WorldWideScience

Sample records for biological systems engineering

  1. 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."

  2. 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.

  3. 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. 

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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....

  9. 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.

  10. 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....

  11. 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.

  12. 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

  13. SYSTEMS BIOLOGY AND METABOLIC ENGINEERING OF ARTHROSPIRA CELL FACTORIES

    Directory of Open Access Journals (Sweden)

    Amornpan Klanchui

    2012-10-01

    Full Text Available Arthrospira are attractive candidates to serve as cell factories for production of many valuable compounds useful for food, feed, fuel and pharmaceutical industries. In connection with the development of sustainable bioprocessing, it is a challenge to design and develop efficient Arthrospira cell factories which can certify effective conversion from the raw materials (i.e. CO2 and sun light into desired products. With the current availability of the genome sequences and metabolic models of Arthrospira, the development of Arthrospira factories can now be accelerated by means of systems biology and the metabolic engineering approach. Here, we review recent research involving the use of Arthrospira cell factories for industrial applications, as well as the exploitation of systems biology and the metabolic engineering approach for studying Arthrospira. The current status of genomics and proteomics through the development of the genome-scale metabolic model of Arthrospira, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies are discussed. At the end, the perspective and future direction on Arthrospira cell factories for industrial biotechnology are presented.

  14. IntegromeDB: an integrated system and biological search engine.

    Science.gov (United States)

    Baitaluk, Michael; Kozhenkov, Sergey; Dubinina, Yulia; Ponomarenko, Julia

    2012-01-19

    With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback.

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

    Science.gov (United States)

    He, Fei; Murabito, Ettore; Westerhoff, Hans V

    2016-04-01

    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 through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways. © 2016 The Author(s).

  16. On the analysis of complex biological supply chains: From Process Systems Engineering to Quantitative Systems Pharmacology.

    Science.gov (United States)

    Rao, Rohit T; Scherholz, Megerle L; Hartmanshenn, Clara; Bae, Seul-A; Androulakis, Ioannis P

    2017-12-05

    The use of models in biology has become particularly relevant as it enables investigators to develop a mechanistic framework for understanding the operating principles of living systems as well as in quantitatively predicting their response to both pathological perturbations and pharmacological interventions. This application has resulted in a synergistic convergence of systems biology and pharmacokinetic-pharmacodynamic modeling techniques that has led to the emergence of quantitative systems pharmacology (QSP). In this review, we discuss how the foundational principles of chemical process systems engineering inform the progressive development of more physiologically-based systems biology models.

  17. Metabolic engineering of Bacillus subtilis fueled by systems biology: Recent advances and future directions.

    Science.gov (United States)

    Liu, Yanfeng; Li, Jianghua; Du, Guocheng; Chen, Jian; Liu, Long

    By combining advanced omics technology and computational modeling, systems biologists have identified and inferred thousands of regulatory events and system-wide interactions of the bacterium Bacillus subtilis, which is commonly used both in the laboratory and in industry. This dissection of the multiple layers of regulatory networks and their interactions has provided invaluable information for unraveling regulatory mechanisms and guiding metabolic engineering. In this review, we discuss recent advances in the systems biology and metabolic engineering of B. subtilis and highlight current gaps in our understanding of global metabolism and global pathway engineering in this organism. We also propose future perspectives in the systems biology of B. subtilis and suggest ways that this approach can be used to guide metabolic engineering. Specifically, although hundreds of regulatory events have been identified or inferred via systems biology approaches, systematic investigation of the functionality of these events in vivo has lagged, thereby preventing the elucidation of regulatory mechanisms and further rational pathway engineering. In metabolic engineering, ignoring the engineering of multilayer regulation hinders metabolic flux redistribution. Post-translational engineering, allosteric engineering, and dynamic pathway analyses and control will also contribute to the modulation and control of the metabolism of engineered B. subtilis, ultimately producing the desired cellular traits. We hope this review will aid metabolic engineers in making full use of available systems biology datasets and approaches for the design and perfection of microbial cell factories through global metabolism optimization. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Importance of systems biology in engineering microbes for biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Mukhopadhyay, Aindrila; Redding, Alyssa M.; Rutherford, Becky J.; Keasling, Jay D.

    2009-12-02

    Microorganisms have been rich sources for natural products, some of which have found use as fuels, commodity chemicals, specialty chemicals, polymers, and drugs, to name a few. The recent interest in production of transportation fuels from renewable resources has catalyzed numerous research endeavors that focus on developing microbial systems for production of such natural products. Eliminating bottlenecks in microbial metabolic pathways and alleviating the stresses due to production of these chemicals are crucial in the generation of robust and efficient production hosts. The use of systems-level studies makes it possible to comprehensively understand the impact of pathway engineering within the context of the entire host metabolism, to diagnose stresses due to product synthesis, and provides the rationale to cost-effectively engineer optimal industrial microorganisms.

  19. Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites

    DEFF Research Database (Denmark)

    Kim, Hyun Uk; Charusanti, Pep; Lee, Sang Yup

    2016-01-01

    Metabolic engineering using systems biology tools is increasingly applied to overproduce secondary metabolites for their potential industrial production. In this Highlight, recent relevant metabolic engineering studies are analyzed with emphasis on host selection and engineering approaches...... for the optimal production of various prokaryotic secondary metabolites: native versus heterologous hosts (e.g., Escherichia coli) and rational versus random approaches. This comparative analysis is followed by discussions on systems biology tools deployed in optimizing the production of secondary metabolites....... The potential contributions of additional systems biology tools are also discussed in the context of current challenges encountered during optimization of secondary metabolite production....

  20. Engineering derivatives from biological systems for advanced aerospace applications

    Science.gov (United States)

    Winfield, Daniel L.; Hering, Dean H.; Cole, David

    1991-01-01

    The present study consisted of a literature survey, a survey of researchers, and a workshop on bionics. These tasks produced an extensive annotated bibliography of bionics research (282 citations), a directory of bionics researchers, and a workshop report on specific bionics research topics applicable to space technology. These deliverables are included as Appendix A, Appendix B, and Section 5.0, respectively. To provide organization to this highly interdisciplinary field and to serve as a guide for interested researchers, we have also prepared a taxonomy or classification of the various subelements of natural engineering systems. Finally, we have synthesized the results of the various components of this study into a discussion of the most promising opportunities for accelerated research, seeking solutions which apply engineering principles from natural systems to advanced aerospace problems. A discussion of opportunities within the areas of materials, structures, sensors, information processing, robotics, autonomous systems, life support systems, and aeronautics is given. Following the conclusions are six discipline summaries that highlight the potential benefits of research in these areas for NASA's space technology programs.

  1. The necessity of a theory of biology for tissue engineering: metabolism-repair systems.

    Science.gov (United States)

    Ganguli, Suman; Hunt, C Anthony

    2004-01-01

    Since there is no widely accepted global theory of biology, tissue engineering and bioengineering lack a theoretical understanding of the systems being engineered. By default, tissue engineering operates with a "reductionist" theoretical approach, inherited from traditional engineering of non-living materials. Long term, that approach is inadequate, since it ignores essential aspects of biology. Metabolism-repair systems are a theoretical framework which explicitly represents two "functional" aspects of living organisms: self-repair and self-replication. Since repair and replication are central to tissue engineering, we advance metabolism-repair systems as a potential theoretical framework for tissue engineering. We present an overview of the framework, and indicate directions to pursue for extending it to the context of tissue engineering. We focus on biological networks, both metabolic and cellular, as one such direction. The construction of these networks, in turn, depends on biological protocols. Together these concepts may help point the way to a global theory of biology appropriate for tissue engineering.

  2. Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology

    DEFF Research Database (Denmark)

    Dvořák, Pavel; Nikel, Pablo Ivan; Damborskýc, Jiří

    2017-01-01

    pollutants with no external intervention, the onset of genetic engineering in the 1980s allowed the possibility of rational design of bacteria to catabolize specific compounds, which could eventually be released into the environment as bioremediation agents. The complexity of this endeavour and the lack...... of fundamental knowledge nonetheless led to the virtual abandonment of such a recombinant DNA-based bioremediation only a decade later. In a twist of events, the last few years have witnessed the emergence of new systemic fields (including systems and synthetic biology, and metabolic engineering) that allow....... In this article, we analyze how contemporary systemic biology is helping to take the design of bioremediation agents back to the core of environmental biotechnology. We inspect a number of recent strategies for catabolic pathway construction and optimization and we bring them together by proposing an engineering...

  3. ‘Can Simple Biological Systems be Built from Standardized Interchangeable Parts?’:Negotiating Biology and Engineering in a Synthetic Biology Competition

    OpenAIRE

    Frow, Emma; Calvert, Jane

    2013-01-01

    Synthetic biology represents a recent attempt to bring engineering principles and practices to working with biology. In practice, the nature of the relationship between engineering and biology in synthetic biology is a subject of ongoing debate. The disciplines of biology and engineering are typically seen to involve differentways of knowing and doing, and to embody different assumptions and objectives. Tensions between these approaches are playing out as the field of synthetic biology is bei...

  4. Engineering a Biological Revolution.

    Science.gov (United States)

    Matheson, Susan

    2017-01-26

    The new field of synthetic biology promises to change health care, computer technology, the production of biofuels, and more. Students participating in the International Genetically Engineered Machine (iGEM) competition are on the front lines of this revolution. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Multiplexed Engineering in Biology.

    Science.gov (United States)

    Rogers, Jameson K; Church, George M

    2016-03-01

    Biotechnology is the manufacturing technology of the future. However, engineering biology is complex, and many possible genetic designs must be evaluated to find cells that produce high levels of a desired drug or chemical. Recent advances have enabled the design and construction of billions of genetic variants per day, but evaluation capacity remains limited to thousands of variants per day. Here we evaluate biological engineering through the lens of the design–build–test cycle framework and highlight the role that multiplexing has had in transforming the design and build steps. We describe a multiplexed solution to the ‘test’ step that is enabled by new research. Achieving a multiplexed test step will permit a fully multiplexed engineering cycle and boost the throughput of biobased product development by up to a millionfold.

  6. Synthetic biology: an emerging engineering discipline.

    Science.gov (United States)

    Cheng, Allen A; Lu, Timothy K

    2012-01-01

    Over the past decade, synthetic biology has emerged as an engineering discipline for biological systems. Compared with other substrates, biology poses a unique set of engineering challenges resulting from an incomplete understanding of natural biological systems and tools for manipulating them. To address these challenges, synthetic biology is advancing from developing proof-of-concept designs to focusing on core platforms for rational and high-throughput biological engineering. These platforms span the entire biological design cycle, including DNA construction, parts libraries, computational design tools, and interfaces for manipulating and probing synthetic circuits. The development of these enabling technologies requires an engineering mindset to be applied to biology, with an emphasis on generalizable techniques in addition to application-specific designs. This review aims to discuss the progress and challenges in synthetic biology and to illustrate areas where synthetic biology may impact biomedical engineering and human health.

  7. Expanding the chemical palate of cells by combining systems biology and metabolic engineering.

    Science.gov (United States)

    Curran, Kathleen A; Alper, Hal S

    2012-07-01

    The field of Metabolic Engineering has recently undergone a transformation that has led to a rapid expansion of the chemical palate of cells. Now, it is conceivable to produce nearly any organic molecule of interest using a cellular host. Significant advances have been made in the production of biofuels, biopolymers and precursors, pharmaceuticals and nutraceuticals, and commodity and specialty chemicals. Much of this rapid expansion in the field has been, in part, due to synergies and advances in the area of systems biology. Specifically, the availability of functional genomics, metabolomics and transcriptomics data has resulted in the potential to produce a wealth of new products, both natural and non-natural, in cellular factories. The sheer amount and diversity of this data however, means that uncovering and unlocking novel chemistries and insights is a non-obvious exercise. To address this issue, a number of computational tools and experimental approaches have been developed to help expedite the design process to create new cellular factories. This review will highlight many of the systems biology enabling technologies that have reduced the design cycle for engineered hosts, highlight major advances in the expanded diversity of products that can be synthesized, and conclude with future prospects in the field of metabolic engineering. Copyright © 2012 Elsevier Inc. All rights reserved.

  8. Synthetic biology: engineering molecular computers

    CERN Multimedia

    CERN. Geneva

    2018-01-01

    Complicated systems cannot survive the rigors of a chaotic environment, without balancing mechanisms that sense, decide upon and counteract the exerted disturbances. Especially so with living organisms, forced by competition to incredible complexities, escalating also their self-controlling plight. Therefore, they compute. Can we harness biological mechanisms to create artificial computing systems? Biology offers several levels of design abstraction: molecular machines, cells, organisms... ranging from the more easily-defined to the more inherently complex. At the bottom of this stack we find the nucleic acids, RNA and DNA, with their digital structure and relatively precise interactions. They are central enablers of designing artificial biological systems, in the confluence of engineering and biology, that we call Synthetic biology. In the first part, let us follow their trail towards an overview of building computing machines with molecules -- and in the second part, take the case study of iGEM Greece 201...

  9. Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology.

    Science.gov (United States)

    Dvořák, Pavel; Nikel, Pablo I; Damborský, Jiří; de Lorenzo, Víctor

    2017-11-15

    Elimination or mitigation of the toxic effects of chemical waste released to the environment by industrial and urban activities relies largely on the catalytic activities of microorganisms-specifically bacteria. Given their capacity to evolve rapidly, they have the biochemical power to tackle a large number of molecules mobilized from their geological repositories through human action (e.g., hydrocarbons, heavy metals) or generated through chemical synthesis (e.g., xenobiotic compounds). Whereas naturally occurring microbes already have considerable ability to remove many environmental pollutants with no external intervention, the onset of genetic engineering in the 1980s allowed the possibility of rational design of bacteria to catabolize specific compounds, which could eventually be released into the environment as bioremediation agents. The complexity of this endeavour and the lack of fundamental knowledge nonetheless led to the virtual abandonment of such a recombinant DNA-based bioremediation only a decade later. In a twist of events, the last few years have witnessed the emergence of new systemic fields (including systems and synthetic biology, and metabolic engineering) that allow revisiting the same environmental pollution challenges through fresh and far more powerful approaches. The focus on contaminated sites and chemicals has been broadened by the phenomenal problems of anthropogenic emissions of greenhouse gases and the accumulation of plastic waste on a global scale. In this article, we analyze how contemporary systemic biology is helping to take the design of bioremediation agents back to the core of environmental biotechnology. We inspect a number of recent strategies for catabolic pathway construction and optimization and we bring them together by proposing an engineering workflow. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Synthetic biology meets tissue engineering.

    Science.gov (United States)

    Davies, Jamie A; Cachat, Elise

    2016-06-15

    Classical tissue engineering is aimed mainly at producing anatomically and physiologically realistic replacements for normal human tissues. It is done either by encouraging cellular colonization of manufactured matrices or cellular recolonization of decellularized natural extracellular matrices from donor organs, or by allowing cells to self-organize into organs as they do during fetal life. For repair of normal bodies, this will be adequate but there are reasons for making unusual, non-evolved tissues (repair of unusual bodies, interface to electromechanical prostheses, incorporating living cells into life-support machines). Synthetic biology is aimed mainly at engineering cells so that they can perform custom functions: applying synthetic biological approaches to tissue engineering may be one way of engineering custom structures. In this article, we outline the 'embryological cycle' of patterning, differentiation and morphogenesis and review progress that has been made in constructing synthetic biological systems to reproduce these processes in new ways. The state-of-the-art remains a long way from making truly synthetic tissues, but there are now at least foundations for future work. © 2016 Authors; published by Portland Press Limited.

  11. Translational systems biology: introduction of an engineering approach to the pathophysiology of the burn patient.

    Science.gov (United States)

    An, Gary; Faeder, James; Vodovotz, Yoram

    2008-01-01

    The pathophysiology of the burn patient manifests the full spectrum of the complexity of the inflammatory response. In the acute phase, inflammation may have negative effects via capillary leak, the propagation of inhalation injury, and development of multiple organ failure. Attempts to mediate these processes remain a central subject of burn care research. Conversely, inflammation is a necessary prologue and component in the later stage processes of wound healing. Despite the volume of information concerning the cellular and molecular processes involved in inflammation, there exists a significant gap between the knowledge of mechanistic pathophysiology and the development of effective clinical therapeutic regimens. Translational systems biology (TSB) is the application of dynamic mathematical modeling and certain engineering principles to biological systems to integrate mechanism with phenomenon and, importantly, to revise clinical practice. This study will review the existing applications of TSB in the areas of inflammation and wound healing, relate them to specific areas of interest to the burn community, and present an integrated framework that links TSB with traditional burn research.

  12. 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 ...

  13. Synthetic biology and metabolic engineering.

    Science.gov (United States)

    Stephanopoulos, Gregory

    2012-11-16

    Metabolic engineering emerged 20 years ago as the discipline occupied with the directed modification of metabolic pathways for the microbial synthesis of various products. As such, it deals with the engineering (design, construction, and optimization) of native as well as non-natural routes of product synthesis, aided in this task by the availability of synthetic DNA, the core enabling technology of synthetic biology. The two fields, however, only partially overlap in their interest in pathway engineering. While fabrication of biobricks, synthetic cells, genetic circuits, and nonlinear cell dynamics, along with pathway engineering, have occupied researchers in the field of synthetic biology, the sum total of these areas does not constitute a coherent definition of synthetic biology with a distinct intellectual foundation and well-defined areas of application. This paper reviews the origins of the two fields and advances two distinct paradigms for each of them: that of unit operations for metabolic engineering and electronic circuits for synthetic biology. In this context, metabolic engineering is about engineering cell factories for the biological manufacturing of chemical and pharmaceutical products, whereas the main focus of synthetic biology is fundamental biological research facilitated by the use of synthetic DNA and genetic circuits.

  14. Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology.

    Science.gov (United States)

    Das, Arya A; Ajayakumar Darsana, T; Jacob, Elizabeth

    2017-03-01

    Experiments in systems biology are generally supported by a computational model which quantitatively estimates the parameters of the system by finding the best fit to the experiment. Mathematical models have proved to be successful in reverse engineering the system. The data generated is interpreted to understand the dynamics of the underlying phenomena. The question we have sought to answer is that - is it possible to use an agent-based approach to re-engineer a biological process, making use of the available knowledge from experimental and modelling efforts? Can the bottom-up approach benefit from the top-down exercise so as to create an integrated modelling formalism for systems biology? We propose a modelling pipeline that learns from the data given by reverse engineering, and uses it for re-engineering the system, to carry out in-silico experiments. A mathematical model that quantitatively predicts co-expression of EGFR-HER2 receptors in activation and trafficking has been taken for this study. The pipeline architecture takes cues from the population model that gives the rates of biochemical reactions, to formulate knowledge-based rules for the particle model. Agent-based simulations using these rules, support the existing facts on EGFR-HER2 dynamics. We conclude that, re-engineering models, built using the results of reverse engineering, opens up the possibility of harnessing the power pack of data which now lies scattered in literature. Virtual experiments could then become more realistic when empowered with the findings of empirical cell biology and modelling studies. Implemented on the Agent Modelling Framework developed in-house. C ++ code templates available in Supplementary material . liz.csir@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  15. Microbial production of natural and non-natural flavonoids: Pathway engineering, directed evolution and systems/synthetic biology.

    Science.gov (United States)

    Pandey, Ramesh Prasad; Parajuli, Prakash; Koffas, Mattheos A G; Sohng, Jae Kyung

    2016-01-01

    In this review, we address recent advances made in pathway engineering, directed evolution, and systems/synthetic biology approaches employed in the production and modification of flavonoids from microbial cells. The review is divided into two major parts. In the first, various metabolic engineering and system/synthetic biology approaches used for production of flavonoids and derivatives are discussed broadly. All the manipulations/engineering accomplished on the microorganisms since 2000 are described in detail along with the biosynthetic pathway enzymes, their sources, structures of the compounds, and yield of each product. In the second part of the review, post-modifications of flavonoids by four major reactions, namely glycosylations, methylations, hydroxylations and prenylations using recombinant strains are described. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Systems Engineering

    OpenAIRE

    Vaughan, William W.

    2016-01-01

    The term “systems engineering” when entered into the Google search page, produces a significant number of results, evidence that systems engineering is recognized as being important for the success of essentially all products. Since most readers of this item will be rather well versed in documents concerning systems engineering, I have elected to share some of the points made on this subject in a document developed by the European Cooperation for Space Standardization (ECSS), a component of t...

  17. Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering

    NARCIS (Netherlands)

    Menolascina, F.; Bellomo, D.; Maiwald, T.; Bevilacqua, V.; Ciminelli, C.; Paradiso, A.; Tommasi, S.

    2009-01-01

    Background: Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the

  18. Recent developments in systems biology and metabolic engineering of plant microbe interactions

    Directory of Open Access Journals (Sweden)

    Vishal Kumar

    2016-09-01

    Full Text Available Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant microbe interactions using gene editing and system biology tools towards the comprehension in improvement of plant traits. Further, system biology tools like FBA, OptKnock and constrain based modeling helps in understanding such interactions as a whole. In addition, various gene editing tools have been summarized and a strategy has been hypothesized for the development of disease free plants. Furthermore, we have tried to summarize the predictions through data retrieved from various types of sources such as high throughput sequencing data (e.g. single nucleotide polymorphism (SNP detection, RNA-seq, proteomics and metabolic models have been reconstructed from such sequences for species communities. It is well known fact that systems biology approaches and modeling of biological networks will enable us to learn the insight of such network and will also help further in understanding these interactions.

  19. Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering.

    Science.gov (United States)

    Menolascina, Filippo; Bellomo, Domenico; Maiwald, Thomas; Bevilacqua, Vitoantonio; Ciminelli, Caterina; Paradiso, Angelo; Tommasi, Stefania

    2009-10-15

    Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the intrinsic characteristics of complex pathologies like cancer: acquiring information for a system understanding of complex reaction networks is time consuming and expensive. Stimulus response experiments (SRE) have been used to gain a deeper insight into the details of biochemical mechanisms underlying cell life and functioning. Optimisation of the input time-profile, however, still remains a major area of research due to the complexity of the problem and its relevance for the task of information retrieval in systems biology-related experiments. We have addressed the problem of quantifying the information associated to an experiment using the Fisher Information Matrix and we have proposed an optimal experimental design strategy based on evolutionary algorithm to cope with the problem of information gathering in Systems Biology. On the basis of the theoretical results obtained in the field of control systems theory, we have studied the dynamical properties of the signals to be used in cell stimulation. The results of this study have been used to develop a microfluidic device for the automation of the process of cell stimulation for system identification. We have applied the proposed approach to the Epidermal Growth Factor Receptor pathway and we observed that it minimises the amount of parametric uncertainty associated to the identified model. A statistical framework based on Monte-Carlo estimations of the uncertainty ellipsoid confirmed the superiority of optimally designed experiments over canonical inputs. The proposed approach can be easily extended to multiobjective formulations that can also take advantage of identifiability analysis. Moreover, the availability of fully automated

  20. Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research

    Directory of Open Access Journals (Sweden)

    Toshitsugu Fujita

    2015-09-01

    Full Text Available Engineered DNA-binding molecules such as transcription activator-like effector (TAL or TALE proteins and the clustered regularly interspaced short palindromic repeats (CRISPR and CRISPR-associated proteins (Cas (CRISPR/Cas system have been used extensively for genome editing in cells of various types and species. The sequence-specific DNA-binding activities of these engineered DNA-binding molecules can also be utilized for other purposes, such as transcriptional activation, transcriptional repression, chromatin modification, visualization of genomic regions, and isolation of chromatin in a locus-specific manner. In this review, we describe applications of these engineered DNA-binding molecules for biological purposes other than genome editing.

  1. An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system

    Directory of Open Access Journals (Sweden)

    Yusuke Kato

    2015-09-01

    Full Text Available Biological containment is a genetic technique that programs dangerous organisms to grow only in the laboratory and to die in the natural environment. Auxotrophy for a substance not found in the natural environment is an ideal biological containment. Here, we constructed an Escherichia coli strain that cannot survive in the absence of the unnatural amino acid 3-iodo-L-tyrosine. This synthetic auxotrophy was achieved by conditional production of the antidote protein against the highly toxic enzyme colicin E3. An amber stop codon was inserted in the antidote gene. The translation of the antidote mRNA was controlled by a translational switch using amber-specific 3-iodo-L-tyrosine incorporation. The antidote is synthesized only when 3-iodo-L-tyrosine is present in the culture medium. The viability of this strain rapidly decreased with less than a 1 h half-life after removal of 3-iodo-L-tyrosine, suggesting that the decay of the antidote causes the host killing by activated colicin E3 in the absence of this unnatural amino acid. The contained strain grew 1.5 times more slowly than the parent strains. The escaper frequency was estimated to be 1.4 mutations (95% highest posterior density 1.1–1.8 per 105 cell divisions. This containment system can be constructed by only plasmid introduction without genome editing, suggesting that this system may be applicable to other microbes carrying toxin-antidote systems similar to that of colicin E3.

  2. Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology.

    Science.gov (United States)

    Li, Jinyang; Liu, Yi; Kim, Eunkyoung; March, John C; Bentley, William E; Payne, Gregory F

    2017-04-01

    The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O 2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H 2 O 2 ) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this

  3. Engineering and Biology: Counsel for a Continued Relationship

    Science.gov (United States)

    Levy, Arnon; Siegal, Mark L.; Soyer, Orkun S.; Wagner, Andreas

    2015-01-01

    Biologists frequently draw on ideas and terminology from engineering. Evolutionary systems biology—with its circuits, switches, and signal processing—is no exception. In parallel with the frequent links drawn between biology and engineering, there is ongoing criticism against this cross-fertilization, using the argument that over-simplistic metaphors from engineering are likely to mislead us as engineering is fundamentally different from biology. In this article, we clarify and reconfigure the link between biology and engineering, presenting it in a more favorable light. We do so by, first, arguing that critics operate with a narrow and incorrect notion of how engineering actually works, and of what the reliance on ideas from engineering entails. Second, we diagnose and diffuse one significant source of concern about appeals to engineering, namely that they are inherently and problematically metaphorical. We suggest that there is plenty of fertile ground left for a continued, healthy relationship between engineering and biology. PMID:26085824

  4. 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.

  5. Systems biology and metabolic engineering of lactic acid bacteria for improved fermented foods

    NARCIS (Netherlands)

    Flahaut, N.A.L.; Vos, de W.M.

    2014-01-01

    Lactic acid bacteria have long been used in industrial dairy and other food fermentations that make use of their metabolic activities leading to products with specific organoleptic properties. Metabolic engineering is a rational approach to steer fermentations toward the production of desired

  6. Design and validation of a dynamic cell-culture system for bone biology research and exogenous tissue-engineering applications.

    Science.gov (United States)

    Allori, Alexander C; Davidson, Edward H; Reformat, Derek D; Sailon, Alexander M; Freeman, James; Vaughan, Adam; Wootton, David; Clark, Elizabeth; Ricci, John L; Warren, Stephen M

    2016-10-01

    Bone lacunocanalicular fluid flow ensures chemotransportation and provides a mechanical stimulus to cells. Traditional static cell-culture methods are ill-suited to study the intricacies of bone biology because they ignore the three-dimensionality of meaningful cellular networks and the lacunocanalicular system; furthermore, reliance on diffusion alone for nutrient supply and waste product removal effectively limits scaffolds to 2-3 mm thickness. In this project, a flow-perfusion system was custom-designed to overcome these limitations: eight adaptable chambers housed cylindrical cell-seeded scaffolds measuring 12 or 24 mm in diameter and 1-10 mm in thickness. The porous scaffolds were manufactured using a three-dimensional (3D) periodic microprinting process and were composed of hydroxyapatite/tricalcium phosphate with variable thicknesses, strut sizes, pore sizes and structural configurations. A multi-channel peristaltic pump drew medium from parallel reservoirs and perfused it through each scaffold at a programmable rate. Hermetically sealed valves permitted sampling or replacement of medium. A gas-permeable membrane allowed for gas exchange. Tubing was selected to withstand continuous perfusion for > 2 months without leakage. Computational modelling was performed to assess the adequacy of oxygen supply and the range of fluid shear stress in the bioreactor-scaffold system, using 12 × 6 mm scaffolds, and these models suggested scaffold design modifications that improved oxygen delivery while enhancing physiological shear stress. This system may prove useful in studying complex 3D bone biology and in developing strategies for engineering thick 3D bone constructs. Copyright © 2013 John Wiley & Sons, Ltd. Copyright © 2013 John Wiley & Sons, Ltd.

  7. Biology: An Important Agricultural Engineering Mechanism

    Science.gov (United States)

    Henderson, S. M.

    1974-01-01

    Describes the field of bioengineering with particular emphasis on agricultural engineering, and presents the results of a survey of schools that combine biology and engineering in their curricula. (JR)

  8. Integrating rehabilitation engineering technology with biologics.

    Science.gov (United States)

    Collinger, Jennifer L; Dicianno, Brad E; Weber, Douglas J; Cui, Xinyan Tracy; Wang, Wei; Brienza, David M; Boninger, Michael L

    2011-06-01

    Rehabilitation engineers apply engineering principles to improve function or to solve challenges faced by persons with disabilities. It is critical to integrate the knowledge of biologics into the process of rehabilitation engineering to advance the field and maximize potential benefits to patients. Some applications in particular demonstrate the value of a symbiotic relationship between biologics and rehabilitation engineering. In this review we illustrate how researchers working with neural interfaces and integrated prosthetics, assistive technology, and biologics data collection are currently integrating these 2 fields. We also discuss the potential for further integration of biologics and rehabilitation engineering to deliver the best technologies and treatments to patients. Engineers and clinicians must work together to develop technologies that meet clinical needs and are accessible to the intended patient population. Copyright © 2011 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

  9. 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).

  10. Engineering Review Information System

    Science.gov (United States)

    Grems, III, Edward G. (Inventor); Henze, James E. (Inventor); Bixby, Jonathan A. (Inventor); Roberts, Mark (Inventor); Mann, Thomas (Inventor)

    2015-01-01

    A disciplinal engineering review computer information system and method by defining a database of disciplinal engineering review process entities for an enterprise engineering program, opening a computer supported engineering item based upon the defined disciplinal engineering review process entities, managing a review of the opened engineering item according to the defined disciplinal engineering review process entities, and closing the opened engineering item according to the opened engineering item review.

  11. Engineering Liposomes and Nanoparticles for Biological Targeting

    DEFF Research Database (Denmark)

    Jølck, Rasmus Irming; Feldborg, Lise Nørkjær; Andersen, Simon

    2011-01-01

    Our ability to engineer nanomaterials for biological and medical applications is continuously increasing, and nanomaterial designs are becoming more and more complex. One very good example of this is the drug delivery field where nanoparticle systems can be used to deliver drugs specifically...... to diseased tissue. In the early days, the design of the nanoparticles was relatively simple, but today we can surface functionalize and manipulate material properties to target diseased tissue and build highly complex drug release mechanisms into our designs. One of the most promising strategies in drug...

  12. Challenges and opportunities in synthetic biology for chemical engineers.

    Science.gov (United States)

    Luo, Yunzi; Lee, Jung-Kul; Zhao, Huimin

    2013-11-15

    Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement.

  13. Challenges and opportunities in synthetic biology for chemical engineers

    Science.gov (United States)

    Luo, Yunzi; Lee, Jung-Kul; Zhao, Huimin

    2012-01-01

    Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement. PMID:24222925

  14. 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.

  15. Introduction to bioengineering: melding of engineering and biological sciences.

    Science.gov (United States)

    Shoureshi, Rahmat A

    2005-04-01

    Engineering has traditionally focused on the external extensions of organisms, such as transportation systems, high-rise buildings, and entertainment systems. In contrast, bioengineering is concerned with inward processes of biologic organisms. Utilization of engineering principles and techniques in the analysis and solution of problems in medicine and biology is the basis for bioengineering. This article discusses subspecialties in bioengineering and presents examples of projects in this discipline.

  16. 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.

  17. Systems engineering simplified

    CERN Document Server

    Cloutier, Robert; Bone, Mary Alice

    2015-01-01

    IntroductionOverviewDiscussion of Common TerminologyThe Case for Systems EngineeringA Brief History of Systems EngineeringSystem ExamplesSummaryThe System Life CycleManaging System Development-The Vee ModelSystem ProductionSystem Utilization and SupportSystem Retirement and DisposalOther Systems Engineering Development ModelsSpiral ModelAgile Model for Systems EngineeringSystem of InterestAbstraction and DecompositionIntegrationDeveloping and Managing RequirementsCyclone Requiremen

  18. International Conference on Medical and Biological Engineering 2017

    CERN Document Server

    2017-01-01

    This volume presents the proceedings of the International Conference on Medical and Biological Engineering held from 16 to 18 March 2017 in Sarajevo, Bosnia and Herzegovina. Focusing on the theme of ‘Pursuing innovation. Shaping the future’, it highlights the latest advancements in Biomedical Engineering and also presents the latest findings, innovative solutions and emerging challenges in this field. Topics include: - Biomedical Signal Processing - Biomedical Imaging and Image Processing - Biosensors and Bioinstrumentation - Bio-Micro/Nano Technologies - Biomaterials - Biomechanics, Robotics and Minimally Invasive Surgery - Cardiovascular, Respiratory and Endocrine Systems Engineering - Neural and Rehabilitation Engineering - Molecular, Cellular and Tissue Engineering - Bioinformatics and Computational Biology - Clinical Engineering and Health Technology Assessment - Health Informatics, E-Health and Telemedicine - Biomedical Engineering Education - Pharmaceutical Engineering.

  19. 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.

  20. Synthetic Biology to Engineer Bacteriophage Genomes.

    Science.gov (United States)

    Rita Costa, Ana; Milho, Catarina; Azeredo, Joana; Pires, Diana Priscila

    2018-01-01

    Recent advances in the synthetic biology field have enabled the development of new molecular biology techniques used to build specialized bacteriophages with new functionalities. Bacteriophages have been engineered towards a wide range of applications including pathogen control and detection, targeted drug delivery, or even assembly of new materials.In this chapter, two strategies that have been successfully used to genetically engineer bacteriophage genomes are addressed: a yeast-based platform and bacteriophage recombineering of electroporated DNA.

  1. Synthetic biology and its alternatives. Descartes, Kant and the idea of engineering biological machines.

    Science.gov (United States)

    Kogge, Werner; Richter, Michael

    2013-06-01

    The engineering-based approach of synthetic biology is characterized by an assumption that 'engineering by design' enables the construction of 'living machines'. These 'machines', as biological machines, are expected to display certain properties of life, such as adapting to changing environments and acting in a situated way. This paper proposes that a tension exists between the expectations placed on biological artefacts and the notion of producing such systems by means of engineering; this tension makes it seem implausible that biological systems, especially those with properties characteristic of living beings, can in fact be produced using the specific methods of engineering. We do not claim that engineering techniques have nothing to contribute to the biotechnological construction of biological artefacts. However, drawing on Descartes's and Kant's thinking on the relationship between the organism and the machine, we show that it is considerably more plausible to assume that distinctively biological artefacts emerge within a paradigm different from the paradigm of the Cartesian machine that underlies the engineering approach. We close by calling for increased attention to be paid to approaches within molecular biology and chemistry that rest on conceptions different from those of synthetic biology's engineering paradigm. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Site systems engineering: Systems engineering management plan

    Energy Technology Data Exchange (ETDEWEB)

    Grygiel, M.L. [Westinghouse Hanford Co., Richland, WA (United States)

    1996-05-03

    The Site Systems Engineering Management Plan (SEMP) is the Westinghouse Hanford Company (WHC) implementation document for the Hanford Site Systems Engineering Policy, (RLPD 430.1) and Systems Engineering Criteria Document and Implementing Directive, (RLID 430.1). These documents define the US Department of Energy (DOE), Richland Operations Office (RL) processes and products to be used at Hanford to implement the systems engineering process at the site level. This SEMP describes the products being provided by the site systems engineering activity in fiscal year (FY) 1996 and the associated schedule. It also includes the procedural approach being taken by the site level systems engineering activity in the development of these products and the intended uses for the products in the integrated planning process in response to the DOE policy and implementing directives. The scope of the systems engineering process is to define a set of activities and products to be used at the site level during FY 1996 or until the successful Project Hanford Management Contractor (PHMC) is onsite as a result of contract award from Request For Proposal DE-RP06-96RL13200. Following installation of the new contractor, a long-term set of systems engineering procedures and products will be defined for management of the Hanford Project. The extent to which each project applies the systems engineering process and the specific tools used are determined by the project`s management.

  3. Synthetic biology approaches to engineer T cells.

    Science.gov (United States)

    Wu, Chia-Yung; Rupp, Levi J; Roybal, Kole T; Lim, Wendell A

    2015-08-01

    There is rapidly growing interest in learning how to engineer immune cells, such as T lymphocytes, because of the potential of these engineered cells to be used for therapeutic applications such as the recognition and killing of cancer cells. At the same time, our knowhow and capability to logically engineer cellular behavior is growing rapidly with the development of synthetic biology. Here we describe how synthetic biology approaches are being used to rationally alter the behavior of T cells to optimize them for therapeutic functions. We also describe future developments that will be important in order to construct safe and precise T cell therapeutics. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Biologi og/eller engineering?

    DEFF Research Database (Denmark)

    Daugbjerg, Peer

    2018-01-01

    Engineering i skolen er en anvendelsesorienteret og problemløsende undervisning, hvor eleverne lærer at udvikle konkrete løsninger på praktiske problemer. I elevernes arbejde indgår faglig viden og teknologi...

  5. Solar engine system

    International Nuclear Information System (INIS)

    Tan, K.K.; Bahrom Sanugi; Chen, L.C.; Chong, K.K.; Jasmy Yunus; Kannan, K.S.; Lim, B.H.; Noriah Bidin; Omar Aliman; Sahar Salehan; Sheikh Ab Rezan Sheikh A H; Tam, C.M.; Chen, Y.T.

    2001-01-01

    This paper reports the revolutionary solar engine system in Universiti Teknologi Malaysia (UTM). The solar engine is a single cylinder stirling engine driven by solar thermal energy. A first prototype solar engine has been built and demonstrated. A new-concept non-imaging focusing heliostat and a recently invented optical receiver are used in the demonstration. Second generation of prototype solar engine is described briefly. In this paper, the solar engine system development is reported. Measurement for the first prototype engine speed, temperature and specifications are presented. The benefits and potential applications for the future solar engine system, especially for the electricity generating aspect are discussed. (Author)

  6. MORE: mixed optimization for reverse engineering--an application to modeling biological networks response via sparse systems of nonlinear differential equations.

    Science.gov (United States)

    Sambo, Francesco; de Oca, Marco A Montes; Di Camillo, Barbara; Toffolo, Gianna; Stützle, Thomas

    2012-01-01

    Reverse engineering is the problem of inferring the structure of a network of interactions between biological variables from a set of observations. In this paper, we propose an optimization algorithm, called MORE, for the reverse engineering of biological networks from time series data. The model inferred by MORE is a sparse system of nonlinear differential equations, complex enough to realistically describe the dynamics of a biological system. MORE tackles separately the discrete component of the problem, the determination of the biological network topology, and the continuous component of the problem, the strength of the interactions. This approach allows us both to enforce system sparsity, by globally constraining the number of edges, and to integrate a priori information about the structure of the underlying interaction network. Experimental results on simulated and real-world networks show that the mixed discrete/continuous optimization approach of MORE significantly outperforms standard continuous optimization and that MORE is competitive with the state of the art in terms of accuracy of the inferred networks.

  7. Biological aspects of tissue-engineered cartilage.

    Science.gov (United States)

    Hoshi, Kazuto; Fujihara, Yuko; Yamawaki, Takanori; Harai, Motohiro; Asawa, Yukiyo; Hikita, Atsuhiko

    2018-04-01

    Cartilage regenerative medicine has been progressed well, and it reaches the stage of clinical application. Among various techniques, tissue engineering, which incorporates elements of materials science, is investigated earnestly, driven by high clinical needs. The cartilage tissue engineering using a poly lactide scaffold has been exploratorily used in the treatment of cleft lip-nose patients, disclosing good clinical results during 3-year observation. However, to increase the reliability of this treatment, not only accumulation of clinical evidence on safety and usefulness of the tissue-engineered products, but also establishment of scientific background on biological mechanisms, are regarded essential. In this paper, we reviewed recent trends of cartilage tissue engineering in clinical practice, summarized experimental findings on cellular and matrix changes during the cartilage regeneration, and discussed the importance of further studies on biological aspects of tissue-engineered cartilage, especially by the histological and the morphological methods.

  8. Challenges of medical and biological engineering and science

    Energy Technology Data Exchange (ETDEWEB)

    Magjarevic, R [University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb (Croatia)

    2004-07-01

    All aspects of biomedical engineering and science, from research and development, education and training, implementation in health care systems, internationalisation and globalisation, and other, new issues are present in the strategy and in action plans of the International Federation for Medical and Biological Engineering (IFMBE) which, with help of a large number of highly motivated volunteers, will stay in leading position in biomedical engineering and science.

  9. Challenges of medical and biological engineering and science

    International Nuclear Information System (INIS)

    Magjarevic, R.

    2004-01-01

    All aspects of biomedical engineering and science, from research and development, education and training, implementation in health care systems, internationalisation and globalisation, and other, new issues are present in the strategy and in action plans of the International Federation for Medical and Biological Engineering (IFMBE) which, with help of a large number of highly motivated volunteers, will stay in leading position in biomedical engineering and science

  10. Battery systems engineering

    CERN Document Server

    Rahn, Christopher D

    2012-01-01

    A complete all-in-one reference on the important interdisciplinary topic of Battery Systems Engineering Focusing on the interdisciplinary area of battery systems engineering, this book provides the background, models, solution techniques, and systems theory that are necessary for the development of advanced battery management systems. It covers the topic from the perspective of basic electrochemistry as well as systems engineering topics and provides a basis for battery modeling for system engineering of electric and hybrid electric vehicle platforms. This original

  11. Hybrid intelligent engineering systems

    CERN Document Server

    Jain, L C; Adelaide, Australia University of

    1997-01-01

    This book on hybrid intelligent engineering systems is unique, in the sense that it presents the integration of expert systems, neural networks, fuzzy systems, genetic algorithms, and chaos engineering. It shows that these new techniques enhance the capabilities of one another. A number of hybrid systems for solving engineering problems are presented.

  12. NASA systems engineering handbook

    Science.gov (United States)

    Shishko, Robert; Aster, Robert; Chamberlain, Robert G.; McDuffee, Patrick; Pieniazek, Les; Rowell, Tom; Bain, Beth; Cox, Renee I.; Mooz, Harold; Polaski, Lou

    1995-06-01

    This handbook brings the fundamental concepts and techniques of systems engineering to NASA personnel in a way that recognizes the nature of NASA systems and environment. It is intended to accompany formal NASA training courses on systems engineering and project management when appropriate, and is designed to be a top-level overview. The concepts were drawn from NASA field center handbooks, NMI's/NHB's, the work of the NASA-wide Systems Engineering Working Group and the Systems Engineering Process Improvement Task team, several non-NASA textbooks and guides, and material from independent systems engineering courses taught to NASA personnel. Five core chapters cover systems engineering fundamentals, the NASA Project Cycle, management issues in systems engineering, systems analysis and modeling, and specialty engineering integration. It is not intended as a directive.

  13. A Multidisciplinary Workshop: Self-Assembling Peptide Systems in Biology, Medicine and Engineering, Crete, Greece, July 1-6, 1999

    Science.gov (United States)

    1999-07-06

    Bombyx mori silk fibroin. Structures with polar ap -s h eets and -turns, stacking with the hydrophobic methyl groups of the alanine units in contact, are...and Science in Crete Preface The idea of organizing this workshop originated from a series of unexpected events. During a visit with Drs. Amalia...and Europe. Biology has asked some fundamental questions about nature and our own being, the origin of species, the development of living systems and

  14. XIV Mediterranean Conference on Medical and Biological Engineering and Computing

    CERN Document Server

    Christofides, Stelios; Pattichis, Constantinos

    2016-01-01

    This volume presents the proceedings of Medicon 2016, held in Paphos, Cyprus. Medicon 2016 is the XIV in the series of regional meetings of the International Federation of Medical and Biological Engineering (IFMBE) in the Mediterranean. The goal of Medicon 2016 is to provide updated information on the state of the art on Medical and Biological Engineering and Computing under the main theme “Systems Medicine for the Delivery of Better Healthcare Services”. Medical and Biological Engineering and Computing cover complementary disciplines that hold great promise for the advancement of research and development in complex medical and biological systems. Research and development in these areas are impacting the science and technology by advancing fundamental concepts in translational medicine, by helping us understand human physiology and function at multiple levels, by improving tools and techniques for the detection, prevention and treatment of disease. Medicon 2016 provides a common platform for the cross fer...

  15. Developmental engineering: a new paradigm for the design and manufacturing of cell-based products. Part II: from genes to networks: tissue engineering from the viewpoint of systems biology and network science.

    Science.gov (United States)

    Lenas, Petros; Moos, Malcolm; Luyten, Frank P

    2009-12-01

    The field of tissue engineering is moving toward a new concept of "in vitro biomimetics of in vivo tissue development." In Part I of this series, we proposed a theoretical framework integrating the concepts of developmental biology with those of process design to provide the rules for the design of biomimetic processes. We named this methodology "developmental engineering" to emphasize that it is not the tissue but the process of in vitro tissue development that has to be engineered. To formulate the process design rules in a rigorous way that will allow a computational design, we should refer to mathematical methods to model the biological process taking place in vitro. Tissue functions cannot be attributed to individual molecules but rather to complex interactions between the numerous components of a cell and interactions between cells in a tissue that form a network. For tissue engineering to advance to the level of a technologically driven discipline amenable to well-established principles of process engineering, a scientifically rigorous formulation is needed of the general design rules so that the behavior of networks of genes, proteins, or cells that govern the unfolding of developmental processes could be related to the design parameters. Now that sufficient experimental data exist to construct plausible mathematical models of many biological control circuits, explicit hypotheses can be evaluated using computational approaches to facilitate process design. Recent progress in systems biology has shown that the empirical concepts of developmental biology that we used in Part I to extract the rules of biomimetic process design can be expressed in rigorous mathematical terms. This allows the accurate characterization of manufacturing processes in tissue engineering as well as the properties of the artificial tissues themselves. In addition, network science has recently shown that the behavior of biological networks strongly depends on their topology and has

  16. The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.

    Science.gov (United States)

    Linshiz, Gregory; Goldberg, Alex; Konry, Tania; Hillson, Nathan J

    2012-01-01

    Synthetic biology is a nascent field that emerged in earnest only around the turn of the millennium. It aims to engineer new biological systems and impart new biological functionality, often through genetic modifications. The design and construction of new biological systems is a complex, multistep process, requiring multidisciplinary collaborative efforts from "fusion" scientists who have formal training in computer science or engineering, as well as hands-on biological expertise. The public has high expectations for synthetic biology and eagerly anticipates the development of solutions to the major challenges facing humanity. This article discusses laboratory practices and the conduct of research in synthetic biology. It argues that the fusion science approach, which integrates biology with computer science and engineering best practices, including standardization, process optimization, computer-aided design and laboratory automation, miniaturization, and systematic management, will increase the predictability and reproducibility of experiments and lead to breakthroughs in the construction of new biological systems. The article also discusses several successful fusion projects, including the development of software tools for DNA construction design automation, recursive DNA construction, and the development of integrated microfluidics systems.

  17. 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.

  18. 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)

  19. Systems Engineering Analysis

    Directory of Open Access Journals (Sweden)

    Alexei Serna M.

    2013-07-01

    Full Text Available The challenges proposed by the development of the new computer systems demand new guidance related to engineer´s education, because they will solve these problems. In the XXI century, system engineers must be able to integrate a number of topics and knowledge disciplines that complement that traditionally has been known as Computer Systems Engineering. We have enough software development engineers, today we need professional engineers for software integration, leaders and system architects that make the most of the technological development for the benefit of society, leaders that integrate sciences to the solutions they build and propose. In this article the current situation of Computer Systems Engineering is analyzed and is presented a theory proposing the need for modifying the approach Universities have given to these careers, to achieve the education of leader engineers according to the needs of this century.

  20. Systems engineering research

    OpenAIRE

    Sahraoui , Abd-El-Kader; Buede , Dennis ,; Sage , Andrew ,

    2008-01-01

    International audience; In this paper, we propose selected research topics that are believed central to progress and growth in the application of systems engineering (SE). As a professional activity, and as an intellectual activity, systems engineering has strong links to such associated disciplines as decision analysis, operation research, project management, quality management, and systems design. When focussing on systems engineering research, we should distinguish between subjects that ar...

  1. Engineering challenges of BioNEMS: the integration of microfluidics, micro- and nanodevices, models and external control for systems biology.

    Science.gov (United States)

    Wikswo, J P; Prokop, A; Baudenbacher, F; Cliffel, D; Csukas, B; Velkovsky, M

    2006-08-01

    Systems biology, i.e. quantitative, postgenomic, postproteomic, dynamic, multiscale physiology, addresses in an integrative, quantitative manner the shockwave of genetic and proteomic information using computer models that may eventually have 10(6) dynamic variables with non-linear interactions. Historically, single biological measurements are made over minutes, suggesting the challenge of specifying 10(6) model parameters. Except for fluorescence and micro-electrode recordings, most cellular measurements have inadequate bandwidth to discern the time course of critical intracellular biochemical events. Micro-array expression profiles of thousands of genes cannot determine quantitative dynamic cellular signalling and metabolic variables. Major gaps must be bridged between the computational vision and experimental reality. The analysis of cellular signalling dynamics and control requires, first, micro- and nano-instruments that measure simultaneously multiple extracellular and intracellular variables with sufficient bandwidth; secondly, the ability to open existing internal control and signalling loops; thirdly, external BioMEMS micro-actuators that provide high bandwidth feedback and externally addressable intracellular nano-actuators; and, fourthly, real-time, closed-loop, single-cell control algorithms. The unravelling of the nested and coupled nature of cellular control loops requires simultaneous recording of multiple single-cell signatures. Externally controlled nano-actuators, needed to effect changes in the biochemical, mechanical and electrical environment both outside and inside the cell, will provide a major impetus for nanoscience.

  2. CDMA systems capacity engineering

    CERN Document Server

    Kim, Kiseon

    2004-01-01

    This new hands-on resource tackles capacity planning and engineering issues that are crucial to optimizing wireless communication systems performance. Going beyond the system physical level and investigating CDMA system capacity at the service level, this volume is the single-source for engineering and analyzing systems capacity and resources.

  3. Computational Intelligence for Engineering Systems

    CERN Document Server

    Madureira, A; Vale, Zita

    2011-01-01

    "Computational Intelligence for Engineering Systems" provides an overview and original analysis of new developments and advances in several areas of computational intelligence. Computational Intelligence have become the road-map for engineers to develop and analyze novel techniques to solve problems in basic sciences (such as physics, chemistry and biology) and engineering, environmental, life and social sciences. The contributions are written by international experts, who provide up-to-date aspects of the topics discussed and present recent, original insights into their own experien

  4. Systems Engineering Management Plan

    International Nuclear Information System (INIS)

    1994-01-01

    The purpose of this Monitored Retrievable Storage (MRS) Project Systems Engineering Management Plan (SEMP) is to define and establish the MRS Project Systems Engineering process that implements the approved policy and requirements of the Office of Civilian Radioactive Waste Management (OCRWM) for the US Department of Energy (DOE). This plan is Volume 5 of the MRS Project Management Plan (PMP). This plan provides the framework for implementation of systems engineering on the MRS Project consistent with DOE Order 4700.1, the OCRWM Program Management System Manual (PMSM), and the OCRWM Systems Engineering Management Plan (SEMP)

  5. 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....

  6. Unified Engineering Software System

    Science.gov (United States)

    Purves, L. R.; Gordon, S.; Peltzman, A.; Dube, M.

    1989-01-01

    Collection of computer programs performs diverse functions in prototype engineering. NEXUS, NASA Engineering Extendible Unified Software system, is research set of computer programs designed to support full sequence of activities encountered in NASA engineering projects. Sequence spans preliminary design, design analysis, detailed design, manufacturing, assembly, and testing. Primarily addresses process of prototype engineering, task of getting single or small number of copies of product to work. Written in FORTRAN 77 and PROLOG.

  7. 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

  8. 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...

  9. Transcription control engineering and applications in synthetic biology

    Directory of Open Access Journals (Sweden)

    Michael D. Engstrom

    2017-09-01

    Full Text Available In synthetic biology, researchers assemble biological components in new ways to produce systems with practical applications. One of these practical applications is control of the flow of genetic information (from nucleic acid to protein, a.k.a. gene regulation. Regulation is critical for optimizing protein (and therefore activity levels and the subsequent levels of metabolites and other cellular properties. The central dogma of molecular biology posits that information flow commences with transcription, and accordingly, regulatory tools targeting transcription have received the most attention in synthetic biology. In this mini-review, we highlight many past successes and summarize the lessons learned in developing tools for controlling transcription. In particular, we focus on engineering studies where promoters and transcription terminators (cis-factors were directly engineered and/or isolated from DNA libraries. We also review several well-characterized transcription regulators (trans-factors, giving examples of how cis- and trans-acting factors have been combined to create digital and analogue switches for regulating transcription in response to various signals. Last, we provide examples of how engineered transcription control systems have been used in metabolic engineering and more complicated genetic circuits. While most of our mini-review focuses on the well-characterized bacterium Escherichia coli, we also provide several examples of the use of transcription control engineering in non-model organisms. Similar approaches have been applied outside the bacterial kingdom indicating that the lessons learned from bacterial studies may be generalized for other organisms.

  10. Transcription control engineering and applications in synthetic biology.

    Science.gov (United States)

    Engstrom, Michael D; Pfleger, Brian F

    2017-09-01

    In synthetic biology, researchers assemble biological components in new ways to produce systems with practical applications. One of these practical applications is control of the flow of genetic information (from nucleic acid to protein), a.k.a. gene regulation. Regulation is critical for optimizing protein (and therefore activity) levels and the subsequent levels of metabolites and other cellular properties. The central dogma of molecular biology posits that information flow commences with transcription, and accordingly, regulatory tools targeting transcription have received the most attention in synthetic biology. In this mini-review, we highlight many past successes and summarize the lessons learned in developing tools for controlling transcription. In particular, we focus on engineering studies where promoters and transcription terminators ( cis -factors) were directly engineered and/or isolated from DNA libraries. We also review several well-characterized transcription regulators ( trans- factors), giving examples of how cis- and trans -acting factors have been combined to create digital and analogue switches for regulating transcription in response to various signals. Last, we provide examples of how engineered transcription control systems have been used in metabolic engineering and more complicated genetic circuits. While most of our mini-review focuses on the well-characterized bacterium Escherichia coli , we also provide several examples of the use of transcription control engineering in non-model organisms. Similar approaches have been applied outside the bacterial kingdom indicating that the lessons learned from bacterial studies may be generalized for other organisms.

  11. 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.

  12. NASA Systems Engineering Handbook

    Science.gov (United States)

    Hirshorn, Steven R.; Voss, Linda D.; Bromley, Linda K.

    2017-01-01

    The update of this handbook continues the methodology of the previous revision: a top-down compatibility with higher level Agency policy and a bottom-up infusion of guidance from the NASA practitioners in the field. This approach provides the opportunity to obtain best practices from across NASA and bridge the information to the established NASA systems engineering processes and to communicate principles of good practice as well as alternative approaches rather than specify a particular way to accomplish a task. The result embodied in this handbook is a top-level implementation approach on the practice of systems engineering unique to NASA. Material used for updating this handbook has been drawn from many sources, including NPRs, Center systems engineering handbooks and processes, other Agency best practices, and external systems engineering textbooks and guides. This handbook consists of six chapters: (1) an introduction, (2) a systems engineering fundamentals discussion, (3) the NASA program project life cycles, (4) systems engineering processes to get from a concept to a design, (5) systems engineering processes to get from a design to a final product, and (6) crosscutting management processes in systems engineering. The chapters are supplemented by appendices that provide outlines, examples, and further information to illustrate topics in the chapters. The handbook makes extensive use of boxes and figures to define, refine, illustrate, and extend concepts in the chapters.

  13. Nuclear propulsion systems engineering

    International Nuclear Information System (INIS)

    Madsen, W.W.; Neuman, J.E.: Van Haaften, D.H.

    1992-01-01

    The Nuclear Energy for Rocket Vehicle Application (NERVA) program of the 1960's and early 1970's was dramatically successful, with no major failures during the entire testing program. This success was due in large part to the successful development of a systems engineering process. Systems engineering, properly implemented, involves all aspects of the system design and operation, and leads to optimization of theentire system: cost, schedule, performance, safety, reliability, function, requirements, etc. The process must be incorporated from the very first and continued to project completion. This paper will discuss major aspects of the NERVA systems engineering effort, and consider the implications for current nuclear propulsion efforts

  14. 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.

  15. 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

  16. 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 ‘‘...

  17. 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.

  18. Cell-free synthetic biology for in vitro prototype engineering.

    Science.gov (United States)

    Moore, Simon J; MacDonald, James T; Freemont, Paul S

    2017-06-15

    Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells. © 2017 The Author(s).

  19. Optomechanical systems engineering

    CERN Document Server

    Kasunic, Keith J

    2015-01-01

    Covers the fundamental principles behind optomechanical design This book emphasizes a practical, systems-level overview of optomechanical engineering, showing throughout how the requirements on the optical system flow down to those on the optomechanical design. The author begins with an overview of optical engineering, including optical fundamentals as well as the fabrication and alignment of optical components such as lenses and mirrors. The concepts of optomechanical engineering are then applied to the design of optical systems, including the structural design of mechanical and optical co

  20. Rotary engine cooling system

    Science.gov (United States)

    Jones, Charles (Inventor); Gigon, Richard M. (Inventor); Blum, Edward J. (Inventor)

    1985-01-01

    A rotary engine has a substantially trochoidal-shaped housing cavity in which a rotor planetates. A cooling system for the engine directs coolant along a single series path consisting of series connected groups of passages. Coolant enters near the intake port, passes downwardly and axially through the cooler regions of the engine, then passes upwardly and axially through the hotter regions. By first flowing through the coolest regions, coolant pressure is reduced, thus reducing the saturation temperature of the coolant and thereby enhancing the nucleate boiling heat transfer mechanism which predominates in the high heat flux region of the engine during high power level operation.

  1. Systems Engineering Workshops | Wind | NREL

    Science.gov (United States)

    Workshops Systems Engineering Workshops The Wind Energy Systems Engineering Workshop is a biennial topics relevant to systems engineering and the wind industry. The presentations and agendas are available for all of the Systems Engineering Workshops: The 1st NREL Wind Energy Systems Engineering Workshop

  2. Plant synthetic biology for molecular engineering of signalling and development.

    Science.gov (United States)

    Nemhauser, Jennifer L; Torii, Keiko U

    2016-03-02

    Molecular genetic studies of model plants in the past few decades have identified many key genes and pathways controlling development, metabolism and environmental responses. Recent technological and informatics advances have led to unprecedented volumes of data that may uncover underlying principles of plants as biological systems. The newly emerged discipline of synthetic biology and related molecular engineering approaches is built on this strong foundation. Today, plant regulatory pathways can be reconstituted in heterologous organisms to identify and manipulate parameters influencing signalling outputs. Moreover, regulatory circuits that include receptors, ligands, signal transduction components, epigenetic machinery and molecular motors can be engineered and introduced into plants to create novel traits in a predictive manner. Here, we provide a brief history of plant synthetic biology and significant recent examples of this approach, focusing on how knowledge generated by the reference plant Arabidopsis thaliana has contributed to the rapid rise of this new discipline, and discuss potential future directions.

  3. Industrial biosystems engineering and biorefinery systems.

    Science.gov (United States)

    Chen, Shulin

    2008-06-01

    The concept of Industrial Biosystems Engineering (IBsE) was suggested as a new engineering branch to be developed for meeting the needs for science, technology and professionals by the upcoming bioeconomy. With emphasis on systems, IBsE builds upon the interfaces between systems biology, bioprocessing, and systems engineering. This paper discussed the background, the suggested definition, the theoretical framework and methodologies of this new discipline as well as its challenges and future development.

  4. Systems engineering management plan

    International Nuclear Information System (INIS)

    Conner, C.W.

    1985-10-01

    The purpose of this Systems Engineering Management Plan (SEMP) is to prescribe the systems engineering procedures to be implemented at the Program level and the minimum requirements for systems engineering at the Program-element level. The Program level corresponds to the Director, OCRWM, or to the organizations within OCRWM to which the Director delegates responsibility for the development of the System and for coordinating and integrating the activities at the Program-element level. The Office of Policy and Outreach (OPO) and the Office of Resource Management (ORM) support the Director at the Program level. The Program-element level corresponds to the organizations within OCRWM (i.e., the Office of Geologic Repositories (OGR) and the Office of Storage and Transportation Systems (OSTS)) with overall responsibility for developing the System elements - that is, the mined geologic disposal system (MGDS), monitored retrievable storage (MRS) (if approved by Congress), and the transportation system

  5. 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.

  6. 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

  7. Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach "reverse pathway engineering".

    Science.gov (United States)

    Liu, Mengjin; Bienfait, Bruno; Sacher, Oliver; Gasteiger, Johann; Siezen, Roland J; Nauta, Arjen; Geurts, Jan M W

    2014-01-01

    The incompleteness of genome-scale metabolic models is a major bottleneck for systems biology approaches, which are based on large numbers of metabolites as identified and quantified by metabolomics. Many of the revealed secondary metabolites and/or their derivatives, such as flavor compounds, are non-essential in metabolism, and many of their synthesis pathways are unknown. In this study, we describe a novel approach, Reverse Pathway Engineering (RPE), which combines chemoinformatics and bioinformatics analyses, to predict the "missing links" between compounds of interest and their possible metabolic precursors by providing plausible chemical and/or enzymatic reactions. We demonstrate the added-value of the approach by using flavor-forming pathways in lactic acid bacteria (LAB) as an example. Established metabolic routes leading to the formation of flavor compounds from leucine were successfully replicated. Novel reactions involved in flavor formation, i.e. the conversion of alpha-hydroxy-isocaproate to 3-methylbutanoic acid and the synthesis of dimethyl sulfide, as well as the involved enzymes were successfully predicted. These new insights into the flavor-formation mechanisms in LAB can have a significant impact on improving the control of aroma formation in fermented food products. Since the input reaction databases and compounds are highly flexible, the RPE approach can be easily extended to a broad spectrum of applications, amongst others health/disease biomarker discovery as well as synthetic biology.

  8. 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...

  9. Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2014

    Energy Technology Data Exchange (ETDEWEB)

    Voigt, Christopher [Massachusetts Institute of Technology

    2014-07-01

    SEED2014 focused on advances in the science and technology emerging from the field of synthetic biology. We broadly define this as technologies that accelerate the process of genetic engineering. It highlighted new tool development, as well as the application of these tools to diverse problems in biotechnology, including therapeutics, industrial chemicals and fuels, natural products, and agriculture. Systems spanned from in vitro experiments and viruses, through diverse bacteria, to eukaryotes (yeast, mammalian cells, plants).

  10. Energy production systems engineering

    CERN Document Server

    Blair, Thomas Howard

    2017-01-01

    Energy Production Systems Engineering presents IEEE, Electrical Apparatus Service Association (EASA), and International Electrotechnical Commission (IEC) standards of engineering systems and equipment in utility electric generation stations. Electrical engineers that practice in the energy industry must understand the specific characteristics of electrical and mechanical equipment commonly applied to energy production and conversion processes, including the mechanical and chemical processes involved, in order to design, operate and maintain electrical systems that support and enable these processes. To aid this understanding, Energy Production Systems Engineeringdescribes the equipment and systems found in various types of utility electric generation stations. This information is accompanied by examples and practice problems. It also addresses common issues of electrical safety that arise in electric generation stations.

  11. 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.

  12. 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...

  13. 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.

  14. System Reliability Engineering

    International Nuclear Information System (INIS)

    Lim, Tae Jin

    2005-02-01

    This book tells of reliability engineering, which includes quality and reliability, reliability data, importance of reliability engineering, reliability and measure, the poisson process like goodness of fit test and the poisson arrival model, reliability estimation like exponential distribution, reliability of systems, availability, preventive maintenance such as replacement policies, minimal repair policy, shock models, spares, group maintenance and periodic inspection, analysis of common cause failure, and analysis model of repair effect.

  15. Systems Engineering Awareness

    Science.gov (United States)

    Lucero, John

    2016-01-01

    The presentation will provide an overview of the fundamentals and principles of Systems Engineering (SE). This includes understanding the processes that are used to assist the engineer in a successful design, build and implementation of solutions. The context of this presentation will be to describe the involvement of SE throughout the life-cycle of a project from cradle to grave. Due to the ever growing number of complex technical problems facing our world, a Systems Engineering approach is desirable for many reasons. The interdisciplinary technical structure of current systems, technical processes representing System Design, Technical Management and Product Realization are instrumental in the development and integration of new technologies into mainstream applications. This tutorial will demonstrate the application of SE tools to these types of problems..

  16. Systems and Control Engineering

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 4; Issue 5. Systems and Control Engineering - Control Systems-Analysis and Design. A Rama Kalyan J R Vengateswaran. General Article Volume 4 Issue 5 May 1999 pp 88-94 ...

  17. 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....

  18. Systems engineering and analysis

    CERN Document Server

    Blanchard, Benjamin S

    2010-01-01

    For senior-level undergraduate and first and second year graduate systems engineering and related courses. A total life-cycle approach to systems and their analysis. This practical introduction to systems engineering and analysis provides the concepts, methodologies, models, and tools needed to understand and implement a total life-cycle approach to systems and their analysis. The authors focus first on the process of bringing systems into being--beginning with the identification of a need and extending that need through requirements determination, functional analysis and allocation, design synthesis, evaluation, and validation, operation and support, phase-out, and disposal. Next, the authors discuss the improvement of systems currently in being, showing that by employing the iterative process of analysis, evaluation, feedback, and modification, most systems in existence can be improved in their affordability, effectiveness, and stakeholder satisfaction.

  19. Systems Safety and Engineering Division

    Data.gov (United States)

    Federal Laboratory Consortium — Volpe's Systems Safety and Engineering Division conducts engineering, research, and analysis to improve transportation safety, capacity, and resiliency. We provide...

  20. Transforming Systems Engineering through Model Centric Engineering

    Science.gov (United States)

    2017-08-08

    Contract No. HQ0034-13-D-0004 Report No. SERC-2017-TR-110 Date: August 8, 2017 Transforming Systems Engineering through Model-Centric... Engineering Technical Report SERC-2017-TR-110 Update: August 8, 2017 Principal Investigator: Mark Blackburn, Stevens Institute of Technology Co...Evangelista Sponsor: U.S. Army Armament Research, Development and Engineering Center (ARDEC), Office of the Deputy Assistant Secretary of Defense for

  1. Systems and Control Engineering

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 4; Issue 1. Systems and Control Engineering - Notions of Control. A Rama Kalyan J R Vengateswaran. General Article Volume 4 Issue 1 January 1999 pp 45-52. Fulltext. Click here to view fulltext PDF. Permanent link:

  2. Microwave system engineering principles

    CERN Document Server

    Raff, Samuel J

    1977-01-01

    Microwave System Engineering Principles focuses on the calculus, differential equations, and transforms of microwave systems. This book discusses the basic nature and principles that can be derived from thermal noise; statistical concepts and binomial distribution; incoherent signal processing; basic properties of antennas; and beam widths and useful approximations. The fundamentals of propagation; LaPlace's Equation and Transmission Line (TEM) waves; interfaces between homogeneous media; modulation, bandwidth, and noise; and communications satellites are also deliberated in this text. This bo

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

    Science.gov (United States)

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

    2010-01-01

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

  4. From Biology to Mathematical Models and Back: Teaching Modeling to Biology Students, and Biology to Math and Engineering Students

    Science.gov (United States)

    McManus, Jeffrey M.; Shaw, Kendrick M.

    2010-01-01

    We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a “live” textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology. PMID:20810957

  5. Tissue Engineering Organs for Space Biology Research

    Science.gov (United States)

    Vandenburgh, H. H.; Shansky, J.; DelTatto, M.; Lee, P.; Meir, J.

    1999-01-01

    Long-term manned space flight requires a better understanding of skeletal muscle atrophy resulting from microgravity. Atrophy most likely results from changes at both the systemic level (e.g. decreased circulating growth hormone, increased circulating glucocorticoids) and locally (e.g. decreased myofiber resting tension). Differentiated skeletal myofibers in tissue culture have provided a model system over the last decade for gaining a better understanding of the interactions of exogenous growth factors, endogenous growth factors, and muscle fiber tension in regulating protein turnover rates and muscle cell growth. Tissue engineering these cells into three dimensional bioartificial muscle (BAM) constructs has allowed us to extend their use to Space flight studies for the potential future development of countermeasures.

  6. Control systems engineering

    CERN Document Server

    Nise, Norman S

    1995-01-01

    This completely updated new edition shows how to use MATLAB to perform control-system calculations. Designed for the professional or engineering student who needs a quick and readable update on designing control systems, the text features a series of tightly focused examples that clearly illustrate each concept of designing control systems. Most chapters conclude with a detailed application from the two case studies that run throughout the book: an antenna asimuth control system and a submarine. The author also refers to many examples of design methods.

  7. Automotive systems engineering

    Energy Technology Data Exchange (ETDEWEB)

    Maurer, Markus [Technische Univ. Braunschweig (Germany). Inst. fuer Regelungstechnik; Winner, Hermann (eds.) [Technische Univ. Darmstadt (Germany). Fachgebiet Fahrzeugtechnik

    2013-06-01

    Innovative state-of-the-art book. Presents brand new results of a joint workshop in the field of automotive systems engineering. Recommendable to students for further reading even though not a primary text book. This book reflects the shift in design paradigm in automobile industry. It presents future innovations, often referred as ''automotive systems engineering''. These cause fundamental innovations in the field of driver assistance systems and electro-mobility as well as fundamental changes in the architecture of the vehicles. New driving functionalities can only be realized if the software programs of multiple electronic control units work together correctly. This volume presents the new and innovative methods which are mandatory to master the complexity of the vehicle of the future.

  8. Engineering Elegant Systems: Postulates, Principles, and Hypotheses of Systems Engineering

    Science.gov (United States)

    Watson, Michael D.

    2018-01-01

    Definition: System Engineering is the engineering discipline which integrates the system functions, system environment, and the engineering disciplines necessary to produce and/or operate an elegant system; Elegant System - A system that is robust in application, fully meeting specified and adumbrated intent, is well structured, and is graceful in operation. Primary Focus: System Design and Integration: Identify system couplings and interactions; Identify system uncertainties and sensitivities; Identify emergent properties; Manage the effectiveness of the system. Engineering Discipline Integration: Manage flow of information for system development and/or operations; Maintain system activities within budget and schedule. Supporting Activities: Process application and execution.

  9. PREFACE: Nanobiology: from physics and engineering to biology

    Science.gov (United States)

    Nussinov, Ruth; Alemán, Carlos

    2006-03-01

    Biological systems are inherently nano in scale. Unlike nanotechnology, nanobiology is characterized by the interplay between physics, materials science, synthetic organic chemistry, engineering and biology. Nanobiology is a new discipline, with the potential of revolutionizing medicine: it combines the tools, ideas and materials of nanoscience and biology; it addresses biological problems that can be studied and solved by nanotechnology; it devises ways to construct molecular devices using biomacromolecules; and it attempts to build molecular machines utilizing concepts seen in nature. Its ultimate aim is to be able to predictably manipulate these, tailoring them to specified needs. Nanobiology targets biological systems and uses biomacromolecules. Hence, on the one hand, nanobiology is seemingly constrained in its scope as compared to general nanotechnology. Yet the amazing intricacy of biological systems, their complexity, and the richness of the shapes and properties provided by the biological polymers, enrich nanobiology. Targeting biological systems entails comprehension of how they work and the ability to use their components in design. From the physical standpoint, ultimately, if we are to understand biology we need to learn how to apply physical principles to figure out how these systems actually work. The goal of nanobiology is to assist in probing these systems at the appropriate length scale, heralding a new era in the biological, physical and chemical sciences. Biology is increasingly asking quantitative questions. Quantitation is essential if we are to understand how the cell works, and the details of its regulation. The physical sciences provide tools and strategies to obtain accurate measurements and simulate the information to allow comprehension of the processes. Nanobiology is at the interface of the physical and the biological sciences. Biology offers to the physical sciences fascinating problems, sophisticated systems and a rich repertoire of

  10. The engineering of cybernetic systems

    Science.gov (United States)

    Fry, Robert L.

    2002-05-01

    This tutorial develops a logical basis for the engineering of systems that operate cybernetically. The term cybernetic system has a clear quantitative definition. It is a system that dynamically matches acquired information to selected actions relative to a computational issue that defines the essential purpose of the system or machine. This notion requires that information and control be further quantified. The logic of questions and assertions as developed by Cox provides one means of doing this. The design and operation of cybernetic systems can be understood by contrasting these kinds of systems with communication systems and information theory as developed by Shannon. The joint logic of questions and assertions can be seen to underlie and be common to both information theory as applied to the design of discrete communication systems and to a theory of discrete general systems. The joint logic captures a natural complementarity between systems that transmit and receive information and those that acquire and act on it. Specific comparisons and contrasts are made between the source rate and channel capacity of a communication system and the acquisition rate and control capacity of a general system. An overview is provided of the joint logic of questions and assertions and the ties that this logic has to both conventional information theory and to a general theory of systems. I-diagrams, the interrogative complement of Venn diagrams, are described as providing valuable reasoning tools. An initial framework is suggested for the design of cybernetic systems. Two examples are given to illustrate this framework as applied to discrete cybernetic systems. These examples include a predator-prey problem as illustrated through "The Dog Chrysippus Pursuing its Prey," and the derivation of a single-neuron system that operates cybernetically and is biologically plausible. Future areas of research are highlighted which require development for a mature engineering framework.

  11. 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...

  12. Framework for systems engineering research

    CSIR Research Space (South Africa)

    Erasmus, L

    2013-08-01

    Full Text Available In this paper a framework is proposed to perform systems engineering research within South Africa. It is proposed that within the reference of the National Research Foundation (NRF) classification of research, systems engineering is a Field...

  13. Is nanotechnology the key to unravel and engineer biological processes?

    Science.gov (United States)

    Navarro, Melba; Planell, Josep A

    2012-01-01

    Regenerative medicine is an emerging field aiming to the development of new reparative strategies to treat degenerative diseases, injury, and trauma through developmental pathways in order to rebuild the architecture of the original injured organ and take over its functionality. Most of the processes and interactions involved in the regenerative process take place at subcellular scale. Nanotechnology provides the tools and technology not only to detect, to measure, or to image the interactions between the different biomolecules and biological entities, but also to control and guide the regenerative process. The relevance of nanotechnology for the development of regenerative medicine as well as an overview of the different tools that contribute to unravel and engineer biological systems are presented in this chapter. In addition, general data about the social impact and global investment in nanotechnology are provided.

  14. Complex engineering systems science meets technology

    CERN Document Server

    Minai, Ali A; Bar-Yam, Yaneer

    2006-01-01

    Every time that we take money out of an ATM, surf the internet or simply turn on a light switch, we enjoy the benefits of complex engineered systems. Systems like power grids and global communication networks are so ubiquitous in our daily lives that we usually take them for granted, only noticing them when they break down. But how do such amazing technologies and infrastructures come to be what they are? How are these systems designed? How do distributed networks work? How are they made to respond rapidly in 'real time'? And as the demands that we place on these systems become increasingly complex, are traditional systems-engineering practices still relevant? This volume examines the difficulties that arise in creating highly complex engineered systems and new approaches that are being adopted. Topics addressed range from the formal representation and classification of distributed networked systems to revolutionary engineering practices inspired by biological evolution. By bringing together the latest resear...

  15. Intelligent systems engineering methodology

    Science.gov (United States)

    Fouse, Scott

    1990-01-01

    An added challenge for the designers of large scale systems such as Space Station Freedom is the appropriate incorporation of intelligent system technology (artificial intelligence, expert systems, knowledge-based systems, etc.) into their requirements and design. This presentation will describe a view of systems engineering which successfully addresses several aspects of this complex problem: design of large scale systems, design with requirements that are so complex they only completely unfold during the development of a baseline system and even then continue to evolve throughout the system's life cycle, design that involves the incorporation of new technologies, and design and development that takes place with many players in a distributed manner yet can be easily integrated to meet a single view of the requirements. The first generation of this methodology was developed and evolved jointly by ISX and the Lockheed Aeronautical Systems Company over the past five years on the Defense Advanced Research Projects Agency/Air Force Pilot's Associate Program, one of the largest, most complex, and most successful intelligent systems constructed to date. As the methodology has evolved it has also been applied successfully to a number of other projects. Some of the lessons learned from this experience may be applicable to Freedom.

  16. 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

  17. 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.

  18. 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 ...

  19. 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....

  20. 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.

  1. Developing systems engineers

    CSIR Research Space (South Africa)

    Goncalves, D

    2008-07-01

    Full Text Available will have rendered him incapable of dealing with the majority of problems that will face him.” (Quoted in [12]). UP has applied the SPICES model, proposed by Harden et al. [12], for developing their medical curriculum. Some aspects of the model... are useful to developing systems engineers and will be considered in SE terms at a relevant level of detail. The SPICES model is contrasted against traditional medical curriculum approaches in TABLE 1. These are two extremes on a continuum. Traditional...

  2. Systems engineering agile design methodologies

    CERN Document Server

    Crowder, James A

    2013-01-01

    This book examines the paradigm of the engineering design process. The authors discuss agile systems and engineering design. The book captures the entire design process (functionbases), context, and requirements to affect real reuse. It provides a methodology for an engineering design process foundation for modern and future systems design. This book captures design patterns with context for actual Systems Engineering Design Reuse and contains a new paradigm in Design Knowledge Management.

  3. 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...

  4. 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),...

  5. 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.

  6. 6th European Conference of the International Federation for Medical and Biological Engineering

    CERN Document Server

    Vasic, Darko

    2015-01-01

    This volume presents the Proceedings of the 6th European Conference of the International Federation for Medical and Biological Engineering (MBEC2014), held in Dubrovnik September 7 – 11, 2014. The general theme of MBEC 2014 is "Towards new horizons in biomedical engineering" The scientific discussions in these conference proceedings include the following themes: - Biomedical Signal Processing - Biomedical Imaging and Image Processing - Biosensors and Bioinstrumentation - Bio-Micro/Nano Technologies - Biomaterials - Biomechanics, Robotics and Minimally Invasive Surgery - Cardiovascular, Respiratory and Endocrine Systems Engineering - Neural and Rehabilitation Engineering - Molecular, Cellular and Tissue Engineering - Bioinformatics and Computational Biology - Clinical Engineering and Health Technology Assessment - Health Informatics, E-Health and Telemedicine - Biomedical Engineering Education

  7. Systems Engineering Leadership Development: Advancing Systems Engineering Excellence

    Science.gov (United States)

    Hall, Phil; Whitfield, Susan

    2011-01-01

    This slide presentation reviews the Systems Engineering Leadership Development Program, with particular emphasis on the work being done in the development of systems engineers at Marshall Space Flight Center. There exists a lack of individuals with systems engineering expertise, in particular those with strong leadership capabilities, to meet the needs of the Agency's exploration agenda. Therefore there is a emphasis on developing these programs to identify and train systems engineers. The presentation reviews the proposed MSFC program that includes course work, and developmental assignments. The formal developmental programs at the other centers are briefly reviewed, including the Point of Contact (POC)

  8. Recent applications of synthetic biology tools for yeast metabolic engineering

    DEFF Research Database (Denmark)

    Jensen, Michael Krogh; Keasling, Jay

    2015-01-01

    to engineer microbial chemical factories has steadily decreased, improvement is still needed. Through the development of synthetic biology tools for key microbial hosts, it should be possible to further decrease the development times and improve the reliability of the resulting microorganism. Together...... with continuous decreases in price and improvements in DNA synthesis, assembly and sequencing, synthetic biology tools will rationalize time-consuming strain engineering, improve control of metabolic fluxes, and diversify screening assays for cellular metabolism. This review outlines some recently developed...... synthetic biology tools and their application to improve production of chemicals and fuels in yeast. Finally, we provide a perspective for the challenges that lie ahead....

  9. 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

  10. 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...

  11. 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...

  12. The bioartificial pancreas (BAP): Biological, chemical and engineering challenges.

    Science.gov (United States)

    Iacovacci, Veronica; Ricotti, Leonardo; Menciassi, Arianna; Dario, Paolo

    2016-01-15

    The bioartificial pancreas (BAP) represents a viable solution for the treatment of type 1 diabetes (T1D). By encapsulating pancreatic cells in a semipermeable membrane to allow nutrient, insulin and glucose exchange, the side effects produced by islets and whole organ transplantation-related immunosuppressive therapy can be circumvented. Several factors, mainly related to materials properties, capsule morphology and biological environment, play a key role in optimizing BAP systems. The BAP is an extremely complex delivery system for insulin. Despite considerable efforts, in some instances meeting with limited degree of success, a BAP capable of restoring physiological pancreas functions without the need for immunosuppressive drugs and of controlling blood glucose levels especially in large animal models and a few clinical trials, does not exist. The state of the art in terms of materials, fabrication techniques and cell sources, as well as the current status of commercial devices and clinical trials, are described in this overview from an interdisciplinary viewpoint. In addition, challenges to the creation of effective BAP systems are highlighted including future perspectives in terms of component integration from both a biological and an engineering viewpoint. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Physiology for engineers applying engineering methods to physiological systems

    CERN Document Server

    Chappell, Michael

    2016-01-01

    This book provides an introduction to qualitative and quantitative aspects of human physiology. It looks at biological and physiological processes and phenomena, including a selection of mathematical models, showing how physiological problems can be mathematically formulated and studied. It also illustrates how a wide range of engineering and physics topics, including electronics, fluid dynamics, solid mechanics and control theory can be used to describe and understand physiological processes and systems. Throughout the text there are introductions to measuring and quantifying physiological processes using both signal and imaging technologies. Physiology for Engineers describes the basic structure and models of cellular systems, the structure and function of the cardiovascular system, the electrical and mechanical activity of the heart and provides an overview of the structure and function of the respiratory and nervous systems. It also includes an introduction to the basic concepts and applications of reacti...

  14. Study of Scramjet Engine System

    OpenAIRE

    苅田, 丈士; KANDA, Takeshi

    2001-01-01

    1. Introduction The scramjet engine for the single-stage-to-orbit (SSTO) aerospace plane has been studied in the ramjet propulsion research division. The problems of the scramjet are (1) combustion, (2) light structure, (3) startability of the inlet, (4) integration of engines, and (5) cooling. The construction of the cooling system is important for the scramjet engine, because of high heat flux during operation. Cooling is not only a problem for the engine itself, but also for the airframe. ...

  15. 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)

  16. NASA System Engineering Design Process

    Science.gov (United States)

    Roman, Jose

    2011-01-01

    This slide presentation reviews NASA's use of systems engineering for the complete life cycle of a project. Systems engineering is a methodical, disciplined approach for the design, realization, technical management, operations, and retirement of a system. Each phase of a NASA project is terminated with a Key decision point (KDP), which is supported by major reviews.

  17. Basic science through engineering? Synthetic modeling and the idea of biology-inspired engineering.

    Science.gov (United States)

    Knuuttila, Tarja; Loettgers, Andrea

    2013-06-01

    Synthetic biology is often understood in terms of the pursuit for well-characterized biological parts to create synthetic wholes. Accordingly, it has typically been conceived of as an engineering dominated and application oriented field. We argue that the relationship of synthetic biology to engineering is far more nuanced than that and involves a sophisticated epistemic dimension, as shown by the recent practice of synthetic modeling. Synthetic models are engineered genetic networks that are implanted in a natural cell environment. Their construction is typically combined with experiments on model organisms as well as mathematical modeling and simulation. What is especially interesting about this combinational modeling practice is that, apart from greater integration between these different epistemic activities, it has also led to the questioning of some central assumptions and notions on which synthetic biology is based. As a result synthetic biology is in the process of becoming more "biology inspired." Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. 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.

  19. Recommendation systems in software engineering

    CERN Document Server

    Robillard, Martin P; Walker, Robert J; Zimmermann, Thomas

    2014-01-01

    With the growth of public and private data stores and the emergence of off-the-shelf data-mining technology, recommendation systems have emerged that specifically address the unique challenges of navigating and interpreting software engineering data.This book collects, structures and formalizes knowledge on recommendation systems in software engineering. It adopts a pragmatic approach with an explicit focus on system design, implementation, and evaluation. The book is divided into three parts: "Part I - Techniques" introduces basics for building recommenders in software engineering, including techniques for collecting and processing software engineering data, but also for presenting recommendations to users as part of their workflow.?"Part II - Evaluation" summarizes methods and experimental designs for evaluating recommendations in software engineering.?"Part III - Applications" describes needs, issues and solution concepts involved in entire recommendation systems for specific software engineering tasks, fo...

  20. Systems metabolic engineering in an industrial setting.

    Science.gov (United States)

    Sagt, Cees M J

    2013-03-01

    Systems metabolic engineering is based on systems biology, synthetic biology, and evolutionary engineering and is now also applied in industry. Industrial use of systems metabolic engineering focuses on strain and process optimization. Since ambitious yields, titers, productivities, and low costs are key in an industrial setting, the use of effective and robust methods in systems metabolic engineering is becoming very important. Major improvements in the field of proteomics and metabolomics have been crucial in the development of genome-wide approaches in strain and process development. This is accompanied by a rapid increase in DNA sequencing and synthesis capacity. These developments enable the use of systems metabolic engineering in an industrial setting. Industrial systems metabolic engineering can be defined as the combined use of genome-wide genomics, transcriptomics, proteomics, and metabolomics to modify strains or processes. This approach has become very common since the technology for generating large data sets of all levels of the cellular processes has developed quite fast into robust, reliable, and affordable methods. The main challenge and scope of this mini review is how to translate these large data sets in relevant biological leads which can be tested for strain or process improvements. Experimental setup, heterogeneity of the culture, and sample pretreatment are important issues which are easily underrated. In addition, the process of structuring, filtering, and visualization of data is important, but also, the availability of a genetic toolbox and equipment for medium/high-throughput fermentation is a key success factor. For an efficient bioprocess, all the different components in this process have to work together. Therefore, mutual tuning of these components is an important strategy.

  1. 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

  2. Morphogenetic Engineering Toward Programmable Complex Systems

    CERN Document Server

    Sayama, Hiroki; Michel, Olivier

    2012-01-01

    Generally, spontaneous pattern formation phenomena are random and repetitive, whereas elaborate devices are the deterministic product of human design. Yet, biological organisms and collective insect constructions are exceptional examples of complex systems that are both self-organized and architectural.   This book is the first initiative of its kind toward establishing a new field of research, Morphogenetic Engineering, to explore the modeling and implementation of “self-architecturing” systems. Particular emphasis is placed on the programmability and computational abilities of self-organization, properties that are often underappreciated in complex systems science—while, conversely, the benefits of self-organization are often underappreciated in engineering methodologies.   Altogether, the aim of this work is to provide a framework for and examples of a larger class of “self-architecturing” systems, while addressing fundamental questions such as   > How do biological organisms carry out morphog...

  3. Dynamic Systems and Control Engineering

    International Nuclear Information System (INIS)

    Kim, Jong Seok

    1994-02-01

    This book deals with introduction of dynamic system and control engineering, frequency domain modeling of dynamic system, temporal modeling of dynamic system, typical dynamic system and automatic control device, performance and stability of control system, root locus analysis, analysis of frequency domain dynamic system, design of frequency domain dynamic system, design and analysis of space, space of control system and digital control system such as control system design of direct digital and digitalization of consecutive control system.

  4. Dynamic Systems and Control Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jong Seok

    1994-02-15

    This book deals with introduction of dynamic system and control engineering, frequency domain modeling of dynamic system, temporal modeling of dynamic system, typical dynamic system and automatic control device, performance and stability of control system, root locus analysis, analysis of frequency domain dynamic system, design of frequency domain dynamic system, design and analysis of space, space of control system and digital control system such as control system design of direct digital and digitalization of consecutive control system.

  5. System safety engineering analysis handbook

    Science.gov (United States)

    Ijams, T. E.

    1972-01-01

    The basic requirements and guidelines for the preparation of System Safety Engineering Analysis are presented. The philosophy of System Safety and the various analytic methods available to the engineering profession are discussed. A text-book description of each of the methods is included.

  6. Power systems engineering and mathematics

    CERN Document Server

    Knight, U G

    1972-01-01

    Power Systems Engineering and Mathematics investigates the application of mathematical aids, particularly the techniques of resource planning, to some of the technical-economic problems of power systems engineering. Topics covered include the process of engineering design and the use of computers in system design and operation; power system planning and operation; time scales and computation in system operation; and load prediction and generation capacity. This volume is comprised of 13 chapters and begins by outlining the stages in the synthesis of designs (or operating states) for engineerin

  7. Systems and Control Engineering

    Indian Academy of Sciences (India)

    design of civil engineering structures has been noted. Protecting ci vil ... R despite disturbing forces such as wind gusts, changes in ambient temperature, etc .. Brief History of ... frequency regulation, boiler control for steam generation, electric.

  8. 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.

  9. 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...

  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. Biological augmentation and tissue engineering approaches in meniscus surgery.

    Science.gov (United States)

    Moran, Cathal J; Busilacchi, Alberto; Lee, Cassandra A; Athanasiou, Kyriacos A; Verdonk, Peter C

    2015-05-01

    The purpose of this review was to evaluate the role of biological augmentation and tissue engineering strategies in meniscus surgery. Although clinical (human), preclinical (animal), and in vitro tissue engineering studies are included here, we have placed additional focus on addressing preclinical and clinical studies reported during the 5-year period used in this review in a systematic fashion while also providing a summary review of some important in vitro tissue engineering findings in the field over the past decade. A search was performed on PubMed for original works published from 2009 to March 31, 2014 using the term "meniscus" with all the following terms: "scaffolds," "constructs," "cells," "growth factors," "implant," "tissue engineering," and "regenerative medicine." Inclusion criteria were the following: English-language articles and original clinical, preclinical (in vivo), and in vitro studies of tissue engineering and regenerative medicine application in knee meniscus lesions published from 2009 to March 31, 2014. Three clinical studies and 18 preclinical studies were identified along with 68 tissue engineering in vitro studies. These reports show the increasing promise of biological augmentation and tissue engineering strategies in meniscus surgery. The role of stem cell and growth factor therapy appears to be particularly useful. A review of in vitro tissue engineering studies found a large number of scaffold types to be of promise for meniscus replacement. Limitations include a relatively low number of clinical or preclinical in vivo studies, in addition to the fact there is as yet no report in the literature of a tissue-engineered meniscus construct used clinically. Neither does the literature provide clarity on the optimal meniscus scaffold type or biological augmentation with which meniscus repair or replacement would be best addressed in the future. There is increasing focus on the role of mechanobiology and biomechanical and

  12. From Biology to Mathematical Models and Back: Teaching Modeling to Biology Students, and Biology to Math and Engineering Students

    Science.gov (United States)

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

    2010-01-01

    We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge…

  13. 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’.

  14. Systems engineering and integration as a foundation for mission engineering

    OpenAIRE

    Beam, David F.

    2015-01-01

    Approved for public release; distribution is unlimited This paper investigates the emerging term mission engineering through the framework of systems engineering and systems integration. Systems engineering concepts, processes, and methodologies are extrapolated for use in conjunction with a systems integration, life-cycle based framework to effect mission engineering. The specific systems engineering concepts of measures of effectiveness, performance and suitability are recommended as fou...

  15. 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.

  16. CellNet: Network Biology Applied to Stem Cell Engineering

    Science.gov (United States)

    Cahan, Patrick; Li, Hu; Morris, Samantha A.; da Rocha, Edroaldo Lummertz; Daley, George Q.; Collins, James J.

    2014-01-01

    SUMMARY Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population, and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. PMID:25126793

  17. Engine systems and methods of operating an engine

    Energy Technology Data Exchange (ETDEWEB)

    Scotto, Mark Vincent

    2018-01-23

    One embodiment of the present invention is a unique method for operating an engine. Another embodiment is a unique engine system. Other embodiments include apparatuses, systems, devices, hardware, methods, and combinations for engines and engine systems. Further embodiments, forms, features, aspects, benefits, and advantages of the present application will become apparent from the description and figures provided herewith.

  18. Engine systems and methods of operating an engine

    Science.gov (United States)

    Scotto, Mark Vincent

    2015-08-25

    One embodiment of the present invention is a unique method for operating an engine. Another embodiment is a unique engine system. Other embodiments include apparatuses, systems, devices, hardware, methods, and combinations for engines and engine systems. Further embodiments, forms, features, aspects, benefits, and advantages of the present application will become apparent from the description and figures provided herewith.

  19. Cell-free protein synthesis enabled rapid prototyping for metabolic engineering and synthetic biology

    Directory of Open Access Journals (Sweden)

    Lihong Jiang

    2018-06-01

    Full Text Available Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade. However, due to complexity of cellular metabolism, the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic engineering. Recently, cell-free protein synthesis system (CFPS has been emerging as an enabling alternative to address challenges in biomanufacturing. This review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits (biosensors to speed up design-build-test (DBT cycles of metabolic engineering and synthetic biology. Keywords: Cell-free protein synthesis, Metabolic pathway optimization, Genetic circuits, Metabolic engineering, Synthetic biology

  20. A Biological Porin Engineered into a Molecular, Nanofluidic Diode

    NARCIS (Netherlands)

    Miedema, Henk; Vrouenraets, Maarten; Wierenga, Jenny; Meijberg, Wim; Robillard, George; Eisenberg, Bob

    2007-01-01

    We changed the nonrectifying biological porin OmpF into a nanofluidic diode. To that end, we engineered a pore that possesses two spatially separated selectivity filters of opposite charge where either cations or anions accumulate. The observed current inhibition under applied reverse bias voltage

  1. 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...

  2. MECHATRONICS SYSTEM ENGINEERING FOR

    DEFF Research Database (Denmark)

    Conrad, Finn; Roli, Francesco

    2005-01-01

    rotary vane actuator for robot manipulators is presented. The contribution proposes mathematical modelling, control and simulation of a novel water hydraulic rotary vane actuator applied to power and control a three-links manipulator. The results include engineering design and test of the proposed...

  3. Engineering Design and Operation Report: Biological ...

    Science.gov (United States)

    Many regions in the United States have excessive levels of ammonia in their drinking water sources (e.g., ground and surface waters) as a result of naturally occurring processes, agricultural and urban runoff, concentrated animal feeding operations, municipal wastewater treatment plants, and other sources. Ammonia is not regulated by the U.S. Environmental Protection Agency (EPA) as a contaminant. Based on a 2003 World Health Organization (WHO) assessment, ammonia levels in groundwater are typically below 0.2 milligrams per liter (mg/L), and do not pose a direct health concern at levels expected in drinking water (WHO 2003); however, they may pose a concern when nitrification of significant levels of ammonia from the source water occurs in the drinking water distribution system. Specifically, this nitrification, which is the conversion of the ammonia to nitrite and nitrate by bacteria, leads to water quality issues, such as potential corrosion problems, oxidant demand, taste and odor complaints, and elevated nitrite levels (Bremer et al.,2001; Fleming et al., 2005; Lee et al., 1980; Odell et al., 1996; Rittman & Snoeyink, 1984; Suffet et al., 1996). The EPA’s regulatory limits for nitrite and nitrate (at the entry point to the distribution system) are 0.1 and 10 mg N/L, respectively. Ammonia in water may also pose problems with water treatment effectiveness. For example, in source waters containing both ammonia and arsenic, the ammonia may negatively impact

  4. Reverse engineering development: Crosstalk opportunities between developmental biology and tissue engineering.

    Science.gov (United States)

    Marcucio, Ralph S; Qin, Ling; Alsberg, Eben; Boerckel, Joel D

    2017-11-01

    The fields of developmental biology and tissue engineering have been revolutionized in recent years by technological advancements, expanded understanding, and biomaterials design, leading to the emerging paradigm of "developmental" or "biomimetic" tissue engineering. While developmental biology and tissue engineering have long overlapping histories, the fields have largely diverged in recent years at the same time that crosstalk opportunities for mutual benefit are more salient than ever. In this perspective article, we will use musculoskeletal development and tissue engineering as a platform on which to discuss these emerging crosstalk opportunities and will present our opinions on the bright future of these overlapping spheres of influence. The multicellular programs that control musculoskeletal development are rapidly becoming clarified, represented by shifting paradigms in our understanding of cellular function, identity, and lineage specification during development. Simultaneously, advancements in bioartificial matrices that replicate the biochemical, microstructural, and mechanical properties of developing tissues present new tools and approaches for recapitulating development in tissue engineering. Here, we introduce concepts and experimental approaches in musculoskeletal developmental biology and biomaterials design and discuss applications in tissue engineering as well as opportunities for tissue engineering approaches to inform our understanding of fundamental biology. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:2356-2368, 2017. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  5. Systems engineering for very large systems

    Science.gov (United States)

    Lewkowicz, Paul E.

    Very large integrated systems have always posed special problems for engineers. Whether they are power generation systems, computer networks or space vehicles, whenever there are multiple interfaces, complex technologies or just demanding customers, the challenges are unique. 'Systems engineering' has evolved as a discipline in order to meet these challenges by providing a structured, top-down design and development methodology for the engineer. This paper attempts to define the general class of problems requiring the complete systems engineering treatment and to show how systems engineering can be utilized to improve customer satisfaction and profit ability. Specifically, this work will focus on a design methodology for the largest of systems, not necessarily in terms of physical size, but in terms of complexity and interconnectivity.

  6. 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.

  7. Engineering Information System (EIS)

    Science.gov (United States)

    1992-01-31

    be availabe and usefu for creating powerful tailored contro and mangeen functions. Mode and Framwork Wirth further elaboration of the EIS portio of...control data and activities of the engineering process. The EIM is a conceptual model of administrative and electroic design information. It records...of the access opeations are derived from the instance variable name and type. An attribute conceptually holds one or more instances of a basic type

  8. System dynamics for mechanical engineers

    CERN Document Server

    Davies, Matthew

    2015-01-01

    This textbook is ideal for mechanical engineering students preparing to enter the workforce during a time of rapidly accelerating technology, where they will be challenged to join interdisciplinary teams. It explains system dynamics using analogies familiar to the mechanical engineer while introducing new content in an intuitive fashion. The fundamentals provided in this book prepare the mechanical engineer to adapt to continuous technological advances with topics outside traditional mechanical engineering curricula by preparing them to apply basic principles and established approaches to new problems. This book also: ·         Reinforces the connection between the subject matter and engineering reality ·         Includes an instructor pack with the online publication that describes in-class experiments with minimal preparation requirements ·         Provides content dedicated to the modeling of modern interdisciplinary technological subjects, including opto-mechanical systems, high...

  9. Systems Engineering a Naval Railgun

    National Research Council Canada - National Science Library

    Bean, John; Shebalin, Paul; Solitario, William

    2006-01-01

    ... to a viable acquisition program. The detailed formulation and application of the railgun systems engineering process will be defined by government acquisition agents and the selected private sector contractors in accordance with United States (US...

  10. Automatic control systems engineering

    International Nuclear Information System (INIS)

    Shin, Yun Gi

    2004-01-01

    This book gives descriptions of automatic control for electrical electronics, which indicates history of automatic control, Laplace transform, block diagram and signal flow diagram, electrometer, linearization of system, space of situation, state space analysis of electric system, sensor, hydro controlling system, stability, time response of linear dynamic system, conception of root locus, procedure to draw root locus, frequency response, and design of control system.

  11. KESS: Knowledge Engineering Support System

    OpenAIRE

    Said, Mohamed Ben; Dougherty, Nini; Anderson, Curtis; Altman, Stanley J.; Bouhaddou, Omar; Warner, Homer R.

    1987-01-01

    KESS (Knowledge Engineering Support System) is a relational information management system created at the University of Utah to document each step in the building of four expert knowledge bases. In weekly knowledge engineering sessions, groups of experts propose decision making criteria and examine information sources in the process of creating HELP knowledge frames. KESS utilizes many-to-many links with multiple files and central link files to track the different kinds of information generate...

  12. 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.

  13. Creating to understand – developmental biology meets engineering in Paris

    NARCIS (Netherlands)

    Kicheva, Anna; Rivron, Nicolas C.

    2017-01-01

    In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation

  14. 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)

  15. 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)

  16. 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,...

  17. Photovoltaic systems engineering

    CERN Document Server

    Messenger, Roger A

    2010-01-01

    BackgroundPopulation and Energy DemandEnergy UnitsCurrent World Energy Use PatternsExponential GrowthHubbert's Gaussian ModelNet Energy, Btu Economics, and the Test for SustainabilityDirect Conversion of Sunlight to Electricity with PhotovoltaicsThe SunThe Solar SpectrumThe Effect of Atmosphere on SunlightSunlight SpecificsCapturing SunlightIntroduction to PV SystemsThe PV CellThe PV ModuleThe PV ArrayEnergy StoragePV System LoadsPV System AvailabilityAssociated System Electronic ComponentsGeneratorsBalance of System (BOS) ComponentsGrid-Connected Utility-Interactive PV SystemsApplicable Codes and StandardsDesign Considerations for Straight Grid-Connected PV SystemsDesign of a System Based on Desired Annual System PerformanceDesign of a System Based on Available Roof SpaceDesign of a Microinverter-Based SystemDesign of a Nominal 21 kW System that Feeds a Three-Phase Distribution PanelDesign of a Nominal 250 kW SystemSystem Performance MonitoringMechanical ConsiderationsImportant Properties of MaterialsEstabli...

  18. Thermostability of biological systems: fundamentals, challenges, and quantification.

    Science.gov (United States)

    He, Xiaoming

    2011-01-01

    This review examines the fundamentals and challenges in engineering/understanding the thermostability of biological systems over a wide temperature range (from the cryogenic to hyperthermic regimen). Applications of the bio-thermostability engineering to either destroy unwanted or stabilize useful biologicals for the treatment of diseases in modern medicine are first introduced. Studies on the biological responses to cryogenic and hyperthermic temperatures for the various applications are reviewed to understand the mechanism of thermal (both cryo and hyperthermic) injury and its quantification at the molecular, cellular and tissue/organ levels. Methods for quantifying the thermophysical processes of the various applications are then summarized accounting for the effect of blood perfusion, metabolism, water transport across cell plasma membrane, and phase transition (both equilibrium and non-equilibrium such as ice formation and glass transition) of water. The review concludes with a summary of the status quo and future perspectives in engineering the thermostability of biological systems.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Fusion systems engineering

    International Nuclear Information System (INIS)

    Anon.

    1977-01-01

    Summaries of research are included for each of the following topics: (1) fusion reactor systems studies, (2) development of blanket processing technology for fusion reactors, (3) safety studies of fusion concepts, (4) the MACK/MACKLIB system for nuclear response functions, and (5) energy storage and power supply systems for fusion reactors

  4. Protein design in systems metabolic engineering for industrial strain development.

    Science.gov (United States)

    Chen, Zhen; Zeng, An-Ping

    2013-05-01

    Accelerating the process of industrial bacterial host strain development, aimed at increasing productivity, generating new bio-products or utilizing alternative feedstocks, requires the integration of complementary approaches to manipulate cellular metabolism and regulatory networks. Systems metabolic engineering extends the concept of classical metabolic engineering to the systems level by incorporating the techniques used in systems biology and synthetic biology, and offers a framework for the development of the next generation of industrial strains. As one of the most useful tools of systems metabolic engineering, protein design allows us to design and optimize cellular metabolism at a molecular level. Here, we review the current strategies of protein design for engineering cellular synthetic pathways, metabolic control systems and signaling pathways, and highlight the challenges of this subfield within the context of systems metabolic engineering. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. MEMS Rotary Engine Power System

    Science.gov (United States)

    Fernandez-Pello, A. Carlos; Pisano, Albert P.; Fu, Kelvin; Walther, David C.; Knobloch, Aaron; Martinez, Fabian; Senesky, Matt; Stoldt, Conrad; Maboudian, Roya; Sanders, Seth; Liepmann, Dorian

    This work presents a project overview and recent research results for the MEMS Rotary Engine Power System project at the Berkeley Sensor & Actuator Center of the University of California at Berkeley. The research motivation for the project is the high specific energy density of hydrocarbon fuels. When compared with the energy density of batteries, hydrocarbon fuels may have as much as 20x more energy. However, the technical challenge is the conversion of hydrocarbon fuel to electricity in an efficient and clean micro engine. A 12.9 mm diameter Wankel engine will be shown that has already generated 4 Watts of power at 9300rpm. In addition, the 1mm and 2.4 mm Wankel engines that BSAC is developing for power generation at the microscale will be discussed. The project goal is to develop electrical power output of 90milliwatts from the 2.4 mm engine. Prototype engine components have already been fabricated and these will be described. The integrated generator design concept utilizes a nickel-iron alloy electroplated in the engine rotor poles, so that the engine rotor also serves as the generator rotor.

  6. Adaptive Systems Engineering: A Medical Paradigm for Practicing Systems Engineering

    Energy Technology Data Exchange (ETDEWEB)

    R. Douglas Hamelin; Ron D. Klingler; Christopher Dieckmann

    2011-06-01

    From its inception in the defense and aerospace industries, SE has applied holistic, interdisciplinary tools and work-process to improve the design and management of 'large, complex engineering projects.' The traditional scope of engineering in general embraces the design, development, production, and operation of physical systems, and SE, as originally conceived, falls within that scope. While this 'traditional' view has expanded over the years to embrace wider, more holistic applications, much of the literature and training currently available is still directed almost entirely at addressing the large, complex, NASA and defense-sized systems wherein the 'ideal' practice of SE provides the cradle-to-grave foundation for system development and deployment. Under such scenarios, systems engineers are viewed as an integral part of the system and project life-cycle from conception to decommissioning. In far less 'ideal' applications, SE principles are equally applicable to a growing number of complex systems and projects that need to be 'rescued' from overwhelming challenges that threaten imminent failure. The medical profession provides a unique analogy for this latter concept and offers a useful paradigm for tailoring our 'practice' of SE to address the unexpected dynamics of applying SE in the real world. In short, we can be much more effective as systems engineers as we change some of the paradigms under which we teach and 'practice' SE.

  7. Synthetic and systems biology for microbial production of commodity chemicals.

    Science.gov (United States)

    Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J; Keasling, Jay D; Martín, Héctor García

    2016-01-01

    The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.

  8. 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...

  9. Industrial and Systems Engineering Applications in NASA

    Science.gov (United States)

    Shivers, Charles H.

    2006-01-01

    A viewgraph presentation on the many applications of Industrial and Systems Engineering used for safe NASA missions is shown. The topics include: 1) NASA Information; 2) Industrial Engineering; 3) Systems Engineering; and 4) Major NASA Programs.

  10. Screening candidate systems engineers: a research design

    CSIR Research Space (South Africa)

    Goncalves, DP

    2009-07-01

    Full Text Available engineering screening methodology that could be used to screen potential systems engineers. According to their design, this can be achieved by defining a system engineering profile according to specific psychological attributes, and using this profile...

  11. Engineering Multiagent Systems - Reflections

    DEFF Research Database (Denmark)

    Villadsen, Jørgen

    2012-01-01

    In the first part I look at a theater performance by artistic director Troels Christian Jakobsen as a multiagent system. It is designed as a self-organising critical system using a framework where within its borders but without a script there is real interaction between the elements of the perfor......In the first part I look at a theater performance by artistic director Troels Christian Jakobsen as a multiagent system. It is designed as a self-organising critical system using a framework where within its borders but without a script there is real interaction between the elements...... of the performance. In the second part I discuss the ideas behind my recent monograph on propositional attitudes and inconsistency tolerance. Natural language sentences are parsed using a categorial grammar and correctness of arguments are decided using a paraconsistent logic. In the third part I present...

  12. Fusion systems engineering

    International Nuclear Information System (INIS)

    Anon.

    1977-01-01

    Information is given on each of the following topics: (1) fusion reactor systems studies, (2) development of blanket processing technology for fusion reactors, (3) safety studies of CTR concepts, and (4) cross section measurements and techniques

  13. Automotive systems engineering

    CERN Document Server

    Winner, Hermann

    2013-01-01

    This book reflects the shift in design paradigm in automobile industry. It presents future innovations, often referred as  “automotive systems engineering”.  These cause fundamental innovations in the field of driver assistance systems and electro-mobility as well as fundamental changes in the architecture of the vehicles. New driving functionalities can only be realized if the software programs of multiple electronic control units work together correctly. This volume presents the new and innovative methods which are mandatory to master the complexity of the vehicle of the future.

  14. Systems Engineering Management Procedures

    Science.gov (United States)

    1966-03-10

    hls -iii-rit. -miiiirme 4 --tandnirdized hle iil*ri oa;iu ’ -enperfrm)a- -yýfefi ~lall uitm l--im eniai~ atar n which will lumPremiiieuiea -. v-imli m...with standard component/part selection. and de- tile total system requirements stated in the Sys- tailed functional and physical interfaces: eval- tern...system survivability requirAent. As physical , interface, time, environment, use of these facility requirements are bei developed, standard perts; and

  15. Computer systems and software engineering

    Science.gov (United States)

    Mckay, Charles W.

    1988-01-01

    The High Technologies Laboratory (HTL) was established in the fall of 1982 at the University of Houston Clear Lake. Research conducted at the High Tech Lab is focused upon computer systems and software engineering. There is a strong emphasis on the interrelationship of these areas of technology and the United States' space program. In Jan. of 1987, NASA Headquarters announced the formation of its first research center dedicated to software engineering. Operated by the High Tech Lab, the Software Engineering Research Center (SERC) was formed at the University of Houston Clear Lake. The High Tech Lab/Software Engineering Research Center promotes cooperative research among government, industry, and academia to advance the edge-of-knowledge and the state-of-the-practice in key topics of computer systems and software engineering which are critical to NASA. The center also recommends appropriate actions, guidelines, standards, and policies to NASA in matters pertinent to the center's research. Results of the research conducted at the High Tech Lab/Software Engineering Research Center have given direction to many decisions made by NASA concerning the Space Station Program.

  16. Object Based Systems Engineering

    Science.gov (United States)

    2011-10-17

    practically impossible where the original SMEs are unavailable or lack perfect recall. 7. Capture the precious and transient logic behind this...complex system. References 1. FITCH, J. Exploiting Decision-to-Requirements Traceability, briefing to NDIA CMMI Conference, November, 2009 2

  17. Systems Security Engineering

    Science.gov (United States)

    2010-08-22

    environment that contains network- borne cybersecurity threats, an argument may be made that the firewall increases overall system functionality by reserving...the number of administered devices. This approach to security analysis is at once old and new. In the early days of eCommerce , security

  18. [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.

  19. 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.

  20. Introducing Model-Based System Engineering Transforming System Engineering through Model-Based Systems Engineering

    Science.gov (United States)

    2014-03-31

    Web  Presentation...Software  .....................................................  20   Figure  6.  Published   Web  Page  from  Data  Collection...the  term  Model  Based  Engineering  (MBE),  Model  Driven  Engineering  ( MDE ),  or  Model-­‐Based  Systems  

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

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Ihekwaba, Adoha

    2007-01-01

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

  2. Fusion systems engineering

    International Nuclear Information System (INIS)

    Anon.

    1978-01-01

    Research during this report period has covered the following areas: (1) fusion reactor systems studies, (2) development of blanket processing technology for fusion reactors, (3) safety studies of fusion concepts, (4) MACKLIB-IV, a new library of nuclear response functions, (5) energy storage and power supply requirements for commercial fusion reactors, (6) blanket/shield design evaluation for commercial fusion reactors, and (7) cross section measurements, evaluations, and techniques

  3. CellNet: network biology applied to stem cell engineering.

    Science.gov (United States)

    Cahan, Patrick; Li, Hu; Morris, Samantha A; Lummertz da Rocha, Edroaldo; Daley, George Q; Collins, James J

    2014-08-14

    Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Security systems engineering overview

    International Nuclear Information System (INIS)

    Steele, B.J.

    1996-01-01

    Crime prevention is on the minds of most people today. The concern for public safety and the theft of valuable assets are being discussed at all levels of government and throughout the public sector. There is a growing demand for security systems that can adequately safeguard people and valuable assets against the sophistication of those criminals or adversaries who pose a threat. The crime in this country has been estimated at $70 billion in direct costs and up to $300 billion in indirect costs. Health insurance fraud alone is estimated to cost American businesses $100 billion. Theft, warranty fraud, and counterfeiting of computer hardware totaled $3 billion in 1994. A threat analysis is a prerequisite to any security system design to assess the vulnerabilities with respect to the anticipated threat. Having established a comprehensive definition of the threat, crime prevention, detection, and threat assessment technologies can be used to address these criminal activities. This talk will outline the process used to design a security system regardless of the level of security. This methodology has been applied to many applications including: government high security facilities; residential and commercial intrusion detection and assessment; anti-counterfeiting/fraud detection technologies (counterfeit currency, cellular phone billing, credit card fraud, health care fraud, passport, green cards, and questionable documents); industrial espionage detection and prevention (intellectual property, computer chips, etc.); and security barrier technology (creation of delay such as gates, vaults, etc.)

  5. Security systems engineering overview

    Science.gov (United States)

    Steele, Basil J.

    1997-01-01

    Crime prevention is on the minds of most people today. The concern for public safety and the theft of valuable assets are being discussed at all levels of government and throughout the public sector. There is a growing demand for security systems that can adequately safeguard people and valuable assets against the sophistication of those criminals or adversaries who pose a threat. The crime in this country has been estimated at 70 billion dollars in direct costs and up to 300 billion dollars in indirect costs. Health insurance fraud alone is estimated to cost American businesses 100 billion dollars. Theft, warranty fraud, and counterfeiting of computer hardware totaled 3 billion dollars in 1994. A threat analysis is a prerequisite to any security system design to assess the vulnerabilities with respect to the anticipated threat. Having established a comprehensive definition of the threat, crime prevention, detection, and threat assessment technologies can be used to address these criminal activities. This talk will outline the process used to design a security system regardless of the level of security. This methodology has been applied to many applications including: government high security facilities; residential and commercial intrusion detection and assessment; anti-counterfeiting/fraud detection technologies; industrial espionage detection and prevention; security barrier technology.

  6. Systems engineering at the nanoscale

    Science.gov (United States)

    Benkoski, Jason J.; Breidenich, Jennifer L.; Wei, Michael C.; Clatterbaughi, Guy V.; Keng, Pei Yuin; Pyun, Jeffrey

    2012-06-01

    Nanomaterials have provided some of the greatest leaps in technology over the past twenty years, but their relatively early stage of maturity presents challenges for their incorporation into engineered systems. Perhaps even more challenging is the fact that the underlying physics at the nanoscale often run counter to our physical intuition. The current state of nanotechnology today includes nanoscale materials and devices developed to function as components of systems, as well as theoretical visions for "nanosystems," which are systems in which all components are based on nanotechnology. Although examples will be given to show that nanomaterials have indeed matured into applications in medical, space, and military systems, no complete nanosystem has yet been realized. This discussion will therefore focus on systems in which nanotechnology plays a central role. Using self-assembled magnetic artificial cilia as an example, we will discuss how systems engineering concepts apply to nanotechnology.

  7. Systems Engineering 2010 Workshop | Wind | NREL

    Science.gov (United States)

    0 Workshop Systems Engineering 2010 Workshop The 1st NREL Wind Energy Systems Engineering Workshop of the system engineering model. In the middle of the model is optimization, metric tracking &M model, capital cost model, and balance of station. Systems engineering represents a holistic

  8. Recent advances in systems metabolic engineering tools and strategies.

    Science.gov (United States)

    Chae, Tong Un; Choi, So Young; Kim, Je Woong; Ko, Yoo-Sung; Lee, Sang Yup

    2017-10-01

    Metabolic engineering has been playing increasingly important roles in developing microbial cell factories for the production of various chemicals and materials to achieve sustainable chemical industry. Nowadays, many tools and strategies are available for performing systems metabolic engineering that allows systems-level metabolic engineering in more sophisticated and diverse ways by adopting rapidly advancing methodologies and tools of systems biology, synthetic biology and evolutionary engineering. As an outcome, development of more efficient microbial cell factories has become possible. Here, we review recent advances in systems metabolic engineering tools and strategies together with accompanying application examples. In addition, we describe how these tools and strategies work together in simultaneous and synergistic ways to develop novel microbial cell factories. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. 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...

  10. 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.)

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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...

  16. Cardiac tissue engineering using perfusion bioreactor systems

    Science.gov (United States)

    Radisic, Milica; Marsano, Anna; Maidhof, Robert; Wang, Yadong; Vunjak-Novakovic, Gordana

    2009-01-01

    This protocol describes tissue engineering of synchronously contractile cardiac constructs by culturing cardiac cell populations on porous scaffolds (in some cases with an array of channels) and bioreactors with perfusion of culture medium (in some cases supplemented with an oxygen carrier). The overall approach is ‘biomimetic’ in nature as it tends to provide in vivo-like oxygen supply to cultured cells and thereby overcome inherent limitations of diffusional transport in conventional culture systems. In order to mimic the capillary network, cells are cultured on channeled elastomer scaffolds that are perfused with culture medium that can contain oxygen carriers. The overall protocol takes 2–4 weeks, including assembly of the perfusion systems, preparation of scaffolds, cell seeding and cultivation, and on-line and end-point assessment methods. This model is well suited for a wide range of cardiac tissue engineering applications, including the use of human stem cells, and high-fidelity models for biological research. PMID:18388955

  17. TWRS Systems Engineering Working Plan

    International Nuclear Information System (INIS)

    Eiholzer, C.R.

    1994-01-01

    The purpose of this Systems Engineering (SE) Working Plan (SEWP) is to describe how the Westinghouse Hanford Company (WHC) Tank Waste Remediation System (TWRS) will implement the SE polity and guidance provided in the Tank Waste Remediation System (TWRS) Systems Engineering Management Plan (SEMP). Sections 2.0 through 4.0 cover how the SE process and management will be performed to develop a technical baseline within TWRS. Section 5.0 covers the plans and schedules to implement the SE process and management within TWRS. Detailed information contained in the TWRS Program SEMP is not repeated in this document. This SEWP and the SE discipline defined within apply to the TWRS Program and new and ongoing TWRS projects or activities, including new facilities and safety. The SE process will be applied to the existing Tank Farm operations where the Richland TWRS Program Office management determines the process appropriate and where value will be added to existing Tank Farm system and operations

  18. 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

  19. Application of Chaos Theory to Engine Systems

    OpenAIRE

    Matsumoto, Kazuhiro; Diebner, Hans H.; Tsuda, Ichiro; Hosoi, Yukiharu

    2008-01-01

    We focus on the control issue for engine systems from the perspective of chaos theory, which is based on the fact that engine systems have a low-dimensional chaotic dynamics. Two approaches are discussed: controlling chaos and harnessing chaos, respectively. We apply Pyragas' chaos control method to an actual engine system. The experimental results show that the chaotic motion of an engine system may be stabilized to a periodic motion. Alternatively, harnessing chaos for engine systems is add...

  20. Aerospace Engineering Systems

    Science.gov (United States)

    VanDalsem, William R.; Livingston, Mary E.; Melton, John E.; Torres, Francisco J.; Stremel, Paul M.

    1999-01-01

    Continuous improvement of aerospace product development processes is a driving requirement across much of the aerospace community. As up to 90% of the cost of an aerospace product is committed during the first 10% of the development cycle, there is a strong emphasis on capturing, creating, and communicating better information (both requirements and performance) early in the product development process. The community has responded by pursuing the development of computer-based systems designed to enhance the decision-making capabilities of product development individuals and teams. Recently, the historical foci on sharing the geometrical representation and on configuration management are being augmented: Physics-based analysis tools for filling the design space database; Distributed computational resources to reduce response time and cost; Web-based technologies to relieve machine-dependence; and Artificial intelligence technologies to accelerate processes and reduce process variability. Activities such as the Advanced Design Technologies Testbed (ADTT) project at NASA Ames Research Center study the strengths and weaknesses of the technologies supporting each of these trends, as well as the overall impact of the combination of these trends on a product development event. Lessons learned and recommendations for future activities will be reported.

  1. 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

  2. Engineering Therapeutic T Cells: From Synthetic Biology to Clinical Trials.

    Science.gov (United States)

    Esensten, Jonathan H; Bluestone, Jeffrey A; Lim, Wendell A

    2017-01-24

    Engineered T cells are currently in clinical trials to treat patients with cancer, solid organ transplants, and autoimmune diseases. However, the field is still in its infancy. The design, and manufacturing, of T cell therapies is not standardized and is performed mostly in academic settings by competing groups. Reliable methods to define dose and pharmacokinetics of T cell therapies need to be developed. As of mid-2016, there are no US Food and Drug Administration (FDA)-approved T cell therapeutics on the market, and FDA regulations are only slowly adapting to the new technologies. Further development of engineered T cell therapies requires advances in immunology, synthetic biology, manufacturing processes, and government regulation. In this review, we outline some of these challenges and discuss the contributions that pathologists can make to this emerging field.

  3. Simple glycolipids of microbes: Chemistry, biological activity and metabolic engineering

    Directory of Open Access Journals (Sweden)

    Ahmad Mohammad Abdel-Mawgoud

    2018-03-01

    Full Text Available Glycosylated lipids (GLs are added-value lipid derivatives of great potential. Besides their interesting surface activities that qualify many of them to act as excellent ecological detergents, they have diverse biological activities with promising biomedical and cosmeceutical applications. Glycolipids, especially those of microbial origin, have interesting antimicrobial, anticancer, antiparasitic as well as immunomodulatory activities. Nonetheless, GLs are hardly accessing the market because of their high cost of production. We believe that experience of metabolic engineering (ME of microbial lipids for biofuel production can now be harnessed towards a successful synthesis of microbial GLs for biomedical and other applications. This review presents chemical groups of bacterial and fungal GLs, their biological activities, their general biosynthetic pathways and an insight on ME strategies for their production.

  4. 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.

  5. Essentials of Project and Systems Engineering Management

    CERN Document Server

    Eisner, Howard S

    2008-01-01

    The Third Edition of Essentials of Project and Systems Engineering Management enables readers to manage the design, development, and engineering of systems effectively and efficiently. The book both defines and describes the essentials of project and systems engineering management and, moreover, shows the critical relationship and interconnection between project management and systems engineering. The author's comprehensive presentation has proven successful in enabling both engineers and project managers to understand their roles, collaborate, and quickly grasp and apply all the basic princip

  6. Method Engineering: Engineering of Information Systems Development Methods and Tools

    NARCIS (Netherlands)

    Brinkkemper, J.N.; Brinkkemper, Sjaak

    1996-01-01

    This paper proposes the term method engineering for the research field of the construction of information systems development methods and tools. Some research issues in method engineering are identified. One major research topic in method engineering is discussed in depth: situational methods, i.e.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering.

    Science.gov (United States)

    Wang, Harris H; Church, George M

    2011-01-01

    Engineering at the scale of whole genomes requires fundamentally new molecular biology tools. Recent advances in recombineering using synthetic oligonucleotides enable the rapid generation of mutants at high efficiency and specificity and can be implemented at the genome scale. With these techniques, libraries of mutants can be generated, from which individuals with functionally useful phenotypes can be isolated. Furthermore, populations of cells can be evolved in situ by directed evolution using complex pools of oligonucleotides. Here, we discuss ways to utilize these multiplexed genome engineering methods, with special emphasis on experimental design and implementation. Copyright © 2011 Elsevier Inc. All rights reserved.

  12. Method Engineering: Engineering of Information Systems Development Methods and Tools

    OpenAIRE

    Brinkkemper, J.N.; Brinkkemper, Sjaak

    1996-01-01

    This paper proposes the term method engineering for the research field of the construction of information systems development methods and tools. Some research issues in method engineering are identified. One major research topic in method engineering is discussed in depth: situational methods, i.e. the configuration of a project approach that is tuned to the project at hand. A language and support tool for the engineering of situational methods are discussed.

  13. Information technology security system engineering methodology

    Science.gov (United States)

    Childs, D.

    2003-01-01

    A methodology is described for system engineering security into large information technology systems under development. The methodology is an integration of a risk management process and a generic system development life cycle process. The methodology is to be used by Security System Engineers to effectively engineer and integrate information technology security into a target system as it progresses through the development life cycle. The methodology can also be used to re-engineer security into a legacy system.

  14. A nuclear power plant system engineering workstation

    International Nuclear Information System (INIS)

    Mason, J.H.; Crosby, J.W.

    1989-01-01

    System engineers offer an approach for effective technical support for operation and maintenance of nuclear power plants. System engineer groups are being set up by most utilities in the United States. Institute of Nuclear Power operations (INPO) and U.S. Nuclear Regulatory Commission (NRC) have endorsed the concept. The INPO Good Practice and a survey of system engineer programs in the southeastern United States provide descriptions of system engineering programs. The purpose of this paper is to describe a process for developing a design for a department-level information network of workstations for system engineering groups. The process includes the following: (1) application of a formal information engineering methodology, (2) analysis of system engineer functions and activities; (3) use of Electric Power Research Institute (EPRI) Plant Information Network (PIN) data; (4) application of the Information Engineering Workbench. The resulting design for this system engineer workstation can provide a reference for design of plant-specific systems

  15. B-2 Systems Engineering Case Study

    Science.gov (United States)

    2007-01-01

    of four small circles on the top view in front of the cockpit and on the bottom view engine bay doors. This air data system has no standard pitot ...Skantze, General, Air Force, Source Selection Advisory Board Chairman Erich Smith, Vought, Test Engineer, Systems Engineer, Chief engineer Henry

  16. 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

  17. Engineered Geothermal System Demonstration Project

    Energy Technology Data Exchange (ETDEWEB)

    Petty, Susan

    2014-06-19

    In June 2009, AltaRock Energy began field work on a project supported by the U.S. Department of Energy entitled “Use of Multiple Stimulations to Improve Economics of Engineered Geothermal Systems in Shallow High Temperature Intrusives.” The goal of the project was to develop an Engineered Geothermal System (EGS) in the portion of The Geysers geothermal field operated by the Northern California Power Agency (NCPA). The project encountered several problems while deepening Well E-7 which culminated in the suspension of field activities in September 2009. Some of the problems encountered are particular to The Geysers area, while others might be encountered in any geothermal field, and they might be avoided in future operations.

  18. PGASO: A synthetic biology tool for engineering a cellulolytic yeast

    Directory of Open Access Journals (Sweden)

    Chang Jui-Jen

    2012-07-01

    Full Text Available Abstract Background To achieve an economical cellulosic ethanol production, a host that can do both cellulosic saccharification and ethanol fermentation is desirable. However, to engineer a non-cellulolytic yeast to be such a host requires synthetic biology techniques to transform multiple enzyme genes into its genome. Results A technique, named Promoter-based Gene Assembly and Simultaneous Overexpression (PGASO, that employs overlapping oligonucleotides for recombinatorial assembly of gene cassettes with individual promoters, was developed. PGASO was applied to engineer Kluyveromycesmarxianus KY3, which is a thermo- and toxin-tolerant yeast. We obtained a recombinant strain, called KR5, that is capable of simultaneously expressing exoglucanase and endoglucanase (both of Trichodermareesei, a beta-glucosidase (from a cow rumen fungus, a neomycin phosphotransferase, and a green fluorescent protein. High transformation efficiency and accuracy were achieved as ~63% of the transformants was confirmed to be correct. KR5 can utilize beta-glycan, cellobiose or CMC as the sole carbon source for growth and can directly convert cellobiose and beta-glycan to ethanol. Conclusions This study provides the first example of multi-gene assembly in a single step in a yeast species other than Saccharomyces cerevisiae. We successfully engineered a yeast host with a five-gene cassette assembly and the new host is capable of co-expressing three types of cellulase genes. Our study shows that PGASO is an efficient tool for simultaneous expression of multiple enzymes in the kefir yeast KY3 and that KY3 can serve as a host for developing synthetic biology tools.

  19. A model of engineering materials inspired by biological tissues

    Directory of Open Access Journals (Sweden)

    Holeček M.

    2009-12-01

    Full Text Available The perfect ability of living tissues to control and adapt their mechanical properties to varying external conditions may be an inspiration for designing engineering materials. An interesting example is the smooth muscle tissue since this "material" is able to change its global mechanical properties considerably by a subtle mechanism within individual muscle cells. Multi-scale continuum models may be useful in designing essentially simpler engineering materials having similar properties. As an illustration we present the model of an incompressible material whose microscopic structure is formed by flexible, soft but incompressible balls connected mutually by linear springs. This simple model, however, shows a nontrivial nonlinear behavior caused by the incompressibility of balls and is very sensitive on some microscopic parameters. It may elucidate the way by which "small" changes in biopolymer networks within individual muscular cells may control the stiffness of the biological tissue, which outlines a way of designing similar engineering materials. The 'balls and springs' material presents also prestress-induced stiffening and allows elucidating a contribution of extracellular fluids into the tissue’s viscous properties.

  20. Genome Engineering and Modification Toward Synthetic Biology for the Production of Antibiotics.

    Science.gov (United States)

    Zou, Xuan; Wang, Lianrong; Li, Zhiqiang; Luo, Jie; Wang, Yunfu; Deng, Zixin; Du, Shiming; Chen, Shi

    2018-01-01

    Antibiotic production is often governed by large gene clusters composed of genes related to antibiotic scaffold synthesis, tailoring, regulation, and resistance. With the expansion of genome sequencing, a considerable number of antibiotic gene clusters has been isolated and characterized. The emerging genome engineering techniques make it possible towards more efficient engineering of antibiotics. In addition to genomic editing, multiple synthetic biology approaches have been developed for the exploration and improvement of antibiotic natural products. Here, we review the progress in the development of these genome editing techniques used to engineer new antibiotics, focusing on three aspects of genome engineering: direct cloning of large genomic fragments, genome engineering of gene clusters, and regulation of gene cluster expression. This review will not only summarize the current uses of genomic engineering techniques for cloning and assembly of antibiotic gene clusters or for altering antibiotic synthetic pathways but will also provide perspectives on the future directions of rebuilding biological systems for the design of novel antibiotics. © 2017 Wiley Periodicals, Inc.

  1. Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes.

    Science.gov (United States)

    Kang, Zhen; Zhang, Junli; Jin, Peng; Yang, Sen

    2015-01-01

    Owing to our limited understanding of the relationship between sequence and function and the interaction between intracellular pathways and regulatory systems, the rational design of enzyme-coding genes and de novo assembly of a brand-new artificial genome for a desired functionality or phenotype are difficult to achieve. As an alternative approach, directed evolution has been widely used to engineer genomes and enzyme-coding genes. In particular, significant developments toward DNA synthesis, DNA assembly (in vitro or in vivo), recombination-mediated genetic engineering, and high-throughput screening techniques in the field of synthetic biology have been matured and widely adopted, enabling rapid semi-rational genome engineering to generate variants with desired properties. In this commentary, these novel tools and their corresponding applications in the directed evolution of genomes and enzymes are discussed. Moreover, the strategies for genome engineering and rapid in vitro enzyme evolution are also proposed.

  2. SMAP Instrument Mechanical System Engineering

    Science.gov (United States)

    Slimko, Eric; French, Richard; Riggs, Benjamin

    2013-01-01

    The Soil Moisture Active Passive (SMAP) mission, scheduled for launch by the end of 2014, is being developed to measure the soil moisture and soil freeze/thaw state on a global scale over a three-year period. The accuracy, resolution, and global coverage of SMAP measurements are invaluable across many science and applications disciplines including hydrology, climate, carbon cycle, and the meteorological, environment, and ecology applications communities. The SMAP observatory is composed of a despun bus and a spinning instrument platform that includes both a deployable 6 meter aperture low structural frequency Astromesh reflector and a spin control system. The instrument section has engendered challenging mechanical system issues associated with the antenna deployment, flexible antenna pointing in the context of a multitude of disturbances, spun section mass properties, spin control system development, and overall integration with the flight system on both mechanical and control system levels. Moreover, the multitude of organizations involved, including two major vendors providing the spin subsystem and reflector boom assembly plus the flight system mechanical and guidance, navigation, and control teams, has led to several unique system engineering challenges. Capturing the key physics associated with the function of the flight system has been challenging due to the many different domains that are applicable. Key interfaces and operational concepts have led to complex negotiations because of the large number of organizations that integrate with the instrument mechanical system. Additionally, the verification and validation concerns associated with the mechanical system have had required far-reaching involvement from both the flight system and other subsystems. The SMAP instrument mechanical systems engineering issues and their solutions are described in this paper.

  3. 4+ Dimensional nuclear systems engineering

    International Nuclear Information System (INIS)

    Suh, Kune Y.

    2009-01-01

    Nuclear power plants (NPPs) require massive quantity of data during the design, construction, operation, maintenance and decommissioning stages because of their special features like size, cost, radioactivity, and so forth. The system engineering thus calls for a fully integrated way of managing the information flow spanning their life cycle. This paper proposes digital systems engineering anchored in three dimensional (3D) computer aided design (CAD) models. The signature in the proposal lies with the four plus dimensional (4 + D) Technology TM , a critical know how for digital management. ESSE (Engineering Super Simulation Emulation) features a 4 + D Technology TM for nuclear energy systems engineering. The technology proposed in the 3D space and time plus cost coordinates, i.e. 4 + D, is the backbone of digital engineering in the nuclear systems design and management. Dased on an integrated 3D configuration management system, ESSE consists of solutions JANUS (Junctional Analysis Neodynamic Unit SoftPower), EURUS (Engineering Utilities Research Unit SoftPower), NOTUS (Neosystemic Optimization Technical Unit SoftPower), VENUS (Virtual Engineering Neocybernetic Unit SoftPower) and INUUS (Informative Neographic Utilities Unit SoftPower). NOTUS contributes to reducing the construction cost of the NPPs by optimizing the component manufacturing procedure and the plant construction process. Planning and scheduling construction projects can thus benefit greatly by integrating traditional management techniques with digital process simulation visualization. The 3D visualization of construction processes and the resulting products intrinsically afford most of the advantages realized by incorporating a purely schedule level detail based the 4 + D system. Problems with equipment positioning and manpower congestion in certain areas can be visualized prior to the actual operation, thus preventing accidents and safety problems such as collision between two machines and losses in

  4. Systems engineering: A problem of perception

    Energy Technology Data Exchange (ETDEWEB)

    Senglaub, M.

    1995-08-01

    The characterization of systems engineering as a discipline, process, procedure or a set of heuristics will have an impact on the implementation strategy, the training methodology, and operational environment. The systems engineering upgrade activities in the New Mexico Weapons Development Center and a search of systems engineering related information provides evidence of a degree of ambiguity in this characterization of systems engineering. A case is made in this article for systems engineering being the engineering discipline applied to the science of complexity. Implications of this characterization and some generic issues are delineated with the goal of providing an enterprise with a starting point for developing its business environment.

  5. Transforming Systems Engineering through Model-Centric Engineering

    Science.gov (United States)

    2018-02-28

    Contract No. HQ0034-13-D-0004 Research Tasks: 48, 118, 141, 157, 170 Report No. SERC-2018-TR-103 Transforming Systems Engineering through...Model-Centric Engineering Technical Report SERC-2018-TR-103 February 28, 2018 Principal Investigator Dr. Mark Blackburn, Stevens Institute of...Systems Engineering Research Center This material is based upon work supported, in whole or in part, by the U.S. Department of Defense through the

  6. Stirling Engine Dynamic System Modeling

    Science.gov (United States)

    Nakis, Christopher G.

    2004-01-01

    The Thermo-Mechanical systems branch at the Glenn Research Center focuses a large amount time on Stirling engines. These engines will be used on missions where solar power is inefficient, especially in deep space. I work with Tim Regan and Ed Lewandowski who are currently developing and validating a mathematical model for the Stirling engines. This model incorporates all aspects of the system including, mechanical, electrical and thermodynamic components. Modeling is done through Simplorer, a program capable of running simulations of the model. Once created and then proven to be accurate, a model is used for developing new ideas for engine design. My largest specific project involves varying key parameters in the model and quantifying the results. This can all be done relatively trouble-free with the help of Simplorer. Once the model is complete, Simplorer will do all the necessary calculations. The more complicated part of this project is determining which parameters to vary. Finding key parameters depends on the potential for a value to be independently altered in the design. For example, a change in one dimension may lead to a proportional change to the rest of the model, and no real progress is made. Also, the ability for a changed value to have a substantial impact on the outputs of the system is important. Results will be condensed into graphs and tables with the purpose of better communication and understanding of the data. With the changing of these parameters, a more optimal design can be created without having to purchase or build any models. Also, hours and hours of results can be simulated in minutes. In the long run, using mathematical models can save time and money. Along with this project, I have many other smaller assignments throughout the summer. My main goal is to assist in the processes of model development, validation and testing.

  7. 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)

  8. Biomedical engineering strategies in system design space.

    Science.gov (United States)

    Savageau, Michael A

    2011-04-01

    Modern systems biology and synthetic bioengineering face two major challenges in relating properties of the genetic components of a natural or engineered system to its integrated behavior. The first is the fundamental unsolved problem of relating the digital representation of the genotype to the analog representation of the parameters for the molecular components. For example, knowing the DNA sequence does not allow one to determine the kinetic parameters of an enzyme. The second is the fundamental unsolved problem of relating the parameters of the components and the environment to the phenotype of the global system. For example, knowing the parameters does not tell one how many qualitatively distinct phenotypes are in the organism's repertoire or the relative fitness of the phenotypes in different environments. These also are challenges for biomedical engineers as they attempt to develop therapeutic strategies to treat pathology or to redirect normal cellular functions for biotechnological purposes. In this article, the second of these fundamental challenges will be addressed, and the notion of a "system design space" for relating the parameter space of components to the phenotype space of bioengineering systems will be focused upon. First, the concept of a system design space will be motivated by introducing one of its key components from an intuitive perspective. Second, a simple linear example will be used to illustrate a generic method for constructing the design space in which qualitatively distinct phenotypes can be identified and counted, their fitness analyzed and compared, and their tolerance to change measured. Third, two examples of nonlinear systems from different areas of biomedical engineering will be presented. Finally, after giving reference to a few other applications that have made use of the system design space approach to reveal important design principles, some concluding remarks concerning challenges and opportunities for further development

  9. Future of Chemical Engineering: Integrating Biology into the Undergraduate ChE Curriculum

    Science.gov (United States)

    Mosto, Patricia; Savelski, Mariano; Farrell, Stephanie H.; Hecht, Gregory B.

    2007-01-01

    Integrating biology in the chemical engineering curriculum seems to be the future for chemical engineering programs nation and worldwide. Rowan University's efforts to address this need include a unique chemical engineering curriculum with an intensive biology component integrated throughout from freshman to senior years. Freshman and Sophomore…

  10. Experiential Engineering through iGEM--An Undergraduate Summer Competition in Synthetic Biology

    Science.gov (United States)

    Mitchell, Rudolph; Dori, Yehudit Judy; Kuldell, Natalie H.

    2011-01-01

    Unlike students in other engineering disciplines, undergraduates in biological engineering typically have limited opportunity to develop design competencies, and even fewer chances to implement their designed projects. The international Genetically Engineered Machines (iGEM) competition is a student Synthetic Biology competition that, in 2009,…

  11. A framework for systems engineering research

    CSIR Research Space (South Africa)

    Erasmus, L

    2013-08-01

    Full Text Available This presentation discusses a framework which is proposed to perform systems engineering research within South Africa and the necessity for hybrid research methods in systems engineering....

  12. 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...

  13. ENGINEERING OF UNIVERSITY INTELLIGENT LEARNING SYSTEMS

    Directory of Open Access Journals (Sweden)

    Vasiliy M. Trembach

    2016-01-01

    Full Text Available In the article issues of engineering intelligent tutoring systems of University with adaptation are considered. The article also dwells on some modern approaches to engineering of information systems. It shows the role of engineering e-learning devices (systems in system engineering. The article describes the basic principles of system engineering and these principles are expanded regarding to intelligent information systems. The structure of intelligent learning systems with adaptation of the individual learning environments based on services is represented in the article.

  14. 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.

  15. 1st Global Conference on Biomedical Engineering & 9th Asian-Pacific Conference on Medical and Biological Engineering

    CERN Document Server

    Wang, Shyh-Hau; Yeh, Ming-Long

    2015-01-01

    This volume presents the proceedings of the 9th Asian-Pacific Conference on Medical and Biological Engineering (APCMBE 2014). The proceedings address a broad spectrum of topics from Bioengineering and Biomedicine, like Biomaterials, Artificial Organs, Tissue Engineering, Nanobiotechnology and Nanomedicine, Biomedical Imaging, Bio MEMS, Biosignal Processing, Digital Medicine, BME Education. It helps medical and biological engineering professionals to interact and exchange their ideas and experiences.

  16. Airbreathing combined cycle engine systems

    Science.gov (United States)

    Rohde, John

    1992-01-01

    The Air Force and NASA share a common interest in developing advanced propulsion systems for commercial and military aerospace vehicles which require efficient acceleration and cruise operation in the Mach 4 to 6 flight regime. The principle engine of interest is the turboramjet; however, other combined cycles such as the turboscramjet, air turborocket, supercharged ejector ramjet, ejector ramjet, and air liquefaction based propulsion are also of interest. Over the past months careful planning and program implementation have resulted in a number of development efforts that will lead to a broad technology base for those combined cycle propulsion systems. Individual development programs are underway in thermal management, controls materials, endothermic hydrocarbon fuels, air intake systems, nozzle exhaust systems, gas turbines and ramjet ramburners.

  17. 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

  18. Towards systems metabolic engineering in Pichia pastoris.

    Science.gov (United States)

    Schwarzhans, Jan-Philipp; Luttermann, Tobias; Geier, Martina; Kalinowski, Jörn; Friehs, Karl

    2017-11-01

    The methylotrophic yeast Pichia pastoris is firmly established as a host for the production of recombinant proteins, frequently outperforming other heterologous hosts. Already, a sizeable amount of systems biology knowledge has been acquired for this non-conventional yeast. By applying various omics-technologies, productivity features have been thoroughly analyzed and optimized via genetic engineering. However, challenging clonal variability, limited vector repertoire and insufficient genome annotation have hampered further developments. Yet, in the last few years a reinvigorated effort to establish P. pastoris as a host for both protein and metabolite production is visible. A variety of compounds from terpenoids to polyketides have been synthesized, often exceeding the productivity of other microbial systems. The clonal variability was systematically investigated and strategies formulated to circumvent untargeted events, thereby streamlining the screening procedure. Promoters with novel regulatory properties were discovered or engineered from existing ones. The genetic tractability was increased via the transfer of popular manipulation and assembly techniques, as well as the creation of new ones. A second generation of sequencing projects culminated in the creation of the second best functionally annotated yeast genome. In combination with landmark physiological insights and increased output of omics-data, a good basis for the creation of refined genome-scale metabolic models was created. The first application of model-based metabolic engineering in P. pastoris showcased the potential of this approach. Recent efforts to establish yeast peroxisomes for compartmentalized metabolite synthesis appear to fit ideally with the well-studied high capacity peroxisomal machinery of P. pastoris. Here, these recent developments are collected and reviewed with the aim of supporting the establishment of systems metabolic engineering in P. pastoris. Copyright © 2017. Published

  19. Development of maintenance engineering system

    International Nuclear Information System (INIS)

    1995-03-01

    Department of JMTR project has developed the Maintenance Engineering System which evaluates the aging tendency of the facilities. The system is used for the repair plan and the replace period of parts, components, equipments or facilities. The system has the data-base which consists of the check data, the inspection data, the trouble data and the repair data at the JMTR since the virgin criticality. The system is utilized maintenance works and concludes the maintenance procedures for the failure components, equipments and facilities. This system has the following characteristics. (1) Anybody can operate the system as easily as word processor. (2) Data are put into by man-machine-interface. (3) The data sheets are with light color and the recognizable arrangements. (4) The system is cost-efficient using commercial personal computers and applications. The research card and the layouts of the input data sheet had been formatted. Data has been begun to be put into the system and to check its functions. The result demonstrates that the system is available for preventive maintenance at the JMTR. (author)

  20. Synthetic biology approaches to engineering the nitrogen symbiosis in cereals.

    Science.gov (United States)

    Rogers, Christian; Oldroyd, Giles E D

    2014-05-01

    Nitrogen is abundant in the earth's atmosphere but, unlike carbon, cannot be directly assimilated by plants. The limitation this places on plant productivity has been circumvented in contemporary agriculture through the production and application of chemical fertilizers. The chemical reduction of nitrogen for this purpose consumes large amounts of energy and the reactive nitrogen released into the environment as a result of fertilizer application leads to greenhouse gas emissions, as well as widespread eutrophication of aquatic ecosystems. The environmental impacts are intensified by injudicious use of fertilizers in many parts of the world. Simultaneously, limitations in the production and supply of chemical fertilizers in other regions are leading to low agricultural productivity and malnutrition. Nitrogen can be directly fixed from the atmosphere by some bacteria and Archaea, which possess the enzyme nitrogenase. Some plant species, most notably legumes, have evolved close symbiotic associations with nitrogen-fixing bacteria. Engineering cereal crops with the capability to fix their own nitrogen could one day address the problems created by the over- and under-use of nitrogen fertilizers in agriculture. This could be achieved either by expression of a functional nitrogenase enzyme in the cells of the cereal crop or through transferring the capability to form a symbiotic association with nitrogen-fixing bacteria. While potentially transformative, these biotechnological approaches are challenging; however, with recent advances in synthetic biology they are viable long-term goals. This review discusses the possibility of these biotechnological solutions to the nitrogen problem, focusing on engineering the nitrogen symbiosis in cereals.

  1. Bacterial genome engineering and synthetic biology: combating pathogens.

    Science.gov (United States)

    Krishnamurthy, Malathy; Moore, Richard T; Rajamani, Sathish; Panchal, Rekha G

    2016-11-04

    The emergence and prevalence of multidrug resistant (MDR) pathogenic bacteria poses a serious threat to human and animal health globally. Nosocomial infections and common ailments such as pneumonia, wound, urinary tract, and bloodstream infections are becoming more challenging to treat due to the rapid spread of MDR pathogenic bacteria. According to recent reports by the World Health Organization (WHO) and Centers for Disease Control and Prevention (CDC), there is an unprecedented increase in the occurrence of MDR infections worldwide. The rise in these infections has generated an economic strain worldwide, prompting the WHO to endorse a global action plan to improve awareness and understanding of antimicrobial resistance. This health crisis necessitates an immediate action to target the underlying mechanisms of drug resistance in bacteria. The advent of new bacterial genome engineering and synthetic biology (SB) tools is providing promising diagnostic and treatment plans to monitor and treat widespread recalcitrant bacterial infections. Key advances in genetic engineering approaches can successfully aid in targeting and editing pathogenic bacterial genomes for understanding and mitigating drug resistance mechanisms. In this review, we discuss the application of specific genome engineering and SB methods such as recombineering, clustered regularly interspaced short palindromic repeats (CRISPR), and bacterial cell-cell signaling mechanisms for pathogen targeting. The utility of these tools in developing antibacterial strategies such as novel antibiotic production, phage therapy, diagnostics and vaccine production to name a few, are also highlighted. The prevalent use of antibiotics and the spread of MDR bacteria raise the prospect of a post-antibiotic era, which underscores the need for developing novel therapeutics to target MDR pathogens. The development of enabling SB technologies offers promising solutions to deliver safe and effective antibacterial therapies.

  2. Security Research on Engineering Database System

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Engine engineering database system is an oriented C AD applied database management system that has the capability managing distributed data. The paper discusses the security issue of the engine engineering database management system (EDBMS). Through studying and analyzing the database security, to draw a series of securi ty rules, which reach B1, level security standard. Which includes discretionary access control (DAC), mandatory access control (MAC) and audit. The EDBMS implem ents functions of DAC, ...

  3. Security Engineering FY17 Systems Aware Cybersecurity

    Science.gov (United States)

    2017-12-07

    Security Engineering – FY17 Systems Aware Cybersecurity Technical Report SERC-2017-TR-114 December 7 2017 Principal Investigator: Dr...December 7, 2017 Copyright © 2017 Stevens Institute of Technology, Systems Engineering Research Center The Systems Engineering Research Center (SERC...supported, in whole or in part, by the U.S. Department of Defense through the Office of the Assistant Secretary of Defense for Research and Engineering (ASD

  4. Proceedings of the European medical and biological engineering conference EMBEC '99 (Part I)

    International Nuclear Information System (INIS)

    Rehak, P.; Hutten, H.

    1999-01-01

    The proceedings books of the EMBEC '99 - European Medical and Biological Engineering Conference - are published in two parts as supplement 2 to the volume 37 of 'Medical and Biological Engineering and Computing', the official journal of the International Federation for Medical and Biological Engineering. More then 800 papers have been arranged in the order of the main topics and the topics of the special sessions of the conference. The paper of INIS relevance were worked up for INIS data bank. (author)

  5. Proceedings of Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2015

    Energy Technology Data Exchange (ETDEWEB)

    Silver, Pamela [Harvard Univ., Cambridge, MA (United States); SEED 2015 Conference Chair; Flach, Evan [American Institute of Chemical Engineers; SEED 2015 Conference Organizer

    2016-10-27

    Synthetic Biology is an emerging discipline that seeks to accelerate the process of engineering biology. As such, the tools are broadly applicable to application areas, including chemicals and biofuels, materials, medicine and agriculture. A characteristic of the field is to look holistically at cellular design, from sensing and genetic circuitry to the manipulation of cellular processes and actuators, to controlling metabolism, to programming multicellular behaviors. Further, the types of cells that are manipulated are broad, from in vitro systems to microbes and fungi to mammalian and plant cells and living animals. Many of the projects in synthetic biology seek to move biochemical functions across organisms. The field is highly interdisciplinary with faculty and students spread across departments that focus on engineering (biological, chemical, electrical, mechanical, civil, computer science) and basic science (biology and systems biology, chemistry, physics). While there have been many one-off workshops and meeting on synthetic biology, the 2014 Synthetic Biology: Engineering, Evolution and Design (SEED) was the first of an annual conference series that serves as a reliable place to pull together the involved disciplines in order to organize and exchange advances in the science and technology in the field. Further, the SEED conferences have a strong focus on industry, with many companies represented and actively participating. A number of these companies have started major efforts in synthetic biology including large companies (e.g., Pfizer, Novartis, Dow, Dupont, BP, Total), smaller companies have recently gone public (e.g., Amyris, Gevo, Intrexon), and many start-ups (e.g., Teslagen, Refactored Materials, Pivot, Genomatica). There are a number of loosely affiliated Synthetic Biology Centers, including ones at MIT, Boston University, UCSD, UCSF, UC-Berkeley, Imperial College, Oxford, and ETH. SEED 2015 will serve as the primary meeting at which international

  6. Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology.

    Science.gov (United States)

    Schmidt, Markus; de Lorenzo, Víctor

    2012-07-16

    The plausible release of deeply engineered or even entirely synthetic/artificial microorganisms raises the issue of their intentional (e.g. bioremediation) or accidental interaction with the Environment. Containment systems designed in the 1980s-1990s for limiting the spread of genetically engineered bacteria and their recombinant traits are still applicable to contemporary Synthetic Biology constructs. Yet, the ease of DNA synthesis and the uncertainty on how non-natural properties and strains could interplay with the existing biological word poses yet again the challenge of designing safe and efficacious firewalls to curtail possible interactions. Such barriers may include xeno-nucleic acids (XNAs) instead of DNA as information-bearing molecules, rewriting the genetic code to make it non-understandable by the existing gene expression machineries, and/or making growth dependent on xenobiotic chemicals. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  7. Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective.

    Science.gov (United States)

    Tadmor, Brigitta; Tidor, Bruce

    2005-09-01

    Progress in the life sciences, including genome sequencing and high-throughput experimentation, offers an opportunity for understanding biology and medicine from a systems perspective. This 'new view', which complements the more traditional component-based approach, involves the integration of biological research with approaches from engineering disciplines and computer science. The result is more than a new set of technologies. Rather, it promises a fundamental reconceptualization of the life sciences based on the development of quantitative and predictive models to describe crucial processes. To achieve this change, learning communities are being formed at the interface of the life sciences, engineering and computer science. Through these communities, research and education will be integrated across disciplines and the challenges associated with multidisciplinary team-based science will be addressed.

  8. Reverse engineering for quality systems

    International Nuclear Information System (INIS)

    Nolan, A.J.

    1995-01-01

    When the age of software engineering began, many companies were faced with a problem of how to support the older, pre-software-engineering, programs. The techniques of reverse engineering and re-engineering were developed to bridge the gap between the past and the present. Although reverse engineering can be used for generating missing documentation, it can also be used as a means to demonstrate quality in these older programs. This paper presents, in the form of a case study, how Rolls-Royce and Associates Limited addressed the quality issues of reverse engineering and re-engineering. (author)

  9. 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

  10. 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.

  11. Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology.

    Science.gov (United States)

    Liljeruhm, Josefine; Funk, Saskia K; Tietscher, Sandra; Edlund, Anders D; Jamal, Sabri; Wistrand-Yuen, Pikkei; Dyrhage, Karl; Gynnå, Arvid; Ivermark, Katarina; Lövgren, Jessica; Törnblom, Viktor; Virtanen, Anders; Lundin, Erik R; Wistrand-Yuen, Erik; Forster, Anthony C

    2018-01-01

    Coral reefs are colored by eukaryotic chromoproteins (CPs) that are homologous to green fluorescent protein. CPs differ from fluorescent proteins (FPs) by intensely absorbing visible light to give strong colors in ambient light. This endows CPs with certain advantages over FPs, such as instrument-free detection uncomplicated by ultra-violet light damage or background fluorescence, efficient Förster resonance energy transfer (FRET) quenching, and photoacoustic imaging. Thus, CPs have found utility as genetic markers and in teaching, and are attractive for potential cell biosensor applications in the field. Most near-term applications of CPs require expression in a different domain of life: bacteria. However, it is unclear which of the eukaryotic CP genes might be suitable and how best to assay them. Here, taking advantage of codon optimization programs in 12 cases, we engineered 14 CP sequences (meffRed, eforRed, asPink, spisPink, scOrange, fwYellow, amilGFP, amajLime, cjBlue, meffBlue, aeBlue, amilCP, tsPurple and gfasPurple) into a palette of Escherichia coli BioBrick plasmids. BioBricks comply with synthetic biology's most widely used, simplified, cloning standard. Differences in color intensities, maturation times and fitness costs of expression were compared under the same conditions, and visible readout of gene expression was quantitated. A surprisingly large variation in cellular fitness costs was found, resulting in loss of color in some overnight liquid cultures of certain high-copy-plasmid-borne CPs, and cautioning the use of multiple CPs as markers in competition assays. We solved these two problems by integrating pairs of these genes into the chromosome and by engineering versions of the same CP with very different colors. Availability of 14 engineered CP genes compared in E. coli , together with chromosomal mutants suitable for competition assays, should simplify and expand CP study and applications. There was no single plasmid-borne CP that combined

  12. 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.

  13. 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...

  14. Laser engineering of microbial systems

    Science.gov (United States)

    Yusupov, V. I.; Gorlenko, M. V.; Cheptsov, V. S.; Minaev, N. V.; Churbanova, E. S.; Zhigarkov, V. S.; Chutko, E. A.; Evlashin, S. A.; Chichkov, B. N.; Bagratashvili, V. N.

    2018-06-01

    A technology of laser engineering of microbial systems (LEMS) based on the method of laser-induced transfer of heterogeneous mixtures containing microorganisms (laser bioprinting) is described. This technology involves laser printing of soil microparticles by focusing near-infrared laser pulses on a specially prepared gel/soil mixture spread onto a gold-coated glass plate. The optimal range of laser energies from the point of view of the formation of stable jets and droplets with minimal negative impact on living systems of giant accelerations, laser pulse irradiation, and Au nanoparticles was found. Microsamples of soil were printed on glucose-peptone-yeast agar plates to estimate the LEMS process influence on structural and morphological microbial diversity. The obtained results were compared with traditionally treated soil samples. It was shown that LEMS technology allows significantly increasing the biodiversity of printed organisms and is effective for isolating rare or unculturable microorganisms.

  15. 23rd International Conference on Systems Engineering

    CERN Document Server

    Zydek, Dawid; Chmaj, Grzegorz

    2015-01-01

    This collection of proceedings from the International Conference on Systems Engineering, Las Vegas, 2014 is orientated toward systems engineering, including topics like aerospace, power systems, industrial automation and robotics, systems theory, control theory, artificial intelligence, signal processing, decision support, pattern recognition and machine learning, information and communication technologies, image processing, and computer vision as well as its applications. The volume’s main focus is on models, algorithms, and software tools that facilitate efficient and convenient utilization of modern achievements in systems engineering.

  16. 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.

  17. Screening candidate systems engineers: exploratory results

    CSIR Research Space (South Africa)

    Gonçalves, D

    2010-09-01

    Full Text Available systems engineers for further development. Data were collected on personality, cognition, values and competence on 21 SE competencies using four computerised assessments. We report on the cognitive style distribution of the participating engineers...

  18. Micromechanics of engineered and biological systems

    Indian Academy of Sciences (India)

    these are available today in microsystems design software but ... Traditionally, silicon micromachining methods have been used ..... current and thermal conduction are both diffu- ...... Micromanipulation for mechanical characterization of cells.

  19. 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.

  20. Integrated engineering system for nuclear facilities building

    International Nuclear Information System (INIS)

    Tomura, H.; Miyamoto, A.; Futami, F.; Yasuda, S.; Ohtomo, T.

    1995-01-01

    In the construction of buildings for nuclear facilities in Japan, construction companies are generally in charge of the building engineering work, coordinating with plant engineering. An integrated system for buildings (PROMOTE: PROductive MOdeling system for Total nuclear Engineering) described here is a building engineering system including the entire life cycle of buildings for nuclear facilities. A Three-dimensional (3D) building model (PRO-model) is to be in the core of the system (PROMOTE). Data sharing in the PROMOTE is also done with plant engineering systems. By providing these basic technical foundations, PROMOTE is oriented toward offering rational, highquality engineering for the projects. The aim of the system is to provide a technical foundation in building engineering. This paper discusses the characteristics of buildings for nuclear facilities and the outline of the PROMOTE. (author)

  1. Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology.

    Science.gov (United States)

    Koutinas, Michalis; Kiparissides, Alexandros; Pistikopoulos, Efstratios N; Mantalaris, Athanasios

    2012-01-01

    The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control and optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals.

  2. 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.

  3. Advances in communication systems and electrical engineering

    CERN Document Server

    Huang, Xu

    2008-01-01

    This volume contains contributions from participants in the 2007 International Multiconference of Engineers and Computer Scientists Topics covered include communications theory, communications protocols, network management, wireless networks, telecommunication, electronics, power engineering, control engineering, signal processing, and industrial applications. The book will offer the states of arts of tremendous advances in communication systems and electrical engineering and also serve as an excellent reference work for researchers and graduate students working with/on communication systems a

  4. Research and engineering assessment of biological solubilization of phosphate

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, R.D.; McIlwain, M.E.; Losinski, S.J.; Taylor, D.D.

    1993-03-01

    This research and engineering assessment examined a microbial phosphate solubilization process as a method of recovering phosphate from phosphorus containing ore compared to the existing wet acid and electric arc methods. A total of 860 microbial isolates, collected from a range of natural environments were tested for their ability to solubilize phosphate from rock phosphate. A bacterium (Pseudomonas cepacia) was selected for extensive characterization and evaluation of the mechanism of phosphate solubilization and of process engineering parameters necessary to recover phosphate from rock phosphate. These studies found that concentration of hydrogen ion and production of organic acids arising from oxidation of the carbon source facilitated microbial solubilization of both pure chemical insoluble phosphate compounds and phosphate rock. Genetic studies found that phosphate solubilization was linked to an enzyme system (glucose dehydrogenase). Process-related studies found that a critical solids density of 1% by weight (ore to liquid) was necessary for optimal solubilization. An engineering analysis evaluated the cost and energy requirements for a 2 million ton per year sized plant, whose size was selected to be comparable to existing wet acid plants.

  5. Integrating system safety into the basic systems engineering process

    Science.gov (United States)

    Griswold, J. W.

    1971-01-01

    The basic elements of a systems engineering process are given along with a detailed description of what the safety system requires from the systems engineering process. Also discussed is the safety that the system provides to other subfunctions of systems engineering.

  6. 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.

  7. Rabi model as a quantum coherent heat engine: From quantum biology to superconducting circuits

    Science.gov (United States)

    Altintas, Ferdi; Hardal, Ali Ü. C.; Müstecaplıoǧlu, Özgür E.

    2015-02-01

    We propose a multilevel quantum heat engine with a working medium described by a generalized Rabi model which consists of a two-level system coupled to a single-mode bosonic field. The model is constructed to be a continuum limit of a quantum biological description of light-harvesting complexes so that it can amplify quantum coherence by a mechanism which is a quantum analog of classical Huygens clocks. The engine operates in a quantum Otto cycle where the working medium is coupled to classical heat baths in the isochoric processes of the four-stroke cycle, while either the coupling strength or the resonance frequency is changed in the adiabatic stages. We found that such an engine can produce work with an efficiency close to the Carnot bound when it operates at low temperatures and in the ultrastrong-coupling regime. The interplay of the effects of quantum coherence and quantum correlations on the engine performance is discussed in terms of second-order coherence, quantum mutual information, and the logarithmic negativity of entanglement. We point out that the proposed quantum Otto engine can be implemented experimentally with modern circuit quantum electrodynamic systems where flux qubits can be coupled ultrastrongly to superconducting transmission-line resonators.

  8. Diesel engine management systems and components

    CERN Document Server

    2014-01-01

    This reference book provides a comprehensive insight into todays diesel injection systems and electronic control. It focusses on minimizing emissions and exhaust-gas treatment. Innovations by Bosch in the field of diesel-injection technology have made a significant contribution to the diesel boom. Calls for lower fuel consumption, reduced exhaust-gas emissions and quiet engines are making greater demands on the engine and fuel-injection systems. Contents History of the diesel engine.- Areas of use for diesel engines.- Basic principles of the diesel engine.- Fuels: Diesel fuel.- Fuels: Alternative fuels.- Cylinder-charge control systems.- Basic principles of diesel fuel-injection.- Overview of diesel fuel-injection systems.- Fuel supply to the low pressure stage.- Overview of discrete cylinder systems.- Unit injector system.- Unit pump system.- Overview of common-rail systems.- High pressure components of the common-rail system.- Injection nozzles.- Nozzle holders.- High pressure lines.- Start assist systems.-...

  9. Multidisciplinary systems engineering architecting the design process

    CERN Document Server

    Crowder, James A; Demijohn, Russell

    2016-01-01

    This book presents Systems Engineering from a modern, multidisciplinary engineering approach, providing the understanding that all aspects of systems design, systems, software, test, security, maintenance and the full life-cycle must be factored in to any large-scale system design; up front, not factored in later. It lays out a step-by-step approach to systems-of-systems architectural design, describing in detail the documentation flow throughout the systems engineering design process. It provides a straightforward look and the entire systems engineering process, providing realistic case studies, examples, and design problems that will enable students to gain a firm grasp on the fundamentals of modern systems engineering.  Included is a comprehensive design problem that weaves throughout the entire text book, concluding with a complete top-level systems architecture for a real-world design problem.

  10. Engineering the mechanical and biological properties of nanofibrous vascular grafts for in situ vascular tissue engineering.

    Science.gov (United States)

    Henry, Jeffrey J D; Yu, Jian; Wang, Aijun; Lee, Randall; Fang, Jun; Li, Song

    2017-08-17

    Synthetic small diameter vascular grafts have a high failure rate, and endothelialization is critical for preventing thrombosis and graft occlusion. A promising approach is in situ tissue engineering, whereby an acellular scaffold is implanted and provides stimulatory cues to guide the in situ remodeling into a functional blood vessel. An ideal scaffold should have sufficient binding sites for biomolecule immobilization and a mechanical property similar to native tissue. Here we developed a novel method to blend low molecular weight (LMW) elastic polymer during electrospinning process to increase conjugation sites and to improve the mechanical property of vascular grafts. LMW elastic polymer improved the elasticity of the scaffolds, and significantly increased the amount of heparin conjugated to the micro/nanofibrous scaffolds, which in turn increased the loading capacity of vascular endothelial growth factor (VEGF) and prolonged the release of VEGF. Vascular grafts were implanted into the carotid artery of rats to evaluate the in vivo performance. VEGF treatment significantly enhanced endothelium formation and the overall patency of vascular grafts. Heparin coating also increased cell infiltration into the electrospun grafts, thus increasing the production of collagen and elastin within the graft wall. This work demonstrates that LMW elastic polymer blending is an approach to engineer the mechanical and biological property of micro/nanofibrous vascular grafts for in situ vascular tissue engineering.

  11. Eighth International Conference on Intelligent Systems and Knowledge Engineering

    CERN Document Server

    Li, Tianrui; ISKE 2013; Foundations of Intelligent Systems; Knowledge Engineering and Management; Practical Applications of Intelligent Systems

    2014-01-01

    "Foundations of Intelligent Systems" presents selected papers from the 2013 International Conference on Intelligent Systems and Knowledge Engineering (ISKE2013). The aim of this conference is to bring together experts from different expertise areas to discuss the state-of-the-art in Intelligent Systems and Knowledge Engineering, and to present new research results and perspectives on future development. The topics in this volume include, but not limited to: Artificial Intelligence Theories, Pattern Recognition, Intelligent System Models, Speech Recognition, Computer Vision, Multi-Agent Systems, Machine Learning, Soft Computing and Fuzzy Systems, Biological Inspired Computation, Game Theory, Cognitive Systems and Information Processing, Computational Intelligence, etc. The proceedings are benefit for both researchers and practitioners who want to utilize intelligent methods in their specific research fields. Dr. Zhenkun Wen is a Professor at the College of Computer and Software Engineering, Shenzhen University...

  12. Biological variability in biomechanical engineering research: Significance and meta-analysis of current modeling practices.

    Science.gov (United States)

    Cook, Douglas; Julias, Margaret; Nauman, Eric

    2014-04-11

    Biological systems are characterized by high levels of variability, which can affect the results of biomechanical analyses. As a review of this topic, we first surveyed levels of variation in materials relevant to biomechanics, and compared these values to standard engineered materials. As expected, we found significantly higher levels of variation in biological materials. A meta-analysis was then performed based on thorough reviews of 60 research studies from the field of biomechanics to assess the methods and manner in which biological variation is currently handled in our field. The results of our meta-analysis revealed interesting trends in modeling practices, and suggest a need for more biomechanical studies that fully incorporate biological variation in biomechanical models and analyses. Finally, we provide some case study example of how biological variability may provide valuable insights or lead to surprising results. The purpose of this study is to promote the advancement of biomechanics research by encouraging broader treatment of biological variability in biomechanical modeling. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Predicting biological system objectives de novo from internal state measurements

    Directory of Open Access Journals (Sweden)

    Maranas Costas D

    2008-01-01

    Full Text Available Abstract Background Optimization theory has been applied to complex biological systems to interrogate network properties and develop and refine metabolic engineering strategies. For example, methods are emerging to engineer cells to optimally produce byproducts of commercial value, such as bioethanol, as well as molecular compounds for disease therapy. Flux balance analysis (FBA is an optimization framework that aids in this interrogation by generating predictions of optimal flux distributions in cellular networks. Critical features of FBA are the definition of a biologically relevant objective function (e.g., maximizing the rate of synthesis of biomass, a unit of measurement of cellular growth and the subsequent application of linear programming (LP to identify fluxes through a reaction network. Despite the success of FBA, a central remaining challenge is the definition of a network objective with biological meaning. Results We present a novel method called Biological Objective Solution Search (BOSS for the inference of an objective function of a biological system from its underlying network stoichiometry as well as experimentally-measured state variables. Specifically, BOSS identifies a system objective by defining a putative stoichiometric "objective reaction," adding this reaction to the existing set of stoichiometric constraints arising from known interactions within a network, and maximizing the putative objective reaction via LP, all the while minimizing the difference between the resultant in silico flux distribution and available experimental (e.g., isotopomer flux data. This new approach allows for discovery of objectives with previously unknown stoichiometry, thus extending the biological relevance from earlier methods. We verify our approach on the well-characterized central metabolic network of Saccharomyces cerevisiae. Conclusion We illustrate how BOSS offers insight into the functional organization of biochemical networks

  14. Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Gregurick, S.; Fredrickson, J. K.; Stevens, R.

    2009-03-01

    Biology has entered a systems-science era with the goal to establish a predictive understanding of the mechanisms of cellular function and the interactions of biological systems with their environment and with each other. Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies. Effectively exploiting these data requires developing a new generation of capabilities for analyzing and managing the information. By revealing the core principles and processes conserved in collective genomes across all biology and by enabling insights into the interplay between an organism's genotype and its environment, systems biology will allow scientific breakthroughs in our ability to project behaviors of natural systems and to manipulate and engineer managed systems. These breakthroughs will benefit Department of Energy (DOE) missions in energy security, climate protection, and environmental remediation.

  15. Environmental Restoration Project - Systems Engineering Management Plan

    International Nuclear Information System (INIS)

    Anderson, T.D.

    1998-06-01

    This Environmental Restoration (ER) Project Systems Engineering Management Plan (SEMP) describes relevant Environmental Restoration Contractor (ERC) management processes and shows how they implement systems engineering. The objective of this SEMP is to explain and demonstrate how systems engineering is being approached and implemented in the ER Project. The application of systems engineering appropriate to the general nature and scope of the project is summarized in Section 2.0. The basic ER Project management approach is described in Section 3.0. The interrelation and integration of project practices and systems engineering are outlined in Section 4.0. Integration with sitewide systems engineering under the Project Hanford Management Contract is described in Section 5.0

  16. Verification and Validation in Systems Engineering

    CERN Document Server

    Debbabi, Mourad; Jarraya, Yosr; Soeanu, Andrei; Alawneh, Luay

    2010-01-01

    "Verification and validation" represents an important process used for the quality assessment of engineered systems and their compliance with the requirements established at the beginning of or during the development cycle. Debbabi and his coauthors investigate methodologies and techniques that can be employed for the automatic verification and validation of systems engineering design models expressed in standardized modeling languages. Their presentation includes a bird's eye view of the most prominent modeling languages for software and systems engineering, namely the Unified Model

  17. A road map for implementing systems engineering

    Energy Technology Data Exchange (ETDEWEB)

    Dean, F.F. [Sandia National Labs., Albuquerque, NM (United States). New Mexico Weapons Systems Engineering Center; Bentz, B.; Bahill, A.T. [Univ. of Arizona, Tucson, AZ (United States)

    1997-02-01

    Studies by academia, industry, and government indicate that applying a sound systems engineering process to development programs is an important tool for preventing cost and schedule overruns and performance deficiencies. There is an enormous body of systems engineering knowledge. Where does one start? How can the principles of systems engineering be applied in the Sandia environment? This road map is intended to be an aid to answering these questions.

  18. Content Analysis in Systems Engineering Acquisition Activities

    Science.gov (United States)

    2016-04-30

    Acquisition Activities Karen Holness, Assistant Professor, NPS Update on the Department of the Navy Systems Engineering Career Competency Model Clifford...systems engineering toolkit . Having a common analysis tool that is easy to use would support the feedback of observed system performance trends from the

  19. Systems Biology for Mapping Genotype-Phenotype Relations in Yeast

    KAUST Repository

    Nielsen, Jens

    2016-01-25

    The yeast Saccharomyces cerevisiae is widely used for production of fuels, chemicals, pharmaceuticals and materials. Through metabolic engineering of this yeast a number of novel new industrial processes have been developed over the last 10 years. Besides its wide industrial use, S. cerevisiae serves as an eukaryal model organism, and many systems biology tools have therefore been developed for this organism. Among these genome-scale metabolic models have shown to be most successful as they easy integrate with omics data and at the same time have been shown to have excellent predictive power. Despite our extensive knowledge of yeast metabolism and its regulation we are still facing challenges when we want to engineer complex traits, such as improved tolerance to toxic metabolites like butanol and elevated temperatures or when we want to engineer the highly complex protein secretory pathway. In this presentation it will be demonstrated how we can combine directed evolution with systems biology analysis to identify novel targets for rational design-build-test of yeast strains that have improved phenotypic properties. In this lecture an overview of systems biology of yeast will be presented together with examples of how genome-scale metabolic modeling can be used for prediction of cellular growth at different conditions. Examples will also be given on how adaptive laboratory evolution can be used for identifying targets for improving tolerance towards butanol, increased temperature and low pH and for improving secretion of heterologous proteins.

  20. Tank waste remediation system engineering plan

    International Nuclear Information System (INIS)

    Rifaey, S.H.

    1998-01-01

    This Engineering Plan describes the engineering process and controls that will be in place to support the Technical Baseline definition and manage its evolution and implementation to the field operations. This plan provides the vision for the engineering required to support the retrieval and disposal mission through Phase 1 and 2, which includes integrated data management of the Technical Baseline. Further, this plan describes the approach for moving from the ''as is'' condition of engineering practice, systems, and facilities to the desired ''to be'' configuration. To make this transition, Tank Waste Remediation System (TWRS) Engineering will become a center of excellence for TWRS which,will perform engineering in the most effective manner to meet the mission. TWRS engineering will process deviations from sitewide systems if necessary to meet the mission most effectively

  1. 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...

  2. CAESY - COMPUTER AIDED ENGINEERING SYSTEM

    Science.gov (United States)

    Wette, M. R.

    1994-01-01

    Many developers of software and algorithms for control system design have recognized that current tools have limits in both flexibility and efficiency. Many forces drive the development of new tools including the desire to make complex system modeling design and analysis easier and the need for quicker turnaround time in analysis and design. Other considerations include the desire to make use of advanced computer architectures to help in control system design, adopt new methodologies in control, and integrate design processes (e.g., structure, control, optics). CAESY was developed to provide a means to evaluate methods for dealing with user needs in computer-aided control system design. It is an interpreter for performing engineering calculations and incorporates features of both Ada and MATLAB. It is designed to be reasonably flexible and powerful. CAESY includes internally defined functions and procedures, as well as user defined ones. Support for matrix calculations is provided in the same manner as MATLAB. However, the development of CAESY is a research project, and while it provides some features which are not found in commercially sold tools, it does not exhibit the robustness that many commercially developed tools provide. CAESY is written in C-language for use on Sun4 series computers running SunOS 4.1.1 and later. The program is designed to optionally use the LAPACK math library. The LAPACK math routines are available through anonymous ftp from research.att.com. CAESY requires 4Mb of RAM for execution. The standard distribution medium is a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format. CAESY was developed in 1993 and is a copyrighted work with all copyright vested in NASA.

  3. Gasoline engine management systems and components

    CERN Document Server

    2015-01-01

    The call for environmentally compatible and economical vehicles necessitates immense efforts to develop innovative engine concepts. Technical concepts such as gasoline direct injection helped to save fuel up to 20 % and reduce CO2-emissions. Descriptions of the cylinder-charge control, fuel injection, ignition and catalytic emission-control systems provides comprehensive overview of today´s gasoline engines. This book also describes emission-control systems and explains the diagnostic systems. The publication provides information on engine-management-systems and emission-control regulations. Contents History of the automobile.- Basics of the gasoline engine.- Fuels.- Cylinder-charge control systems.- Gasoline injection systems over the years.- Fuel supply.- Manifold fuel injection.- Gasoline direct injection.- Operation of gasoline engines on natural gas.- Ignition systems over the years.- Inductive ignition systems.- Ignition coils.- Spark plugs.- Electronic control.- Sensors.- Electronic control unit.- Exh...

  4. Model-Based Systems Engineering in Concurrent Engineering Centers

    Science.gov (United States)

    Iwata, Curtis; Infeld, Samantha; Bracken, Jennifer Medlin; McGuire, Melissa; McQuirk, Christina; Kisdi, Aron; Murphy, Jonathan; Cole, Bjorn; Zarifian, Pezhman

    2015-01-01

    Concurrent Engineering Centers (CECs) are specialized facilities with a goal of generating and maturing engineering designs by enabling rapid design iterations. This is accomplished by co-locating a team of experts (either physically or virtually) in a room with a narrow design goal and a limited timeline of a week or less. The systems engineer uses a model of the system to capture the relevant interfaces and manage the overall architecture. A single model that integrates other design information and modeling allows the entire team to visualize the concurrent activity and identify conflicts more efficiently, potentially resulting in a systems model that will continue to be used throughout the project lifecycle. Performing systems engineering using such a system model is the definition of model-based systems engineering (MBSE); therefore, CECs evolving their approach to incorporate advances in MBSE are more successful in reducing time and cost needed to meet study goals. This paper surveys space mission CECs that are in the middle of this evolution, and the authors share their experiences in order to promote discussion within the community.

  5. Advances in polymeric systems for tissue engineering and biomedical applications.

    Science.gov (United States)

    Ravichandran, Rajeswari; Sundarrajan, Subramanian; Venugopal, Jayarama Reddy; Mukherjee, Shayanti; Ramakrishna, Seeram

    2012-03-01

    The characteristics of tissue engineered scaffolds are major concerns in the quest to fabricate ideal scaffolds for tissue engineering applications. The polymer scaffolds employed for tissue engineering applications should possess multifunctional properties such as biocompatibility, biodegradability and favorable mechanical properties as it comes in direct contact with the body fluids in vivo. Additionally, the polymer system should also possess biomimetic architecture and should support stem cell adhesion, proliferation and differentiation. As the progress in polymer technology continues, polymeric biomaterials have taken characteristics more closely related to that desired for tissue engineering and clinical needs. Stimuli responsive polymers also termed as smart biomaterials respond to stimuli such as pH, temperature, enzyme, antigen, glucose and electrical stimuli that are inherently present in living systems. This review highlights the exciting advancements in these polymeric systems that relate to biological and tissue engineering applications. Additionally, several aspects of technology namely scaffold fabrication methods and surface modifications to confer biological functionality to the polymers have also been discussed. The ultimate objective is to emphasize on these underutilized adaptive behaviors of the polymers so that novel applications and new generations of smart polymeric materials can be realized for biomedical and tissue engineering applications. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Advancing Systems Engineering Excellence: The Marshall Systems Engineering Leadership Development Program

    Science.gov (United States)

    Hall, Philip; Whitfield, Susan

    2011-01-01

    As NASA undertakes increasingly complex projects, the need for expert systems engineers and leaders in systems engineering is becoming more pronounced. As a result of this issue, the Agency has undertaken an initiative to develop more systems engineering leaders through its Systems Engineering Leadership Development Program; however, the NASA Office of the Chief Engineer has also called on the field Centers to develop mechanisms to strengthen their expertise in systems engineering locally. In response to this call, Marshall Space Flight Center (MSFC) has developed a comprehensive development program for aspiring systems engineers and systems engineering leaders. This presentation will summarize the two-level program, which consists of a combination of training courses and on-the-job, developmental training assignments at the Center to help develop stronger expertise in systems engineering and technical leadership. In addition, it will focus on the success the program has had in its pilot year. The program hosted a formal kickoff event for Level I on October 13, 2009. The first class includes 42 participants from across MSFC and Michoud Assembly Facility (MAF). A formal call for Level II is forthcoming. With the new Agency focus on research and development of new technologies, having a strong pool of well-trained systems engineers is becoming increasingly more critical. Programs such as the Marshall Systems Engineering Leadership Development Program, as well as those developed at other Centers, help ensure that there is an upcoming generation of trained systems engineers and systems engineering leaders to meet future design challenges.

  7. 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.

  8. A demonstration of expert systems applications in transportation engineering : volume I, transportation engineers and expert systems.

    Science.gov (United States)

    1987-01-01

    Expert systems, a branch of artificial-intelligence studies, is introduced with a view to its relevance in transportation engineering. Knowledge engineering, the process of building expert systems or transferring knowledge from human experts to compu...

  9. Systems Engineering Analysis for Office Space Management

    Science.gov (United States)

    2017-09-01

    ENGINEERING ANALYSIS FOR OFFICE SPACE MANAGEMENT by James E. Abellana September 2017 Thesis Advisor: Diana Angelis Second Reader: Walter E. Owen...Master’s thesis 4. TITLE AND SUBTITLE SYSTEMS ENGINEERING ANALYSIS FOR OFFICE SPACE MANAGEMENT 5. FUNDING NUMBERS 6. AUTHOR(S) James E. Abellana 7...of the systems engineering method, this thesis develops a multicriteria decision-making framework applicable to space allocation decisions for

  10. Vehicle Systems Engineering and Integration Activities

    Science.gov (United States)

    2012-08-31

    liter turbo diesel Bolt on armor required upgraded suspension, engine, and steering Mattracks or wheels Imbalance in cupola required motorized...liter turbo diesel engine, a new transmission, improved suspension and frame for an increased armor capability, 1,800- 4,400 lb payload and GVW 18,000...space (14 cubic feet), enhanced 6500 turbo diesel engine, higher capacity transmission, air induction system and exhaust systems. Lessons

  11. 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...

  12. When one model is not enough: Combining epistemic tools in systems biology

    DEFF Research Database (Denmark)

    Green, Sara

    2013-01-01

    . The conceptual repertoire of Rheinberger’s historical epistemology offers important insights for an analysis of the modelling practice. I illustrate this with a case study on network modeling in systems biology where engineering approaches are applied to the study of biological systems. I shall argue...

  13. Principles of Sociology in Systems Engineering

    Science.gov (United States)

    Watson, Michael D.; Andrews, James G.; Larsen, Jordan A.

    2017-01-01

    Systems engineering involves both the integration of the system and the integration of the disciplines which develop and operate the system. Integrating the disciplines is a sociological effort to bring together different groups, often with different terminology, to achieve a common goal, the system. The focus for the systems engineer is information flow through the organization, between the disciplines, to ensure the system is developed and operated with all relevant information informing system decisions. Robert K. Merton studied the sociological principles of the sciences and the sociological principles he developed apply to systems engineering. Concepts such as specification of ignorance, common terminology, opportunity structures, role-sets, and the reclama (reconsideration) process are all important sociological approaches that should be employed by the systems engineer. In bringing the disciplines together, the systems engineer must also be wary of social ambivalence, social anomie, social dysfunction, insider-outsider behavior, unintended consequences, and the self-fulfilling prophecy. These sociological principles provide the systems engineer with key approaches to manage the information flow through the organization as the disciplines are integrated and share their information. This also helps identify key sociological barriers to information flow through the organization. This paper will discuss this theoretical basis for the application of sociological principles to systems engineering.

  14. 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...

  15. Applying Systems Engineering on Energy Challenges

    NARCIS (Netherlands)

    Safi, J.; Muller, G.; Bonnema, Gerrit Maarten

    2012-01-01

    Systems engineering is a discipline with methods and techniques to address complex problems. We want to study how Systems Engineering methods can help to address today's grand challenges, such as the energy problem. The first step is problem definition which aims at articulating the problem in its

  16. 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

  17. 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...

  18. Holarchical Systems and Emotional Holons : Biologically-Inspired System Designs for Control of Autonomous Aerial Vehicles

    Science.gov (United States)

    Ippolito, Corey; Plice, Laura; Pisanich, Greg

    2003-01-01

    The BEES (Bio-inspired Engineering for Exploration Systems) for Mars project at NASA Ames Research Center has the goal of developing bio-inspired flight control strategies to enable aerial explorers for Mars scientific investigations. This paper presents a summary of our ongoing research into biologically inspired system designs for control of unmanned autonomous aerial vehicle communities for Mars exploration. First, we present cooperative design considerations for robotic explorers based on the holarchical nature of biological systems and communities. Second, an outline of an architecture for cognitive decision making and control of individual robotic explorers is presented, modeled after the emotional nervous system of cognitive biological systems. Keywords: Holarchy, Biologically Inspired, Emotional UAV Flight Control

  19. Systems Engineering of Electric and Hybrid Vehicles

    Science.gov (United States)

    Kurtz, D. W.; Levin, R. R.

    1986-01-01

    Technical paper notes systems engineering principles applied to development of electric and hybrid vehicles such that system performance requirements support overall program goal of reduced petroleum consumption. Paper discusses iterative design approach dictated by systems analyses. In addition to obvious peformance parameters of range, acceleration rate, and energy consumption, systems engineering also considers such major factors as cost, safety, reliability, comfort, necessary supporting infrastructure, and availability of materials.

  20. Designing a 'neotissue' using the principles of biology, chemistry and engineering.

    Science.gov (United States)

    Nannaparaju, Madhusudhan; Oragui, Emeka; Khan, Wasim S

    2012-01-01

    The traditional methods of treating musculoskeletal injuries and disorders are not completely effective and have several limitations. Tissue engineering involves using the principles of biology, chemistry and engineering to design a 'neotissue' that augments a malfunctioning in vivo tissue. The main requirements for functional engineered tissue include reparative cellular components that proliferate on a scaffold grown within a bioreactor that provides specific biochemical and physical signals to regulate cell differentiation and tissue assembly. In this review we provide an overview of the biology of common musculoskeletal tissue and discuss their common pathologies. We also describe the commonly used stem cells, scaffolds and bioreactors and evaluate their role in issue engineering.

  1. 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.

  2. Practical Application of Sociology in Systems Engineering

    Science.gov (United States)

    Watson, Michael D.; Andrews, James G.; Eckley, Jeri Cassel; Culver, Michael L.

    2017-01-01

    Systems engineering involves both the integration of the system and the integration of the disciplines which develop and operate the system. Integrating the disciplines is a sociological effort to bring together different groups, who often have different terminology, to achieve a common goal, the system. The focus for the systems engineer is information flow through the organization, between the disciplines, to ensure the system is developed and operated will all relevant information informing system decisions. The practical application of the sociology in systems engineering brings in various organizational development concepts including the principles of planned renegotiation and the application of principles to address information barriers created by organizational culture. Concepts such as specification of ignorance, consistent terminology, opportunity structures, role-sets, and the reclama (reconsideration) process are all important sociological approaches that help address the organizational social structure (culture). In bringing the disciplines together, the systems engineer must also be wary of social ambivalence, social anomie, social dysfunction, and insider-outsider behavior. Unintended consequences can result when these social issues are present. These issues can occur when localized subcultures shift from the overarching organizational culture, or when the organizational culture prevents achievement of system goals. These sociological principles provide the systems engineer with key approaches to manage the information flow through the organization as the disciplines are integrated and share their information and provides key sociological barriers to information flow through the organization. This paper will discuss the practical application of sociological principles to systems engineering.

  3. The characteristics of mechanical engineering systems

    CERN Document Server

    Holmes, R

    1977-01-01

    The Characteristics of Mechanical Engineering Systems focuses on the characteristics that must be considered when designing a mechanical engineering system. Mechanical systems are presented on the basis of component input-output relationships, paying particular attention to lumped-parameter problems and the interrelationships between lumped components or """"black-boxes"""" in an engineering system. Electric motors and generators are treated in an elementary manner, and the principles involved are explained as far as possible from physical and qualitative reasoning. This book is comprised of

  4. Visualizing systems engineering data with Java

    International Nuclear Information System (INIS)

    Barter, R; Vinzant, A.

    1998-01-01

    Systems Engineers are required to deal with complex sets of data. To be useful, the data must be managed effectively, and presented in meaningful terms to a wide variety of information consumers. Two software patterns are presented as the basis for exploring the visualization of systems engineering data. The Model, View, Controller pattern defines an information management system architecture. The Entity, Relation, Attribute pattern defines the information model. MVC Views then form the basis for the user interface between the information consumer and the MVC Controller/Model combination. A Java tool set is described for exploring alternative views into the underlying complex data structures encountered in systems engineering

  5. Rethinking the Systems Engineering Process in Light of Design Thinking

    Science.gov (United States)

    2016-04-30

    systems engineering process models (Blanchard & Fabrycky, 1990) and the majority of engineering design education (Dym et al., 2005). The waterfall model ...Engineering Career Competency Model Clifford Whitcomb, Systems Engineering Professor, NPS Corina White, Systems Engineering Research Associate, NPS...Postgraduate School (NPS) in Monterey, CA. He teaches and conducts research in the design of enterprise systems, systems modeling , and system

  6. System for measuring engine exhaust constituents

    International Nuclear Information System (INIS)

    Carduner, K.R.; Colvin, A.D.; Leong, D.Y.W.

    1992-01-01

    This patent describes a system for measuring an automotive engine exhaust constituent. It comprises: a meter for determining the mass of air flowing through the engine and for generating an engine airflow signal corresponding to the airflow; sample handling apparatus; diluent adding means; processor means. This patent also describes a method for using an analyzer to determine the amount of lubricating oil consumed by an automotive engine. It comprises: determining the amount of sulfur dioxide within the room air being drawn into the engine; maintaining a constant total flow comprised of a constant fraction of the engine's exhaust gas and a diluent gas through the analyzer, while: determining the amount of sulfur dioxide contained within the engine's exhaust, determining the amount of sulfur dioxide contained within the engine's exhaust, while operating the engine on room air; determining an efficiency factor for the analyzer; and using the efficiency factor and the concentration of sulfur in the engine oil and the amounts of sulfur dioxide determined in steps a and d to determine the amount of lubrication oil leaving the engine through its exhaust

  7. 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.

  8. Software And Systems Engineering Risk Management

    Science.gov (United States)

    2010-04-01

    RSKM 2004 COSO Enterprise RSKM Framework 2006 ISO/IEC 16085 Risk Management Process 2008 ISO/IEC 12207 Software Lifecycle Processes 2009 ISO/IEC...1 Software And Systems Engineering Risk Management John Walz VP Technical and Conferences Activities, IEEE Computer Society Vice-Chair Planning...Software & Systems Engineering Standards Committee, IEEE Computer Society US TAG to ISO TMB Risk Management Working Group Systems and Software

  9. Systems engineering: A formal approach. Part 1: System concepts

    Science.gov (United States)

    Vanhee, K. M.

    1993-03-01

    Engineering is the scientific discipline focused on the creation of new artifacts that are supposed to be of some use to our society. Different types of artifacts require different engineering approaches. However, in all these disciplines the development of a new artifact is divided into stages. Three stages can always be recognized: Analysis, Design, and Realization. The book considers only the first two stages of the development process. It focuses on a specific type of artifacts, called discrete dynamic systems. These systems consist of active components of actors that consume and produce passive components or tokens. Three subtypes are studied in more detail: business systems (like a factory or restaurant), information systems (whether automated or not), and automated systems (systems that are controlled by an automated information system). The first subtype is studied by industrial engineers, the last by software engineers and electrical engineers, whereas the second is a battlefield for all three disciplines. The union of these disciplines is called systems engineering.

  10. Introducing Molecular Biology to Environmental Engineers through Development of a New Course.

    Science.gov (United States)

    Oerther, Daniel B.

    2002-01-01

    Introduces a molecular biology course designed for environmental engineering majors using 16S ribosomal ribonucleic acid-targeted technology that allows students to identify and study microorganisms in bioreactor environments. (Contains 17 references.) (YDS)

  11. Contemporary issues in systems science and engineering

    CERN Document Server

    Zhou, M; Weijnen, M

    2015-01-01

    This volume provides a comprehensive overview of all important areas in systems science and engineering and poses the issues and challenges in these areas in order to deal with ever-increasingly complex systems and newly emergent applications. The topics range from discrete event systems, distributed intelligent systems, grey systems, and enterprise information systems to conflict resolution, robotics and intelligent sensing, smart grids, and system of systems approaches. Individual chapters are written by leading experts in the field.

  12. 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.

  13. Process Systems Engineering Education: Learning by Research

    Science.gov (United States)

    Abbas, A.; Alhammadi, H. Y.; Romagnoli, J. A.

    2009-01-01

    In this paper, we discuss our approach in teaching the final-year course Process Systems Engineering. Students are given ownership of the course by transferring to them the responsibility of learning. A project-based group environment stimulates learning while solving a real engineering problem. We discuss postgraduate student involvement and how…

  14. Pragmatic electrical engineering systems and instruments

    CERN Document Server

    Eccles, William

    2011-01-01

    Pragmatic Electrical Engineering: Systems and Instruments is about some of the non-energy parts of electrical systems, the parts that control things and measure physical parameters. The primary topics are control systems and their characterization, instrumentation, signals, and electromagnetic compatibility. This text features a large number of completely worked examples to aid the reader in understanding how the various principles fit together.While electric engineers may find this material useful as a review, engineers in other fields can use this short lecture text as a modest introduction

  15. Nuclear engine system simulation (NESS) program update

    International Nuclear Information System (INIS)

    Scheil, C.M.; Pelaccio, D.G.; Petrosky, L.J.

    1993-01-01

    The second phase of development of a Nuclear Thermal Propulsion (NTP) engine system design analysis code has been completed. The standalone, versatile Nuclear Engine System Simulation (NESS) code provides an accurate, detailed assessment of engine system operating performance, weight, and sizes. The critical information is required to support ongoing and future engine system and stage design study efforts. This recent development effort included incorporation of an updated solid-core nuclear thermal reactor model that yields a reduced core weight and higher fuel power density when compared to a NERVA type reactor. NESS can now analyze expander, gas generator, and bleed cycles, along with multi-redundant propellant pump feed systems. Performance and weight of efficient multi-stage axial turbopump can now be determined, in addition to the traditional centrifugal pump

  16. Engineering Design of an Adaptive Leg Prosthesis Using Biological Principles

    DEFF Research Database (Denmark)

    Lenau, Torben Anker; Dentel, Andy; Invarsdottir, Thorunn

    2010-01-01

    The biomimetic design process is explored through a design case: An adaptive leg prosthesis. The aim is to investigate if the biomimetic design process can be carried out with a minimum of biological knowledge and without using advanced design methods. In the design case biomimetic design was suc...... was successfully carried out using library search resulting in 14 biological analogies for the design problem 'shape adaption'. It is proposed that search results are handled using special cards describing the biological phenomena and the functional principles....

  17. OCRWM Systems Engineering Management Plan (SEMP)

    International Nuclear Information System (INIS)

    1994-06-01

    The Office of Civilian Radioactive Waste Management Systems Engineering Management Plan (OCRWM SEMP) specifies the technical management approach for the development of the waste management system, and specifies the approach for the development of each of the system elements -- the waste acceptance system, the transportation system, the Monitored Retrievable Storage (MRS) facility, and the mined geologic disposal system, which includes site characterization activity. The SEMP also delineates how systems engineering will be used by OCRWM to describe the system development process; it identifies responsibilities for its implementation, and specifies the minimum requirements for systems engineering. It also identifies the close interrelationship of system engineering and licensing processes. This SEMP, which is a combined OCRWM and M ampersand O SEMP, is part of the top-level program documentation and is prepared in accordance with the direction provided in the Program Management System Manual (PMSM). The relationship of this document to other top level documents in the CRWMS document hierarchy is defined in the PMSM. A systems engineering management plan for each project, which specifies the actions to be taken in implementing systems engineering at the project level, shall be prepared by the respective project managers. [''Program'' refers to the CRWMS-wide activity and ''project'' refers to that level responsible for accomplishing the specific activities of that segment of the program.] The requirements for the project level SEMPs are addressed in Section 4.2.2.2. They represent the minimum set of requirements, and do not preclude the broadening of systems engineering activities to meet the specific needs of each project

  18. A systems engineering primer for every engineer and scientist

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, William R.

    2001-12-10

    The Systems Engineering (SE) staff at LBNL has generated the following artifacts to assist projects with implementing a systems approach: (1) The present document that focuses on the what, why, and when of SE. It also provides a simple case-study to illustrate several SE tasks. (2) A web site with primary emphasis on the project life-cycle and workflow, (http://www-eng.LBNL.gov/Systems/index.html). It includes: SE guidelines and principles; A list of in-house tools; Templates; Case studies with ''how to'' examples; and Links to useful SE material. These sources are living documents to be updated as necessary. The viewpoint adopted in this document is that what LBNL engineers and scientists need is a set of principles and guiding practices for developing R and D systems rather than a ''cookbook''. There are many excellent ''how to'' resources such as the ''INCOSE Systems Engineering Handbook'' to guide those in search of more details. The SE staff is another resource available to consult and support projects. This document specifies SE principles and activities that are applicable to all LBNL projects independent of their specific differences. Each project should tailor the SE implementation to meet its individual needs and culture including project-specific resources, procedures, products, and tools.

  19. A systems engineering primer for every engineer and scientist

    International Nuclear Information System (INIS)

    Edwards, William R.

    2001-01-01

    The Systems Engineering (SE) staff at LBNL has generated the following artifacts to assist projects with implementing a systems approach: (1) The present document that focuses on the what, why, and when of SE. It also provides a simple case-study to illustrate several SE tasks. (2) A web site with primary emphasis on the project life-cycle and workflow, (http://www-eng.LBNL.gov/Systems/index.html). It includes: SE guidelines and principles; A list of in-house tools; Templates; Case studies with ''how to'' examples; and Links to useful SE material. These sources are living documents to be updated as necessary. The viewpoint adopted in this document is that what LBNL engineers and scientists need is a set of principles and guiding practices for developing R and D systems rather than a ''cookbook''. There are many excellent ''how to'' resources such as the ''INCOSE Systems Engineering Handbook'' to guide those in search of more details. The SE staff is another resource available to consult and support projects. This document specifies SE principles and activities that are applicable to all LBNL projects independent of their specific differences. Each project should tailor the SE implementation to meet its individual needs and culture including project-specific resources, procedures, products, and tools

  20. A design concept of parallel elasticity extracted from biological muscles for engineered actuators.

    Science.gov (United States)

    Chen, Jie; Jin, Hongzhe; Iida, Fumiya; Zhao, Jie

    2016-08-23

    Series elastic actuation that takes inspiration from biological muscle-tendon units has been extensively studied and used to address the challenges (e.g. energy efficiency, robustness) existing in purely stiff robots. However, there also exists another form of passive property in biological actuation, parallel elasticity within muscles themselves, and our knowledge of it is limited: for example, there is still no general design strategy for the elasticity profile. When we look at nature, on the other hand, there seems a universal agreement in biological systems: experimental evidence has suggested that a concave-upward elasticity behaviour is exhibited within the muscles of animals. Seeking to draw possible design clues for elasticity in parallel with actuators, we use a simplified joint model to investigate the mechanisms behind this biologically universal preference of muscles. Actuation of the model is identified from general biological joints and further reduced with a specific focus on muscle elasticity aspects, for the sake of easy implementation. By examining various elasticity scenarios, one without elasticity and three with elasticity of different profiles, we find that parallel elasticity generally exerts contradictory influences on energy efficiency and disturbance rejection, due to the mechanical impedance shift thus caused. The trade-off analysis between them also reveals that concave parallel elasticity is able to achieve a more advantageous balance than linear and convex ones. It is expected that the results could contribute to our further understanding of muscle elasticity and provide a theoretical guideline on how to properly design parallel elasticity behaviours for engineering systems such as artificial actuators and robotic joints.

  1. The role of mechanics in biological and bio-inspired systems.

    Science.gov (United States)

    Egan, Paul; Sinko, Robert; LeDuc, Philip R; Keten, Sinan

    2015-07-06

    Natural systems frequently exploit intricate multiscale and multiphasic structures to achieve functionalities beyond those of man-made systems. Although understanding the chemical make-up of these systems is essential, the passive and active mechanics within biological systems are crucial when considering the many natural systems that achieve advanced properties, such as high strength-to-weight ratios and stimuli-responsive adaptability. Discovering how and why biological systems attain these desirable mechanical functionalities often reveals principles that inform new synthetic designs based on biological systems. Such approaches have traditionally found success in medical applications, and are now informing breakthroughs in diverse frontiers of science and engineering.

  2. Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

    DEFF Research Database (Denmark)

    Aziz, Ramy K.; Monk, Jonathan M.; Lewis, R. M.

    2015-01-01

    Mathematical models of metabolism from bacterial systems biology have proven their utility across multiple fields, for example metabolic engineering, growth phenotype simulation, and biological discovery. The usefulness of the models stems from their ability to compute a link between genotype...... of metabolic models, and highlight one potential application of systems biology to drug discovery and translational medicine....

  3. Thermodynamic Optimality criteria for biological systems in linear irreversible thermodynamics

    International Nuclear Information System (INIS)

    Chimal, J C; Sánchez, N; Ramírez, PR

    2017-01-01

    In this paper the methodology of the so-called Linear Irreversible Thermodynamics (LIT) is applied; although traditionally used locally to study general systems in non-equilibrium states in which it is consider both internal and external contributions to the entropy increments in order to analyze the efficiency of two coupled processes with generalized fluxes J 1 , J 2 and their corresponding forces X 1 , X 2 . We extend the former analysis to takes into account two different operating regimes namely: Omega Function and Efficient Power criterion, respectively. Results show analogies in the optimal performance between and we can say that there exist a criteria of optimization which can be used specially for biological systems where a good design of the biological parameters made by nature at maximum efficient power conditions lead to more efficient engines than those at the maximum power conditions or ecological conditions. (paper)

  4. 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…

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. Advancing the science of forest hydrology A challenge to agricultural and biological engineers

    Science.gov (United States)

    Devendra Amatya; Wayne Skaggs; Carl Trettin

    2009-01-01

    For more than a century, agricultural and biological engineers have provided major advances in science, engineering, and technology to increase food and fiber production to meet the demands of a rapidly growing global population. The land base for these technological advances has originated largely from forested lands, which have experienced dramatic declines over the...

  10. Hybrid cognitive engine for radio systems adaptation

    KAUST Repository

    Alqerm, Ismail; Shihada, Basem

    2017-01-01

    of our hybrid engine is validated using software defined radios implementation and simulation in multi-carrier environment. The system throughput, signal to noise and interference ratio, and packet error rate are obtained and compared with other schemes

  11. System Engineering Process Realization Toolkit, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA faces many systems engineering challenges as it seeks to conduct exploration and science missions concurrently. One such challenge is implementing a repeatable...

  12. Framework to investigate emergence in system engineering

    CSIR Research Space (South Africa)

    Oosthuizen, R

    2011-09-01

    Full Text Available System Engineering is the process of identifying, implementing and maintaining solutions to real world problems. Some problems tend to be messy with no single solution or set of effective and accurate requirements, often resulting in implementation...

  13. Applying systems engineering in the civil engineering industry : an analysis of systems engineering projects of a Dutch water board

    NARCIS (Netherlands)

    de Graaf, R. S. (Robin); Vromen, R. M.(Rick); Boes, J. (Hans)

    2017-01-01

    The past decade, practice and literature have shown an increasing interest in Systems Engineering (SE) in the civil engineering industry. The aim of this study is to analyse to what extent SE is applied in six civil engineering SE projects of a Dutch water board. The projects were analysed using a

  14. 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....

  15. Prevention of Preharvest Sprouting through Hormone Engineering and Germination Recovery by Chemical Biology.

    Science.gov (United States)

    Nonogaki, Mariko; Nonogaki, Hiroyuki

    2017-01-01

    Vivipary, germination of seeds on the maternal plant, is observed in nature and provides ecological advantages in certain wild species, such as mangroves. However, precocious seed germination in agricultural species, such as preharvest sprouting (PHS) in cereals, is a serious issue for food security. PHS reduces grain quality and causes economical losses to farmers. PHS can be prevented by translating the basic knowledge of hormone biology in seeds into technologies. Biosynthesis of abscisic acid (ABA), which is an essential hormone for seed dormancy, can be engineered to enhance dormancy and prevent PHS. Enhancing nine- cis -epoxycarotenoid dioxygenase (NCED), a rate-limiting enzyme of ABA biosynthesis, through a chemically induced gene expression system, has successfully been used to suppress germination of Arabidopsis seeds. The more advanced system NCED positive-feedback system, which amplifies ABA biosynthesis in a seed-specific manner without chemical induction, has also been developed. The proofs of concept established in the model species are now ready to be applied to crops. A potential problem is recovery of germination from hyperdormant crop grains. Hyperdormancy induced by the NCED systems can be reversed by inducing counteracting genes, such as NCED RNA interference or gibberellin (GA) biosynthesis genes. Alternatively, seed sensitivity to ABA can be modified to rescue germination using the knowledge of chemical biology. ABA antagonists, which were developed recently, have great potential to recover germination from the hyperdormant seeds. Combination of the dormancy-imposing and -releasing approaches will establish a comprehensive technology for PHS prevention and germination recovery.

  16. Complex Adaptive Systems of Systems (CASOS) engineering environment.

    Energy Technology Data Exchange (ETDEWEB)

    Detry, Richard Joseph; Linebarger, John Michael; Finley, Patrick D.; Maffitt, S. Louise; Glass, Robert John, Jr.; Beyeler, Walter Eugene; Ames, Arlo Leroy

    2012-02-01

    Complex Adaptive Systems of Systems, or CASoS, are vastly complex physical-socio-technical systems which we must understand to design a secure future for the nation. The Phoenix initiative implements CASoS Engineering principles combining the bottom up Complex Systems and Complex Adaptive Systems view with the top down Systems Engineering and System-of-Systems view. CASoS Engineering theory and practice must be conducted together to develop a discipline that is grounded in reality, extends our understanding of how CASoS behave and allows us to better control the outcomes. The pull of applications (real world problems) is critical to this effort, as is the articulation of a CASoS Engineering Framework that grounds an engineering approach in the theory of complex adaptive systems of systems. Successful application of the CASoS Engineering Framework requires modeling, simulation and analysis (MS and A) capabilities and the cultivation of a CASoS Engineering Community of Practice through knowledge sharing and facilitation. The CASoS Engineering Environment, itself a complex adaptive system of systems, constitutes the two platforms that provide these capabilities.

  17. Reverse engineering biological networks :applications in immune responses to bio-toxins.

    Energy Technology Data Exchange (ETDEWEB)

    Martino, Anthony A.; Sinclair, Michael B.; Davidson, George S.; Haaland, David Michael; Timlin, Jerilyn Ann; Thomas, Edward Victor; Slepoy, Alexander; Zhang, Zhaoduo; May, Elebeoba Eni; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-12-01

    Our aim is to determine the network of events, or the regulatory network, that defines an immune response to a bio-toxin. As a model system, we are studying T cell regulatory network triggered through tyrosine kinase receptor activation using a combination of pathway stimulation and time-series microarray experiments. Our approach is composed of five steps (1) microarray experiments and data error analysis, (2) data clustering, (3) data smoothing and discretization, (4) network reverse engineering, and (5) network dynamics analysis and fingerprint identification. The technological outcome of this study is a suite of experimental protocols and computational tools that reverse engineer regulatory networks provided gene expression data. The practical biological outcome of this work is an immune response fingerprint in terms of gene expression levels. Inferring regulatory networks from microarray data is a new field of investigation that is no more than five years old. To the best of our knowledge, this work is the first attempt that integrates experiments, error analyses, data clustering, inference, and network analysis to solve a practical problem. Our systematic approach of counting, enumeration, and sampling networks matching experimental data is new to the field of network reverse engineering. The resulting mathematical analyses and computational tools lead to new results on their own and should be useful to others who analyze and infer networks.

  18. Engineering management of large scale systems

    Science.gov (United States)

    Sanders, Serita; Gill, Tepper L.; Paul, Arthur S.

    1989-01-01

    The organization of high technology and engineering problem solving, has given rise to an emerging concept. Reasoning principles for integrating traditional engineering problem solving with system theory, management sciences, behavioral decision theory, and planning and design approaches can be incorporated into a methodological approach to solving problems with a long range perspective. Long range planning has a great potential to improve productivity by using a systematic and organized approach. Thus, efficiency and cost effectiveness are the driving forces in promoting the organization of engineering problems. Aspects of systems engineering that provide an understanding of management of large scale systems are broadly covered here. Due to the focus and application of research, other significant factors (e.g., human behavior, decision making, etc.) are not emphasized but are considered.

  19. Systems Engineering Model for ART Energy Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Mendez Cruz, Carmen Margarita [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Rochau, Gary E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Wilson, Mollye C. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-02-01

    The near-term objective of the EC team is to establish an operating, commercially scalable Recompression Closed Brayton Cycle (RCBC) to be constructed for the NE - STEP demonstration system (demo) with the lowest risk possible. A systems engineering approach is recommended to ensure adequate requirements gathering, documentation, and mode ling that supports technology development relevant to advanced reactors while supporting crosscut interests in potential applications. A holistic systems engineering model was designed for the ART Energy Conversion program by leveraging Concurrent Engineering, Balance Model, Simplified V Model, and Project Management principles. The resulting model supports the identification and validation of lifecycle Brayton systems requirements, and allows designers to detail system-specific components relevant to the current stage in the lifecycle, while maintaining a holistic view of all system elements.

  20. Systems Engineering Assessment & Workforce Development Plan

    Science.gov (United States)

    2012-11-05

    Government or its technical domains. Other fields, such as culinary and healthcare, have also identified these emerging and growing issues (Calhoun...et al. (2009). "The Art and Science of Systems Engineering." Systems Research Forum 3(2): 81-100. Shenhar, A. and B. Sauser, Eds. (2009). Systems

  1. Review of Microfluidic Photobioreactor Technology for Metabolic Engineering and Synthetic Biology of Cyanobacteria and Microalgae

    Directory of Open Access Journals (Sweden)

    Ya-Tang Yang

    2016-10-01

    Full Text Available One goal of metabolic engineering and synthetic biology for cyanobacteria and microalgae is to engineer strains that can optimally produce biofuels and commodity chemicals. However, the current workflow is slow and labor intensive with respect to assembly of genetic parts and characterization of production yields because of the slow growth rates of these organisms. Here, we review recent progress in the microfluidic photobioreactors and identify opportunities and unmet needs in metabolic engineering and synthetic biology. Because of the unprecedented experimental resolution down to the single cell level, long-term real-time monitoring capability, and high throughput with low cost, microfluidic photobioreactor technology will be an indispensible tool to speed up the development process, advance fundamental knowledge, and realize the full potential of metabolic engineering and synthetic biology for cyanobacteria and microalgae.

  2. Hybrid cognitive engine for radio systems adaptation

    KAUST Repository

    Alqerm, Ismail

    2017-07-20

    Network efficiency and proper utilization of its resources are essential requirements to operate wireless networks in an optimal fashion. Cognitive radio aims to fulfill these requirements by exploiting artificial intelligence techniques to create an entity called cognitive engine. Cognitive engine exploits awareness about the surrounding radio environment to optimize the use of radio resources and adapt relevant transmission parameters. In this paper, we propose a hybrid cognitive engine that employs Case Based Reasoning (CBR) and Decision Trees (DTs) to perform radio adaptation in multi-carriers wireless networks. The engine complexity is reduced by employing DTs to improve the indexing methodology used in CBR cases retrieval. The performance of our hybrid engine is validated using software defined radios implementation and simulation in multi-carrier environment. The system throughput, signal to noise and interference ratio, and packet error rate are obtained and compared with other schemes in different scenarios.

  3. A discussion of molecular biology methods for protein engineering

    CSIR Research Space (South Africa)

    Zawaira, A

    2011-09-01

    Full Text Available A number of molecular biology techniques are available to generate variants from a particular start gene for eventual protein expression. The authors discuss the basic principles of these methods in a repertoire that may be used to achieve...

  4. Micropropagation, genetic engineering, and molecular biology of Populus

    Science.gov (United States)

    N. B. Klopfenstein; Y. W. Chun; M. -S. Kim; M. A. Ahuja; M. C. Dillon; R. C. Carman; L. G. Eskew

    1997-01-01

    Thirty-four Populus biotechnology chapters, written by 85 authors, are comprised in 5 sections: 1) in vitro culture (micropropagation, somatic embryogenesis, protoplasts, somaclonal variation, and germplasm preservation); 2) transformation and foreign gene expression; 3) molecular biology (molecular/genetic characterization); 4) biotic and abiotic resistance (disease,...

  5. Nuclear reactor engineering: Reactor systems engineering. Fourth edition, Volume Two

    International Nuclear Information System (INIS)

    Glasstone, S.; Sesonske, A.

    1994-01-01

    This new edition of this classic reference combines broad yet in-depth coverage of nuclear engineering principles with practical descriptions of their application in the design and operation of nuclear power plants. Extensively updated, the fourth edition includes new materials on reactor safety and risk analysis, regulation, fuel management, waste management and operational aspects of nuclear power. This volume contains the following: the systems concept, design decisions, and information tools; energy transport; reactor fuel management and energy cost considerations; environmental effects of nuclear power and waste management; nuclear reactor safety and regulation; power reactor systems; plant operations; and advanced plants and the future

  6. Tank waste remediation system systems engineering management plan

    International Nuclear Information System (INIS)

    Peck, L.G.

    1998-01-01

    This Systems Engineering Management Plan (SEMP) describes the Tank Waste Remediation System (TWRS) implementation of the US Department of Energy (DOE) systems engineering policy provided in 97-IMSD-193. The SEMP defines the products, process, organization, and procedures used by the TWRS Project to implement the policy. The SEMP will be used as the basis for tailoring the systems engineering applications to the development of the physical systems and processes necessary to achieve the desired end states of the program. It is a living document that will be revised as necessary to reflect changes in systems engineering guidance as the program evolves. The US Department of Energy-Headquarters has issued program management guidance, DOE Order 430. 1, Life Cycle Asset Management, and associated Good Practice Guides that include substantial systems engineering guidance

  7. Requirements engineering for software and systems

    CERN Document Server

    Laplante, Phillip A

    2014-01-01

    Solid requirements engineering has increasingly been recognized as the key to improved, on-time and on-budget delivery of software and systems projects. This book provides practical teaching for graduate and professional systems and software engineers. It uses extensive case studies and exercises to help students grasp concepts and techniques. With a focus on software-intensive systems, this text provides a probing and comprehensive review of recent developments in intelligent systems, soft computing techniques, and their diverse applications in manufacturing. The second edition contains 100% revised content and approximately 30% new material

  8. Human engineering in mobile radwaste systems

    International Nuclear Information System (INIS)

    Jones, D.; McMahon, J.; Motl, G.

    1988-01-01

    To a large degree, mobile radwaste systems are replacing installed plant systems at US nuclear plants due to regulatory obsolescence, high capital and maintenance costs, and increased radiation exposure. Well over half the power plants in the United States now use some sort of mobile system similar to those offered by LN Technologies Corporation. Human engineering is reflected in mobile radwaste system design due to concerns about safety, efficiency, and cost. The radwaste services business is so competitive that vendors must reflect human engineering in several areas of equipment design in order to compete. The paper discusses radiation exposure control, contamination control, compact components, maintainability, operation, and transportability

  9. Reusable Rocket Engine Turbopump Health Management System

    Science.gov (United States)

    Surko, Pamela

    1994-01-01

    A health monitoring expert system software architecture has been developed to support condition-based health monitoring of rocket engines. Its first application is in the diagnosis decisions relating to the health of the high pressure oxidizer turbopump (HPOTP) of Space Shuttle Main Engine (SSME). The post test diagnostic system runs off-line, using as input the data recorded from hundreds of sensors, each running typically at rates of 25, 50, or .1 Hz. The system is invoked after a test has been completed, and produces an analysis and an organized graphical presentation of the data with important effects highlighted. The overall expert system architecture has been developed and documented so that expert modules analyzing other line replaceable units may easily be added. The architecture emphasizes modularity, reusability, and open system interfaces so that it may be used to analyze other engines as well.

  10. Current Hitachi knowledge engineering systems: an overview

    Energy Technology Data Exchange (ETDEWEB)

    Masui, S; Maeda, A; Masuishi, T [Hitachi, Ltd., Tokyo (Japan)

    1992-02-01

    In order to bring the knowledge engineering technology up to the practical phase, Hitachi has provided several knowledge engineering system products, including expert system building tools, knowledge acquisition tools, and many kinds of stand-alone and build-in expert systems in both the business and process control fields. In this review article, an overview of Hitachi{prime}s recent knowledge systems is described, which includes a trend analysis on recent market recognition. In addition, to introduce the Hitachi{prime}s current activities, a new product, a user interface building tool, and a new method of tuning fuzzy membership functions using a neuro-computing algorithm are also described. Furthermore, it is pointed out that not only practical tools and methodologies, but also a practical development team, including a planning section, a cooperating expert, a user section, and experienced knowledge engineers, is needed to achieve practical expert systems. 20 refs., 10 figs., 1 tab.

  11. Advances in reliability and system engineering

    CERN Document Server

    Davim, J

    2017-01-01

    This book presents original studies describing the latest research and developments in the area of reliability and systems engineering. It helps the reader identifying gaps in the current knowledge and presents fruitful areas for further research in the field. Among others, this book covers reliability measures, reliability assessment of multi-state systems, optimization of multi-state systems, continuous multi-state systems, new computational techniques applied to multi-state systems and probabilistic and non-probabilistic safety assessment.

  12. 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

  13. 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.

  14. NVESTIGATION OF INTERNATIONAL ENGINEERING LICENSURE SYSTEMS

    Directory of Open Access Journals (Sweden)

    Selim BARADAN

    2009-01-01

    Full Text Available In many countries, engineers are legally required to register to a "licensure" system, which is founded on education and experience criteria and administered by a government body, to use the "engineer" title and offer professional services to the public. In today's globalized world, international alliances such as FEANI, APEC and EMF award engineers with European, APEC and International Professional engineer titles within a framework of mutual recognition of qualifications enabling them to practice outside their own country. This article examines such international licensure systems, particularly their administration processes and registration criteria, and discusses how current licensure procedures in Turkey should be revamped in case of joining an international alliance such as European Union.

  15. The art and science of Systems Engineering

    Directory of Open Access Journals (Sweden)

    Jerome Longrew

    2014-12-01

    Full Text Available In this work are collected years of experience and the work of systems engineering, and debates centered in the industry leadership, of engineer and instructors around the world. A recurrent issue in this experiences and discussions is that community used a lot of terms and titles more diffused with the aim of achieve an agreement toward a common comprehension of this area of knowledge. Besides, it does not matter how are divided the functions and responsibilities among teams, the obligatoriness is ensure that this be clears and are run as a functional whole. The goal is provide a wide definition of systems engineer, described the characteristics of behave of highly effective engineered, and make explicit the expectations of the same.

  16. 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.

  17. Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2015

    Science.gov (United States)

    2015-12-01

    yield stability. Transgenic approach plays an important role in crop improvement. Currently, transgenes are randomly inserted into maize genome...Improve Microbial Biofuel Production - Mary Dunlop, University of Vermont 2:30-3:00 PM Targeted Integration of Genes into the Maize Genome Facilitated...highlights gaps in the present understanding of M13 biology. Understanding the subtleties of regulation will be important for maximally ex- ploiting the

  18. User engineering: A new look at system engineering

    Science.gov (United States)

    Mclaughlin, Larry L.

    1987-01-01

    User Engineering is a new System Engineering perspective responsible for defining and maintaining the user view of the system. Its elements are a process to guide the project and customer, a multidisciplinary team including hard and soft sciences, rapid prototyping tools to build user interfaces quickly and modify them frequently at low cost, and a prototyping center for involving users and designers in an iterative way. The main consideration is reducing the risk that the end user will not or cannot effectively use the system. The process begins with user analysis to produce cognitive and work style models, and task analysis to produce user work functions and scenarios. These become major drivers of the human computer interface design which is presented and reviewed as an interactive prototype by users. Feedback is rapid and productive, and user effectiveness can be measured and observed before the system is built and fielded. Requirements are derived via the prototype and baselined early to serve as an input to the architecture and software design.

  19. Software engineering practices for control system reliability

    International Nuclear Information System (INIS)

    S. K. Schaffner; K. S White

    1999-01-01

    This paper will discuss software engineering practices used to improve Control System reliability. The authors begin with a brief discussion of the Software Engineering Institute's Capability Maturity Model (CMM) which is a framework for evaluating and improving key practices used to enhance software development and maintenance capabilities. The software engineering processes developed and used by the Controls Group at the Thomas Jefferson National Accelerator Facility (Jefferson Lab), using the Experimental Physics and Industrial Control System (EPICS) for accelerator control, are described. Examples are given of how their procedures have been used to minimized control system downtime and improve reliability. While their examples are primarily drawn from their experience with EPICS, these practices are equally applicable to any control system. Specific issues addressed include resource allocation, developing reliable software lifecycle processes and risk management

  20. BIOPROCESS SYSTEMS ENGINEERING: TRANSFERRING TRADITIONAL PROCESS ENGINEERING PRINCIPLES TO INDUSTRIAL BIOTECHNOLOGY

    Directory of Open Access Journals (Sweden)

    Michalis Koutinas

    2012-10-01

    Full Text Available The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control and optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals.

  1. Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology

    Directory of Open Access Journals (Sweden)

    Michalis Koutinas

    2012-10-01

    Full Text Available The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control & optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals.

  2. Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

    Energy Technology Data Exchange (ETDEWEB)

    Madhavan, Aravind [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Rajiv Gandhi Centre for Biotechnology, Trivandrum (India); Jose, Anju Alphonsa; Binod, Parameswaran; Sindhu, Raveendran, E-mail: sindhurgcb@gmail.com; Sukumaran, Rajeev K. [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Pandey, Ashok [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Center for Innovative and Applied Bioprocessing, Mohali, Punjab (India); Castro, Galliano Eulogio [Dpt. Ingeniería Química, Ambiental y de los Materiales Edificio, Universidad de Jaén, Jaén (Spain)

    2017-04-25

    The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.

  3. Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

    Directory of Open Access Journals (Sweden)

    Raveendran Sindhu

    2017-04-01

    Full Text Available The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.

  4. Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

    International Nuclear Information System (INIS)

    Madhavan, Aravind; Jose, Anju Alphonsa; Binod, Parameswaran; Sindhu, Raveendran; Sukumaran, Rajeev K.; Pandey, Ashok; Castro, Galliano Eulogio

    2017-01-01

    The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.

  5. Industrial deployment of system engineering methods

    CERN Document Server

    Romanovsky, Alexander

    2013-01-01

    A formal method is not the main engine of a development process, its contribution is to improve system dependability by motivating formalisation where useful. This book summarizes the results of the DEPLOY research project on engineering methods for dependable systems through the industrial deployment of formal methods in software development. The applications considered were in automotive, aerospace, railway, and enterprise information systems, and microprocessor design.  The project introduced a formal method, Event-B, into several industrial organisations and built on the lessons learned to

  6. Synthetic biology for engineering acetyl coenzyme a metabolism in yeast

    DEFF Research Database (Denmark)

    Nielsen, Jens

    2014-01-01

    The yeast Saccharomyces cerevisiae is a widely used cell factory for the production of fuels, chemicals, and pharmaceuticals. The use of this cell factory for cost-efficient production of novel fuels and chemicals requires high yields and low by-product production. Many industrially interesting...... chemicals are biosynthesized from acetyl coenzyme A (acetyl-CoA), which serves as a central precursor metabolite in yeast. To ensure high yields in production of these chemicals, it is necessary to engineer the central carbon metabolism so that ethanol production is minimized (or eliminated) and acetyl...

  7. An initial bibliometric analysis and mapping of systems engineering research

    CSIR Research Space (South Africa)

    Oosthuizen, Rudolph

    2016-07-01

    Full Text Available Systems engineering is still a growing field that depends on continuous research to develop and mature. Research in systems engineering is difficult and the classic approaches for other engineering disciplines may not be sufficient. Additional...

  8. Telecommunications system reliability engineering theory and practice

    CERN Document Server

    Ayers, Mark L

    2012-01-01

    "Increasing system complexity require new, more sophisticated tools for system modeling and metric calculation. Bringing the field up to date, this book provides telecommunications engineers with practical tools for analyzing, calculating, and reporting availability, reliability, and maintainability metrics. It gives the background in system reliability theory and covers in-depth applications in fiber optic networks, microwave networks, satellite networks, power systems, and facilities management. Computer programming tools for simulating the approaches presented, using the Matlab software suite, are also provided"

  9. 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 ...

  10. 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

  11. Integrated Control System Engineering Support.

    Science.gov (United States)

    1984-12-01

    Advanced Medium Range Air to Air Missile ASTEC Advanced Speech Technology Experimental Configuration BA Body Axis BCIU Bus Control Interface Unit BMU Bus...support nreeded to tie an ASTEC speech recognition system into the DIGISYN fJcility and support an FIGR experiment designed to investigate the voice...information passed to the PDP computer consisted of integers which represented words or phrases recognized by the ASTEC recognition system. An interface

  12. 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.

  13. The collective biology of the gene: Towards genetic dynamics engineering

    International Nuclear Information System (INIS)

    Chela-Flores, J.

    1985-11-01

    Chromatin dynamics is studied in terms of coupled vibrations (phonon pairing); this is shown to lead to a collective variable Δ, interpreted as a gene inhibition factor, which behaves as a biological switch turned off, not only by enzymatic action or metabolic energy, but also by means of an external probe:irradiation. We discuss the inactivation of the X chromosome and puffing. The relevance of being able to modulate Δ is emphasized, since it is equivalent to controlling chromatin dynamics without interfering with chromatin structure, unlike in the usual recombinant DNA techniques. (author)

  14. Interactions of nanomaterials and biological systems: implications to personalized nanomedicine☆

    Science.gov (United States)

    Zhang, Xue-Qing; Xu, Xiaoyang; Bertrand, Nicolas; Pridgen, Eric; Swami, Archana; Farokhzad, Omid C.

    2012-01-01

    The application of nanotechnology to personalized medicine provides an unprecedented opportunity to improve the treatment of many diseases. Nanomaterials offer several advantages as therapeutic and diagnostic tools due to design flexibility, small sizes, large surface-to-volume ratio, and ease of surface modification with multivalent ligands to increase avidity for target molecules. Nanomaterials can be engineered to interact with specific biological components, allowing them to benefit from the insights provided by personalized medicine techniques. To tailor these interactions, a comprehensive knowledge of how nanomaterials interact with biological systems is critical. Herein, we discuss how the interactions of nanomaterials with biological systems can guide their design for diagnostic, imaging and drug delivery purposes. A general overview of nanomaterials under investigation is provided with an emphasis on systems that have reached clinical trials. Finally, considerations for the development of personalized nanomedicines are summarized such as the potential toxicity, scientific and technical challenges in fabricating them, and regulatory and ethical issues raised by the utilization of nanomaterials. PMID:22917779

  15. OCRWM Systems Engineering Management Plan (SEMP)

    International Nuclear Information System (INIS)

    1990-03-01

    The Nuclear Waste Policy Act of 1982 established the Office of Civilian Radioactive Waste Management (OCRWM) in the Department of Energy (DOE) to implement a program for the safe and permanent disposal of spent nuclear fuel and high-level radioactive waste. To achieve this objective, the OCRWM is developing an integrated waste-management system consisting of three elements: the transportation system, the monitored retrievable storage (MRS) facility, and the mined geologic disposal system (MGDS). The development of such a system requires management of many diverse disciplines that are involved in research, siting, design, licensing, and external interactions. The purpose of this Systems Engineering Management Plan (SEMP) is to prescribe how the systems-engineering process will be implemented in the development of the waste-management system. Systems engineering will be used by the OCRWM to manage, integrate, and document all aspects of the technical development of the waste-management system and its system elements to ensure that the requirements of the waste-management program are met. It will be applied to all technical activities of the OCRWM program. It will be used by the OCRWM to specify the sequence of technical activities necessary to define the requirements the waste-management system must satisfy, to develop the waste-management system, to relate system elements to each other, and to determine how the waste-management system can be optimized to most effectively satisfy the requirements. Furthermore, systems engineering will be used in the management of Program activities at the program, program-element, and project levels by specifying procedures, studies, reviews, and documentation requirements. 9 refs., 1 fig

  16. Cognitive systems engineering in health care

    CERN Document Server

    Bisantz, Ann M; Fairbanks, Rollin J

    2014-01-01

    Cognitive Engineering for Better Health Care Systems, Ann M. Bisantz, Rollin J. Fairbanks, and Catherine M. BurnsThe Role of Cognitive Engineering in Improving Clinical Decision Support, Anne Miller and Laura MilitelloTeam Cognitive Work Analysis as an Approach for Understanding Teamwork in Health Care, Catherine M. BurnsCognitive Engineering Design of an Emergency Department Information System, Theresa K. Guarrera, Nicolette M. McGeorge, Lindsey N. Clark, David T. LaVergne, Zachary A. Hettinger, Rollin J. Fairbanks, and Ann M. BisantzDisplays for Health Care Teams: A Conceptual Framework and Design Methodology, Avi ParushInformation Modeling for Cognitive Work in a Health Care System, Priyadarshini R. PennathurSupport for ICU Clinician Cognitive Work through CSE, Christopher Nemeth, Shilo Anders, Jeffrey Brown, Anna Grome, Beth Crandall, and Jeremy PamplinMatching Cognitive Aids and the "Real Work" of Health Care in Support of Surgical Microsystem Teamwork, Sarah Henrickson Parker and Shawna J. PerryEngageme...

  17. Cognitive Systems Engineering: The Next 30 Years

    Science.gov (United States)

    Feary, Michael

    2012-01-01

    This presentation is part of panel discussion on Cognitive Systems Engineering. The purpose of this panel is to discuss the challenges and future directions of Cognitive Systems Engineering for the next 30 years. I intended to present the work we have been doing with the Aviation Safety program and Space Human Factors Engineering project on Work Domain Analysis and some areas of Research Focus. Specifically, I intend to focus on the shift on the need to understand and model attention in mixed-initiative systems, the need for methods which can generate results to be used in trade-off decisions, and the need to account for a range of human behavior in the design.

  18. Engineering education as a complex system

    Science.gov (United States)

    Gattie, David K.; Kellam, Nadia N.; Schramski, John R.; Walther, Joachim

    2011-12-01

    This paper presents a theoretical basis for cultivating engineering education as a complex system that will prepare students to think critically and make decisions with regard to poorly understood, ill-structured issues. Integral to this theoretical basis is a solution space construct developed and presented as a benchmark for evaluating problem-solving orientations that emerge within students' thinking as they progress through an engineering curriculum. It is proposed that the traditional engineering education model, while analytically rigorous, is characterised by properties that, although necessary, are insufficient for preparing students to address complex issues of the twenty-first century. A Synthesis and Design Studio model for engineering education is proposed, which maintains the necessary rigor of analysis within a uniquely complex yet sufficiently structured learning environment.

  19. 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.

  20. 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.

  1. Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops.

    Science.gov (United States)

    Shih, Patrick M; Liang, Yan; Loqué, Dominique

    2016-07-01

    The Green Revolution has fuelled an exponential growth in human population since the mid-20th century. Due to population growth, food and energy demands will soon surpass supply capabilities. To overcome these impending problems, significant improvements in genetic engineering will be needed to complement breeding efforts in order to accelerate the improvement of agronomical traits. The new field of plant synthetic biology has emerged in recent years and is expected to support rapid, precise, and robust engineering of plants. In this review, we present recent advances made in the field of plant synthetic biology, specifically in genome editing, transgene expression regulation, and bioenergy crop engineering, with a focus on traits related to lignocellulose, oil, and soluble sugars. Ultimately, progress and innovation in these fields may facilitate the development of beneficial traits in crop plants to meet society's bioenergy needs. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

  2. 46 CFR 121.620 - Propulsion engine control systems.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Propulsion engine control systems. 121.620 Section 121... Propulsion engine control systems. (a) A vessel must have two independent means of controlling each propulsion engine. Control must be provided for the engine speed, direction of shaft rotation, and engine...

  3. A methodology to annotate systems biology markup language models with the synthetic biology open language.

    Science.gov (United States)

    Roehner, Nicholas; Myers, Chris J

    2014-02-21

    Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, has often failed in translation and application to new projects, a problem exacerbated by a lack of engineering standards that combine descriptions of the structure and function of DNA. To address this need, this paper describes a methodology to connect the systems biology markup language (SBML) to the synthetic biology open language (SBOL), existing standards that describe biochemical models and DNA components, respectively. Our methodology involves first annotating SBML model elements such as species and reactions with SBOL DNA components. A graph is then constructed from the model, with vertices corresponding to elements within the model and edges corresponding to the cause-and-effect relationships between these elements. Lastly, the graph is traversed to assemble the annotating DNA components into a composite DNA component, which is used to annotate the model itself and can be referenced by other composite models and DNA components. In this way, our methodology can be used to build up a hierarchical library of models annotated with DNA components. Such a library is a useful input to any future genetic technology mapping algorithm that would automate the process of composing DNA components to satisfy a behavioral specification. Our methodology for SBML-to-SBOL annotation is implemented in the latest version of our genetic design automation (GDA) software tool, iBioSim.

  4. The electric power engineering handbook power systems

    CERN Document Server

    2012-01-01

    Power Systems, Third Edition (part of the five-volume set, The Electric Power Engineering Handbook) covers all aspects of power system protection, dynamics, stability, operation, and control. Under the editorial guidance of L.L. Grigsby, a respected and accomplished authority in power engineering, and section editors Andrew Hanson, Pritindra Chowdhuri, Gerry Sheble, and Mark Nelms, this carefully crafted reference includes substantial new and revised contributions from worldwide leaders in the field. This content provides convenient access to overviews and detailed information on a diverse arr

  5. Targeting engineering synchronization in chaotic systems

    Science.gov (United States)

    Bhowmick, Sourav K.; Ghosh, Dibakar

    2016-07-01

    A method of targeting engineering synchronization states in two identical and mismatch chaotic systems is explained in detail. The method is proposed using linear feedback controller coupling for engineering synchronization such as mixed synchronization, linear and nonlinear generalized synchronization and targeting fixed point. The general form of coupling design to target any desire synchronization state under unidirectional coupling with the help of Lyapunov function stability theory is derived analytically. A scaling factor is introduced in the coupling definition to smooth control without any loss of synchrony. Numerical results are done on two mismatch Lorenz systems and two identical Sprott oscillators.

  6. Engineered Barrier System: Physical and Chemical Environment

    International Nuclear Information System (INIS)

    Dixon, P.

    2004-01-01

    The conceptual and predictive models documented in this Engineered Barrier System: Physical and Chemical Environment Model report describe the evolution of the physical and chemical conditions within the waste emplacement drifts of the repository. The modeling approaches and model output data will be used in the total system performance assessment (TSPA-LA) to assess the performance of the engineered barrier system and the waste form. These models evaluate the range of potential water compositions within the emplacement drifts, resulting from the interaction of introduced materials and minerals in dust with water seeping into the drifts and with aqueous solutions forming by deliquescence of dust (as influenced by atmospheric conditions), and from thermal-hydrological-chemical (THC) processes in the drift. These models also consider the uncertainty and variability in water chemistry inside the drift and the compositions of introduced materials within the drift. This report develops and documents a set of process- and abstraction-level models that constitute the engineered barrier system: physical and chemical environment model. Where possible, these models use information directly from other process model reports as input, which promotes integration among process models used for total system performance assessment. Specific tasks and activities of modeling the physical and chemical environment are included in the technical work plan ''Technical Work Plan for: In-Drift Geochemistry Modeling'' (BSC 2004 [DIRS 166519]). As described in the technical work plan, the development of this report is coordinated with the development of other engineered barrier system analysis model reports

  7. Metabolic Engineering for Production of Biorenewable Fuels and Chemicals: Contributions of Synthetic Biology

    Directory of Open Access Journals (Sweden)

    Laura R. Jarboe

    2010-01-01

    Full Text Available Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemical-based production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use of metabolic engineering and synthetic biology in biocatalyst engineering for biorenewable fuels and chemicals production, such as ethanol, butanol, acetate, lactate, succinate, alanine, and xylitol. We also examine the existing challenges in this area and discuss strategies for improving biocatalyst tolerance to chemical inhibitors.

  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. A Vision for Systems Engineering Applied to Wind Energy (Presentation)

    Energy Technology Data Exchange (ETDEWEB)

    Felker, F.; Dykes, K.

    2015-01-01

    This presentation was given at the Third Wind Energy Systems Engineering Workshop on January 14, 2015. Topics covered include the importance of systems engineering, a vision for systems engineering as applied to wind energy, and application of systems engineering approaches to wind energy research and development.

  10. Engineering Algorithms for Finding Patterns in Biological Data

    DEFF Research Database (Denmark)

    Nielsen, Jesper

    2011-01-01

    similarity scores. Association mapping is a technique based on using large amounts of data on Single Nucleotide Polymorphisms (SNPs) to statistically infer associations between segments of DNA and effects in the host. Within the area of association mapping we develop an efficient file format and software...... library, called SNPFile. The file format is able to store both large amounts of SNP data and associated metadata, such as ids and affected-status of samples. Thus the file format can both speed-up SNP data access and simplify data management significantly. On the topic of molecular biological data, we...... analyze data from an experiment on exosome knockout. The exosome is a complex with a role in RNA degradation. We find that knockout of the exosome stabilize hitherto unknown RNA transcripts upstream active transcription start sites. With respect to Hidden Markov Models we develop two fast algorithms. We...

  11. Biomaterials — where biology, physics, chemistry, engineering and medicine meet

    Science.gov (United States)

    Hing, K. A.

    2008-03-01

    The success or failure of an implant material in the body depends on a complex interaction between a synthetic 'foreign body' and the 'host tissue'. These interactions occur at many levels from the sub-microscopic level, where subtle changes in the surface physio-chemistry can substantially alter the nature of the biomaterial-host tissue interface, through the microscopical level (e.g. sensitivity to surface topography) to the macrostructural level (e.g. dependence on scaffold porosity). Thus the factors that control these responses are not only biologically determined but also mechanically, physically and chemically mediated, although identifying where one starts and the other finishes can be difficult. Design of a successful medical device has therefore to call on expertise within a wide range of disciplines. In terms of both investigating the basic science behind the factors which orchestrate a biological response and developing research tools that enable study of these responses. However, a medical device must also meet the economic and practical demands of health care professionals who will ultimately be using it in the clinic. Bone graft substitute materials are used in orthopaedics as an alternative or adjunct to autografting, a practice where the patient 'donates' bone from a healthy site to aid bone repair at a damaged or diseased site. These materials are used in a wide range of procedures from total hip revision to spinal fusion and their evolution over the last 10 years illustrates how an interdisciplinary approach has benefited their development and may lead to further innovation in the future.

  12. Biomimicry, Biofabrication, and Biohybrid Systems: The Emergence and Evolution of Biological Design.

    Science.gov (United States)

    Raman, Ritu; Bashir, Rashid

    2017-10-01

    The discipline of biological design has a relatively short history, but has undergone very rapid expansion and development over that time. This Progress Report outlines the evolution of this field from biomimicry to biofabrication to biohybrid systems' design, showcasing how each subfield incorporates bioinspired dynamic adaptation into engineered systems. Ethical implications of biological design are discussed, with an emphasis on establishing responsible practices for engineering non-natural or hypernatural functional behaviors in biohybrid systems. This report concludes with recommendations for implementing biological design into educational curricula, ensuring effective and responsible practices for the next generation of engineers and scientists. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Offshore Wind Energy Systems Engineering Curriculum Development

    Energy Technology Data Exchange (ETDEWEB)

    McGowan, Jon G. [Univ. of Massachusetts, Amherst, MA (United States); Manwell, James F. [Univ. of Massachusetts, Amherst, MA (United States); Lackner, Matthew A. [Univ. of Massachusetts, Amherst, MA (United States)

    2012-12-31

    Utility-scale electricity produced from offshore wind farms has the potential to contribute significantly to the energy production of the United States. In order for the U.S. to rapidly develop these abundant resources, knowledgeable scientists and engineers with sound understanding of offshore wind energy systems are critical. This report summarizes the development of an upper-level engineering course in "Offshore Wind Energy Systems Engineering." This course is designed to provide students with a comprehensive knowledge of both the technical challenges of offshore wind energy and the practical regulatory, permitting, and planning aspects of developing offshore wind farms in the U.S. This course was offered on a pilot basis in 2011 at the University of Massachusetts and the National Renewable Energy Laboratory (NREL), TU Delft, and GL Garrad Hassan have reviewed its content. As summarized in this report, the course consists of 17 separate topic areas emphasizing appropriate engineering fundamentals as well as development, planning, and regulatory issues. In addition to the course summary, the report gives the details of a public Internet site where references and related course material can be obtained. This course will fill a pressing need for the education and training of the U.S. workforce in this critically important area. Fundamentally, this course will be unique due to two attributes: an emphasis on the engineering and technical aspects of offshore wind energy systems, and a focus on offshore wind energy issues specific to the United States.

  14. Engineering of complex systems: The impact of systems engineering at NASA

    Science.gov (United States)

    Kludze, Ave-Klutse Kodzo Paaku

    The "true" impact or value of systems engineering to an organization unfortunately appears not to have been well-studied and understood. The principles of systems engineering are highly encouraged by NASA at all levels, and most practitioners, both internal and external to NASA, intuitively "believe" it adds some value to the development of complex systems by producing them faster, better and cheaper. This research, in trying to fill a gap that exists in the systems engineering literature, analyzes data collected within NASA and other sources external to NASA (INCOSE) for comparisons. Analyses involving a number of case studies performed on selected NASA projects are presented to draw attention to the impact systems engineering had or could have had on these projects. This research clearly shows that systems engineering does add value to projects within and outside NASA. The research results further demonstrate that systems engineering has been beneficial not only to NASA but also to organizations within which INCOSE members work. It was determined, however, that systems engineering does not operate in a vacuum and may not always guarantee success through mere application. During this research, it was discovered that the lack of or inadequate application of systems engineering in the development of complex systems may result in cost overruns, poor technical performance, project delays, and in some cases unmitigated risk with disastrous consequences including the loss of life and property. How much is saved (in terms of cost, schedule) or improved (in terms of technical performance) as a result of its implementation may never be known precisely, but by indirectly measuring its value or impact on a project, percentages of project budget spent on systems engineering activities and any schedule reductions or performance enhancements realized could be determined. According to this research, systems engineering is not a waste of time and resources; in most cases, it is

  15. Metasynthetic computing and engineering of complex systems

    CERN Document Server

    Cao, Longbing

    2015-01-01

    Provides a comprehensive overview and introduction to the concepts, methodologies, analysis, design and applications of metasynthetic computing and engineering. The author: Presents an overview of complex systems, especially open complex giant systems such as the Internet, complex behavioural and social problems, and actionable knowledge discovery and delivery in the big data era. Discusses ubiquitous intelligence in complex systems, including human intelligence, domain intelligence, social intelligence, network intelligence, data intelligence and machine intelligence, and their synergy thro

  16. 5th European Conference of the International Federation for Medical and Biological Engineering

    CERN Document Server

    European IFMBE MBEC : Cooperation for Effective Healthcare

    2012-01-01

    This volume presents the 5th European Conference of the International Federation for Medical and Biological Engineering (EMBEC),  held in Budapest, 14-18 September, 2011. The scientific discussion on the conference and in this conference proceedings include the following issues: - Signal & Image Processing - ICT - Clinical Engineering and Applications - Biomechanics and Fluid Biomechanics - Biomaterials and Tissue Repair - Innovations and Nanotechnology - Modeling and Simulation - Education and Professional

  17. Radio systems engineering a tutorial approach

    CERN Document Server

    Santos, Héctor J De Los; Ponte, Juan

    2015-01-01

    This book is intended for readers who already have knowledge of devices and circuits for radio-frequency (RF) and microwave communication and are ready to study the systems engineering-level aspects of modern radio communications systems. The authors provide a general overview of radio systems with their components, focusing on the analog parts of the system and their non-idealities. Based on the physical functionality of the various building blocks of a modern radio system, block parameters are derived, which allows the examination of their influence on the overall system performance. The dis

  18. Ionic interactions in biological and physical systems: a variational treatment.

    Science.gov (United States)

    Eisenberg, Bob

    2013-01-01

    Chemistry is about chemical reactions. Chemistry is about electrons changing their configurations as atoms and molecules react. Chemistry has for more than a century studied reactions as if they occurred in ideal conditions of infinitely dilute solutions. But most reactions occur in salt solutions that are not ideal. In those solutions everything (charged) interacts with everything else (charged) through the electric field, which is short and long range extending to the boundaries of the system. Mathematics has recently been developed to deal with interacting systems of this sort. The variational theory of complex fluids has spawned the theory of liquid crystals (or vice versa). In my view, ionic solutions should be viewed as complex fluids, particularly in the biological and engineering context. In both biology and electrochemistry ionic solutions are mixtures highly concentrated (to approximately 10 M) where they are most important, near electrodes, nucleic ids, proteins, active sites of enzymes, and ionic channels. Ca2+ is always involved in biological solutions because the concentration (really free energy per mole) of Ca2+ in a particular location is the signal that controls many biological functions. Such interacting systems are not simple fluids, and it is no wonder that analysis of interactions, such as the Hofmeister series, rooted in that tradition has not succeeded as one would hope. Here, we present a variational treatment of ard spheres in a frictional dielectric with the hope that such a treatment of an lectrolyte as a complex fluid will be productive. The theory automatically extends to spatially nonuniform boundary conditions and the nonequilibrium systems and flows they produce. The theory is unavoidably self-consistent since differential equations are derived (not assumed) from models of (Helmholtz free) nergy and dissipation of the electrolyte. The origin of the Hofmeister series is (in my view) an inverse problem that becomes well posed when

  19. Micro electromechanical systems (MEMS) for mechanical engineers

    Energy Technology Data Exchange (ETDEWEB)

    Lee, A. P., LLNL

    1996-11-18

    The ongoing advances in Microelectromechanical Systems (MEMS) are providing man-kind the freedom to travel to dimensional spaces never before conceivable. Advances include new fabrication processes, new materials, tailored modeling tools, new fabrication machines, systems integration, and more detailed studies of physics and surface chemistry as applied to the micro scale. In the ten years since its inauguration, MEMS technology is penetrating industries of automobile, healthcare, biotechnology, sports/entertainment, measurement systems, data storage, photonics/optics, computer, aerospace, precision instruments/robotics, and environment monitoring. It is projected that by the turn of the century, MEMS will impact every individual in the industrial world, totaling sales up to $14 billion (source: System Planning Corp.). MEMS programs in major universities have spawned up all over the United States, preparing the brain-power and expertise for the next wave of MEMS breakthroughs. It should be pointed out that although MEMS has been initiated by electrical engineering researchers through the involvement of IC fabrication techniques, today it has evolved such that it requires a totally multi-disciplinary team to develop useful devices. Mechanical engineers are especially crucial to the success of MEMS development, since 90% of the physical realm involved is mechanical. Mechanical engineers are needed for the design of MEMS, the analysis of the mechanical system, the design of testing apparatus, the implementation of analytical tools, and the packaging process. Every single aspect of mechanical engineering is being utilized in the MEMS field today, however, the impact could be more substantial if more mechanical engineers are involved in the systems level designing. In this paper, an attempt is made to create the pathways for a mechanical engineer to enter in the MEMS field. Examples of application in optics and medical devices will be used to illustrate how mechanical

  20. Biologically improved nanofibrous scaffolds for cardiac tissue engineering

    Energy Technology Data Exchange (ETDEWEB)

    Bhaarathy, V. [Centre for Nanofibers and Nanotechnology, NUSNNI, Faculty of Engineering, National University of Singapore, 117576 (Singapore); Department of Nanoscience and Technology, School of Physical Sciences, Bharathiar University, Coimbatore 641046 (India); Lee Kong Chian School of Medicine, Nanyang Technological University, 138673 (Singapore); Venugopal, J., E-mail: nnijrv@nus.edu.sg [Centre for Nanofibers and Nanotechnology, NUSNNI, Faculty of Engineering, National University of Singapore, 117576 (Singapore); Gandhimathi, C. [Centre for Nanofibers and Nanotechnology, NUSNNI, Faculty of Engineering, National University of Singapore, 117576 (Singapore); Ponpandian, N.; Mangalaraj, D. [Department of Nanoscience and Technology, School of Physical Sciences, Bharathiar University, Coimbatore 641046 (India); Ramakrishna, S. [Centre for Nanofibers and Nanotechnology, NUSNNI, Faculty of Engineering, National University of Singapore, 117576 (Singapore)

    2014-11-01

    Nanofibrous structure developed by electrospinning technology provides attractive extracellular matrix conditions for the anchorage, migration and differentiation of stem cells, including those responsible for regenerative medicine. Recently, biocomposite nanofibers consisting of two or more polymeric blends are electrospun more tidily in order to obtain scaffolds with desired functional and mechanical properties depending on their applications. The study focuses on one such an attempt of using copolymer Poly(L-lactic acid)-co-poly (ε-caprolactone) (PLACL), silk fibroin (SF) and Aloe Vera (AV) for fabricating biocomposite nanofibrous scaffolds for cardiac tissue engineering. SEM micrographs of fabricated electrospun PLACL, PLACL/SF and PLACL/SF/AV nanofibrous scaffolds are porous, beadless, uniform nanofibers with interconnected pores and obtained fibre diameter in the range of 459 ± 22 nm, 202 ± 12 nm and 188 ± 16 nm respectively. PLACL, PLACL/SF and PLACL/SF/AV electrospun mats obtained at room temperature with an elastic modulus of 14.1 ± 0.7, 9.96 ± 2.5 and 7.0 ± 0.9 MPa respectively. PLACL/SF/AV nanofibers have more desirable properties to act as flexible cell supporting scaffolds compared to PLACL for the repair of myocardial infarction (MI). The PLACL/SF and PLACL/SF/AV nanofibers had a contact angle of 51 ± 12° compared to that of 133 ± 15° of PLACL alone. Cardiac cell proliferation was increased by 21% in PLACL/SF/AV nanofibers compared to PLACL by day 6 and further increased to 42% by day 9. Confocal analysis for cardiac expression proteins myosin and connexin 43 was observed better by day 9 compared to all other nanofibrous scaffolds. The results proved that the fabricated PLACL/SF/AV nanofibrous scaffolds have good potentiality for the regeneration of infarcted myocardium in cardiac tissue engineering. - Highlights: • Fabricated nanofibrous scaffolds are porous, beadless and uniform structures. • PLACL/SF/AV nanofibers improve the

  1. Biologically improved nanofibrous scaffolds for cardiac tissue engineering

    International Nuclear Information System (INIS)

    Bhaarathy, V.; Venugopal, J.; Gandhimathi, C.; Ponpandian, N.; Mangalaraj, D.; Ramakrishna, S.

    2014-01-01

    Nanofibrous structure developed by electrospinning technology provides attractive extracellular matrix conditions for the anchorage, migration and differentiation of stem cells, including those responsible for regenerative medicine. Recently, biocomposite nanofibers consisting of two or more polymeric blends are electrospun more tidily in order to obtain scaffolds with desired functional and mechanical properties depending on their applications. The study focuses on one such an attempt of using copolymer Poly(L-lactic acid)-co-poly (ε-caprolactone) (PLACL), silk fibroin (SF) and Aloe Vera (AV) for fabricating biocomposite nanofibrous scaffolds for cardiac tissue engineering. SEM micrographs of fabricated electrospun PLACL, PLACL/SF and PLACL/SF/AV nanofibrous scaffolds are porous, beadless, uniform nanofibers with interconnected pores and obtained fibre diameter in the range of 459 ± 22 nm, 202 ± 12 nm and 188 ± 16 nm respectively. PLACL, PLACL/SF and PLACL/SF/AV electrospun mats obtained at room temperature with an elastic modulus of 14.1 ± 0.7, 9.96 ± 2.5 and 7.0 ± 0.9 MPa respectively. PLACL/SF/AV nanofibers have more desirable properties to act as flexible cell supporting scaffolds compared to PLACL for the repair of myocardial infarction (MI). The PLACL/SF and PLACL/SF/AV nanofibers had a contact angle of 51 ± 12° compared to that of 133 ± 15° of PLACL alone. Cardiac cell proliferation was increased by 21% in PLACL/SF/AV nanofibers compared to PLACL by day 6 and further increased to 42% by day 9. Confocal analysis for cardiac expression proteins myosin and connexin 43 was observed better by day 9 compared to all other nanofibrous scaffolds. The results proved that the fabricated PLACL/SF/AV nanofibrous scaffolds have good potentiality for the regeneration of infarcted myocardium in cardiac tissue engineering. - Highlights: • Fabricated nanofibrous scaffolds are porous, beadless and uniform structures. • PLACL/SF/AV nanofibers improve the

  2. 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.

  3. 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…

  4. 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…

  5. Biologically inspired robotic inspectors: the engineering reality and future outlook (Keynote address)

    Science.gov (United States)

    Bar-Cohen, Yoseph

    2005-04-01

    Human errors have long been recognized as a major factor in the reliability of nondestructive evaluation results. To minimize such errors, there is an increasing reliance on automatic inspection tools that allow faster and consistent tests. Crawlers and various manipulation devices are commonly used to perform variety of inspection procedures that include C-scan with contour following capability to rapidly inspect complex structures. The emergence of robots has been the result of the need to deal with parts that are too complex to handle by a simple automatic system. Economical factors are continuing to hamper the wide use of robotics for inspection applications however technology advances are increasingly changing this paradigm. Autonomous robots, which may look like human, can potentially address the need to inspect structures with configuration that are not predetermined. The operation of such robots that mimic biology may take place at harsh or hazardous environments that are too dangerous for human presence. Biomimetic technologies such as artificial intelligence, artificial muscles, artificial vision and numerous others are increasingly becoming common engineering tools. Inspired by science fiction, making biomimetic robots is increasingly becoming an engineering reality and in this paper the state-of-the-art will be reviewed and the outlook for the future will be discussed.

  6. Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method.

    Science.gov (United States)

    Tien, Shin-Ming; Hsu, Chih-Yuan; Chen, Bor-Sen

    2016-01-01

    Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella's rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the "brake component" in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each "brake component" were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the "brake component". Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate "brake component" in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.

  7. Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method.

    Directory of Open Access Journals (Sweden)

    Shin-Ming Tien

    Full Text Available Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella's rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the "brake component" in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each "brake component" were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the "brake component". Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate "brake component" in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.

  8. Engineering design of systems models and methods

    CERN Document Server

    Buede, Dennis M

    2009-01-01

    The ideal introduction to the engineering design of systems-now in a new edition. The Engineering Design of Systems, Second Edition compiles a wealth of information from diverse sources to provide a unique, one-stop reference to current methods for systems engineering. It takes a model-based approach to key systems engineering design activities and introduces methods and models used in the real world. Features new to this edition include: * The addition of Systems Modeling Language (SysML) to several of the chapters, as well as the introduction of new terminology * Additional material on partitioning functions and components * More descriptive material on usage scenarios based on literature from use case development * Updated homework assignments * The software product CORE (from Vitech Corporation) is used to generate the traditional SE figures and the software product MagicDraw UML with SysML plugins (from No Magic, Inc.) is used for the SysML figures This book is designed to be an introductory reference ...

  9. High efficiency stoichiometric internal combustion engine system

    Science.gov (United States)

    Winsor, Richard Edward; Chase, Scott Allen

    2009-06-02

    A power system including a stoichiometric compression ignition engine in which a roots blower is positioned in the air intake for the engine to control air flow. Air flow is decreased during part power conditions to maintain the air-fuel ratio in the combustion chamber of the engine at stoichiometric, thus enabling the use of inexpensive three-way catalyst to reduce oxides of nitrogen. The roots blower is connected to a motor generator so that when air flow is reduced, electrical energy is stored which is made available either to the roots blower to temporarily increase air flow or to the system electrical load and thus recapture energy that would otherwise be lost in reducing air flow.

  10. The future of metabolic engineering and synthetic biology: towards a systematic practice.

    Science.gov (United States)

    Yadav, Vikramaditya G; De Mey, Marjan; Lim, Chin Giaw; Ajikumar, Parayil Kumaran; Stephanopoulos, Gregory

    2012-05-01

    Industrial biotechnology promises to revolutionize conventional chemical manufacturing in the years ahead, largely owing to the excellent progress in our ability to re-engineer cellular metabolism. However, most successes of metabolic engineering have been confined to over-producing natively synthesized metabolites in E. coli and S. cerevisiae. A major reason for this development has been the descent of metabolic engineering, particularly secondary metabolic engineering, to a collection of demonstrations rather than a systematic practice with generalizable tools. Synthetic biology, a more recent development, faces similar criticisms. Herein, we attempt to lay down a framework around which bioreaction engineering can systematize itself just like chemical reaction engineering. Central to this undertaking is a new approach to engineering secondary metabolism known as 'multivariate modular metabolic engineering' (MMME), whose novelty lies in its assessment and elimination of regulatory and pathway bottlenecks by re-defining the metabolic network as a collection of distinct modules. After introducing the core principles of MMME, we shall then present a number of recent developments in secondary metabolic engineering that could potentially serve as its facilitators. It is hoped that the ever-declining costs of de novo gene synthesis; the improved use of bioinformatic tools to mine, sort and analyze biological data; and the increasing sensitivity and sophistication of investigational tools will make the maturation of microbial metabolic engineering an autocatalytic process. Encouraged by these advances, research groups across the world would take up the challenge of secondary metabolite production in simple hosts with renewed vigor, thereby adding to the range of products synthesized using metabolic engineering. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. 6th International Conference on Knowledge and Systems Engineering

    CERN Document Server

    Le, Anh-Cuong; Huynh, Van-Nam

    2015-01-01

    This volume contains papers presented at the Sixth International Conference on Knowledge and Systems Engineering (KSE 2014), which was held in Hanoi, Vietnam, during 9–11 October, 2014. The conference was organized by the University of Engineering and Technology, Vietnam National University, Hanoi. Besides the main track of contributed papers, this proceedings  feature the results of four special sessions focusing on specific topics of interest and three invited keynote speeches. The book gathers a total of 51 carefully reviewed papers describing recent advances and development on various topics including knowledge discovery and data mining, natural language processing, expert systems, intelligent decision making, computational biology, computational modeling, optimization algorithms, and industrial applications.

  12. 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)

  13. 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)

  14. The engineering of microprocessor systems guidelines on system development

    CERN Document Server

    1979-01-01

    The Engineering of Microprocessor Systems: Guidelines on System Development provides economical and technical guidance for use when incorporating microprocessors in products or production processes and assesses the alternatives that are available. This volume is part of Project 0251 undertaken by The Electrical Research Association, which aims to give managers and development engineers advice and comment on the development process and the hardware and software needed to support the engineering of microprocessor systems. The results of Phase 1 of the five-phase project are contained in this fir

  15. 20th Annual Systems Engineering Conference, Thursday, Volume 4

    Science.gov (United States)

    2017-10-26

    20th Annual Systems Engineering Conference October 23-26, 2017 | Waterford at Springfield | Springfield, VA NDIA.org/systemsengineering...Conference Program SYSTEMS ENGINEERING CONFERENCE 2 Welcome to the NDIA Systems Engineering Conference On behalf of the National Defense Industrial...Association’s Systems Engineering Division, I would like to extend a very warm welcome to the 20th Annual Systems Engineering Conference. Yes, the 20th Annual

  16. System Engineering of Photonic Systems for Space Application

    Science.gov (United States)

    Watson, Michael D.; Pryor, Jonathan E.

    2014-01-01

    The application of photonics in space systems requires tight integration with the spacecraft systems to ensure accurate operation. This requires some detailed and specific system engineering to properly incorporate the photonics into the spacecraft architecture and to guide the spacecraft architecture in supporting the photonics devices. Recent research in product focused, elegant system engineering has led to a system approach which provides a robust approach to this integration. Focusing on the mission application and the integration of the spacecraft system physics incorporation of the photonics can be efficiently and effectively accomplished. This requires a clear understanding of the driving physics properties of the photonics device to ensure proper integration with no unintended consequences. The driving physics considerations in terms of optical performance will be identified for their use in system integration. Keywords: System Engineering, Optical Transfer Function, Optical Physics, Photonics, Image Jitter, Launch Vehicle, System Integration, Organizational Interaction

  17. Hybrid printing of mechanically and biologically improved constructs for cartilage tissue engineering applications

    International Nuclear Information System (INIS)

    Xu Tao; Binder, Kyle W; Albanna, Mohammad Z; Dice, Dennis; Zhao Weixin; Yoo, James J; Atala, Anthony

    2013-01-01

    Bioprinting is an emerging technique used to fabricate viable, 3D tissue constructs through the precise deposition of cells and hydrogels in a layer-by-layer fashion. Despite the ability to mimic the native properties of tissue, printed 3D constructs that are composed of naturally-derived biomaterials still lack structural integrity and adequate mechanical properties for use in vivo, thus limiting their development for use in load-bearing tissue engineering applications, such as cartilage. Fabrication of viable constructs using a novel multi-head deposition system provides the ability to combine synthetic polymers, which have higher mechanical strength than natural materials, with the favorable environment for cell growth provided by traditional naturally-derived hydrogels. However, the complexity and high cost associated with constructing the required robotic system hamper the widespread application of this approach. Moreover, the scaffolds fabricated by these robotic systems often lack flexibility, which further restrict their applications. To address these limitations, advanced fabrication techniques are necessary to generate complex constructs with controlled architectures and adequate mechanical properties. In this study, we describe the construction of a hybrid inkjet printing/electrospinning system that can be used to fabricate viable tissues for cartilage tissue engineering applications. Electrospinning of polycaprolactone fibers was alternated with inkjet printing of rabbit elastic chondrocytes suspended in a fibrin–collagen hydrogel in order to fabricate a five-layer tissue construct of 1 mm thickness. The chondrocytes survived within the printed hybrid construct with more than 80% viability one week after printing. In addition, the cells proliferated and maintained their basic biological properties within the printed layered constructs. Furthermore, the fabricated constructs formed cartilage-like tissues both in vitro and in vivo as evidenced by the

  18. Intelligent Systems For Aerospace Engineering: An Overview

    Science.gov (United States)

    KrishnaKumar, K.

    2003-01-01

    Intelligent systems are nature-inspired, mathematically sound, computationally intensive problem solving tools and methodologies that have become extremely important for advancing the current trends in information technology. Artificially intelligent systems currently utilize computers to emulate various faculties of human intelligence and biological metaphors. They use a combination of symbolic and sub-symbolic systems capable of evolving human cognitive skills and intelligence, not just systems capable of doing things humans do not do well. Intelligent systems are ideally suited for tasks such as search and optimization, pattern recognition and matching, planning, uncertainty management, control, and adaptation. In this paper, the intelligent system technologies and their application potential are highlighted via several examples.

  19. A cylinder pressure based engine management system

    Energy Technology Data Exchange (ETDEWEB)

    Truscott, A.; Noble, A. [Ricardo Consulting Engineers Ltd. (United Kingdom); Mueller, R.; Hart, M.; Kroetz, G.; Eickhoff, M. [DaimlerChrysler AG (Germany); Cavalloni, C.; Gnielka, M. [Kistler Instrumente AG (Switzerland)

    2000-07-01

    Worldwide demands on fuel economy and lower emissions from automotive vehicles have led to stringent requirements in the development of Engine Management Systems (EMS). Cylinder Pressure based Engine Management Systems (CPEMS) provide a way forward in EMS technology by combining intelligent control algorithms with innovative sensing techniques. The full utilisation of model-based control and diagnostics to provide improvements in cost, efficiency, emissions and comfort requires the close monitoring of engine conditions. This is made possible with the advent of new inexpensive sensor materials that can withstand the harsh environment of the combustion chamber. AENEAS is a collaborative project undertaken by Ricardo, DaimlerChrysler and Kistler, with financial support from the European Commission and the Swiss Government, aimed at demonstrating the major benefits of CPEMS technology. This paper describes the application of CPEMS technology to a spark ignition (SI) engine. It describes how the combination of model based algorithms, incorporating physical principles, and cylinder pressure sensing can provide an effective means of engine control and diagnostics. Results are presented to demonstrate the benefits of this new technology. (author)

  20. Systems Engineering as a tool; Verktoeyet Systems Engineering : struktur fra start til maal

    Energy Technology Data Exchange (ETDEWEB)

    Carlsen, Randi

    2002-07-01

    Systems engineering integrates all types of specialists and disciplines into teams that try to create a structured development process from concept via production to operation. The idea is that by using systems engineering, projects can be completed efficiently and successfully. It is important that the individual participant in a project understands that he or she works within a system and that there is a need for skill, comprehensiveness and communication. Systems engineering comprises system design, computer aided design, cybernetics and mecatronics. The article describes the use of systems engineering in a student project in which a heat pump will be used to utilize the energy potential of ground water primarily to heat the visitors' area in a mine museum in Kongsberg, Norway.

  1. Engineering Education as a Complex System

    Science.gov (United States)

    Gattie, David K.; Kellam, Nadia N.; Schramski, John R.; Walther, Joachim

    2011-01-01

    This paper presents a theoretical basis for cultivating engineering education as a complex system that will prepare students to think critically and make decisions with regard to poorly understood, ill-structured issues. Integral to this theoretical basis is a solution space construct developed and presented as a benchmark for evaluating…

  2. Practice-based systems engineering programme

    CSIR Research Space (South Africa)

    Goncalves, D

    2010-08-01

    Full Text Available the required system engineering competencies is introduced. A practice-based approach is presented as part of the solution, including the roles of universities, students and industry within this approach. Finally we elaborate on a proposed curriculum for a...

  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. Systems engineering approach for future automotive microcontroller solutions; Systems-Engineering-Ansatz zur Entwicklung zukuenftiger Mikrocontroller

    Energy Technology Data Exchange (ETDEWEB)

    Hilgert, J.; Turski, K.; Vollhardt, S. [NEC Electronics Europe, Duesseldorf (Germany)

    2005-09-01

    In the future, microcontrollers used in automotive applications will have to meet escalating demands from different areas. For this reason, NEC Electronics (Europe) regards the concept of Systems Engineering as the key to handling the development of the complex system vehicle. This article describes how the Systems Engineering approach is applied to the development of new microcontrollers. The example used is the development platform for NEC's upcoming gateway product. (orig.)

  8. Execution Of Systems Integration Principles During Systems Engineering Design

    Science.gov (United States)

    2016-09-01

    application utilized a paper-based approach to systems design. The customer directed utilization of an SE Waterfall process model . These new...regarding requirements, stakeholders, testing, and system boundaries. Additionally, this thesis discusses use of systems architecture frameworks and models ...and the consistent use of model - based systems engineering throughout development. Lastly, it proposes formal methods language for improving models

  9. 46 CFR 184.620 - Propulsion engine control systems.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Propulsion engine control systems. 184.620 Section 184... Communications Systems § 184.620 Propulsion engine control systems. (a) A vessel must have two independent means of controlling each propulsion engine. Control must be provided for the engine speed, direction of...

  10. Electronic ignition system for internal combustion engines

    Energy Technology Data Exchange (ETDEWEB)

    Crowder, L W

    1980-11-20

    Mechanical ignition adjustment devices are sensitive to many effects, for example breakage, faults due to manufacturing tolerances, play in the linkage and the effect of a dirty or corrosive environment. It is therefore the purpose of the invention to provide an electronic ignition system which avoids the disadvantages of a mechanical system. The invention provides adjustment of the ignition point, which gives advance of the ignition timing with increasing speed. An output signal is formed, which supersedes the signal supplied by the electronic control system, so that the ignition is advanced. This also occurs with a larger crankshaft angle before top dead centre of the engine. The electronic control system combines with a source of AC time signals which has a generator as electrical transmitter and a DC battery and ignition coil. The rotor of the electrical generator is driven synchronised with the engine. Structural and functional details of the transistor control circuits are given in 5 patent claims.

  11. 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.

  12. 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...

  13. 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....

  14. The Future of Metabolic Engineering and Synthetic Biology: Towards a Systematic Practice

    Science.gov (United States)

    Yadav, Vikramaditya G.; De Mey, Marjan; Lim, Chin Giaw; Ajikumar, Parayil Kumaran; Stephanopoulos, Gregory

    2012-01-01

    Industrial biotechnology promises to revolutionize conventional chemical manufacturing in the years ahead, largely owing to the excellent progress in our ability to re-engineer cellular metabolism. However, most successes of metabolic engineering have been confined to over-producing natively synthesized metabolites in E. coli and S. cerevisiae. A major reason for this development has been the descent of metabolic engineering, particularly secondary metabolic engineering, to a collection of demonstrations rather than a systematic practice with generalizable tools. Synthetic biology, a more recent development, faces similar criticisms. Herein, we attempt to lay down a framework around which bioreaction engineering can systematize itself just like chemical reaction engineering. Central to this undertaking is a new approach to engineering secondary metabolism known as ‘multivariate modular metabolic engineering’ (MMME), whose novelty lies in its assessment and elimination of regulatory and pathway bottlenecks by re-defining the metabolic network as a collection of distinct modules. After introducing the core principles of MMME, we shall then present a number of recent developments in secondary metabolic engineering that could potentially serve as its facilitators. It is hoped that the ever-declining costs of de novo gene synthesis; the improved use of bioinformatic tools to mine, sort and analyze biological data; and the increasing sensitivity and sophistication of investigational tools will make the maturation of microbial metabolic engineering an autocatalytic process. Encouraged by these advances, research groups across the world would take up the challenge of secondary metabolite production in simple hosts with renewed vigor, thereby adding to the range of products synthesized using metabolic engineering. PMID:22629571

  15. WFIRST: Coronagraph Systems Engineering and Performance Budgets

    Science.gov (United States)

    Poberezhskiy, Ilya; cady, eric; Frerking, Margaret A.; Kern, Brian; Nemati, Bijan; Noecker, Martin; Seo, Byoung-Joon; Zhao, Feng; Zhou, Hanying

    2018-01-01

    The WFIRST coronagraph instrument (CGI) will be the first in-space coronagraph using active wavefront control to directly image and characterize mature exoplanets and zodiacal disks in reflected starlight. For CGI systems engineering, including requirements development, CGI performance is predicted using a hierarchy of performance budgets to estimate various noise components — spatial and temporal flux variations — that obscure exoplanet signals in direct imaging and spectroscopy configurations. These performance budgets are validated through a robust integrated modeling and testbed model validation efforts.We present the performance budgeting framework used by WFIRST for the flow-down of coronagraph science requirements, mission constraints, and observatory interfaces to measurable instrument engineering parameters.

  16. Systems engineering real estate development projects

    Science.gov (United States)

    Gusakova, Elena; Titarenko, Boris; Stepanov, Vitaliy

    2017-10-01

    In recent years, real estate development has accumulated a wealth of experience in implementing major projects, which requires comprehension and systematization. The scientific instrument of system engineering is studied in the article and is substantively interpreted with reference to real estate development projects. The most perspective approaches and models are substantiated, allowing strategically to plan the life cycle of the project as a whole, and also to solve the engineering butt problems of the project. The relevance of further scientific studies of regularities and specifics of the life cycle of real estate development projects conducted at the Moscow State University of Economics and Management at the ISTA department is shown.

  17. Principles of e-learning systems engineering

    CERN Document Server

    Gilbert, Lester

    2008-01-01

    The book integrates the principles of software engineering with the principles of educational theory, and applies them to the problems of e-learning development, thus establishing the discipline of E-learning systems engineering. For the first time, these principles are collected and organised into the coherent framework that this book provides. Both newcomers to and established practitioners in the field are provided with integrated and grounded advice on theory and practice. The book presents strong practical and theoretical frameworks for the design and development of technology-based mater

  18. 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...

  19. The systems engineering overview and process (from the Systems Engineering Management Guide, 1990)

    Science.gov (United States)

    1993-01-01

    The past several decades have seen the rise of large, highly interactive systems that are on the forward edge of technology. As a result of this growth and the increased usage of digital systems (computers and software), the concept of systems engineering has gained increasing attention. Some of this attention is no doubt due to large program failures which possibly could have been avoided, or at least mitigated, through the use of systems engineering principles. The complexity of modern day weapon systems requires conscious application of systems engineering concepts to ensure producible, operable and supportable systems that satisfy mission requirements. Although many authors have traced the roots of systems engineering to earlier dates, the initial formalization of the systems engineering process for military development began to surface in the mid-1950s on the ballistic missile programs. These early ballistic missile development programs marked the emergence of engineering discipline 'specialists' which has since continued to grow. Each of these specialties not only has a need to take data from the overall development process, but also to supply data, in the form of requirements and analysis results, to the process. A number of technical instructions, military standards and specifications, and manuals were developed as a result of these development programs. In particular, MILSTD-499 was issued in 1969 to assist both government and contractor personnel in defining the systems engineering effort in support of defense acquisition programs. This standard was updated to MIL-STD499A in 1974, and formed the foundation for current application of systems engineering principles to military development programs.

  20. 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.

  1. Systems Engineering Management Training at Naval Air Systems Command

    National Research Council Canada - National Science Library

    Rebel, James

    2000-01-01

    Within the past few years, the Naval Air Systems Command (NAVAIR) has undergone several major changes including an engineering reorganization from a matrix organization to an Integrated Program Team/Competency Aligned Organization (IPT/CAO...

  2. System engineering approach to GPM retrieval algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Rose, C. R. (Chris R.); Chandrasekar, V.

    2004-01-01

    System engineering principles and methods are very useful in large-scale complex systems for developing the engineering requirements from end-user needs. Integrating research into system engineering is a challenging task. The proposed Global Precipitation Mission (GPM) satellite will use a dual-wavelength precipitation radar to measure and map global precipitation with unprecedented accuracy, resolution and areal coverage. The satellite vehicle, precipitation radars, retrieval algorithms, and ground validation (GV) functions are all critical subsystems of the overall GPM system and each contributes to the success of the mission. Errors in the radar measurements and models can adversely affect the retrieved output values. Ground validation (GV) systems are intended to provide timely feedback to the satellite and retrieval algorithms based on measured data. These GV sites will consist of radars and DSD measurement systems and also have intrinsic constraints. One of the retrieval algorithms being studied for use with GPM is the dual-wavelength DSD algorithm that does not use the surface reference technique (SRT). The underlying microphysics of precipitation structures and drop-size distributions (DSDs) dictate the types of models and retrieval algorithms that can be used to estimate precipitation. Many types of dual-wavelength algorithms have been studied. Meneghini (2002) analyzed the performance of single-pass dual-wavelength surface-reference-technique (SRT) based algorithms. Mardiana (2003) demonstrated that a dual-wavelength retrieval algorithm could be successfully used without the use of the SRT. It uses an iterative approach based on measured reflectivities at both wavelengths and complex microphysical models to estimate both No and Do at each range bin. More recently, Liao (2004) proposed a solution to the Do ambiguity problem in rain within the dual-wavelength algorithm and showed a possible melting layer model based on stratified spheres. With the No and Do

  3. Ignition system for an internal combustion engine

    Energy Technology Data Exchange (ETDEWEB)

    Imhof, G

    1977-05-12

    The invention pertains to ignition systems for internal combustion engines; in particular, these are used in the engines of modern small motorcycles, where power is supplied by means of a so-called flywheel magneto, so that there is no need for an additional battery. The invention will prevent back-kicking. This is achieved by the following means: in the right direction of rotation of the internal combustion engine, due to an axial magnetic unsymmetry of the rotor, a voltage component that can switch the electronic switch will occur only in one of the two parts of the control winding at the point of ignition. In the wrong direction of rotation, on the other hand, this voltage component will only occur in the other part of the control winding and will act in direction on a diode connected in parallel to this part of the winding.

  4. Integration and framing between system engineering, enterprise engineering and whole of society

    CSIR Research Space (South Africa)

    Erasmus, Louwrence D

    2017-07-01

    Full Text Available with the semantic theoretical constructs of systems levels of Boulding’s General Systems Theory. The construct of systems hierarchy levels addresses the progression from complicated engineered levels to the complexity of human interaction with engineered... predicates in: • A theory of the systems engineering process (Doeben-Henisch, et al., 2008) (Erasmus & Doeben-Henisch, 2011a) • A theory of systems engineering management (SEMBASE) (Erasmus & Doeben-Henisch, 2011b). In the structuralist programme...

  5. Biological engineering applications of feedforward neural networks designed and parameterized by genetic algorithms.

    Science.gov (United States)

    Ferentinos, Konstantinos P

    2005-09-01

    Two neural network (NN) applications in the field of biological engineering are developed, designed and parameterized by an evolutionary method based on the evolutionary process of genetic algorithms. The developed systems are a fault detection NN model and a predictive modeling NN system. An indirect or 'weak specification' representation was used for the encoding of NN topologies and training parameters into genes of the genetic algorithm (GA). Some a priori knowledge of the demands in network topology for specific application cases is required by this approach, so that the infinite search space of the problem is limited to some reasonable degree. Both one-hidden-layer and two-hidden-layer network architectures were explored by the GA. Except for the network architecture, each gene of the GA also encoded the type of activation functions in both hidden and output nodes of the NN and the type of minimization algorithm that was used by the backpropagation algorithm for the training of the NN. Both models achieved satisfactory performance, while the GA system proved to be a powerful tool that can successfully replace the problematic trial-and-error approach that is usually used for these tasks.

  6. Can Man Control His Biological Evolution? A Symposium on Genetic Engineering. Genetic Engineering

    Science.gov (United States)

    Ramsey, Paul

    1972-01-01

    Presented are issues related to genetic engineering. Increased knowledge of techniques to manipulate genes are apt to create confusion about moral values in relation to unborn babies and other living organisms on earth. Human beings may use this knowledge to disturb the balance maintained by nature. (PS)

  7. Systems Engineering for Space Exploration Medical Capabilities

    Science.gov (United States)

    Mindock, Jennifer; Reilly, Jeffrey; Rubin, David; Urbina, Michelle; Hailey, Melinda; Hanson, Andrea; Burba, Tyler; McGuire, Kerry; Cerro, Jeffrey; Middour, Chris; hide

    2017-01-01

    Human exploration missions that reach destinations beyond low Earth orbit, such as Mars, will present significant new challenges to crew health management. For the medical system, lack of consumable resupply, evacuation opportunities, and real-time ground support are key drivers toward greater autonomy. Recognition of the limited mission and vehicle resources available to carry out exploration missions motivates the Exploration Medical Capability (ExMC) Element's approach to enabling the necessary autonomy. The Element's work must integrate with the overall exploration mission and vehicle design efforts to successfully provide exploration medical capabilities. ExMC is applying systems engineering principles and practices to accomplish its goals. This paper discusses the structured and integrative approach that is guiding the medical system technical development. Assumptions for the required levels of care on exploration missions, medical system goals, and a Concept of Operations are early products that capture and clarify stakeholder expectations. Model-Based Systems Engineering techniques are then applied to define medical system behavior and architecture. Interfaces to other flight and ground systems, and within the medical system are identified and defined. Initial requirements and traceability are established, which sets the stage for identification of future technology development needs. An early approach for verification and validation, taking advantage of terrestrial and near-Earth exploration system analogs, is also defined to further guide system planning and development.

  8. DIDACTIC ENGINEERING: DESIGNING NEW GENERATION LEARNING SYSTEMS

    Directory of Open Access Journals (Sweden)

    Nail K. Nuriyev

    2016-09-01

    Full Text Available Introduction: the article deals with the organisation of training activities in the man-made environment. Didactic engineering is seen as a methodology within which problems of didactics are solved with application of pedagogical, psychological, engineering methods. It is obvious that in order to implement the training of future engineers in a competence-based format (according to educational standard a new type of teaching system is needed, with new capacities (properties. These systems should set each student towards the development of professionally significant (key abilities, taking into account his/her psychological characteristics; ensure training on the verge of permissible difficulties (developing training, and thereby achieve rapid development of key skills, through his/her zone of “immediate development”; to diagnose the quality of possession of a competence in the academic sense. For the objectivity and reliability of assessment of the level and depth of learned knowledge it is necessary to generate this evaluation in a metric format. As a result, we created a didactic system, which combines all the listed properties and the properties of classical systems. This allowed us to construct a new generation of didactic systems. Materials and Methods: the research is based on a systematic analysis of the activity of an engineer; on models of “zones of immediate development” by L. S. Vygotsky; on “developmental education” by L. N. Zankova; on the use of pedagogical and psychological patterns as well as taxonomic methods, didactic engineering, theory of probability and mathematical statistics. Results: constructed is a model for training engineers in the metric format of competence, which envisages a rapid development of students project and constructive abilit ies based on their knowledge learned. Discussion and Conclusions: the parameters defining the probability of engineer’s success have been described; the taxonomic scale

  9. Adaptive vibration isolation system for diesel engine

    Institute of Scientific and Technical Information of China (English)

    YANG Tie-jun; ZHANG Xin-yu; XIAO You-hong; HUANG Jin-e; LIU Zhi-gang

    2004-01-01

    An active two-stage isolation mounting, on which servo-hydraulic system is used as the actuator (secondary vibration source) and a diesel engine is used as primary vibration source, has been built. The upper mass of the mounting is composed of a 495diesel and an electrical eddy current dynamometer. The lower mass is divided into four small masses to which servo-hydraulic actuator and rubber isolators are attached. According to the periodical characteristics of diesel vibration signals, a multi-point adaptive strategy based on adaptive comb filtered algorithm is applied to active multi-direction coupled vibrations control for the engine. The experimental results demonstrate that a good suppression in the effective range of phase compensation in secondary path (within 100Hz) at different operation conditions is achieved, and verify that this strategy is effective. The features of the active system, the development activities carried out on the system and experimental results are discussed in the paper.

  10. NPP site selection: A systems engineering approach

    Energy Technology Data Exchange (ETDEWEB)

    Pwani, Henry; Kamanja, Florah; Zolkaffly, Zulfakar; Jung, J. C. [KEPCO International Nuclear Graduate School, Ulsan (Korea, Republic of)

    2012-10-15

    The necessity for improved decision making concerning the siting and licensing of major power facilities has been accelerated in the past decade by the increased environmental consciousness of the public and by the energy crisis. These problems are exceedingly complex due to their multiple objective nature, the many interest groups, the long range time horizons, and the inherent uncertainties of the potential impacts of any decision. Along with the relatively objective economic and engineering concerns, the more subjective factors involving safety, environmental, and social issues are crucial to the problem. The preferences of the general public, as consumers, the utility companies, as builders and operators of power plant facilities, and environmentalists and the government must be accounted for in analyzing power plant siting and licensing issues. We advocate for a systems engineering approach that articulates stake holder's requirements, expert judgements, and a systems decision making approach. The appropriateness and application of systems decision making process is illustrated in this paper.

  11. NPP site selection: A systems engineering approach

    International Nuclear Information System (INIS)

    Pwani, Henry; Kamanja, Florah; Zolkaffly, Zulfakar; Jung, J. C.

    2012-01-01

    The necessity for improved decision making concerning the siting and licensing of major power facilities has been accelerated in the past decade by the increased environmental consciousness of the public and by the energy crisis. These problems are exceedingly complex due to their multiple objective nature, the many interest groups, the long range time horizons, and the inherent uncertainties of the potential impacts of any decision. Along with the relatively objective economic and engineering concerns, the more subjective factors involving safety, environmental, and social issues are crucial to the problem. The preferences of the general public, as consumers, the utility companies, as builders and operators of power plant facilities, and environmentalists and the government must be accounted for in analyzing power plant siting and licensing issues. We advocate for a systems engineering approach that articulates stake holder's requirements, expert judgements, and a systems decision making approach. The appropriateness and application of systems decision making process is illustrated in this paper

  12. Engineering embedded systems physics, programs, circuits

    CERN Document Server

    Hintenaus, Peter

    2015-01-01

    This is a textbook for graduate and final-year-undergraduate computer-science and electrical-engineering students interested in the hardware and software aspects of embedded and cyberphysical systems design. It is comprehensive and self-contained, covering everything from the basics to case-study implementation. Emphasis is placed on the physical nature of the problem domain and of the devices used. The reader is assumed to be familiar on a theoretical level with mathematical tools like ordinary differential equation and Fourier transforms. In this book these tools will be put to practical use. Engineering Embedded Systems begins by addressing basic material on signals and systems, before introducing to electronics. Treatment of digital electronics accentuating synchronous circuits and including high-speed effects proceeds to micro-controllers, digital signal processors and programmable logic. Peripheral units and decentralized networks are given due weight. The properties of analog circuits and devices like ...

  13. 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.

  14. Engineered Barrier System: Physical and Chemical Environment

    Energy Technology Data Exchange (ETDEWEB)

    P. Dixon

    2004-04-26

    The conceptual and predictive models documented in this Engineered Barrier System: Physical and Chemical Environment Model report describe the evolution of the physical and chemical conditions within the waste emplacement drifts of the repository. The modeling approaches and model output data will be used in the total system performance assessment (TSPA-LA) to assess the performance of the engineered barrier system and the waste form. These models evaluate the range of potential water compositions within the emplacement drifts, resulting from the interaction of introduced materials and minerals in dust with water seeping into the drifts and with aqueous solutions forming by deliquescence of dust (as influenced by atmospheric conditions), and from thermal-hydrological-chemical (THC) processes in the drift. These models also consider the uncertainty and variability in water chemistry inside the drift and the compositions of introduced materials within the drift. This report develops and documents a set of process- and abstraction-level models that constitute the engineered barrier system: physical and chemical environment model. Where possible, these models use information directly from other process model reports as input, which promotes integration among process models used for total system performance assessment. Specific tasks and activities of modeling the physical and chemical environment are included in the technical work plan ''Technical Work Plan for: In-Drift Geochemistry Modeling'' (BSC 2004 [DIRS 166519]). As described in the technical work plan, the development of this report is coordinated with the development of other engineered barrier system analysis model reports.

  15. 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.

  16. Combustion pressure-based engine management system

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, R.; Hart, M. [DaimlerChrysler, Stuttart (Germany); Truscott, A.; Noble, A. [Ricardo, Shoreham-by-Sea (United Kingdom); Kroetz, G.; Richter, C. [DaimlerChrysler, Munchen (Germany); Cavalloni, C. [Kistler Instruments AG, Winterthur (Switzerland)

    2000-07-01

    In order to fulfill future emissions and OBD regulations, whilst meeting increasing demands for driveability and refinement, new technologies for SI engines have to be found in terms of sensors and algorithms for engine control units. One promising way, explored in the AENEAS collaborative project between DaimlerChrysler, Kistler, Ricardo and the European Commission, is to optimize the behavior of the system by using in-cylinder measurements and analysing them with modern control algorithms. In this paper a new engine management system based on combustion pressure sensing is presented. The pressure sensor is designed to give a reliable and accurate signal of the full pressure trace during a working cycle. With the application of new technologies low cost manufacturing appears to be achievable, so that an application in mass production can be considered. Furthermore, model-based algorithms were developed to allow optimal control of the engine based on the in-cylinder measurements. The algorithms incorporate physical principles to improve efficiency, emissions and to reduce the parameterisation effort. In the paper, applications of the combustion pressure signal for air mass estimation, knock detection, ignition control cam phase detection and diagnosis are discussed. (author)

  17. Genome Engineering with TALE and CRISPR Systems in Neuroscience.

    Science.gov (United States)

    Lee, Han B; Sundberg, Brynn N; Sigafoos, Ashley N; Clark, Karl J

    2016-01-01

    Recent advancement in genome engineering technology is changing the landscape of biological research and providing neuroscientists with an opportunity to develop new methodologies to ask critical research questions. This advancement is highlighted by the increased use of programmable DNA-binding agents (PDBAs) such as transcription activator-like effector (TALE) and RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems. These PDBAs fused or co-expressed with various effector domains allow precise modification of genomic sequences and gene expression levels. These technologies mirror and extend beyond classic gene targeting methods contributing to the development of novel tools for basic and clinical neuroscience. In this Review, we discuss the recent development in genome engineering and potential applications of this technology in the field of neuroscience.

  18. Genome Engineering with TALE and CRISPR Systems in Neuroscience

    Science.gov (United States)

    Lee, Han B.; Sundberg, Brynn N.; Sigafoos, Ashley N.; Clark, Karl J.

    2016-01-01

    Recent advancement in genome engineering technology is changing the landscape of biological research and providing neuroscientists with an opportunity to develop new methodologies to ask critical research questions. This advancement is highlighted by the increased use of programmable DNA-binding agents (PDBAs) such as transcription activator-like effector (TALE) and RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems. These PDBAs fused or co-expressed with various effector domains allow precise modification of genomic sequences and gene expression levels. These technologies mirror and extend beyond classic gene targeting methods contributing to the development of novel tools for basic and clinical neuroscience. In this Review, we discuss the recent development in genome engineering and potential applications of this technology in the field of neuroscience. PMID:27092173

  19. 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.

  20. 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.