WorldWideScience

Sample records for systems biology driven

  1. Precision medicine driven by cancer systems biology.

    Science.gov (United States)

    Filipp, Fabian V

    2017-03-01

    Molecular insights from genome and systems biology are influencing how cancer is diagnosed and treated. We critically evaluate big data challenges in precision medicine. The melanoma research community has identified distinct subtypes involving chronic sun-induced damage and the mitogen-activated protein kinase driver pathway. In addition, despite low mutation burden, non-genomic mitogen-activated protein kinase melanoma drivers are found in membrane receptors, metabolism, or epigenetic signaling with the ability to bypass central mitogen-activated protein kinase molecules and activating a similar program of mitogenic effectors. Mutation hotspots, structural modeling, UV signature, and genomic as well as non-genomic mechanisms of disease initiation and progression are taken into consideration to identify resistance mutations and novel drug targets. A comprehensive precision medicine profile of a malignant melanoma patient illustrates future rational drug targeting strategies. Network analysis emphasizes an important role of epigenetic and metabolic master regulators in oncogenesis. Co-occurrence of driver mutations in signaling, metabolic, and epigenetic factors highlights how cumulative alterations of our genomes and epigenomes progressively lead to uncontrolled cell proliferation. Precision insights have the ability to identify independent molecular pathways suitable for drug targeting. Synergistic treatment combinations of orthogonal modalities including immunotherapy, mitogen-activated protein kinase inhibitors, epigenetic inhibitors, and metabolic inhibitors have the potential to overcome immune evasion, side effects, and drug resistance.

  2. Current trends and new challenges of databases and web applications for systems driven biological research

    Directory of Open Access Journals (Sweden)

    Pradeep Kumar eSreenivasaiah

    2010-12-01

    Full Text Available Dynamic and rapidly evolving nature of systems driven research imposes special requirements on the technology, approach, design and architecture of computational infrastructure including database and web application. Several solutions have been proposed to meet the expectations and novel methods have been developed to address the persisting problems of data integration. It is important for researchers to understand different technologies and approaches. Having familiarized with the pros and cons of the existing technologies, researchers can exploit its capabilities to the maximum potential for integrating data. In this review we discuss the architecture, design and key technologies underlying some of the prominent databases (DBs and web applications. We will mention their roles in integration of biological data and investigate some of the emerging design concepts and computational technologies that are likely to have a key role in the future of systems driven biomedical research.

  3. Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

    Science.gov (United States)

    Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

    2018-01-01

    Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

  4. Quantitative, high-resolution proteomics for data-driven systems biology

    DEFF Research Database (Denmark)

    Cox, J.; Mann, M.

    2011-01-01

    Systems biology requires comprehensive data at all molecular levels. Mass spectrometry (MS)-based proteomics has emerged as a powerful and universal method for the global measurement of proteins. In the most widespread format, it uses liquid chromatography (LC) coupled to high-resolution tandem...... primary structure of proteins including posttranslational modifications, to localize proteins to organelles, and to determine protein interactions. Here, we describe the principles of analysis and the areas of biology where proteomics can make unique contributions. The large-scale nature of proteomics...... data and its high accuracy pose special opportunities as well as challenges in systems biology that have been largely untapped so far....

  5. 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

  6. Arena3D: visualizing time-driven phenotypic differences in biological systems

    Directory of Open Access Journals (Sweden)

    Secrier Maria

    2012-03-01

    Full Text Available Abstract Background Elucidating the genotype-phenotype connection is one of the big challenges of modern molecular biology. To fully understand this connection, it is necessary to consider the underlying networks and the time factor. In this context of data deluge and heterogeneous information, visualization plays an essential role in interpreting complex and dynamic topologies. Thus, software that is able to bring the network, phenotypic and temporal information together is needed. Arena3D has been previously introduced as a tool that facilitates link discovery between processes. It uses a layered display to separate different levels of information while emphasizing the connections between them. We present novel developments of the tool for the visualization and analysis of dynamic genotype-phenotype landscapes. Results Version 2.0 introduces novel features that allow handling time course data in a phenotypic context. Gene expression levels or other measures can be loaded and visualized at different time points and phenotypic comparison is facilitated through clustering and correlation display or highlighting of impacting changes through time. Similarity scoring allows the identification of global patterns in dynamic heterogeneous data. In this paper we demonstrate the utility of the tool on two distinct biological problems of different scales. First, we analyze a medium scale dataset that looks at perturbation effects of the pluripotency regulator Nanog in murine embryonic stem cells. Dynamic cluster analysis suggests alternative indirect links between Nanog and other proteins in the core stem cell network. Moreover, recurrent correlations from the epigenetic to the translational level are identified. Second, we investigate a large scale dataset consisting of genome-wide knockdown screens for human genes essential in the mitotic process. Here, a potential new role for the gene lsm14a in cytokinesis is suggested. We also show how phenotypic

  7. What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform

    NARCIS (Netherlands)

    Swat, Maciej; Kiełbasa, Szymon M.; Polak, Sebastian; Olivier, Brett; Bruggeman, Frank J.; Tulloch, Mark Quinton; Snoep, Jacky L.; Verhoeven, Arthur J.; Westerhoff, Hans V.

    2011-01-01

    The utility of model repositories is discussed in the context of systems biology (SB). It is shown how such repositories, and in particular their live versions, can be used for computational SB: we calculate the robustness of the yeast glycolytic network with respect to perturbations of one of its

  8. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    study and understand the function of biological systems, particu- larly, the response of such .... understand the organisation and behaviour of prokaryotic sys- tems. ... relationship of the structure of a target molecule to its ability to bind a certain ...

  9. EVALUATING THE ECOLOGICAL RESILIENT DRIVEN PERFORMANCE OF A TROPICAL WASTE STABILIZATION POND SYSTEM USING ECOLOGICAL SIGNATURE OF BIOLOGICAL INTEGRITY

    Directory of Open Access Journals (Sweden)

    Susmita Lahiri Ganguly

    2015-06-01

    Full Text Available Using ecological signature of biological integrity as a measure of performance, the reclamation efficiency of waste stabilization ponds was evaluated over a period of four years in a tropical sewage treatment plant – cum fish culture consisting of two anaerobic, two facultative and four maturation ponds located serially across the sewage effluent gradient. The four maturation ponds were used for batch culture of fish. Samples of surface and bottom water as well as surface sediment were collected twice a month from different ponds of the system and examined for some nutrient cycling bacteria, primary production, chlorophyll content of micro-algae, phytoplankton, zooplankton abundance, fish growth and water quality parameters. Computation of ecological signature using aerobic mineralization index for heterotrophic and ammonifying bacteria revealed steady increase across the sewage effluent gradient. The heterotrophic and ammonifying bacterial populations appeared to have a direct function with the concentrations of chemical oxygen demand of water. The sum of total scores for different optimal conditions for fish growth increased as a function of the distance from the source of effluent implying that ecological resilience of the waste stabilization ponds has been accomplished by the sedimentation, chelation, and biological functional attributes mediated through redundancy of different subsystems, self- purification capacity of the system as a whole.

  10. Increasing URM Undergraduate Student Success through Assessment-Driven Interventions: A Multiyear Study Using Freshman-Level General Biology as a Model System

    Science.gov (United States)

    Carmichael, Mary C.; St. Clair, Candace; Edwards, Andrea M.; Barrett, Peter; McFerrin, Harris; Davenport, Ian; Awad, Mohamed; Kundu, Anup; Ireland, Shubha Kale

    2016-01-01

    Xavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students. In this multiyear study with ~5500 participants, data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course. The three hour-long exams were common and…

  11. Mechanically driven interface propagation in biological tissues

    International Nuclear Information System (INIS)

    Ranft, Jonas; Joanny, Jean-François; Aliee, Maryam; Jülicher, Frank; Prost, Jacques

    2014-01-01

    Many biological tissues consist of more than one cell type. We study the dynamics of an interface between two different cell populations as it occurs during the growth of a tumor in a healthy host tissue. Recent work suggests that the rates of cell division and cell death are under mechanical control, characterized by a homeostatic pressure. The difference in the homeostatic pressures of two cell types drives the propagation of the interface, corresponding to the invasion of one cell type into the other. We derive a front propagation equation that takes into account the coupling between cell number balance and tissue mechanics. We show that in addition to pulled fronts, pushed-front solutions occur as a result of convection driven by mechanics. (paper)

  12. On Rank Driven Dynamical Systems

    Science.gov (United States)

    Veerman, J. J. P.; Prieto, F. J.

    2014-08-01

    We investigate a class of models related to the Bak-Sneppen (BS) model, initially proposed to study evolution. The BS model is extremely simple and yet captures some forms of "complex behavior" such as self-organized criticality that is often observed in physical and biological systems. In this model, random fitnesses in are associated to agents located at the vertices of a graph . Their fitnesses are ranked from worst (0) to best (1). At every time-step the agent with the worst fitness and some others with a priori given rank probabilities are replaced by new agents with random fitnesses. We consider two cases: The exogenous case where the new fitnesses are taken from an a priori fixed distribution, and the endogenous case where the new fitnesses are taken from the current distribution as it evolves. We approximate the dynamics by making a simplifying independence assumption. We use Order Statistics and Dynamical Systems to define a rank-driven dynamical system that approximates the evolution of the distribution of the fitnesses in these rank-driven models, as well as in the BS model. For this simplified model we can find the limiting marginal distribution as a function of the initial conditions. Agreement with experimental results of the BS model is excellent.

  13. EVALUATING THE ECOLOGICAL RESILIENT DRIVEN PERFORMANCE OF A TROPICAL WASTE STABILIZATION POND SYSTEM USING ECOLOGICAL SIGNATURE OF BIOLOGICAL INTEGRITY

    OpenAIRE

    Susmita Lahiri Ganguly; Dipanwita Sarkar Paria; B. B. Jana

    2015-01-01

    Using ecological signature of biological integrity as a measure of performance, the reclamation efficiency of waste stabilization ponds was evaluated over a period of four years in a tropical sewage treatment plant – cum fish culture consisting of two anaerobic, two facultative and four maturation ponds located serially across the sewage effluent gradient. The four maturation ponds were used for batch culture of fish. Samples of surface and bottom water as well as surface sediment were collec...

  14. PC driven integrated vacuum system

    International Nuclear Information System (INIS)

    Curuia, M.; Culcer, M.; Brandea, I.; Anghel, M.

    2001-01-01

    The paper presents a integrated vacuum system which was designed and manufactured in our institute. The main parts of this system are the power supply unit for turbo-melecular pumps and the vacuummeter. Both parts of the system are driven by means of a personal computer using a serial communication, according to the RS 232 hardware standard.(author)

  15. 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).

  16. Noise-driven phenomena in hysteretic systems

    CERN Document Server

    Dimian, Mihai

    2014-01-01

    Noise-Driven Phenomena in Hysteretic Systems provides a general approach to nonlinear systems with hysteresis driven by noisy inputs, which leads to a unitary framework for the analysis of various stochastic aspects of hysteresis. This book includes integral, differential and algebraic models that are used to describe scalar and vector hysteretic nonlinearities originating from various areas of science and engineering. The universality of the authors approach is also reflected by the diversity of the models used to portray the input noise, from the classical Gaussian white noise to its impulsive forms, often encountered in economics and biological systems, and pink noise, ubiquitous in multi-stable electronic systems. The book is accompanied by HysterSoft© - a robust simulation environment designed to perform complex hysteresis modeling – that can be used by the reader to reproduce many of the results presented in the book as well as to research both disruptive and constructive effects of noise in hysteret...

  17. Increasing URM Undergraduate Student Success through Assessment-Driven Interventions: A Multiyear Study Using Freshman-Level General Biology as a Model System

    Science.gov (United States)

    Carmichael, Mary C.; St. Clair, Candace; Edwards, Andrea M.; Barrett, Peter; McFerrin, Harris; Davenport, Ian; Awad, Mohamed; Kundu, Anup; Ireland, Shubha Kale

    2016-01-01

    Xavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students. In this multiyear study with ∼5500 participants, data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course. The three hour-long exams were common and administered concurrently to all students. New exam questions were developed using Bloom’s taxonomy, and exam results were analyzed statistically with validated assessment tools. All but the comprehensive final exam were returned to students for self-evaluation and remediation. Among other approaches, course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters. Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 72.9% (2010) to 83.5% (2015). Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions. Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20% increase in the course pass rates over time, also for the high-risk population. These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention, particularly for our academically at-risk students. PMID:27543637

  18. Biological conversion system

    Science.gov (United States)

    Scott, C.D.

    A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

  19. Resonances in a periodically driven bosonic system

    NARCIS (Netherlands)

    Quelle, Anton; de Morais Smith, Cristiane

    2017-01-01

    Periodically driven systems are a common topic in modern physics. In optical lattices specifically, driving is at the origin of many interesting phenomena. However, energy is not conserved in driven systems, and under periodic driving, heating of a system is a real concern. In an effort to better

  20. Systems Biology and Health Systems Complexity in;

    NARCIS (Netherlands)

    Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

    2016-01-01

    Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

  1. Nutritional Systems Biology

    DEFF Research Database (Denmark)

    Jensen, Kasper

    and network biology has the potential to increase our understanding of how small molecules affect metabolic pathways and homeostasis, how this perturbation changes at the disease state, and to what extent individual genotypes contribute to this. A fruitful strategy in approaching and exploring the field...... biology research. The paper also shows as a proof-of-concept that a systems biology approach to diet is meaningful and demonstrates some basic principles on how to work with diet systematic. The second chapter of this thesis we developed the resource NutriChem v1.0. A foodchemical database linking...... sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...

  2. Transmutation and accelerator driven systems

    International Nuclear Information System (INIS)

    Shapira, J.P.

    2001-01-01

    Full text: Today, countries who are presently involved in nuclear energy are facing many challenges to maintain this option open for the next few decades. Among them, management of nuclear wastes produced in nuclear reactors and in fuel cycle operations has become a very strong environmental issue among the public. In most countries with sizeable commercial nuclear programs, deep geological disposal of ultimate highly active and long-lived nuclear wastes is considered as the reference long-term management scheme. But, many questions arise on the possibility to demonstrate that such wastes can be dealt in such a way as to protect the future generations and the environment. The characteristics of nuclear wastes, the various back end policies concerning spent fuels and the nuclear wastes long-term management options will be first described. Then recent proposals, based on transmutation, especially those using accelerator driven systems (ADS) and/or thorium will be presented. Finally, the possibility for the nuclear physics community to play a part in alleviating the nuclear wastes burden will be pointed out. (author)

  3. Systems biology at work

    NARCIS (Netherlands)

    Martins Dos Santos, V.A.P.; Damborsky, J.

    2010-01-01

    In his editorial overview for the 2008 Special Issue on this topic, the late Jaroslav Stark pointedly noted that systems biology is no longer a niche pursuit, but a recognized discipline in its own right “noisily” coming of age [1]. Whilst general underlying principles and basic techniques are now

  4. Plant Systems Biology (editorial)

    Science.gov (United States)

    In June 2003, Plant Physiology published an Arabidopsis special issue devoted to plant systems biology. The intention of Natasha Raikhel and Gloria Coruzzi, the two editors of this first-of-its-kind issue, was ‘‘to help nucleate this new effort within the plant community’’ as they considered that ‘‘...

  5. Biophysics and systems biology.

    Science.gov (United States)

    Noble, Denis

    2010-03-13

    Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

  6. On fusion driven systems (FDS) for transmutation

    Energy Technology Data Exchange (ETDEWEB)

    Aagren, O (Uppsala Univ., Aangstroem laboratory, div. of electricity, Uppsala (Sweden)); Moiseenko, V.E. (Inst. of Plasma Physics, National Science Center, Kharkov Inst. of Physics and Technology, Kharkov (Ukraine)); Noack, K. (Forschungszentrum Dresden-Rossendorf (Germany))

    2008-10-15

    This report gives a brief description of ongoing activities on fusion driven systems (FDS) for transmutation of the long-lived radioactive isotopes in the spent nuclear waste from fission reactors. Driven subcritical systems appears to be the only option for efficient minor actinide burning. Driven systems offer a possibility to increase reactor safety margins. A comparatively simple fusion device could be sufficient for a fusion-fission machine, and transmutation may become the first industrial application of fusion. Some alternative schemes to create strong fusion neutron fluxes are presented

  7. On fusion driven systems (FDS) for transmutation

    International Nuclear Information System (INIS)

    Aagren, O; Moiseenko, V.E.; Noack, K.

    2008-10-01

    This report gives a brief description of ongoing activities on fusion driven systems (FDS) for transmutation of the long-lived radioactive isotopes in the spent nuclear waste from fission reactors. Driven subcritical systems appears to be the only option for efficient minor actinide burning. Driven systems offer a possibility to increase reactor safety margins. A comparatively simple fusion device could be sufficient for a fusion-fission machine, and transmutation may become the first industrial application of fusion. Some alternative schemes to create strong fusion neutron fluxes are presented

  8. Shock propagation in locally driven granular systems

    Science.gov (United States)

    Joy, Jilmy P.; Pathak, Sudhir N.; Das, Dibyendu; Rajesh, R.

    2017-09-01

    We study shock propagation in a system of initially stationary hard spheres that is driven by a continuous injection of particles at the origin. The disturbance created by the injection of energy spreads radially outward through collisions between particles. Using scaling arguments, we determine the exponent characterizing the power-law growth of this disturbance in all dimensions. The scaling functions describing the various physical quantities are determined using large-scale event-driven simulations in two and three dimensions for both elastic and inelastic systems. The results are shown to describe well the data from two different experiments on granular systems that are similarly driven.

  9. Epithelioid Sarcoma: Opportunities for Biology-driven Targeted Therapy

    Directory of Open Access Journals (Sweden)

    Jonathan eNoujaim

    2015-08-01

    Full Text Available Epithelioid sarcoma is a soft tissue sarcoma of children and young adults for which the preferred treatment for localised disease is wide surgical resection. Medical management is to a great extent undefined, and therefore for patients with regional and distal metastases, the development of targeted therapies is greatly desired. In this review we will summarize clinically-relevant biomarkers (e.g., SMARCB1, CA125, dysadherin and others with respect to targeted therapeutic opportunities. We will also examine the role of EGFR, mTOR and polykinase inhibitors (e.g., sunitinib in the management of local and disseminated disease. Towards building a consortium of pharmaceutical, academic and non-profit collaborators, we will discuss the state of resources for investigating epithelioid sarcoma with respect to cell line resources, tissue banks, and registries so that a roadmap can be developed towards effective biology-driven therapies.

  10. Epithelioid Sarcoma: Opportunities for Biology-Driven Targeted Therapy.

    Science.gov (United States)

    Noujaim, Jonathan; Thway, Khin; Bajwa, Zia; Bajwa, Ayeza; Maki, Robert G; Jones, Robin L; Keller, Charles

    2015-01-01

    Epithelioid sarcoma (ES) is a soft tissue sarcoma of children and young adults for which the preferred treatment for localized disease is wide surgical resection. Medical management is to a great extent undefined, and therefore for patients with regional and distal metastases, the development of targeted therapies is greatly desired. In this review, we will summarize clinically relevant biomarkers (e.g., SMARCB1, CA125, dysadherin, and others) with respect to targeted therapeutic opportunities. We will also examine the role of EGFR, mTOR, and polykinase inhibitors (e.g., sunitinib) in the management of local and disseminated disease. Toward building a consortium of pharmaceutical, academic, and non-profit collaborators, we will discuss the state of resources for investigating ES with respect to cell line resources, tissue banks, and registries so that a roadmap can be developed toward effective biology-driven therapies.

  11. 7th Annual Systems Biology Symposium: Systems Biology and Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Galitski, Timothy P.

    2008-04-01

    Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

  12. Integrative radiation systems biology

    International Nuclear Information System (INIS)

    Unger, Kristian

    2014-01-01

    Maximisation of the ratio of normal tissue preservation and tumour cell reduction is the main concept of radiotherapy alone or combined with chemo-, immuno- or biologically targeted therapy. The foremost parameter influencing this ratio is radiation sensitivity and its modulation towards a more efficient killing of tumour cells and a better preservation of normal tissue at the same time is the overall aim of modern therapy schemas. Nevertheless, this requires a deep understanding of the molecular mechanisms of radiation sensitivity in order to identify its key players as potential therapeutic targets. Moreover, the success of conventional approaches that tried to statistically associate altered radiation sensitivity with any molecular phenotype such as gene expression proofed to be somewhat limited since the number of clinically used targets is rather sparse. However, currently a paradigm shift is taking place from pure frequentistic association analysis to the rather holistic systems biology approach that seeks to mathematically model the system to be investigated and to allow the prediction of an altered phenotype as the function of one single or a signature of biomarkers. Integrative systems biology also considers the data from different molecular levels such as the genome, transcriptome or proteome in order to partially or fully comprehend the causal chain of molecular mechanisms. An example for the application of this concept currently carried out at the Clinical Cooperation Group “Personalized Radiotherapy in Head and Neck Cancer” of the Helmholtz-Zentrum München and the LMU Munich is described. This review article strives for providing a compact overview on the state of the art of systems biology, its actual challenges, potential applications, chances and limitations in radiation oncology research working towards improved personalised therapy concepts using this relatively new methodology

  13. Comments to accelerator-driven system

    International Nuclear Information System (INIS)

    Taka aki, Matsumoto

    2003-01-01

    Accelerator-driven system (ADS) that was a subcritical nuclear reactor driven by a high power proton accelerator was recently studied by several large organisations over the world. This paper described two comments for ADS: philosophical and technological ones. The latter was made from a view point of micro ball lightning (BL) that was newly discovered by the author. Negative and positive aspects of micro BL for ADS were discussed. (author)

  14. Logical analysis of biological systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian

    2005-01-01

    R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005.......R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005....

  15. Test-driven modeling of embedded systems

    DEFF Research Database (Denmark)

    Munck, Allan; Madsen, Jan

    2015-01-01

    To benefit maximally from model-based systems engineering (MBSE) trustworthy high quality models are required. From the software disciplines it is known that test-driven development (TDD) can significantly increase the quality of the products. Using a test-driven approach with MBSE may have...... a similar positive effect on the quality of the system models and the resulting products and may therefore be desirable. To define a test-driven model-based systems engineering (TD-MBSE) approach, we must define this approach for numerous sub disciplines such as modeling of requirements, use cases...... suggest that our method provides a sound foundation for rapid development of high quality system models....

  16. PC driven integrated vacuum system

    International Nuclear Information System (INIS)

    Curuia, Marian; Culcer, Mihai; Brandea, Iulian; Anghel, Mihai

    2001-01-01

    The monitoring of industrial plants by virtual instrumentation represents the most modern trend in the domain of electronic equipment. The integrated vacuum system presented here has several facilities, including the automated data storing of measurement results on hard disk and providing warning messages for operators when the measured parameters are lower or higher upper than the fixed values. The system can also work stand-alone, receiving the commands from the keyboards placed on his front panel but, when it is included in a automation complex system, a remote control from PC is necessary . Both parts of the system, power supply unit for turbo-molecular pump and the vacuum gage, are controlled by an 80C31 microcontroller. Because this microcontroller has a built-in circuitry for a serial communication, we established a serial communication between the PC and the power supply unit for turbo-molecular pump and the vacuum gage, according to the RS-232 hardware standard. As software, after careful evaluation of several options, we chose to develop a hybrid software packing using two different software development tools: LabVIEW, and assembly language. We chose LabVIEW because it is dedicated to data acquisition and communications, containing libraries for data collection, analysis, display and storage. (authors)

  17. Quantitative system validation in model driven design

    DEFF Research Database (Denmark)

    Hermanns, Hilger; Larsen, Kim Guldstrand; Raskin, Jean-Francois

    2010-01-01

    The European STREP project Quasimodo1 develops theory, techniques and tool components for handling quantitative constraints in model-driven development of real-time embedded systems, covering in particular real-time, hybrid and stochastic aspects. This tutorial highlights the advances made, focus...

  18. Mammalian Synthetic Biology: Engineering Biological Systems.

    Science.gov (United States)

    Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

    2017-06-21

    The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

  19. Resonances in a periodically driven bosonic system

    Science.gov (United States)

    Quelle, Anton; Smith, Cristiane Morais

    2017-11-01

    Periodically driven systems are a common topic in modern physics. In optical lattices specifically, driving is at the origin of many interesting phenomena. However, energy is not conserved in driven systems, and under periodic driving, heating of a system is a real concern. In an effort to better understand this phenomenon, the heating of single-band systems has been studied, with a focus on disorder- and interaction-induced effects, such as many-body localization. Nevertheless, driven systems occur in a much wider context than this, leaving room for further research. Here, we fill this gap by studying a noninteracting model, characterized by discrete, periodically spaced energy levels that are unbounded from above. We couple these energy levels resonantly through a periodic drive, and discuss the heating dynamics of this system as a function of the driving protocol. In this way, we show that a combination of stimulated emission and absorption causes the presence of resonant stable states. This will serve to elucidate the conditions under which resonant driving causes heating in quantum systems.

  20. Resonances in a periodically driven bosonic system.

    Science.gov (United States)

    Quelle, Anton; Smith, Cristiane Morais

    2017-11-01

    Periodically driven systems are a common topic in modern physics. In optical lattices specifically, driving is at the origin of many interesting phenomena. However, energy is not conserved in driven systems, and under periodic driving, heating of a system is a real concern. In an effort to better understand this phenomenon, the heating of single-band systems has been studied, with a focus on disorder- and interaction-induced effects, such as many-body localization. Nevertheless, driven systems occur in a much wider context than this, leaving room for further research. Here, we fill this gap by studying a noninteracting model, characterized by discrete, periodically spaced energy levels that are unbounded from above. We couple these energy levels resonantly through a periodic drive, and discuss the heating dynamics of this system as a function of the driving protocol. In this way, we show that a combination of stimulated emission and absorption causes the presence of resonant stable states. This will serve to elucidate the conditions under which resonant driving causes heating in quantum systems.

  1. Vlasov dynamics of periodically driven systems

    Science.gov (United States)

    Banerjee, Soumyadip; Shah, Kushal

    2018-04-01

    Analytical solutions of the Vlasov equation for periodically driven systems are of importance in several areas of plasma physics and dynamical systems and are usually approximated using ponderomotive theory. In this paper, we derive the plasma distribution function predicted by ponderomotive theory using Hamiltonian averaging theory and compare it with solutions obtained by the method of characteristics. Our results show that though ponderomotive theory is relatively much easier to use, its predictions are very restrictive and are likely to be very different from the actual distribution function of the system. We also analyse all possible initial conditions which lead to periodic solutions of the Vlasov equation for periodically driven systems and conjecture that the irreducible polynomial corresponding to the initial condition must only have squares of the spatial and momentum coordinate. The resulting distribution function for other initial conditions is aperiodic and can lead to complex relaxation processes within the plasma.

  2. Electromagnetic fields in biological systems

    National Research Council Canada - National Science Library

    Lin, James C

    2012-01-01

    "Focusing on exposure, induced fields, and absorbed energy, this volume covers the interaction of electromagnetic fields and waves with biological systems, spanning static fields to terahertz waves...

  3. Accelerating Science Driven System Design With RAMP

    Energy Technology Data Exchange (ETDEWEB)

    Wawrzynek, John [Univ. of California, Berkeley, CA (United States)

    2015-05-01

    Researchers from UC Berkeley, in collaboration with the Lawrence Berkeley National Lab, are engaged in developing an Infrastructure for Synthesis with Integrated Simulation (ISIS). The ISIS Project was a cooperative effort for “application-driven hardware design” that engages application scientists in the early parts of the hardware design process for future generation supercomputing systems. This project served to foster development of computing systems that are better tuned to the application requirements of demanding scientific applications and result in more cost-effective and efficient HPC system designs. In order to overcome long conventional design-cycle times, we leveraged reconfigurable devices to aid in the design of high-efficiency systems, including conventional multi- and many-core systems. The resulting system emulation/prototyping environment, in conjunction with the appropriate intermediate abstractions, provided both a convenient user programming experience and retained flexibility, and thus efficiency, of a reconfigurable platform. We initially targeted the Berkeley RAMP system (Research Accelerator for Multiple Processors) as that hardware emulation environment to facilitate and ultimately accelerate the iterative process of science-driven system design. Our goal was to develop and demonstrate a design methodology for domain-optimized computer system architectures. The tangible outcome is a methodology and tools for rapid prototyping and design-space exploration, leading to highly optimized and efficient HPC systems.

  4. Model Driven Development of Data Sensitive Systems

    DEFF Research Database (Denmark)

    Olsen, Petur

    2014-01-01

    storage systems, where the actual values of the data is not relevant for the behavior of the system. For many systems the values are important. For instance the control flow of the system can be dependent on the input values. We call this type of system data sensitive, as the execution is sensitive...... to the values of variables. This theses strives to improve model-driven development of such data-sensitive systems. This is done by addressing three research questions. In the first we combine state-based modeling and abstract interpretation, in order to ease modeling of data-sensitive systems, while allowing...... efficient model-checking and model-based testing. In the second we develop automatic abstraction learning used together with model learning, in order to allow fully automatic learning of data-sensitive systems to allow learning of larger systems. In the third we develop an approach for modeling and model-based...

  5. Excited states in biological systems

    International Nuclear Information System (INIS)

    Cilento, G.; Zinner, K.; Bechara, E.J.H.; Duran, N.; Baptista, R.C. de; Shimizu, Y.; Augusto, O.; Faljoni-Alario, A.; Vidigal, C.C.C.; Oliveira, O.M.M.F.; Haun, M.

    1979-01-01

    Some aspects of bioluminescence related to bioenergetics are discussed: 1. chemical generation of excited species, by means of two general processes: electron transference and cyclic - and linear peroxide cleavage; 2. biological systems capable of generating excited states and 3. biological functions of these states, specially the non-emissive ones (tripletes). The production and the role of non-emissive excited states in biological systems are analysed, the main purpose of the study being the search for non-emissive states. Experiences carried out in biological systems are described; results and conclusions are given. (M.A.) [pt

  6. Telemetry System of Biological Parameters

    Directory of Open Access Journals (Sweden)

    Jan Spisak

    2005-01-01

    Full Text Available The mobile telemetry system of biological parameters serves for reading and wireless data transfer of measured values of selected biological parameters to an outlying computer. It concerns basically long time monitoring of vital function of car pilot.The goal of this projects is to propose mobile telemetry system for reading, wireless transfer and processing of biological parameters of car pilot during physical and psychical stress. It has to be made with respect to minimal consumption, weight and maximal device mobility. This system has to eliminate signal noise, which is created by biological artifacts and disturbances during the data transfer.

  7. Mapping biological systems to network systems

    CERN Document Server

    Rathore, Heena

    2016-01-01

    The book presents the challenges inherent in the paradigm shift of network systems from static to highly dynamic distributed systems – it proposes solutions that the symbiotic nature of biological systems can provide into altering networking systems to adapt to these changes. The author discuss how biological systems – which have the inherent capabilities of evolving, self-organizing, self-repairing and flourishing with time – are inspiring researchers to take opportunities from the biology domain and map them with the problems faced in network domain. The book revolves around the central idea of bio-inspired systems -- it begins by exploring why biology and computer network research are such a natural match. This is followed by presenting a broad overview of biologically inspired research in network systems -- it is classified by the biological field that inspired each topic and by the area of networking in which that topic lies. Each case elucidates how biological concepts have been most successfully ...

  8. On stability of accelerator driven systems

    International Nuclear Information System (INIS)

    Makai, Mihaly

    2003-01-01

    An unsolved problem of energy production in nuclear reactors is the waste management. A large portion of the nuclear waste is the spent fuel. At present, two possibilities are seen. The first one is to 'wrap up' all the radioactive waste safely and to bury it at a remote quiet place where it can rest undisturbed until its activity decreases to a tolerable level. The second one is to exploit the excitation energy still present in the nuclear waste. In order to release that energy, the spent fuel is bombarded by high energy particles obtained from an accelerator. The resulting system is called accelerator driven system (ADS). In an ADS, the spent fuel forms a subcritical reactor, which is driven by an external source. (author)

  9. Weapon plutonium in accelerator driven power system

    International Nuclear Information System (INIS)

    Shvedov, O.V.; Murin, B.P.; Kochurov, B.P.; Shubin, Yu.M.; Volk, V.I.; Bogdanov, P.V.

    1997-01-01

    Accelerator Driven Systems are planned to be developed for the use (or destruction) of dozens of tons of weapon-grade Plutonium (W-Pu) resulted from the reducing of nuclear weapons. In the paper are compared the parameters of various types of accelerators, the physical properties of various types of targets and blankets, and the results of fuel cycle simulation. Some economical aspects are also discussed

  10. Static Analysis for Systems Biology

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis; Rosa, D. Schuch da

    2004-01-01

    This paper shows how static analysis techniques can help understanding biological systems. Based on a simple example we illustrate the outcome of performing three different analyses extracting information of increasing precision. We conclude by reporting on the potential impact and exploitation o...... of these techniques in systems biology....

  11. Systems biology and medicine

    Indian Academy of Sciences (India)

    work could potentially provide us with ways to identify drug ... appropriately balance cause, effect, and context of a given clinical ... would not provide answers/solutions to multitude of tasks that were ... a major challenge of contemporary biology is to embark on an ... nificantly govern the life and responsiveness of cells.

  12. A stress driven growth model for soft tissue considering biological availability

    International Nuclear Information System (INIS)

    Oller, S; Bellomo, F J; Nallim, L G; Armero, F

    2010-01-01

    Some of the key factors that regulate growth and remodeling of tissues are fundamentally mechanical. However, it is important to take into account the role of bioavailability together with the stresses and strains in the processes of normal or pathological growth. In this sense, the model presented in this work is oriented to describe the growth of soft biological tissue under 'stress driven growth' and depending on the biological availability of the organism. The general theoretical framework is given by a kinematic formulation in large strain combined with the thermodynamic basis of open systems. The formulation uses a multiplicative decomposition of deformation gradient, splitting it in a growth part and visco-elastic part. The strains due to growth are incompatible and are controlled by an unbalanced stresses related to a homeostatic state. Growth implies a volume change with an increase of mass maintaining constant the density. One of the most interesting features of the proposed model is the generation of new tissue taking into account the contribution of mass to the system controlled through biological availability. Because soft biological tissues in general have a hierarchical structure with several components (usually a soft matrix reinforced with collagen fibers), the developed growth model is suitable for the characterization of the growth of each component. This allows considering a different behavior for each of them in the context of a generalized theory of mixtures. Finally, we illustrate the response of the model in case of growth and atrophy with an application example.

  13. The Case for "Story-Driven" Biology Education

    Science.gov (United States)

    Schattner, Peter

    2015-01-01

    Can learning molecular biology and genetics be enjoyable? Of course it can. Biologists know their field is exciting and fascinating and that learning how cells and molecules shape the living world is extraordinarily interesting. But can students who are not already inclined towards science also be convinced that learning molecular biology is…

  14. "A mission-driven discipline": the growth of conservation biology.

    Science.gov (United States)

    Meine, Curt; Soulé, Michael; Noss, Reed E

    2006-06-01

    Conservation biology emerged in the mid-1980s, drawing on established disciplines and integrating them in pursuit of a coherent goal: the protection and perpetuation of the Earth's biological diversity. Opportunistic in its borrowing and application of knowledge, conservation biology had its roots within the established biological sciences and resource management disciplines but has continually incorporated insights from the empirical experience of resource managers, from the social sciences and humanities, and from diverse cultural sources. The Society for Conservation Biology (SCB) has represented the field's core constituency, while expanding that constituency in keeping with the field's integrative spirit. Conservation Biology has served as SCB's flagship publication, promoting research, dialog, debate, and application of the field's essential concepts. Over the last 20 years the field, SCB, and the journal have evolved to meet changing conservation needs, to explore gaps in our knowledge base, to incorporate new information from related fields, to build professional capacity, and to provide expanded opportunities for international participation. In turn, the field, SCB, and journal have prompted change in related fields, organizations, and publications. In its dedication to advancing the scientific foundations of biodiversity conservation and placing that science at the service of society in a world whose variety, wildness, and beauty we care for conservation biology represents both a continuation and radical reconfiguration of the traditional relationship between science and conservation.

  15. Quantum Effects in Biological Systems

    CERN Document Server

    2016-01-01

    Since the last decade the study of quantum mechanical phenomena in biological systems has become a vibrant field of research. Initially sparked by evidence of quantum effects in energy transport that is instrumental for photosynthesis, quantum biology asks the question of how methods and models from quantum theory can help us to understand fundamental mechanisms in living organisms. This approach entails a paradigm change challenging the related disciplines: The successful framework of quantum theory is taken out of its low-temperature, microscopic regimes and applied to hot and dense macroscopic environments, thereby extending the toolbox of biology and biochemistry at the same time. The Quantum Effects in Biological Systems conference is a platform for researchers from biology, chemistry and physics to present and discuss the latest developments in the field of quantum biology. After meetings in Lisbon (2009), Harvard (2010), Ulm (2011), Berkeley (2012), Vienna (2013), Singapore (2014) and Florence (2015),...

  16. Asymptotic work distributions in driven bistable systems

    International Nuclear Information System (INIS)

    Nickelsen, D; Engel, A

    2012-01-01

    The asymptotic tails of the probability distributions of thermodynamic quantities convey important information about the physics of nanoscopic systems driven out of equilibrium. We apply a recently proposed method to analytically determine the asymptotics of work distributions in Langevin systems to an one-dimensional model of single-molecule force spectroscopy. The results are in excellent agreement with numerical simulations, even in the centre of the distributions. We compare our findings with a recent proposal for an universal form of the asymptotics of work distributions in single-molecule experiments.

  17. Heuristic Strategies in Systems Biology

    Directory of Open Access Journals (Sweden)

    Fridolin Gross

    2016-06-01

    Full Text Available Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences.

  18. Statistical mechanics of driven diffusive systems

    CERN Document Server

    Schmittmann, B

    1995-01-01

    Far-from-equilibrium phenomena, while abundant in nature, are not nearly as well understood as their equilibrium counterparts. On the theoretical side, progress is slowed by the lack of a simple framework, such as the Boltzmann-Gbbs paradigm in the case of equilibrium thermodynamics. On the experimental side, the enormous structural complexity of real systems poses serious obstacles to comprehension. Similar difficulties have been overcome in equilibrium statistical mechanics by focusing on model systems. Even if they seem too simplistic for known physical systems, models give us considerable insight, provided they capture the essential physics. They serve as important theoretical testing grounds where the relationship between the generic physical behavior and the key ingredients of a successful theory can be identified and understood in detail. Within the vast realm of non-equilibrium physics, driven diffusive systems form a subset with particularly interesting properties. As a prototype model for these syst...

  19. Compartmental study of biological systems

    International Nuclear Information System (INIS)

    Moretti, J.L.

    1975-01-01

    The compartmental analysis of biological system is dealt with on several chapters devoted successively to: terminology; a mathematical and symbolic account of a system at equilibrium; different compartment systems; analysis of the experimental results. For this it is pointed out that the application of compartmental systems to biological phenomena is not always without danger. Sometimes the compartmental system established in a reference subject fails to conform in the patient. The compartments can divide into two or join together, completely changing the aspect of the system so that parameters calculated with the old model become entirely false. The conclusion is that the setting up of a compartmental system to represent a biological phenomenon is a tricky undertaking and the results must be constantly criticized and questioned [fr

  20. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many...

  1. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many......In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...

  2. Informing biological design by integration of systems and synthetic biology.

    Science.gov (United States)

    Smolke, Christina D; Silver, Pamela A

    2011-03-18

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Development trend of radiation biology research-systems radiation biology

    International Nuclear Information System (INIS)

    Min Rui

    2010-01-01

    Radiation biology research has past 80 years. We have known much more about fundamentals, processes and results of biology effects induced by radiation and various factors that influence biology effects wide and deep, however many old and new scientific problems occurring in the field of radiation biology research remain to be illustrated. To explore and figure these scientific problems need systemic concept, methods and multi dimension view on the base of considerations of complexity of biology system, diversity of biology response, temporal and spatial process of biological effects during occurrence, and complex feed back network of biological regulations. (authors)

  4. Minor actinide transmutation in accelerator driven systems

    Energy Technology Data Exchange (ETDEWEB)

    Friess, Friederike [IANUS, TU Darmstadt (Germany)

    2015-07-01

    Transmutation of radioactive waste, the legacy of nuclear energy use, gains rising interest. This includes the development of facilities able to transmute minor actinides (MA) into stable or short-lived isotopes before final disposal. The most common proposal is to use a double-strata approach with accelerator-driven-systems (ADS) for the efficient transmutation of MA and power reactors to dispose plutonium. An ADS consists of a sub-critical core that reaches criticality with neutrons supplied by a spallation target. An MCNP model of the ADS system Multi Purpose Research Reactor for Hightech Applications will be presented. Depletion calculations have been performed for both standard MOX fuel and transmutation fuel with an increased content of minor actinides. The resulting transmutation rates for MAs are compared to published values. Special attention is given to selected fission products such as Tc-99 and I-129, which impact the radiation from the spent fuel significantly.

  5. From systems biology to systems biomedicine.

    Science.gov (United States)

    Antony, Paul M A; Balling, Rudi; Vlassis, Nikos

    2012-08-01

    Systems Biology is about combining theory, technology, and targeted experiments in a way that drives not only data accumulation but knowledge as well. The challenge in Systems Biomedicine is to furthermore translate mechanistic insights in biological systems to clinical application, with the central aim of improving patients' quality of life. The challenge is to find theoretically well-chosen models for the contextually correct and intelligible representation of multi-scale biological systems. In this review, we discuss the current state of Systems Biology, highlight the emergence of Systems Biomedicine, and highlight some of the topics and views that we think are important for the efficient application of Systems Theory in Biomedicine. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Inverse problems in systems biology

    International Nuclear Information System (INIS)

    Engl, Heinz W; Lu, James; Müller, Stefan; Flamm, Christoph; Schuster, Peter; Kügler, Philipp

    2009-01-01

    Systems biology is a new discipline built upon the premise that an understanding of how cells and organisms carry out their functions cannot be gained by looking at cellular components in isolation. Instead, consideration of the interplay between the parts of systems is indispensable for analyzing, modeling, and predicting systems' behavior. Studying biological processes under this premise, systems biology combines experimental techniques and computational methods in order to construct predictive models. Both in building and utilizing models of biological systems, inverse problems arise at several occasions, for example, (i) when experimental time series and steady state data are used to construct biochemical reaction networks, (ii) when model parameters are identified that capture underlying mechanisms or (iii) when desired qualitative behavior such as bistability or limit cycle oscillations is engineered by proper choices of parameter combinations. In this paper we review principles of the modeling process in systems biology and illustrate the ill-posedness and regularization of parameter identification problems in that context. Furthermore, we discuss the methodology of qualitative inverse problems and demonstrate how sparsity enforcing regularization allows the determination of key reaction mechanisms underlying the qualitative behavior. (topical review)

  7. Nanoscale technology in biological systems

    CERN Document Server

    Greco, Ralph S; Smith, R Lane

    2004-01-01

    Reviewing recent accomplishments in the field of nanobiology Nanoscale Technology in Biological Systems introduces the application of nanoscale matrices to human biology. It focuses on the applications of nanotechnology fabrication to biomedical devices and discusses new physical methods for cell isolation and manipulation and intracellular communication at the molecular level. It also explores the application of nanobiology to cardiovascular diseases, oncology, transplantation, and a range of related disciplines. This book build a strong background in nanotechnology and nanobiology ideal for

  8. Traffic and related self-driven many-particle systems

    Science.gov (United States)

    Helbing, Dirk

    2001-10-01

    Since the subject of traffic dynamics has captured the interest of physicists, many surprising effects have been revealed and explained. Some of the questions now understood are the following: Why are vehicles sometimes stopped by ``phantom traffic jams'' even though drivers all like to drive fast? What are the mechanisms behind stop-and-go traffic? Why are there several different kinds of congestion, and how are they related? Why do most traffic jams occur considerably before the road capacity is reached? Can a temporary reduction in the volume of traffic cause a lasting traffic jam? Under which conditions can speed limits speed up traffic? Why do pedestrians moving in opposite directions normally organize into lanes, while similar systems ``freeze by heating''? All of these questions have been answered by applying and extending methods from statistical physics and nonlinear dynamics to self-driven many-particle systems. This article considers the empirical data and then reviews the main approaches to modeling pedestrian and vehicle traffic. These include microscopic (particle-based), mesoscopic (gas-kinetic), and macroscopic (fluid-dynamic) models. Attention is also paid to the formulation of a micro-macro link, to aspects of universality, and to other unifying concepts, such as a general modeling framework for self-driven many-particle systems, including spin systems. While the primary focus is upon vehicle and pedestrian traffic, applications to biological or socio-economic systems such as bacterial colonies, flocks of birds, panics, and stock market dynamics are touched upon as well.

  9. Driven topological systems in the classical limit

    Science.gov (United States)

    Duncan, Callum W.; Öhberg, Patrik; Valiente, Manuel

    2017-03-01

    Periodically driven quantum systems can exhibit topologically nontrivial behavior, even when their quasienergy bands have zero Chern numbers. Much work has been conducted on noninteracting quantum-mechanical models where this kind of behavior is present. However, the inclusion of interactions in out-of-equilibrium quantum systems can prove to be quite challenging. On the other hand, the classical counterpart of hard-core interactions can be simulated efficiently via constrained random walks. The noninteracting model, proposed by Rudner et al. [Phys. Rev. X 3, 031005 (2013), 10.1103/PhysRevX.3.031005], has a special point for which the system is equivalent to a classical random walk. We consider the classical counterpart of this model, which is exact at a special point even when hard-core interactions are present, and show how these quantitatively affect the edge currents in a strip geometry. We find that the interacting classical system is well described by a mean-field theory. Using this we simulate the dynamics of the classical system, which show that the interactions play the role of Markovian, or time-dependent disorder. By comparing the evolution of classical and quantum edge currents in small lattices, we find regimes where the classical limit considered gives good insight into the quantum problem.

  10. Workshop Introduction: Systems Biology and Biological Models

    Science.gov (United States)

    As we consider the future of toxicity testing, the importance of applying biological models to this problem is clear. Modeling efforts exist along a continuum with respect to the level of organization (e.g. cell, tissue, organism) linked to the resolution of the model. Generally,...

  11. Systems biology approach to bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

    2012-06-01

    Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

  12. Motility-driven glass and jamming transitions in biological tissues

    Science.gov (United States)

    Bi, Dapeng; Yang, Xingbo; Marchetti, M. Cristina; Manning, M. Lisa

    2017-01-01

    Cell motion inside dense tissues governs many biological processes, including embryonic development and cancer metastasis, and recent experiments suggest that these tissues exhibit collective glassy behavior. To make quantitative predictions about glass transitions in tissues, we study a self-propelled Voronoi (SPV) model that simultaneously captures polarized cell motility and multi-body cell-cell interactions in a confluent tissue, where there are no gaps between cells. We demonstrate that the model exhibits a jamming transition from a solid-like state to a fluid-like state that is controlled by three parameters: the single-cell motile speed, the persistence time of single-cell tracks, and a target shape index that characterizes the competition between cell-cell adhesion and cortical tension. In contrast to traditional particulate glasses, we are able to identify an experimentally accessible structural order parameter that specifies the entire jamming surface as a function of model parameters. We demonstrate that a continuum Soft Glassy Rheology model precisely captures this transition in the limit of small persistence times, and explain how it fails in the limit of large persistence times. These results provide a framework for understanding the collective solid-to-liquid transitions that have been observed in embryonic development and cancer progression, which may be associated with Epithelial-to-Mesenchymal transition in these tissues. PMID:28966874

  13. Community-driven computational biology with Debian Linux.

    Science.gov (United States)

    Möller, Steffen; Krabbenhöft, Hajo Nils; Tille, Andreas; Paleino, David; Williams, Alan; Wolstencroft, Katy; Goble, Carole; Holland, Richard; Belhachemi, Dominique; Plessy, Charles

    2010-12-21

    The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers.

  14. Systems biology: the reincarnation of systems theory applied in biology?

    Science.gov (United States)

    Wolkenhauer, O

    2001-09-01

    With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task. This is, however, not the first time that systems theory has been applied in modelling cellular processes. Notably in the 1960s systems theory and biology enjoyed considerable interest among eminent scientists, mathematicians and engineers. Why did these early attempts vanish from research agendas? Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen. Rosen emerged from the early developments in the 1960s as a main critic but also developed a new alternative perspective to living systems, a concept that deserves a fresh look in the post-genome era of bioinformatics.

  15. Kinetic parameters for source driven systems

    International Nuclear Information System (INIS)

    Dulla, S.; Ravetto, P.; Carta, M.; D'Angelo, A.

    2006-01-01

    The definition of the characteristic kinetic parameters of a subcritical source-driven system constitutes an interesting problem in reactor physics with important consequences for practical applications. Consistent and physically meaningful values of the parameters allow to obtain accurate results from kinetic simulation tools and to correctly interpret kinetic experiments. For subcritical systems a preliminary problem arises for the adoption of a suitable weighting function to be used in the projection procedure to derive a point model. The present work illustrates a consistent factorization-projection procedure which leads to the definition of the kinetic parameters in a straightforward manner. The reactivity term is introduced coherently with the generalized perturbation theory applied to the source multiplication factor ks, which is thus given a physical role in the kinetic model. The effective prompt lifetime is introduced on the assumption that a neutron generation can be initiated by both the fission process and the source emission. Results are presented for simplified configurations to fully comprehend the physical features and for a more complicated highly decoupled system treated in transport theory. (authors)

  16. Tunable promoters in systems biology

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Jensen, Peter Ruhdal

    2005-01-01

    The construction of synthetic promoter libraries has represented a major breakthrough in systems biology, enabling the subtle tuning of enzyme activities. A number of tools are now available that allow the modulation of gene expression and the detection of changes in expression patterns. But, how...

  17. 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.

  18. Uncertainty assessment for accelerator-driven systems

    International Nuclear Information System (INIS)

    Finck, P. J.; Gomes, I.; Micklich, B.; Palmiotti, G.

    1999-01-01

    The concept of a subcritical system driven by an external source of neutrons provided by an accelerator ADS (Accelerator Driver System) has been recently revived and is becoming more popular in the world technical community with active programs in Europe, Russia, Japan, and the U.S. A general consensus has been reached in adopting for the subcritical component a fast spectrum liquid metal cooled configuration. Both a lead-bismuth eutectic, sodium and gas are being considered as a coolant; each has advantages and disadvantages. The major expected advantage is that subcriticality avoids reactivity induced transients. The potentially large subcriticality margin also should allow for the introduction of very significant quantities of waste products (minor Actinides and Fission Products) which negatively impact the safety characteristics of standard cores. In the U.S. these arguments are the basis for the development of the Accelerator Transmutation of Waste (ATW), which has significant potential in reducing nuclear waste levels. Up to now, neutronic calculations have not attached uncertainties on the values of the main nuclear integral parameters that characterize the system. Many of these parameters (e.g., degree of subcriticality) are crucial to demonstrate the validity and feasibility of this concept. In this paper we will consider uncertainties related to nuclear data only. The present knowledge of the cross sections of many isotopes that are not usually utilized in existing reactors (like Bi, Pb-207, Pb-208, and also Minor Actinides and Fission Products) suggests that uncertainties in the integral parameters will be significantly larger than for conventional reactor systems, and this raises concerns on the neutronic performance of those systems

  19. Dynamical critical phenomena in driven-dissipative systems.

    Science.gov (United States)

    Sieberer, L M; Huber, S D; Altman, E; Diehl, S

    2013-05-10

    We explore the nature of the Bose condensation transition in driven open quantum systems, such as exciton-polariton condensates. Using a functional renormalization group approach formulated in the Keldysh framework, we characterize the dynamical critical behavior that governs decoherence and an effective thermalization of the low frequency dynamics. We identify a critical exponent special to the driven system, showing that it defines a new dynamical universality class. Hence critical points in driven systems lie beyond the standard classification of equilibrium dynamical phase transitions. We show how the new critical exponent can be probed in experiments with driven cold atomic systems and exciton-polariton condensates.

  20. Systems Biology-an interdisciplinary approach.

    Science.gov (United States)

    Friboulet, Alain; Thomas, Daniel

    2005-06-15

    System-level approaches in biology are not new but foundations of "Systems Biology" are achieved only now at the beginning of the 21st century [Kitano, H., 2001. Foundations of Systems Biology. MIT Press, Cambridge, MA]. The renewed interest for a system-level approach is linked to the progress in collecting experimental data and to the limits of the "reductionist" approach. System-level understanding of native biological and pathological systems is needed to provide potential therapeutic targets. Examples of interdisciplinary approach in Systems Biology are described in U.S., Japan and Europe. Robustness in biology, metabolic engineering and idiotypic networks are discussed in the framework of Systems Biology.

  1. Mathematical methods in systems biology.

    Science.gov (United States)

    Kashdan, Eugene; Duncan, Dominique; Parnell, Andrew; Schattler, Heinz

    2016-12-01

    The editors of this Special Issue of Mathematical Biosciences and Engineering were the organizers for the Third International Workshop "Mathematical Methods in System Biology" that took place on June 15-18, 2015 at the University College Dublin in Ireland. As stated in the workshop goals, we managed to attract a good mix of mathematicians and statisticians working on biological and medical applications with biologists and clinicians interested in presenting their challenging problems and looking to find mathematical and statistical tools for their solutions.

  2. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Bor-Sen Chen

    2013-10-01

    Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  3. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  4. Carbon nanomaterials in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Pu Chun Ke [Laboratory of Single-Molecule Biophysics and Polymer Physics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634 (United States); Qiao Rui [Department of Mechanical Engineering, Clemson University, Clemson, SC 29634 (United States)

    2007-09-19

    This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

  5. Systems Biology of the Fluxome

    Directory of Open Access Journals (Sweden)

    Miguel A. Aon

    2015-07-01

    Full Text Available The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. Systems biology-inspired computational methods for translating metabolomics data into fluxomics provide a direct functional, dynamic readout of metabolic networks. When combined with appropriate experimental design, these methods deliver insightful knowledge about cellular function under diverse conditions. The use of computational models accounting for detailed kinetics and regulatory mechanisms allow us to unravel the control and regulatory properties of the fluxome under steady and time-dependent behaviors. This approach extends the analysis of complex systems from description to prediction, including control of complex dynamic behavior ranging from biological rhythms to catastrophic lethal arrhythmias. The powerful quantitative metabolomics-fluxomics approach will help our ability to engineer unicellular and multicellular organisms evolve from trial-and-error to a more predictable process, and from cells to organ and organisms.

  6. Carbon nanomaterials in biological systems

    International Nuclear Information System (INIS)

    Pu Chun Ke; Qiao Rui

    2007-01-01

    This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

  7. Analyzing the Biology on the System Level

    OpenAIRE

    Tong, Wei

    2016-01-01

    Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

  8. Biological Potential in Serpentinizing Systems

    Science.gov (United States)

    Hoehler, Tori M.

    2016-01-01

    Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

  9. Anion binding in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Feiters, Martin C [Department of Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Meyer-Klaucke, Wolfram [EMBL Hamburg Outstation at DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Kostenko, Alexander V; Soldatov, Alexander V [Faculty of Physics, Southern Federal University, Sorge 5, Rostov-na-Donu, 344090 (Russian Federation); Leblanc, Catherine; Michel, Gurvan; Potin, Philippe [Centre National de la Recherche Scientifique and Universite Pierre et Marie Curie Paris-VI, Station Biologique de Roscoff, Place Georges Teissier, BP 74, F-29682 Roscoff cedex, Bretagne (France); Kuepper, Frithjof C [Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, Scotland (United Kingdom); Hollenstein, Kaspar; Locher, Kaspar P [Institute of Molecular Biology and Biophysics, ETH Zuerich, Schafmattstrasse 20, Zuerich, 8093 (Switzerland); Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R, E-mail: m.feiters@science.ru.n [Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft (Netherlands)

    2009-11-15

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L{sub 3} (2p{sub 3/2}) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  10. Anion binding in biological systems

    International Nuclear Information System (INIS)

    Feiters, Martin C; Meyer-Klaucke, Wolfram; Kostenko, Alexander V; Soldatov, Alexander V; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Kuepper, Frithjof C; Hollenstein, Kaspar; Locher, Kaspar P; Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R

    2009-01-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L 3 (2p 3/2 ) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  11. Anion binding in biological systems

    Science.gov (United States)

    Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

    2009-11-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  12. Materials issues in accelerator driven-systems

    International Nuclear Information System (INIS)

    Al Mazouzi, A.

    2008-01-01

    Full text of publication follows. Nuclear energy has to cope with critical topics to resolve the economical question of increasing energy demand and, in particular, the public acceptability demands: - increasing the absolute safety of the installations; - managing more efficiently the nuclear waste; In that respect, the development of a new type of nuclear installation coping with above constraints of technological as well as socio-economical nature may be of high importance for the future of sustainable energy provision. An accelerator-driven system (ADS) - a subcritical core, operated as a waste burner for minor actinides (MAs) and long-lived fission products (LLFPs) or as nuclear amplifier for energy production, fed with primary neutrons by a spallation source - has the potential to cope with above constraints and to pave the way to a more environmentally safe and acceptable nuclear energy production. Within the framework of EUROTRANS, the European community has launched a broad R and D programme in collaboration with partners from Europe and abroad (USA, Japan), to address the technical, technological and fundamental issues related to the realisation of an experimental machine that is intended to allow: - continuation, and extension of the present knowledge towards ADS, in the field of reactor materials, fuel and reactor physics research; - enhancement and triggering of new R and D activities such as nuclear waste transmutation, ADS technology, liquid metal embrittlement, The present lecture will cover the main aspects of the design of an experimental XT-ADS taking as example the work that has been performed at SCK.CEN within MYRRHA project. The safety aspect of such machine will be addressed on terms of structural material performance, with emphasis on issues related to the interaction between structural materials (austenitic and ferritic martensitic steels) and the liquid metal coolant (lead-alloys). Finally, a discussion will be given on the open issues and

  13. System driven technology selection for future European launch systems

    Science.gov (United States)

    Baiocco, P.; Ramusat, G.; Sirbi, A.; Bouilly, Th.; Lavelle, F.; Cardone, T.; Fischer, H.; Appel, S.

    2015-02-01

    In the framework of the next generation launcher activity at ESA, a top-down approach and a bottom-up approach have been performed for the identification of promising technologies and alternative conception of future European launch vehicles. The top-down approach consists in looking for system-driven design solutions and the bottom-up approach features design solutions leading to substantial advantages for the system. The main investigations have been focused on the future launch vehicle technologies. Preliminary specifications have been used in order to permit sub-system design to find the major benefit for the overall launch system. The development cost, non-recurring and recurring cost, industrialization and operational aspects have been considered as competitiveness factors for the identification and down-selection of the most interesting technologies. The recurring cost per unit payload mass has been evaluated. The TRL/IRL has been assessed and a preliminary development plan has been traced for the most promising technologies. The potentially applicable launch systems are Ariane and VEGA evolution. The main FLPP technologies aim at reducing overall structural mass, increasing structural margins for robustness, metallic and composite containment of cryogenic hydrogen and oxygen propellants, propellant management subsystems, elements significantly reducing fabrication and operational costs, avionics, pyrotechnics, etc. to derive performing upper and booster stages. Application of the system driven approach allows creating performing technology demonstrators in terms of need, demonstration objective, size and cost. This paper outlines the process of technology down selection using a system driven approach, the accomplishments already achieved in the various technology fields up to now, as well as the potential associated benefit in terms of competitiveness factors.

  14. Nonlinear dynamics in biological systems

    CERN Document Server

    Carballido-Landeira, Jorge

    2016-01-01

    This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied math...

  15. High power radiation guiding systems for laser driven accelerators

    International Nuclear Information System (INIS)

    Cutolo, A.

    1985-01-01

    This paper reviews the main problems encountered in the design of an optical system for transmitting high fluence radiation in a laser driven accelerator. Particular attention is devoted to the analysis of mirror and waveguide systems. (orig.)

  16. Problems in the neutron dynamics of source-driven systems

    International Nuclear Information System (INIS)

    Ravetto, P.

    2001-01-01

    The present paper presents some neutronic features of source-driven neutron multiplying systems, with special regards to dynamics, discussing the validity and limitations of classical methods, developed for systems in the vicinity of criticality. Specific characteristics, such as source dominance and the role of delayed neutron emissions are illustrated. Some dynamic peculiarities of innovative concepts proposed for accelerator-driven systems, such as fluid-fuel, are also discussed. The second portion of the work formulates the quasi-static methods for source-driven systems, evidencing its novel features and presenting some numerical results. (author)

  17. Real-space renormalization group approach to driven diffusive systems

    Energy Technology Data Exchange (ETDEWEB)

    Hanney, T [SUPA and School of Physics, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ (United Kingdom); Stinchcombe, R B [Theoretical Physics, 1 Keble Road, Oxford, OX1 3NP (United Kingdom)

    2006-11-24

    We introduce a real-space renormalization group procedure for driven diffusive systems which predicts both steady state and dynamic properties. We apply the method to the boundary driven asymmetric simple exclusion process and recover exact results for the steady state phase diagram, as well as the crossovers in the relaxation dynamics for each phase.

  18. Real-space renormalization group approach to driven diffusive systems

    International Nuclear Information System (INIS)

    Hanney, T; Stinchcombe, R B

    2006-01-01

    We introduce a real-space renormalization group procedure for driven diffusive systems which predicts both steady state and dynamic properties. We apply the method to the boundary driven asymmetric simple exclusion process and recover exact results for the steady state phase diagram, as well as the crossovers in the relaxation dynamics for each phase

  19. Coherent states of the driven Rydberg atom: Quantum-classical correspondence of periodically driven systems

    International Nuclear Information System (INIS)

    Vela-Arevalo, Luz V.; Fox, Ronald F.

    2005-01-01

    A methodology to calculate generalized coherent states for a periodically driven system is presented. We study wave packets constructed as a linear combination of suitable Floquet states of the three-dimensional Rydberg atom in a microwave field. The driven coherent states show classical space localization, spreading, and revivals and remain localized along the classical trajectory. The microwave strength and frequency have a great effect in the localization of Floquet states, since quasienergy avoided crossings produce delocalization of the Floquet states, showing that tuning of the parameters is very important. Using wavelet-based time-frequency analysis, the classical phase-space structure is determined, which allows us to show that the driven coherent state is located in a large regular region in which the z coordinate is in resonance with the external field. The expectation values of the wave packet show that the driven coherent state evolves along the classical trajectory

  20. [Network structures in biological systems].

    Science.gov (United States)

    Oleskin, A V

    2013-01-01

    Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

  1. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  2. Systems biology and biomarker discovery

    Energy Technology Data Exchange (ETDEWEB)

    Rodland, Karin D.

    2010-12-01

    Medical practitioners have always relied on surrogate markers of inaccessible biological processes to make their diagnosis, whether it was the pallor of shock, the flush of inflammation, or the jaundice of liver failure. Obviously, the current implementation of biomarkers for disease is far more sophisticated, relying on highly reproducible, quantitative measurements of molecules that are often mechanistically associated with the disease in question, as in glycated hemoglobin for the diagnosis of diabetes [1] or the presence of cardiac troponins in the blood for confirmation of myocardial infarcts [2]. In cancer, where the initial symptoms are often subtle and the consequences of delayed diagnosis often drastic for disease management, the impetus to discover readily accessible, reliable, and accurate biomarkers for early detection is compelling. Yet despite years of intense activity, the stable of clinically validated, cost-effective biomarkers for early detection of cancer is pathetically small and still dominated by a handful of markers (CA-125, CEA, PSA) first discovered decades ago. It is time, one could argue, for a fresh approach to the discovery and validation of disease biomarkers, one that takes full advantage of the revolution in genomic technologies and in the development of computational tools for the analysis of large complex datasets. This issue of Disease Markers is dedicated to one such new approach, loosely termed the 'Systems Biology of Biomarkers'. What sets the Systems Biology approach apart from other, more traditional approaches, is both the types of data used, and the tools used for data analysis - and both reflect the revolution in high throughput analytical methods and high throughput computing that has characterized the start of the twenty first century.

  3. Radical production in biological systems

    International Nuclear Information System (INIS)

    Johnson, J.R.; Akabani, G.

    1994-10-01

    This paper describes our effort to develop a metric for radiation exposure that is more fundamental than adsorbed dose and upon which a metric for exposure to chemicals could be based. This metric is based on the production of radicals by the two agents. Radicals produced by radiation in biological systems commonly assumed to be the same as those produced in water despite the presence of a variety of complex molecules. This may explain why the extensive efforts to describe the relationship between energy deposition (track structure) and molecular damage to DNA, based on the spectrum of radicals produced, have not been successful in explaining simple biological effects such as cell killing. Current models assume that DNA and its basic elements are immersed in water-like media and only model the production and diffusion of water-based radicals and their interaction with DNA structures; these models lack the cross sections associated with each macro-component of DNA and only treat water-based radicals. It has been found that such models are not realistic because DNA is not immersed in pure water. A computer code capable of simulating electron tracks, low-energy electrons, energy deposition in small molecules, and radical production and diffusion in water like media has been developed. This code is still in at a primitive stage and development is continuing. It is being used to study radical production by radiation, and radical diffusion and interactions in simple molecular systems following their production. We are extending the code to radical production by chemicals to complement our PBPK modeling efforts. It therefore has been developed primarily for use with radionuclides that are in biological materials, and not for radiation fields

  4. Integrating phosphoproteomics in systems biology

    Directory of Open Access Journals (Sweden)

    Yu Liu

    2014-07-01

    Full Text Available Phosphorylation of serine, threonine and tyrosine plays significant roles in cellular signal transduction and in modifying multiple protein functions. Phosphoproteins are coordinated and regulated by a network of kinases, phosphatases and phospho-binding proteins, which modify the phosphorylation states, recognize unique phosphopeptides, or target proteins for degradation. Detailed and complete information on the structure and dynamics of these networks is required to better understand fundamental mechanisms of cellular processes and diseases. High-throughput technologies have been developed to investigate phosphoproteomes in model organisms and human diseases. Among them, mass spectrometry (MS-based technologies are the major platforms and have been widely applied, which has led to explosive growth of phosphoproteomic data in recent years. New bioinformatics tools are needed to analyze and make sense of these data. Moreover, most research has focused on individual phosphoproteins and kinases. To gain a more complete knowledge of cellular processes, systems biology approaches, including pathways and networks modeling, have to be applied to integrate all components of the phosphorylation machinery, including kinases, phosphatases, their substrates, and phospho-binding proteins. This review presents the latest developments of bioinformatics methods and attempts to apply systems biology to analyze phosphoproteomics data generated by MS-based technologies. Challenges and future directions in this field will be also discussed.

  5. Systems biology of fungal infection

    Directory of Open Access Journals (Sweden)

    Fabian eHorn

    2012-04-01

    Full Text Available Elucidation of pathogenicity mechanisms of the most important human pathogenic fungi, Aspergillus fumigatus and Candida albicans, has gained great interest in the light of the steadily increasing number of cases of invasive fungal infections.A key feature of these infections is the interaction of the different fungal morphotypes with epithelial and immune effector cells in the human host. Because of the high level of complexity, it is necessary to describe and understand invasive fungal infection by taking a systems biological approach, i.e., by a comprehensive quantitative analysis of the non-linear and selective interactions of a large number of functionally diverse, and frequently multifunctional, sets of elements, e.g., genes, proteins, metabolites, which produce coherent and emergent behaviours in time and space. The recent advances in systems biology will now make it possible to uncover the structure and dynamics of molecular and cellular cause-effect relationships within these pathogenic interactions.We review current efforts to integrate omics and image-based data of host-pathogen interactions into network and spatio-temporal models. The modelling will help to elucidate pathogenicity mechanisms and to identify diagnostic biomarkers and potential drug targets for therapy and could thus pave the way for novel intervention strategies based on novel antifungal drugs and cell therapy.

  6. Dynamical systems in population biology

    CERN Document Server

    Zhao, Xiao-Qiang

    2017-01-01

    This research monograph provides an introduction to the theory of nonautonomous semiflows with applications to population dynamics. It develops dynamical system approaches to various evolutionary equations such as difference, ordinary, functional, and partial differential equations, and pays more attention to periodic and almost periodic phenomena. The presentation includes persistence theory, monotone dynamics, periodic and almost periodic semiflows, basic reproduction ratios, traveling waves, and global analysis of prototypical population models in ecology and epidemiology. Research mathematicians working with nonlinear dynamics, particularly those interested in applications to biology, will find this book useful. It may also be used as a textbook or as supplementary reading for a graduate special topics course on the theory and applications of dynamical systems. Dr. Xiao-Qiang Zhao is a University Research Professor at Memorial University of Newfoundland, Canada. His main research interests involve applied...

  7. Institute for Genomics and Systems Biology

    Science.gov (United States)

    Institute for Genomics and Systems Biology Discover. Predict. Improve. Advancing Human and , 2015 See all Research Papers Featured Video Introduction to Systems Biology Video: Introduction to Systems Biology News Jack Gilbert Heading UChicago Startup that Aims to Predict Behavior of Trillions of

  8. Answering biological questions: Querying a systems biology database for nutrigenomics

    NARCIS (Netherlands)

    Evelo, C.T.; Bochove, K. van; Saito, J.T.

    2011-01-01

    The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A

  9. Nuclear data requirements for accelerator driven sub-critical systems

    Indian Academy of Sciences (India)

    The development of accelerator driven sub-critical systems (ADSS) require significant amount of new nuclear data in extended energy regions as well as for a variety of new materials. This paper reviews these perspectives in the Indian context.

  10. Accelerator driven radiation clean nuclear power system conceptual research symposium

    International Nuclear Information System (INIS)

    Zhao Zhixiang

    2000-06-01

    The R and D of ADS (Accelerators Driven Subcritical System) in China introduced. 31 theses are presented. It includes the basic principle of ADS, accelerators, sub-critical reactors, neutron physics, nuclear data, partitioning and transmutation

  11. Chip Integrated, Hybrid EHD/Capillary Driven Thermal Management System

    Data.gov (United States)

    National Aeronautics and Space Administration — Chip-Integrated, Hybrid EHD/Capillary-Driven Thermal Management System is a two year that will leverage independently attained yet related prototype hardware...

  12. Controller synthesis for negative imaginary systems: a data driven approach

    KAUST Repository

    Mabrok, Mohamed; Petersen, Ian R.

    2016-01-01

    -driven controller synthesis methodology for NI systems is presented. In this approach, measured frequency response data of the plant is used to construct the controller frequency response at every frequency by minimising a cost function. Then, this controller

  13. Fostering synergy between cell biology and systems biology.

    Science.gov (United States)

    Eddy, James A; Funk, Cory C; Price, Nathan D

    2015-08-01

    In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  14. Data-driven modelling of LTI systems using symbolic regression

    NARCIS (Netherlands)

    Khandelwal, D.; Toth, R.; Van den Hof, P.M.J.

    2017-01-01

    The aim of this project is to automate the task of data-driven identification of dynamical systems. The underlying goal is to develop an identification tool that models a physical system without distinguishing between classes of systems such as linear, nonlinear or possibly even hybrid systems. Such

  15. Quantum Dynamics in Biological Systems

    Science.gov (United States)

    Shim, Sangwoo

    In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

  16. Editorial overview : Systems biology for biotechnology

    NARCIS (Netherlands)

    Heinemann, Matthias; Pilpel, Yitzhak

    About 15 years ago, systems biology was introduced as a novel approach to biological research. On the one side, its introduction was a result of the recognition that through solely the reductionist approach, we would ulti- mately not be able to understand how biological systems function as a whole.

  17. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

    2011-08-11

    Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

  18. Proliferation Potential of Accelerator-Driven Systems: Feasibility Calculations

    International Nuclear Information System (INIS)

    Riendeau, C.D.; Moses, D.L.; Olson, A.P.

    1998-01-01

    Accelerator-driven systems for fissile materials production have been proposed and studied since the early 1950s. Recent advances in beam power levels for small accelerators have raised the possibility that such use could be feasible for a potential proliferator. The objective of this study is to review the state of technology development for accelerator-driven spallation neutron sources and subcritical reactors. Energy and power requirements were calculated for a proton accelerator-driven neutron spallation source and subcritical reactors to produce a significant amount of fissile material--plutonium

  19. Magnetic Actuation of Biological Systems

    Science.gov (United States)

    Lauback, Stephanie D.

    Central to the advancement of many biomedical and nanotechnology capabilities is the capacity to precisely control the motion of micro and nanostructures. These applications range from single molecule experiments to cell isolation and separation, to drug delivery and nanomachine manipulation. This dissertation focuses on actuation of biological micro- and nano-entities through the use of weak external magnetic fields, superparamagnetic beads, and ferromagnetic thin films. The magnetic platform presents an excellent method for actuation of biological systems due to its ability to directly control the motion of an array of micro and nanostructures in real-time with calibrated picoNewton forces. The energy landscape of two ferromagnetic thin film patterns (disks and zigzag wires) is experimentally explored and compared to corresponding theoretical models to quantify the applied forces and trajectories of superparamagnetic beads due to the magnetic traps. A magnetic method to directly actuate DNA nanomachines in real-time with nanometer resolution and sub-second response times using micromagnetic control was implemented through the use of stiff DNA micro-levers which bridged the large length scale mismatch between the micro-actuator and the nanomachine. Compared to current alternative methods which are limited in the actuation speeds and the number of reconfiguration states of DNA constructs, this magnetic approach enables fast actuation (˜ milliseconds) and reconfigurable conformations achieved through a continuous range of finely tuned steps. The system was initially tested through actuation of the stiff arm tethered to the surface, and two prototype DNA nanomachines (rotor and hinge) were successfully actuated using the stiff mechanical lever. These results open new possibilities in the development of functional robotic systems at the molecular scale. In exploiting the use of DNA stiff levers, a new technique was also developed to investigate the emergence of the

  20. Data driven propulsion system weight prediction model

    Science.gov (United States)

    Gerth, Richard J.

    1994-10-01

    The objective of the research was to develop a method to predict the weight of paper engines, i.e., engines that are in the early stages of development. The impetus for the project was the Single Stage To Orbit (SSTO) project, where engineers need to evaluate alternative engine designs. Since the SSTO is a performance driven project the performance models for alternative designs were well understood. The next tradeoff is weight. Since it is known that engine weight varies with thrust levels, a model is required that would allow discrimination between engines that produce the same thrust. Above all, the model had to be rooted in data with assumptions that could be justified based on the data. The general approach was to collect data on as many existing engines as possible and build a statistical model of the engines weight as a function of various component performance parameters. This was considered a reasonable level to begin the project because the data would be readily available, and it would be at the level of most paper engines, prior to detailed component design.

  1. System and safety studies of accelerator driven transmutation systems

    International Nuclear Information System (INIS)

    Gudowski, W.; Wallenius, J.; Tucek, K.; Eriksson, Marcus; Carlsson, Johan; Seltborg, P.; Cetnar, J.

    2001-05-01

    The research on safety of Accelerator-Driven Transmutation Systems (ADS) at the department has been focused on: a) ADS core design and development of advanced nuclear fuel optimised for high transmutation rates and good safety features; b) analysis of ADS-dynamics c) computer code and nuclear data development relevant for simulation and optimization of ADS; d) participation in ADS experiments including 1 MW spallation target manufacturing, subcritical experiments MUSE (CEA-Cadarache). Moreover, during the reporting period the EU-project 'IABAT', co-ordinated by the department has been finished and 4 other projects have been initiated in the frame of the 5th European Framework Programme. Most of the research topics reported in this paper are referred to appendices, which have been published in the open literature. The topics, which are not yet published, are described here in more details

  2. System and safety studies of accelerator driven transmutation systems

    Energy Technology Data Exchange (ETDEWEB)

    Gudowski, W.; Wallenius, J.; Tucek, K.; Eriksson, Marcus; Carlsson, Johan; Seltborg, P.; Cetnar, J. [Royal Inst. of Technology, Stockholm (Sweden). Dept. of Nuclear and Reactor Physics

    2001-05-01

    The research on safety of Accelerator-Driven Transmutation Systems (ADS) at the department has been focused on: a) ADS core design and development of advanced nuclear fuel optimised for high transmutation rates and good safety features; b) analysis of ADS-dynamics c) computer code and nuclear data development relevant for simulation and optimization of ADS; d) participation in ADS experiments including 1 MW spallation target manufacturing, subcritical experiments MUSE (CEA-Cadarache). Moreover, during the reporting period the EU-project 'IABAT', co-ordinated by the department has been finished and 4 other projects have been initiated in the frame of the 5th European Framework Programme. Most of the research topics reported in this paper are referred to appendices, which have been published in the open literature. The topics, which are not yet published, are described here in more details.

  3. Scheduling Driven Partitioning of Heterogeneous Embedded Systems

    DEFF Research Database (Denmark)

    Pop, Paul; Eles, Petru; Peng, Zebo

    1998-01-01

    In this paper we present an algorithm for system level hardware/software partitioning of heterogeneous embedded systems. The system is represented as an abstract graph which captures both data-flow and the flow of control. Given an architecture consisting of several processors, ASICs and shared...... busses, our partitioning algorithm finds the partitioning with the smallest hardware cost and is able to predict and guarantee the performance of the system in terms of worst case delay....

  4. Model driven geo-information systems development

    NARCIS (Netherlands)

    Morales Guarin, J.M.; Ferreira Pires, Luis; van Sinderen, Marten J.; Williams, A.D.

    Continuous change of user requirements has become a constant for geo-information systems. Designing systems that can adapt to such changes requires an appropriate design methodology that supports abstraction, modularity and other mechanisms to capture the essence of the system and help controlling

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

    Science.gov (United States)

    Engelhardt, Benjamin; Frőhlich, Holger; Kschischo, Maik

    2016-02-11

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

  6. Applicability of Computational Systems Biology in Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning; Hadrup, Niels; Audouze, Karine Marie Laure

    2014-01-01

    be used to establish hypotheses on links between the chemical and human diseases. Such information can also be applied for designing more intelligent animal/cell experiments that can test the established hypotheses. Here, we describe how and why to apply an integrative systems biology method......Systems biology as a research field has emerged within the last few decades. Systems biology, often defined as the antithesis of the reductionist approach, integrates information about individual components of a biological system. In integrative systems biology, large data sets from various sources...... and databases are used to model and predict effects of chemicals on, for instance, human health. In toxicology, computational systems biology enables identification of important pathways and molecules from large data sets; tasks that can be extremely laborious when performed by a classical literature search...

  7. Opimization of fusion-driven fissioning systems

    International Nuclear Information System (INIS)

    Chapin, D.L.; Mills, R.G.

    1976-01-01

    Potential advantages of hybrid or fusion/fission systems can be exploited in different ways. With selection of the 238 U-- 239 Pu fuel cycle, we show that the system has greatest value as a power producer. Numerical examples of relative revenue from power production vs. 239 Pu production are discussed, and possible plant characteristics described. The analysis tends to show that the hybrid may be more economically attractive than pure fusion systems

  8. Promoting Student Inquiry Using "Zea Mays" (Corn) Cultivars for Hypothesis-Driven Experimentation in a Majors Introductory Biology Course

    Science.gov (United States)

    Blair, Amy C.; Peters, Brenda J.; Bendixen, Conrad W.

    2014-01-01

    The AAAS Vision and Change report (2011) recommends incorporating student research experiences into the biology curriculum at the undergraduate level. This article describes, in detail, how "Zea mays" (corn) cultivars were used as a model for a hypothesis-driven short-term research project in an introductory biology course at a small…

  9. Metabolomics: Definitions and Significance in Systems Biology.

    Science.gov (United States)

    Klassen, Aline; Faccio, Andréa Tedesco; Canuto, Gisele André Baptista; da Cruz, Pedro Luis Rocha; Ribeiro, Henrique Caracho; Tavares, Marina Franco Maggi; Sussulini, Alessandra

    2017-01-01

    Nowadays, there is a growing interest in deeply understanding biological mechanisms not only at the molecular level (biological components) but also the effects of an ongoing biological process in the organism as a whole (biological functionality), as established by the concept of systems biology. Within this context, metabolomics is one of the most powerful bioanalytical strategies that allow obtaining a picture of the metabolites of an organism in the course of a biological process, being considered as a phenotyping tool. Briefly, metabolomics approach consists in identifying and determining the set of metabolites (or specific metabolites) in biological samples (tissues, cells, fluids, or organisms) under normal conditions in comparison with altered states promoted by disease, drug treatment, dietary intervention, or environmental modulation. The aim of this chapter is to review the fundamentals and definitions used in the metabolomics field, as well as to emphasize its importance in systems biology and clinical studies.

  10. MODEL DRIVEN DEVELOPMENT OF ONLINE BANKING SYSTEMS

    Directory of Open Access Journals (Sweden)

    Bresfelean Vasile Paul

    2011-07-01

    Full Text Available In case of online applications the cycle of software development varies from the routine. The online environment, the variety of users, the treatability of the mass of information created by them, the reusability and the accessibility from different devices are all factors of these systems complexity. The use of model drive approach brings several advantages that ease up the development process. Working prototypes that simplify client relationship and serve as the base of model tests can be easily made from models describing the system. These systems make possible for the banks clients to make their desired actions from anywhere. The user has the possibility of accessing information or making transactions.

  11. Systems biology of personalized nutrition

    NARCIS (Netherlands)

    Ommen, B. van; Broek, T. van den; Hoogh, I. de; Erk, M. van; Someren, E. van; Rouhani-Rankouhi, T.; Anthony, J.C.; Hogenelst, K.; Pasman, W.; Boorsma, A.; Wopereis, S.

    2017-01-01

    Personalized nutrition is fast becoming a reality due to a number of technological, scientific, and societal developments that complement and extend current public health nutrition recommendations. Personalized nutrition tailors dietary recommendations to specific biological requirements on the

  12. Quantum thermodynamics for driven dissipative bosonic systems

    Science.gov (United States)

    Ochoa, Maicol A.; Zimbovskaya, Natalya; Nitzan, Abraham

    2018-02-01

    We investigate two prototypical dissipative bosonic systems under slow driving and arbitrary system-bath coupling strength, recovering their dynamic evolution as well as the heat and work rates, and we verify that thermodynamic laws are respected. Specifically, we look at the damped harmonic oscillator and the damped two-level system. For the former, we study independently the slow time-dependent perturbation in the oscillator frequency and in the coupling strength. For the latter, we concentrate on the slow modulation of the energy gap between the two levels. Importantly, we are able to find the entropy production rates for each case without explicitly defining nonequilibrium extensions for the entropy functional. This analysis also permits the definition of phenomenological friction coefficients in terms of structural properties of the system-bath composite.

  13. Modeling the Thermosphere as a Driven-Dissipative Thermodynamic System

    Science.gov (United States)

    2013-03-01

    8 Figure 2: Illustration of the geocentric solar magnetospheric coordinate system............15 Figure 3: Diagram of the...to test new methods of modeling the thermospheric environment. Thermosphere as a Driven-Dissipative Thermodynamic System One approach for modeling... approach uses empirical coupling and relaxation constants to model the 4 input of energy to the thermosphere from the solar wind during

  14. Information system design for demand-driven supply networks

    OpenAIRE

    Selk, Bernhard

    2004-01-01

    Information system design for demand-driven supply networks : integrating CRM & SCM / B. Selk, K. Turowski, C. Winnewisser. - In: EIS : Fourth International ICSC Symposium on Engineering of Intelligent Systems, EIS 2004. [Elektronische Ressource]. - Millet, Alberta : ICSC Interdisciplinary Research Canada, 2004. - 8 S. auf CD-ROM

  15. International conference on sub-critical accelerator driven systems. Proceedings

    International Nuclear Information System (INIS)

    Litovkina, L.P.; Titarenko, Yu.E.

    1999-01-01

    The International Meeting on Sub-Critical Accelerator Driven Systems was organized by the State Scientific Center - Institute for Theoretical and Experimental Physics with participation of Atomic Ministry of RF. The Meeting objective was to analyze the recent achievements and tendencies of the accelerator-driven systems development. The Meeting program covers a broad range of problems including the accelerator-driven systems (ADS) conceptual design; analyzing the ADS role in nuclear fuel cycle; accuracy of modeling the main parameters of ADS; conceptual design of high-current accelerators. Moreover, the results of recent experimental and theoretical studies on nuclear data accumulation to support the ADS technologies are presented. About 70 scientists from the main scientific centers of Russia, as well as scientists from USA, France, Belgium, India, and Yugoslavia, attended the meeting and presented 44 works [ru

  16. Data-Driven Control of Refrigeration System

    DEFF Research Database (Denmark)

    Vinther, Kasper

    Refrigeration is used in a wide range of applications, e.g., for storage of food at low temperatures to prolong shelf life and in air conditioning for occupancy comfort. The main focus of this thesis is control of supermarket refrigeration systems. This market is very competitive and it is import......Refrigeration is used in a wide range of applications, e.g., for storage of food at low temperatures to prolong shelf life and in air conditioning for occupancy comfort. The main focus of this thesis is control of supermarket refrigeration systems. This market is very competitive...... traditionally are a pressure and a temperature sensor. In this thesis, a novel maximum slope-seeking (MSS) control method is developed. This has resulted in a control implementation, which successfully has been able to control the evaporator superheat in four widely different refrigeration system test...... problems. The method utilizes the qualitative nonlinearity in the system and harmonic analysis of a perturbation signal to reach an unknown, but suitable, operating point. Another important control task in refrigeration systems is to maintain the temperature of the refrigerated space or foodstuff within...

  17. Portable database driven control system for SPEAR

    Energy Technology Data Exchange (ETDEWEB)

    Howry, S.; Gromme, T.; King, A.; Sullenberger, M.

    1985-04-01

    The new computer control system software for SPEAR is presented as a transfer from the PEP system. Features of the target ring (SPEAR) such as symmetries, magnet groupings, etc., are all contained in a design file which is read by both people and computer. People use it as documentation; a program reads it to generate the database structure, which becomes the center of communication for all the software. Geometric information, such as element positions and lengths, and CAMAC I/O routing information is entered into the database as it is developed. Since application processes refer only to the database and since they do so only in generic terms, almost all of this software (representing more then fifteen man years) is transferred with few changes. Operator console menus (touchpanels) are also transferred with only superficial changes for the same reasons. The system is modular: the CAMAC I/O software is all in one process; the menu control software is a process; the ring optics model and the orbit model are separate processes, each of which runs concurrently with about 15 others in the multiprogramming environment of the VAX/VMS operating system. 10 refs., 1 fig.

  18. Portable database driven control system for SPEAR

    International Nuclear Information System (INIS)

    Howry, S.; Gromme, T.; King, A.; Sullenberger, M.

    1985-04-01

    The new computer control system software for SPEAR is presented as a transfer from the PEP system. Features of the target ring (SPEAR) such as symmetries, magnet groupings, etc., are all contained in a design file which is read by both people and computer. People use it as documentation; a program reads it to generate the database structure, which becomes the center of communication for all the software. Geometric information, such as element positions and lengths, and CAMAC I/O routing information is entered into the database as it is developed. Since application processes refer only to the database and since they do so only in generic terms, almost all of this software (representing more then fifteen man years) is transferred with few changes. Operator console menus (touchpanels) are also transferred with only superficial changes for the same reasons. The system is modular: the CAMAC I/O software is all in one process; the menu control software is a process; the ring optics model and the orbit model are separate processes, each of which runs concurrently with about 15 others in the multiprogramming environment of the VAX/VMS operating system. 10 refs., 1 fig

  19. Dynamic Data Driven Applications Systems (DDDAS)

    Science.gov (United States)

    2012-05-03

    response) – Earthquakes, hurricanes, tornados, wildfires, floods, landslides, tsunamis, … • Critical Infrastructure systems – Electric-powergrid...Multiphase Flow Weather and Climate Structural Mechanics Seismic Processing Aerodynamics Geophysical Fluids Quantum Chemistry Actinide Chemistry...Alloys • Approach and Objectives:  Consider porous SMAs:  similar macroscopic behavior but mass /weight is less, and thus attractive for

  20. Philosophy of Systems and Synthetic Biology

    DEFF Research Database (Denmark)

    Green, Sara

    2017-01-01

    This entry aims to clarify how systems and synthetic biology contribute to and extend discussions within philosophy of science. Unlike fields such as developmental biology or molecular biology, systems and synthetic biology are not easily demarcated by a focus on a specific subject area or level...... of organization. Rather, they are characterized by the development and application of mathematical, computational, and synthetic modeling strategies in response to complex problems and challenges within the life sciences. Proponents of systems and synthetic biology often stress the necessity of a perspective...... that goes beyond the scope of molecular biology and genetic engineering, respectively. With the emphasis on systems and interaction networks, the approaches explicitly engage in one of the oldest philosophical discussions on the relationship between parts and wholes, or between reductionism and holism...

  1. Micro-separation toward systems biology.

    Science.gov (United States)

    Liu, Bi-Feng; Xu, Bo; Zhang, Guisen; Du, Wei; Luo, Qingming

    2006-02-17

    Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

  2. Collaborative Systems Driven Aircraft Configuration Design Optimization

    OpenAIRE

    Shiva Prakasha, Prajwal; Ciampa, Pier Davide; Nagel, Björn

    2016-01-01

    A Collaborative, Inside-Out Aircraft Design approach is presented in this paper. An approach using physics based analysis to evaluate the correlations between the airframe design, as well as sub-systems integration from the early design process, and to exploit the synergies within a simultaneous optimization process. Further, the disciplinary analysis modules involved in the optimization task are located in different organization. Hence, the Airframe and Subsystem design tools are integrated ...

  3. The Database Driven ATLAS Trigger Configuration System

    CERN Document Server

    Martyniuk, Alex; The ATLAS collaboration

    2015-01-01

    This contribution describes the trigger selection configuration system of the ATLAS low- and high-level trigger (HLT) and the upgrades it received in preparation for LHC Run 2. The ATLAS trigger configuration system is responsible for applying the physics selection parameters for the online data taking at both trigger levels and the proper connection of the trigger lines across those levels. Here the low-level trigger consists of the already existing central trigger (CT) and the new Level-1 Topological trigger (L1Topo), which has been added for Run 2. In detail the tasks of the configuration system during the online data taking are Application of the selection criteria, e.g. energy cuts, minimum multiplicities, trigger object correlation, at the three trigger components L1Topo, CT, and HLT On-the-fly, e.g. rate-dependent, generation and application of prescale factors to the CT and HLT to adjust the trigger rates to the data taking conditions, such as falling luminosity or rate spikes in the detector readout ...

  4. Biological Systems Thinking for Control Engineering Design

    Directory of Open Access Journals (Sweden)

    D. J. Murray-Smith

    2004-01-01

    Full Text Available Artificial neural networks and genetic algorithms are often quoted in discussions about the contribution of biological systems thinking to engineering design. This paper reviews work on the neuromuscular system, a field in which biological systems thinking could make specific contributions to the development and design of automatic control systems for mechatronics and robotics applications. The paper suggests some specific areas in which a better understanding of this biological control system could be expected to contribute to control engineering design methods in the future. Particular emphasis is given to the nonlinear nature of elements within the neuromuscular system and to processes of neural signal processing, sensing and system adaptivity. Aspects of the biological system that are of particular significance for engineering control systems include sensor fusion, sensor redundancy and parallelism, together with advanced forms of signal processing for adaptive and learning control. 

  5. Phase transformations and systems driven far from equilibrium

    International Nuclear Information System (INIS)

    Ma, E.; Atzmon, M.; Bellon, P.; Trivedi, R.

    1998-01-01

    This volume compiles invited and contributed papers that were presented at Symposium B of the 1997 Materials Research Society Fall Meeting, Phase Transformations and Systems Driven Far From Equilibrium, which was held December 1--5, in Boston, Massachusetts. While this symposium followed the tradition of previous MRS symposia on the fundamental topic of phase transformations, this year the emphasis was on materials systems driven far from equilibrium. The central theme of the majority of the work presented is the understanding of the thermodynamics and kinetics of phase transformations, with significant coverage of metastable materials and externally forced transformations driven, for example, by energy beams or mechanical deformation. The papers are arranged in seven sections: solidification theory and experiments; nucleation; solid state transformations and microstructural evolution; beam-induced transformations; amorphous solids; interfacial and thin film transformations; and nanophases and mechanical alloying. One hundred three papers have been processed separately for inclusion on the data base

  6. Impact of Thermodynamic Principles in Systems Biology

    NARCIS (Netherlands)

    Heijnen, J.J.

    2010-01-01

    It is shown that properties of biological systems which are relevant for systems biology motivated mathematical modelling are strongly shaped by general thermodynamic principles such as osmotic limit, Gibbs energy dissipation, near equilibria and thermodynamic driving force. Each of these aspects

  7. Aspergilli: Systems biology and industrial applications

    DEFF Research Database (Denmark)

    Knuf, Christoph; Nielsen, Jens

    2012-01-01

    possible to implement systems biology tools to advance metabolic engineering. These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology....

  8. Systems biology in critical-care nursing.

    Science.gov (United States)

    Schallom, Lynn; Thimmesch, Amanda R; Pierce, Janet D

    2011-01-01

    Systems biology applies advances in technology and new fields of study including genomics, transcriptomics, proteomics, and metabolomics to the development of new treatments and approaches of care for the critically ill and injured patient. An understanding of systems biology enhances a nurse's ability to implement evidence-based practice and to educate patients and families on novel testing and therapies. Systems biology is an integrated and holistic view of humans in relationship with the environment. Biomarkers are used to measure the presence and severity of disease and are rapidly expanding in systems biology endeavors. A systems biology approach using predictive, preventive, and participatory involvement is being utilized in a plethora of conditions of critical illness and injury including sepsis, cancer, pulmonary disease, and traumatic injuries.

  9. Marine biological data and information management system

    Digital Repository Service at National Institute of Oceanography (India)

    Sarupria, J.S.

    Indian National Oceanographic Data Centre (INODC) is engaged in developing a marine biological data and information management system (BIODIMS). This system will contain the information on zooplankton in the water column, zoobenthic biomass...

  10. Graphics processing units in bioinformatics, computational biology and systems biology.

    Science.gov (United States)

    Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

    2017-09-01

    Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

  11. A Systematic Review of Published Respondent-Driven Sampling Surveys Collecting Behavioral and Biologic Data.

    Science.gov (United States)

    Johnston, Lisa G; Hakim, Avi J; Dittrich, Samantha; Burnett, Janet; Kim, Evelyn; White, Richard G

    2016-08-01

    Reporting key details of respondent-driven sampling (RDS) survey implementation and analysis is essential for assessing the quality of RDS surveys. RDS is both a recruitment and analytic method and, as such, it is important to adequately describe both aspects in publications. We extracted data from peer-reviewed literature published through September, 2013 that reported collected biological specimens using RDS. We identified 151 eligible peer-reviewed articles describing 222 surveys conducted in seven regions throughout the world. Most published surveys reported basic implementation information such as survey city, country, year, population sampled, interview method, and final sample size. However, many surveys did not report essential methodological and analytical information for assessing RDS survey quality, including number of recruitment sites, seeds at start and end, maximum number of waves, and whether data were adjusted for network size. Understanding the quality of data collection and analysis in RDS is useful for effectively planning public health service delivery and funding priorities.

  12. Economics of fusion driven symbiotic energy systems

    International Nuclear Information System (INIS)

    Renier, J.P.; Hoffman, T.J.

    1979-01-01

    The economic analysis of symbiotic energy systems in which U233 (to fuel advanced converters burning U233 fuel) is generated in blankets surrounding fusioning D-T plasma's depends on factors such as the plasma performance parameters, ore costs, and the relative costs of Fusion Breeders (CTR) to Advanced Fission Converters. The analysis also depends on detailed information such as initial, final makeup fuel requirements, fuel isotopics, reprocessing and fabrication costs, reprocessing losses (1%) and delays (2 years), the cost of money, and the effect of the underutilization of the factory thermal installation at the beginning of cycle. In this paper we present the results of calculations of overall fuel cycle and power costs, ore requirements, proliferation resistance and possibilities for grid expansion, based on detailed mass and energy flow diagrams and standard US INFCE cost data and introduction constraints, for realistic symbiotic scenarios involving CTR's (used as drivers) and denatured CANDU's (used as U233 burners). We compare the results with those obtained for other strategies involving heterogeneous LMFBR's which burn Pu to produce U233 for U233-burners such as the advanced CANDU converters

  13. Water-driven micromotors for rapid photocatalytic degradation of biological and chemical warfare agents.

    Science.gov (United States)

    Li, Jinxing; Singh, Virendra V; Sattayasamitsathit, Sirilak; Orozco, Jahir; Kaufmann, Kevin; Dong, Renfeng; Gao, Wei; Jurado-Sanchez, Beatriz; Fedorak, Yuri; Wang, Joseph

    2014-11-25

    Threats of chemical and biological warfare agents (CBWA) represent a serious global concern and require rapid and efficient neutralization methods. We present a highly effective micromotor strategy for photocatalytic degradation of CBWA based on light-activated TiO2/Au/Mg microspheres that propel autonomously in natural water and obviate the need for external fuel, decontaminating reagent, or mechanical agitation. The activated TiO2/Au/Mg micromotors generate highly reactive oxygen species responsible for the efficient destruction of the cell membranes of the anthrax simulant Bacillus globigii spore, as well as rapid and complete in situ mineralization of the highly persistent organophosphate nerve agents into nonharmful products. The water-driven propulsion of the TiO2/Au/Mg micromotors facilitates efficient fluid transport and dispersion of the photogenerated reactive oxidative species and their interaction with the CBWA. Coupling of the photocatalytic surface of the micromotors and their autonomous water-driven propulsion thus leads to a reagent-free operation which holds a considerable promise for diverse "green" defense and environmental applications.

  14. Feedback dynamics and cell function: Why systems biology is called Systems Biology.

    Science.gov (United States)

    Wolkenhauer, Olaf; Mesarovic, Mihajlo

    2005-05-01

    A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

  15. Genomes, Phylogeny, and Evolutionary Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  16. Dataset-driven research for improving recommender systems for learning

    NARCIS (Netherlands)

    Verbert, Katrien; Drachsler, Hendrik; Manouselis, Nikos; Wolpers, Martin; Vuorikari, Riina; Duval, Erik

    2011-01-01

    Verbert, K., Drachsler, H., Manouselis, N., Wolpers, M., Vuorikari, R., & Duval, E. (2011). Dataset-driven research for improving recommender systems for learning. In Ph. Long, & G. Siemens (Eds.), Proceedings of 1st International Conference Learning Analytics & Knowledge (pp. 44-53). February,

  17. Nonlinear dynamics of a parametrically driven sine-Gordon system

    DEFF Research Database (Denmark)

    Grønbech-Jensen, Niels; Kivshar, Yuri S.; Samuelsen, Mogens Rugholm

    1993-01-01

    We consider a sine-Gordon system, driven by an ac parametric force in the presence of loss. It is demonstrated that a breather can be maintained in a steady state at half of the external frequency. In the small-amplitude limit the effect is described by an effective nonlinear Schrodinger equation...

  18. Reactivity Monitoring of Accelerator-Driven Nuclear Reactor Systems

    NARCIS (Netherlands)

    Uyttenhove, W.

    2016-01-01

    This thesis provides a methodology and set-up of a reactivity monitoring tool for Accelerator-Driven Systems (ADS). The reactivity monitoring tool should guarantee the operation of an ADS at a safe margin from criticality. Robustness is assured in different aspects of the monitoring tool: the choice

  19. Introduction of fusion driven subcritical system plasma design

    International Nuclear Information System (INIS)

    Bin Wu

    2003-01-01

    Fusion driven subcritical nuclear system (FDS) is a multifunctional hybrid reactor, which could breed nuclear fuel, transmute long-lived wastes, producing tritium and so on. This paper presents an introduction of FDS plasma design. Several different advance equilibrium configurations have been proposed and a 1.5-D discharge simulation of FDS was also present

  20. Concept evaluation of nuclear fusion driven symbiotic energy systems

    International Nuclear Information System (INIS)

    Renier, J.P.; Hoffman, T.J.

    1979-01-01

    This paper analyzes systems based on D-T and semi-catalyzed D-D fusion-powered U233 breeders. Two different blanket types were used: metallic thorium pebble-bed blankets with a batch reprocessing mode and a molten salt blanket with on-line continuous or batch reprocessing. All fusion-driven blankets are assumed to have spherical geometries, with a 85% closure. Neutronics depletion calculations were performed with a revised version of the discrete ordinates code XSDRN-PM, using multigroup (100 neutron, 21 gamma-ray groups) coupled cross-section libraries. These neutronics calculations are coupled with a scenario optimization and cost analysis code. Also, the fusion burn was shaped so as to keep the blanket maximum power density below a preset value, and to improve the performance of the fusion-driven systems. The fusion-driven symbiotes are compared with LMFBR-driven energy systems. The nuclear fission breeders that were used as drivers have parameters characteristic of heterogeneous, oxide LMFBRs. They are net plutonium users - the plutonium is obtained from the discharges of LWRs - and U233 is bred in the fission breeder thorium blankets. The analyses of the symbiotic energy systems were performed at equilibrium, at maximum rate of grid expansion, and for a given nuclear power demand

  1. Accelerator-driven transmutation reactor analysis code system (ATRAS)

    Energy Technology Data Exchange (ETDEWEB)

    Sasa, Toshinobu; Tsujimoto, Kazufumi; Takizuka, Takakazu; Takano, Hideki [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1999-03-01

    JAERI is proceeding a design study of the hybrid type minor actinide transmutation system which mainly consist of an intense proton accelerator and a fast subcritical core. Neutronics and burnup characteristics of the accelerator-driven system is important from a view point of the maintenance of subcriticality and energy balance during the system operation. To determine those characteristics accurately, it is necessary to involve reactions at high-energy region, which are not treated on ordinary reactor analysis codes. The authors developed a code system named ATRAS to analyze the neutronics and burnup characteristics of accelerator-driven subcritical reactor systems. ATRAS has a function of burnup analysis taking account of the effect of spallation neutron source. ATRAS consists of a spallation analysis code, a neutron transport codes and a burnup analysis code. Utility programs for fuel exchange, pre-processing and post-processing are also incorporated. (author)

  2. Periodic and quasiperiodic revivals in periodically driven interacting quantum systems

    Science.gov (United States)

    Luitz, David J.; Lazarides, Achilleas; Bar Lev, Yevgeny

    2018-01-01

    Recently it has been shown that interparticle interactions generically destroy dynamical localization in periodically driven systems, resulting in diffusive transport and heating. In this Rapid Communication we rigorously construct a family of interacting driven systems which are dynamically localized and effectively decoupled from the external driving potential. We show that these systems exhibit tunable periodic or quasiperiodic revivals of the many-body wave function and thus of all physical observables. By numerically examining spinless fermions on a one-dimensional lattice we show that the analytically obtained revivals of such systems remain stable for finite systems with open boundary conditions while having a finite lifetime in the presence of static spatial disorder. We find this lifetime to be inversely proportional to the disorder strength.

  3. Quantum revivals in periodically driven systems close to nonlinear resonances

    International Nuclear Information System (INIS)

    Saif, Farhan; Fortunato, Mauro

    2002-01-01

    We calculate the quantum revival time for a wave packet initially well localized in a one-dimensional potential in the presence of an external periodic modulating field. The dependence of the revival time on various parameters of the driven system is shown analytically. As an example of an application of our approach, we compare the analytically obtained values of the revival time for various modulation strengths with the numerically computed ones in the case of a driven gravitational cavity. We show that they are in very good agreement

  4. Group decision support system for customer-driven product design

    Science.gov (United States)

    Lin, Zhihang; Chen, Hang; Chen, Kuen; Che, Ada

    2000-10-01

    This paper describes the work on the development of a group decision support system for customer driven product design. The customer driven is to develop products, which meet all customer requirements in whole life cycle of products. A process model of decision during product primary design is proposed to formulate the structured, semi-structured and unstructured decision problems. The framework for the decision support system is presented that integrated both advances in the group decision making and distributed artificial intelligent. The system consists of the product primary design tool kit and the collaborative platform with multi-agent structure. The collaborative platform of the system and the product primary design tool kit, including the VOC (Voice of Customer) tool, QFD (Quality Function Deployment) tool, the Conceptual design tool, Reliability analysis tool and the cost and profit forecasting tool, are indicated.

  5. Network-driven design principles for neuromorphic systems

    OpenAIRE

    Partzsch, Johannes; Sch?ffny, Rene

    2015-01-01

    Synaptic connectivity is typically the most resource-demanding part of neuromorphic systems. Commonly, the architecture of these systems is chosen mainly on technical considerations. As a consequence, the potential for optimization arising from the inherent constraints of connectivity models is left unused. In this article, we develop an alternative, network-driven approach to neuromorphic architecture design. We describe methods to analyse performance of existing neuromorphic architectures i...

  6. Documentation Driven Development for Complex Real-Time Systems

    Science.gov (United States)

    2004-12-01

    This paper presents a novel approach for development of complex real - time systems , called the documentation-driven development (DDD) approach. This... time systems . DDD will also support automated software generation based on a computational model and some relevant techniques. DDD includes two main...stakeholders to be easily involved in development processes and, therefore, significantly improve the agility of software development for complex real

  7. A Model-Driven Development Method for Management Information Systems

    Science.gov (United States)

    Mizuno, Tomoki; Matsumoto, Keinosuke; Mori, Naoki

    Traditionally, a Management Information System (MIS) has been developed without using formal methods. By the informal methods, the MIS is developed on its lifecycle without having any models. It causes many problems such as lack of the reliability of system design specifications. In order to overcome these problems, a model theory approach was proposed. The approach is based on an idea that a system can be modeled by automata and set theory. However, it is very difficult to generate automata of the system to be developed right from the start. On the other hand, there is a model-driven development method that can flexibly correspond to changes of business logics or implementing technologies. In the model-driven development, a system is modeled using a modeling language such as UML. This paper proposes a new development method for management information systems applying the model-driven development method to a component of the model theory approach. The experiment has shown that a reduced amount of efforts is more than 30% of all the efforts.

  8. An engineering design approach to systems biology.

    Science.gov (United States)

    Janes, Kevin A; Chandran, Preethi L; Ford, Roseanne M; Lazzara, Matthew J; Papin, Jason A; Peirce, Shayn M; Saucerman, Jeffrey J; Lauffenburger, Douglas A

    2017-07-17

    Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.

  9. Hysteretic behavior of spin-crossover noise driven system

    Energy Technology Data Exchange (ETDEWEB)

    Gudyma, Iurii [Department of General Physics, Chernivtsi National University, Chernivtsi 58012 (Ukraine); Maksymov, Artur, E-mail: maxyartur@gmail.com [Department of General Physics, Chernivtsi National University, Chernivtsi 58012 (Ukraine); Advanced Materials Research Institute, University of New Orleans, LA 70148 (United States); Dimian, Mihai [Department of Electrical and Computer Engineering, Howard University, Washington DC, 20059 (United States); Faculty of Electrical Engineering and Computer Science, Stefan cel Mare University, Suceava 720229 (Romania)

    2016-04-01

    The influence of white Gaussian noise on hysteretic behavior of spin-crossover system is analyzed in the framework of stochastic Langevin dynamics. Various stochastic simulations are performed and several important properties of spin-transition in spin-crossover system driven by noise are reproduced. The numerical results are tested against the stationary probability function and the associated dynamic potential obtained from Fokker–Planck equation corresponding to spin-crossover Langevin dynamics. The dependence of light-induced optical hysteresis width and non-hysteretic transition curve slope on the noise intensity is illustrated. The role of low-spin and high-spin phase stabilities in the hysteretic behavior of noise-driven spin-crossover system is discussed.

  10. Nonadiabatic population transfer in a driven four-level system

    International Nuclear Information System (INIS)

    Prants, S.V.

    1994-01-01

    The coherent dynamics of a four-level quantum system with an arbitrary level configuration is described analytically in the modulated polychromatic laser field. The method of dynamical symmetries is invoked to develop the formalism for explicit calculation of the evolution matrix of the system in the resonance fields. The method is free of the usual adiabatic-passage, weak-field approximations, and approximation of the slowly varying amplitudes. The conditions for occurrence of the coherent effects of the total inversion and the total depletion of the initial level of a system driven simultaneously driven simultaneously at several transitions by the laser pulses of arbitrary shape are derived analytically. The obtained results can be applied to problems of the control of quantum processes in multilevel atoms and molecules. 14 refs

  11. Dynamic Systems Driven by Non-Poissonian Impulses

    DEFF Research Database (Denmark)

    Nielsen, Søren R.K.; Iwankiewicz, R.

    interarrival times. The moment equations for the augmented Poisson driven system are derived and closed by an ordinary cumulant neglect closure at the order N=4. The obtained moments are compared with these obtained by Monte Carlo simulations for both the original process with lognormally distributed......Dynamic systems under random trains of impulses driven by renewal point processes are studied. Then the system state variables no longer form a Markov vector as it is in the case of Poisson impulses. A general format is given for the replacing an ordinary renewal process by an equivalent Poisson...... process at the expense of the introduction of auxiliary state variables. A technique is devised for truncating the hierarchy of stochastic equations governing the auxiliary state variables. For the generalized Erlang process, suitable for approximating a wide class of renewal processes, the technique...

  12. Universality in driven-dissipative quantum many-body systems

    International Nuclear Information System (INIS)

    Sieberer, L.M.

    2015-01-01

    Recent experimental investigations of condensation phenomena in driven-dissipative quantum many-body systems raise the question of what kind of novel universal behavior can emerge under non-equilibrium conditions. We explore various aspects of universality in this context. Our results are of relevance for a variety of open quantum systems on the interface of quantum optics and condensed matter physics, ranging from exciton-polariton condensates to cold atomic gases. In Part I we characterize the dynamical critical behavior at the Bose-Einstein condensation phase transition in driven open quantum systems in three spatial dimensions. Although thermodynamic equilibrium conditions are emergent at low frequencies, the approach to this thermalized low-frequency regime is described by a critical exponent which is specific to the non-equilibrium transition, and places the latter beyond the standard classification of equilibrium dynamical critical behavior. Our theoretical approach is based on the functional renormalization group within the framework of Keldysh non-equilibrium field theory, which is equivalent to a microscopic description of the open system dynamics in terms of a many-body quantum master equation. Universal behavior in the coherence properties of driven-dissipative condensates in reduced dimensions is investigated in Part II. We show that driven two-dimensional Bose systems cannot exhibit algebraic order as in thermodynamic equilibrium, unless they are sufficiently anisotropic. However, we find evidence that even isotropic systems may have a finite superfluidity fraction. In one-dimensional systems, non-equilibrium conditions are traceable in the behavior of the autocorrelation function. We obtain these results by mapping the long-wavelength condensate dynamics onto the Kardar-Parisi-Zhang equation. In Part III we show that systems in thermodynamic equilibrium have a specific symmetry, which makes them distinct from generic driven open systems. The novel

  13. Controller synthesis for negative imaginary systems: a data driven approach

    KAUST Repository

    Mabrok, Mohamed

    2016-02-17

    The negative imaginary (NI) property occurs in many important applications. For instance, flexible structure systems with collocated force actuators and position sensors can be modelled as negative imaginary systems. In this study, a data-driven controller synthesis methodology for NI systems is presented. In this approach, measured frequency response data of the plant is used to construct the controller frequency response at every frequency by minimising a cost function. Then, this controller response is used to identify the controller transfer function using system identification methods. © The Institution of Engineering and Technology 2016.

  14. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  15. Neutron Transport Methods for Accelerator-Driven Systems

    International Nuclear Information System (INIS)

    Nicholas Tsoulfanidis; Elmer Lewis

    2005-01-01

    The objective of this project has been to develop computational methods that will enable more effective analysis of Accelerator Driven Systems (ADS). The work is centered at the University of Missouri at Rolla, with a subcontract at Northwestern University, and close cooperation with the Nuclear Engineering Division at Argonne National Laboratory. The work has fallen into three categories. First, the treatment of the source for neutrons originating from the spallation target which drives the neutronics calculations of the ADS. Second, the generalization of the nodal variational method to treat the R-Z geometry configurations frequently needed for scoping calculations in Accelerator Driven Systems. Third, the treatment of void regions within variational nodal methods as needed to treat the accelerator beam tube

  16. A Cost Benefit Analysis of an Accelerator Driven Transmutation System

    International Nuclear Information System (INIS)

    Westlen, D.; Gudowski, W.; Wallenius, J.; Tucek, K.

    2002-01-01

    This paper estimates the economical costs and benefits associated with a nuclear waste transmutation strategy. An 800 MWth, fast neutron spectrum, subcritical core design has been used in the study (the so called Sing-Sing Core). Three different fuel cycle scenarios have been compared. The main purpose of the paper has been to identify the cost drivers of a partitioning and transmutation strategy, and to estimate the cost of electricity generated in a nuclear park with operating accelerator driven systems. It has been found that directing all transuranic discharges from spent light water reactor (LWR) uranium oxide (UOX) fuel to accelerator driven systems leads to a cost increase for nuclear power of 50±15%, while introduction of a mixed oxide (MOX) burning step in the LWRs diminishes the cost penalty to 35±10%. (authors)

  17. Theory of many-body localization in periodically driven systems

    International Nuclear Information System (INIS)

    Abanin, Dmitry A.; De Roeck, Wojciech; Huveneers, François

    2016-01-01

    We present a theory of periodically driven, many-body localized (MBL) systems. We argue that MBL persists under periodic driving at high enough driving frequency: The Floquet operator (evolution operator over one driving period) can be represented as an exponential of an effective time-independent Hamiltonian, which is a sum of quasi-local terms and is itself fully MBL. We derive this result by constructing a sequence of canonical transformations to remove the time-dependence from the original Hamiltonian. When the driving evolves smoothly in time, the theory can be sharpened by estimating the probability of adiabatic Landau–Zener transitions at many-body level crossings. In all cases, we argue that there is delocalization at sufficiently low frequency. We propose a phase diagram of driven MBL systems.

  18. Entanglement replication in driven dissipative many-body systems.

    Science.gov (United States)

    Zippilli, S; Paternostro, M; Adesso, G; Illuminati, F

    2013-01-25

    We study the dissipative dynamics of two independent arrays of many-body systems, locally driven by a common entangled field. We show that in the steady state the entanglement of the driving field is reproduced in an arbitrarily large series of inter-array entangled pairs over all distances. Local nonclassical driving thus realizes a scale-free entanglement replication and long-distance entanglement distribution mechanism that has immediate bearing on the implementation of quantum communication networks.

  19. Variable speed gas engine-driven air compressor system

    Science.gov (United States)

    Morgan, J. R.; Ruggles, A. E.; Chen, T. N.; Gehret, J.

    1992-11-01

    Tecogen Inc. and Ingersoll-Rand Co. as a subcontractor have designed a nominal 150-hp gas engine-driven air compressor utilizing the TECODRIVE 8000 engine and the Ingersoll-Rand 178.5-mm twin screw compressor. Phase 1 included the system engineering and design, economic and applications studies, and a draft commercialization plan. Phase 2 included controls development, laboratory prototype construction, and performance testing. The testing conducted verified that the compressor meets all design specifications.

  20. Omics/systems biology and cancer cachexia.

    Science.gov (United States)

    Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

    2016-06-01

    Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

  1. Ashing vs. electric generation in accelerator driven system

    International Nuclear Information System (INIS)

    Solanilla, Roberto B.

    1999-01-01

    Accelerator Driven Systems have been conceived as an alternative for the processing of the radioactive wastes contained in spent fuel elements from nuclear power plants. These systems are formed by the coupling of a nuclear reactor - preferably a subcritical reactor - with a particle accelerator providing particles with energy in the order of the GeV. The long-lived fission products and actinides of the spent fuels are transformed by nuclear reactions in stable isotopes or in short-lived radioisotopes. The basic parameters for the electric energy production of the different systems are analysed. (author)

  2. Keldysh field theory for driven open quantum systems.

    Science.gov (United States)

    Sieberer, L M; Buchhold, M; Diehl, S

    2016-09-01

    Recent experimental developments in diverse areas-ranging from cold atomic gases to light-driven semiconductors to microcavity arrays-move systems into the focus which are located on the interface of quantum optics, many-body physics and statistical mechanics. They share in common that coherent and driven-dissipative quantum dynamics occur on an equal footing, creating genuine non-equilibrium scenarios without immediate counterpart in equilibrium condensed matter physics. This concerns both their non-thermal stationary states and their many-body time evolution. It is a challenge to theory to identify novel instances of universal emergent macroscopic phenomena, which are tied unambiguously and in an observable way to the microscopic drive conditions. In this review, we discuss some recent results in this direction. Moreover, we provide a systematic introduction to the open system Keldysh functional integral approach, which is the proper technical tool to accomplish a merger of quantum optics and many-body physics, and leverages the power of modern quantum field theory to driven open quantum systems.

  3. Data-Driven H∞ Control for Nonlinear Distributed Parameter Systems.

    Science.gov (United States)

    Luo, Biao; Huang, Tingwen; Wu, Huai-Ning; Yang, Xiong

    2015-11-01

    The data-driven H∞ control problem of nonlinear distributed parameter systems is considered in this paper. An off-policy learning method is developed to learn the H∞ control policy from real system data rather than the mathematical model. First, Karhunen-Loève decomposition is used to compute the empirical eigenfunctions, which are then employed to derive a reduced-order model (ROM) of slow subsystem based on the singular perturbation theory. The H∞ control problem is reformulated based on the ROM, which can be transformed to solve the Hamilton-Jacobi-Isaacs (HJI) equation, theoretically. To learn the solution of the HJI equation from real system data, a data-driven off-policy learning approach is proposed based on the simultaneous policy update algorithm and its convergence is proved. For implementation purpose, a neural network (NN)- based action-critic structure is developed, where a critic NN and two action NNs are employed to approximate the value function, control, and disturbance policies, respectively. Subsequently, a least-square NN weight-tuning rule is derived with the method of weighted residuals. Finally, the developed data-driven off-policy learning approach is applied to a nonlinear diffusion-reaction process, and the obtained results demonstrate its effectiveness.

  4. Decision Making in Biological Systems

    DEFF Research Database (Denmark)

    Tian, Chengzhe

    This thesis consists of five projects in three topics with a shared theme of understanding cellular decision-making processes with mathematical modeling. In the first topic, we address the possible interaction between bacterial Toxin-Antitoxin (TA) systems and stringent response alarmone guanosin...

  5. Diffusion-advection within dynamic biological gaps driven by structural motion

    Science.gov (United States)

    Asaro, Robert J.; Zhu, Qiang; Lin, Kuanpo

    2018-04-01

    To study the significance of advection in the transport of solutes, or particles, within thin biological gaps (channels), we examine theoretically the process driven by stochastic fluid flow caused by random thermal structural motion, and we compare it with transport via diffusion. The model geometry chosen resembles the synaptic cleft; this choice is motivated by the cleft's readily modeled structure, which allows for well-defined mechanical and physical features that control the advection process. Our analysis defines a Péclet-like number, AD, that quantifies the ratio of time scales of advection versus diffusion. Another parameter, AM, is also defined by the analysis that quantifies the full potential extent of advection in the absence of diffusion. These parameters provide a clear and compact description of the interplay among the well-defined structural, geometric, and physical properties vis-a ̀-vis the advection versus diffusion process. For example, it is found that AD˜1 /R2 , where R is the cleft diameter and hence diffusion distance. This curious, and perhaps unexpected, result follows from the dependence of structural motion that drives fluid flow on R . AM, on the other hand, is directly related (essentially proportional to) the energetic input into structural motion, and thereby to fluid flow, as well as to the mechanical stiffness of the cleftlike structure. Our model analysis thus provides unambiguous insight into the prospect of competition of advection versus diffusion within biological gaplike structures. The importance of the random, versus a regular, nature of structural motion and of the resulting transient nature of advection under random motion is made clear in our analysis. Further, by quantifying the effects of geometric and physical properties on the competition between advection and diffusion, our results clearly demonstrate the important role that metabolic energy (ATP) plays in this competitive process.

  6. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

  7. New superconducting cyclotron driven scanning proton therapy systems

    International Nuclear Information System (INIS)

    Klein, Hans-Udo; Baumgarten, Christian; Geisler, Andreas; Heese, Juergen; Hobl, Achim; Krischel, Detlef; Schillo, Michael; Schmidt, Stefan; Timmer, Jan

    2005-01-01

    Since one and a half decades ACCEL is investing in development and engineering of state of the art particle-therapy systems. A new medical superconducting 250 MeV proton cyclotron with special focus on the present and future beam requirements of fast scanning treatment systems has been designed. The first new ACCEL medical proton cyclotron is under commissioning at PSI for their PROSCAN proton therapy facility having undergone successful factory tests especially of the closed loop cryomagnetic system. The second cyclotron is part of ACCEL's integrated proton therapy system for Europe's first clinical center, RPTC in Munich. The cyclotron, the energy selection system, the beamline as well as the four gantries and patient positioners have been installed. The scanning system and major parts of the control software have already been tested. We will report on the concept of ACCEL's superconducting cyclotron driven scanning proton therapy systems and the current status of the commissioning work at PSI and RPTC

  8. Systems Biology and Stem Cell Pluripotency

    DEFF Research Database (Denmark)

    Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

    2016-01-01

    Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...

  9. The art and practice of systems biology in medicine: Mapping patterns of relationships

    NARCIS (Netherlands)

    Greef, J. van der; Martin, S.; Juhasz, P.; Adourian, A.; Plasterer, T.; Verheij, E.R.; McBurney, R.N.

    2007-01-01

    Systems biology has developed in recent years from a technology-driven enterprise to a new strategic tool in Life Sciences, particularly for innovative drug discovery and drug development. Combining the ultimate in systems phenotyping with in-depth investigations of biomolecular mechanisms will

  10. Stability properties of cold blanket systems for current driven modes

    International Nuclear Information System (INIS)

    Ohlsson, D.

    1977-12-01

    The stability problem of the boundary regions of cold blanket systems with induced currents parallel to the lines of force is formulated. Particular interest is focused on two types of modes: first electrostatic modes driven by the combined effects of a transverse resistivity gradient due to a spatially non-uniform electron temperature and a longitudinal current, second electromagnetic kink like modes driven by the torque arising from a transverse current density gradient and magnetic field perturbations. It is found that the combination of various dissipative and neutral gas effects introduces strong stabilizing effects within specific parameter ranges. For particular steady-state models investigated it is shown that these effects become of importance in laboratory plasmas at relatively high densities, low temperatures and moderate magnetic field strengths. Stability diagrams based on specific steady-state cold plasma blanket models will be presented

  11. ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

    Science.gov (United States)

    Huan, Tianxiao; Sivachenko, Andrey Y; Harrison, Scott H; Chen, Jake Y

    2008-08-12

    New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed. We developed ProteoLens as a JAVA-based visual analytic software tool for creating, annotating and exploring multi-scale biological networks. It supports direct database connectivity to either Oracle or PostgreSQL database tables/views, on which SQL statements using both Data Definition Languages (DDL) and Data Manipulation languages (DML) may be specified. The robust query languages embedded directly within the visualization software help users to bring their network data into a visualization context for annotation and exploration. ProteoLens supports graph/network represented data in standard Graph Modeling Language (GML) formats, and this enables interoperation with a wide range of other visual layout tools. The architectural design of ProteoLens enables the de-coupling of complex network data visualization tasks into two distinct phases: 1) creating network data association rules, which are mapping rules between network node IDs or edge IDs and data attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation of graph nodes and edges

  12. Tunable promoters in synthetic and systems biology

    DEFF Research Database (Denmark)

    Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

    2012-01-01

    in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available......Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central...... for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression...

  13. Data driven information system for supervision of judicial open

    Directory of Open Access Journals (Sweden)

    Ming LI

    2016-08-01

    Full Text Available Aiming at the four outstanding problems of informationized supervision for judicial publicity, the judicial public data is classified based on data driven to form the finally valuable data. Then, the functional structure, technical structure and business structure of the data processing system are put forward, including data collection module, data reduction module, data analysis module, data application module and data security module, etc. The development of the data processing system based on these structures can effectively reduce work intensity of judicial open iformation management, summarize the work state, find the problems, and promote the level of judicial publicity.

  14. Role of accelerator-driven systems in waste incineration scenarios

    Energy Technology Data Exchange (ETDEWEB)

    Salvatores, M.; Slessarev, I.; Tchistiakov, A. [CEA Centre d`Etudes de Cadarache, 13 - Saint-Paul-lez-Durance (France). Direction des Reacteurs Nucleaires; Spiro, M.; Terrien, Y.; Mouney, H.; Vergnes, J.

    1997-12-31

    At CEA accelerator-driven systems (ADS) are studied in the frame of the R and D required to answer the request of a law voted in 1991 by the French Parliament, `to search for solutions allowing to partition and transmute long lived radioactive wastes, in order to reduce their volume and toxicity`. These systems (called `INCAs`) are still at a conceptual level. However, the role of ADS has been clarified as a first step, and this will be the subject of the present paper. (author)

  15. ? filtering for stochastic systems driven by Poisson processes

    Science.gov (United States)

    Song, Bo; Wu, Zheng-Guang; Park, Ju H.; Shi, Guodong; Zhang, Ya

    2015-01-01

    This paper investigates the ? filtering problem for stochastic systems driven by Poisson processes. By utilising the martingale theory such as the predictable projection operator and the dual predictable projection operator, this paper transforms the expectation of stochastic integral with respect to the Poisson process into the expectation of Lebesgue integral. Then, based on this, this paper designs an ? filter such that the filtering error system is mean-square asymptotically stable and satisfies a prescribed ? performance level. Finally, a simulation example is given to illustrate the effectiveness of the proposed filtering scheme.

  16. Modelling of two-zone accelerator-driven systems

    Directory of Open Access Journals (Sweden)

    V. A. Babenko

    2012-09-01

    Full Text Available Neutron-physical modelings of two-zone subcritical reactor driven by high-intensity neutron generator are considered. The cascade principle in subcritical reactors, the use of which can hypothetically substantially amplify the neutron flux from the external source is discussed in this article. The theoretical preconditions of the cascade principle are discussed, and the directions of practical realization of the cascade subcritical system are considered, namely the possible methods of neutron feedback between reactor sections elimination. The results of Monte Carlo neutron-physical modeling of the cascade subcritical systems are presented and discussed.

  17. Electromagnetic Properties Analysis on Hybrid-driven System of Electromagnetic Motor

    Science.gov (United States)

    Zhao, Jingbo; Han, Bingyuan; Bei, Shaoyi

    2018-01-01

    The hybrid-driven system made of permanent-and electromagnets applied in the electromagnetic motor was analyzed, equivalent magnetic circuit was used to establish the mathematical models of hybrid-driven system, based on the models of hybrid-driven system, the air gap flux, air-gap magnetic flux density, electromagnetic force was proposed. Taking the air-gap magnetic flux density and electromagnetic force as main research object, the hybrid-driven system was researched. Electromagnetic properties of hybrid-driven system with different working current modes is studied preliminary. The results shown that analysis based on hybrid-driven system can improve the air-gap magnetic flux density and electromagnetic force more effectively and can also guarantee the output stability, the effectiveness and feasibility of the hybrid-driven system are verified, which proved theoretical basis for the design of hybrid-driven system.

  18. Fluctuation-Driven Transport in Biological Nanopores. A 3D Poisson–Nernst–Planck Study

    Directory of Open Access Journals (Sweden)

    Marcel Aguilella-Arzo

    2017-03-01

    Full Text Available Living systems display a variety of situations in which non-equilibrium fluctuations couple to certain protein functions yielding astonishing results. Here we study the bacterial channel OmpF under conditions similar to those met in vivo, where acidic resistance mechanisms are known to yield oscillations in the electric potential across the cell membrane. We use a three-dimensional structure-based theoretical approach to assess the possibility of obtaining fluctuation-driven transport. Our calculations show that remarkably high voltages would be necessary to observe the actual transport of ions against their concentration gradient. The reasons behind this are the mild selectivity of this bacterial pore and the relatively low efficiencies of the oscillating signals characteristic of membrane cells (random telegraph noise and thermal noise.

  19. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    Science.gov (United States)

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  20. A RADIANT AIR-CONDITIONING SYSTEM USING SOLAR-DRIVEN

    Directory of Open Access Journals (Sweden)

    S. A. ABDALLA

    2006-12-01

    Full Text Available Every air-conditioning system needs some fresh air to provide adequate ventilation air required to remove moisture, gases like ammonia and hydrogen sulphide, disease organisms, and heat from occupied spaces. However, natural ventilation is difficult to control because urban areas outside air is often polluted and cannot be supplied to inner spaces before being filtered. Besides the high electrical demand of refrigerant compression units used by most air-conditioning systems, and fans used to transport the cool air through the thermal distribution system draw a significant amount of electrical energy in comparison with electrical energy used by the building thermal conditioning systems. Part of this electricity heats the cooled air; thereby add to the internal thermal cooling peak load. In addition, refrigerant compression has both direct and indirect negative effects on the environment on both local and global scales. In seeking for innovative air-conditioning systems that maintain and improve indoor air quality under potentially more demanding performance criteria without increasing environmental impact, this paper presents radiant air-conditioning system which uses a solar-driven liquid desiccant evaporative cooler. The paper describes the proposed solar-driven liquid desiccant evaporative cooling system and the method used for investigating its performance in providing cold water for a radiant air-conditioning system in Khartoum (Central Sudan. The results of the investigation show that the system can operate in humid as well as dry climates and that employing such a system reduces air-conditioning peak electrical demands as compared to vapour compression systems.

  1. Thermodynamic stability of driven open systems and control of phase separation by electro-autocatalysis.

    Science.gov (United States)

    Bazant, Martin Z

    2017-07-01

    Motivated by the possibility of electrochemical control of phase separation, a variational theory of thermodynamic stability is developed for driven reactive mixtures, based on a nonlinear generalization of the Cahn-Hilliard and Allen-Cahn equations. The Glansdorff-Prigogine stability criterion is extended for driving chemical work, based on variations of nonequilibrium Gibbs free energy. Linear stability is generally determined by the competition of chemical diffusion and driven autocatalysis. Novel features arise for electrochemical systems, related to controlled total current (galvanostatic operation), concentration-dependent exchange current (Butler-Volmer kinetics), and negative differential reaction resistance (Marcus kinetics). The theory shows how spinodal decomposition can be controlled by solo-autocatalytic charge transfer, with only a single faradaic reaction. Experimental evidence is presented for intercalation and electrodeposition in rechargeable batteries, and further applications are discussed in solid state ionics, electrovariable optics, electrochemical precipitation, and biological pattern formation.

  2. Policy Driven Development: Flexible Policy Insertion for Large Scale Systems.

    Science.gov (United States)

    Demchak, Barry; Krüger, Ingolf

    2012-07-01

    The success of a software system depends critically on how well it reflects and adapts to stakeholder requirements. Traditional development methods often frustrate stakeholders by creating long latencies between requirement articulation and system deployment, especially in large scale systems. One source of latency is the maintenance of policy decisions encoded directly into system workflows at development time, including those involving access control and feature set selection. We created the Policy Driven Development (PDD) methodology to address these development latencies by enabling the flexible injection of decision points into existing workflows at runtime , thus enabling policy composition that integrates requirements furnished by multiple, oblivious stakeholder groups. Using PDD, we designed and implemented a production cyberinfrastructure that demonstrates policy and workflow injection that quickly implements stakeholder requirements, including features not contemplated in the original system design. PDD provides a path to quickly and cost effectively evolve such applications over a long lifetime.

  3. Data-Driven Assistance Functions for Industrial Automation Systems

    International Nuclear Information System (INIS)

    Windmann, Stefan; Niggemann, Oliver

    2015-01-01

    The increasing amount of data in industrial automation systems overburdens the user in process control and diagnosis tasks. One possibility to cope with these challenges consists of using smart assistance systems that automatically monitor and optimize processes. This article deals with aspects of data-driven assistance systems such as assistance functions, process models and data acquisition. The paper describes novel approaches for self-diagnosis and self-optimization, and shows how these assistance functions can be integrated in different industrial environments. The considered assistance functions are based on process models that are automatically learned from process data. Fault detection and isolation is based on the comparison of observations of the real system with predictions obtained by application of the process models. The process models are further employed for energy efficiency optimization of industrial processes. Experimental results are presented for fault detection and energy efficiency optimization of a drive system. (paper)

  4. Systems biology solutions for biochemical production challenges

    DEFF Research Database (Denmark)

    Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus

    2017-01-01

    There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics...... characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity...... compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains...

  5. Systems biology solutions for biochemical production challenges.

    Science.gov (United States)

    Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus; Herrgård, Markus J

    2017-06-01

    There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains for biofuels and -chemicals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  6. Advances in Optimizing Weather Driven Electric Power Systems.

    Science.gov (United States)

    Clack, C.; MacDonald, A. E.; Alexander, A.; Dunbar, A. D.; Xie, Y.; Wilczak, J. M.

    2014-12-01

    The importance of weather-driven renewable energies for the United States (and global) energy portfolio is growing. The main perceived problems with weather-driven renewable energies are their intermittent nature, low power density, and high costs. The National Energy with Weather System Simulator (NEWS) is a mathematical optimization tool that allows the construction of weather-driven energy sources that will work in harmony with the needs of the system. For example, it will match the electric load, reduce variability, decrease costs, and abate carbon emissions. One important test run included existing US carbon-free power sources, natural gas power when needed, and a High Voltage Direct Current power transmission network. This study shows that the costs and carbon emissions from an optimally designed national system decrease with geographic size. It shows that with achievable estimates of wind and solar generation costs, that the US could decrease its carbon emissions by up to 80% by the early 2030s, without an increase in electric costs. The key requirement would be a 48 state network of HVDC transmission, creating a national market for electricity not possible in the current AC grid. These results were found without the need for storage. Further, we tested the effect of changing natural gas fuel prices on the optimal configuration of the national electric power system. Another test that was carried out was an extension to global regions. The extension study shows that the same properties found in the US study extend to the most populous regions of the planet. The extra test is a simplified version of the US study, and is where much more research can be carried out. We compare our results to other model results.

  7. A universal piezo-driven ultrasonic cell microinjection system.

    Science.gov (United States)

    Huang, Haibo; Mills, James K; Lu, Cong; Sun, Dong

    2011-08-01

    Over the past decade, the rapid development of biotechnologies such as gene injection, in-vitro fertilization, intracytoplasmic sperm injection (ICSI) and drug development have led to great demand for highly automated, high precision equipment for microinjection. Recently a new cell injection technology using piezo-driven pipettes with a very small mercury column was proposed and successfully applied in ICSI to a variety of mammal species. Although this technique significantly improves the survival rates of the ICSI process, shortcomings due to the toxicity of mercury and damage to the cell membrane due to large lateral tip oscillations of the injector pipette may limit its application. In this paper, a new cell injection system for automatic batch injection of suspended cells is developed. A new design of the piezo-driven cell injector is proposed for automated suspended cell injection. This new piezo-driven cell injector design relocates the piezo oscillation actuator to the injector pipette which eliminates the vibration effect on other parts of the micromanipulator. A small piezo stack is sufficient to perform the cell injection process. Harmful lateral tip oscillations of the injector pipette are reduced substantially without the use of a mercury column. Furthermore, ultrasonic vibration micro-dissection (UVM) theory is utilized to analyze the piezo-driven cell injection process, and the source of the lateral oscillations of the injector pipette is investigated. From preliminary experiments of cell injection of a large number of zebrafish embryos (n = 200), the injector pipette can easily pierce through the cell membrane at a low injection speed and almost no deformation of the cell wall, and with a high success rate(96%) and survival rate(80.7%) This new injection approach shows good potential for precision injection with less damage to the injected cells.

  8. Synthetic Biology: Advancing Biological Frontiers by Building Synthetic Systems

    OpenAIRE

    Chen, Yvonne Yu-Hsuan; Galloway, Kate E; Smolke, Christina D

    2012-01-01

    Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field.

  9. Solar thermally driven cooling systems: Some investigation results and perspectives

    International Nuclear Information System (INIS)

    Ajib, Salman; Günther, Wolfgang

    2013-01-01

    Highlights: ► Two types of solar thermally driven absorption refrigeration machines (ARMs) have been investigated. ► We investigated the influence of the operating conditions on the effectiveness of the ARMs. ► The influence of the flow rate of the work solution on the effectiveness of the ARMs has been tested. ► Two laboratory test plants have been built and tested under different operating conditions. - Abstract: A big increase in the number of solar thermal cooling installations and research efforts could be seen over the last years worldwide. Especially the producers of solar thermal collectors and systems have been looking for thermal chillers in the small capacity range to provide air conditioning for one or two family houses. Furthermore, many developments aim to increase the efficiency of the system and to decrease the specific costs of the produced refrigeration capacity. The growth in the use of solar thermal cooling systems amounted about 860% from 52 units in 2004 to 450 units in 2009 [1]. This tendency is expected to be continuously in the next years. The practical examinations on solar thermally driven absorption machines with refrigeration capacity of 15, 10 and 5 kW have shown that this technology has a good chance to be standardized and to replace partly the conventional one. These systems can save more primary energy at high fraction of solar thermally driving by suitable control and regulation of the system. The investing costs still higher as the conventional one, however, the operating costs are less than the conventional one. The Coefficient of Performance (COP) depends on the kind of the system, work temperatures and conditions as well as the refrigeration capacity of the systems. It lies between 0.4 and 1.2. In the framework of the research on this field, we built, tested and measured two prototypes. After measuring the first prototype, the chillers were redesigned to reduce internal heat losses and make the heat and mass transfer

  10. Community-driven development for computational biology at Sprints, Hackathons and Codefests.

    Science.gov (United States)

    Möller, Steffen; Afgan, Enis; Banck, Michael; Bonnal, Raoul J P; Booth, Timothy; Chilton, John; Cock, Peter J A; Gumbel, Markus; Harris, Nomi; Holland, Richard; Kalaš, Matúš; Kaján, László; Kibukawa, Eri; Powel, David R; Prins, Pjotr; Quinn, Jacqueline; Sallou, Olivier; Strozzi, Francesco; Seemann, Torsten; Sloggett, Clare; Soiland-Reyes, Stian; Spooner, William; Steinbiss, Sascha; Tille, Andreas; Travis, Anthony J; Guimera, Roman; Katayama, Toshiaki; Chapman, Brad A

    2014-01-01

    Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how

  11. The physics design of accelerator-driven transmutation systems

    International Nuclear Information System (INIS)

    Venneri, F.

    1995-01-01

    Nuclear systems under study in the Los Alamos Accelerator-Driven Transmutation Technology program (ADTT) will allow the destruction of nuclear spent fuel and weapons-return plutonium, as well as the production of nuclear energy from the thorium cycle, without a long-lived radioactive waste stream. The subcritical systems proposed represent a radical departure from traditional nuclear concepts (reactors), yet the actual implementation of ADTT systems is based on modest extrapolations of existing technology. These systems strive to keep the best that the nuclear technology has developed over the years, within a sensible conservative design envelope and eventually manage to offer a safer, less expensive and more environmentally sound approach to nuclear power

  12. The physics design of accelerator-driven transmutation systems

    Energy Technology Data Exchange (ETDEWEB)

    Venneri, F. [Los Alamos National Laboratory, NM (United States)

    1995-10-01

    Nuclear systems under study in the Los Alamos Accelerator-Driven Transmutation Technology program (ADTT) will allow the destruction of nuclear spent fuel and weapons-return plutonium, as well as the production of nuclear energy from the thorium cycle, without a long-lived radioactive waste stream. The subcritical systems proposed represent a radical departure from traditional nuclear concepts (reactors), yet the actual implementation of ADTT systems is based on modest extrapolations of existing technology. These systems strive to keep the best that the nuclear technology has developed over the years, within a sensible conservative design envelope and eventually manage to offer a safe, less expensive and more environmentally sound approach to nuclear power.

  13. Systems Biology — the Broader Perspective

    Directory of Open Access Journals (Sweden)

    Jonathan Bard

    2013-06-01

    Full Text Available Systems biology has two general aims: a narrow one, which is to discover how complex networks of proteins work, and a broader one, which is to integrate the molecular and network data with the generation and function of organism phenotypes. Doing all this involves complex methodologies, but underpinning the subject are more general conceptual problems about upwards and downwards causality, complexity and information storage, and their solutions provide the constraints within which these methodologies can be used. This essay considers these general aspects and the particular role of protein networks; their functional outputs are often the processes driving phenotypic change and physiological function—networks are, in a sense, the units of systems biology much as proteins are for molecular biology. It goes on to argue that the natural language for systems-biological descriptions of biological phenomena is the mathematical graph (a set of connected facts of the general form [process] (e.g., [activates] . Such graphs not only integrate events at different levels but emphasize the distributed nature of control as well as displaying a great deal of data. The implications and successes of these ideas for physiology, pharmacology, development and evolution are briefly considered. The paper concludes with some challenges for the future.

  14. Model-driven dependability assessment of software systems

    CERN Document Server

    Bernardi, Simona; Petriu, Dorina C

    2013-01-01

    In this book, the authors present cutting-edge model-driven techniques for modeling and analysis of software dependability. Most of them are based on the use of UML as software specification language. From the software system specification point of view, such techniques exploit the standard extension mechanisms of UML (i.e., UML profiling). UML profiles enable software engineers to add non-functional properties to the software model, in addition to the functional ones. The authors detail the state of the art on UML profile proposals for dependability specification and rigorously describe the t

  15. Present status and issues for accelerator driven transmutation system

    International Nuclear Information System (INIS)

    Mizumoto, Motoharu

    2003-01-01

    Proper treatment of high-level nuclear wastes (HLW) that are produced in operation of nuclear power plants is one of the most important problems for further utilization of nuclear energy. The purpose of the accelerator driven nuclear waste transmutation system (ADS) is to transmute these nuclei to stable or short-lived nuclei by various radiation-induced nuclear reactions. When ADS for HLW can be realized, burden to deep geological disposal can be considerably reduced. In the paper, present status and issues for ADS will be discussed. (author)

  16. System on chip module configured for event-driven architecture

    Science.gov (United States)

    Robbins, Kevin; Brady, Charles E.; Ashlock, Tad A.

    2017-10-17

    A system on chip (SoC) module is described herein, wherein the SoC modules comprise a processor subsystem and a hardware logic subsystem. The processor subsystem and hardware logic subsystem are in communication with one another, and transmit event messages between one another. The processor subsystem executes software actors, while the hardware logic subsystem includes hardware actors, the software actors and hardware actors conform to an event-driven architecture, such that the software actors receive and generate event messages and the hardware actors receive and generate event messages.

  17. Transmutation of 129I Using an Accelerator-Driven System

    International Nuclear Information System (INIS)

    Nishihara, Kenji; Takano, Hideki

    2002-01-01

    A conceptual blanket design for 129 I transmutation is proposed for an accelerator-driven system (ADS) that is designed to transmute minor actinides (MAs). In this ADS, 250 kg/yr of MA and 56 kg/yr of iodine are simultaneously transmuted, and they correspond to the quantities generated from ∼10 units of existing light water reactors. Furthermore, an introduction scenario and the benefit of iodine transmutation are studied for future introduction of fast breeder reactors. It is shown that the transmutation of iodine benefits the concept of underground disposal

  18. A Quality-Driven Methodology for Information Systems Integration

    Directory of Open Access Journals (Sweden)

    Iyad Zikra

    2017-10-01

    Full Text Available Information systems integration is an essential instrument for organizations to attain advantage in today’s growing and fast changing business and technology landscapes. Integration solutions generate added value by combining the functionality and services of heterogeneous and diverse systems. Existing integration environments tend to rely heavily on technical, platform-dependent skills. Consequently, the solutions that they enable are not optimally aligned with the envisioned business goals of the organization. Furthermore, the gap between the goals and the solutions complicates the task of evaluating the quality of integration solutions. To address these challenges, we propose a quality-driven, model-driven methodology for designing and developing integration solutions. The methodology spans organizational and systems design details, providing a holistic view of the integration solution and its underlying business goals. A multi-view meta-model provides the basis for the integration design. Quality factors that affect various aspects of the integration solution guide and inform the progress of the methodology. An example business case is presented to demonstrate the application of the methodology.

  19. Discrete changes of current statistics in periodically driven stochastic systems

    International Nuclear Information System (INIS)

    Chernyak, Vladimir Y; Sinitsyn, N A

    2010-01-01

    We demonstrate that the counting statistics of currents in periodically driven ergodic stochastic systems can show sharp changes of some of its properties in response to continuous changes of the driving protocol. To describe this effect, we introduce a new topological phase factor in the evolution of the moment generating function which is akin to the topological geometric phase in the evolution of a periodically driven quantum mechanical system with time-reversal symmetry. This phase leads to the prediction of a sign change for the difference of the probabilities to find even and odd numbers of particles transferred in a stochastic system in response to cyclic evolution of control parameters. The driving protocols that lead to this sign change should enclose specific degeneracy points in the space of control parameters. The relation between the topology of the paths in the control parameter space and the sign changes can be described in terms of the first Stiefel–Whitney class of topological invariants. (letter)

  20. Design of SGLT2 Inhibitors for the Treatment of Type 2 Diabetes: A History Driven by Biology to Chemistry.

    Science.gov (United States)

    Cai, Wenqing; Jiang, Linlin; Xie, Yafei; Liu, Yuqiang; Liu, Wei; Zhao, Guilong

    2015-01-01

    A brief history of the design of sodium-dependent glucose cotransporter 2 (SGLT2) inhibitors is reviewed. The design of O-glucoside SGLT2 inhibitors by structural modification of phlorizin, a naturally occurring O-glucoside, in the early stage was a process mainly driven by biology with anticipation of improving SGLT2/SGLT1 selectivity and increasing metabolic stability. Discovery of dapagliflozin, a pioneering C-glucoside SGLT2 inhibitor developed by Bristol-Myers Squibb, represents an important milestone in this history. In the second stage, the design of C-glycoside SGLT2 inhibitors by modifications of the aglycone and glucose moiety of dapagliflozin, an original structural template for almost all C-glycoside SGLT2 inhibitors, was mainly driven by synthetic organic chemistry due to the challenge of designing dapagliflozin derivatives that are patentable, biologically active and synthetically accessible. Structure-activity relationships (SAR) of the SGLT2 inhibitors are also discussed.

  1. Heat Driven Cooling in District Energy Systems; Vaermedriven Kyla

    Energy Technology Data Exchange (ETDEWEB)

    Rydstrand, Magnus; Martin, Viktoria; Westermark, Mats [Royal Inst. of Technology, Stockholm (Sweden). Dept. of Chemical Engineering and Technology

    2004-07-01

    high costs. However heat sinks are unavoidable from a system perspective and there are potential cost savings since a low-pressure steam turbines will not be required if heat driven cooling is implemented. The fuel utilization for some technologies (not necessarily the best technology) was evaluated in two different scenarios: 1) with electricity production from coal; and 2) with electricity production from natural gas. It is shown in the scenarios that the heat driven cooling technologies give lower fuel consumption as compared producing electricity as an intermediate product before cooling is produced. Further it should be noted that electricity is produced, not consumed, if heat is used directly for the production of cooling. We claim that cost effective solutions for district heat driven chillers and/or combined production of electricity and district cooling can be found in all climates with high enough density of heating and cooling demands. It was found that district heat driven chillers can be very energy efficient in warm and humid climates since desiccant systems are an effective way of handling latent cooling loads. In dry climates, with low latent loads, water distributed cooling has a large potential and absorption cooling will give high fuel utilization seen from a system perspective. In climates where water shortage is a problem it is possible that the temperature lift of the conventional absorption chiller has to be increased in order to be able to use dry cooling towers. The temperature lift can be increased by changing the chiller design or by using a different working pair. Heat driven cooling can be integrated into an energy system in different ways. In USA and Japan, district heating is not well developed. Instead small, distributed combined heat and power (CHP) plants with high exhaust temperatures are widespread. Cooling is often produced, in these regions, through absorption cooling (using heat from CHP) or compression chillers depending on

  2. Alternative definitions of kinetic parameters for accelerator driven systems

    International Nuclear Information System (INIS)

    Talamo, Alberto; Gohar, Yousry; Dulla, Sandra; Ravetto, Piero

    2012-01-01

    Highlights: ► New definition of kinetic parameters for accelerator driven systems. ► Difference between effective and average delayed neutron fraction. ► Difference between effective and average prompt neutron lifetime. ► Effect of the neutron source (Cf, D–D, D–T) on k src . ► Effect of the (n, xn) reactions and source energy-angle distribution on k src . - Abstract: This study introduces a new formulation of kinetic parameters for accelerator driven systems and it is structured into two parts. The first part is dedicated to the classic definition of the kinetic parameters and compares different calculation methodologies. The second part considers a new definition of the kinetic parameters for subcritical assemblies, with particular emphasis on the delayed neutron fraction and the prompt neutron lifetime. This new definition takes into account neutrons from the external neutron source and (n, xn) reactions, which increase the fraction of prompt neutrons. The developed theoretical framework has been applied by Monte Carlo and deterministic calculations to the YALINA Thermal subcritical assembly located in Belarus. This facility can be driven by californium, deuterium–deuterium (D–D), or deuterium–tritium (D–T) external neutron sources. For the D–T neutron source, (n, xn) reactions must be taken into account in order to produce accurate results because the average energy of D–T source neutrons is 14.1 MeV, a value which is much higher than the threshold energy of the (n, 2n) cross section of uranium isotopes.

  3. Systems Biology for Organotypic Cell Cultures

    Energy Technology Data Exchange (ETDEWEB)

    Grego, Sonia [RTI International, Research Triangle Park, NC (United States); Dougherty, Edward R. [Texas A & M Univ., College Station, TX (United States); Alexander, Francis J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Auerbach, Scott S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Berridge, Brian R. [GlaxoSmithKline, Research Triangle Park, NC (United States); Bittner, Michael L. [Translational Genomics Research Inst., Phoenix, AZ (United States); Casey, Warren [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Cooley, Philip C. [RTI International, Research Triangle Park, NC (United States); Dash, Ajit [HemoShear Therapeutics, Charlottesville, VA (United States); Ferguson, Stephen S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Fennell, Timothy R. [RTI International, Research Triangle Park, NC (United States); Hawkins, Brian T. [RTI International, Research Triangle Park, NC (United States); Hickey, Anthony J. [RTI International, Research Triangle Park, NC (United States); Kleensang, Andre [Johns Hopkins Univ., Baltimore, MD (United States). Center for Alternatives to Animal Testing; Liebman, Michael N. [IPQ Analytics, Kennett Square, PA (United States); Martin, Florian [Phillip Morris International, Neuchatel (Switzerland); Maull, Elizabeth A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Paragas, Jason [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Qiao, Guilin [Defense Threat Reduction Agency, Ft. Belvoir, VA (United States); Ramaiahgari, Sreenivasa [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Sumner, Susan J. [RTI International, Research Triangle Park, NC (United States); Yoon, Miyoung [The Hamner Inst. for Health Sciences, Research Triangle Park, NC (United States); ScitoVation, Research Triangle Park, NC (United States)

    2016-08-04

    Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data. This consensus report summarizes the discussions held.

  4. Client and event driven data hub system at CDF

    International Nuclear Information System (INIS)

    Kilminster, Ben; McFarland, Kevin; Vaiciulis, Tony; Matsunaga, Hiroyuki; Shimojima, Makoto

    2001-01-01

    The Consumer-Server Logger (CSL) system at the Collider Detector at Fermilab is a client and event driven data hub capable of receiving physics events from multiple connections, and logging them to multiple streams while distributing them to multiple online analysis programs (consumers). Its multiple-partitioned design allows data flowing through different paths of the detector sub-systems to be processed separately. The CSL system, using a set of internal memory buffers and message queues mapped to the location of events within its programs, and running on an SGI 2200 Server, is able to process at least the required 20 MB/s of constant event logging (75 Hz of 250 KB events) while also filtering up to 10 MB/s to consumers requesting specific types of events

  5. Data-driven system to predict academic grades and dropout

    Science.gov (United States)

    Rovira, Sergi; Puertas, Eloi

    2017-01-01

    Nowadays, the role of a tutor is more important than ever to prevent students dropout and improve their academic performance. This work proposes a data-driven system to extract relevant information hidden in the student academic data and, thus, help tutors to offer their pupils a more proactive personal guidance. In particular, our system, based on machine learning techniques, makes predictions of dropout intention and courses grades of students, as well as personalized course recommendations. Moreover, we present different visualizations which help in the interpretation of the results. In the experimental validation, we show that the system obtains promising results with data from the degree studies in Law, Computer Science and Mathematics of the Universitat de Barcelona. PMID:28196078

  6. Promoting Systems Thinking through Biology Lessons

    Science.gov (United States)

    Riess, Werner; Mischo, Christoph

    2010-01-01

    This study's goal was to analyze various teaching approaches within the context of natural science lessons, especially in biology. The main focus of the paper lies on the effectiveness of different teaching methods in promoting systems thinking in the field of Education for Sustainable Development. The following methods were incorporated into the…

  7. Systems Biology of Glucocorticoids in Muscle Disease

    Science.gov (United States)

    2010-10-01

    Introduction Duchenne muscular dystrophy (DMD) is the most common and incurable muscular dystrophy of childhood. Muscle regeneration fails with...SUBJECT TERMS Duchenne Muscular dystrophy , Glucocorticoids, Systems biology, Drug mechanism 16. SECURITY CLASSIFICATION OF: U 17. LIMITATION...better targeted and more effective therapies for Duchenne muscular dystrophy dynamically. This MDA grant proposal is led by Dr. Eric Hoffman, and it

  8. Modular microfluidic system for biological sample preparation

    Science.gov (United States)

    Rose, Klint A.; Mariella, Jr., Raymond P.; Bailey, Christopher G.; Ness, Kevin Dean

    2015-09-29

    A reconfigurable modular microfluidic system for preparation of a biological sample including a series of reconfigurable modules for automated sample preparation adapted to selectively include a) a microfluidic acoustic focusing filter module, b) a dielectrophoresis bacteria filter module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter.

  9. Radiological/biological/aerosol removal system

    Science.gov (United States)

    Haslam, Jeffery J

    2015-03-17

    An air filter replacement system for existing buildings, vehicles, arenas, and other enclosed airspaces includes a replacement air filter for replacing a standard air filter. The replacement air filter has dimensions and air flow specifications that allow it to replace the standard air filter. The replacement air filter includes a filter material that removes radiological or biological or aerosol particles.

  10. Notions of radiation chemistry in biological systems

    International Nuclear Information System (INIS)

    Mastro, N.L. del.

    1989-10-01

    The present paper examines some aspects of the direct and indirect biological radiation effects: pair formation, free radicals, superoxide ion, hydrogen peroxide, hydroxyl radical, oxygen singlet together with the endogen radioprotector mechanisms of organisms and the ways in which an improved radioresistance of biochemical systems can be achieved. (author) [pt

  11. Performance evaluation of solar photovoltaic panel driven refrigeration system

    Science.gov (United States)

    Rajoria, C. S.; Singh, Dharmendra; Gupta, Pankaj Kumar

    2018-03-01

    The solar photovoltaic (PV) panel driven refrigeration system employs solar PV panel and play a vital role when combined with storage batteries. The variation in performance of solar PV panel driven refrigeration system has been experimentally investigated in this paper. The change in battery voltage is analyzed with respect to panel size. Different series and parallel combinations have been applied on four solar PV panels of 35W each to get 24V. With the above combination a current in the range of 3-5 ampere has been obtained depending upon the solar intensity. A refrigerator of 110 W and 50 liters is used in the present investigation which requires 0.80 ampere AC at 230 V. The required current and voltage has been obtained from an inverter which draws about 7 ampere DC from the battery bank at 24V. The compressor of the refrigerator consumed 110W which required a PV panel size of 176 W approximately. It is important to note that the compressor consumed about 300W for first 50 milliseconds, 130 W for next five seconds and gradually comes to 110 W in 65 seconds. Thus panel size should be such that it may compensate for the initial load requirement.

  12. Data driven CAN node reliability assessment for manufacturing system

    Science.gov (United States)

    Zhang, Leiming; Yuan, Yong; Lei, Yong

    2017-01-01

    The reliability of the Controller Area Network(CAN) is critical to the performance and safety of the system. However, direct bus-off time assessment tools are lacking in practice due to inaccessibility of the node information and the complexity of the node interactions upon errors. In order to measure the mean time to bus-off(MTTB) of all the nodes, a novel data driven node bus-off time assessment method for CAN network is proposed by directly using network error information. First, the corresponding network error event sequence for each node is constructed using multiple-layer network error information. Then, the generalized zero inflated Poisson process(GZIP) model is established for each node based on the error event sequence. Finally, the stochastic model is constructed to predict the MTTB of the node. The accelerated case studies with different error injection rates are conducted on a laboratory network to demonstrate the proposed method, where the network errors are generated by a computer controlled error injection system. Experiment results show that the MTTB of nodes predicted by the proposed method agree well with observations in the case studies. The proposed data driven node time to bus-off assessment method for CAN networks can successfully predict the MTTB of nodes by directly using network error event data.

  13. 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...... of a system thereby suggesting new ways of thinking specific toxicological endpoints. Furthermore, computational methods can serve as valuable input for the hypothesis generating phase of the preparations of a research project....

  14. A second inheritance system: the extension of biology through culture.

    Science.gov (United States)

    Whiten, Andrew

    2017-10-06

    By the mid-twentieth century (thus following the 'Modern Synthesis' in evolutionary biology), the behavioural sciences offered only the sketchy beginnings of a scientific literature documenting evidence for cultural inheritance in animals-the transmission of traditional behaviours via learning from others (social learning). By contrast, recent decades have seen a massive growth in the documentation of such cultural phenomena, driven by long-term field studies and complementary laboratory experiments. Here, I review the burgeoning scope of discoveries in this field, which increasingly suggest that this 'second inheritance system', built on the shoulders of the primary genetic inheritance system, occurs widely among vertebrates and possibly in invertebrates too. Its novel characteristics suggest significant implications for our understanding of evolutionary biology. I assess the extent to which this second system extends the scope of evolution, both by echoing principal properties of the primary, organic evolutionary system, and going beyond it in significant ways. This is well established in human cultural evolution; here, I address animal cultures more generally. The further major, and related, question concerns the extent to which the consequences of widespread animal cultural transmission interact with the primary, genetically based inheritance systems, shaping organic evolution.

  15. Metabolomics for functional genomics, systems biology, and biotechnology.

    Science.gov (United States)

    Saito, Kazuki; Matsuda, Fumio

    2010-01-01

    Metabolomics now plays a significant role in fundamental plant biology and applied biotechnology. Plants collectively produce a huge array of chemicals, far more than are produced by most other organisms; hence, metabolomics is of great importance in plant biology. Although substantial improvements have been made in the field of metabolomics, the uniform annotation of metabolite signals in databases and informatics through international standardization efforts remains a challenge, as does the development of new fields such as fluxome analysis and single cell analysis. The principle of transcript and metabolite cooccurrence, particularly transcriptome coexpression network analysis, is a powerful tool for decoding the function of genes in Arabidopsis thaliana. This strategy can now be used for the identification of genes involved in specific pathways in crops and medicinal plants. Metabolomics has gained importance in biotechnology applications, as exemplified by quantitative loci analysis, prediction of food quality, and evaluation of genetically modified crops. Systems biology driven by metabolome data will aid in deciphering the secrets of plant cell systems and their application to biotechnology.

  16. How synthetic membrane systems contribute to the understanding of lipid-driven endocytosis.

    Science.gov (United States)

    Schubert, Thomas; Römer, Winfried

    2015-11-01

    Synthetic membrane systems, such as giant unilamellar vesicles and solid supported lipid bilayers, have widened our understanding of biological processes occurring at or through membranes. Artificial systems are particularly suited to study the inherent properties of membranes with regard to their components and characteristics. This review critically reflects the emerging molecular mechanism of lipid-driven endocytosis and the impact of model membrane systems in elucidating the complex interplay of biomolecules within this process. Lipid receptor clustering induced by binding of several toxins, viruses and bacteria to the plasma membrane leads to local membrane bending and formation of tubular membrane invaginations. Here, lipid shape, and protein structure and valency are the essential parameters in membrane deformation. Combining observations of complex cellular processes and their reconstitution on minimal systems seems to be a promising future approach to resolve basic underlying mechanisms. This article is part of a Special Issue entitled: Mechanobiology. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Systems biology and p4 medicine: past, present, and future.

    Science.gov (United States)

    Hood, Leroy

    2013-04-01

    Studying complex biological systems in a holistic rather than a "one gene or one protein" at a time approach requires the concerted effort of scientists from a wide variety of disciplines. The Institute for Systems Biology (ISB) has seamlessly integrated these disparate fields to create a cross-disciplinary platform and culture in which "biology drives technology drives computation." To achieve this platform/culture, it has been necessary for cross-disciplinary ISB scientists to learn one another's languages and work together effectively in teams. The focus of this "systems" approach on disease has led to a discipline denoted systems medicine. The advent of technological breakthroughs in the fields of genomics, proteomics, and, indeed, the other "omics" is catalyzing striking advances in systems medicine that have and are transforming diagnostic and therapeutic strategies. Systems medicine has united genomics and genetics through family genomics to more readily identify disease genes. It has made blood a window into health and disease. It is leading to the stratification of diseases (division into discrete subtypes) for proper impedance match against drugs and the stratification of patients into subgroups that respond to environmental challenges in a similar manner (e.g. response to drugs, response to toxins, etc.). The convergence of patient-activated social networks, big data and their analytics, and systems medicine has led to a P4 medicine that is predictive, preventive, personalized, and participatory. Medicine will focus on each individual. It will become proactive in nature. It will increasingly focus on wellness rather than disease. For example, in 10 years each patient will be surrounded by a virtual cloud of billions of data points, and we will have the tools to reduce this enormous data dimensionality into simple hypotheses about how to optimize wellness and avoid disease for each individual. P4 medicine will be able to detect and treat perturbations in

  18. Data-Driven Predictive Direct Load Control of Refrigeration Systems

    DEFF Research Database (Denmark)

    Shafiei, Seyed Ehsan; Knudsen, Torben; Wisniewski, Rafal

    2015-01-01

    A predictive control using subspace identification is applied for the smart grid integration of refrigeration systems under a direct load control scheme. A realistic demand response scenario based on regulation of the electrical power consumption is considered. A receding horizon optimal control...... is proposed to fulfil two important objectives: to secure high coefficient of performance and to participate in power consumption management. Moreover, a new method for design of input signals for system identification is put forward. The control method is fully data driven without an explicit use of model...... against real data. The performance improvement results in a 22% reduction in the energy consumption. A comparative simulation is accomplished showing the superiority of the method over the existing approaches in terms of the load following performance....

  19. Selection of initial events of accelerator driven subcritical system

    International Nuclear Information System (INIS)

    Wang Qianglong; Hu Liqin; Wang Jiaqun; Li Yazhou; Yang Zhiyi

    2013-01-01

    The Probabilistic Safety Assessment (PSA) is an important tool in reactor safety analysis and a significant reference to the design and operation of reactor. It is the origin and foundation of the PSA for a reactor to select the initial events. Accelerator Driven Subcritical System (ADS) has advanced design characteristics, complicated subsystems and little engineering and operating experience, which makes it much more difficult to identify the initial events of ADS. Based on the current design project of ADS, the system's safety characteristics and special issues were analyzed in this article. After a series of deductions with Master Logic Diagram (MLD) and considering the relating experience of other advanced research reactors, a preliminary initial events was listed finally, which provided the foundation for the next safety assessment. (authors)

  20. Chaste: A test-driven approach to software development for biological modelling

    KAUST Repository

    Pitt-Francis, Joe

    2009-12-01

    Chaste (\\'Cancer, heart and soft-tissue environment\\') is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence. Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling. Program summary: Program title: Chaste. Catalogue identifier: AEFD_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFD_v1_0.html. Program obtainable from: CPC Program Library, Queen\\'s University, Belfast, N. Ireland. Licensing provisions: LGPL 2.1. No. of lines in distributed program, including test data, etc.: 5 407 321. No. of bytes in distributed program, including test data, etc.: 42 004 554. Distribution format: tar.gz. Programming language: C++. Operating system: Unix. Has the code been vectorised or parallelized?: Yes. Parallelized using MPI. RAM:< 90   Megabytes for two of the scenarios described in Section 6 of the manuscript (Monodomain re-entry on a slab or Cylindrical crypt simulation). Up to 16 Gigabytes (distributed across processors) for full resolution bidomain cardiac simulation. Classification: 3. External routines: Boost, CodeSynthesis XSD, CxxTest, HDF5, METIS, MPI, PETSc, Triangle, Xerces. Nature of problem: Chaste may be used for solving coupled ODE and PDE systems arising from modelling biological systems. Use of Chaste in two application areas are described in this paper: cardiac

  1. Systems Biology and P4 Medicine: Past, Present, and Future

    Directory of Open Access Journals (Sweden)

    Leroy Hood

    2013-04-01

    Full Text Available Studying complex biological systems in a holistic rather than a “one gene or one protein” at a time approach requires the concerted effort of scientists from a wide variety of disciplines. The Institute for Systems Biology (ISB has seamlessly integrated these disparate fields to create a cross-disciplinary platform and culture in which “biology drives technology drives computation.” To achieve this platform/culture, it has been necessary for cross-disciplinary ISB scientists to learn one another’s languages and work together effectively in teams. The focus of this “systems” approach on disease has led to a discipline denoted systems medicine. The advent of technological breakthroughs in the fields of genomics, proteomics, and, indeed, the other “omics” is catalyzing striking advances in systems medicine that have and are transforming diagnostic and therapeutic strategies. Systems medicine has united genomics and genetics through family genomics to more readily identify disease genes. It has made blood a window into health and disease. It is leading to the stratification of diseases (division into discrete subtypes for proper impedance match against drugs and the stratification of patients into subgroups that respond to environmental challenges in a similar manner (e.g. response to drugs, response to toxins, etc.. The convergence of patient-activated social networks, big data and their analytics, and systems medicine has led to a P4 medicine that is predictive, preventive, personalized, and participatory. Medicine will focus on each individual. It will become proactive in nature. It will increasingly focus on wellness rather than disease. For example, in 10 years each patient will be surrounded by a virtual cloud of billions of data points, and we will have the tools to reduce this enormous data dimensionality into simple hypotheses about how to optimize wellness and avoid disease for each individual. P4 medicine will be able to

  2. Computational Model of a Biomass Driven Absorption Refrigeration System

    Directory of Open Access Journals (Sweden)

    Munyeowaji Mbikan

    2017-02-01

    Full Text Available The impact of vapour compression refrigeration is the main push for scientists to find an alternative sustainable technology. Vapour absorption is an ideal technology which makes use of waste heat or renewable heat, such as biomass, to drive absorption chillers from medium to large applications. In this paper, the aim was to investigate the feasibility of a biomass driven aqua-ammonia absorption system. An estimation of the solid biomass fuel quantity required to provide heat for the operation of a vapour absorption refrigeration cycle (VARC is presented; the quantity of biomass required depends on the fuel density and the efficiency of the combustion and heat transfer systems. A single-stage aqua-ammonia refrigeration system analysis routine was developed to evaluate the system performance and ascertain the rate of energy transfer required to operate the system, and hence, the biomass quantity needed. In conclusion, this study demonstrated the results of the performance of a computational model of an aqua-ammonia system under a range of parameters. The model showed good agreement with published experimental data.

  3. Boundary conditions for open quantum systems driven far from equilibrium

    Science.gov (United States)

    Frensley, William R.

    1990-07-01

    This is a study of simple kinetic models of open systems, in the sense of systems that can exchange conserved particles with their environment. The system is assumed to be one dimensional and situated between two particle reservoirs. Such a system is readily driven far from equilibrium if the chemical potentials of the reservoirs differ appreciably. The openness of the system modifies the spatial boundary conditions on the single-particle Liouville-von Neumann equation, leading to a non-Hermitian Liouville operator. If the open-system boundary conditions are time reversible, exponentially growing (unphysical) solutions are introduced into the time dependence of the density matrix. This problem is avoided by applying time-irreversible boundary conditions to the Wigner distribution function. These boundary conditions model the external environment as ideal particle reservoirs with properties analogous to those of a blackbody. This time-irreversible model may be numerically evaluated in a discrete approximation and has been applied to the study of a resonant-tunneling semiconductor diode. The physical and mathematical properties of the irreversible kinetic model, in both its discrete and its continuum formulations, are examined in detail. The model demonstrates the distinction in kinetic theory between commutator superoperators, which may become non-Hermitian to describe irreversible behavior, and anticommutator superoperators, which remain Hermitian and are used to evaluate physical observables.

  4. Set membership experimental design for biological systems

    Directory of Open Access Journals (Sweden)

    Marvel Skylar W

    2012-03-01

    Full Text Available Abstract Background Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. Results In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. Conclusions The practicability of our approach is illustrated with a case study. This

  5. Optoelectronic system and apparatus for connection to biological systems

    Science.gov (United States)

    Okandan, Murat; Nielson, Gregory N.

    2018-03-06

    The present invention relates to a biological probe structure, as well as apparatuses, systems, and methods employing this structure. In particular embodiments, the structure includes a hermetically sealed unit configured to receive and transmit one or more optical signals. Furthermore, the structure can be implanted subcutaneously and interrogated externally. In this manner, a minimally invasive method can be employed to detect, treat, and/or assess the biological target. Additional methods and systems are also provided.

  6. A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

    Science.gov (United States)

    Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

    2016-06-17

    Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

  7. MYRRHA project: an Accelerator Driven System (ADS) Prototype

    Energy Technology Data Exchange (ETDEWEB)

    Ait Abderrahim, H

    2000-07-01

    The goal of the MYRRHA project is to investigate the design, development and realisation of a versatile neutron source based on an Accelerator Driven System (ADS). Efforts in 1999 were focussed on the optimisation of a high-performance device with a maximum neutron flux for MA irradiation experiments of 1.10{sup 1}'5 n/cm{sup 2}.s with neutron energies exceeding 0.75 MeV and about 3.10{sup 15} n/cm{sup 2}.s for all energies. Design proposals for different MYRRHA ADS components including the accelerator and the spallation source were elaborated. Potential applications of an ADS neutron source as well as various engineering aspects are discussed.

  8. MYRRHA: a multipurpose accelerator driven system for research and development

    International Nuclear Information System (INIS)

    Tichelen Van, K.; Malambu, E.; Benoit, Ph.; Kupschus, P.; Ait Abderrahim, H.; Vandeplassche, D.; Ternier, S.; Jongen, Y.

    2001-01-01

    The development of a new nuclear installation that is able to fulfil the economical, social, environmental and technological demands, is a cornerstone for the future provision of sustainable energy. Accelerator Driven Systems (ADS) can pave the way for a more environmentally safe and acceptable nuclear energy production. Fundamental and applied R and D are crucial in the development of ADS technologies and demand the availability of appropriate prototype installations. In answer to this need and in order to update its current irradiation potential, the Belgian Nuclear Research Centre (SCK·CEN), in partnership with Ion Beam Applications s. a. (IBA), is launching the MYRRHA project. It is focussed on the design, development and realisation of a modular and flexible irradiation facility based on the ADS concept. This paper describes the concept, the applications foreseen in the MYRRHA installation and the accompanying design activities currently being performed at SCK·CEN and IBA. (authors)

  9. Economic analysis of the fusion-driven subcritical system

    International Nuclear Information System (INIS)

    Huang Desuo; Wu Yican; Chu Delin; Hu Liqin

    2004-01-01

    The economic performance of the Fusion-Driven Subcritical system (FDS) is discussed. At first, as an example, the impacts of parameters, such as plasma aspect-ratio, elongation, normalized beta, on-axis toroidal field and the blanket energy-gain are analyzed on the costs of the typical case (moderate aspect-ratio) of FDS. Then, the economic characteristics of the 3 possible scenarios of FDS are estimated with respect to the neutronics parameters. The results calculated with the SYSCODE developed by the FDS team show that the cost of electricity of Scenario-1 (low aspect-ratio) and Scenario-2 (moderate aspect-ratio) of FDS is cheaper than that of pure fusion power plant at the same plane size (1 GW e ). The cost of electricity of the FDS power plant depends heavily on the functions of blanket and the blanket energy-gain. (authors)

  10. Radiological Hazard of Spallation Products in Accelerator-Driven System

    International Nuclear Information System (INIS)

    Saito, M.; Stankovskii, A.; Artisyuk, V.; Korovin, Yu.; Shmelev, A.; Titarenko, Yu.

    2002-01-01

    The central issue underlying this paper is related to elucidating the hazard of radioactive spallation products that might be an important factor affecting the design option of accelerator-driven systems (ADSs). Hazard analysis based on the concept of Annual Limit on Intake identifies alpha-emitting isotopes of rare earths (REs) (dysprosium, gadolinium, and samarium) as the dominant contributors to the overall toxicity of traditional (W, Pb, Pb-Bi) targets. The matter is addressed from several points of view: code validation to simulate their yields, choice of material for the neutron producing targets, and challenging the beam type. The paper quantitatively determines the domain in which the toxicity of REs exceeds that of polonium activation products broadly discussed now in connection with advertising lead-bismuth technology for the needs of ADSs

  11. MYRRHA: A multipurpose accelerator driven system for research and development

    International Nuclear Information System (INIS)

    Van Tichelen, K.; Malambu, E.; Benoit, Ph.; Kupschus, P.; Ait Abderrahim, H.

    2000-01-01

    The development of a new nuclear installation that is able to fulfil the economical, social, environmental and technological demands, is of first importance for the future of sustainable energy provision. Accelerator Driven Systems can pave the way for a more environ- mentally safe and acceptable nuclear energy production. Fundamental and applied R and D are crucial in the development of ADS technologies and demand the availability of appropriate prototype installations. In answer to this need and in order to update its current irradiation potential, the Belgian Nuclear Research Centre (SCK.CEN) has launched the Myrrha project. It is focussed on the design, development and realisation of a modular and flexible irradiation facility based on ADS. This paper describes the concept, the applications fore- seen in the Myrrha installation and the accompanying design activities currently being performed at SCK.CEN. (authors)

  12. MYRRHA project: an Accelerator Driven System (ADS) Prototype

    International Nuclear Information System (INIS)

    Ait Abderrahim, H.

    2000-01-01

    The goal of the MYRRHA project is to investigate the design, development and realisation of a versatile neutron source based on an Accelerator Driven System (ADS). Efforts in 1999 were focussed on the optimisation of a high-performance device with a maximum neutron flux for MA irradiation experiments of 1.10 1 '5 n/cm 2 .s with neutron energies exceeding 0.75 MeV and about 3.10 15 n/cm 2 .s for all energies. Design proposals for different MYRRHA ADS components including the accelerator and the spallation source were elaborated. Potential applications of an ADS neutron source as well as various engineering aspects are discussed

  13. Thermal hydraulics of accelerator driven system: validation and analysis

    International Nuclear Information System (INIS)

    Kumari, I.; Khanna, A.

    2014-01-01

    This paper presents validation of RELAP5/Mod4.0 code modified to incorporate Lead Bismuth Eutectic (LBE)fluid properties for simulation of Accelerator Driven System (ADS) against Barone's NACIE facility.Results of mass flow rates (MFR), Reynolds number, heat transfer coefficients, temperatures and temperature difference for three powers (10.8, 21.7 and 32.5 kW) under natural circulation of LBE match with Barone's values within 7%,18%,37%, 5% and 8% of relative error respectively. After this validation Indian ADS for thermal power of 15 kW has been simulated. Simulated profiles of temperature, MFR and pressure drop LBE and air are reported. Air and LBE temperatures of present work match with literature design values within 5% of relative error. (author)

  14. Safety and control of accelerator-driven subcritical systems

    Energy Technology Data Exchange (ETDEWEB)

    Rief, H. [Ispra Establishment (Italy); Takahashi, H. [Brookhaven National Laboratory, Long Island, NY (United States)

    1995-10-01

    To study control and safety of accelertor driven nuclear systems, a one point kinetic model was developed and programed. It deals with fast transients as a function of reactivity insertion. Doppler feedback, and the intensity of an external neutron source. The model allows for a simultaneous calculation of an equivalent critical reactor. It was validated by a comparison with a benchmark specified by the Nuclear Energy Agency Committee of Reactor Physics. Additional features are the possibility of inserting a linear or quadratic time dependent reactivity ramp which may account for gravity induced accidents like earthquakes, the possibility to shut down the external neutron source by an exponential decay law of the form exp({minus}t/{tau}), and a graphical display of the power and reactivity changes. The calculations revealed that such boosters behave quite benignly even if they are only slightly subcritical.

  15. Network-driven design principles for neuromorphic systems

    Directory of Open Access Journals (Sweden)

    Johannes ePartzsch

    2015-10-01

    Full Text Available Synaptic connectivity is typically the most resource-demanding part of neuromorphic systems. Commonly, the architecture of these systems is chosen mainly on technical considerations. As a consequence, the potential for optimization arising from the inherent constraints of connectivity models is left unused. In this article, we develop an alternative, network-driven approach to neuromorphic architecture design. We describe methods to analyse performance of existing neuromorphic architectures in emulating certain connectivity models. Furthermore, we show step-by-step how to derive a neuromorphic architecture from a given connectivity model. For this, we introduce a generalized description for architectures with a synapse matrix, which takes into account shared use of circuit components for reducing total silicon area. Architectures designed with this approach are fitted to a connectivity model, essentially adapting to its connection density. They are guaranteeing faithful reproduction of the model on chip, while requiring less total silicon area. In total, our methods allow designers to implement more area-efficient neuromorphic systems and verify usability of the connectivity resources in these systems.

  16. Network-driven design principles for neuromorphic systems.

    Science.gov (United States)

    Partzsch, Johannes; Schüffny, Rene

    2015-01-01

    Synaptic connectivity is typically the most resource-demanding part of neuromorphic systems. Commonly, the architecture of these systems is chosen mainly on technical considerations. As a consequence, the potential for optimization arising from the inherent constraints of connectivity models is left unused. In this article, we develop an alternative, network-driven approach to neuromorphic architecture design. We describe methods to analyse performance of existing neuromorphic architectures in emulating certain connectivity models. Furthermore, we show step-by-step how to derive a neuromorphic architecture from a given connectivity model. For this, we introduce a generalized description for architectures with a synapse matrix, which takes into account shared use of circuit components for reducing total silicon area. Architectures designed with this approach are fitted to a connectivity model, essentially adapting to its connection density. They are guaranteeing faithful reproduction of the model on chip, while requiring less total silicon area. In total, our methods allow designers to implement more area-efficient neuromorphic systems and verify usability of the connectivity resources in these systems.

  17. Computer codes and methods for simulating accelerator driven systems

    International Nuclear Information System (INIS)

    Sartori, E.; Byung Chan Na

    2003-01-01

    A large set of computer codes and associated data libraries have been developed by nuclear research and industry over the past half century. A large number of them are in the public domain and can be obtained under agreed conditions from different Information Centres. The areas covered comprise: basic nuclear data and models, reactor spectra and cell calculations, static and dynamic reactor analysis, criticality, radiation shielding, dosimetry and material damage, fuel behaviour, safety and hazard analysis, heat conduction and fluid flow in reactor systems, spent fuel and waste management (handling, transportation, and storage), economics of fuel cycles, impact on the environment of nuclear activities etc. These codes and models have been developed mostly for critical systems used for research or power generation and other technological applications. Many of them have not been designed for accelerator driven systems (ADS), but with competent use, they can be used for studying such systems or can form the basis for adapting existing methods to the specific needs of ADS's. The present paper describes the types of methods, codes and associated data available and their role in the applications. It provides Web addresses for facilitating searches for such tools. Some indications are given on the effect of non appropriate or 'blind' use of existing tools to ADS. Reference is made to available experimental data that can be used for validating the methods use. Finally, some international activities linked to the different computational aspects are described briefly. (author)

  18. Operational Characteristics of an Accelerator Driven Fissile Solution System

    International Nuclear Information System (INIS)

    Kimpland, Robert Herbert

    2016-01-01

    Operational characteristics represent the set of responses that a nuclear system exhibits during normal operation. Operators rely on this behavior to assess the status of the system and to predict the consequences of off-normal events. These characteristics largely refer to the relationship between power and system operating conditions. The static and dynamic behavior of a chain-reacting system, operating at sufficient power, is primarily governed by reactivity effects. The science of reactor physics has identified and evaluated a number of such effects, including Doppler broadening and shifts in the thermal neutron spectrum. Often these reactivity effects are quantified in the form of feedback coefficients that serve as coupling coefficients relating the neutron population and the physical mechanisms that drive reactivity effects, such as fissile material temperature and density changes. The operational characteristics of such nuclear systems usually manifest themselves when perturbations between system power (neutron population) and system operating conditions arise. Successful operation of such systems requires the establishment of steady equilibrium conditions. However, prior to obtaining the desired equilibrium (steady-state) conditions, an approach from zero-power (startup) must occur. This operational regime may possess certain limiting system conditions that must be maintained to achieve effective startup. Once steady-state is achieved, a key characteristic of this operational regime is the level of stability that the system possesses. Finally, a third operational regime, shutdown, may also possess limiting conditions of operation that must be maintained. This report documents the operational characteristics of a ''generic'' Accelerator Driven Fissile Solution (ADFS) system during the various operational regimes of startup, steady-state operation, and shutdown. Typical time-dependent behavior for each operational regime will be illustrated, and key system

  19. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    GPSR: A Resource for Genomics Proteomics and Systems Biology · Simple Calculation Programs for Biology Immunological Methods · Simple Calculation Programs for Biology Methods in Molecular Biology · Simple Calculation Programs for Biology Other Methods · PowerPoint Presentation · Slide 6 · Slide 7 · Prediction of ...

  20. Complex biological and bio-inspired systems

    Energy Technology Data Exchange (ETDEWEB)

    Ecke, Robert E [Los Alamos National Laboratory

    2009-01-01

    The understanding and characterization ofthe fundamental processes of the function of biological systems underpins many of the important challenges facing American society, from the pathology of infectious disease and the efficacy ofvaccines, to the development of materials that mimic biological functionality and deliver exceptional and novel structural and dynamic properties. These problems are fundamentally complex, involving many interacting components and poorly understood bio-chemical kinetics. We use the basic science of statistical physics, kinetic theory, cellular bio-chemistry, soft-matter physics, and information science to develop cell level models and explore the use ofbiomimetic materials. This project seeks to determine how cell level processes, such as response to mechanical stresses, chemical constituents and related gradients, and other cell signaling mechanisms, integrate and combine to create a functioning organism. The research focuses on the basic physical processes that take place at different levels ofthe biological organism: the basic role of molecular and chemical interactions are investigated, the dynamics of the DNA-molecule and its phylogenetic role are examined and the regulatory networks of complex biochemical processes are modeled. These efforts may lead to early warning algorithms ofpathogen outbreaks, new bio-sensors to detect hazards from pathomic viruses to chemical contaminants. Other potential applications include the development of efficient bio-fuel alternative-energy processes and the exploration ofnovel materials for energy usages. Finally, we use the notion of 'coarse-graining,' which is a method for averaging over less important degrees of freedom to develop computational models to predict cell function and systems-level response to disease, chemical stress, or biological pathomic agents. This project supports Energy Security, Threat Reduction, and the missions of the DOE Office of Science through its efforts to

  1. Life: An Introduction to Complex Systems Biology

    CERN Document Server

    Kaneko, Kunihiko

    2006-01-01

    What is life? Has molecular biology given us a satisfactory answer to this question? And if not, why, and how to carry on from there? This book examines life not from the reductionist point of view, but rather asks the question: what are the universal properties of living systems and how can one construct from there a phenomenological theory of life that leads naturally to complex processes such as reproductive cellular systems, evolution and differentiation? The presentation has been deliberately kept fairly non-technical so as to address a broad spectrum of students and researchers from the natural sciences and informatics.

  2. Two-level systems driven by large-amplitude fields

    Science.gov (United States)

    Nori, F.; Ashhab, S.; Johansson, J. R.; Zagoskin, A. M.

    2009-03-01

    We analyze the dynamics of a two-level system subject to driving by large-amplitude external fields, focusing on the resonance properties in the case of driving around the region of avoided level crossing. In particular, we consider three main questions that characterize resonance dynamics: (1) the resonance condition, (2) the frequency of the resulting oscillations on resonance, and (3) the width of the resonance. We identify the regions of validity of different approximations. In a large region of the parameter space, we use a geometric picture in order to obtain both a simple understanding of the dynamics and quantitative results. The geometric approach is obtained by dividing the evolution into discrete time steps, with each time step described by either a phase shift on the basis states or a coherent mixing process corresponding to a Landau-Zener crossing. We compare the results of the geometric picture with those of a rotating wave approximation. We also comment briefly on the prospects of employing strong driving as a useful tool to manipulate two-level systems. S. Ashhab, J.R. Johansson, A.M. Zagoskin, F. Nori, Two-level systems driven by large-amplitude fields, Phys. Rev. A 75, 063414 (2007). S. Ashhab et al, unpublished.

  3. Advanced Computational Models for Accelerator-Driven Systems

    International Nuclear Information System (INIS)

    Talamo, A.; Ravetto, P.; Gudowsk, W.

    2012-01-01

    In the nuclear engineering scientific community, Accelerator Driven Systems (ADSs) have been proposed and investigated for the transmutation of nuclear waste, especially plutonium and minor actinides. These fuels have a quite low effective delayed neutron fraction relative to uranium fuel, therefore the subcriticality of the core offers a unique safety feature with respect to critical reactors. The intrinsic safety of ADS allows the elimination of the operational control rods, hence the reactivity excess during burnup can be managed by the intensity of the proton beam, fuel shuffling, and eventually by burnable poisons. However, the intrinsic safety of a subcritical system does not guarantee that ADSs are immune from severe accidents (core melting), since the decay heat of an ADS is very similar to the one of a critical system. Normally, ADSs operate with an effective multiplication factor between 0.98 and 0.92, which means that the spallation neutron source contributes little to the neutron population. In addition, for 1 GeV incident protons and lead-bismuth target, about 50% of the spallation neutrons has energy below 1 MeV and only 15% of spallation neutrons has energies above 3 MeV. In the light of these remarks, the transmutation performances of ADS are very close to those of critical reactors.

  4. System biology and the project Encode

    Directory of Open Access Journals (Sweden)

    M. Yu. Obolenskaya

    2014-08-01

    Full Text Available The goal of this review is to give an incipient knowledge on the background of system biology, the premises to its assignment as a new branch of biology, its principles, methodology and its great achievements in identification of functional elements of human genome and regulation of their concordant­ and differential activity. The short characteristics of functional elements including the protein-coding sequences and those coding noncoding RNAs, the DNAse 1 hypersensitivity sites and methylated CpG islets, modified histones and specific 3D structure of chromatin, are represented. The topology of transcription factors network with its main motifs, hierar­chy, combination and association of transcription factors and their allelic specificity are highlighted­.

  5. Engineering biological systems toward a sustainable bioeconomy.

    Science.gov (United States)

    Lopes, Mateus Schreiner Garcez

    2015-06-01

    The nature of our major global risks calls for sustainable innovations to decouple economic growth from greenhouse gases emission. The development of sustainable technologies has been negatively impacted by several factors including sugar production costs, production scale, economic crises, hydraulic fracking development and the market inability to capture externality costs. However, advances in engineering of biological systems allow bridging the gap between exponential growth of knowledge about biology and the creation of sustainable value chains for a broad range of economic sectors. Additionally, industrial symbiosis of different biobased technologies can increase competitiveness and sustainability, leading to the development of eco-industrial parks. Reliable policies for carbon pricing and revenue reinvestments in disruptive technologies and in the deployment of eco-industrial parks could boost the welfare while addressing our major global risks toward the transition from a fossil to a biobased economy.

  6. Biological Therapy in Systemic Lupus Erythematosus

    Directory of Open Access Journals (Sweden)

    Mariana Postal

    2012-01-01

    Full Text Available Systemic lupus erythematosus (SLE is a prototypic inflammatory autoimmune disorder characterized by multisystem involvement and fluctuating disease activity. Symptoms range from rather mild manifestations such as rash or arthritis to life-threatening end-organ manifestations. Despite new and improved therapy having positively impacted the prognosis of SLE, a subgroup of patients do not respond to conventional therapy. Moreover, the risk of fatal outcomes and the damaging side effects of immunosuppressive therapies in SLE call for an improvement in the current therapeutic management. New therapeutic approaches are focused on B-cell targets, T-cell downregulation and costimulatory blockade, cytokine inhibition, and the modulation of complement. Several biological agents have been developed, but this encouraging news is associated with several disappointments in trials and provide a timely moment to reflect on biologic therapy in SLE.

  7. Multiway modeling and analysis in stem cell systems biology

    Directory of Open Access Journals (Sweden)

    Vandenberg Scott L

    2008-07-01

    Full Text Available Abstract Background Systems biology refers to multidisciplinary approaches designed to uncover emergent properties of biological systems. Stem cells are an attractive target for this analysis, due to their broad therapeutic potential. A central theme of systems biology is the use of computational modeling to reconstruct complex systems from a wealth of reductionist, molecular data (e.g., gene/protein expression, signal transduction activity, metabolic activity, etc.. A number of deterministic, probabilistic, and statistical learning models are used to understand sophisticated cellular behaviors such as protein expression during cellular differentiation and the activity of signaling networks. However, many of these models are bimodal i.e., they only consider row-column relationships. In contrast, multiway modeling techniques (also known as tensor models can analyze multimodal data, which capture much more information about complex behaviors such as cell differentiation. In particular, tensors can be very powerful tools for modeling the dynamic activity of biological networks over time. Here, we review the application of systems biology to stem cells and illustrate application of tensor analysis to model collagen-induced osteogenic differentiation of human mesenchymal stem cells. Results We applied Tucker1, Tucker3, and Parallel Factor Analysis (PARAFAC models to identify protein/gene expression patterns during extracellular matrix-induced osteogenic differentiation of human mesenchymal stem cells. In one case, we organized our data into a tensor of type protein/gene locus link × gene ontology category × osteogenic stimulant, and found that our cells expressed two distinct, stimulus-dependent sets of functionally related genes as they underwent osteogenic differentiation. In a second case, we organized DNA microarray data in a three-way tensor of gene IDs × osteogenic stimulus × replicates, and found that application of tensile strain to a

  8. Adaptable data management for systems biology investigations

    Directory of Open Access Journals (Sweden)

    Burdick David

    2009-03-01

    Full Text Available Abstract Background Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage. Results The adaptable data management system discussed is designed to support the seamless mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry. We use different content graphs to represent different views upon the data. These views are designed for different roles: equipment specific views are used to gather instrumentation information; data processing oriented views are provided to enable the rapid development of analysis applications; and research project specific views are used to organize information for individual research experiments. This management system allows for both the rapid introduction of new types of information and the evolution of the knowledge it represents. Conclusion Data management is an important aspect of any research enterprise. It is the foundation on which most applications are built, and must be easily extended to serve new functionality for new scientific areas. We have found that adopting a three-tier architecture for data management, built around distributed standardized content repositories, allows us to rapidly develop new applications to support a diverse user community.

  9. Thorium utilization in heavy water moderated Accelerator Driven Systems

    International Nuclear Information System (INIS)

    Bajpai, Anil; Degweker, S.B.; Ghosh, Biplab

    2011-01-01

    Research on Accelerator Driven Systems (ADSs) is being carried out around the world primarily with the objective of waste transmutation. Presently, the volume of waste in India is small and therefore there is little incentive to develop ADS based waste transmutation technology immediately. With limited indigenous U availability and the presence of large Th deposits in the country, there is a clear incentive to develop Th related technologies. India also has vast experience in design, construction and operation of heavy water moderated reactors. Heavy water moderated reactors employing solid Th fuels can be self sustaining, but the discharge burnups are too low to be economical. A possible way to improve the performance such reactors is to use an external neutron source as is done in ADS. This paper discusses our studies on Th utilization in heavy water moderated ADSs. The study is carried out at the lattice level. The time averaged k-infinity of the Th bundle from zero burnup up to the discharge burnup is taken to be the same as the core (ensemble) averaged k-infinity. For the purpose of the analysis we have chosen standard PHWR and AHWR assemblies. Variation of the pitch and coolant (H 2 O/D 2 O) are studied. Both, the once through cycle and the recycling option are studied. In the latter case the study is carried out for various enrichments (% 233 U in Th) of the recycled Th fuel bundles. The code DTF as modified for lattice and burnup calculations (BURNTRAN) was used for carrying out the study. The once through cycle represents the most attractive ADS concept (Th burner ADS) possible for Th utilization. It avoids reprocessing of Th spent fuel and in the ideal situation the use of any fissile material either initially or for sustaining itself. The gain in this system is however rather low requiring a high power accelerator and a substantial fraction of the power generated to be fed back to the accelerator. The self sustaining Th-U cycle in a heavy moderated ADS

  10. Transmutation of nuclear waste in accelerator-driven systems

    CERN Document Server

    Herrera-Martínez, A

    2004-01-01

    Today more than ever energy is not only a cornerstone of human development, but also a key to the environmental sustainability of economic activity. In this context, the role of nuclear power may be emphasized in the years to come. Nevertheless, the problems of nuclear waste, safety and proliferation still remain to be solved. It is believed that the use of accelerator-driven systems (ADSs) for nuclear waste transmutation and energy production would address these problems in a simple, clean and economically viable, and therefore sustainable, manner. This thesis covers the major nuclear physics aspects of ADSs, in particular the spallation process and the core neutronics specific to this type of systems. The need for accurate nuclear data is described, together with a detailed analysis of the specific isotopes and energy ranges in which this data needs to be improved and the impact of their uncertainty. Preliminary experimental results for some of these isotopes, produced by the Neutron Time-of-Flight (n_TOF) ...

  11. Macroscopic multigroup constants for accelerator driven system core calculation

    International Nuclear Information System (INIS)

    Heimlich, Adino; Santos, Rubens Souza dos

    2011-01-01

    The high-level wastes stored in facilities above ground or shallow repositories, in close connection with its nuclear power plant, can take almost 106 years before the radiotoxicity became of the order of the background. While the disposal issue is not urgent from a technical viewpoint, it is recognized that extended storage in the facilities is not acceptable since these ones cannot provide sufficient isolation in the long term and neither is it ethical to leave the waste problem to future generations. A technique to diminish this time is to transmute these long-lived elements into short-lived elements. The approach is to use an Accelerator Driven System (ADS), a sub-critical arrangement which uses a Spallation Neutron Source (SNS), after separation the minor actinides and the long-lived fission products (LLFP), to convert them to short-lived isotopes. As an advanced reactor fuel, still today, there is a few data around these type of core systems. In this paper we generate macroscopic multigroup constants for use in calculations of a typical ADS fuel, take into consideration, the ENDF/BVI data file. Four energy groups are chosen to collapse the data from ENDF/B-VI data file by PREPRO code. A typical MOX fuel cell is used to validate the methodology. The results are used to calculate one typical subcritical ADS core. (author)

  12. Analysis of Intelligent Transportation Systems Using Model-Driven Simulations

    Directory of Open Access Journals (Sweden)

    Alberto Fernández-Isabel

    2015-06-01

    Full Text Available Intelligent Transportation Systems (ITSs integrate information, sensor, control, and communication technologies to provide transport related services. Their users range from everyday commuters to policy makers and urban planners. Given the complexity of these systems and their environment, their study in real settings is frequently unfeasible. Simulations help to address this problem, but present their own issues: there can be unintended mistakes in the transition from models to code; their platforms frequently bias modeling; and it is difficult to compare works that use different models and tools. In order to overcome these problems, this paper proposes a framework for a model-driven development of these simulations. It is based on a specific modeling language that supports the integrated specification of the multiple facets of an ITS: people, their vehicles, and the external environment; and a network of sensors and actuators conveniently arranged and distributed that operates over them. The framework works with a model editor to generate specifications compliant with that language, and a code generator to produce code from them using platform specifications. There are also guidelines to help researchers in the application of this infrastructure. A case study on advanced management of traffic lights with cameras illustrates its use.

  13. Expert system driven fuzzy control application to power reactors

    International Nuclear Information System (INIS)

    Tsoukalas, L.H.; Berkan, R.C.; Upadhyaya, B.R.; Uhrig, R.E.

    1990-01-01

    For the purpose of nonlinear control and uncertainty/imprecision handling, fuzzy controllers have recently reached acclaim and increasing commercial application. The fuzzy control algorithms often require a ''supervisory'' routine that provides necessary heuristics for interface, adaptation, mode selection and other implementation issues. Performance characteristics of an on-line fuzzy controller depend strictly on the ability of such supervisory routines to manipulate the fuzzy control algorithm and enhance its control capabilities. This paper describes an expert system driven fuzzy control design application to nuclear reactor control, for the automated start-up control of the Experimental Breeder Reactor-II. The methodology is verified through computer simulations using a valid nonlinear model. The necessary heuristic decisions are identified that are vitally important for the implemention of fuzzy control in the actual plant. An expert system structure incorporating the necessary supervisory routines is discussed. The discussion also includes the possibility of synthesizing the fuzzy, exact and combined reasoning to include both inexact concepts, uncertainty and fuzziness, within the same environment

  14. It's the System, Stupid: How Systems Biology Is Transforming.

    Science.gov (United States)

    2010-01-01

    So far, little is known about systems biology and its potential for changing how we diagnose and treat disease. That will change soon, say the systems experts, who advise payers to begin learning now about how it could make healthcare efficient.

  15. Systems Biology: Impressions from a Newcomer Graduate Student in 2016

    Science.gov (United States)

    Simpson, Melanie Rae

    2016-01-01

    As a newcomer, the philosophical basis of systems biology seems intuitive and appealing, the underlying philosophy being that the whole of a living system cannot be completely understood by the study of its individual parts. Yet answers to the questions "What is systems biology?" and "What constitutes a systems biology approach in…

  16. The Feasibility of Systems Thinking in Biology Education

    Science.gov (United States)

    Boersma, Kerst; Waarlo, Arend Jan; Klaassen, Kees

    2011-01-01

    Systems thinking in biology education is an up and coming research topic, as yet with contrasting feasibility claims. In biology education systems thinking can be understood as thinking backward and forward between concrete biological objects and processes and systems models representing systems theoretical characteristics. Some studies claim that…

  17. Biological diversity in the patent system.

    Directory of Open Access Journals (Sweden)

    Paul Oldham

    Full Text Available Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI established by the Global Biodiversity Information Facility (GBIF and Encyclopedia of Life (EOL. We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8-1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on

  18. Nuclear magnetic resonance applications in biological systems

    International Nuclear Information System (INIS)

    Jiang Ling; Liu Maili

    2011-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is a state-of-the-art technology which has been widely applied in biological systems over the past decades. It is a powerful tool for macromolecular structure determination in solution, and has the unique advantage of being capable of elucidating the structure and dynamic behavior of proteins during vital biomedical processes. In this review, we introduce the recent progress in NMR techniques for studying the structure, interaction and dynamics of proteins. The methods for NMR based drug discovery and metabonomics are also briefly introduced. (authors)

  19. System for determining sizes of biological macromolecules

    International Nuclear Information System (INIS)

    Nelson, R.M.; Danby, P.C.

    1987-01-01

    An electrophoresis system for determining the sizes of radiolabelled biological macromolecules is described. It comprises a cell containing an electrophoresis gel and having at least one lane, a voltage source connected across the gel for effecting the movement of macromolecules in the lane, a detector fixed relative to the moving molecules for generating electrical pulses responsive to signals emitted by the radiolabelled molecules; a pulse processor for counting the pulse rate, and a computational device for comparing the pulse rate to a predetermined value. (author)

  20. Feasibility analysis of constant TRU feeding in waste transmutation system using accelerator-driven subcritical system

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kun Jai; Cho, Nam Zin; Jo, Chang Keun; Park, Chang Je; Kim, Do Sam; Park, Jeong Hwan [Korea Advanced Institute of Science and Technology, Taejon (Korea)

    1999-03-01

    It is probable that the issue of nuclear spent fuel and high-level waste can have negative impact on the future expansion of nuclear power programs. Accelerator-driven nuclear waste transmutation with constant composition TRU feeding which satisfies non-proliferation condition will help establish the long-range nuclear waste disposal strategy. In this study, current status of accelerator-driven transmutation of waste technology, and feasibility analysis of constant composition TRU feeding system were investigated. We ascertained that solid system using constant composition TRU is feasible with the the capability of transmutation. (author). 13 refs., 53 figs., 20 tabs.

  1. Chaste: A test-driven approach to software development for biological modelling

    KAUST Repository

    Pitt-Francis, Joe; Pathmanathan, Pras; Bernabeu, Miguel O.; Bordas, Rafel; Cooper, Jonathan; Fletcher, Alexander G.; Mirams, Gary R.; Murray, Philip; Osborne, James M.; Walter, Alex; Chapman, S. Jon; Garny, Alan; van Leeuwen, Ingeborg M.M.; Maini, Philip K.; Rodrí guez, Blanca; Waters, Sarah L.; Whiteley, Jonathan P.; Byrne, Helen M.; Gavaghan, David J.

    2009-01-01

    Chaste ('Cancer, heart and soft-tissue environment') is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology

  2. Dynamics of Change in Human-Driven and Natural Systems: Fast Forward, Slow Motion, Same Movie? A Case Study from Plant Protection

    Directory of Open Access Journals (Sweden)

    Didier Andrivon

    2012-03-01

    Full Text Available Evolutionary biology and evolutionary ecology deal with change in species and ecosystems over time, and propose mechanisms to explain and predict these. In particular, they look for generic elements that will drive any organism or phylum to adaptive changes or to extinction. This paper, using examples from the field of plant protection against pests and diseases, shows that the patterns of change observed in natural and in human-driven systems are comparable, and proposes that their similarities result from the same mechanisms operating at different paces. Human-driven systems can thus be seen simply as ‘fast-forward’ versions of natural systems, making them tractable tools to test and predict elements from evolutionary theory. Conversely, the convergence between natural and human-driven systems opens opportunities for a more widespread use of evolutionary theory when analyzing and optimizing any human-driven system, or predicting its adaptability to changing conditions.

  3. Dielectric relaxation in biological systems physical principles, methods, and applications

    CERN Document Server

    Feldman, Yuri

    2015-01-01

    This title covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems.

  4. Redefining plant systems biology: from cell to ecosystem

    NARCIS (Netherlands)

    Keurentjes, J.J.B.; Angenent, G.C.; Dicke, M.; Martins Dos Santos, V.A.P.; Molenaar, J.; Van der Putten, W.H.; de Ruiter, P.C.; Struik, P.C.; Thomma, B.P.H.J.

    2011-01-01

    Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase

  5. An Integrated Biological Control System At Hanford

    International Nuclear Information System (INIS)

    Johnson, A.R.; Caudill, J.G.; Giddings, R.F.; Rodriguez, J.M.; Roos, R.C.; Wilde, J.W.

    2010-01-01

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimate spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  6. AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

    Energy Technology Data Exchange (ETDEWEB)

    JOHNSON AR; CAUDILL JG; GIDDINGS RF; RODRIGUEZ JM; ROOS RC; WILDE JW

    2010-02-11

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimated spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  7. Thermal hydraulics of accelerator driven system windowless targets

    Directory of Open Access Journals (Sweden)

    Bruno ePanella

    2015-07-01

    Full Text Available The study of the fluid dynamics of the windowless spallation target of an Accelerator Driven System (ADS is presented. Several target mockup configurations have been investigated: the first one was a symmetrical target, that was made by two concentric cylinders, the other configurations are not symmetrical. In the experiments water has been used as hydraulic equivalent to lead-bismuth eutectic fluid. The experiments have been carried out at room temperature and flow rate up to 24 kg/s. The fluid velocity components have been measured by an ultrasound technique. The velocity field of the liquid within the target region either for the approximately axial-symmetrical configuration or for the not symmetrical ones as a function of the flow rate and the initial liquid level is presented. A comparison of experimental data with the prediction of the finite volume FLUENT code is also presented. Moreover the results of a 2D-3D numerical analysis that investigates the effect on the steady state thermal and flow fields due to the insertion of guide vanes in the windowless target unit of the EFIT project ADS nuclear reactor are presented, by analysing both the cold flow case (absence of power generation and the hot flow case (nominal power generation inside the target unit.

  8. Orbitally-driven magnetism in light actinide systems

    International Nuclear Information System (INIS)

    Cooper, B.R.; Los Alamos National Lab.

    1987-01-01

    We are interested in understanding the solid-state behavior characteristic of the transition regime between itinerant (bonding) and localized (correlated ionic) f-electron behavior in light actinide (uranium, neptunium and plutonium) systems. For the light actinides, the degree of f-electron localization is sensitive to chemical environment and varies widely depending on specific compound or alloy. It is important for any meaningful theory to reflect this sensitivity to chemical environment. We have focussed our attention initially on magnetic behavior, since the pertinent orbitally-driven magnetic behavior is both interesting in itself and valuable as a diagnostic tool for the f-electron behavior and sensitivity to chemical environment. The key aspect of the electronic behavior is the hybridization (mixing) of the f electrons with band electrons of other than f atomic parentage. To treat effects of hybridization quantitatively, we transform the physical mixing mathematically to resonant scattering of band electrons off f electrons. Anisotropic magnetic properties provide a way to measure the weighting of resonant scattering channels, and this weighting reflects the sensitivity to chemical environment. (orig.)

  9. Structural Identifiability of Dynamic Systems Biology Models.

    Science.gov (United States)

    Villaverde, Alejandro F; Barreiro, Antonio; Papachristodoulou, Antonis

    2016-10-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.

  10. Stochastic transport processes in discrete biological systems

    CERN Document Server

    Frehland, Eckart

    1982-01-01

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

  11. Model checking biological systems described using ambient calculus

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Priami, Corrado; Qualia, Paola

    2005-01-01

    Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005.......Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005....

  12. Calculating life? Duelling discourses in interdisciplinary systems biology.

    Science.gov (United States)

    Calvert, Jane; Fujimura, Joan H

    2011-06-01

    A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences. Copyright © 2010 Elsevier Ltd. All rights reserved.

  13. KIPT accelerator-driven system design and performance

    International Nuclear Information System (INIS)

    Gohar, Y.; Bolshinsky, I.; Karnaukhov, I.

    2015-01-01

    facilities and it can be used for studying accelerator-driven systems. The facility utilisation study shows that this neutron source facility has excellent capability for producing different medical isotopes. Several horizontal neutron channels are incorporated to perform basic research, including cold neutron source. This paper highlights the design, the performed analyses, and the current status of the facility. (authors)

  14. Microbial stress tolerance for biofuels. Systems biology

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zonglin Lewis (ed.) [National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL (United States)

    2012-07-01

    The development of sustainable and renewable biofuels is attracting growing interest. It is vital to develop robust microbial strains for biocatalysts that are able to function under multiple stress conditions. This Microbiology Monograph provides an overview of methods for studying microbial stress tolerance for biofuels applications using a systems biology approach. Topics covered range from mechanisms to methodology for yeast and bacteria, including the genomics of yeast tolerance and detoxification; genetics and regulation of glycogen and trehalose metabolism; programmed cell death; high gravity fermentations; ethanol tolerance; improving biomass sugar utilization by engineered Saccharomyces; the genomics on tolerance of Zymomonas mobilis; microbial solvent tolerance; control of stress tolerance in bacterial host organisms; metabolomics for ethanologenic yeast; automated proteomics work cell systems for strain improvement; and unification of gene expression data for comparable analyses under stress conditions. (orig.)

  15. Spatial Structures and Regulation in Biological Systems

    DEFF Research Database (Denmark)

    Yde, Pernille

    , and the other is the spatial regulation of biological systems, here related to different aspects of the inflammatory response. All systems are studied using computational modelling and mathematical analysis. The first part of the thesis explores different protein aggregation scenarios. In Chapter 1, we consider...... a previously studied and very general aggregation model describing frangible linear filaments. This model is especially relevant for the growth of amyloid fibres, that have been related to a number of serious human diseases, and which are known to grow in an accelerated self-enhanced manner.We derive...... model of the tissue and show how coupled cells are able to function as an excitable medium and propagate waves of high cytokine concentration through the tissue. If the internal regulation in the cells is over-productive, the model predicts a continuous amplification of cytokines, which spans the entire...

  16. Molecular profiles to biology and pathways: a systems biology approach.

    Science.gov (United States)

    Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

    2016-06-16

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

  17. An Unprecedented Revolution in Medicinal Chemistry Driven by the Progress of Biological Science.

    Science.gov (United States)

    Chou, Kuo-Chen

    2017-01-01

    The eternal or ultimate goal of medicinal chemistry is to find most effective ways to treat various diseases and extend human beings' life as long as possible. Human being is a biological entity. To realize such an ultimate goal, the inputs or breakthroughs from the advances in biological science are no doubt most important that may even drive medicinal science into a revolution. In this review article, we are to address this from several different angles. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  18. Interaction-driven versus disorder-driven transport in ultra-dilute GaAs two-dimensional hole systems

    Science.gov (United States)

    Huang, Jian; Pfeiffer, L. N.; West, K. W.

    2012-02-01

    It is well-known that the insulating behavior in the two-dimensional metal-to-insulator transition demonstrates a finite temperature conduction via hopping. Recently, however, some very strongly interacting higher purity two-dimensional electron systems at temperatures T->0 demonstrate certain nonactivated insulating behaviors that are absent in more disordered systems. Through measuring in dark the T-dependence of the conductivity of ultra-high quality 2D holes with charge densities down to 7x10^8 cm-2, an approximate power-law behavior is identified. Moreover, for the lowest charge densities, the exponent exhibits a linearly decreasing density-dependence which suggests an interaction-driven nature. Such an electron state is fragile to even a slight increase of disorder which causes a crossover from nonactivated to activated conduction. The non-activated conduction may well be an universal interaction-driven signature of an electron state of strongly correlated (semiquantum) liquid.

  19. On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

    Science.gov (United States)

    Gomez-Ramirez, Jaime; Sanz, Ricardo

    2013-09-01

    One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Evidence of market-driven size-selective fishing and the mediating effects of biological and institutional factors

    Science.gov (United States)

    Reddy, Sheila M. W.; Wentz, Allison; Aburto-Oropeza, Octavio; Maxey, Martin; Nagavarapu, Sriniketh; Leslie, Heather M.

    2014-01-01

    Market demand is often ignored or assumed to lead uniformly to the decline of resources. Yet little is known about how market demand influences natural resources in particular contexts, or the mediating effects of biological or institutional factors. Here, we investigate this problem by examining the Pacific red snapper (Lutjanus peru) fishery around La Paz, Mexico, where medium or “plate-sized” fish are sold to restaurants at a premium price. If higher demand for plate-sized fish increases the relative abundance of the smallest (recruit size class) and largest (most fecund) fish, this may be a market mechanism to increase stocks and fishermen’s revenues. We tested this hypothesis by estimating the effect of prices on the distribution of catch across size classes using daily records of prices and catch. We linked predictions from this economic choice model to a staged-based model of the fishery to estimate the effects on the stock and revenues from harvest. We found that the supply of plate-sized fish increased by 6%, while the supply of large fish decreased by 4% as a result of a 13% price premium for plate-sized fish. This market-driven size selection increased revenues (14%) but decreased total fish biomass (−3%). However, when market-driven size selection was combined with limited institutional constraints, both fish biomass (28%) and fishermen’s revenue (22%) increased. These results show that the direction and magnitude of the effects of market demand on biological populations and human behavior can depend on both biological attributes and institutional constraints. Fisheries management may capitalize on these conditional effects by implementing size-based regulations when economic and institutional incentives will enhance compliance, as in the case we describe here, or by creating compliance enhancing conditions for existing regulations. PMID:23865225

  1. Evidence of market-driven size-selective fishing and the mediating effects of biological and institutional factors.

    Science.gov (United States)

    Reddy, Sheila M W; Wentz, Allison; Aburto-Oropeza, Octavio; Maxey, Martin; Nagavarapu, Sriniketh; Leslie, Heather M

    2013-06-01

    Market demand is often ignored or assumed to lead uniformly to the decline of resources. Yet little is known about how market demand influences natural resources in particular contexts, or the mediating effects of biological or institutional factors. Here, we investigate this problem by examining the Pacific red snapper (Lutjanus peru) fishery around La Paz, Mexico, where medium or "plate-sized" fish are sold to restaurants at a premium price. If higher demand for plate-sized fish increases the relative abundance of the smallest (recruit size class) and largest (most fecund) fish, this may be a market mechanism to increase stocks and fishermen's revenues. We tested this hypothesis by estimating the effect of prices on the distribution of catch across size classes using daily records of prices and catch. We linked predictions from this economic choice model to a staged-based model of the fishery to estimate the effects on the stock and revenues from harvest. We found that the supply of plate-sized fish increased by 6%, while the supply of large fish decreased by 4% as a result of a 13% price premium for plate-sized fish. This market-driven size selection increased revenues (14%) but decreased total fish biomass (-3%). However, when market-driven size selection was combined with limited institutional constraints, both fish biomass (28%) and fishermen's revenue (22%) increased. These results show that the direction and magnitude of the effects of market demand on biological populations and human behavior can depend on both biological attributes and institutional constraints. Fisheries management may capitalize on these conditional effects by implementing size-based regulations when economic and institutional incentives will enhance compliance, as in the case we describe here, or by creating compliance enhancing conditions for existing regulations.

  2. Stabilization of breathers in a parametrically driven sine-Gordon system with loss

    DEFF Research Database (Denmark)

    Grønbech-Jensen, N.; Kivshar, Yu. S.; Samuelsen, Mogens Rugholm

    1991-01-01

    We demonstrate that in a parametrically driven sine-Gordon system with loss, a breather, if driven, can be maintained in a steady state at half the external frequency. In the small-amplitude limit the system is described by the effective perturbed nonlinear Schrödinger equation. For an arbitrary...

  3. A Timing-Driven Partitioning System for Multiple FPGAs

    Directory of Open Access Journals (Sweden)

    Kalapi Roy

    1996-01-01

    Full Text Available Field-programmable systems with multiple FPGAs on a PCB or an MCM are being used by system designers when a single FPGA is not sufficient. We address the problem of partitioning a large technology mapped FPGA circuit onto multiple FPGA devices of a specific target technology. The physical characteristics of the multiple FPGA system (MFS pose additional constraints to the circuit partitioning algorithms: the capacity of each FPGA, the timing constraints, the number of I/Os per FPGA, and the pre-designed interconnection patterns of each FPGA and the package. Existing partitioning techniques which minimize just the cut sizes of partitions fail to satisfy the above challenges. We therefore present a timing driven N-way partitioning algorithm based on simulated annealing for technology-mapped FPGA circuits. The signal path delays are estimated during partitioning using a timing model specific to a multiple FPGA architecture. The model combines all possible delay factors in a system with multiple FPGA chips of a target technology. Furthermore, we have incorporated a new dynamic net-weighting scheme to minimize the number of pin-outs for each chip. Finally, we have developed a graph-based global router for pin assignment which can handle the pre-routed connections of our MFS structure. In order to reduce the time spent in the simulated annealing phase of the partitioner, clusters of circuit components are identified by a new linear-time bottom-up clustering algorithm. The annealing-based N-way partitioner executes four times faster using the clusters as opposed to a flat netlist with improved partitioning results. For several industrial circuits, our approach outperforms the recursive min-cut bi-partitioning algorithm by 35% in terms of nets cut. Our approach also outperforms an industrial FPGA partitioner by 73% on average in terms of unroutable nets. Using the performance optimization capabilities in our approach we have successfully partitioned the

  4. Notions of similarity for systems biology models.

    Science.gov (United States)

    Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knüpfer, Christian; Liebermeister, Wolfram; Waltemath, Dagmar

    2018-01-01

    Systems biology models are rapidly increasing in complexity, size and numbers. When building large models, researchers rely on software tools for the retrieval, comparison, combination and merging of models, as well as for version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of 'similarity' may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here we survey existing methods for the comparison of models, introduce quantitative measures for model similarity, and discuss potential applications of combined similarity measures. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on a combination of different model aspects. The six aspects that we define as potentially relevant for similarity are underlying encoding, references to biological entities, quantitative behaviour, qualitative behaviour, mathematical equations and parameters and network structure. We argue that future similarity measures will benefit from combining these model aspects in flexible, problem-specific ways to mimic users' intuition about model similarity, and to support complex model searches in databases. © The Author 2016. Published by Oxford University Press.

  5. Hydrogen production from biomass by biological systems

    International Nuclear Information System (INIS)

    Sharifan, H.R.; Qader, S.

    2009-01-01

    Hydrogen gas is seen as a future energy carrier, not involved in 'greenhouse' gas and its released energy in combustion can be converted to electric power. Biological system with low energy can produce hydrogen compared to electrochemical hydrogen production via solar battery-based water splitting which requires the use of solar batteries with high energy requirements. The biological hydrogen production occurs in microalgae and cyanobacteria by photosynthesis. They consume biochemical energy to produce molecular hydrogen. Hydrogen in some algae is an anaerobic production in the absence of light. In cyanobacteria the hydrogen production simultaneously happens with nitrogen fixation, and also catalyzed by nitrogenase as a side reaction. Hydrogen production by photosynthetic bacteria is mediated by nitrogenase activity, although hydrogenases may be active for both hydrogen production and hydrogen uptake under some conditions. Genetic studies on photosynthetic microorganisms have markedly increased in recent times, relatively few genetic engineering studies have focused on altering the characteristics of these microorganisms, particularly with respect to enhancing the hydrogen-producing capabilities of photosynthetic bacteria and cyanobacteria. (author)

  6. 3S - Systematic, systemic, and systems biology and toxicology.

    Science.gov (United States)

    Smirnova, Lena; Kleinstreuer, Nicole; Corvi, Raffaella; Levchenko, Andre; Fitzpatrick, Suzanne C; Hartung, Thomas

    2018-01-01

    A biological system is more than the sum of its parts - it accomplishes many functions via synergy. Deconstructing the system down to the molecular mechanism level necessitates the complement of reconstructing functions on all levels, i.e., in our conceptualization of biology and its perturbations, our experimental models and computer modelling. Toxicology contains the somewhat arbitrary subclass "systemic toxicities"; however, there is no relevant toxic insult or general disease that is not systemic. At least inflammation and repair are involved that require coordinated signaling mechanisms across the organism. However, the more body components involved, the greater the challenge to reca-pitulate such toxicities using non-animal models. Here, the shortcomings of current systemic testing and the development of alternative approaches are summarized. We argue that we need a systematic approach to integrating existing knowledge as exemplified by systematic reviews and other evidence-based approaches. Such knowledge can guide us in modelling these systems using bioengineering and virtual computer models, i.e., via systems biology or systems toxicology approaches. Experimental multi-organ-on-chip and microphysiological systems (MPS) provide a more physiological view of the organism, facilitating more comprehensive coverage of systemic toxicities, i.e., the perturbation on organism level, without using substitute organisms (animals). The next challenge is to establish disease models, i.e., micropathophysiological systems (MPPS), to expand their utility to encompass biomedicine. Combining computational and experimental systems approaches and the chal-lenges of validating them are discussed. The suggested 3S approach promises to leverage 21st century technology and systematic thinking to achieve a paradigm change in studying systemic effects.

  7. Computational Modeling of Biological Systems From Molecules to Pathways

    CERN Document Server

    2012-01-01

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

  8. A Magnetic Sensor System for Biological Detection

    KAUST Repository

    Li, Fuquan

    2015-01-01

    Magnetic biosensors detect biological targets through sensing the stray field of magnetic beads which label the targets. Commonly, magnetic biosensors employ the “sandwich” method to immobilize biological targets, i.e., the targets are sandwiched

  9. Hologenomics: Systems-Level Host Biology.

    Science.gov (United States)

    Theis, Kevin R

    2018-01-01

    The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations. Regardless of the conclusion on the hologenome concept as an evolutionary hypothesis, a hologenomic perspective has applied value as a systems-level framework for host biology, including in medicine. Specifically, it emphasizes investigating the multivarious and dynamic interactions between patient genomes and the genomes of their diverse microbiota when attempting to elucidate etiologies of complex, noninfectious diseases.

  10. System and safety studies of accelerator driven transmutation systems. Annual report 1999

    International Nuclear Information System (INIS)

    Gudowski, Waclaw; Wallenius, Jan; Eriksson, Marcus; Carlsson, Johan; Seltborg, Per; Tucek, Kamil

    2000-05-01

    In 1996, SKB commenced funding of the project 'System and safety studies of accelerator driven transmutation systems and development of a spallation target'. The aim of the project was stated as: Development of a complete code for simulation of transmutation processes in an accelerator driven system. Application of the code for analysis of neutron flux, transmutation rates, reactivity changes, toxicity and radiation damages in the transmutation core. Build up of competence regarding issues related to spallation targets, development of research activities regarding relevant material issues. Performing of basic experiments in order to investigate the adequacy of using the spallation. target as a neutron source for a transmutation system, and participation in the planning and implementation of an international demonstration experiment. In the present report, activities within and related to the framework of the project, performed at the department of Nuclear and Reactor Physics at the Royal Institute of Technology during 1999, are accounted for

  11. System and safety studies of accelerator driven transmutation systems. Annual report 1997

    International Nuclear Information System (INIS)

    Wallenius, J.; Carlsson, Johan; Gudowski, W.

    1997-12-01

    In November 1996, SKB started financing of the project ''System and safety studies of accelerator driven transmutation systems and development of a spallation target''. The aim of the project was stated as: 1) Development of a complete code for simulation of transmutation processes in an accelerator driven system. Application of the code for analysis of neutron flux, transmutation rates, reactivity changes, toxicity and radiation damages in the transmutation core. 2) Build up of competence regarding issues related to spallation targets development of research activities regarding relevant material issues. Performing of basic experiments in order to investigate the adequacy of using the spallation target as a neutron source for a transmutation system, and participation in the planning and implementation of an international demonstration-experiment. In the present report, activities within the framework of the project performed at the department of Nuclear and Reactor Physics at the Royal Institute of Technology during 1997, are accounted for

  12. System and safety studies of accelerator driven transmutation systems. Annual report 1997

    Energy Technology Data Exchange (ETDEWEB)

    Wallenius, J.; Carlsson, Johan; Gudowski, W. [Royal Inst. of Tech., Stockholm (Sweden). Dept. of Nuclear and Reactor Physics

    1997-12-01

    In November 1996, SKB started financing of the project ``System and safety studies of accelerator driven transmutation systems and development of a spallation target``. The aim of the project was stated as: 1) Development of a complete code for simulation of transmutation processes in an accelerator driven system. Application of the code for analysis of neutron flux, transmutation rates, reactivity changes, toxicity and radiation damages in the transmutation core. 2) Build up of competence regarding issues related to spallation targets development of research activities regarding relevant material issues. Performing of basic experiments in order to investigate the adequacy of using the spallation target as a neutron source for a transmutation system, and participation in the planning and implementation of an international demonstration-experiment. In the present report, activities within the framework of the project performed at the department of Nuclear and Reactor Physics at the Royal Institute of Technology during 1997, are accounted for. 13 refs, 6 figs.

  13. System and safety studies of accelerator driven transmutation systems. Annual report 1999

    Energy Technology Data Exchange (ETDEWEB)

    Gudowski, Waclaw; Wallenius, Jan; Eriksson, Marcus; Carlsson, Johan; Seltborg, Per; Tucek, Kamil [Royal Inst. of Tech., Stockholm (Sweden). Dept. of Nuclear and Reactor Physics

    2000-05-01

    In 1996, SKB commenced funding of the project 'System and safety studies of accelerator driven transmutation systems and development of a spallation target'. The aim of the project was stated as: Development of a complete code for simulation of transmutation processes in an accelerator driven system. Application of the code for analysis of neutron flux, transmutation rates, reactivity changes, toxicity and radiation damages in the transmutation core. Build up of competence regarding issues related to spallation targets, development of research activities regarding relevant material issues. Performing of basic experiments in order to investigate the adequacy of using the spallation. target as a neutron source for a transmutation system, and participation in the planning and implementation of an international demonstration experiment. In the present report, activities within and related to the framework of the project, performed at the department of Nuclear and Reactor Physics at the Royal Institute of Technology during 1999, are accounted for.

  14. Present status of laser driven fusion--fission energy systems

    International Nuclear Information System (INIS)

    Maniscalco, J.A.; Hansen, L.F.

    1978-01-01

    The potential of laser fusion driven hybrids to produce fissile fuel and/or electricity has been investigated in the laser program at the Lawrence Livermore Laboratory (LLL) for several years. Our earlier studies used neutronic methods of analysis to estimate hybrid performance. The results were encouraging, but it was apparent that a more accurate assessment of the hybrid's potential would require studies which treat the engineering, environmental, and economic issues as well as the neutronic aspects. More recently, we have collaborated with Bechtel and Westinghouse Corporations in two engineering design studies of laser fusion driven hybrid power plants. With Bechtel, we have been engaged in a joint effort to design a laser fusion driven hybrid which emphasizes fissile fuel production while the primary objective of our joint effort with Westinghouse has been to design a hybrid which emphasizes power production. The hybrid designs which have resulted from these two studies are briefly described and analyzed by considering their most important operational parameters

  15. Biomarkers of Nanoparticles Impact on Biological Systems

    Science.gov (United States)

    Mikhailenko, V.; Ieleiko, L.; Glavin, A.; Sorochinska, J.

    Studies of nanoscale mineral fibers have demonstrated that the toxic and carcinogenic effects are related to the surface area and surface activity of inhaled particles. Particle surface characteristics are considered to be key factors in the generation of free radicals and reactive oxygen species and are related to the development of apoptosis or cancer. Existing physico-chemical methods do not always allow estimation of the nanoparticles impact on organismal and cellular levels. The aim of this study was to develop marker system for evaluation the toxic and carcinogenic effects of nanoparticles on cells. The markers are designed with respect to important nanoparticles characteristics for specific and sensitive assessment of their impact on biological system. We have studied DNA damage, the activity of xanthine oxidoreductase influencing the level of free radicals, bioenergetic status, phospholipids profile and formation of 1H-NMR-visible mobile lipid domains in Ehrlich carcinoma cells. The efficiency of the proposed marker system was tested in vivo and in vitro with the use of C60 fullerene nanoparticles and multiwalled carbon nanotubes. Our data suggest that multiwalled carbon nanotubes and fullerene C60 may pose genotoxic effect, change energy metabolism and membrane structure, alter free radical level via xanthine oxidase activation and cause mobile lipid domains formation as determined in vivo and in vitro studies on Ehrlich carcinoma cells.

  16. Systems Biology of Metabolism: Annual Review of Biochemistry

    DEFF Research Database (Denmark)

    Nielsen, Jens

    2017-01-01

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are descr...

  17. Second-Order Multiagent Systems with Event-Driven Consensus Control

    Directory of Open Access Journals (Sweden)

    Jiangping Hu

    2013-01-01

    Full Text Available Event-driven control scheduling strategies for multiagent systems play a key role in future use of embedded microprocessors of limited resources that gather information and actuate the agent control updates. In this paper, a distributed event-driven consensus problem is considered for a multi-agent system with second-order dynamics. Firstly, two kinds of event-driven control laws are, respectively, designed for both leaderless and leader-follower systems. Then, the input-to-state stability of the closed-loop multi-agent system with the proposed event-driven consensus control is analyzed and the bound of the inter-event times is ensured. Finally, some numerical examples are presented to validate the proposed event-driven consensus control.

  18. MYRRHA: a multipurpose accelerator driven system for research and development

    International Nuclear Information System (INIS)

    Benoit, Ph.; Ait Abderrahim, H.; Kupschus, P.; Malambu, E.; Tichelen, K. van; Arien, B.; Vermeersch, F.; Jongen, Y.; Vandeplassche, D.; Ternier, S.

    2001-01-01

    SCK-CEN, the Belgian Nuclear Research Centre, and IBA s.a., Ion Beam Application, a world leader in accelerator technology, want to fulfil a prominent role in the Accelerator Driven Systems field and are designing an ADS prototype, the MYRRHA Project, and conducting an associated R and D programme. The partners are foreseeing MYRRHA as a first step towards the European ADS-Demo facility. The project focuses primarily on ADS related research, i.e. structural materials and nuclear fuel research, liquid metals and associated aspects, sub-critical reactor physics and subsequently on applications such as waste transmutation, radioisotope production and safety research on sub-critical systems. In this respect, the MYRRHA system should become a new major research infrastructure for the European partners presently involved in the ADS Demo development, supporting and enabling the international R and D programs. Ion Beam Applications, the Belgium world leader in particle accelerators, had joined the MYRRHA Project to perform the accelerator development. Currently the study and preliminary conceptual design of the MYRRHA system is going on and an intensive R and D programme is conducted to assess the most risky points of the present design. This study will define the final choice of the characteristics of the facility depending on the selected fields of application to be achieved. The MYRRHA concept, as it is today, is based on the coupling of an upgraded commercial proton accelerator with a spallation target surrounded by a subcritical neutron-multiplying medium. Its design is determined by the versatility m applications that should be made possible. Further technical and/or strategic developments of the project might change the concept. A cyclotron, based on positive ion acceleration technology brings the protons up to an energy level of 350 MeV. The nominal current is 5 mA of protons. The spallation target system consists in a circuit with, at the upper part, a free

  19. Validation of Portable Muscle Tone Measurement Device Based on a Motor-Driven System

    National Research Council Canada - National Science Library

    Chen, Jia-Jin

    2001-01-01

    .... The aim of this study is to extend a sophisticated motor-driven measurement system, developed in our previous research, as a validation platform for developing a portable muscle tone measurement system...

  20. A SYSTEMIC VISION OF BIOLOGY: OVERCOMING LINEARITY

    Directory of Open Access Journals (Sweden)

    M. Mayer

    2005-07-01

    Full Text Available Many  authors have proposed  that contextualization of reality  is necessary  to teach  Biology, empha- sizing students´ social and  economic realities.   However, contextualization means  more than  this;  it is related  to working with  different kinds of phenomena  and/or objects  which enable  the  expression of scientific concepts.  Thus,  contextualization allows the integration of different contents.  Under this perspective,  the  objectives  of this  work were to articulate different  biology concepts  in order  to de- velop a systemic vision of biology; to establish  relationships with other areas of knowledge and to make concrete the  cell molecular  structure and organization as well as their  implications  on living beings´ environment, using  contextualization.  The  methodology  adopted  in this  work  was based  on three aspects:  interdisciplinarity, contextualization and development of competences,  using energy:  its flux and transformations as a thematic axis and  an approach  which allowed the  interconnection between different situations involving  these  concepts.   The  activities developed  were:  1.   dialectic exercise, involving a movement around  micro and macroscopic aspects,  by using questions  and activities,  sup- ported  by the use of alternative material  (as springs, candles on the energy, its forms, transformations and  implications  in the  biological way (microscopic  concepts;  2, Construction of molecular  models, approaching the concepts of atom,  chemical bonds and bond energy in molecules; 3. Observations de- veloped in Manguezal¨(mangrove swamp  ecosystem (Itapissuma, PE  were used to work macroscopic concepts  (as  diversity  and  classification  of plants  and  animals,  concerning  to  energy  flow through food chains and webs. A photograph register of all activities  along the course plus texts

  1. Data-Driven Cyber-Physical Systems via Real-Time Stream Analytics and Machine Learning

    OpenAIRE

    Akkaya, Ilge

    2016-01-01

    Emerging distributed cyber-physical systems (CPSs) integrate a wide range of heterogeneous components that need to be orchestrated in a dynamic environment. While model-based techniques are commonly used in CPS design, they be- come inadequate in capturing the complexity as systems become larger and extremely dynamic. The adaptive nature of the systems makes data-driven approaches highly desirable, if not necessary.Traditionally, data-driven systems utilize large volumes of static data sets t...

  2. Trans-algorithmic nature of learning in biological systems.

    Science.gov (United States)

    Shimansky, Yury P

    2018-05-02

    Learning ability is a vitally important, distinctive property of biological systems, which provides dynamic stability in non-stationary environments. Although several different types of learning have been successfully modeled using a universal computer, in general, learning cannot be described by an algorithm. In other words, algorithmic approach to describing the functioning of biological systems is not sufficient for adequate grasping of what is life. Since biosystems are parts of the physical world, one might hope that adding some physical mechanisms and principles to the concept of algorithm could provide extra possibilities for describing learning in its full generality. However, a straightforward approach to that through the so-called physical hypercomputation so far has not been successful. Here an alternative approach is proposed. Biosystems are described as achieving enumeration of possible physical compositions though random incremental modifications inflicted on them by active operating resources (AORs) in the environment. Biosystems learn through algorithmic regulation of the intensity of the above modifications according to a specific optimality criterion. From the perspective of external observers, biosystems move in the space of different algorithms driven by random modifications imposed by the environmental AORs. A particular algorithm is only a snapshot of that motion, while the motion itself is essentially trans-algorithmic. In this conceptual framework, death of unfit members of a population, for example, is viewed as a trans-algorithmic modification made in the population as a biosystem by environmental AORs. Numerous examples of AOR utilization in biosystems of different complexity, from viruses to multicellular organisms, are provided.

  3. Ecological and biological systems under extreme conditions

    Energy Technology Data Exchange (ETDEWEB)

    Zlobin, V S; Nenishkiene, V B

    1989-01-01

    The behaviour of biological and ecological systems under extreme conditions (high and low temperatures, electromagnetic fields of different frequencies, ultraviolet. X-ray and gamma radiation) is analyzed. The ecosystems of macro- and microalgae living in salt, brackinsh and fresh waters are considered in the evolutional aspect basing on their chemical and biochemical composition taking into account the mechanism of radionuclide uptake by water plant cells, osmotic regulation, water and ice structures, combined water in a living organism. The problems of life-support in cosmic flights and of mastering the planets of the Solar system, for instance Mars and Venus, utilizing some microalgae and bacteria with high adaptive properties are discussed. Abnormal water points and their role in the metabolism of a water plant cell are estimated. The 'life niches' are determined at the temperatures exceeding 100 deg C and the possibility of existence for living organisms in high pressure and temperature is grounded. Attempts are made to change the metabolism of the plant and animal cell by subjecting it to the action of electromagnetic and thermal fields, heavy water, chemical and pharmocological substances changing the structure of bound water. 333 refs.; 79 tabs.

  4. Drawing inspiration from biological optical systems

    Science.gov (United States)

    Wolpert, H. D.

    2009-08-01

    Bio-Mimicking/Bio-Inspiration: How can we not be inspired by Nature? Life has evolved on earth over the last 3.5 to 4 billion years. Materials formed during this time were not toxic; they were created at low temperatures and low pressures unlike many of the materials developed today. The natural materials formed are self-assembled, multifunctional, nonlinear, complex, adaptive, self-repairing and biodegradable. The designs that failed are fossils. Those that survived are the success stories. Natural materials are mostly formed from organics, inorganic crystals and amorphous phases. The materials make economic sense by optimizing the design of the structures or systems to meet multiple needs. We constantly "see" many similar strategies in approaches, between man and nature, but we seldom look at the details of natures approaches. The power of image processing, in many of natures creatures, is a detail that is often overlooked. Seldon does the engineer interact with the biologist and learn what nature has to teach us. The variety and complexity of biological materials and the optical systems formed should inspire us.

  5. Complexity, Analysis and Control of Singular Biological Systems

    CERN Document Server

    Zhang, Qingling; Zhang, Xue

    2012-01-01

    Complexity, Analysis and Control of Singular Biological Systems follows the control of real-world biological systems at both ecological and phyisological levels concentrating on the application of now-extensively-investigated singular system theory. Much effort has recently been dedicated to the modelling and analysis of developing bioeconomic systems and the text establishes singular examples of these, showing how proper control can help to maintain sustainable economic development of biological resources. The book begins from the essentials of singular systems theory and bifurcations before tackling  the use of various forms of control in singular biological systems using examples including predator-prey relationships and viral vaccination and quarantine control. Researchers and graduate students studying the control of complex biological systems are shown how a variety of methods can be brought to bear and practitioners working with the economics of biological systems and their control will also find the ...

  6. An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence.

    Science.gov (United States)

    Sahoo, Satya S; Bodenreider, Olivier; Rutter, Joni L; Skinner, Karen J; Sheth, Amit P

    2008-10-01

    This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. RESOURCE PAGE: http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/

  7. Network Reconstruction of Dynamic Biological Systems

    OpenAIRE

    Asadi, Behrang

    2013-01-01

    Inference of network topology from experimental data is a central endeavor in biology, since knowledge of the underlying signaling mechanisms a requirement for understanding biological phenomena. As one of the most important tools in bioinformatics area, development of methods to reconstruct biological networks has attracted remarkable attention in the current decade. Integration of different data types can lead to remarkable improvements in our ability to identify the connectivity of differe...

  8. Systems biology of microbial exopolysaccharides production

    Directory of Open Access Journals (Sweden)

    Ozlem eAtes

    2015-12-01

    Full Text Available Exopolysaccharides (EPS produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture and medicine. EPSs are mainly associated with high-value applications and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore a systems-based approach constitutes an important step towards understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan and dextran.

  9. Systems Biology of Microbial Exopolysaccharides Production.

    Science.gov (United States)

    Ates, Ozlem

    2015-01-01

    Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.

  10. Iterative Systems Biology for Medicine – time for advancing from network signature to mechanistic equations

    KAUST Repository

    Gomez-Cabrero, David

    2017-05-09

    The rise and growth of Systems Biology following the sequencing of the human genome has been astounding. Early on, an iterative wet-dry methodology was formulated which turned out as a successful approach in deciphering biological complexity. Such type of analysis effectively identified and associated molecular network signatures operative in biological processes across different systems. Yet, it has proven difficult to distinguish between causes and consequences, thus making it challenging to attack medical questions where we require precise causative drug targets and disease mechanisms beyond a web of associated markers. Here we review principal advances with regard to identification of structure, dynamics, control, and design of biological systems, following the structure in the visionary review from 2002 by Dr. Kitano. Yet, here we find that the underlying challenge of finding the governing mechanistic system equations enabling precision medicine remains open thus rendering clinical translation of systems biology arduous. However, stunning advances in raw computational power, generation of high-precision multi-faceted biological data, combined with powerful algorithms hold promise to set the stage for data-driven identification of equations implicating a fundamental understanding of living systems during health and disease.

  11. Municipal wastewater biological nutrient removal driven by the fermentation liquid of dairy wastewater.

    Science.gov (United States)

    Liu, Hui; Chen, Yinguang; Wu, Jiang

    2017-11-01

    Carbon substrate is required by biological nutrient removal (BNR) microorganism, but it is usually insufficient in the influent of many municipal wastewater treatment plants. In this study the use of ethanol-enriched fermentation liquid, which was derived from dairy wastewater, as the preferred carbon substrate of BNR was reported. First, the application of dairy wastewater and food processing wastewater and their fermentation liquid as the carbon substrate of BNR was compared in the short-term tests. The fermented wastewater showed higher BNR performance than the unfermented one, and the fermentation liquid of dairy wastewater (FL-DW), which was obtained under pH 8 and fermentation time of 6 day, exhibited the highest phosphorus (95.5%) and total nitrogen (97.6%) removal efficiencies due to its high ethanol content (57.9%). Then, the long-term performance of FL-DW acting as the carbon substrate of BNR was compared with that of acetate and ethanol, and the FL-DW showed the greatest phosphorus and total nitrogen removal. Further investigation showed that the use of FL-DW caused the highest polyhydroxyalkanoates (PHAs) synthesis in BNR microbial cells, and more PHAs were used for phosphorus uptake and denitrification rather than glycogen synthesis and microbial growth. The FL-DW can be used as a preferred carbon substrate for BNR microbes. AB: aerobic end sludge active biomass; BNR: biological nutrient removal; DW: dairy wastewater; FL-DW: fermentation liquid of dairy wastewater; FPW: food processing wastewater; FL-FPW: fermentation liquid of food processing wastewater; PHAs: polyhydroxyalkanoates; PHB: poly-3-hydroxybutyrate; PHV: poly-3-hydroxyvalerate; PH2MV: poly-3-hydroxy-2- methylvalerate; PAOs: phosphorus accumulating organisms; SBR: sequencing batch reactor; SOP: soluble ortho-phosphorus; TN: total nitrogen; TSS: total suspended solids; VSS: volatile suspended solids; VFAs: volatile fatty acids; WWTPs: wastewater treatment plants.

  12. Decomposing the effects of ocean warming on chlorophyll a concentrations into physically and biologically driven contributions

    International Nuclear Information System (INIS)

    Olonscheck, D; Hofmann, M; Schellnhuber, H J; Worm, B

    2013-01-01

    Recently compiled observational data suggest a substantial decline in the global median chlorophyll a concentration over the 20th century, a trend that appears to be linked to ocean warming. Several modelling studies have considered changes in the ocean’s physical structure as a possible cause, while experimental work supports a biological mechanism, namely an observed increase in zooplankton grazing rate that outpaces phytoplankton production at higher temperatures. Here, we present transient simulations derived from a coupled ocean general circulation and carbon cycle model forced by atmospheric fields under unabated anthropogenic global warming (IPCC SRES A1FI scenario). The simulations account for both physical and biological mechanisms, and can reproduce about one quarter of the observed chlorophyll a decline during the 20th century, when using realistically parameterized temperature sensitivity of zooplankton metabolism (Q 10 between 2 and 4) and phytoplankton growth (Q 10 ∼ 1.9). Therefore, we have employed and re-calibrated the standard ecosystem model which assumes a lower temperature sensitivity of zooplankton grazing (Q 10 = 1.1049) by re-scaling phytoplankton growth rates and zooplankton grazing rates. Our model projects a global chlorophyll a decline of >50% by the end of the 21st century. While phytoplankton abundance and chlorophyll a experience pronounced negative effects, primary production and zooplankton concentrations are less sensitive to ocean warming. Although changes in physical structure play an important role, much of the simulated change in chlorophyll a and productivity is related to the uneven temperature sensitivity of the marine ecosystem. (letter)

  13. Toxicity of silver nanoparticles in biological systems: Does the complexity of biological systems matter?

    Science.gov (United States)

    Vazquez-Muñoz, Roberto; Borrego, Belen; Juárez-Moreno, Karla; García-García, Maritza; Mota Morales, Josué D; Bogdanchikova, Nina; Huerta-Saquero, Alejandro

    2017-07-05

    Currently, nanomaterials are more frequently in our daily life, specifically in biomedicine, electronics, food, textiles and catalysis just to name a few. Although nanomaterials provide many benefits, recently their toxicity profiles have begun to be explored. In this work, the toxic effects of silver nanoparticles (35nm-average diameter and Polyvinyl-Pyrrolidone-coated) on biological systems of different levels of complexity was assessed in a comprehensive and comparatively way, through a variety of viability and toxicological assays. The studied organisms included viruses, bacteria, microalgae, fungi, animal and human cells (including cancer cell lines). It was found that biological systems of different taxonomical groups are inhibited at concentrations of silver nanoparticles within the same order of magnitude. Thus, the toxicity of nanomaterials on biological/living systems, constrained by their complexity, e.g. taxonomic groups, resulted contrary to the expected. The fact that cells and virus are inhibited with a concentration of silver nanoparticles within the same order of magnitude could be explained considering that silver nanoparticles affects very primitive cellular mechanisms by interacting with fundamental structures for cells and virus alike. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Quantifying electron transfer reactions in biological systems

    DEFF Research Database (Denmark)

    Sjulstok, Emil Sjulstok; Olsen, Jógvan Magnus Haugaard; Solov'yov, Ilia A

    2015-01-01

    which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between...

  15. Systems biology: properties of reconstructed networks

    National Research Council Canada - National Science Library

    Palsson, Bernhard

    2006-01-01

    ... between the mathematical ideas and biological processes are made clear, the book reflects the irreversible trend of increasing mathematical content in biology education. Therefore to assist both teacher and student, Palsson provides problem sets, projects, and PowerPoint slides in an associated web site and keeps the presentation in the book concrete with illustrat...

  16. Advances in pulsed-power-driven radiography system design

    International Nuclear Information System (INIS)

    Portillo, Salvador; Hinshelwood, David D.; Rovang, Dean Curtis; Cordova, Steve Ray; Oliver, Bryan Velten; Weber, Bruce V.; Welch, Dale Robert; Shelton, Bradley Allen; Sceiford, Matthew E.; Cooperstein, Gerald; Gignac, Raymond Edward; Puetz, Elizabeth A.; Rose, David Vincent; Barker, Dennis L.; Van De Valde, David M.; Droemer, Darryl W.; Wilkins, Frank Lee; Molina, Isidro; Jaramillo, Deanna M.; Swanekamp, Stephen Brian; Commisso, Robert J.; Bailey, Vernon Leslie; Maenchen, John Eric; Johnson, David Lee; Griffin, Fawn A.; Hahn, Kelly Denise; Smith, Ian

    2004-01-01

    Flash x-ray radiography has undergone a transformation in recent years with the resurgence of interest in compact, high intensity pulsed-power-driven electron beam sources. The radiographic requirements and the choice of a consistent x-ray source determine the accelerator parameters, which can be met by demonstrated Induction Voltage Adder technologies. This paper reviews the state of the art and the recent advances which have improved performance by over an order of magnitude in beam brightness and radiographic utility.

  17. Accelerator driven systems for energy production and waste incineration: Physics, design and related nuclear data

    Energy Technology Data Exchange (ETDEWEB)

    Herman, M; Stanculescu, A [International Atomic Energy Agency, Vienna (Austria); Paver, N [University of Trieste and INFN, Trieste (Italy)

    2003-06-15

    This volume contains the notes of lectures given at the workshops 'Hybrid Nuclear Systems for Energy Production, Utilisation of Actinides and Transmutation of Long-lived Radioactive Waste' and 'Nuclear Data for Science and Technology: Accelerator Driven Waste Incineration', held at the Abdus Salam ICTP in September 2001. The subject of the first workshop was focused on the so-called Accelerator Driven Systems, and covered the most important physics and technological aspects of this innovative field. The second workshop was devoted to an exhaustive survey on the acquisition, evaluation, retrieval and validation of the nuclear data relevant to the design of Accelerator Driven Systems.

  18. Transmutation of fission products in reactors and accelerator-driven systems

    International Nuclear Information System (INIS)

    Janssen, A.J.

    1994-01-01

    Energy flows and mass flows in several scenarios are considered. Economical and safety aspects of the transmutation scenarios are compared. It is difficult to find a sound motivation for the transmutation of fission products with accelerator-driven systems. If there would be any hesitation in transmuting fission products in nuclear reactors, there would be an even stronger hesitation to use accelerator-driven systems, mainly because of their lower energy efficiency and their poor cost effectiveness. The use of accelerator-driven systems could become a 'meaningful' option only if nuclear energy would be banished completely. (orig./HP)

  19. Accelerator driven systems for energy production and waste incineration: Physics, design and related nuclear data

    International Nuclear Information System (INIS)

    Herman, M.; Stanculescu, A.; Paver, N.

    2003-01-01

    This volume contains the notes of lectures given at the workshops 'Hybrid Nuclear Systems for Energy Production, Utilisation of Actinides and Transmutation of Long-lived Radioactive Waste' and 'Nuclear Data for Science and Technology: Accelerator Driven Waste Incineration', held at the Abdus Salam ICTP in September 2001. The subject of the first workshop was focused on the so-called Accelerator Driven Systems, and covered the most important physics and technological aspects of this innovative field. The second workshop was devoted to an exhaustive survey on the acquisition, evaluation, retrieval and validation of the nuclear data relevant to the design of Accelerator Driven Systems

  20. Isotopic fractionation of tritium in biological systems.

    Science.gov (United States)

    Le Goff, Pierre; Fromm, Michel; Vichot, Laurent; Badot, Pierre-Marie; Guétat, Philippe

    2014-04-01

    Isotopic fractionation of tritium is a highly relevant issue in radiation protection and requires certain radioecological considerations. Sound evaluation of this factor is indeed necessary to determine whether environmental compartments are enriched/depleted in tritium or if tritium is, on the contrary, isotopically well-distributed in a given system. The ubiquity of tritium and the standard analytical methods used to assay it may induce biases in both the measurement and the signification that is accorded to the so-called fractionation: based on an exhaustive review of the literature, we show how, sometimes large deviations may appear. It is shown that when comparing the non-exchangeable fraction of organically bound tritium (neOBT) to another fraction of tritium (e.g. tritiated water) the preparation of samples and the measurement of neOBT reported frequently led to underestimation of the ratio of tritium to hydrogen (T/H) in the non-exchangeable compartment by a factor of 5% to 50%. In the present study, corrections are proposed for most of the biological matrices studied so far. Nevertheless, the values of isotopic fractionation reported in the literature remain difficult to compare with each other, especially since the physical quantities and units often vary between authors. Some improvements are proposed to better define what should encompass the concepts of exchangeable and non-exchangeable fractions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Toward mechanical systems biology in bone.

    Science.gov (United States)

    Trüssel, Andreas; Müller, Ralph; Webster, Duncan

    2012-11-01

    Cyclic mechanical loading is perhaps the most important physiological factor regulating bone mass and shape in a way which balances optimal strength with minimal weight. This bone adaptation process spans multiple length and time scales. Forces resulting from physiological exercise at the organ scale are sensed at the cellular scale by osteocytes, which reside inside the bone matrix. Via biochemical pathways, osteocytes orchestrate the local remodeling action of osteoblasts (bone formation) and osteoclasts (bone resorption). Together these local adaptive remodeling activities sum up to strengthen bone globally at the organ scale. To resolve the underlying mechanisms it is required to identify and quantify both cause and effect across the different scales. Progress has been made at the different scales experimentally. Computational models of bone adaptation have been developed to piece together various experimental observations at the different scales into coherent and plausible mechanisms. However additional quantitative experimental validation is still required to build upon the insights which have already been achieved. In this review we discuss emerging as well as state of the art experimental and computational techniques and how they might be used in a mechanical systems biology approach to further our understanding of the mechanisms governing load induced bone adaptation, i.e., ways are outlined in which experimental and computational approaches could be coupled, in a quantitative manner to create more reliable multiscale models of bone.

  2. Interactomes, manufacturomes and relational biology: analogies between systems biology and manufacturing systems

    Science.gov (United States)

    2011-01-01

    Background We review and extend the work of Rosen and Casti who discuss category theory with regards to systems biology and manufacturing systems, respectively. Results We describe anticipatory systems, or long-range feed-forward chemical reaction chains, and compare them to open-loop manufacturing processes. We then close the loop by discussing metabolism-repair systems and describe the rationality of the self-referential equation f = f (f). This relationship is derived from some boundary conditions that, in molecular systems biology, can be stated as the cardinality of the following molecular sets must be about equal: metabolome, genome, proteome. We show that this conjecture is not likely correct so the problem of self-referential mappings for describing the boundary between living and nonliving systems remains an open question. We calculate a lower and upper bound for the number of edges in the molecular interaction network (the interactome) for two cellular organisms and for two manufacturomes for CMOS integrated circuit manufacturing. Conclusions We show that the relevant mapping relations may not be Abelian, and that these problems cannot yet be resolved because the interactomes and manufacturomes are incomplete. PMID:21689427

  3. Adapting to Biology: Maintaining Container-Closure System Compatibility with the Therapeutic Biologic Revolution.

    Science.gov (United States)

    Degrazio, Dominick

    Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to the dimension of evolving therapeutic biologics. Important concerns associated with this changeover are becoming forefront, as challenges develop of varying complexity uncommon with the synthesis and production of traditional drugs. Therefore, alternative measures must be established that aim to preserve the efficacy and functionality of a biologic that might not be implemented for small molecules. Conserving protein stability is relative to perpetuating a net equilibrium of both intrinsic and extrinsic factors. Key to sustaining this balance is the ability of container-closure systems to maintain their compatibility with the ever-changing dynamics of therapeutic biologics. Failure to recognize and adjust the material properties of packaging components to support compatibility with therapeutic biologics can compromise patient safety, drug productivity, and biological stability. This review will examine the differences between small-molecule drugs and therapeutic biologics, lay a basic foundation for understanding the stability of therapeutic biologics, and demonstrate potential sources of container-closure systems' incompatibilities with therapeutic biologics at a mechanistic level. Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to recombinantly derived therapeutic biologics. Concerns associated with this transformation are becoming prominent, as therapeutic biologics are uncharacteristic to small-molecule drugs. Maintaining the stability of a therapeutic biologic is a combination of balancing intrinsic factors and external elements within the biologic's microenvironment. An important aspect of this balance is relegated to the overall compatibility of primary, parenteral container-closure systems with therapeutic biologics

  4. Radionuclide Imaging Technologies for Biological Systems

    Energy Technology Data Exchange (ETDEWEB)

    Howell, Calvin R. [Duke Univ., Durham, NC (United States); Reid, Chantal D. [Duke Univ., Durham, NC (United States); Weisenberger, Andrew G. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

    2014-05-14

    The main objective of this project is to develop technologies and experimental techniques for studying the dynamics of physiological responses of plants to changes in their interface with the local environment and to educate a new generation of scientists in an interdisciplinary environment of biology, physics and engineering. Also an important goal is to perform measurements to demonstrate the new data that can be produced and made available to the plant-biology community using the imaging technologies and experimental techniques developed in this project. The study of the plant-environment interface includes a wide range of topics in plant physiology, e.g., the root-soil interface, resource availability, impact of herbivores, influence of microbes on root surface, and responses to toxins in the air and soil. The initial scientific motivation for our work is to improve understanding of the mechanisms for physiological responses to abrupt changes in the local environment, in particular, the responses that result in short-term adjustments in resource (e.g., sugars, nutrients and water) allocations. Data of time-dependent responses of plants to environmental changes are essential in developing mechanistic models for substance intake and resource allocation. Our approach is to use radioisotope tracing techniques to study whole-plant and plant organ (e.g., leaves, stems, roots) dynamical responses to abrupt changes in environmental conditions such as concentration of CO2 in the atmosphere, nutrient availability and lighting. To this aim we are collaborating with the Radiation Detector and Imaging Group at the Thomas Jefferson National Laboratory Facility (JLab) to develop gamma-ray and beta particle imaging systems optimized for plant studies. The radioisotope tracing measurements are conducted at the Phytotron facility at Duke University. The Phytotron is a controlled environment plant research facility with a variety of plant growth chambers. One chamber

  5. Anomalous edge states and the bulk-edge correspondence for periodically-driven two dimensional systems

    DEFF Research Database (Denmark)

    Rudner, Mark Spencer; Lindner, Netanel; Berg, Erez

    2013-01-01

    revealed phenomena that cannot be characterized by analogy to the topological classification framework for static systems. In particular, in driven systems in two dimensions (2D), robust chiral edge states can appear even though the Chern numbers of all the bulk Floquet bands are zero. Here, we elucidate...... the crucial distinctions between static and driven 2D systems, and construct a new topological invariant that yields the correct edge-state structure in the driven case. We provide formulations in both the time and frequency domains, which afford additional insight into the origins of the “anomalous” spectra...... that arise in driven systems. Possibilities for realizing these phenomena in solid-state and cold-atomic systems are discussed....

  6. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Nielsen, Jens; Jewett, Michael Christopher

    2008-01-01

    in the industrial application of this yeast. Developments in genomics and high-throughput systems biology tools are enhancing one's ability to rapidly characterize cellular behaviour, which is valuable in the field of metabolic engineering where strain characterization is often the bottleneck in strain development...... programmes. Here, the impact of systems biology on metabolic engineering is reviewed and perspectives on the role of systems biology in the design of cell factories are given....

  7. Modelling of a biologically inspired robotic fish driven by compliant parts

    International Nuclear Information System (INIS)

    Daou, Hadi El; Salumäe, Taavi; Kruusmaa, Maarja; Chambers, Lily D; Megill, William M

    2014-01-01

    Inspired by biological swimmers such as fish, a robot composed of a rigid head, a compliant body and a rigid caudal fin was built. It has the geometrical properties of a subcarangiform swimmer of the same size. The head houses a servo-motor which actuates the compliant body and the caudal fin. It achieves this by applying a concentrated moment on a point near the compliant body base. In this paper, the dynamics of the compliant body driving the robotic fish is modelled and experimentally validated. Lighthill’s elongated body theory is used to define the hydrodynamic forces on the compliant part and Rayleigh proportional damping is used to model damping. Based on the assumed modes method, an energetic approach is used to write the equations of motion of the compliant body and to compute the relationship between the applied moment and the resulting lateral deflections. Experiments on the compliant body were carried out to validate the model predictions. The results showed that a good match was achieved between the measured and predicted deformations. A discussion of the swimming motions between the real fish and the robot is presented. (paper)

  8. Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

    DEFF Research Database (Denmark)

    Green, Sara; Serban, Maria; Scholl, Raphael

    2018-01-01

    of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological...... strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties...

  9. Seasonal allergic rhinitis and systems biology-oriented biomarker discovery

    NARCIS (Netherlands)

    Baars, E.W.; Nierop, A.F.M.; Savelkoul, H.F.J.

    2015-01-01

    There is an increasing interest in science and medicine in the systems approach. Instead of the reductionist approach that focuses on the physical and chemical properties of the individual components, systems biology aims to describe, understand, and explain from the complex biological systems

  10. Breeding system and pollination biology of the semidomesticated ...

    African Journals Online (AJOL)

    Breeding system and pollination biology of the semidomesticated fruit tree, Tamarindus indica L. (Leguminosae: Caesalpinioideae ): Implications for fruit production, selective breeding, and conservation of genetic resources.

  11. How do biological systems escape 'chaotic' state?

    Indian Academy of Sciences (India)

    B J Rao

    2018-02-13

    Feb 13, 2018 ... Lorencova 2016), sociology, physics, computer science, economics and even biology ... dynamic complexity associated with them at multiple levels? .... Social anthropology and the science of chaos (Oxford: Berghahn Books).

  12. Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes

    Directory of Open Access Journals (Sweden)

    de Hoon Michiel JL

    2007-02-01

    Full Text Available Abstract Background Computational prediction methods are currently used to identify genes in prokaryote genomes. However, identification of the correct translation initiation sites remains a difficult task. Accurate translation initiation sites (TISs are important not only for the annotation of unknown proteins but also for the prediction of operons, promoters, and small non-coding RNA genes, as this typically makes use of the intergenic distance. A further problem is that most existing methods are optimized for Escherichia coli data sets; applying these methods to newly sequenced bacterial genomes may not result in an equivalent level of accuracy. Results Based on a biological representation of the translation process, we applied Bayesian statistics to create a score function for predicting translation initiation sites. In contrast to existing programs, our combination of methods uses supervised learning to optimally use the set of known translation initiation sites. We combined the Ribosome Binding Site (RBS sequence, the distance between the translation initiation site and the RBS sequence, the base composition of the start codon, the nucleotide composition (A-rich sequences following start codons, and the expected distribution of the protein length in a Bayesian scoring function. To further increase the prediction accuracy, we also took into account the operon orientation. The outcome of the procedure achieved a prediction accuracy of 93.2% in 858 E. coli genes from the EcoGene data set and 92.7% accuracy in a data set of 1243 Bacillus subtilis 'non-y' genes. We confirmed the performance in the GC-rich Gamma-Proteobacteria Herminiimonas arsenicoxydans, Pseudomonas aeruginosa, and Burkholderia pseudomallei K96243. Conclusion Hon-yaku, being based on a careful choice of elements important in translation, improved the prediction accuracy in B. subtilis data sets and other bacteria except for E. coli. We believe that most remaining

  13. Seabed resident event driven profiling system (SREP). Concept, design and tests

    Digital Repository Service at National Institute of Oceanography (India)

    Mascarenhas, A.A.M.Q.; Afzulpurkar, S.; Maurya, P.K.; Fernandes, L.; Madhan, R.; Desa, E.S.; Dabolkar, N.A.; Navelkar, G.S.; Naik, L.; Shetye, V.G.; Shetty, N.B.; Prabhudesai, S.P.; Nagvekar, S.; Vimalakumari, D.

    The seabed resident event driven profiling system (SREP) described here offers a novel, optimized approach to profiling in coastal waters from seabed to sea surface during the rough seas encountered in the southwest monsoon season (June...

  14. Autonomous Soil Assessment System: A Data-Driven Approach to Planetary Mobility Hazard Detection

    Science.gov (United States)

    Raimalwala, K.; Faragalli, M.; Reid, E.

    2018-04-01

    The Autonomous Soil Assessment System predicts mobility hazards for rovers. Its development and performance are presented, with focus on its data-driven models, machine learning algorithms, and real-time sensor data fusion for predictive analytics.

  15. Chip Integrated, Hybrid EHD/Capillary Driven Thermal Management System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Chip-Integrated, Hybrid EHD/Capillary-Driven Thermal Management System is a two year that will leverage independently attained yet related prototype hardware...

  16. Industrial systems biology and its impact on synthetic biology of yeast cell factories.

    Science.gov (United States)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-06-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  17. Industrial systems biology and its impact on synthetic biology of yeast cell factories

    DEFF Research Database (Denmark)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-01-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

  18. A Magnetic Sensor System for Biological Detection

    KAUST Repository

    Li, Fuquan

    2015-05-01

    Magnetic biosensors detect biological targets through sensing the stray field of magnetic beads which label the targets. Commonly, magnetic biosensors employ the “sandwich” method to immobilize biological targets, i.e., the targets are sandwiched between a bio-functionalized sensor surface and bio-functionalized magnetic beads. This method has been used very successfully in different application, but its execution requires a rather elaborate procedure including several washing and incubation steps. This dissertation investigates a new magnetic biosensor concept, which enables a simple and effective detection of biological targets. The biosensor takes advantage of the size difference between bare magnetic beads and compounds of magnetic beads and biological targets. First, the detection of super-paramagnetic beads via magnetic tunnel junction (MTJ) sensors is implemented. Frequency modulation is used to enhance the signal-to-noise ratio, enabling the detection of a single magnetic bead. Second, the concept of the magnetic biosensor is investigated theoretically. The biosensor consists of an MTJ sensor, which detects the stray field of magnetic beads inside of a trap on top of the MTJ. A microwire between the trap and the MTJ is used to attract magnetic beads to the trapping well by applying a current to it. The MTJ sensor’s output depends on the number of beads inside the trap. If biological targets are in the sample solution, the beads will form bead compounds consisting of beads linked to the biological targets. Since bead compounds are larger than bare beads, the number of beads inside the trapping well will depend on the presence of biological targets. Hence, the output of the MTJ sensor will depend on the biological targets. The dependences of sensor signals on the sizes of the MTJ sensor, magnetic beads and biological targets are studied to find the optimum constellations for the detection of specific biological targets. The optimization is demonstrated

  19. Numerical simulation of nonlinear dynamical systems driven by commutative noise

    International Nuclear Information System (INIS)

    Carbonell, F.; Biscay, R.J.; Jimenez, J.C.; Cruz, H. de la

    2007-01-01

    The local linearization (LL) approach has become an effective technique for the numerical integration of ordinary, random and stochastic differential equations. One of the reasons for this success is that the LL method achieves a convenient trade-off between numerical stability and computational cost. Besides, the LL method reproduces well the dynamics of nonlinear equations for which other classical methods fail. However, in the stochastic case, most of the reported works has been focused in Stochastic Differential Equations (SDE) driven by additive noise. This limits the applicability of the LL method since there is a number of interesting dynamics observed in equations with multiplicative noise. On the other hand, recent results show that commutative noise SDEs can be transformed into a random differential equation (RDE) by means of a random diffeomorfism (conjugacy). This paper takes advantages of such conjugacy property and the LL approach for defining a LL scheme for SDEs driven by commutative noise. The performance of the proposed method is illustrated by means of numerical simulations

  20. Event-Driven Contrastive Divergence for Spiking Neuromorphic Systems

    Directory of Open Access Journals (Sweden)

    Emre eNeftci

    2014-01-01

    Full Text Available Restricted Boltzmann Machines (RBMs and Deep Belief Networks have been demonstrated to perform efficiently in variety of applications, such as dimensionality reduction, feature learning, and classification. Their implementation on neuromorphic hardware platforms emulating large-scale networks of spiking neurons can have significant advantages from the perspectives of scalability, power dissipation and real-time interfacing with the environment. However the traditional RBM architecture and the commonly used training algorithm known as Contrastive Divergence (CD are based on discrete updates and exact arithmetics which do not directly map onto a dynamical neural substrate. Here, we present an event-driven variation of CD to train a RBM constructed with Integrate & Fire (I&F neurons, that is constrained by the limitations of existing and near future neuromorphic hardware platforms. Our strategy is based on neural sampling, which allows us to synthesize a spiking neural network that samples from a target Boltzmann distribution. The reverberating activity of the network replaces the discrete steps of the CD algorithm, while Spike Time Dependent Plasticity (STDP carries out the weight updates in an online, asynchronous fashion.We demonstrate our approach by training an RBM composed of leaky I&F neurons with STDP synapses to learn a generative model of the MNIST hand-written digit dataset, and by testing it in recognition, generation and cue integration tasks. Our results contribute to a machine learning-driven approach for synthesizing networks of spiking neurons capable of carrying out practical, high-level functionality.

  1. Event-driven contrastive divergence for spiking neuromorphic systems.

    Science.gov (United States)

    Neftci, Emre; Das, Srinjoy; Pedroni, Bruno; Kreutz-Delgado, Kenneth; Cauwenberghs, Gert

    2013-01-01

    Restricted Boltzmann Machines (RBMs) and Deep Belief Networks have been demonstrated to perform efficiently in a variety of applications, such as dimensionality reduction, feature learning, and classification. Their implementation on neuromorphic hardware platforms emulating large-scale networks of spiking neurons can have significant advantages from the perspectives of scalability, power dissipation and real-time interfacing with the environment. However, the traditional RBM architecture and the commonly used training algorithm known as Contrastive Divergence (CD) are based on discrete updates and exact arithmetics which do not directly map onto a dynamical neural substrate. Here, we present an event-driven variation of CD to train a RBM constructed with Integrate & Fire (I&F) neurons, that is constrained by the limitations of existing and near future neuromorphic hardware platforms. Our strategy is based on neural sampling, which allows us to synthesize a spiking neural network that samples from a target Boltzmann distribution. The recurrent activity of the network replaces the discrete steps of the CD algorithm, while Spike Time Dependent Plasticity (STDP) carries out the weight updates in an online, asynchronous fashion. We demonstrate our approach by training an RBM composed of leaky I&F neurons with STDP synapses to learn a generative model of the MNIST hand-written digit dataset, and by testing it in recognition, generation and cue integration tasks. Our results contribute to a machine learning-driven approach for synthesizing networks of spiking neurons capable of carrying out practical, high-level functionality.

  2. The aims of systems biology: between molecules and organisms.

    Science.gov (United States)

    Noble, D

    2011-05-01

    The systems approach to biology has a long history. Its recent rapid resurgence at the turn of the century reflects the problems encountered in interpreting the sequencing of the genome and the failure of that immense achievement to provide rapid and direct solutions to major multi-factorial diseases. This paper argues that systems biology is necessarily multilevel and that there is no privileged level of causality in biological systems. It is an approach rather than a separate discipline. Functionality arises from biological networks that interact with the genome, the environment and the phenotype. This view of biology is very different from the gene-centred views of neo-Darwinism and molecular biology. In neuroscience, the systems approach leads naturally to 2 important conclusions: first, that the idea of 'programs' in the brain is confusing, and second, that the self is better interpreted as a process than as an object. © Georg Thieme Verlag KG Stuttgart · New York.

  3. Climate-driven population divergence in sex-determining systems

    NARCIS (Netherlands)

    Pen, Ido; Uller, Tobias; Feldmeyer, Barbara; Harts, Anna; While, Geoffrey M.; Wapstra, Erik

    2010-01-01

    Sex determination is a fundamental biological process, yet its mechanisms are remarkably diverse(1,2). In vertebrates, sex can be determined by inherited genetic factors or by the temperature experienced during embryonic development(2,3). However, the evolutionary causes of this diversity remain

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

    CERN Document Server

    Noji, Sumihare; Ueno, Naoto; Maini, Philip

    2003-01-01

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

  5. A review of imaging techniques for systems biology

    Directory of Open Access Journals (Sweden)

    Po Ming J

    2008-08-01

    Full Text Available Abstract This paper presents a review of imaging techniques and of their utility in system biology. During the last decade systems biology has matured into a distinct field and imaging has been increasingly used to enable the interplay of experimental and theoretical biology. In this review, we describe and compare the roles of microscopy, ultrasound, CT (Computed Tomography, MRI (Magnetic Resonance Imaging, PET (Positron Emission Tomography, and molecular probes such as quantum dots and nanoshells in systems biology. As a unified application area among these different imaging techniques, examples in cancer targeting are highlighted.

  6. Hierarchical structure of biological systems: a bioengineering approach.

    Science.gov (United States)

    Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

    2014-01-01

    A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems.

  7. On the interplay between mathematics and biology: hallmarks toward a new systems biology.

    Science.gov (United States)

    Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M; Alghamdi, Mohammed Ali

    2015-03-01

    This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Programming Morphogenesis through Systems and Synthetic Biology.

    Science.gov (United States)

    Velazquez, Jeremy J; Su, Emily; Cahan, Patrick; Ebrahimkhani, Mo R

    2018-04-01

    Mammalian tissue development is an intricate, spatiotemporal process of self-organization that emerges from gene regulatory networks of differentiating stem cells. A major goal in stem cell biology is to gain a sufficient understanding of gene regulatory networks and cell-cell interactions to enable the reliable and robust engineering of morphogenesis. Here, we review advances in synthetic biology, single cell genomics, and multiscale modeling, which, when synthesized, provide a framework to achieve the ambitious goal of programming morphogenesis in complex tissues and organoids. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. About using of ion accelerators in accelerator driven systems

    Energy Technology Data Exchange (ETDEWEB)

    Chigrinov, S; Kevitskaya, A; Petlevskij, V; Rutkovskaya, C [Belarussian Academy of Sciences, Minsk-Sosny (Belarus). Radiation Physics and Chemistry Inst.

    1997-12-31

    The prospects of using deuteron and alpha particle beams in Accelerator Driven Molten Salt Breeder for simultaneous production of uranium 233 and of thermal power are discussed, disregarding the problems of reactor construction and design. It is shown that by replacing the proton beam by beams of deuterons or alpha particles the energy cost of one neutron can be reduced from 11.5 MeV down to 9.3-10 MeV. The average energy of neutrons increases from 17.7 MeV to 24.3 MeV or 28.2 MeV, respectively. Thus, the gain in the number of fissile nuclei and in thermal power production of at least 1.2 - 1.3 times can be expected in ACMB. (J.U.). 1 tab., 3 figs., 4 refs.

  10. Network science of biological systems at different scales: A review

    Science.gov (United States)

    Gosak, Marko; Markovič, Rene; Dolenšek, Jurij; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž; Perc, Matjaž

    2018-03-01

    Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present

  11. SEEK: a systems biology data and model management platform.

    NARCIS (Netherlands)

    Wolstencroft, K.J.; Owen, S.; Krebs, O.; Nguyen, Q.; Stanford, N.J.; Golebiewski, M.; Weidemann, A.; Bittkowski, M.; An, L.; Shockley, D.; Snoep, J.L.; Mueller, W.; Goble, C.

    2015-01-01

    Background: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems

  12. Plant Systems Biology at the Single-Cell Level.

    Science.gov (United States)

    Libault, Marc; Pingault, Lise; Zogli, Prince; Schiefelbein, John

    2017-11-01

    Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Tracing organizing principles: Learning from the history of systems biology

    DEFF Research Database (Denmark)

    Green, Sara; Wolkenhauer, Olaf

    2014-01-01

    on this historical background in order to increase the understanding of the motivation behind the search for general principles and to clarify different epistemic aims within systems biology. We pinpoint key aspects of earlier approaches that also underlie the current practice. These are i) the focus on relational......With the emergence of systems biology, the identification of organizing principles is being highlighted as a key research aim. Researchers attempt to “reverse engineer” the functional organization of biological systems using methodologies from mathematics, engineering and computer science while...... taking advantage of data produced by new experimental techniques. While systems biology is a relatively new approach, the quest for general principles of biological organization dates back to systems theoretic approaches in early and mid-twentieth century. The aim of this paper is to draw...

  14. Yeast systems biology to unravel the network of life

    DEFF Research Database (Denmark)

    Mustacchi, Roberta; Hohmann, S; Nielsen, Jens

    2006-01-01

    Systems biology focuses on obtaining a quantitative description of complete biological systems, even complete cellular function. In this way, it will be possible to perform computer-guided design of novel drugs, advanced therapies for treatment of complex diseases, and to perform in silico design....... Furthermore, it serves as an industrial workhorse for production of a wide range of chemicals and pharmaceuticals. Systems biology involves the combination of novel experimental techniques from different disciplines as well as functional genomics, bioinformatics and mathematical modelling, and hence no single...... laboratory has access to all the necessary competences. For this reason the Yeast Systems Biology Network (YSBN) has been established. YSBN will coordinate research efforts, in yeast systems biology and, through the recently obtained EU funding for a Coordination Action, it will be possible to set...

  15. General Purpose Data-Driven System Monitoring for Space Operations

    Data.gov (United States)

    National Aeronautics and Space Administration — Modern space propulsion and exploration system designs are becoming increasingly sophisticated and complex. Determining the health state of these systems using...

  16. Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

    Science.gov (United States)

    Jalili, Mahdi

    2018-03-01

    I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

  17. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

    NARCIS (Netherlands)

    He, F.; Murabito, E.; Westerhoff, H.V.

    2016-01-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out throughin silicotheoretical studies with the aim to guide and complement furtherin vitroandin vivoexperimental

  18. Biological Detection System Technologies Technology and Industrial Base Study. A Primer on Biological Detection Technologies

    National Research Council Canada - National Science Library

    2001-01-01

    .... and Canadian military personnel. In light of these concerns both defense departments have increased efforts to develop and field biological agent detection systems to help protect their military forces and fixed assets...

  19. The Systems Biology Research Tool: evolvable open-source software

    Directory of Open Access Journals (Sweden)

    Wright Jeremiah

    2008-06-01

    Full Text Available Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology. Conclusion The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability, to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.

  20. Scaling for Dynamical Systems in Biology.

    Science.gov (United States)

    Ledder, Glenn

    2017-11-01

    Asymptotic methods can greatly simplify the analysis of all but the simplest mathematical models and should therefore be commonplace in such biological areas as ecology and epidemiology. One essential difficulty that limits their use is that they can only be applied to a suitably scaled dimensionless version of the original dimensional model. Many books discuss nondimensionalization, but with little attention given to the problem of choosing the right scales and dimensionless parameters. In this paper, we illustrate the value of using asymptotics on a properly scaled dimensionless model, develop a set of guidelines that can be used to make good scaling choices, and offer advice for teaching these topics in differential equations or mathematical biology courses.

  1. Magnetic biosensor system to detect biological targets

    KAUST Repository

    Li, Fuquan

    2012-09-01

    Magneto-resistive sensors in combination with magnetic beads provide sensing platforms, which are small in size and highly sensitive. These platforms can be fully integrated with microchannels and electronics to enable devices capable of performing complex tasks. Commonly, a sandwich method is used that requires a specific coating of the sensor\\'s surface to immobilize magnetic beads and biological targets on top of the sensor. This paper concerns a micro device to detect biological targets using magnetic concentration, magnetic as well as mechanical trapping and magnetic sensing. Target detection is based on the size difference between bare magnetic beads and magnetic beads with targets attached. This method remedies the need for a coating layer and reduces the number of steps required to run an experiment. © 2012 IEEE.

  2. Design of Efficient Sound Systems for Low Voltage Battery Driven Applications

    DEFF Research Database (Denmark)

    Iversen, Niels Elkjær; Oortgiesen, Rien; Knott, Arnold

    2016-01-01

    The efficiency of portable battery driven sound systems is crucial as it relates to both the playback time and cost of the system. This paper presents design considerations when designing such systems. This include loudspeaker and amplifier design. Using a low resistance voice coil realized...

  3. Air driven fiber optic coupled pulser system for ZT-40

    International Nuclear Information System (INIS)

    Nunnally, W.C.; Brousseau, A.T.

    1977-01-01

    The design, construction, and operation of an air powered fiber optic coupled pulser system for initiating various high-voltage systems in the ZT-40 experiment is displayed. The air fiber optic system provides complete electrical isolation of the experimental high-voltage circuits from the digital timing and control circuits. In addition, this pulser system prevents cross talk between individual output channels and eliminates trigger system ground loops. The system uses an additional fiber optic bundle to confirm pulser output in the screen room

  4. Disposition of nuclear waste using subcritical accelerator-driven systems

    International Nuclear Information System (INIS)

    Venneri, F.; Li, N.; Williamson, M.; Houts, M.; Lawrence, G.

    1998-01-01

    Spent fuel from nuclear power plants contains large quantities of Pu, other actinides, and fission products (FP). This creates challenges for permanent disposal because of the long half-lives of some isotopes and the potential for diversion of the fissile material. Two issues of concern for the US repository concept are: (1) long-term radiological risk peaking tens-of-thousands of years in the future; and (2) short-term thermal loading (decay heat) that limits capacity. An accelerator-driven neutron source can destroy actinides through fission, and can convert long-lived fission products to shorter-lived or stable isotopes. Studies over the past decade have established that accelerator transmutation of waste (ATW) can have a major beneficial impact on the nuclear waste problem. Specifically, the ATW concept the authors are evaluating: (1) destroys over 99.9% of the actinides; (2) destroys over 99.9% of the Tc and I; (3) separates Sr-90 and Cs-137; (4) separates uranium from the spent fuel; (5) produces electric power

  5. Synthetic Biology: Engineering Living Systems from Biophysical Principles.

    Science.gov (United States)

    Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

    2017-03-28

    Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  6. Towards cross-hierarchy simulation of collisionless driven reconnection in an open system

    OpenAIRE

    R., HORIUCHI; H., OHTANI; A., ISHIZAWA

    2006-01-01

    The basic idea of a cross-hierarchy model for magnetic reconnection in an open system is proposed, where a microscopic system is surrounded by a macroscopic system and the interaction between the two systems is expressed by the plasma inflow and outflow through the system boundary. Collisionless driven reconnection in two-dimensional and three-dimensional open systems is demonstrated using an open particle simulation model developed as a microscopic part of a cross-hierarchy model. It is foun...

  7. A framework for semantic driven electronic examination system for ...

    African Journals Online (AJOL)

    The framework is implemented using Java programming language and a prototype of the proposed system is tested and compared with the existing system. Results show that words that are synonymous to any given correct answer are equally recognize as correct option. Hence, the e - examination system reliability, ...

  8. Nonequilibrium steady states and resonant tunneling in time-periodically driven systems with interactions

    Science.gov (United States)

    Qin, Tao; Hofstetter, Walter

    2018-03-01

    Time-periodically driven systems are a versatile toolbox for realizing interesting effective Hamiltonians. Heating, caused by excitations to high-energy states, is a challenge for experiments. While most setups so far address the relatively weakly interacting regime, it is of general interest to study heating in strongly correlated systems. Using Floquet dynamical mean-field theory, we study nonequilibrium steady states (NESS) in the Falicov-Kimball model, with time-periodically driven kinetic energy or interaction. We systematically investigate the nonequilibrium properties of the NESS. For a driven kinetic energy, we show that resonant tunneling, where the interaction is an integer multiple of the driving frequency, plays an important role in the heating. In the strongly correlated regime, we show that this can be well understood using Fermi's golden rule and the Schrieffer-Wolff transformation for a time-periodically driven system. We furthermore demonstrate that resonant tunneling can be used to control the population of Floquet states to achieve "photodoping." For driven interactions introduced by an oscillating magnetic field near a widely adopted Feshbach resonance, we find that the double occupancy is strongly modulated. Our calculations apply to shaken ultracold-atom systems and to solid-state systems in a spatially uniform but time-dependent electric field. They are also closely related to lattice modulation spectroscopy. Our calculations are helpful to understand the latest experiments on strongly correlated Floquet systems.

  9. Speech-driven environmental control systems--a qualitative analysis of users' perceptions.

    Science.gov (United States)

    Judge, Simon; Robertson, Zoë; Hawley, Mark; Enderby, Pam

    2009-05-01

    To explore users' experiences and perceptions of speech-driven environmental control systems (SPECS) as part of a larger project aiming to develop a new SPECS. The motivation for this part of the project was to add to the evidence base for the use of SPECS and to determine the key design specifications for a new speech-driven system from a user's perspective. Semi-structured interviews were conducted with 12 users of SPECS from around the United Kingdom. These interviews were transcribed and analysed using a qualitative method based on framework analysis. Reliability is the main influence on the use of SPECS. All the participants gave examples of occasions when their speech-driven system was unreliable; in some instances, this unreliability was reported as not being a problem (e.g., for changing television channels); however, it was perceived as a problem for more safety critical functions (e.g., opening a door). Reliability was cited by participants as the reason for using a switch-operated system as back up. Benefits of speech-driven systems focused on speech operation enabling access when other methods were not possible; quicker operation and better aesthetic considerations. Overall, there was a perception of increased independence from the use of speech-driven environmental control. In general, speech was considered a useful method of operating environmental controls by the participants interviewed; however, their perceptions regarding reliability often influenced their decision to have backup or alternative systems for certain functions.

  10. Model and information abstraction for description-driven systems

    International Nuclear Information System (INIS)

    Estrella, F.; McClatchey, R.; Kovacs, Z.; Goff, J.-M.L.

    2001-01-01

    A crucial factor in the creation of adaptable systems dealing with changing requirements is the suitability of the underlying technology in allowing the evolution of the system. A reflective system utilizes an open architecture where implicit system aspects are reified to become explicit first-class (meta-data) objects. These implicit system aspects are often fundamental structures which are inaccessible and immutable, and their reification as meta-data objects can serve as the basis for changes and extensions to the system, making it self-describing. To address the evolvability issue, the author proposes a reflective architecture based on two orthogonal abstractions-model abstraction and information abstraction. In this architecture the modeling abstractions allow for the separation of the description meta-data from the system aspects they represent so that they can be managed and versioned independently, asynchronously and explicitly

  11. Behaviors of tritium in terrestrial biological system

    International Nuclear Information System (INIS)

    Inomata, Tsuyako

    1983-01-01

    The in vivo behaviors of HTO- 3 H in food chain models in experimental animals were described. Of pregnant mice that had ingested HTO and drinking water alone for 19 days, the total 3 H content in the tissue/wet weight was greater by 20% in fetuses and newborns than in mothers, and the proportion of tissue-bound 3 H was 8-24% in mothers and 3% in fetuses. The mean 3 H concentration in the free water in tissues was about 36% of ingested HTO. When only 3 H foods were ingested for 18 days, the total 3 H content in the tissue/wet weight showed no marked difference among the mother, fetuses and newborns, nor did the bound 3 H level show great differences. With respect to the tissue distribution of 3 H, only the incorporation rate by the mother's brain from HTO was satisfactory, whereas in other organs, the mother, fetuses and newborns showed higher incorporation rates from 3 H foods. The ratio of specific radioactivity of soft tissue 3 H in mothers to HTO in drinking water exceeded 1 only for the spleen, but other tissues showed no biological concentration. Again, no biological concentration was observed with 3 H foods. Environmental HTO did not result in biological concentration of 3 H in mother mice that had ingested 3 H foods, but 3 H was rather diluted. Tissues other than the spleen showed similar values of 3 H ingestion from environmental HTO through all routes. However, the proportion of bound 3 H in the total 3 H in the soft tissue was about 1.4-1.6 times that on ingestion of HTO alone. (Chiba, N.)

  12. Optical Biosensors to Explore Biological Systems

    DEFF Research Database (Denmark)

    Palanco, Marta Espina; Mogensen, Klaus Bo; Andersen, Nils H. Skovgaard

    2016-01-01

    their capability to work in biosensor devices. For example, Raman spectroscopy can be non-invasive and can provide 1 μm of spatial resolution in 1 second of collection time, well suited for sensing. Moreover, it may give information at the single cell and even approaching the single molecule scale. Here we present...... protein may be used as an efficient sensor in an organic environment via a biomimetic membrane model. The combination of both biomimetic membranes and protein membranes as a signal transduction medium has interesting applications in biology and medicine. It is crucial that the matrix where a protein...

  13. Model-Driven Test Generation of Distributed Systems

    Science.gov (United States)

    Easwaran, Arvind; Hall, Brendan; Schweiker, Kevin

    2012-01-01

    This report describes a novel test generation technique for distributed systems. Utilizing formal models and formal verification tools, spe cifically the Symbolic Analysis Laboratory (SAL) tool-suite from SRI, we present techniques to generate concurrent test vectors for distrib uted systems. These are initially explored within an informal test validation context and later extended to achieve full MC/DC coverage of the TTEthernet protocol operating within a system-centric context.

  14. Simulator for an Accelerator-Driven Subcritical Fissile Solution System

    International Nuclear Information System (INIS)

    Klein, Steven Karl; Day, Christy M.; Determan, John C.

    2015-01-01

    LANL has developed a process to generate a progressive family of system models for a fissile solution system. This family includes a dynamic system simulation comprised of coupled nonlinear differential equations describing the time evolution of the system. Neutron kinetics, radiolytic gas generation and transport, and core thermal hydraulics are included in the DSS. Extensions to explicit operation of cooling loops and radiolytic gas handling are embedded in these systems as is a stability model. The DSS may then be converted to an implementation in Visual Studio to provide a design team the ability to rapidly estimate system performance impacts from a variety of design decisions. This provides a method to assist in optimization of the system design. Once design has been generated in some detail the C++ version of the system model may then be implemented in a LabVIEW user interface to evaluate operator controls and instrumentation and operator recognition and response to off-normal events. Taken as a set of system models the DSS, Visual Studio, and LabVIEW progression provides a comprehensive set of design support tools.

  15. Simulator for an Accelerator-Driven Subcritical Fissile Solution System

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Steven Karl [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Day, Christy M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Determan, John C. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-09-14

    LANL has developed a process to generate a progressive family of system models for a fissile solution system. This family includes a dynamic system simulation comprised of coupled nonlinear differential equations describing the time evolution of the system. Neutron kinetics, radiolytic gas generation and transport, and core thermal hydraulics are included in the DSS. Extensions to explicit operation of cooling loops and radiolytic gas handling are embedded in these systems as is a stability model. The DSS may then be converted to an implementation in Visual Studio to provide a design team the ability to rapidly estimate system performance impacts from a variety of design decisions. This provides a method to assist in optimization of the system design. Once design has been generated in some detail the C++ version of the system model may then be implemented in a LabVIEW user interface to evaluate operator controls and instrumentation and operator recognition and response to off-normal events. Taken as a set of system models the DSS, Visual Studio, and LabVIEW progression provides a comprehensive set of design support tools.

  16. Noninvasive biological sensor system for detection of drunk driving.

    Science.gov (United States)

    Murata, Kohji; Fujita, Etsunori; Kojima, Shigeyuki; Maeda, Shinitirou; Ogura, Yumi; Kamei, Tsutomu; Tsuji, Toshio; Kaneko, Shigehiko; Yoshizumi, Masao; Suzuki, Nobutaka

    2011-01-01

    Systems capable of monitoring the biological condition of a driver and issuing warnings during instances of drowsiness have recently been studied. Moreover, many researchers have reported that biological signals, such as brain waves, pulsation waves, and heart rate, are different between people who have and have not consumed alcohol. Currently, we are developing a noninvasive system to detect individuals driving under the influence of alcohol by measuring biological signals. We used the frequency time series analysis to attempt to distinguish between normal and intoxicated states of a person as the basis of the sensing system.

  17. Preliminary analysis of advanced equilibrium configuration for the fusion-driven subcritical system

    International Nuclear Information System (INIS)

    Chu Delin; Wu Bin; Wu Yican

    2003-01-01

    The Fusion-Driven Subcritical System (FDS) is a subcritical nuclear energy system driven by fusion neutron source. In this paper, an advanced plasma configuration for FDS system has been proposed, which aims at high beta, high bootstrap current and good confinement. A fixed-boundary equilibrium code has been used to obtain ideal equilibrium configuration. In order to determine the feasibility of FDS operation, a two-dimensional time-dependent free boundary simulation code has been adopted to simulate time-scale evolution of plasma current profile and boundary position. By analyses, the Reversed Shear mode as the most attractive one has been recommended for the FDS equilibrium configuration design

  18. Continuous Energy Improvement in Motor Driven Systems - A Guidebook for Industry

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert A. McCoy and John G. Douglass

    2014-02-01

    This guidebook provides a step-by-step approach to developing a motor system energy-improvement action plan. An action plan includes which motors should be repaired or replaced with higher efficiency models, recommendations on maintaining a spares inventory, and discussion of improvements in maintenance practices. The guidebook is the successor to DOE’s 1997 Energy Management for Motor Driven Systems. It builds on its predecessor publication by including topics such as power transmission systems and matching driven equipment to process requirements in addition to motors.

  19. Reduced equations of motion for quantum systems driven by diffusive Markov processes.

    Science.gov (United States)

    Sarovar, Mohan; Grace, Matthew D

    2012-09-28

    The expansion of a stochastic Liouville equation for the coupled evolution of a quantum system and an Ornstein-Uhlenbeck process into a hierarchy of coupled differential equations is a useful technique that simplifies the simulation of stochastically driven quantum systems. We expand the applicability of this technique by completely characterizing the class of diffusive Markov processes for which a useful hierarchy of equations can be derived. The expansion of this technique enables the examination of quantum systems driven by non-Gaussian stochastic processes with bounded range. We present an application of this extended technique by simulating Stark-tuned Förster resonance transfer in Rydberg atoms with nonperturbative position fluctuations.

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Bullinger Eric

    2006-12-01

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

  2. A systems biology approach to study systemic inflammation.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2014-01-01

    Systemic inflammation needs a precise control on the sequence and magnitude of occurring events. The high throughput data on the host-pathogen interactions gives us an opportunity to have a glimpse on the systemic inflammation. In this article, a dynamic Candida albicans-zebrafish interactive infectious network is built as an example to demonstrate how systems biology approach can be used to study systematic inflammation. In particular, based on microarray data of C. albicans and zebrafish during infection, the hyphal growth, zebrafish, and host-pathogen intercellular PPI networks were combined to form an integrated infectious PPI network that helps us understand the systematic mechanisms underlying the pathogenicity of C. albicans and the immune response of the host. The signaling pathways for morphogenesis and hyphal growth of C. albicans were 2 significant interactions found in the intercellular PPI network. Two cellular networks were also developed corresponding to the different infection stages (adhesion and invasion), and then compared with each other to identify proteins to gain more insight into the pathogenic role of hyphal development in the C. albicans infection process. Important defense-related proteins in zebrafish were predicted using the same approach. This integrated network consisting of intercellular invasion and cellular defense processes during infection can improve medical therapies and facilitate development of new antifungal drugs.

  3. Setting planned leadtimes in customer-order-driven assembly systems

    NARCIS (Netherlands)

    Atan, Z.; Kok, de A.G.; Dellaert, N.P.; Janssen, F.B.S.L.P.; Boxel, van R.

    2016-01-01

    We study an assembly system with a number of parallel multistage processes feeding a multistage final assembly process. Each stage has a stochastic throughput time. We assume that the system is controlled by planned leadtimes at each stage. From these planned leadtimes the start and due times of all

  4. Observation-Driven Configuration of Complex Software Systems

    Science.gov (United States)

    Sage, Aled

    2010-06-01

    The ever-increasing complexity of software systems makes them hard to comprehend, predict and tune due to emergent properties and non-deterministic behaviour. Complexity arises from the size of software systems and the wide variety of possible operating environments: the increasing choice of platforms and communication policies leads to ever more complex performance characteristics. In addition, software systems exhibit different behaviour under different workloads. Many software systems are designed to be configurable so that policies can be chosen to meet the needs of various stakeholders. For complex software systems it can be difficult to accurately predict the effects of a change and to know which configuration is most appropriate. This thesis demonstrates that it is useful to run automated experiments that measure a selection of system configurations. Experiments can find configurations that meet the stakeholders' needs, find interesting behavioural characteristics, and help produce predictive models of the system's behaviour. The design and use of ACT (Automated Configuration Tool) for running such experiments is described, in combination a number of search strategies for deciding on the configurations to measure. Design Of Experiments (DOE) is discussed, with emphasis on Taguchi Methods. These statistical methods have been used extensively in manufacturing, but have not previously been used for configuring software systems. The novel contribution here is an industrial case study, applying the combination of ACT and Taguchi Methods to DC-Directory, a product from Data Connection Ltd (DCL). The case study investigated the applicability of Taguchi Methods for configuring complex software systems. Taguchi Methods were found to be useful for modelling and configuring DC- Directory, making them a valuable addition to the techniques available to system administrators and developers.

  5. System and safety studies of accelerator driven systems for transmutation. Annual report 2007

    International Nuclear Information System (INIS)

    Arzhanov, Vasily; Fokau, Andrei; Persson, Calle; Runevall, Odd; Sandberg, Nils; Tesinsky, Milan; Wallenius, Janne; Youpeng Zhang

    2008-05-01

    Within the project 'System and safety studies of accelerator driven systems for transmutation', research on design and safety of sub-critical reactors for recycling of minor actinides is performed. During 2007, the reactor physics division at KTH has calculated safety parameters for EFIT-400 with cermet fuel, permitting to start the transient safety analysis. The accuracy of different reactivity meters applied to the YALINA facility was assessed and neutron detection studies were performed. A model to address deviations from point kinetic behaviour was developed. Studies of basic radiation damage physics included calculations of vacancy formation and activation enthalpies in bcc niobium. In order to predict the oxygen potential of inert matrix fuels, a thermo-chemical model for mixed actinide oxides was implemented in a phase equilibrium code

  6. System and safety studies of accelerator driven systems for transmutation. Annual report 2007

    Energy Technology Data Exchange (ETDEWEB)

    Arzhanov, Vasily; Fokau, Andrei; Persson, Calle; Runevall, Odd; Sandberg, Nils; Tesinsky, Milan; Wallenius, Janne; Youpeng Zhang (Div. of Reactor Physics, Royal Institute of Technology, Stockholm (Sweden))

    2008-05-15

    Within the project 'System and safety studies of accelerator driven systems for transmutation', research on design and safety of sub-critical reactors for recycling of minor actinides is performed. During 2007, the reactor physics division at KTH has calculated safety parameters for EFIT-400 with cermet fuel, permitting to start the transient safety analysis. The accuracy of different reactivity meters applied to the YALINA facility was assessed and neutron detection studies were performed. A model to address deviations from point kinetic behaviour was developed. Studies of basic radiation damage physics included calculations of vacancy formation and activation enthalpies in bcc niobium. In order to predict the oxygen potential of inert matrix fuels, a thermo-chemical model for mixed actinide oxides was implemented in a phase equilibrium code

  7. A biology-driven approach identifies the hypoxia gene signature as a predictor of the outcome of neuroblastoma patients

    Directory of Open Access Journals (Sweden)

    Fardin Paolo

    2010-07-01

    Full Text Available Abstract Background Hypoxia is a condition of low oxygen tension occurring in the tumor microenvironment and it is related to poor prognosis in human cancer. To examine the relationship between hypoxia and neuroblastoma, we generated and tested an in vitro derived hypoxia gene signature for its ability to predict patients' outcome. Results We obtained the gene expression profile of 11 hypoxic neuroblastoma cell lines and we derived a robust 62 probesets signature (NB-hypo taking advantage of the strong discriminating power of the l1-l2 feature selection technique combined with the analysis of differential gene expression. We profiled gene expression of the tumors of 88 neuroblastoma patients and divided them according to the NB-hypo expression values by K-means clustering. The NB-hypo successfully stratifies the neuroblastoma patients into good and poor prognosis groups. Multivariate Cox analysis revealed that the NB-hypo is a significant independent predictor after controlling for commonly used risk factors including the amplification of MYCN oncogene. NB-hypo increases the resolution of the MYCN stratification by dividing patients with MYCN not amplified tumors in good and poor outcome suggesting that hypoxia is associated with the aggressiveness of neuroblastoma tumor independently from MYCN amplification. Conclusions Our results demonstrate that the NB-hypo is a novel and independent prognostic factor for neuroblastoma and support the view that hypoxia is negatively correlated with tumors' outcome. We show the power of the biology-driven approach in defining hypoxia as a critical molecular program in neuroblastoma and the potential for improvement in the current criteria for risk stratification.

  8. Multi-level and hybrid modelling approaches for systems biology.

    Science.gov (United States)

    Bardini, R; Politano, G; Benso, A; Di Carlo, S

    2017-01-01

    During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The information collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the different parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different system levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field.

  9. Data analysis using a data base driven graphics animation system

    International Nuclear Information System (INIS)

    Schwieder, D.H.; Stewart, H.D.; Curtis, J.N.

    1985-01-01

    A graphics animation system has been developed at the Idaho National Engineering Laboratory (INEL) to assist engineers in the analysis of large amounts of time series data. Most prior attempts at computer animation of data involve the development of large and expensive problem-specific systems. This paper discusses a generalized interactive computer animation system designed to be used in a wide variety of data analysis applications. By using relational data base storage of graphics and control information, considerable flexibility in design and development of animated displays is achieved

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

    Science.gov (United States)

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

    2015-08-21

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

  11. Optical response in a laser-driven quantum pseudodot system

    Energy Technology Data Exchange (ETDEWEB)

    Kilic, D. Gul [Physics Department, Graduate School of Natural and Applied Sciences, Dokuz Eylül University, 35390 Izmir (Turkey); Sakiroglu, S., E-mail: serpil.sakiroglu@deu.edu.tr [Physics Department, Faculty of Science, Dokuz Eylül University, 35390 Izmir (Turkey); Ungan, F.; Yesilgul, U. [Department of Optical Engineering, Faculty of Technology, Cumhuriyet University, 58140 Sivas (Turkey); Kasapoglu, E. [Physics Department, Faculty of Science, Cumhuriyet University, 58140 Sivas (Turkey); Sari, H. [Department of Primary Education, Faculty of Education, Cumhuriyet University, 58140 Sivas (Turkey); Sokmen, I. [Physics Department, Faculty of Science, Dokuz Eylül University, 35390 Izmir (Turkey)

    2017-03-15

    We investigate theoretically the intense laser-induced optical absorption coefficients and refractive index changes in a two-dimensional quantum pseudodot system under an uniform magnetic field. The effects of non-resonant, monochromatic intense laser field upon the system are treated within the framework of high-frequency Floquet approach in which the system is supposed to be governed by a laser-dressed potential. Linear and nonlinear absorption coefficients and relative changes in the refractive index are obtained by means of the compact-density matrix approach and iterative method. The results of numerical calculations for a typical GaAs quantum dot reveal that the optical response depends strongly on the magnitude of external magnetic field and characteristic parameters of the confinement potential. Moreover, we have demonstrated that the intense laser field modifies the confinement and thereby causes remarkable changes in the linear and nonlinear optical properties of the system.

  12. Optical response in a laser-driven quantum pseudodot system

    International Nuclear Information System (INIS)

    Kilic, D. Gul; Sakiroglu, S.; Ungan, F.; Yesilgul, U.; Kasapoglu, E.; Sari, H.; Sokmen, I.

    2017-01-01

    We investigate theoretically the intense laser-induced optical absorption coefficients and refractive index changes in a two-dimensional quantum pseudodot system under an uniform magnetic field. The effects of non-resonant, monochromatic intense laser field upon the system are treated within the framework of high-frequency Floquet approach in which the system is supposed to be governed by a laser-dressed potential. Linear and nonlinear absorption coefficients and relative changes in the refractive index are obtained by means of the compact-density matrix approach and iterative method. The results of numerical calculations for a typical GaAs quantum dot reveal that the optical response depends strongly on the magnitude of external magnetic field and characteristic parameters of the confinement potential. Moreover, we have demonstrated that the intense laser field modifies the confinement and thereby causes remarkable changes in the linear and nonlinear optical properties of the system.

  13. Design of a Hydraulic Motor System Driven by Compressed Air

    Directory of Open Access Journals (Sweden)

    Jyun-Jhe Yu

    2013-06-01

    Full Text Available This paper presents the design of a highly efficient pneumatic motor system. The air engine is currently the most generally used device to convert potential energy of compressed air into mechanical energy. However, the efficiency of the air engines is too low to provide sufficient operating range for the vehicle. In this study, the energy contained in compressed air/pressurized hydraulic oil is transformed by a hydraulic motor to mechanical energy to enhance the efficiency of using air power. To evaluate the theoretical efficiency, the principle of balance of energy is applied. The theoretical efficiency of converting air into hydraulic energy is found to be a function of pressure; thus, the maximum converting efficiency can be determined. To confirm the theoretical evaluation, a prototype of the pneumatic hydraulic system is built. The experiment verifies that the theoretical evaluation of the system efficiency is reasonable, and that the layout of the system is determined by the results of theoretical evaluation.

  14. Eccentric Mounting and Adjustment System for Belt Driven Devices

    National Research Council Canada - National Science Library

    Hansen, David N

    2008-01-01

    .... The system includes a housing fixed to the engine, a socket rotatable in pawl-and-ratchet fashion within the housing, and a socket aperture eccentrically disposed relative to the socket's axis...

  15. Analysis of Fuel Cell Driven Ground Source Heat Pump Systems in Community Buildings

    Directory of Open Access Journals (Sweden)

    Jong-Keun Shin

    2013-05-01

    Full Text Available In the present study, a fuel cell driven ground source heat pump (GSHP system is applied in a community building and heat pump system performance is analyzed by computational methods. Conduction heat transfer between the brine pipe and ground is analyzed by TEACH code in order to predict the performance of the heat pump system. The predicted coefficient of performance (COP of the heat pump system and the energy cost were compared with the variation of the location of the objective building, the water saturation rate of the soil, and the driven powers of the heat pump system. Compared to the late-night electricity driven system, a significant reduction of energy cost can be accomplished by employing the fuel cell driven heat pump system. This is due to the low cost of electricity production of the fuel cell system and to the application of the recovered waste heat generated during the electricity production process to the heating of the community building.

  16. An experimental and analytical study of a buoyancy driven cooling system for a particle accelerator

    International Nuclear Information System (INIS)

    Campbell, B.; Ranganathan, R.

    1993-05-01

    A buoyancy driven closed-loop cooling system that transports the heat generated in a particle accelerator to the ambient has been evaluated both through experiments performed earlier and analysis techniques developed elsewhere. Excellent comparisons between measurements and calculations have been obtained. The model illustrates the feasibility (from a heat transfer viewpoint) of such a cooling system for a particle accelerator

  17. An experimental and analytical study of a buoyancy driven cooling system for a particle accelerator

    International Nuclear Information System (INIS)

    Campbell, B.; Ranganathan, R.

    1993-01-01

    A buoyancy driven closed-loop cooling system that transports the heat generated in a particle accelerator to the ambient has been evaluated both through experiments performed earlier and analysis techniques developed elsewhere. Excellent comparisons between measurements and calculations have been obtained. The model illustrates the feasibility (from a heat transfer viewpoint) of such a cooling system for a particle accelerator

  18. State Estimation for Linear Systems Driven Simultaneously by Wiener and Poisson Processes.

    Science.gov (United States)

    1978-12-01

    The state estimation problem of linear stochastic systems driven simultaneously by Wiener and Poisson processes is considered, especially the case...where the incident intensities of the Poisson processes are low and the system is observed in an additive white Gaussian noise. The minimum mean squared

  19. Towards Ontology-Driven Information Systems: Guidelines to the Creation of New Methodologies to Build Ontologies

    Science.gov (United States)

    Soares, Andrey

    2009-01-01

    This research targeted the area of Ontology-Driven Information Systems, where ontology plays a central role both at development time and at run time of Information Systems (IS). In particular, the research focused on the process of building domain ontologies for IS modeling. The motivation behind the research was the fact that researchers have…

  20. Microcontroller-driven fluid-injection system for atomic force microscopy.

    Science.gov (United States)

    Kasas, S; Alonso, L; Jacquet, P; Adamcik, J; Haeberli, C; Dietler, G

    2010-01-01

    We present a programmable microcontroller-driven injection system for the exchange of imaging medium during atomic force microscopy. Using this low-noise system, high-resolution imaging can be performed during this process of injection without disturbance. This latter circumstance was exemplified by the online imaging of conformational changes in DNA molecules during the injection of anticancer drug into the fluid chamber.

  1. Future cooperative communication systems driven by social mobile networks

    DEFF Research Database (Denmark)

    Blázovics, L.; Varga, C.; Bamford, W.

    2011-01-01

    In this work we are underlining the importance of social mobile networks for upcoming cooperative communication systems. The assumption of this work is that future mobile communication systems will incorporate user cooperation, i.e. a combination of cellular access in parallel with ongoing short...... cases. By the example of the Gedda-Headz gaming community, possible links between cooperative mobile communication and social mobile networks are shown....

  2. A clinician-driven home care delivery system.

    Science.gov (United States)

    August, D A; Faubion, W C; Ryan, M L; Haggerty, R H; Wesley, J R

    1993-12-01

    The financial, entrepreneurial, administrative, and legal forces acting within the home care arena make it difficult for clinicians to develop and operate home care initiatives within an academic setting. HomeMed is a clinician-initiated and -directed home care delivery system wholly owned by the University of Michigan. The advantages of a clinician-directed system include: Assurance that clinical and patient-based factors are the primary determinants of strategic and procedural decisions; Responsiveness of the system to clinician needs; Maintenance of an important role for the referring physician in home care; Economical clinical research by facilitation of protocol therapy in ambulatory and home settings; Reduction of lengths of hospital stays through clinician initiatives; Incorporation of outcome analysis and other research programs into the mission of the system; Clinician commitment to success of the system; and Clinician input on revenue use. Potential disadvantages of a clinician-based system include: Entrepreneurial, financial, and legal naivete; Disconnection from institutional administrative and data management resources; and Inadequate clinician interest and commitment. The University of Michigan HomeMed experience demonstrates a model of clinician-initiated and -directed home care delivery that has been innovative, profitable, and clinically excellent, has engendered broad physician, nurse, pharmacist, and social worker enthusiasm, and has supported individual investigator clinical protocols as well as broad outcomes research initiatives. It is concluded that a clinician-initiated and -directed home care program is feasible and effective, and in some settings may be optimal.

  3. Genome Scale Modeling in Systems Biology: Algorithms and Resources

    Science.gov (United States)

    Najafi, Ali; Bidkhori, Gholamreza; Bozorgmehr, Joseph H.; Koch, Ina; Masoudi-Nejad, Ali

    2014-01-01

    In recent years, in silico studies and trial simulations have complemented experimental procedures. A model is a description of a system, and a system is any collection of interrelated objects; an object, moreover, is some elemental unit upon which observations can be made but whose internal structure either does not exist or is ignored. Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. This review highlights some of most popular and important modeling algorithms, tools, and emerging standards for representing, simulating and analyzing cellular networks in five sections. Also, we try to show these concepts by means of simple example and proper images and graphs. Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems. We provide an overview of all processes used in modeling and simulating biological networks in such a way that they can become easily understandable for researchers with both biological and mathematical backgrounds. Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches to augment and assist in the development of a fully quantitative understanding of cellular dynamics. PMID:24822031

  4. Sensitivity analysis approaches applied to systems biology models.

    Science.gov (United States)

    Zi, Z

    2011-11-01

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

  5. A system for success: BMC Systems Biology, a new open access journal

    OpenAIRE

    Webb Penelope A; Hodgkinson Matt J

    2007-01-01

    Abstract BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

  6. A system for success: BMC Systems Biology, a new open access journal.

    Science.gov (United States)

    Hodgkinson, Matt J; Webb, Penelope A

    2007-09-04

    BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

  7. Data-driven design of fault diagnosis and fault-tolerant control systems

    CERN Document Server

    Ding, Steven X

    2014-01-01

    Data-driven Design of Fault Diagnosis and Fault-tolerant Control Systems presents basic statistical process monitoring, fault diagnosis, and control methods, and introduces advanced data-driven schemes for the design of fault diagnosis and fault-tolerant control systems catering to the needs of dynamic industrial processes. With ever increasing demands for reliability, availability and safety in technical processes and assets, process monitoring and fault-tolerance have become important issues surrounding the design of automatic control systems. This text shows the reader how, thanks to the rapid development of information technology, key techniques of data-driven and statistical process monitoring and control can now become widely used in industrial practice to address these issues. To allow for self-contained study and facilitate implementation in real applications, important mathematical and control theoretical knowledge and tools are included in this book. Major schemes are presented in algorithm form and...

  8. Hamiltonian-Driven Adaptive Dynamic Programming for Continuous Nonlinear Dynamical Systems.

    Science.gov (United States)

    Yang, Yongliang; Wunsch, Donald; Yin, Yixin

    2017-08-01

    This paper presents a Hamiltonian-driven framework of adaptive dynamic programming (ADP) for continuous time nonlinear systems, which consists of evaluation of an admissible control, comparison between two different admissible policies with respect to the corresponding the performance function, and the performance improvement of an admissible control. It is showed that the Hamiltonian can serve as the temporal difference for continuous-time systems. In the Hamiltonian-driven ADP, the critic network is trained to output the value gradient. Then, the inner product between the critic and the system dynamics produces the value derivative. Under some conditions, the minimization of the Hamiltonian functional is equivalent to the value function approximation. An iterative algorithm starting from an arbitrary admissible control is presented for the optimal control approximation with its convergence proof. The implementation is accomplished by a neural network approximation. Two simulation studies demonstrate the effectiveness of Hamiltonian-driven ADP.

  9. System and safety studies of accelerator driven transmutation systems. Annual report 1998

    International Nuclear Information System (INIS)

    Wallenius, J.; Gudowski, W.; Carlsson, Johan; Eriksson, Marcus; Tucek, K.

    1998-12-01

    This annual report describes the accelerator-driven transmutation project conducted at the Department of Nuclear and Reactor Physics at the Royal Institute of Technology. The main results are: development of the simulation tools for accelerator-driven transmutation calculations including an integrated Monte-Carlo burnup module and improvements of neutron energy fission yield simulations, processing of the evacuated nuclear data files including preparation of the temperature dependent neutron cross-sections, development of nuclear data for a medium energy range for some isotopes, development of the models and codes for radiation damage simulations, system studies for the spent fuel transmuter, based on heavy metal coolant and advanced nuclear fuel, contribution to the spallation target design being manufactured in IPPE, Obninsk, and accelerator reliability studies. Moreover a lot of efforts were put to further develop existing international collaboration with the most active research groups in the world together with educational activities in Sweden including a number of meetings and workshops and a graduate course in transmutation. This project has been conducted in close collaboration with the EU-project 'Impact of the accelerator based technologies on nuclear fission safety' - IABAT and in bilateral cooperation with different foreign research groups

  10. System and safety studies of accelerator driven transmutation systems. Annual report 1998

    Energy Technology Data Exchange (ETDEWEB)

    Wallenius, J.; Gudowski, W.; Carlsson, Johan; Eriksson, Marcus; Tucek, K. [Royal Inst. of Tech., Stockholm (Sweden). Dept. of Nuclear and Reactor Physics

    1998-12-01

    This annual report describes the accelerator-driven transmutation project conducted at the Department of Nuclear and Reactor Physics at the Royal Institute of Technology. The main results are: development of the simulation tools for accelerator-driven transmutation calculations including an integrated Monte-Carlo burnup module and improvements of neutron energy fission yield simulations, processing of the evacuated nuclear data files including preparation of the temperature dependent neutron cross-sections, development of nuclear data for a medium energy range for some isotopes, development of the models and codes for radiation damage simulations, system studies for the spent fuel transmuter, based on heavy metal coolant and advanced nuclear fuel, contribution to the spallation target design being manufactured in IPPE, Obninsk, and accelerator reliability studies. Moreover a lot of efforts were put to further develop existing international collaboration with the most active research groups in the world together with educational activities in Sweden including a number of meetings and workshops and a graduate course in transmutation. This project has been conducted in close collaboration with the EU-project `Impact of the accelerator based technologies on nuclear fission safety` - IABAT and in bilateral cooperation with different foreign research groups 31 refs, 23 figs

  11. Technical and economic assessment of photovoltaic-driven desalination systems

    International Nuclear Information System (INIS)

    Al-Karaghouli, Ali; Renne, David; Kazmerski, Lawrence L.

    2010-01-01

    Solar desalination systems are approaching technical and cost viability for producing fresh-water, a commodity of equal importance to energy in many arid and coastal regions worldwide. Solar photovoltaics (PV) represent an ideal, clean alternative to fossil fuels, especially for remote communities such as grid-limited villages or isolated islands. These applications for water production in remote areas are the first to be nearing cost-competitiveness due to decreasing PV prices and increasing fossil fuel prices over the last five years. The electricity produced from PV systems for desalination applications can be used for electro-mechanical devices such as pumps or in direct-current (DC) devices. Reverse osmosis (RO) and electrodialysis (ED) desalination units are the most favorable alternatives to be coupled with PV systems. RO usually operates on alternating current (AC) for the pumps, thus requiring a DC/AC inverter. In contrast, electrodialysis uses DC for the electrodes at the cell stack, and hence, it can use the energy supplied from the PV panels with some minor power conditioning. Energy storage is critical and batteries are required for sustained operation. In this paper, we discuss the operational features and system designs of typical PV-RO and PV-ED systems in terms of their suitability and optimization for PV operation. For PV-RO and PV-ED systems, we evaluate their electricity need, capital and operational costs, and fresh-water production costs. We cover ongoing and projected research and development activities, with estimates of their potential economics. We discuss the feasibility of future solar desalination based on expected (or predicted) improvements in technology of the desalination and PV systems. Examples are provided for Middle East and other parts of the World. (author)

  12. PC driven integrated system for vacuum making and control

    International Nuclear Information System (INIS)

    Curuia, Marian; Culcer, Mihai; Brandea, Iulian

    2000-01-01

    The vacuum systems, are utilised in many technological plants. Some of these plants cover a big area, with high distances between workstations. For this reason the remote control is necessary, but is this not excepts the local control system, which may be performed for local supervision, control or shut down. The utilised software was the package LabView, which is a dedicate software for industrial automation. LabView is a conventional graphic program which has characteristic modules necessary for commands and data measurements from industrial processes. With this software we can simulate the instruments used in automation. The program which was realized has been defined as virtual instrument ( VI ), and it is realized of the 'front panel' computer utility interface and the 'block diagram' source code of the program, in which can be find also the subprograms (subVI) with the icons and the afferent connections. This connections are necessary to connect the electronic drive system to computer. The versatility of the software realised the communication between computer and the afferent modules of electric drive system through the serial port (COM1 or COM2). The main parts of this system are: -electronic drive unit; -interface relay unit; -central processing unit. The entire behaviour of system is progressing under the computer supervision, which accomplishes the following operations: - start and stop command for pump; - the NOMINAL or STAND BY operation command; -taking over of the signal to rotational frequency transducer and displays the results; -command the degassing of pump heater. The command of electric drive system with the virtual instrumentation represents the most modern trend in the field of electronic devices. The virtual device which was achieved offers an complex 'on-line' automation with many possibilities to be extended. (authors)

  13. A systems biology approach to study glucose repression in the yeast Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Westergaard, Steen Lund; Soberano de Oliveira, Ana Paula; Bro, Christoffer

    2007-01-01

    in repression of a wide range of genes involved to utilization of alternative carbon sources. In this work, we applied a systems biology approach to study the interaction between these two pathways. Through genome-wide transcription analysis of strains with disruption of HXK2, GRR1, MIG1, the combination of MIG......1 and MIG2, and the parentel strain, we identified 393 genes to have significantly changed expression levels. To identify co-regulation patterns in the different strains we applied principal component analysis. Disruption of either GRR1 or HXK2 were both found to have profound effects...... reporter metabolites, and found that there is a high degree of consistency between the identified reporter metabolites and the physiological effects observed in the different mutants . Our systems biology approach points to close interaction between the two pathways, and our metabolism driven analysis...

  14. Systems biology of neutrophil differentiation and immune response

    DEFF Research Database (Denmark)

    Theilgaard-Mönch, Kim; Porse, Bo T; Borregaard, Niels

    2005-01-01

    Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies. These stu......Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies....... These studies have identified a plethora of novel effector proteins stored in the granules of neutrophils. In addition, these studies provide evidence that neutrophil differentiation and immune response are governed by a highly coordinated transcriptional programme that regulates cellular fate and function...

  15. Advancing metabolic engineering through systems biology of industrial microorganisms.

    Science.gov (United States)

    Dai, Zongjie; Nielsen, Jens

    2015-12-01

    Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Advancing metabolic engineering through systems biology of industrial microorganisms

    DEFF Research Database (Denmark)

    Dai, Zongjie; Nielsen, Jens

    2015-01-01

    resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review......Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable...... the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further....

  17. Systems biology approaches to the study of cardiovascular drugs

    NARCIS (Netherlands)

    Nikolsky, Y.; Kleemann, R.

    2010-01-01

    Atherogenic lipids and chronic inflammation drive the development of cardiovascular disorders such as atherosclerosis. Many cardiovascular drugs target the liver which is involved in the formation of lipid and inflammatory risk factors. With robust systems biology tools and comprehensive

  18. Strategies for structuring interdisciplinary education in Systems Biology

    DEFF Research Database (Denmark)

    Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure

    2016-01-01

    function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material...... and example curricula. As university education at the Bachelor’s level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master’s level, as it offers a more flexible framework. Our team of experts and active...... performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master’s programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii...

  19. An intention driven hand functions task training robotic system.

    Science.gov (United States)

    Tong, K Y; Ho, S K; Pang, P K; Hu, X L; Tam, W K; Fung, K L; Wei, X J; Chen, P N; Chen, M

    2010-01-01

    A novel design of a hand functions task training robotic system was developed for the stroke rehabilitation. It detects the intention of hand opening or hand closing from the stroke person using the electromyography (EMG) signals measured from the hemiplegic side. This training system consists of an embedded controller and a robotic hand module. Each hand robot has 5 individual finger assemblies capable to drive 2 degrees of freedom (DOFs) of each finger at the same time. Powered by the linear actuator, the finger assembly achieves 55 degree range of motion (ROM) at the metacarpophalangeal (MCP) joint and 65 degree range of motion (ROM) at the proximal interphalangeal (PIP) joint. Each finger assembly can also be adjusted to fit for different finger length. With this task training system, stroke subject can open and close their impaired hand using their own intention to carry out some of the daily living tasks.

  20. Test-Driven, Model-Based Systems Engineering

    DEFF Research Database (Denmark)

    Munck, Allan

    Hearing systems have evolved over many years from simple mechanical devices (horns) to electronic units consisting of microphones, amplifiers, analog filters, loudspeakers, batteries, etc. Digital signal processors replaced analog filters to provide better performance end new features. Central....... This thesis concerns methods for identifying, selecting and implementing tools for various aspects of model-based systems engineering. A comprehensive method was proposed that include several novel steps such as techniques for analyzing the gap between requirements and tool capabilities. The method...... was verified with good results in two case studies for selection of a traceability tool (single-tool scenario) and a set of modeling tools (multi-tool scenarios). Models must be subjected to testing to allow engineers to predict functionality and performance of systems. Test-first strategies are known...

  1. Patterning in systems driven by nonlocal external forces.

    Science.gov (United States)

    Luneville, L; Mallick, K; Pontikis, V; Simeone, D

    2016-11-01

    This work focuses on systems displaying domain patterns resulting from competing external and internal dynamics. To this end, we introduce a Lyapunov functional capable of describing the steady states of systems subject to external forces, by adding nonlocal terms to the Landau Ginzburg free energy of the system. Thereby, we extend the existing methodology treating long-range order interactions, to the case of external nonlocal forces. By studying the quadratic term of this Lyapunov functional, we compute the phase diagram in the temperature versus external field and we determine all possible modulated phases (domain patterns) as a function of the external forces and the temperature. Finally, we investigate patterning in chemical reactive mixtures and binary mixtures under irradiation, and we show that the last case opens the path toward micro-structural engineering of materials.

  2. OASIS: a COBOL-11 menu-driven information system

    International Nuclear Information System (INIS)

    Lee, W.F. Jr.

    1982-01-01

    Oak Ridge National Laboratory's Automated Safeguards Information System (OASIS) is a near real-time nuclear materials/precious metals safeguard and accountability control system. Using COBOL and RSTS/E on a dedicated 11/34, the system performs on-line inventory update, inquiry and report functions. Processed transactions consisting of intra-laboratory movements, on-site receipts and off-site shipments are maintained for inquiry and report preparation. A secure, controlled but friendly user environment is maintained by chaining between menu and data manipulation tasks. The use of menus, security and access control, screen manipulation, file access and contention, word processing activities, task size problems and other aspects of this application will be discussed

  3. Electron versus proton accelerator driven sub-critical system performance using TRIGA reactors at power

    International Nuclear Information System (INIS)

    Carta, M.; Burgio, N.; D'Angelo, A.; Santagata, A.; Petrovich, C.; Schikorr, M.; Beller, D.; Felice, L. S.; Imel, G.; Salvatores, M.

    2006-01-01

    This paper provides a comparison of the performance of an electron accelerator-driven experiment, under discussion within the Reactor Accelerator Coupling Experiments (RACE) Project, being conducted within the U.S. Dept. of Energy's Advanced Fuel Cycle Initiative (AFCI), and of the proton-driven experiment TRADE (TRIGA Accelerator Driven Experiment) originally planned at ENEA-Casaccia in Italy. Both experiments foresee the coupling to sub-critical TRIGA core configurations, and are aimed to investigate the relevant kinetic and dynamic accelerator-driven systems (ADS) core behavior characteristics in the presence of thermal reactivity feedback effects. TRADE was based on the coupling of an upgraded proton cyclotron, producing neutrons via spallation reactions on a tantalum (Ta) target, with the core driven at a maximum power around 200 kW. RACE is based on the coupling of an Electron Linac accelerator, producing neutrons via photoneutron reactions on a tungsten-copper (W-Cu) or uranium (U) target, with the core driven at a maximum power around 50 kW. The paper is focused on analysis of expected dynamic power response of the RACE core following reactivity and/or source transients. TRADE and RACE target-core power coupling coefficients are compared and discussed. (authors)

  4. Category of Metabolic-Replication Systems in Biology and Medicine

    OpenAIRE

    I. C. Baianu

    2012-01-01

    Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life's origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important questio...

  5. Stochastic chemical kinetics theory and (mostly) systems biological applications

    CERN Document Server

    Érdi, Péter; Lente, Gabor

    2014-01-01

    This volume reviews the theory and simulation methods of stochastic kinetics by integrating historical and recent perspectives, presents applications, mostly in the context of systems biology and also in combustion theory. In recent years, due to the development in experimental techniques, such as optical imaging, single cell analysis, and fluorescence spectroscopy, biochemical kinetic data inside single living cells have increasingly been available. The emergence of systems biology brought renaissance in the application of stochastic kinetic methods.

  6. A protable Database driven control system for SPEAR

    International Nuclear Information System (INIS)

    Howry, S.; Gromme, T.; King, A.; Sullenberger, M.

    1985-01-01

    The new computer control system software for SPEAR is presented as a transfer from the PEP system. Features of the target ring (SPEAR) such as symmetries, magnet groupings, etc., are all contained in a design file which is read by both people and computer. People use it as documentation; a program reads it to generate the database structure, which becomes the center of communication for all the software. Geometric information, such as element positions and lengths, and CAMAC I/O routing information is entered into the database as it is developed. Since application processes refer only to the database and since they do so only in generic terms, almost all of this software (representing more then fifteen man years) is transferred with few changes. Operator console menus (touchpanels) are also transferred with only superficial changes for the same reasons. The system is modular: the CAMAC I/O software is all in one process; the menu control software is a process; the ring optics model and the orbit model are separate processes, each of which runs concurrently with about 15 others in the multiprogramming environment of the VAX/VMS operating system

  7. Stability of impulsive systems driven by renewal processes

    NARCIS (Netherlands)

    Guerreiro Tome Antunes, D.J.; Hespanha, J.P.; Silvestre, C.J.

    2009-01-01

    Necessary and sufficient conditions are provided for stochastic stability and mean exponential stability of impulsive systems with jumps triggered by a renewal process, that is, the intervals between jumps are independent and identically distributed. The conditions for stochastic stability can be

  8. Density-Driven segregation in Binary and Ternary Granular Systems

    NARCIS (Netherlands)

    Windows-Yule, Kit; Parker, David

    2015-01-01

    We present a first experimental study of density-induced segregation within a three-dimensional, vibrofluidised, ternary granular system. Using Positron Emission Particle Tracking (PEPT), we study the steady-state particle distributions achieved by binary and ternary granular beds under a variety of

  9. Exploring Synthetic and Systems Biology at the University of Edinburgh.

    Science.gov (United States)

    Fletcher, Liz; Rosser, Susan; Elfick, Alistair

    2016-06-15

    The Centre for Synthetic and Systems Biology ('SynthSys') was originally established in 2007 as the Centre for Integrative Systems Biology, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC). Today, SynthSys embraces an extensive multidisciplinary community of more than 200 researchers from across the University with a common interest in synthetic and systems biology. Our research is broad and deep, addressing a diversity of scientific questions, with wide ranging impact. We bring together the power of synthetic biology and systems approaches to focus on three core thematic areas: industrial biotechnology, agriculture and the environment, and medicine and healthcare. In October 2015, we opened a newly refurbished building as a physical hub for our new U.K. Centre for Mammalian Synthetic Biology funded by the BBSRC/EPSRC/MRC as part of the U.K. Research Councils' Synthetic Biology for Growth programme. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  10. Implementation of 252Cf-source-driven power spectrum density measurement system

    International Nuclear Information System (INIS)

    Ren Yong; Wei Biao; Feng Peng; Li Jiansheng; Ye Cenming

    2012-01-01

    The principle of 252 Cf-source-driven power spectrum density measurement method is introduced. A measurement system and platform is realized accordingly, which is a combination of hardware and software, for measuring nuclear parameters. The detection method of neutron pulses based on an ultra-high-speed data acquisition card (three channels, 1 GHz sampling rate, 1 ns synchronization) is described, and the data processing process and the power spectrum density algorithm on PC are designed. This 252 Cf-source-driven power spectrum density measurement system can effectively obtain the nuclear tag parameters of nuclear random processes, such as correlation function and power spectrum density. (authors)

  11. Feasibility of waste transmutation using accelerator-driven IRIS subcritical system

    International Nuclear Information System (INIS)

    Petroviae, B.; Carelli, M.; Paramonov, D.

    2001-01-01

    Waste transmutation is considered for reducing radio-toxicity of nuclear waste generated in power reactors. Accelerator driven subcritical systems (ADS) offer certain advantages over the use of nuclear reactors. Transmutation of fission products (e.g. 99 Tc) generally requires thermal neutron spectrum, while for actinides fast spectrum provides better performance. Proposed solutions to this problem include a multi-strata approach as well as a multi-zone (thermal/fast-spectrum) single systems. In this paper we examine the feasibility of employing a dual-spectrum two-zone accelerator-driven IRIS subcritical for waste transmutation. (author)

  12. RBAC Driven Least Privilege Architecture For Control Systems

    Energy Technology Data Exchange (ETDEWEB)

    Hull, Julie [Honeywell International Inc., Golden Valley, MN (United States); Markham, Mark [Honeywell International Inc., Golden Valley, MN (United States)

    2014-01-25

    The concept of role based access control (RBAC) within the IT environment has been studied by researchers and was supported by NIST (circa 1992). This earlier work highlighted the benefits of RBAC which include reduced administrative workload and policies which are easier to analyze and apply. The goals of this research were to expand the application of RBAC in the following ways. Apply RBAC to the control systems environment: The typical RBAC model within the IT environment is used to control a user’s access to files. Within the control system environment files are replaced with measurement (e.g., temperature) and control (e.g. valve) points organized as a hierarchy of control assets (e.g. a boiler, compressor, refinery unit). Control points have parameters (e.g., high alarm limit, set point, etc.) associated with them. The RBAC model is extended to support access to points and their parameters based upon roles while at the same time allowing permissions for the points to be defined at the asset level or point level directly. In addition, centralized policy administration with distributed access enforcement mechanisms was developed to support the distributed architecture of distributed control systems and SCADA; Extend the RBAC model to include access control for software and devices: The established RBAC approach is to assign users to roles. This work extends that notion by first breaking the control system down into three layers 1) users, 2) software and 3) devices. An RBAC model is then created for each of these three layers. The result is that RBAC can be used to define machine-to-machine policy enforced via the IP security (IPsec) protocol. This highlights the potential to use RBAC for machine-to-machine connectivity within the internet of things; and Enable dynamic policy based upon the operating mode of the system: The IT environment is generally static with respect to policy. However, large cyber physical systems such as industrial controls have various

  13. Fast removal of oxygen from biological systems

    International Nuclear Information System (INIS)

    Dewey, D.L.; Michael, B.D.

    1975-01-01

    Reference is made to the fact that if radiation is given at a high enough dose rate, the biological effect of oxygen is less than at low dose rates. Examples are given of 'break-point' experiments showing the effect. It is stated that the rapid removal of a substance by radiation is not confined to oxygen: the only criterion required to demonstrate the effect is that the chemical causes a measurable sensitization or protection at a concentration small enough so that it can be depleted at a relatively low dose of radiation. Sufficient confidence is now placed in the effect that it can be used the other way round; that is, to measure the position of the break-point and from this measurement determine the oxygen concentration at the target site at the instant before irradiation. Examples are given of the use of the high dose rate technique for measuring the oxygen concentration inside mammalian cells (Chinese hamster cells). The effects of partial pressures of inert gases, and the effect of elevated gas pressures, are discussed. (U.K.)

  14. Primary energy-transformations in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Lehninger, A.L.

    1980-10-01

    In this paper I shall review the main outlines of current research on the molecular aspects of the primary energy-coupling mechanisms in cells, those carried out by energy-transducing membranes. They include the capture of solar energy by the chloroplast membranes of green plants, used to generate carbohydrates and molecular oxygen from carbon dioxide and water, and the counterpart of photosynthesis, the process of respiration in heterotrophic organisms, in which reduced organic products generated by photosynthesis are oxidized at the expense of dioxygen to form carbon dioxide and water. Although the cycling of dioxygen, carbon dioxide, and organic matter between the plant and animal worlds is well known, it is not generally appreciated that the magnitude of biological energy flux in these cycles is huge compared to the total energy flux in man-made devices. A major consequence is that the concentration of carbon dioxide in the atmosphere has been increasing at a significant rate, at a time when there is also a decrease, at least in some parts of the world, in the counterbalancing utilization of CO/sub 2/ by green plants, due to deforestation. The greenhouse effect of increased atmospheric CO/sub 2/ may not only change the earth's climate, but also may influence the rate of photosynthesis. It is also not generally appreciated that energy flow in the biosphere leads to production of enormous amounts of organic matter potentially useful in furnishing man's energy requirements.

  15. Measurable Control System Security through Ideal Driven Technical Metrics

    Energy Technology Data Exchange (ETDEWEB)

    Miles McQueen; Wayne Boyer; Sean McBride; Marie Farrar; Zachary Tudor

    2008-01-01

    The Department of Homeland Security National Cyber Security Division supported development of a small set of security ideals as a framework to establish measurable control systems security. Based on these ideals, a draft set of proposed technical metrics was developed to allow control systems owner-operators to track improvements or degradations in their individual control systems security posture. The technical metrics development effort included review and evaluation of over thirty metrics-related documents. On the bases of complexity, ambiguity, or misleading and distorting effects the metrics identified during the reviews were determined to be weaker than necessary to aid defense against the myriad threats posed by cyber-terrorism to human safety, as well as to economic prosperity. Using the results of our metrics review and the set of security ideals as a starting point for metrics development, we identified thirteen potential technical metrics - with at least one metric supporting each ideal. Two case study applications of the ideals and thirteen metrics to control systems were then performed to establish potential difficulties in applying both the ideals and the metrics. The case studies resulted in no changes to the ideals, and only a few deletions and refinements to the thirteen potential metrics. This led to a final proposed set of ten core technical metrics. To further validate the security ideals, the modifications made to the original thirteen potential metrics, and the final proposed set of ten core metrics, seven separate control systems security assessments performed over the past three years were reviewed for findings and recommended mitigations. These findings and mitigations were then mapped to the security ideals and metrics to assess gaps in their coverage. The mappings indicated that there are no gaps in the security ideals and that the ten core technical metrics provide significant coverage of standard security issues with 87% coverage. Based

  16. System chemical biology studies of endocrine disruptors

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Oprea, Tudor I.

    Endocrine disrupting chemicals (EDCs) alter hormonal balance and other physiological systems through inappropriate developmental or adult exposure, perturbing the reproductive function of further generations. While disruption of key receptors (e.g., estrogen, androgen, and thyroid) at the ligand...

  17. Process-driven selection of information systems for healthcare

    Science.gov (United States)

    Mills, Stephen F.; Yeh, Raymond T.; Giroir, Brett P.; Tanik, Murat M.

    1995-05-01

    Integration of networking and data management technologies such as PACS, RIS and HIS into a healthcare enterprise in a clinically acceptable manner is a difficult problem. Data within such a facility are generally managed via a combination of manual hardcopy systems and proprietary, special-purpose data processing systems. Process modeling techniques have been successfully applied to engineering and manufacturing enterprises, but have not generally been applied to service-based enterprises such as healthcare facilities. The use of process modeling techniques can provide guidance for the placement, configuration and usage of PACS and other informatics technologies within the healthcare enterprise, and thus improve the quality of healthcare. Initial process modeling activities conducted within the Pediatric ICU at Children's Medical Center in Dallas, Texas are described. The ongoing development of a full enterprise- level model for the Pediatric ICU is also described.

  18. Solvable Family of Driven-Dissipative Many-Body Systems

    Science.gov (United States)

    Foss-Feig, Michael; Young, Jeremy T.; Albert, Victor V.; Gorshkov, Alexey V.; Maghrebi, Mohammad F.

    2017-11-01

    Exactly solvable models have played an important role in establishing the sophisticated modern understanding of equilibrium many-body physics. Conversely, the relative scarcity of solutions for nonequilibrium models greatly limits our understanding of systems away from thermal equilibrium. We study a family of nonequilibrium models, some of which can be viewed as dissipative analogues of the transverse-field Ising model, in that an effectively classical Hamiltonian is frustrated by dissipative processes that drive the system toward states that do not commute with the Hamiltonian. Surprisingly, a broad and experimentally relevant subset of these models can be solved efficiently. We leverage these solutions to compute the effects of decoherence on a canonical trapped-ion-based quantum computation architecture, and to prove a no-go theorem on steady-state phase transitions in a many-body model that can be realized naturally with Rydberg atoms or trapped ions.

  19. Design of a Hydraulic Motor System Driven by Compressed Air

    OpenAIRE

    Shaw, Dein; Yu, Jyun-Jhe; Chieh, Cheng

    2013-01-01

    This paper presents the design of a highly efficient pneumatic motor system. The air engine is currently the most generally used device to convert potential energy of compressed air into mechanical energy. However, the efficiency of the air engines is too low to provide sufficient operating range for the vehicle. In this study, the energy contained in compressed air/pressurized hydraulic oil is transformed by a hydraulic motor to mechanical energy to enhance the efficiency of using air power....

  20. Stochastic systems driven by alpha-stable noises

    DEFF Research Database (Denmark)

    Ditlevsen, Ove Dalager; Ditlevsen, P.

    1998-01-01

    with observed data. In particular the tailsof the observed response distributions may even for linear systems be more fat than the tails obtained for Gaussianwhite noise input. Also the excitation may show jumps that cannot be modeled by Gaussian white noise. The paper supports the possibility of using...... the larger class of so-calledalpha-stable white noises to provide a better fit. A geophysical application concerning ice age climate variations is described....

  1. Schedulability-Driven Communication Synthesis for Time Triggered Embedded Systems

    DEFF Research Database (Denmark)

    Pop, Paul; Eles, Petru; Peng, Zebo

    1999-01-01

    We present an approach to static priority preemptive process scheduling for the synthesis of hard real-time distributed embedded systems where communication plays an important role. The communication model is based on a time-triggered protocol. We have developed an analysis for the communication...... delays proposing four different message scheduling policies over a time-triggered communication channel. Optimization strategies for the synthesis of communication are developed, and the four approaches to message scheduling are compared using extensive experiments....

  2. Schedulability-Driven Communication Synthesis for Time Triggered Embedded Systems

    DEFF Research Database (Denmark)

    Pop, Paul; Eles, Petru; Peng, Zebo

    2004-01-01

    We present an approach to static priority preemptive process scheduling for the synthesis of hard real-time distributed embedded systems where communication plays an important role. The communication model is based on a time-triggered protocol. We have developed an analysis for the communication...... delays with four different message scheduling policies over a time-triggered communication channel. Optimization strategies for the synthesis of communication are developed, and the four approaches to message scheduling are compared using extensive experiments....

  3. Accelerator driven systems (ADS): A principal neutronics and transmutation potential

    International Nuclear Information System (INIS)

    Slessarev, I.

    1997-01-01

    An accelerator-based system using a beam of high energy protons to produce supplementary neutrons as a result of spallation processes in a target is investigated. The spallation neutrons are successively used to feed a subcritical blanket where they create a neutron surplus available for incineration of those long-lived toxic nuclei which require neutrons (long-lived fission products and minor actinides), and enhance the deterministic safety features for reactivity-type of accidents

  4. Schedulability-Driven Communication Synthesis for Time Triggered Embedded Systems

    DEFF Research Database (Denmark)

    Pop, Paul; Eles, Petru; Peng, Zebo

    2006-01-01

    We present an approach to static priority preemptive process scheduling for the synthesis of hard real-time distributed embedded systems where communication plays an important role. The communication model is based on a time-triggered protocol. We have developed an analysis for the communication...... delays proposing four different message scheduling policies over a time-triggered communication channel. Optimization strategies for the synthesis of communication are developed, and the four approaches to message scheduling are compared using extensive experiments...

  5. Design Tools for Dynamic, Data-Driven, Stream Mining Systems

    Science.gov (United States)

    2015-01-01

    growth in technologies for sensing and computation has contributed to large increases in the volume of data that must be managed and analyzed in many...recognition, speaker identification, pattern recognition) and wireless communication (e.g., GSM, digital radio, NFC , Bluetooth), as well as control...systems for performance and energy consumption. In Proceedings of the IEEE Real-Time Technology and Applications Symposium, pages 124–132, 2003. [49

  6. A Generic Language for Biological Systems based on Bigraphs

    DEFF Research Database (Denmark)

    Damgaard, Troels Christoffer; Krivine, Jean

    Several efforts have shown that process calculi developed for reasoning about concurrent and mobile systems may be employed for modelling biological systems at the molecular level. In this paper, we initiate investigation of the meta-language framework bigraphical reactive systems, due to Milner et...

  7. Amino acid catabolism-directed biofuel production in Clostridium sticklandii: An insight into model-driven systems engineering

    Directory of Open Access Journals (Sweden)

    C Sangavai

    2017-12-01

    Full Text Available Model-driven systems engineering has been more fascinating process for the microbial production of biofuel and bio-refineries in chemical and pharmaceutical industries. Genome-scale modeling and simulations have been guided for metabolic engineering of Clostridium species for the production of organic solvents and organic acids. Among them, Clostridium sticklandii is one of the potential organisms to be exploited as a microbial cell factory for biofuel production. It is a hyper-ammonia producing bacterium and is able to catabolize amino acids as important carbon and energy sources via Stickland reactions and the development of the specific pathways. Current genomic and metabolic aspects of this bacterium are comprehensively reviewed herein, which provided information for learning about protein catabolism-directed biofuel production. It has a metabolic potential to drive energy and direct solventogenesis as well as acidogenesis from protein catabolism. It produces by-products such as ethanol, acetate, n-butanol, n-butyrate and hydrogen from amino acid catabolism. Model-driven systems engineering of this organism would improve the performance of the industrial sectors and enhance the industrial economy by using protein-based waste in environment-friendly ways. Keywords: Biofuel, Amino acid catabolism, Genome-scale model, Metabolic engineering, Systems biology, ABE fermentation, Clostridium sticklandii

  8. Generating a fractal butterfly Floquet spectrum in a class of driven SU(2) systems

    International Nuclear Information System (INIS)

    Wang Jiao; Gong Jiangbin

    2010-01-01

    A scheme for generating a fractal butterfly Floquet spectrum, first proposed by Wang and Gong [Phys. Rev. A 77, 031405(R) (2008)], is extended to driven SU(2) systems such as a driven two-mode Bose-Einstein condensate. A class of driven systems without a link with the Harper-model context is shown to have an intriguing butterfly Floquet spectrum. The found butterfly spectrum shows remarkable deviations from the known Hofstadter's butterfly. In addition, the level crossings between Floquet states of the same parity and between Floquet states of different parities are studied and highlighted. The results are relevant to studies of fractal statistics, quantum chaos, and coherent destruction of tunneling, as well as the validity of mean-field descriptions of Bose-Einstein condensates.

  9. Generating a fractal butterfly Floquet spectrum in a class of driven SU(2) systems

    Science.gov (United States)

    Wang, Jiao; Gong, Jiangbin

    2010-02-01

    A scheme for generating a fractal butterfly Floquet spectrum, first proposed by Wang and Gong [Phys. Rev. A 77, 031405(R) (2008)], is extended to driven SU(2) systems such as a driven two-mode Bose-Einstein condensate. A class of driven systems without a link with the Harper-model context is shown to have an intriguing butterfly Floquet spectrum. The found butterfly spectrum shows remarkable deviations from the known Hofstadter’s butterfly. In addition, the level crossings between Floquet states of the same parity and between Floquet states of different parities are studied and highlighted. The results are relevant to studies of fractal statistics, quantum chaos, and coherent destruction of tunneling, as well as the validity of mean-field descriptions of Bose-Einstein condensates.

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

    Science.gov (United States)

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

    2014-11-01

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

  11. Biological oceanography of the red oceanic system

    Science.gov (United States)

    Theil, Hjalmar; Weikert, Horst

    1. In 1977, 1979 and 1980-81, investigations were carried out which aimed at evaluating the potential risks from mining metalliferous muds precipating in the Atlantis II Deep of the central Red Sea. This environmental research was initiated by the Saudi Sudanese Red Sea Joint Commission in order to avoid any danger for the Red Sea ecosystem. The broad environmental research programme coherent studies in physical, chemical, biological, and geological oceanography as well as toxicological investigations in the oceanic and in reef zones. We summarise the results from our biological fiels studies in the open sea. 2. The biological investigations were concentrated on the area of the Atlantis II Deep. Benthos was sampled between 700-2000m. For comparison a few samples were also taken further north in the central Red Sea, and to east and west along the flanking deep terraces (500-1000m). Plankton studies covered the total water column above the Deep, and were extended along the axial through to north and south. 3. Benthos sampling was carried out using a heavy closing trawl, a large box grab (box size 50 × 50 cm), Van Veen grabs and traps; photographic surveys were made a phototrap and a photosled. Community respiration was measured with a ship-board method using grab subsamples. Nutrient concentrations, seston and phytoplankton standing stocks as well as in situ primary production were determined from hydrocast samples. Data on zooplankton and micronekton composition and standing stock were obtained from samples collected using different multiple opening-and-closing nets equipped with 100 μm, 300 μm, and 1000 μm mesh sizes. Daily and ontogenetical vertical migration patterns were studied by comparisons of data from midday and midnight tows. 4. Throughout the whole area the sediment is a pteropod ooze containing low contentrations of organic matter; measured organic carbon and nitrogen contents were 0.5 and 0.05% respectively, and chloroplastic pigment equivalents

  12. Stochastic resonance in bistable systems driven by harmonic noise

    International Nuclear Information System (INIS)

    Neiman, A.; Schimansky-Geier, L.

    1994-01-01

    We study stochastic resonance in a bistable system which is excited simultaneously by white and harmonic noise which we understand as the signal. In our case the spectral line of the signal has a finite width as it occurs in many real situations. Using techniques of cumulant analysis as well as computer simulations we find that the effect of stochastic resonance is preserved in the case of harmonic noise excitation. Moreover we show that the width of the spectral line of the signal at the output can be decreased via stochastic resonance. The last could be of importance in the practical using of the stochastic resonance

  13. Modeling life the mathematics of biological systems

    CERN Document Server

    Garfinkel, Alan; Guo, Yina

    2017-01-01

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

  14. Amoxicillin in a biological water recovery system

    International Nuclear Information System (INIS)

    Morse, A.; Jackson, A.; Rainwater, K.; Pickering, K.

    2002-01-01

    Pharmaceuticals are new contaminants of concern in the aquatic environment, having been identified in groundwater, surface water, and residential tap water. Possible sources of pharmaceuticals include household wastewaters, runoff from feedlots, or waste discharges from pharmaceutical manufacturing plants. When surface water or groundwater supplies impacted by pharmaceuticals are used in drinking water production, the contaminants may reduce drinking water quality. Many pharmaceuticals, such as amoxicillin, pass through the body largely unmetabolized and directly enter wastewater collection systems. Pharmaceuticals are designed to persist in the body long enough to have the desired therapeutic effect. Therefore, they may also have the ability to persist in the environment (Seiler et al, 1999). The purpose of this work is to determine the overall transformation potential of a candidate pharmaceutical in wastewater treatment with specific emphasis on recycle systems. Amoxicillin is the selected pharmaceutical agent, an orally absorbed broad-spectrum antibiotic with a variety of clinical uses including ear, nose, and throat infections and lower respiratory tract infections. Experiments were conducted using an anaerobic reactor (with NO 3 - and NO 2 - as the e - acceptors) followed by a two-phase nitrifying tubular reactor. Influent composed of water, urine and surfactant was spiked with amoxicillin and fed into the wastewater recycle system. The concentration of amoxicillin in the feed and effluent was quantified using an HPLC. Results from this study include potential for long-term buildup in recycled systems, accumulation of breakdown products and possible transfer of antibiotic resistance to microorganisms in the system effluent. In addition, the results of this study may provide information on contamination potential for communities that are considering supplementing drinking water supplies with recovered wastewater or for entities considering a closed loop

  15. A cable-driven locomotor training system for restoration of gait in human SCI.

    Science.gov (United States)

    Wu, Ming; Hornby, T George; Landry, Jill M; Roth, Heidi; Schmit, Brian D

    2011-02-01

    A novel cable-driven robotic locomotor training system was developed to provide compliant assistance/resistance forces to the legs during treadmill training in patients with incomplete spinal cord injury (SCI). Eleven subjects with incomplete SCI were recruited to participate in two experiments to test the feasibility of the robotic gait training system. Specifically, 10 subjects participated in one experimental session to test the characteristics of the robotic gait training system and one subject participated in repeated testing sessions over 8 weeks with the robotic device to test improvements in locomotor function. Limb kinematics were recorded in one experiment to evaluate the system characteristics of the cable-driven locomotor trainer and the overground gait speed and 6 min walking distance were evaluated at pre, 4 and 8 weeks post treadmill training of a single subject as well. The results indicated that the cable driven robotic gait training system improved the kinematic performance of the leg during treadmill walking and had no significant impact on the variability of lower leg trajectory, suggesting a high backdrivability of the cable system. In addition, results from a patient with incomplete SCI indicated that prolonged robotic gait training using the cable robot improved overground gait speed. Results from this study suggested that a cable driven robotic gait training system is effective in improving leg kinematic performance, yet allows variability of gait kinematics. Thus, it seems feasible to improve the locomotor function in human SCI using this cable driven robotic system, warranting testing with a larger group of patients. Copyright © 2010 Elsevier B.V. All rights reserved.

  16. A European roadmap for developing accelerator driven systems (ADS) for nuclear waste incineration. Executive summary

    International Nuclear Information System (INIS)

    The European Technical Working Group on ADS

    2001-01-01

    In 1998 the Research Ministers of France, Italy and Spain, set up a Ministers' Advisors Group on the use of accelerator driven systems (ADS) for nuclear waste transmutation. This led to the establishing of a technical working group under the chairmanship of Prof. Carlo Rubbia to identify the critical technical issues and to prepare a 'Roadmap' for a demonstration programme to be performed within 12 years. In the following Roadmap, the technical working group (consisting of representatives from Austria, Belgium, Finland, France, Germany, Italy, Portugal, Spain, Sweden and the JRC) has identified the steps necessary to start the construction of an experimental accelerator driven system towards the end of the decade. This is considered as an essential prerequisite to assess the safe and efficient behaviour of such systems for a large-scale deployment for transmutation purposes in the first half of this century. The development and deployment of accelerator driven systems requires three steps: a comprehensive mid- and long-term R and D program, to develop the single elements and components of the system. This includes development of new fuels and fuel cycle systems; planning, design, construction and operation of an Experimental Accelerator Driven System for the demonstration of the concept; planning, design, construction and operation of a large size prototype accelerator driven systems with subsequent large-scale deployment. Following a first phase of R and D focused on the understanding of the basic principles of ADS (already partly underway), the programmes should be streamlined and focused on a practical demonstration of the key issues. These demonstrations should cover high intensity proton accelerators (beam currents in the range 1-20 mA), spallation targets of high power (of power in excess of 1 megawatt), and their effective coupling with a sub-critical core. Cost estimates are taken into account as well as the ADS activities in Japan and USA

  17. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  18. Two-level systems driven by large-amplitude fields

    International Nuclear Information System (INIS)

    Ashhab, S.; Johansson, J. R.; Zagoskin, A. M.; Nori, Franco

    2007-01-01

    We analyze the dynamics of a two-level system subject to driving by large-amplitude external fields, focusing on the resonance properties in the case of driving around the region of avoided level crossing. In particular, we consider three main questions that characterize resonance dynamics: (1) the resonance condition (2) the frequency of the resulting oscillations on resonance, and (3) the width of the resonance. We identify the regions of validity of different approximations. In a large region of the parameter space, we use a geometric picture in order to obtain both a simple understanding of the dynamics and quantitative results. The geometric approach is obtained by dividing the evolution into discrete time steps, with each time step described by either a phase shift on the basis states or a coherent mixing process corresponding to a Landau-Zener crossing. We compare the results of the geometric picture with those of a rotating wave approximation. We also comment briefly on the prospects of employing strong driving as a useful tool to manipulate two-level systems

  19. Antimatter Driven P-B11 Fusion Propulsion System

    Science.gov (United States)

    Kammash, Terry; Martin, James; Godfroy, Thomas

    2002-01-01

    One of the major advantages of using P-B11 fusion fuel is that the reaction produces only charged particles in the form of three alpha particles and no neutrons. A fusion concept that lends itself to this fuel cycle is the Magnetically Insulated Inertial Confinement Fusion (MICF) reactor whose distinct advantage lies in the very strong magnetic field that is created when an incident particle (or laser) beam strikes the inner wall of the target pellet. This field serves to thermally insulate the hot plasma from the metal wall thereby allowing thc plasma to burn for a long time and produce a large energy magnification. If used as a propulsion device, we propose using antiprotons to drive the system which we show to be capable of producing very large specific impulse and thrust. By way of validating the confinement propenies of MICF we will address a proposed experiment in which pellets coated with P-B11 fuel at the appropriate ratio will be zapped by a beam of antiprotons that enter the target through a hole. Calculations showing the density and temperature of the generated plasma along with the strength of the magnetic field and other properties of the system will be presented and discussed.

  20. Construction of a Linux based chemical and biological information system.

    Science.gov (United States)

    Molnár, László; Vágó, István; Fehér, András

    2003-01-01

    A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

  1. Circadian systems biology: When time matters

    Directory of Open Access Journals (Sweden)

    Luise Fuhr

    2015-01-01

    In this manuscript we review the combination of experimental methodologies, bioinformatics and theoretical models that have been essential to explore this remarkable timing-system. Such an integrative and interdisciplinary approach may provide new strategies with regard to chronotherapeutic treatment and new insights concerning the restoration of the circadian timing in clock-associated diseases.

  2. 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...

  3. Maximum Principle for General Controlled Systems Driven by Fractional Brownian Motions

    International Nuclear Information System (INIS)

    Han Yuecai; Hu Yaozhong; Song Jian

    2013-01-01

    We obtain a maximum principle for stochastic control problem of general controlled stochastic differential systems driven by fractional Brownian motions (of Hurst parameter H>1/2). This maximum principle specifies a system of equations that the optimal control must satisfy (necessary condition for the optimal control). This system of equations consists of a backward stochastic differential equation driven by both fractional Brownian motions and the corresponding underlying standard Brownian motions. In addition to this backward equation, the maximum principle also involves the Malliavin derivatives. Our approach is to use conditioning and Malliavin calculus. To arrive at our maximum principle we need to develop some new results of stochastic analysis of the controlled systems driven by fractional Brownian motions via fractional calculus. Our approach of conditioning and Malliavin calculus is also applied to classical system driven by standard Brownian motions while the controller has only partial information. As a straightforward consequence, the classical maximum principle is also deduced in this more natural and simpler way.

  4. 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.

  5. Challenge-driven attention: interacting frontal and brainstem systems

    Directory of Open Access Journals (Sweden)

    Rajeev D S Raizada

    2008-03-01

    Full Text Available The world is an unpredictable place, presenting challenges that fl uctuate from moment to moment. However, the neural systems for responding to such challenges are far from fully understood. Using fMRI, we studied an audiovisual task in which the trials' diffi culty and onset times varied unpredictably. Two regions were found to increase their activation for challenging trials, with their activities strongly correlated: right frontal cortex and the brainstem. The frontal area matched regions found in previous human studies of cognitive control, and activated in a graded manner with increasing task diffi culty. The brainstem responded only to the most diffi cult trials, showing a phasic activity pattern paralleling locus coeruleus recordings in monkeys. These results reveal a bridge between animal and human studies, and suggest interacting roles for the brainstem and right frontal cortex: the brainstem may signal that an attentional challenge is occurring, while right frontal cortex allocates cognitive resources in response.

  6. An induction Linac driven heavy-ion fusion systems model

    International Nuclear Information System (INIS)

    Zuckerman, D.S.; Driemeyer, D.E.; Waganer, L.M.; Dudziak, D.J.

    1988-01-01

    A computerized systems model of a heavy-ion fusion (HIF) reactor power plant is presented. The model can be used to analyze the behavior and projected costs of a commercial power plant using an induction linear accelerator (Linac) as a driver. Each major component of the model (targets, reactor cavity, Linac, beam transport, power flow, balance of plant, and costing) is discussed. Various target, reactor cavity, Linac, and beam transport schemes are examined and compared. The preferred operating regime for such a power plant is also examined. The results show that HIF power plants can compete with other advanced energy concepts at the 1000-MW (electric) power level [cost of electricity (COE) -- 50 mill/kW . h] provided that the cost savings predicted for Linacs using higher charge-state ions (+3) can be realized

  7. Dissipation-driven quantum phase transitions in collective spin systems

    International Nuclear Information System (INIS)

    Morrison, S; Parkins, A S

    2008-01-01

    We consider two different collective spin systems subjected to strong dissipation-on the same scale as interaction strengths and external fields-and show that either continuous or discontinuous dissipative quantum phase transitions can occur as the dissipation strength is varied. First, we consider a well-known model of cooperative resonance fluorescence that can exhibit a second-order quantum phase transition, and analyse the entanglement properties near the critical point. Next, we examine a dissipative version of the Lipkin-Meshkov-Glick interacting collective spin model, where we find that either first- or second-order quantum phase transitions can occur, depending only on the ratio of the interaction and external field parameters. We give detailed results and interpretation for the steady-state entanglement in the vicinity of the critical point, where it reaches a maximum. For the first-order transition we find that the semiclassical steady states exhibit a region of bistability. (fast track communication)

  8. Comparative Study on Photovoltaic Pumping Systems Driven by Different Motors Optimized with Sliding Mode Control

    Directory of Open Access Journals (Sweden)

    Abdelhak Bouchakour

    2017-06-01

    Full Text Available This study investigates the performance of three different photovoltaic (PV water pumping systems driven by three types of motors, namely a separately excited DC motor (DCM, an asynchronous motor (ASM, and a permanent magnet synchronous motor (PMSM, via a DC/DC buck-boost converter coupled to a centrifugal pump. The purpose of this study is to implement a fast and robust control for this type of a nonlinear system, controlled by sliding mode (SM. This paper presents an SM control technique for controlling a DC/DC buck-boost converter to transfer the maximum power delivered by the PV generator. Each component is studied and analyzed to simulate the global system in MATLAB/SIMULINK. The three systems are then compared to determine the overall effectiveness of the proposed command. The study concludes that the ASM-driven PV system yields highly favorable results and requires less maintenance compared with other systems.

  9. Data-driven modeling and real-time distributed control for energy efficient manufacturing systems

    International Nuclear Information System (INIS)

    Zou, Jing; Chang, Qing; Arinez, Jorge; Xiao, Guoxian

    2017-01-01

    As manufacturers face the challenges of increasing global competition and energy saving requirements, it is imperative to seek out opportunities to reduce energy waste and overall cost. In this paper, a novel data-driven stochastic manufacturing system modeling method is proposed to identify and predict energy saving opportunities and their impact on production. A real-time distributed feedback production control policy, which integrates the current and predicted system performance, is established to improve the overall profit and energy efficiency. A case study is presented to demonstrate the effectiveness of the proposed control policy. - Highlights: • A data-driven stochastic manufacturing system model is proposed. • Real-time system performance and energy saving opportunity identification method is developed. • Prediction method for future potential system performance and energy saving opportunity is developed. • A real-time distributed feedback control policy is established to improve energy efficiency and overall system profit.

  10. An online model composition tool for system biology models.

    Science.gov (United States)

    Coskun, Sarp A; Cicek, A Ercument; Lai, Nicola; Dash, Ranjan K; Ozsoyoglu, Z Meral; Ozsoyoglu, Gultekin

    2013-09-05

    There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user's input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well.

  11. An innovative ultra-capacitor driven shape memory alloy actuator with an embedded control system

    International Nuclear Information System (INIS)

    Li, Peng; Song, Gangbing

    2014-01-01

    In this paper, an innovative ultra-capacitor driven shape memory alloy (SMA) actuator with an embedded control system is proposed targeting high power high-duty cycle SMA applications. The ultra-capacitor, which is capable of delivering massive amounts of instantaneous current in a compact dimension for high power applications, is chosen as the main component of the power supply. A specialized embedded system is designed from the ground up to control the ultra-capacitor driven SMA system. The control of the ultra-capacitor driven SMA is different from that of a regular constant voltage powered SMA system in that the energy and the voltage of the ultra-capacitor decrease as the system load increases. The embedded control system is also different from a computer-based control system in that it has limited computational power, and the control algorithm has to be designed to be simple while effective so that it can fit into the embedded system environment. The problem of a variable voltage power source induced by the use of the ultra-capacitor is solved by using a fuzzy PID (proportional integral and derivative) control. The method of using an ultra-capacitor to drive SMA actuators enabled SMA as a good candidate for high power high-duty cycle applications. The proposed embedded control system provides a good and ready-to-use solution for SMA high power applications. (paper)

  12. The Model-Driven openETCS Paradigm for Secure, Safe and Certifiable Train Control Systems

    DEFF Research Database (Denmark)

    Peleska, Jan; Feuser, Johannes; Haxthausen, Anne Elisabeth

    2012-01-01

    -driven openETCS approach, a threat analysis is performed, identifying both safety and security hazards that may be common to all model-based development paradigms for safety-critical railway control systems, or specific to the openETCS approach. In the subsequent sections state-of-the-art methods suitable...

  13. Transition to Collisionless Ion-Temperature-Gradient-Driven Plasma Turbulence: A Dynamical Systems Approach

    International Nuclear Information System (INIS)

    Kolesnikov, R.A.; Krommes, J.A.

    2005-01-01

    The transition to collisionless ion-temperature-gradient-driven plasma turbulence is considered by applying dynamical systems theory to a model with 10 degrees of freedom. The study of a four-dimensional center manifold predicts a 'Dimits shift' of the threshold for turbulence due to the excitation of zonal flows and establishes (for the model) the exact value of that shift

  14. Grazing management, resilience and the dynamics of a fire driven rangeland system

    NARCIS (Netherlands)

    Anderies, J.M.; Janssen, M.A.; Walker, B.H.

    2002-01-01

    We developed a stylized mathematical model to explore the effects of physical, ecological, and economic factors on the resilience of a managed fire-driven rangeland system. Depending on grazing pressure, the model exhibits one of three distinct configurations: a fire-dominated, grazing-dominated, or

  15. Model-driven design-space exploration for embedded systems: the Octopus Toolset

    NARCIS (Netherlands)

    Basten, T.; van Benthum, E.; Geilen, M.C.W.; Hendriks, M.; Houben, F.; Igna, G.; Reckers, F.J.; Smet, de S.; Somers, L.J.A.M.; Teeselink, Egbert; Trcka, N.; Vaandrager, F.W.; Verriet, J.H.; Voorhoeve, M.; Yang, Y.; Margaria, T.; Steffen, B.

    2010-01-01

    The complexity of today’s embedded systems and their development trajectories requires a systematic, model-driven design approach, supported by tooling wherever possible. Only then, development trajectories become manageable, with high-quality, cost-effective results. This paper introduces the

  16. A scenario-driven approach for value, risk and cost analysis in system architecting for innovation

    NARCIS (Netherlands)

    Ionita, M.T.; America, P.H.M.; Hammer, D.K.; Obbink, J.H.; Trienekens, J.J.M.; Magee, J.; Szyperski, C.; Bosch, J.

    2004-01-01

    We present a quantitative method for scenario-driven value, risk, and cost analysis when proposing new system architectures for innovation projects. The method helps to articulate the relative benefits and/or disadvantages of the proposed set of scenarios in the early architecting phases of a new

  17. Optical gain in an optically driven three-level ? system in atomic Rb vapor

    Science.gov (United States)

    Ballmann, C. W.; Yakovlev, V. V.

    2018-06-01

    In this work, we report experimentally achieved optical gain of a weak probe beam in a three-level ? system in a low density Rubidium vapor cell driven by a single pump beam. The maximum measured gain of the probe beam was about 0.12%. This work could lead to new approaches for enhancing molecular spectroscopy applications.

  18. Accelerator-driven nuclear synergetic systems-an overview of the research activities in Sweden

    International Nuclear Information System (INIS)

    Conde, H.; Baecklin, A.; Carius, S.

    1995-01-01

    The rapid development of the accelerator technology which enables the construction of reliable and very intense neutron sources has initiated a growing interest for accelerator driven transmutation systems in Sweden. After the Specialist Meeting on Accelerator-Driven Transmutation Technology for Radwaste and other Applications on 24-28 June 1991 at Saltsjoebaden, Sweden, the research activities oriented towards accelerator-driven systems have been started at several research centers in Sweden. Also the governmental agencies responsible for the spent fuel policy showed a positive attitude to these activities through a limited financial support, particularly for studies of the safety aspects of these systems. Also the nuclear power industry and utilities show a positive interest in the research on these concepts. The present paper presents an overview of the Swedish research activities on accelerator-driven systems and the proposed future coordination, organizations and prospects for this research in the context of the national nuclear energy and spent fuel policy. The Swedish perspective for international cooperation is also described

  19. Accelerator Driven Sub-Critical System for the Radioactive Waste Transmutation

    International Nuclear Information System (INIS)

    Avramovic, I.; Pesic, M.

    2008-01-01

    Spent nuclear fuel discharged from nuclear power plants is the main problem during design of radioactive waste disposal. Most of the hazard stems from only a few chemical elements. The radiotoxicity of these elements can be efficiently reduced using partitioning and transmutation in fast reactors and accelerator driven subcritical systems. (author)

  20. Accelerator-driven nuclear synergetic systems-an overview of the research activities in Sweden

    Energy Technology Data Exchange (ETDEWEB)

    Conde, H.; Baecklin, A.; Carius, S. [Uppsala Univ. (Sweden)] [and others

    1995-10-01

    The rapid development of the accelerator technology which enables the construction of reliable and very intense neutron sources has initiated a growing interest for accelerator driven transmutation systems in Sweden. After the Specialist Meeting on Accelerator-Driven Transmutation Technology for Radwaste and other Applications on 24-28 June 1991 at Saltsjoebaden, Sweden, the research activities oriented towards accelerator-driven systems have been started at several research centers in Sweden. Also the governmental agencies responsible for the spent fuel policy showed a positive attitude to these activities through a limited financial support, particularly for studies of the safety aspects of these systems. Also the nuclear power industry and utilities show a positive interest in the research on these concepts. The present paper presents an overview of the Swedish research activities on accelerator-driven systems and the proposed future coordination, organizations and prospects for this research in the context of the national nuclear energy and spent fuel policy. The Swedish perspective for international cooperation is also described.