability of accurate product-specific exposure information is essential in the pharmacovigilance of biologicals, because differences in the safety profile may emerge between products containing the same active substance. In spontaneous adverse drug reaction (ADR) re

  14. 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)

  15. 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.

  16. 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...

  17. 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...

  18. 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...

  19. 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.

  20. 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.

  1. 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.

  2. Basic Principle of Molecular Dynamics and Application in The Filed of Biologic Molecules Simulation%分子动力学模拟及在生物大分子模拟领域的应用

    Institute of Scientific and Technical Information of China (English)

    刘冠辰

    2015-01-01

    简要介绍了分子动力学的发展历史、基本理论、基本步骤以及其作为基本研究手段来进行生物大分子模拟领域的应用。%This article briefly describes the molecular dynamics of development history,basic theory,basic steps and basic research as a means to carry out simulation in the field of application of biological macromolecules.

  3. 基于MSPH方法模拟激光对树脂基复合材料的辐照效应%MSPH method applied to simulate the irradiation effect of resin composites irradiated by laser

    Institute of Scientific and Technical Information of China (English)

    陈敏孙; 江厚满; 刘泽金

    2012-01-01

    Complicated physical and chemical changes such as thermal decomposition, ablation, evaporation even complicated interface problem may take place while resin composites irradiated by laser. In view of the mesh free particle methods have advantages on dealing with problems of large deformation, mesh distortion and laser ablation, the modified smoothed particle hydrodynamics method (MSPH) was applied to numerical simulating the three-dimensional temperature field model of resin composites irradiated by laser. By comparing the simulation results with the experimental results, the applicability of MSPH to simulate the irradiation effects of resin composites irradiated by laser was studied. Numerical simulation results indicate that MSPH is fit for modeling the irradiation effects of resin composites irradiated by laser. Furthermore, MSPH is also a valuable numerical method in the domain of laser interaction with matter.%树脂基复合材料在激光辐照下通常会发生复杂的物理化学变化,可能涉及材料热分解、烧蚀、汽化和比较复杂的界面问题.鉴于无网格粒子法在处理大变形、网格畸变和材料烧蚀等问题时有优势,利用改进的光滑粒子方法对激光辐照下复合材料树脂基热解时的三维温度场模型进行数值求解.将数值模拟结果与实验结果进行对比,考察了改进的光滑粒子方法对所考虑问题的适用性.结果表明:改进的光滑粒子方法适合于模拟激光对树脂基复合材料的辐照效应,在激光与物质相互作用领域,该方法也是值得关注的一种数值方法.

  4. Simulation of the respiratory model of tract of Publication 66 of the ICRP and their use in biological analysis; Simulacion del modelo de tracto respiratorio de la Publicacion 66 de la ICRP y su utilizacion en bioanalisis

    Energy Technology Data Exchange (ETDEWEB)

    Puerta, A. [Universidad Nacional de Colombia, Medellin (Colombia). Facultad de Ciencias. Dept. de Fisica; Bertelli, L.; Lipsztein, J. [Instituto de Radioprotecao e Dosimetria (IRD), Rio de Janeiro, RJ (Brazil)

    2001-07-01

    The International Commission Radiological Protection, ICRP in its publications 67, 68, 69 and 71 provides the loss of systematic activity of the radioactive materials by the routes of excretion and recirculation, as well as effective dose by incorporation unit coefficient, using the model of respiratory tract proposed by the ICRP, in its Publication 66, but it does not provide information on as these models in biological analysis are used. There are some specific studies for inhalation of uranium compounds made by Bertelli and collaborators using the new model of the lung. In this work it have been done a simulation of the model of respiratory tract of ICRP 66 of such form that it can be used in-vitro and in-vivo biological analysis. In order to verify the simulation were used systemic models for adult of planuin, lead, uranium, bismuth and their respective descendants and the comparison with the coefficients of dose provided by the ICRP. Finally, it shows the estimation of the temporary distribution of activity in devices and the excrete of these radionuclides and in addition the model for gases and steam in the conditions is verified that the ICRP proposes.

  5. Simulation Study of Radiant Floor Heating Applied in the Station Hall with Large Space%地板辐射采暖在大空间候车厅应用的模拟研究

    Institute of Scientific and Technical Information of China (English)

    尹海文

    2015-01-01

    为说明地板辐射采暖在大空间候车站的应用可行性,简要介绍了地板辐射采暖的原理及特点,采用CFD技术对低温地板辐射采暖的铁路车站候车厅温度场和速度场进行数值模拟研究,通过分析室内空气温度梯度、地板表面温度、候车区的热舒适性(PMV)及不满意率(PPD),对候车厅等高大空间采用低温地板辐射采暖的设计方案进行验证,计算结果表明 PMV-PPD 满足国际标准ISO7730推荐值,说明地板辐射采暖在大空间建筑应用是一种较舒适的采暖方式。%In order to testify the feasibility of the radiant floor heating applied in the station hall with large space, the theory and characteristic of radiant floor is introduced and the CFD technique is employed to simulate the temperature and velocity distribution in a station hall with large space. The temperature gradient of indoor air, floor surface temperature, PMV and PPD are used to evaluate the effect of the design scheme. The simulation results show that the PMV-PPD can meet the recommended value of the international standard, ISO7730 and the radiant floor heating is suitable for the large space.

  6. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

    Science.gov (United States)

    Boldon, Lauren; Laliberte, Fallon; Liu, Li

    2015-01-01

    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. PMID:25721341

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. Applied statistical thermodynamics

    CERN Document Server

    Lucas, Klaus

    1991-01-01

    The book guides the reader from the foundations of statisti- cal thermodynamics including the theory of intermolecular forces to modern computer-aided applications in chemical en- gineering and physical chemistry. The approach is new. The foundations of quantum and statistical mechanics are presen- ted in a simple way and their applications to the prediction of fluid phase behavior of real systems are demonstrated. A particular effort is made to introduce the reader to expli- cit formulations of intermolecular interaction models and to show how these models influence the properties of fluid sy- stems. The established methods of statistical mechanics - computer simulation, perturbation theory, and numerical in- tegration - are discussed in a style appropriate for newcom- ers and are extensively applied. Numerous worked examples illustrate how practical calculations should be carried out.

  13. 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...

  14. Simulations in nanobiotechnology

    CERN Document Server

    Eom, Kilho

    2011-01-01

    Introduction to Simulations in NanobiotechnologyKilho EomSimulations in Biological SciencesModeling the Interface between Biological and Synthetic Components in Hybrid NanosystemsRogan Carr, Jeffrey Comer, and Aleksei AksimentievCoarse-Grained Modeling of Large Protein Complexes for Understanding Their Conformational DynamicsKilho Eom, Gwonchan Yoon, Jae In Kim, and Sungsoo NaContinuum Modeling and Simulation of Membrane ProteinsXi ChenExploring the Energy Landscape of Biopolymers U

  15. 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)

  16. 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.

  17. 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...

  18. Psychological effects of sustained operations in a simulated NBC (nuclear, biological or chemical) environment on M1 tank crews. Technical report, May-June 1985

    Energy Technology Data Exchange (ETDEWEB)

    Munro, I.; Rauch, T.M.; Banderet, L.E.; Lussier, A.R.; Tharion, W.J.

    1987-07-03

    Forty-eight M1 crewmen were tested in a temperate climate under conditions simulating 72-hour operations in an area contaminated with chemical agents. Over 50% of the crewman voluntarily withdrew from the test, and maximum unit endurance did not exceed 32 hours. Two problems were found to be related to endurance failure. Soldiers who withdrew reported more intense symptoms associated with respiratory distress than did those who remained in the test. In addition, soldiers who withdrew experienced greater cognitive difficulties. Near-term countermeasures, assessed in some test iterations, showed no significant endurance-extending effects. Alternative solutions based on the identified problems were proposed.

  19. X射线源的静电自会聚电子枪的计算机模拟%Simulation of Electrostatic Self-Focusing Lanthanum Hexaboride Electron Gun Applied in X-Ray Source

    Institute of Scientific and Technical Information of China (English)

    于海波; 林祖伦; 祁康成; 曹贵川; 王小菊

    2015-01-01

    High power, high current density, fine focus X-ray sources are widely used in the field of industrial nondestructive testing, medical imaging, security technology, and so on. An electrostatic self-focusing lanthanum hexaboride electron gun applied in X-ray source is designed using electron beam simulation (EBS) software. The electron gun consists of three parts: a lanthanum hexaboride thermionic emitter, a focusing electrode with a trapezoidal focusing groove and a rectangular hole, and an anode. The simulated results show that the inclination angle of focusing electrode has strong influence on electron focusing property and the best inclination angle is 46°. The anode current and the uniformity of the distribution are decreased with increasing the distance between the gate and cathode, and the best distance between the gate and cathode value is 0.3 mm.%高功率、大电流密度、细聚焦X射线源在工业无损探伤、医学成像、安全技术等领域具有广泛的应用。本文设计了一种用于X射线管的静电自会聚电子枪,该电子枪包括三部分:LaB6热阴极发射体、带有矩形孔和斜槽的聚焦极、阳极。采用EBS粒子束模拟软件对该电子枪的结构进行了模拟仿真。仿真结果表明:电子枪的聚焦能力主要取决于聚焦极倾角,当聚焦极倾角为46°时,达到理想的电子束聚焦效果;随着阴栅距的增加,阳极电流以及束斑电流分布均匀性显著降低,当阴栅距为0.3 mm,可在工艺条件允许下,得到具有较大阳极电流以及理想电流分布的电子束。

  20. 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.

  1. 数字锁相测试用畸变电网信号模拟装置%Design of Distorted Simulation Signal Device Applied in Digital Phase-Lock

    Institute of Scientific and Technical Information of China (English)

    李海舰; 赵仁德; 许强

    2013-01-01

    A simulated three - phase distorted grid signal device is designed for digital real - time phase -locked technique. The digital signal processor TMS320F2812 is chosen as the core controller. Based on die serial communication between PC and DSP, the modulation signal parameters including frequency, amplitude and phase can be realized in real - time, and program of abrupt changes in frequency, amplitude and phase is designed. Distorted grid signal is achieved by a second order active low pass filter. Experimental results show the signal can be applied to supply harmonic distortion signal for digital real - time phase - lock algorithm.%设计了一种能够为数字锁相技术提供三相畸变电网电压和电流信号的模拟装置.选取TMS320F2812DSP作为控制核心,通过上位机与DSP通信,实时传递信号基波频率、基波和各次谐波的幅值和相位偏移参数,编写信号频率突变、幅值突变、相位偏移定点程序.DSP输出的PWM波形经过二阶有源低通滤波器滤波,获得所需要的模拟三相畸变电网电压和电流信号.ANF锁相实验结果表明装置产生的信号可直接输入到DSP、单片机中,为数字锁相算法提供畸变电网信号.

  2. "Heart-cut" bidimensional achiral-chiral liquid chromatography applied to the evaluation of stereoselective metabolism, in vivo biological activity and brain response to chiral drug candidates targeting the central nervous system.

    Science.gov (United States)

    Battisti, Umberto M; Citti, Cinzia; Larini, Martina; Ciccarella, Giuseppe; Stasiak, Natalia; Troisi, Luigino; Braghiroli, Daniela; Parenti, Carlo; Zoli, Michele; Cannazza, Giuseppe

    2016-04-22

    A "heart-cut" two-dimensional achiral-chiral liquid chromatography triple-quadrupole mass spectrometry method (LC-LC-MS/MS) was developed and coupled to in vivo cerebral microdialysis to evaluate the brain response to the chiral compound (±)-7-chloro-5-(3-furanyl)-3-methyl-3,4-dihydro-2H-1,2,4-benzothiadiazine-1,1-dioxide ((±)-1), a potent positive allosteric modulator (PAM) of AMPA receptor. The method was successfully employed to evaluate also its stereoselective metabolism and in vitro biological activity. In particular, the LC achiral method developed, employs a pentafluorinated silica based column (Discovery HS-F5) to separate dopamine, acetylcholine, serotonin, (±)-1 and its two hepatic metabolites. In the "heart-cut" two-dimension achiral-chiral configuration, (±)-1 and (±)-1-d4 eluted from the achiral column (1st dimension), were transferred to a polysaccharide-based chiral column (2nd dimension, Chiralcel OD-RH) by using an automatic six-port valve. Single enantiomers of (±)-1 were separated and detected using electrospray positive ionization mode and quantified in selected reaction monitoring mode. The method was validated and showed good performance in terms of linearity, accuracy and precision. The new method employed showed several possible applications in the evaluation of: (a) brain response to neuroactive compounds by measuring variations in the brain extracellular levels of selected neurotransmitters and other biomarkers; (b) blood brain barrier penetration of drug candidates by measuring the free concentration of the drug in selected brain areas; (c) the presence of drug metabolites in the brain extracellular fluid that could prove very useful during drug discovery; (d) a possible stereoselective metabolization or blood brain barrier stereoselective crossing of chiral drugs. Finally, compared to the methods reported in the literature, this technique avoids the necessity of euthanizing an animal at each time point to measure drug

  3. Applying Biomimetic Algorithms for Extra-Terrestrial Habitat Generation

    Science.gov (United States)

    Birge, Brian

    2012-01-01

    The objective is to simulate and optimize distributed cooperation among a network of robots tasked with cooperative excavation on an extra-terrestrial surface. Additionally to examine the concept of directed Emergence among a group of limited artificially intelligent agents. Emergence is the concept of achieving complex results from very simple rules or interactions. For example, in a termite mound each individual termite does not carry a blueprint of how to make their home in a global sense, but their interactions based strictly on local desires create a complex superstructure. Leveraging this Emergence concept applied to a simulation of cooperative agents (robots) will allow an examination of the success of non-directed group strategy achieving specific results. Specifically the simulation will be a testbed to evaluate population based robotic exploration and cooperative strategies while leveraging the evolutionary teamwork approach in the face of uncertainty about the environment and partial loss of sensors. Checking against a cost function and 'social' constraints will optimize cooperation when excavating a simulated tunnel. Agents will act locally with non-local results. The rules by which the simulated robots interact will be optimized to the simplest possible for the desired result, leveraging Emergence. Sensor malfunction and line of sight issues will be incorporated into the simulation. This approach falls under Swarm Robotics, a subset of robot control concerned with finding ways to control large groups of robots. Swarm Robotics often contains biologically inspired approaches, research comes from social insect observation but also data from among groups of herding, schooling, and flocking animals. Biomimetic algorithms applied to manned space exploration is the method under consideration for further study.

  4. Kinetic Modeling of Biological Systems

    Energy Technology Data Exchange (ETDEWEB)

    Resat, Haluk; Petzold, Linda; Pettigrew, Michel F.

    2009-04-21

    The dynamics of how its constituent components interact define the spatio-temporal response of a natural system to stimuli. Modeling the kinetics of the processes that represent a biophysical system has long been pursued with the aim of improving our understanding of the studied system. Due to the unique properties of biological systems, in addition to the usual difficulties faced in modeling the dynamics of physical or chemical systems, biological simulations encounter difficulties that result from intrinsic multiscale and stochastic nature of the biological processes. This chapter discusses the implications for simulation of models involving interacting species with very low copy numbers, which often occur in biological systems and give rise to significant relative fluctuations. The conditions necessitating the use of stochastic kinetic simulation methods and the mathematical foundations of the stochastic simulation algorithms are presented. How the well-organized structural hierarchies often seen in biological systems can lead to multiscale problems, and possible ways to address the encountered computational difficulties are discussed. We present the details of the existing kinetic simulation methods, and discuss their strengths and shortcomings. A list of the publicly available kinetic simulation tools and our reflections for future prospects are also provided.

  5. 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...

  6. 五种土壤处理除草剂对刺萼龙葵的生物活性研究%Study on the Biological Activity of 5 Soil-applied Herbicides Against Solanum rostratum

    Institute of Scientific and Technical Information of China (English)

    张少逸; 张朝贤; 王金信; 黄红娟; 张建华; 曹坳程; 魏守辉

    2012-01-01

    To screen for safe and effective soil-applied herbicides to prevent and control of buffalobur, pot experiments were conducted to evaluate the control effect of 5 preemergent herbicides against buffalobur, and greenhouse bioassay were further conducted for the herbicides with better control effects. The results showed that the tox-icity of acetochlor was the highest, while that of pendimethalin was the lowest, the ED90 were 41. 43 and 748. 56 g a. i. /hm2 , respectively. The order of toxicity was acetochlor > clomazone > alachlor > s-metolachlor > pendimethalin. Based on consideration of herbicidal activity and recommended rate, the 5 herbicides could be used to control buffalobur at lower dose than recommended.%为筛选防治刺萼龙葵的安全、高效的土壤处理除草剂,采用温室盆栽法对5种土壤处理除草剂进行了室内生物测定.结果表明,乙草胺对刺萼龙葵活性最高,ED90为41.43 g a.i./hm2;二甲戊灵最低,ED90为748.56 g a.i./hm2.5种除草剂ED90由高到低的顺序为乙草胺>异噁草松>甲草胺>精异丙甲草胺>二甲戊灵.综合考虑药剂活性及其推荐剂量,乙草胺、异噁草松、甲草胺、精异丙甲草胺和二甲戊灵均可在低于推荐剂量下用于防除刺萼龙葵.

  7. Simulation tools

    CERN Document Server

    Jenni, F

    2006-01-01

    In the last two decades, simulation tools made a significant contribution to the great progress in development of power electronics. Time to market was shortened and development costs were reduced drastically. Falling costs, as well as improved speed and precision, opened new fields of application. Today, continuous and switched circuits can be mixed. A comfortable number of powerful simulation tools is available. The users have to choose the best suitable for their application. Here a simple rule applies: The best available simulation tool is the tool the user is already used to (provided, it can solve the task). Abilities, speed, user friendliness and other features are continuously being improved—even though they are already powerful and comfortable. This paper aims at giving the reader an insight into the simulation of power electronics. Starting with a short description of the fundamentals of a simulation tool as well as properties of tools, several tools are presented. Starting with simplified models ...

  8. Practical biological spread-out Bragg peak design of carbon beam

    CERN Document Server

    Kim, Chang Hyeuk; Chang, Seduk; Jang, Hong Suk; Kim, Jeong Hwan; Park, Dong Wook; Hwang, Won Taek; Yang, Tea-Keun

    2015-01-01

    The carbon beams show more advantages on the biological properties compared with proton beams in radiation therapy. The carbon beam shows high linear energy transfer (LET) to medium and it increases the relative biological effectiveness (RBE). To design spread-out Bragg peak (SOBP) of biological dose using carbon beam, a practical method was purposed by using the linear-quadratic (LQ) model and Geant4 based Monte Carlo simulation code. The various Bragg peak profiles and LET was calculated for each slice at the target region. To generate appropriate biological SOBP, a set of weighting factor, which is a power function in terms of energy step, was applied to the obtained each physical dose. The designed biological SOBP showed 1.34 % of uniformity.

  9. Drug Delivery Through the Skin: Molecular Simulations of Barrier Lipids to Design more Effective Noninvasive Dermal and Transdermal Delivery Systems for Small Molecules Biologics and Cosmetics

    Energy Technology Data Exchange (ETDEWEB)

    J Torin Huzil; S Sivaloganathan; M Kohandel; M Foldvari

    2011-12-31

    The delivery of drugs through the skin provides a convenient route of administration that is often preferable to injection because it is noninvasive and can typically be self-administered. These two factors alone result in a significant reduction of medical complications and improvement in patient compliance. Unfortunately, a significant obstacle to dermal and transdermal drug delivery alike is the resilient barrier that the epidermal layers of the skin, primarily the stratum corneum, presents for the diffusion of exogenous chemical agents. Further advancement of transdermal drug delivery requires the development of novel delivery systems that are suitable for modern, macromolecular protein and nucleotide therapeutic agents. Significant effort has already been devoted to obtain a functional understanding of the physical barrier properties imparted by the epidermis, specifically the membrane structures of the stratum corneum. However, structural observations of membrane systems are often hindered by low resolutions, making it difficult to resolve the molecular mechanisms related to interactions between lipids found within the stratum corneum. Several models describing the molecular diffusion of drug molecules through the stratum corneum have now been postulated, where chemical permeation enhancers are thought to disrupt the underlying lipid structure, resulting in enhanced permeability. Recent investigations using biphasic vesicles also suggested a possibility for novel mechanisms involving the formation of complex polymorphic lipid phases. In this review, we discuss the advantages and limitations of permeation-enhancing strategies and how computational simulations, at the atomic scale, coupled with physical observations can provide insight into the mechanisms of diffusion through the stratum corneum.

  10. Simulated influence of postweaning production system on performance of different biological types of cattle: II. Carcass composition, retail product, and quality.

    Science.gov (United States)

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

    1995-03-01

    A computer simulation model was used to characterize the response in carcass composition, retail product, and quality of 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, and finished at either a low (1.0 kg) or high (1.36 kg) ADG. The backgrounding systems were a high ADG (.9 kg) for 111, 167, or 222 d, a medium ADG (.5 kg) for 200, 300, or 400 d, a low ADG (.25 kg) for 300 or 400 d and 0 d backgrounding. For specific genotype x production system combinations, results showed that carcasses of compensating steers may be either leaner, not different in fatness, or fatter than carcasses of steers put on a finishing diet directly after weaning. Systems in which steers gained a greater proportion of the final slaughter weight over long durations of growth restriction resulted in leaner carcasses. There were 12 common production systems in which 13 of the genotypes produced a carcass with a maximum of 28% fat or with a marbling score of 11 or greater. These results suggest sire breeds used to produce these steers can be used over a wide range of nutritional and management environments, and that a mixed group of steers can be fed and managed similarly from weaning to slaughter to produce a carcass with a specified composition, retail product, or quality.

  11. A fast integral equation method for simulating high-field radio frequency coil arrays in magnetic resonance imaging

    International Nuclear Information System (INIS)

    A fast full-wave numerical approach was developed for simulating high-field multi-channel radio-frequency (RF) receive coil arrays in magnetic resonance imaging. To improve the efficiency, the impedance matrix was compressed by a multilevel adaptive cross approximation method. Furthermore, careful organization of multiple coil simulations was applied so that the impedance matrix associated with biological subjects is constructed and pre-conditioned only once. Numerical examples demonstrate the efficacy of the proposed approach for RF coil simulations.

  12. Surface-water quantity and quality, aquatic biology, stream geomorphology, and groundwater-flow simulation for National Guard Training Center at Fort Indiantown Gap, Pennsylvania, 2002-05

    Science.gov (United States)

    Langland, Michael J.; Cinotto, Peter J.; Chichester, Douglas C.; Bilger, Michael D.; Brightbill, Robin A.

    2010-01-01

    Base-line and long-term monitoring of water resources of the National Guard Training Center at Fort Indiantown Gap in south-central Pennsylvania began in 2002. Results of continuous monitoring of streamflow and turbidity and monthly and stormflow water-quality samples from two continuous-record long-term stream sites, periodic collection of water-quality samples from five miscellaneous stream sites, and annual collection of biological data from 2002 to 2005 at 27 sites are discussed. In addition, results from a stream-geomorphic analysis and classification and a regional groundwater-flow model are included. Streamflow at the facility was above normal for the 2003 through 2005 water years and extremely high-flow events occurred in 2003 and in 2004. Water-quality samples were analyzed for nutrients, sediments, metals, major ions, pesticides, volatile and semi-volatile organic compounds, and explosives. Results indicated no exceedances for any constituent (except iron) above the primary and secondary drinking-water standards or health-advisory levels set by the U.S. Environmental Protection Agency. Iron concentrations were naturally elevated in the groundwater within the watershed because of bedrock lithology. The majority of the constituents were at or below the method detection limit. Sediment loads were dominated by precipitation due to the remnants of Hurricane Ivan in September 2004. More than 60 percent of the sediment load measured during the entire study was transported past the streamgage in just 2 days during that event. Habitat and aquatic-invertebrate data were collected in the summers of 2002-05, and fish data were collected in 2004. Although 2002 was a drought year, 2003-05 were above-normal flow years. Results indicated a wide diversity in invertebrates, good numbers of taxa (distinct organisms), and on the basis of a combination of metrics, the majority of the 27 sites indicated no or slight impairment. Fish-metric data from 25 sites indicated results

  13. Desarrollo de un Simulador de Secado para Materiales Biológicos Development of a Simulation Model for Drying Biological Materials

    Directory of Open Access Journals (Sweden)

    R. Olivas-Vargas

    2004-01-01

    Full Text Available En este artículo, se proponen dos modelos para describir el proceso de secado y el deterioro que ocurre en el procesamiento de materiales biológicos, partiendo de datos experimentales. El estudio fue desarrollado utilizando chile jalapeño (Capsicum annuum L. y manzana en rebanadas como materias primas. El deterioro fue evaluado mediante cambio en la capacidad de rehidratación en chile jalapeño y cambios en el color en manzana. El modelo de secado propuesto se utilizó con las ecuaciones clásicas usadas en esta operación unitaria para predecir el tiempo de proceso. Tomando estos modelos, se desarrolló un software de análisis y predicción de los balances de masa y energía, como una herramienta de utilidad en el escalamiento o diseño de sistemas de secado, así como el daño que el material va a sufrir. El software desarrollado tuvo un excelente desempeño en materiales que muestran poca dispersión de los datos experimentalesTwo models, based on experimental data, that describe the process of drying and the deterioration that occurs during the processing of biological materials, are proposed in this article. Jalapeño pepper (Capsicum annuum L. and apple slices were used for generation of experimental data. Rehydration capability on jalapeño pepper and color changes on apple slices were used for measurement of deterioration. The proposed drying model was used with the classic equations this unit operation to predict the processing time. Based on these models, a computer program for the analysis and prediction of the mass and energy balances was developed as a useful tool in the scaling or design of the drying systems, as well as the damage that the material will suffer. The software developed showed an excellent performance when experimental data have low dispersion

  14. 情景式模拟教学在急诊教学中的应用效果研究%Study on the effect of applying scene simulation in clinical teaching of emergency medicine

    Institute of Scientific and Technical Information of China (English)

    苟君臣; 汪庆; 徐春梅; 马杰; 付成; 陈安海

    2015-01-01

    Objective To investigate effect of scene simulation in clinical teaching of emergency medicine.Methods 90 ca-ses of medical staff in department of emergency were randomly divided into experimental group and control group, with 45 cases each. The teaching method of 3 hours training on first aid knowledge and skills was applied in experimental group, and then they were divided into groups of 5, simulated the process of different emergency scene for rescuing critical patients that designed by the supervisor.The control group was trained with traditional teaching mode, in which the supervisor as the leading and students play the passive role.Af-ter the internship in emergency department, test performance, practice assessment results and clinical information feedback were com-pared between the two groups.Results The mean scores of test performance of experimental group and control group were(92.98 ± 2.71) and (85.29 ±6.24), respectively.The difference between two groups were statistically significantly(t=4.999,P<0.05). Experimental group was given 6 good in practice assessment, and control group was given 1 good and 5 bad.43 good and 2 medium were given to experimental group in clinical information feedback, and 26 good, 10 medium, 9 bad were given to control group.The difference between two groups were statistically significantly(Z=-4.275,P<0.01).Conclusions Scene simulation teaching mode can improve first aid skills, communication ability, teamwork spirit of clinical emergency medical staff, aiming to meet further needs of modern emergency teaching, so it is worthy of being popularized and applied clinically.%目的:探讨情景式模拟教学在急诊实习医护人员教学中的应用效果。方法急诊科实习医护人员90名随机分为实验组和对照组,每组45名。实验组教学方法为急救知识及技能培训3学时,然后由导师设计不同危重患者抢救现场,实习医护人员5人一组,演练抢救流程;对照组采用

  15. Simulated influence of postweaning production system on performance of different biological types of cattle: II. Carcass composition, retail product, and quality.

    Science.gov (United States)

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

    1995-03-01

    A computer simulation model was used to characterize the response in carcass composition, retail product, and quality of 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, and finished at either a low (1.0 kg) or high (1.36 kg) ADG. The backgrounding systems were a high ADG (.9 kg) for 111, 167, or 222 d, a medium ADG (.5 kg) for 200, 300, or 400 d, a low ADG (.25 kg) for 300 or 400 d and 0 d backgrounding. For specific genotype x production system combinations, results showed that carcasses of compensating steers may be either leaner, not different in fatness, or fatter than carcasses of steers put on a finishing diet directly after weaning. Systems in which steers gained a greater proportion of the final slaughter weight over long durations of growth restriction resulted in leaner carcasses. There were 12 common production systems in which 13 of the genotypes produced a carcass with a maximum of 28% fat or with a marbling score of 11 or greater. These results suggest sire breeds used to produce these steers can be used over a wide range of nutritional and management environments, and that a mixed group of steers can be fed and managed similarly from weaning to slaughter to produce a carcass with a specified composition, retail product, or quality. PMID:7608000

  16. Case Studies in Biology.

    Science.gov (United States)

    Zeakes, Samuel J.

    1989-01-01

    A case study writing exercise used in a course on parasitology was found to be a powerful learning experience for students because it involved discipline-based technical writing and terminology, brought the students in as evaluators, applied current learning, caused interaction among all students, and simulated real professional activities. (MSE)

  17. Fusion of biological membranes

    Indian Academy of Sciences (India)

    K Katsov; M Müller; M Schick

    2005-06-01

    The process of membrane fusion has been examined by Monte Carlo simulation, and is found to be very different than the conventional picture. The differences in mechanism lead to several predictions, in particular that fusion is accompanied by transient leakage. This prediction has recently been verified. Self-consistent field theory is applied to examine the free energy barriers in the different scenarios.

  18. Simulating Nuclear and Electronic Quantum Effects in Enzymes.

    Science.gov (United States)

    Wang, L; Isborn, C M; Markland, T E

    2016-01-01

    An accurate treatment of the structures and dynamics that lead to enhanced chemical reactivity in enzymes requires explicit treatment of both electronic and nuclear quantum effects. The former can be captured in ab initio molecular dynamics (AIMD) simulations, while the latter can be included by performing ab initio path integral molecular dynamics (AI-PIMD) simulations. Both AIMD and AI-PIMD simulations have traditionally been computationally prohibitive for large enzymatic systems. Recent developments in streaming computer architectures and new algorithms to accelerate path integral simulations now make these simulations practical for biological systems, allowing elucidation of enzymatic reactions in unprecedented detail. In this chapter, we summarize these recent developments and discuss practical considerations for applying AIMD and AI-PIMD simulations to enzymes. PMID:27498646

  19. Biological Oceanography

    Science.gov (United States)

    Abbott, M. R.

    1984-01-01

    Within the framework of global biogeochemical cycles and ocean productivity, there are two areas that will be of particular interest to biological oceanography in the 1990s. The first is the mapping in space time of the biomass and productivity of phytoplankton in the world ocean. The second area is the coupling of biological and physical processes as it affects the distribution and growth rate of phytoplankton biomass. Certainly other areas will be of interest to biological oceanographers, but these two areas are amenable to observations from satellites. Temporal and spatial variability is a regular feature of marine ecosystems. The temporal and spatial variability of phytoplankton biomass and productivity which is ubiquitous at all time and space scales in the ocean must be characterized. Remote sensing from satellites addresses these problems with global observations of mesocale (2 to 20 days, 10 to 200 km) features over a long period of time.

  20. Computer Simulation in Chemical Kinetics

    Science.gov (United States)

    Anderson, Jay Martin

    1976-01-01

    Discusses the use of the System Dynamics technique in simulating a chemical reaction for kinetic analysis. Also discusses the use of simulation modelling in biology, ecology, and the social sciences, where experimentation may be impractical or impossible. (MLH)