Science.gov

Sample records for synthetic model systems

  1. A system model and inversion for synthetic aperture radar imaging.

    PubMed

    Soumekh, M

    1992-01-01

    A system model and its corresponding inversion for synthetic aperture radar (SAR) imaging are presented. The system model incorporates the spherical nature of a radar's radiation pattern at far field. The inverse method based on this model performs a spatial Fourier transform (Doppler processing) on the recorded signals with respect to the available coordinates of a translational radar (SAR) or target (inverse SAR). It is shown that the transformed data provide samples of the spatial Fourier transform of the target's reflectivity function. The inverse method can be modified to incorporate deviations of the radar's motion from its prescribed straight line path. The effects of finite aperture on resolution, reconstruction, and sampling constraints for the imaging problem are discussed.

  2. Rigid Biological Systems as Models for Synthetic Composites

    NASA Astrophysics Data System (ADS)

    Mayer, George

    2005-11-01

    Advances that have been made in understanding the mechanisms underlying the mechanical behavior of a number of biological materials (namely mollusk shells and sponge spicules) are discussed here. Attempts at biomimicry of the structure of a nacreous layer of a mollusk shell have shown reasonable success. However, they have revealed additional issues that must be addressed if new synthetic composite materials that are based on natural systems are to be constructed. Some of the important advantages and limitations of copying from nature are also described here.

  3. A Unique Model Platform for C4 Plant Systems and Synthetic Biology

    DTIC Science & Technology

    2015-12-10

    AFRL-AFOSR-JP-TR-2016-0001 A Unique Model Platform for C4 Plant Systems and Synthetic Biology Lars Nielsen THE UNIVERSITY OF QUEENSLAND Final Report...3. DATES COVERED 03-06-2014 to 02-06-2015 4. TITLE AND SUBTITLE A Unique Model Platform for C4 Plant Systems and Synthetic Biology 5a...Platform for C4 Plant Systems and Synthetic Biology 5a. CONTRACT NUMBER FA2386-14-1-4028 5b. GRANT NUMBER Grant AOARD-14IOA042 144028 5c

  4. Evolvable synthetic neural system

    NASA Technical Reports Server (NTRS)

    Curtis, Steven A. (Inventor)

    2009-01-01

    An evolvable synthetic neural system includes an evolvable neural interface operably coupled to at least one neural basis function. Each neural basis function includes an evolvable neural interface operably coupled to a heuristic neural system to perform high-level functions and an autonomic neural system to perform low-level functions. In some embodiments, the evolvable synthetic neural system is operably coupled to one or more evolvable synthetic neural systems in a hierarchy.

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

    PubMed

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

    2015-08-21

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

  6. MSW to synthetic natural gas: System modeling and thermodynamics assessment.

    PubMed

    Zhu, Lin; Zhang, Le; Fan, Junming; Jiang, Peng; Li, Luling

    2016-02-01

    To achieve environmental-friendly and energy-efficiency synthetic natural gas (SNG) production routing from municipal solid waste (MSW), a MSW-to-SNG process is unprecedentedly presented in this work, of which the designed configuration is developed and simulated with the aid of Aspen Plus. In addition, sensitivity analyses on major operation parameters, such as equivalence volume ratio (ER), steam-to-MSW mass ratio (S/M) and methanation pressure, are performed with the discussion of process efficiencies and SNG quality. In parallel, the comparison analysis is considered by adopting various MSW material. In this work, the composition of SNG mainly consists of 87.7% CH4, 2.9% CO2, 2.3% H2 and 7.1% N2. And lower heating value (LHV) together with Wobbe index of SNG are separately 31.66MJ/Nm(3) and 45.90MJ/Nm(3). Moreover, the wood-to-SNG, MSW-to-SNG and coal-to-SNG processes are carried out to demonstrate the superiority of the MSW-to-SNG process. The results reveal that the MSW-to-SNG process is a promising option to dispose MSW environmentally, meanwhile converting MSW to the valuable SNG.

  7. Synthetical Reliability Analysis Model of CNC Software System

    NASA Astrophysics Data System (ADS)

    Xu, Yue; Xia, Yinjie; Wan, Yi

    CNC technology is the core of advanced manufacturing technology, and CNC software system is the very important part of numerical control system. The entire CNC system will not work normally, once the potential failure makes the software invalid. As to the current study of CNC sysytem, in use of the FAULT glitch tree, established a glitch tree for the CNC system; find the minimum cut sets with Fussed method and then according to the probability of several common glitches, make quantitative analysis in the reliability of the CNC system so that scientific ways can be provided for the reliability design, maintenance and management of the CNC system.

  8. EOID System Model Validation, Metrics, and Synthetic Clutter Generation

    DTIC Science & Technology

    2003-09-30

    Our long-term goal is to accurately predict the capability of the current generation of laser-based underwater imaging sensors to perform Electro ... Optic Identification (EOID) against relevant targets in a variety of realistic environmental conditions. The models will predict the impact of

  9. Synthetic Vision Systems

    NASA Technical Reports Server (NTRS)

    Prinzel, L.J.; Kramer, L.J.

    2009-01-01

    A synthetic vision system is an aircraft cockpit display technology that presents the visual environment external to the aircraft using computer-generated imagery in a manner analogous to how it would appear to the pilot if forward visibility were not restricted. The purpose of this chapter is to review the state of synthetic vision systems, and discuss selected human factors issues that should be considered when designing such displays.

  10. A Model of a Synthetic Biological Communication Interface between Mammalian Cells and Mechatronic Systems.

    PubMed

    Heyde, Keith C; Ruder, Warren C

    2016-12-01

    The creation of communication interfaces between abiotic and biotic systems represents a significant research challenge. In this work, we design and model a system linking the biochemical signaling pathways of mammalian cells to the actions of a mobile robotic prosthesis. We envision this system as a robotic platform carrying an optically monitored bioreactor that harbors mammalian cells. The cellular, optical signal is captured by an onboard fluorescent microscope and converted into an electronic signal. We first present a design for the overall cell-robot system, with a specific focus on the design of the synthetic gene networks needed for the system. We use these synthetic networks to encode motion commands within the cell's endogenous, oscillatory calcium signaling pathways. We then describe a potential system whereby this oscillatory signal could be outputted and monitored as a change in cellular fluorescence. Next, we use the changes resulting from the synthetic biological modifications as new parameters in a simulation of a well-established mathematical model for intracellular calcium signaling. The resulting signal is processed in the frequency domain, with specific frequencies activating cognate robot motion subroutines.

  11. A Model of a Synthetic Biological Communication Interface between Mammalian Cells and Mechatronic Systems.

    PubMed

    Heyde, Keith Cameron; Ruder, Warren Christopher

    2016-10-25

    The creation of communication interfaces between abiotic and biotic systems represents a significant research challenge. In this work, we design and model a system linking the biochemical signaling pathways of mammalian cells to the actions of a mobile robotic prosthesis. We envision this system as a robotic platform carrying an optically monitored bioreactor that harbors mammalian cells. The cellular, optical signal is captured by an onboard fluorescent microscope and converted into an electronic signal. We first present a design for the overall cellrobot system, with a specific focus on the design of the synthetic gene networks needed for the system. We use these synthetic networks to encode motion commands within the cell's endogenous, oscillatory calcium signaling pathways. We then describe a potential system whereby this oscillatory signal could be outputted and monitored as a change in cellular fluorescence. Next, we use the changes resulting from the synthetic biological modifications as new parameters in a simulation of a wellestablished mathematical model for intracellular calcium signaling. The resulting signal is processed in the frequency domain, with specific frequencies activating cognate robot motion subroutines.

  12. Modeling Transport Through Synthetic Nanopores

    PubMed Central

    Aksimentiev, Aleksei; Brunner, Robert K.; Cruz-Chú, Eduardo; Comer, Jeffrey; Schulten, Klaus

    2011-01-01

    Nanopores in thin synthetic membranes have emerged as convenient tools for high-throughput single-molecule manipulation and analysis. Because of their small sizes and their ability to selectively transport solutes through otherwise impermeable membranes, nanopores have numerous potential applications in nanobiotechnology. For most applications, properties of the nanopore systems have to be characterize at the atomic level, which is currently beyond the limit of experimental methods. Molecular dynamics (MD) simulations can provide the desired information, however several technical challenges have to be met before this method can be applied to synthetic nanopore systems. Here, we highlight our recent work on modeling synthetic nanopores of the most common types. First, we describe a novel graphical tool for setting up all-atom systems incorporating inorganic materials and biomolecules. Next, we illustrate the application of the MD method for silica, silicon nitride, and polyethylene terephthalate nanopores. Following that, we describe a method for modeling synthetic surfaces using a bias potential. Future directions for tool development and nanopore modeling are briefly discussed at the end of this article. PMID:21909347

  13. SMART-DS: Synthetic Models for Advanced, Realistic Testing: Distribution Systems and Scenarios

    SciTech Connect

    Hodge, Bri-Mathias; Palmintier, Bryan

    2016-03-03

    This presentation provides an overview of full-scale, high-quality, synthetic distribution system data set(s) for testing distribution automation algorithms, distributed control approaches, ADMS capabilities, and other emerging distribution technologies.

  14. Synthetic quantum systems

    NASA Astrophysics Data System (ADS)

    Cahill, Reginald T.

    2002-10-01

    So far proposed quantum computers use fragile and environmentally sensitive natural quantum systems. Here we explore the new notion that synthetic quantum systems suitable for quantum computation may be fabricated from smart nanostructures using topological excitations of a stochastic neural-type network that can mimic natural quantum systems. These developments are a technological application of process physics which is an information theory of reality in which space and quantum phenomena are emergent, and so indicates the deep origins of quantum phenomena. Analogous complex stochastic dynamical systems have recently been proposed within neurobiology to deal with the emergent complexity of biosystems, particularly the biodynamics of higher brain function. The reasons for analogous discoveries in fundamental physics and neurobiology are discussed.

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

    PubMed

    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.

  16. BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

    PubMed

    Gorochowski, Thomas E; Matyjaszkiewicz, Antoni; Todd, Thomas; Oak, Neeraj; Kowalska, Kira; Reid, Stephen; Tsaneva-Atanasova, Krasimira T; Savery, Nigel J; Grierson, Claire S; di Bernardo, Mario

    2012-01-01

    Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI) recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.

  17. Agent-based modelling in synthetic biology

    PubMed Central

    2016-01-01

    Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions. PMID:27903820

  18. Using synthetic model systems to understand charge separation and spin dynamics in photosynthetic reaction centers.

    SciTech Connect

    Wasielewski, M. R.

    1998-08-27

    Our current work in modeling reaction center dynamics has resulted in the observation of each major spin-dependent photochemical pathway that is observed in reaction centers. The development of new, simpler model systems has permitted us to probe deeply into the mechanistic issues that drive these dynamics. Based on these results we have returned to biomimetic chlorophyll-based electron donors to mimic these dynamics. Future studies will focus on the details of electronic structure and energetic of both the donor-acceptor molecules and their surrounding environment that dictate the mechanistic pathways and result in efficient photosynthetic charge separation.

  19. Synthetic population system user guide

    SciTech Connect

    Roberts, D.J.

    1998-03-01

    The Los Alamos National Laboratory (LANL) TRansportation Analysis SIMulatiuon System (TRANSIMS) synthetic population system (SYN) is designed to produce populations (family households, non-family households, and group quarters) that are statistically equivalent to actual populations when compared at the level of block group or higher. The methodology used by this system is described in a report entitled Creating Synthetic Baseline Populations. The inputs to the system are US Census Bureau data (STF3A and PUMS) and MABLE/GEOCORR data. Census Bureau STF3A and PUMS data formats are commonly used and are available on CD-ROM from the Census Bureau. These data inputs will not be described in any detail in this guide. The primary function of MABLE/GEOCORR data is to cross-reference STF3 block group data to PUMS areas. The outputs of the system are files that contain family household, non-family household, and group quarters data in the form of household and person records. SYN will run on a variety of Unix platforms.

  20. Toward a synthetic economic systems modeling tool for sustainable exploitation of ecosystems.

    PubMed

    Richardson, Colin; Courvisanos, Jerry; Crawford, John W

    2011-02-01

    Environmental resources that underpin the basic human needs of water, energy, and food are predicted to become in such short supply by 2050 that global security and the well-being of millions will be under threat. These natural commodities have been allowed to reach crisis levels of supply because of a failure of economic systems to sustain them. This is largely because there have been no means of integrating their exploitation into any economic model that effectively addresses ecological systemic failures in a way that provides an integrated ecological-economic tool that can monitor and evaluate market and policy targets. We review the reasons for this and recent attempts to address the problem while identifying outstanding issues. The key elements of a policy-oriented economic model that integrates ecosystem processes are described and form the basis of a proposed new synthesis approach. The approach is illustrated by an indicative case study that develops a simple model for rainfed and irrigated food production in the Murray-Darling basin of southeastern Australia.

  1. Using X-band Weather Radar Measurements to Monitor the Integrity of Digital Elevation Models for Synthetic Vision Systems

    NASA Technical Reports Server (NTRS)

    Young, Steve; UijtdeHaag, Maarten; Sayre, Jonathon

    2003-01-01

    Synthetic Vision Systems (SVS) provide pilots with displays of stored geo-spatial data representing terrain, obstacles, and cultural features. As comprehensive validation is impractical, these databases typically have no quantifiable level of integrity. Further, updates to the databases may not be provided as changes occur. These issues limit the certification level and constrain the operational context of SVS for civil aviation. Previous work demonstrated the feasibility of using a realtime monitor to bound the integrity of Digital Elevation Models (DEMs) by using radar altimeter measurements during flight. This paper describes an extension of this concept to include X-band Weather Radar (WxR) measurements. This enables the monitor to detect additional classes of DEM errors and to reduce the exposure time associated with integrity threats. Feature extraction techniques are used along with a statistical assessment of similarity measures between the sensed and stored features that are detected. Recent flight-testing in the area around the Juneau, Alaska Airport (JNU) has resulted in a comprehensive set of sensor data that is being used to assess the feasibility of the proposed monitor technology. Initial results of this assessment are presented.

  2. Protoplaneary Dynamics Uncovered through Synthetic Spectral Modeling

    NASA Astrophysics Data System (ADS)

    Kronberg, Martin

    2010-01-01

    One of the key problems in planetary formation research is to determine the properties and dynamics of protoplaneary accretion disks where all planetary formation occurs. An increasingly useful probe into these systems is near infrared spectroscopy of ro-vibrational CO emission. The goal of the study is to develop techniques that utilize synthetic spectra generated via a modeling algorithm fitted to actual spectral data gathered from protoplanetary systems to determine specific properties of the system. We currently have a working algorithm which generates synthetic spectra based upon a number of degenerate parameters. In order to generate the best fit given the degenerate nature of the parameters we are developing a Monte Carlo algorithm that will determine local as well as absolute minima in a ten dimensional surface plot. Once this is completed we will utilize two CONDOR clusters to generate fits for hundreds of known protoplanetary systems.The result will be the largest, most descriptive database of protoplanetary systems, an essential tool for planetary and stellar researchers. This project was funded by a partnership between the National Science Foundation (NSF AST-0552798), Research Experiences for Undergraduates (REU), and the Department of Defense (DoD) ASSURE (Awards to Stimulate and Support Undergraduate Research Experiences) programs.

  3. Systems approaches for synthetic biology: a pathway toward mammalian design.

    PubMed

    Rekhi, Rahul; Qutub, Amina A

    2013-01-01

    We review methods of understanding cellular interactions through computation in order to guide the synthetic design of mammalian cells for translational applications, such as regenerative medicine and cancer therapies. In doing so, we argue that the challenges of engineering mammalian cells provide a prime opportunity to leverage advances in computational systems biology. We support this claim systematically, by addressing each of the principal challenges to existing synthetic bioengineering approaches-stochasticity, complexity, and scale-with specific methods and paradigms in systems biology. Moreover, we characterize a key set of diverse computational techniques, including agent-based modeling, Bayesian network analysis, graph theory, and Gillespie simulations, with specific utility toward synthetic biology. Lastly, we examine the mammalian applications of synthetic biology for medicine and health, and how computational systems biology can aid in the continued development of these applications.

  4. Synthetic biology of minimal living cells: primitive cell models and semi-synthetic cells.

    PubMed

    Stano, Pasquale

    2010-09-01

    This article summarizes a contribution presented at the ESF 2009 Synthetic Biology focused on the concept of the minimal requirement for life and on the issue of constructive (synthetic) approaches in biological research. The attempts to define minimal life within the framework of autopoietic theory are firstly described, and a short report on the development of autopoietic chemical systems based on fatty acid vesicles, which are relevant as primitive cell models is given. These studies can be used as a starting point for the construction of more complex systems, firstly being inspired by possible origins of life scenarioes (and therefore by considering primitive functions), then by considering an approach based on modern biomacromolecular-encoded functions. At this aim, semi-synthetic minimal cells are defined as those man-made vesicle-based systems that are composed of the minimal number of genes, proteins, biomolecules and which can be defined as living. Recent achievements on minimal sized semi-synthetic cells are then discussed, and the kind of information obtained is recognized as being distinctively derived by a constructive approach. Synthetic biology is therefore a fundamental tool for gaining basic knowledge about biosystems, and it should not be confined at all to the engineering side.

  5. Synthetic biology of minimal living cells: primitive cell models and semi-synthetic cells

    PubMed Central

    2010-01-01

    This article summarizes a contribution presented at the ESF 2009 Synthetic Biology focused on the concept of the minimal requirement for life and on the issue of constructive (synthetic) approaches in biological research. The attempts to define minimal life within the framework of autopoietic theory are firstly described, and a short report on the development of autopoietic chemical systems based on fatty acid vesicles, which are relevant as primitive cell models is given. These studies can be used as a starting point for the construction of more complex systems, firstly being inspired by possible origins of life scenarioes (and therefore by considering primitive functions), then by considering an approach based on modern biomacromolecular-encoded functions. At this aim, semi-synthetic minimal cells are defined as those man-made vesicle-based systems that are composed of the minimal number of genes, proteins, biomolecules and which can be defined as living. Recent achievements on minimal sized semi-synthetic cells are then discussed, and the kind of information obtained is recognized as being distinctively derived by a constructive approach. Synthetic biology is therefore a fundamental tool for gaining basic knowledge about biosystems, and it should not be confined at all to the engineering side. PMID:21886680

  6. How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology.

    PubMed

    Gonze, Didier; Abou-Jaoudé, Wassim; Ouattara, Djomangan Adama; Halloy, José

    2011-01-01

    The recent advance of genetic studies and the rapid accumulation of molecular data, together with the increasing performance of computers, led researchers to design more and more detailed mathematical models of biological systems. Many modeling approaches rely on ordinary differential equations (ODE) which are based on standard enzyme kinetics. Michaelis-Menten and Hill functions are indeed commonly used in dynamical models in systems and synthetic biology because they provide the necessary nonlinearity to make the dynamics nontrivial (i.e., limit-cycle oscillations or multistability). For most of the systems modeled, the actual molecular mechanism is unknown, and the enzyme equations should be regarded as phenomenological. In this chapter, we discuss the validity and accuracy of these approximations. In particular, we focus on the validity of the Michaelis-Menten function for open systems and on the use of Hill kinetics to describe transcription rates of regulated genes. Our discussion is illustrated by numerical simulations of prototype systems, including the Repressilator (a genetic oscillator) and the Toggle Switch model (a bistable system). We systematically compare the results obtained with the compact version (based on Michaelis-Menten and Hill functions) with its corresponding developed versions (based on "elementary" reaction steps and mass action laws). We also discuss the use of compact approaches to perform stochastic simulations (Gillespie algorithm). On the basis of these results, we argue that using compact models is suitable to model qualitatively biological systems.

  7. Flight Testing an Integrated Synthetic Vision System

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Arthur, Jarvis J., III; Bailey, Randall E.; Prinzel, Lawrence J., III

    2005-01-01

    NASA's Synthetic Vision Systems (SVS) project is developing technologies with practical applications to eliminate low visibility conditions as a causal factor to civil aircraft accidents while replicating the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. A major thrust of the SVS project involves the development/demonstration of affordable, certifiable display configurations that provide intuitive out-the-window terrain and obstacle information with advanced pathway guidance for transport aircraft. The SVS concept being developed at NASA encompasses the integration of tactical and strategic Synthetic Vision Display Concepts (SVDC) with Runway Incursion Prevention System (RIPS) alerting and display concepts, real-time terrain database integrity monitoring equipment (DIME), and Enhanced Vision Systems (EVS) and/or improved Weather Radar for real-time object detection and database integrity monitoring. A flight test evaluation was jointly conducted (in July and August 2004) by NASA Langley Research Center and an industry partner team under NASA's Aviation Safety and Security, Synthetic Vision System project. A Gulfstream GV aircraft was flown over a 3-week period in the Reno/Tahoe International Airport (NV) local area and an additional 3-week period in the Wallops Flight Facility (VA) local area to evaluate integrated Synthetic Vision System concepts. The enabling technologies (RIPS, EVS and DIME) were integrated into the larger SVS concept design. This paper presents experimental methods and the high level results of this flight test.

  8. Synthetic Flight Training System Study

    DTIC Science & Technology

    1983-12-23

    System Component Development Program (VSCDP) as a baseline. In addition, the study investiqated commonality issues of such subsystems as motion...Combat Development Command issued the first in a series of what are now entitled Training Device Requirements (TDR) documents for the development of the...study’s basic issues of visual technology application and commonality are analyzed. The study focuses on approximately five prinicpal organizations

  9. Synthetic Ecology of Microbes: Mathematical Models and Applications.

    PubMed

    Zomorrodi, Ali R; Segrè, Daniel

    2016-02-27

    As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.

  10. Synthetic quantitative MRI through relaxometry modelling

    PubMed Central

    Mohammadi, Siawoosh; Weiskopf, Nikolaus

    2016-01-01

    Abstract Quantitative MRI (qMRI) provides standardized measures of specific physical parameters that are sensitive to the underlying tissue microstructure and are a first step towards achieving maps of biologically relevant metrics through in vivo histology using MRI. Recently proposed models have described the interdependence of qMRI parameters. Combining such models with the concept of image synthesis points towards a novel approach to synthetic qMRI, in which maps of fundamentally different physical properties are constructed through the use of biophysical models. In this study, the utility of synthetic qMRI is investigated within the context of a recently proposed linear relaxometry model. Two neuroimaging applications are considered. In the first, artefact‐free quantitative maps are synthesized from motion‐corrupted data by exploiting the over‐determined nature of the relaxometry model and the fact that the artefact is inconsistent across the data. In the second application, a map of magnetization transfer (MT) saturation is synthesized without the need to acquire an MT‐weighted volume, which directly leads to a reduction in the specific absorption rate of the acquisition. This feature would be particularly important for ultra‐high field applications. The synthetic MT map is shown to provide improved segmentation of deep grey matter structures, relative to segmentation using T 1‐weighted images or R 1 maps. The proposed approach of synthetic qMRI shows promise for maximizing the extraction of high quality information related to tissue microstructure from qMRI protocols and furthering our understanding of the interrelation of these qMRI parameters. PMID:27753154

  11. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

    PubMed Central

    Lomnitz, Jason G.; Savageau, Michael A.

    2016-01-01

    Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

  12. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems.

    PubMed

    Lomnitz, Jason G; Savageau, Michael A

    2016-01-01

    Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

  13. Towards synthetic molecular motors: a model elastic-network study

    NASA Astrophysics Data System (ADS)

    Sarkar, Amartya; Flechsig, Holger; Mikhailov, Alexander S.

    2016-04-01

    Protein molecular motors play a fundamental role in biological cells and development of their synthetic counterparts is a major challenge. Here, we show how a model motor system with the operation mechanism resembling that of muscle myosin can be designed at the concept level, without addressing the implementation aspects. The model is constructed as an elastic network, similar to the coarse-grained descriptions used for real proteins. We show by numerical simulations that the designed synthetic motor can operate as a deterministic or Brownian ratchet and that there is a continuous transition between such two regimes. The motor operation under external load, approaching the stall condition, is also analysed.

  14. Synthetic bounds for semi-Markov reliability models

    NASA Technical Reports Server (NTRS)

    White, A. L.

    1985-01-01

    Upper and lower bounds are derived for the probability of failure for a class of highly reliable process control computers. The bounds are synthetic in the sense that the descriptions of component failure and system recovery are assumed to be obtained from different sources. The reliability model is constructed under the assumption that the processes are independent.

  15. Simpson's paradox in a synthetic microbial system.

    PubMed

    Chuang, John S; Rivoire, Olivier; Leibler, Stanislas

    2009-01-09

    The maintenance of "public" or "common good" producers is a major question in the evolution of cooperation. Because nonproducers benefit from the shared resource without bearing its cost of production, they may proliferate faster than producers. We established a synthetic microbial system consisting of two Escherichia coli strains of common-good producers and nonproducers. Depending on the population structure, which was varied by forming groups with different initial compositions, an apparently paradoxical situation could be attained in which nonproducers grew faster within each group, yet producers increased overall. We show that a simple way to generate the variance required for this effect is through stochastic fluctuations via population bottlenecks. The synthetic approach described here thus provides a way to study generic mechanisms of natural selection.

  16. Synthetic Vision Systems - Operational Considerations Simulation Experiment

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Williams, Steven P.; Bailey, Randall E.; Glaab, Louis J.

    2007-01-01

    Synthetic vision is a computer-generated image of the external scene topography that is generated from aircraft attitude, high-precision navigation information, and data of the terrain, obstacles, cultural features, and other required flight information. A synthetic vision system (SVS) enhances this basic functionality with real-time integrity to ensure the validity of the databases, perform obstacle detection and independent navigation accuracy verification, and provide traffic surveillance. Over the last five years, NASA and its industry partners have developed and deployed SVS technologies for commercial, business, and general aviation aircraft which have been shown to provide significant improvements in terrain awareness and reductions in the potential for Controlled-Flight-Into-Terrain incidents/accidents compared to current generation cockpit technologies. It has been hypothesized that SVS displays can greatly improve the safety and operational flexibility of flight in Instrument Meteorological Conditions (IMC) to a level comparable to clear-day Visual Meteorological Conditions (VMC), regardless of actual weather conditions or time of day. An experiment was conducted to evaluate SVS and SVS-related technologies as well as the influence of where the information is provided to the pilot (e.g., on a Head-Up or Head-Down Display) for consideration in defining landing minima based upon aircraft and airport equipage. The "operational considerations" evaluated under this effort included reduced visibility, decision altitudes, and airport equipage requirements, such as approach lighting systems, for SVS-equipped aircraft. Subjective results from the present study suggest that synthetic vision imagery on both head-up and head-down displays may offer benefits in situation awareness; workload; and approach and landing performance in the visibility levels, approach lighting systems, and decision altitudes tested.

  17. Crop monitoring & yield forecasting system based on Synthetic Aperture Radar (SAR) and process-based crop growth model: Development and validation in South and South East Asian Countries

    NASA Astrophysics Data System (ADS)

    Setiyono, T. D.

    2014-12-01

    Accurate and timely information on rice crop growth and yield helps governments and other stakeholders adapting their economic policies and enables relief organizations to better anticipate and coordinate relief efforts in the wake of a natural catastrophe. Such delivery of rice growth and yield information is made possible by regular earth observation using space-born Synthetic Aperture Radar (SAR) technology combined with crop modeling approach to estimate yield. Radar-based remote sensing is capable of observing rice vegetation growth irrespective of cloud coverage, an important feature given that in incidences of flooding the sky is often cloud-covered. The system allows rapid damage assessment over the area of interest. Rice yield monitoring is based on a crop growth simulation and SAR-derived key information, particularly start of season and leaf growth rate. Results from pilot study sites in South and South East Asian countries suggest that incorporation of SAR data into crop model improves yield estimation for actual yields. Remote-sensing data assimilation into crop model effectively capture responses of rice crops to environmental conditions over large spatial coverage, which otherwise is practically impossible to achieve. Such improvement of actual yield estimates offers practical application such as in a crop insurance program. Process-based crop simulation model is used in the system to ensure climate information is adequately captured and to enable mid-season yield forecast.

  18. Southern San Andreas-San Jacinto fault system slip rates estimated from earthquake cycle models constrained by GPS and interferometric synthetic aperture radar observations

    NASA Astrophysics Data System (ADS)

    Lundgren, Paul; Hetland, Eric A.; Liu, Zhen; Fielding, Eric J.

    2009-02-01

    We use ground geodetic and interferometric synthetic aperture radar satellite observations across the southern San Andreas (SAF)-San Jacinto (SJF) fault systems to constrain their slip rates and the viscosity structure of the lower crust and upper mantle on the basis of periodic earthquake cycle, Maxwell viscoelastic, finite element models. Key questions for this system are the SAF and SJF slip rates, the slip partitioning between the two main branches of the SJF, and the dip of the SAF. The best-fitting models generally have a high-viscosity lower crust (η = 1021 Pa s) overlying a lower-viscosity upper mantle (η = 1019 Pa s). We find considerable trade-offs between the relative time into the current earthquake cycle of the San Jacinto fault and the upper mantle viscosity. With reasonable assumptions for the relative time in the earthquake cycle, the partition of slip is fairly robust at around 24-26 mm/a for the San Jacinto fault system and 16-18 mm/a for the San Andreas fault. Models for two subprofiles across the SAF-SJF systems suggest that slip may transfer from the western (Coyote Creek) branch to the eastern (Clark-Superstition hills) branch of the SJF from NW to SE. Across the entire system our best-fitting model gives slip rates of 2 ± 3, 12 ± 9, 12 ± 9, and 17 ± 3 mm/a for the Elsinore, Coyote Creek, Clark, and San Andreas faults, respectively, where the large uncertainties in the slip rates for the SJF branches reflect the large uncertainty in the slip rate partitioning within the SJF system.

  19. Specifications of Standards in Systems and Synthetic Biology.

    PubMed

    Schreiber, Falk; Bader, Gary D; Golebiewski, Martin; Hucka, Michael; Kormeier, Benjamin; Le Novère, Nicolas; Myers, Chris; Nickerson, David; Sommer, Björn; Waltemath, Dagmar; Weise, Stephan

    2015-09-04

    Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation). Systems and synthetic biology is a relatively novel area, and it is only in the last decade that the standardisation of data, information, and models related to systems and synthetic biology has become a community-wide effort. Several open standards have been established and are under continuous development as a community initiative. COMBINE, the ‘COmputational Modeling in BIology’ NEtwork has been established as an umbrella initiative to coordinate and promote the development of the various community standards and formats for computational models. There are yearly two meeting, HARMONY (Hackathons on Resources for Modeling in Biology), Hackathon-type meetings with a focus on development of the support for standards, and COMBINE forums, workshop-style events with oral presentations, discussion, poster, and breakout sessions for further developing the standards. For more information see http://co.mbine.org/. So far the different standards were published and made accessible through the standards’ web- pages or preprint services. The aim of this special issue is to provide a single, easily accessible and citable platform for the publication of standards in systems and synthetic biology. This special issue is intended to serve as a central access point to standards and related initiatives in systems and synthetic biology, it will be published annually to provide an opportunity for standard development groups to communicate updated specifications.

  20. Synthetic organisms and self-designing systems

    SciTech Connect

    Dress, W.B.

    1989-01-01

    This paper examines the need for complex, adaptive solutions to certain types of complex problems typified by the Strategic Defense System and NASA's Space Station and Mars Rover. Since natural systems have evolved with capabilities of intelligent behavior in complex, dynamic situations, it is proposed that biological principles be identified and abstracted for application to certain problems now facing industry defense, and space exploration. Two classes of artificial neural networks are presented/endash/a non-adaptive network used as a genetically determined ''retina,'' and a frequency-coded network as an adaptive ''brain.'' The role of a specific environment coupled with a system of artificial neural networks having simulated sensors and effectors is seen as an ecosystem. Evolution of synthetic organisms within this ecosystem provides a powerful optimization methodology for creating intelligent systems able to function successfully in any desired environment. A complex software system involving a simulation of an environment and a program designed to cope with that environment are presented. Reliance on adaptive systems, as found in nature, is only part of the proposed answer, though an essential one. The second part of the proposed method makes use of an additional biological metaphor/endash/that of natural selection/endash/to solve the dynamic optimization problems that every intelligent system eventually faces. A third area of concern in developing an adaptive, intelligent system is that of real-time computing. It is recognized that many of the problems now being explored in this area have their parallels in biological organisms, and many of the performance issues facing artificial neural networks may find resolution in the methodology of real-time computing. 30 refs., 4 figs.

  1. A synthetic aperture acoustic prototype system

    NASA Astrophysics Data System (ADS)

    Luke, Robert H.; Bishop, Steven S.; Chan, Aaron M.; Gugino, Peter M.; Donzelli, Thomas P.; Soumekh, Mehrdad

    2015-05-01

    A novel quasi-monostatic system operating in a side-scan synthetic aperture acoustic (SAA) imaging mode is presented. This research project's objectives are to explore the military utility of outdoor continuous sound imaging of roadside foliage and target detection. The acoustic imaging method has several military relevant advantages such as being immune to RF jamming, superior spatial resolution as compared to 0.8-2.4 GHz ground penetrating radar (GPR), capable of standoff side and forward-looking scanning, and relatively low cost, weight and size when compared to GPR technologies. The prototype system's broadband 2-17 kHz LFM chirp transceiver is mounted on a manned all-terrain vehicle. Targets are positioned within the acoustic main beam at slant ranges of two to seven meters and on surfaces such as dirt, grass, gravel and weathered asphalt and with an intervening metallic chain link fence. Acoustic image reconstructions and signature plots result in means for literal interpretation and quantifiable analyses.

  2. Towards a whole-cell modeling approach for synthetic biology

    NASA Astrophysics Data System (ADS)

    Purcell, Oliver; Jain, Bonny; Karr, Jonathan R.; Covert, Markus W.; Lu, Timothy K.

    2013-06-01

    Despite rapid advances over the last decade, synthetic biology lacks the predictive tools needed to enable rational design. Unlike established engineering disciplines, the engineering of synthetic gene circuits still relies heavily on experimental trial-and-error, a time-consuming and inefficient process that slows down the biological design cycle. This reliance on experimental tuning is because current modeling approaches are unable to make reliable predictions about the in vivo behavior of synthetic circuits. A major reason for this lack of predictability is that current models view circuits in isolation, ignoring the vast number of complex cellular processes that impinge on the dynamics of the synthetic circuit and vice versa. To address this problem, we present a modeling approach for the design of synthetic circuits in the context of cellular networks. Using the recently published whole-cell model of Mycoplasma genitalium, we examined the effect of adding genes into the host genome. We also investigated how codon usage correlates with gene expression and find agreement with existing experimental results. Finally, we successfully implemented a synthetic Goodwin oscillator in the whole-cell model. We provide an updated software framework for the whole-cell model that lays the foundation for the integration of whole-cell models with synthetic gene circuit models. This software framework is made freely available to the community to enable future extensions. We envision that this approach will be critical to transforming the field of synthetic biology into a rational and predictive engineering discipline.

  3. Computational models for synthetic marine infrared clutter

    NASA Astrophysics Data System (ADS)

    Constantikes, Kim T.; Zysnarski, Adam H.

    1996-06-01

    The next generation of ship defense missiles will need to engage stealthy, passive, sea-skimming missiles. Detection and guidance will occur against a background of sea surface and horizon which can present significant clutter problems for infrared seekers, particularly when targets are comparatively dim. We need a variety of sea clutter models: statistical image models for signal processing algorithm design, clutter occurrence models for systems effectiveness assessment, and constructive image models for synthesizing very large field-of-view (FOV) images with high spatial and temporal resolution. We have implemented and tested such a constructive model. First principle models of water waves and light transport provide a computationally intensive clutter model implemented as a raytracer. Our models include sea, sky, and solar radiance; reflectance; attenuating atmospheres; constructive solid geometry targets; target and water wave dynamics; and simple sensor image formation.

  4. Building synthetic systems to learn nature's design principles.

    PubMed

    Davidson, Eric A; Windram, Oliver P F; Bayer, Travis S

    2012-01-01

    Evolution undoubtedly shapes the architecture of biological systems, yet it is unclear which features of regulatory, metabolic, and signalling circuits have adaptive significance and how the architecture of these circuits constrains or promotes evolutionary processes, such as adaptation to new environments. Experimentally rewiring circuits using genetic engineering and constructing novel circuits in living cells allows direct testing and validation of hypotheses in evolutionary systems biology. Building synthetic genetic systems enables researchers to explore regions of the genotype-phenotype and fitness landscapes that may be inaccessible to more traditional analysis. Here, we review the strategies that allow synthetic systems to be constructed and how evolutionary design principles have advanced these technologies. We also describe how building small genetic regulatory systems can provide insight on the trade-offs that constrain adaptation and can shape the structure of biological networks. In the future, the possibility of building biology de novo at the genome scale means that increasingly sophisticated models of the evolutionary dynamics of networks can be proposed and validated, and will allow us to recreate ancestral systems in the lab. This interplay between evolutionary systems theory and engineering design may illuminate the fundamental limits of performance, robustness, and evolvability of living systems.

  5. Computational Modeling And Analysis Of Synthetic Jets

    NASA Technical Reports Server (NTRS)

    Mittal, Rajat; Cattafesta, Lou

    2005-01-01

    In the last report we focused on the study of 3D synthetic jets of moderate jet aspect-ratio. Jets in quiescent and cross-flow cases were investigated. Since most of the synthetic jets in practical applications are found to be of large aspect ratio, the focus was shifted to studying synthetic jets of large aspect ratio. In the current year, further progress has been made by studying jets of aspect ratio 8 and infinity. Some other aspects of the jet, like the vorticity flux is looked into apart from analyzing the vortex dynamics, velocity profiles and the other dynamical characteristics of the jet which allows us to extract some insight into the effect of these modifications on the jet performance. Also, efforts were made to qualitatively validate the simulated results with the NASA Langley test cases at higher jet Reynolds number for the quiescent jet case.

  6. Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development.

    PubMed

    Paddon, Chris J; Keasling, Jay D

    2014-05-01

    Recent developments in synthetic biology, combined with continued progress in systems biology and metabolic engineering, have enabled the engineering of microorganisms to produce heterologous molecules in a manner that was previously unfeasible. The successful synthesis and recent entry of semi-synthetic artemisinin into commercial production is the first demonstration of the potential of synthetic biology for the development and production of pharmaceutical agents. In this Review, we describe the metabolic engineering and synthetic biology approaches that were used to develop this important antimalarial drug precursor. This not only demonstrates the incredible potential of the available technologies but also illuminates how lessons learned from this work could be applied to the production of other pharmaceutical agents.

  7. Exploring Synthetic and Systems Biology at the University of Edinburgh.

    PubMed

    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.

  8. Metabolic modelling in the development of cell factories by synthetic biology

    PubMed Central

    Jouhten, Paula

    2012-01-01

    Cell factories are commonly microbial organisms utilized for bioconversion of renewable resources to bulk or high value chemicals. Introduction of novel production pathways in chassis strains is the core of the development of cell factories by synthetic biology. Synthetic biology aims to create novel biological functions and systems not found in nature by combining biology with engineering. The workflow of the development of novel cell factories with synthetic biology is ideally linear which will be attainable with the quantitative engineering approach, high-quality predictive models, and libraries of well-characterized parts. Different types of metabolic models, mathematical representations of metabolism and its components, enzymes and metabolites, are useful in particular phases of the synthetic biology workflow. In this minireview, the role of metabolic modelling in synthetic biology will be discussed with a review of current status of compatible methods and models for the in silico design and quantitative evaluation of a cell factory. PMID:24688669

  9. Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects.

    PubMed

    Liu, Yanfeng; Shin, Hyun-dong; Li, Jianghua; Liu, Long

    2015-02-01

    Metabolic engineering facilitates the rational development of recombinant bacterial strains for metabolite overproduction. Building on enormous advances in system biology and synthetic biology, novel strategies have been established for multivariate optimization of metabolic networks in ensemble, spatial, and dynamic manners such as modular pathway engineering, compartmentalization metabolic engineering, and metabolic engineering guided by genome-scale metabolic models, in vitro reconstitution, and systems and synthetic biology. Herein, we summarize recent advances in novel metabolic engineering strategies. Combined with advancing kinetic models and synthetic biology tools, more efficient new strategies for improving cellular properties can be established and applied for industrially important biochemical production.

  10. Bridging the gap between systems biology and synthetic biology

    PubMed Central

    Liu, Di; Hoynes-O’Connor, Allison; Zhang, Fuzhong

    2013-01-01

    Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, systems biology provides the knowledge necessary for the development of synthetic biology tools, which in turn facilitates the manipulation and understanding of complex biological systems. Thus, the combination of systems and synthetic biology has huge potential for studying and engineering microbes, especially to perform advanced tasks, such as producing biofuels. Although there have been very few studies in integrating systems and synthetic biology, existing examples have demonstrated great power in extending microbiological capabilities. This review focuses on recent efforts in microbiological genomics, transcriptomics, proteomics, and metabolomics, aiming to fill the gap between systems and synthetic biology. PMID:23898328

  11. Mechanistically Consistent Reduced Models of Synthetic Gene Networks

    PubMed Central

    Mier-y-Terán-Romero, Luis; Silber, Mary; Hatzimanikatis, Vassily

    2013-01-01

    Designing genetic networks with desired functionalities requires an accurate mathematical framework that accounts for the essential mechanistic details of the system. Here, we formulate a time-delay model of protein translation and mRNA degradation by systematically reducing a detailed mechanistic model that explicitly accounts for the ribosomal dynamics and the cleaving of mRNA by endonucleases. We exploit various technical and conceptual advantages that our time-delay model offers over the mechanistic model to probe the behavior of a self-repressing gene over wide regions of parameter space. We show that a heuristic time-delay model of protein synthesis of a commonly used form yields a notably different prediction for the parameter region where sustained oscillations occur. This suggests that such heuristics can lead to erroneous results. The functional forms that arise from our systematic reduction can be used for every system that involves transcription and translation and they could replace the commonly used heuristic time-delay models for these processes. The results from our analysis have important implications for the design of synthetic gene networks and stress that such design must be guided by a combination of heuristic models and mechanistic models that include all relevant details of the process. PMID:23663853

  12. Synthetic thrombus model for in vitro studies of laser thrombolysis

    SciTech Connect

    Hermes, R.E.; Trajkovska, K.

    1998-07-01

    Laser thrombolysis is the controlled ablation of a thrombus (blood clot) blockage in a living arterial system. Theoretical modeling of the interaction of laser light with thrombi relies on the ability to perform in vitro experiments with well characterized surrogate materials. A synthetic thrombus formulation may offer more accurate results when compared to in vivo clinical experiments. The authors describe the development of new surrogate materials based on formulations incorporating chick egg, guar gum, modified food starch, and a laser light absorbing dye. The sound speed and physical consistency of the materials were very close to porcine (arterial) and human (venous) thrombi. Photographic and videotape recordings of pulsed dye laser ablation experiments under various experimental conditions were used to evaluate the new material as compared to in vitro tests with human (venous) thrombus. The characteristics of ablation and mass removal were similar to that of real thrombi, and therefore provide a more realistic model for in vitro laser thrombolysis when compared to gelatin.

  13. Wildfire simulation using LES with synthetic-velocity SGS models

    NASA Astrophysics Data System (ADS)

    McDonough, J. M.; Tang, Tingting

    2016-11-01

    Wildland fires are becoming more prevalent and intense worldwide as climate change leads to warmer, drier conditions; and large-eddy simulation (LES) is receiving increasing attention for fire spread predictions as computing power continues to improve (see, e.g.,). We report results from wildfire simulations over general terrain employing implicit LES for solution of the incompressible Navier-Stokes (N.-S.) and thermal energy equations with Boussinesq approximation, altered with Darcy, Forchheimer and Brinkman extensions, to represent forested regions as porous media with varying (in both space and time) porosity and permeability. We focus on subgrid-scale (SGS) behaviors computed with a synthetic-velocity model, a discrete dynamical system, based on the poor man's N.-S. equations and investigate the ability of this model to produce fire whirls (tornadoes of fire) at the (unresolved) SGS level. Professor, Mechanical Engineering and Mathematics.

  14. Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing

    PubMed Central

    Garcia-Ojalvo, Jordi; Elowitz, Michael B.; Strogatz, Steven H.

    2004-01-01

    Diverse biochemical rhythms are generated by thousands of cellular oscillators that somehow manage to operate synchronously. In fields ranging from circadian biology to endocrinology, it remains an exciting challenge to understand how collective rhythms emerge in multicellular structures. Using mathematical and computational modeling, we study the effect of coupling through intercell signaling in a population of Escherichia coli cells expressing a synthetic biological clock. Our results predict that a diverse and noisy community of such genetic oscillators interacting through a quorum-sensing mechanism should self-synchronize in a robust way, leading to a substantially improved global rhythmicity in the system. As such, the particular system of coupled genetic oscillators considered here might be a good candidate to provide the first quantitative example of a synchronization transition in a population of biological oscillators. PMID:15256602

  15. A Heritable Recombination system for synthetic Darwinian evolution in yeast.

    PubMed

    Romanini, Dante W; Peralta-Yahya, Pamela; Mondol, Vanessa; Cornish, Virginia W

    2012-12-21

    Genetic recombination is central to the generation of molecular diversity and enhancement of evolutionary fitness in living systems. Methods such as DNA shuffling that recapitulate this diversity mechanism in vitro are powerful tools for engineering biomolecules with useful new functions by directed evolution. Synthetic biology now brings demand for analogous technologies that enable the controlled recombination of beneficial mutations in living cells. Thus, here we create a Heritable Recombination system centered around a library cassette plasmid that enables inducible mutagenesis via homologous recombination and subsequent combination of beneficial mutations through sexual reproduction in Saccharomyces cerevisiae. Using repair of nonsense codons in auxotrophic markers as a model, Heritable Recombination was optimized to give mutagenesis efficiencies of up to 6% and to allow successive repair of different markers through two cycles of sexual reproduction and recombination. Finally, Heritable Recombination was employed to change the substrate specificity of a biosynthetic enzyme, with beneficial mutations in three different active site loops crossed over three continuous rounds of mutation and selection to cover a total sequence diversity of 10(13). Heritable Recombination, while at an early stage of development, breaks the transformation barrier to library size and can be immediately applied to combinatorial crossing of beneficial mutations for cell engineering, adding important features to the growing arsenal of next generation molecular biology tools for synthetic biology.

  16. A resource dependent protein synthesis model for evaluating synthetic circuits.

    PubMed

    Halter, Wolfgang; Montenbruck, Jan Maximilian; Tuza, Zoltan A; Allgöwer, Frank

    2017-03-09

    Reliable in silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the Ribosome Flow Model and among other things describes the movement of RNA-polymerase and ribosomes on mRNA and DNA templates, respectively. By analyzing the convergence properties of this model based upon geometric considerations, we present additional insights into the dynamic mechanisms of the process of protein synthesis. Further, we demonstrate how this model can be used to evaluate the performance of synthetic gene circuits under different loading scenarios.

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

    PubMed

    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.

  18. Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

    PubMed Central

    Lewis, Daniel D.; Villarreal, Fernando D.; Wu, Fan; Tan, Cheemeng

    2014-01-01

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems. PMID:25538941

  19. Synthetic aperture radar autofocus based on a bilinear model.

    PubMed

    Liu, Kuang-Hung; Wiesel, Ami; Munson, David C

    2012-05-01

    Autofocus algorithms are used to restore images in nonideal synthetic aperture radar imaging systems. In this paper, we propose a bilinear parametric model for the unknown image and the nuisance phase parameters and derive an efficient maximum-likelihood autofocus (MLA) algorithm. In the special case of a simple image model and a narrow range of look angles, MLA coincides with the successful multichannel autofocus (MCA). MLA can be interpreted as a generalization of MCA to a larger class of models with a larger range of look angles. We analyze its advantages over previous extensions of MCA in terms of identifiability conditions and noise sensitivity. As a byproduct, we also propose numerical approximations to the difficult constant modulus quadratic program that lies at the core of these algorithms. We demonstrate the superior performance of our proposed methods using computer simulations in both the correct and mismatched system models. MLA performs better than other methods, both in terms of the mean squared error and visual quality of the restored image.

  20. Alternative Watson-Crick Synthetic Genetic Systems.

    PubMed

    Benner, Steven A; Karalkar, Nilesh B; Hoshika, Shuichi; Laos, Roberto; Shaw, Ryan W; Matsuura, Mariko; Fajardo, Diego; Moussatche, Patricia

    2016-11-01

    In its "grand challenge" format in chemistry, "synthesis" as an activity sets out a goal that is substantially beyond current theoretical and technological capabilities. In pursuit of this goal, scientists are forced across uncharted territory, where they must answer unscripted questions and solve unscripted problems, creating new theories and new technologies in ways that would not be created by hypothesis-directed research. Thus, synthesis drives discovery and paradigm changes in ways that analysis cannot. Described here are the products that have arisen so far through the pursuit of one grand challenge in synthetic biology: Recreate the genetics, catalysis, evolution, and adaptation that we value in life, but using genetic and catalytic biopolymers different from those that have been delivered to us by natural history on Earth. The outcomes in technology include new diagnostic tools that have helped personalize the care of hundreds of thousands of patients worldwide. In science, the effort has generated a fundamentally different view of DNA, RNA, and how they work.

  1. Research and application of a hybrid model based on dynamic fuzzy synthetic evaluation for establishing air quality forecasting and early warning system: A case study in China.

    PubMed

    Xu, Yunzhen; Du, Pei; Wang, Jianzhou

    2017-04-01

    As the atmospheric environment pollution has been becoming more and more serious in China, it is highly desirable to develop a scientific and effective early warning system that plays a great significant role in analyzing and monitoring air quality. However, establishing a robust early warning system for warning the public in advance and ameliorating air quality is not only an extremely challenging task but also a public concerned problem for human health. Most previous studies are focused on improving the prediction accuracy, which usually ignore the significance of uncertainty information and comprehensive evaluation concerning air pollutants. Therefore, in this paper a novel robust early warning system was successfully developed, which consists of three modules: evaluation module, forecasting module and characteristics estimating module. In this system, a new dynamic fuzzy synthetic evaluation is proposed and applied to determine air quality levels and primary pollutants, which can be regarded as the research objectives; Moreover, to further mine and analyze the characteristics of air pollutants, four different distribution functions and interval forecasting method are also employed that can not only provide predictive range, confidence level and the other uncertain information of the pollutants future values, but also assist decision-makers in reducing and controlling the emissions of atmospheric pollutants. Case studies utilizing hourly PM2.5, PM10 and SO2 data collected from Tianjin and Shanghai in China are applied as illustrative examples to estimate the effectiveness and efficiency of the proposed system. Experimental results obviously indicated that the developed novel early warning system is much suitable for analyzing and monitoring air pollution, which can also add a novel viable option for decision-makers.

  2. The Application of Lidar to Synthetic Vision System Integrity

    NASA Technical Reports Server (NTRS)

    Campbell, Jacob L.; UijtdeHaag, Maarten; Vadlamani, Ananth; Young, Steve

    2003-01-01

    One goal in the development of a Synthetic Vision System (SVS) is to create a system that can be certified by the Federal Aviation Administration (FAA) for use at various flight criticality levels. As part of NASA s Aviation Safety Program, Ohio University and NASA Langley have been involved in the research and development of real-time terrain database integrity monitors for SVS. Integrity monitors based on a consistency check with onboard sensors may be required if the inherent terrain database integrity is not sufficient for a particular operation. Sensors such as the radar altimeter and weather radar, which are available on most commercial aircraft, are currently being investigated for use in a real-time terrain database integrity monitor. This paper introduces the concept of using a Light Detection And Ranging (LiDAR) sensor as part of a real-time terrain database integrity monitor. A LiDAR system consists of a scanning laser ranger, an inertial measurement unit (IMU), and a Global Positioning System (GPS) receiver. Information from these three sensors can be combined to generate synthesized terrain models (profiles), which can then be compared to the stored SVS terrain model. This paper discusses an initial performance evaluation of the LiDAR-based terrain database integrity monitor using LiDAR data collected over Reno, Nevada. The paper will address the consistency checking mechanism and test statistic, sensitivity to position errors, and a comparison of the LiDAR-based integrity monitor to a radar altimeter-based integrity monitor.

  3. Kapitza problem for the magnetic moments of synthetic antiferromagnetic systems

    SciTech Connect

    Dzhezherya, Yu. I.; Demishev, K. O.; Korenivskii, V. N.

    2012-08-15

    The dynamics of magnetization in synthetic antiferromagnetic systems with the magnetic dipole coupling in a rapidly oscillating field has been examined. It has been revealed that the system can behave similar to the Kapitza pendulum. It has been shown that an alternating magnetic field can be efficiently used to control the magnetic state of a cell of a synthetic antiferromagnet. Analytical relations have been obtained between the parameters of such an antiferromagnet and an external magnetic field at which certain quasistationary states are implemented.

  4. The use of synthetic input sequences in time series modeling

    NASA Astrophysics Data System (ADS)

    de Oliveira, Dair José; Letellier, Christophe; Gomes, Murilo E. D.; Aguirre, Luis A.

    2008-08-01

    In many situations time series models obtained from noise-like data settle to trivial solutions under iteration. This Letter proposes a way of producing a synthetic (dummy) input, that is included to prevent the model from settling down to a trivial solution, while maintaining features of the original signal. Simulated benchmark models and a real time series of RR intervals from an ECG are used to illustrate the procedure.

  5. A SEASAT-A synthetic aperture imaging radar system

    NASA Technical Reports Server (NTRS)

    Jordan, R. L.; Rodgers, D. H.

    1975-01-01

    The SEASAT, a synthetic aperture imaging radar system is the first radar system of its kind designed for the study of ocean wave patterns from orbit. The basic requirement of this system is to generate continuous radar imagery with a 100 km swath with 25m resolution from an orbital altitude of 800 km. These requirements impose unique system design problems. The end to end data system described including interactions of the spacecraft, antenna, sensor, telemetry link, and data processor. The synthetic aperture radar system generates a large quantity of data requiring the use of an analog link with stable local oscillator encoding. The problems associated in telemetering the radar information with sufficient fidelity to synthesize an image on the ground is described as well as the selected solutions to the problems.

  6. Synthetic biology: advancing the design of diverse genetic systems

    PubMed Central

    Wang, Yen-Hsiang; Wei, Kathy Y.; Smolke, Christina D.

    2013-01-01

    A main objective of synthetic biology is to make the process of designing genetically-encoded biological systems more systematic, predictable, robust, scalable, and efficient. The examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from a simple genetic switch to search-and-destroy systems. While significant advances in synthesis capabilities support the potential for the implementation of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Synthetic biology offers much promise in developing systems to address challenges faced in manufacturing, the environment and sustainability, and health and medicine, but the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems. PMID:23413816

  7. Transfer of Instrument Training and the Synthetic Flight Training System.

    ERIC Educational Resources Information Center

    Caro, Paul W.

    One phase of an innovative flight training program, its development, and initial administration is described in this paper. The operational suitability test activities related to a determination of the transfer of instrument training value of the Army's Synthetic Flight Training System (SFTS) Device 2B24. Sixteen active Army members of an Officer…

  8. Antenna dimensions of synthetic aperture radar systems on satellites

    NASA Technical Reports Server (NTRS)

    Richter, K. R.

    1973-01-01

    Design of a synthetic aperture radar (SAR) for a satellite must take into account the limitation in weight and dimensions of the antenna. The lower limits of the antenna area are derived from the conditions of unambiguity of the SAR system. This result is applied to estimate the antenna requirements for SARs on satellites in circular orbits of various altitudes around Earth and Venus.

  9. Ambiguities in spaceborne synthetic aperture radar systems

    NASA Technical Reports Server (NTRS)

    Li, F. K.; Johnson, W. T. K.

    1983-01-01

    An examination of aspects of spaceborne SAR time delay and Doppler ambiguities has led to the formulation of an accurate method for the evaluation of the ratio of ambiguity intensities to that of the signal, which has been applied to the nominal SAR system on Seasat. After discussing the variation of this ratio as a function of orbital latitude and attitude control error, it is shown that the detailed range migration-azimuth phase history of an ambiguity is different from that of a signal, so that the images of ambiguities are dispersed. Seasat SAR dispersed images are presented, and their dispersions are eliminated through an adjustment of the processing parameters. A method is also presented which uses a set of multiple pulse repetition sequences to determine the Doppler centroid frequency absolute values for SARs with high carrier frequencies and poor attitude measurements.

  10. Study on key techniques for synthetic aperture ladar system

    NASA Astrophysics Data System (ADS)

    Cao, Changqing; Zeng, Xiaodong; Feng, Zhejun; Zhang, Wenrui; Su, Lei

    2008-03-01

    The spatial resolution of a conventional imaging LADAR system is constrained by the diffraction limit of the telescope aperture. The purpose of this work is to investigate Synthetic Aperture Imaging LADAR (SAIL), which employs aperture synthesis with coherent laser radar to overcome the diffraction limit and achieve fine-resolution, long range, two-dimensional imaging with modest aperture diameters. Because of many advantages, LADAR based on synthetic aperture theory is becoming research hotspot and practicality. Synthetic Aperture LADAR (SAL) technology satisfies the critical need for reliable, long-range battlefield awareness. An image that takes radar tens of seconds to produce can be produced in a few thousands of a second at optical frequencies. While radar waves respond to macroscopic features such as corners, edges, and facets, laser waves interact with microscopic surface characteristics, which results in imagery that appears more familiar and is more easily interpreted. SAL could provide high resolution optical/infrared imaging. In the present paper we have tried to answer three questions: (1) the process of collecting the samples over the large "synthetic" aperture; (2) differences between SAR and SAL; (3) the key techniques for SAL system. The principle and progress of SAL are introduced and a typical SAL system is described. Beam stabilization, chirp laser, and heterodyne detection, which are among the most challenging aspects of SAL, are discussed in detail.

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

    PubMed

    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.

  12. Experiments with the Mesoscale Atmospheric Simulation System (MASS) using the synthetic relative humidity

    NASA Technical Reports Server (NTRS)

    Chang, Chia-Bo

    1994-01-01

    This study is intended to examine the impact of the synthetic relative humidity on the model simulation of mesoscale convective storm environment. The synthetic relative humidity is derived from the National Weather Services surface observations, and non-conventional sources including aircraft, radar, and satellite observations. The latter sources provide the mesoscale data of very high spatial and temporal resolution. The synthetic humidity data is used to complement the National Weather Services rawinsonde observations. It is believed that a realistic representation of initial moisture field in a mesoscale model is critical for the model simulation of thunderstorm development, and the formation of non-convective clouds as well as their effects on the surface energy budget. The impact will be investigated based on a real-data case study using the mesoscale atmospheric simulation system developed by Mesoscale Environmental Simulations Operations, Inc. The mesoscale atmospheric simulation system consists of objective analysis and initialization codes, and the coarse-mesh and fine-mesh dynamic prediction models. Both models are a three dimensional, primitive equation model containing the essential moist physics for simulating and forecasting mesoscale convective processes in the atmosphere. The modeling system is currently implemented at the Applied Meteorology Unit, Kennedy Space Center. Two procedures involving the synthetic relative humidity to define the model initial moisture fields are considered. It is proposed to perform several short-range (approximately 6 hours) comparative coarse-mesh simulation experiments with and without the synthetic data. They are aimed at revealing the model sensitivities should allow us both to refine the specification of the observational requirements, and to develop more accurate and efficient objective analysis schemes. The goal is to advance the MASS (Mesoscal Atmospheric Simulation System) modeling expertise so that the model

  13. Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

    PubMed

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-10-11

    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.

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

    PubMed Central

    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

  15. Scaling Reversible Adhesion in Synthetic and Biological Systems

    NASA Astrophysics Data System (ADS)

    Bartlett, Michael; Irschick, Duncan; Crosby, Alfred

    2013-03-01

    High capacity, easy release polymer adhesives, as demonstrated by a gecko's toe, present unique opportunities for synthetic design. However, without a framework that connects biological and synthetic adhesives from basic nanoscopic features to macroscopic systems, synthetic mimics have failed to perform favorably at large length scales. Starting from an energy balance, we develop a scaling approach to understand unstable interfacial fracture over multiple length scales. The simple theory reveals that reversibly adhesive polymers do not rely upon fibrillar features but require contradicting attributes: maximum compliance normal to the substrate and minimum compliance in the loading direction. We use this counterintuitive criterion to create reversible, easy release adhesives at macroscopic sizes (100 cm2) with unprecedented force capacities on the order of 3000 N. Importantly, we achieve this without fibrillar features, supporting our predictions and emphasizing the importance of subsurface anatomy in biological adhesive systems. Our theory describes adhesive force capacity as a function of material properties and geometry and is supported by over 1000 experiments, spanning both synthetic and biological adhesives, with agreement over 14 orders of magnitude in adhesive force.

  16. JAK/STAT signalling--an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology.

    PubMed

    Blätke, Mary Ann; Dittrich, Anna; Rohr, Christian; Heiner, Monika; Schaper, Fred; Marwan, Wolfgang

    2013-06-01

    Mathematical models of molecular networks regulating biological processes in cells or organisms are most frequently designed as sets of ordinary differential equations. Various modularisation methods have been applied to reduce the complexity of models, to analyse their structural properties, to separate biological processes, or to reuse model parts. Taking the JAK/STAT signalling pathway with the extensive combinatorial cross-talk of its components as a case study, we make a natural approach to modularisation by creating one module for each biomolecule. Each module consists of a Petri net and associated metadata and is organised in a database publically accessible through a web interface (). The Petri net describes the reaction mechanism of a given biomolecule and its functional interactions with other components including relevant conformational states. The database is designed to support the curation, documentation, version control, and update of individual modules, and to assist the user in automatically composing complex models from modules. Biomolecule centred modules, associated metadata, and database support together allow the automatic creation of models by considering differential gene expression in given cell types or under certain physiological conditions or states of disease. Modularity also facilitates exploring the consequences of alternative molecular mechanisms by comparative simulation of automatically created models even for users without mathematical skills. Models may be selectively executed as an ODE system, stochastic, or qualitative models or hybrid and exported in the SBML format. The fully automated generation of models of redesigned networks by metadata-guided modification of modules representing biomolecules with mutated function or specificity is proposed.

  17. Numerical modeling of active separation control by synthetic jets

    NASA Astrophysics Data System (ADS)

    Aram, Shawn

    Zero-Net Mass-Flux (ZNMF) actuators or synthetic jet actuators are versatile micro scale devices with numerous applications in the field of fluid mechanics. The primary focus of the current work is to use time-accurate simulations to study the interaction of these jets with cross flows and to optimize their performance for the control of boundary layer separation. This study consists of four parts. In the first part, a class of phenomenology-based models is proposed to reproduce the flow associated with synthetic jets in grazing flows and simplify the task of ZNMF-based flow control simulations. The proposed models have a non-uniform jet velocity profile with only two spatial degrees of freedom and a uniform slip velocity on the slot-flow boundary. A comparison of key integral quantities associated with the momentum, energy and vorticity fluxes shows that the models with a non-uniform jet velocity during the expulsion phase and uniform jet velocity during the ingestion phase can predict these quantities with good accuracy, whereas a simple plug flow model with a zero slip and uniform jet velocity under-predicts these three quantities during the expulsion phase. Based on our initial analysis, three of the simplest models are selected for further study, including an assessment of their performance for a canonical separated flow at different forcing frequencies. A key finding is that a simple plug-flow type model can predict incorrect trends for separation reduction with the jet frequency. A preliminary attempt is also made to provide empirical closure to these models. The effect of synthetic jets orientation on its interaction with a zero pressure gradient laminar boundary layer is explored in the second part. A rectangular slot is chosen in this study and streamwise and spanwise orientations of this slot are examined. The orientation of the slot is found to have a significant impact on its interaction with the boundary layer. The dominant feature in the streamwise

  18. Synthetic Fluorophores for Visualizing Biomolecules in Living Systems

    PubMed Central

    Martynov, V. I.; Pakhomov, A. A.; Popova, N. V.; Deyev, I. E.; Petrenko, A. G.

    2016-01-01

    The last decade has witnessed significant advance in the imaging of living systems using fluorescent markers. This progress has been primarily associated with the discovery of different spectral variants of fluorescent proteins. However, the fluorescent protein technology has its own limitations and, in some cases, the use of low-molecular-weight fluorophores is preferable. In this review, we describe the arsenal of synthetic fluorescent tools that are currently in researchers’ hands and span virtually the entire spectrum, from the UV to visible and, further, to the near-infrared region. An overview of recent advances in site-directed introduction of synthetic fluorophores into target cellular objects is provided. Application of these fluorescent probes to the solution of a wide range of biological problems, in particular, to the determination of local ion concentrations and pH in living systems, is discussed. PMID:28050265

  19. A digital calibration method for synthetic aperture radar systems

    NASA Technical Reports Server (NTRS)

    Larson, Richard W.; Jackson, P. L.; Kasischke, Eric S.

    1988-01-01

    A basic method to calibrate imagery from synthetic aperture radar (SAR) systems is presented. SAR images are calibrated by monitoring all the terms of the radar equation. This procedure includes the use of both external (calibrated reference reflectors) and internal (system-generated calibration signals) sources to monitor the total SAR system transfer function. To illustrate the implementation of the procedure, two calibrated SAR images (X-band, 3.2-cm wavelength) are presented, along with the radar cross-section measurements of specific scenes within each image. The sources of error within the SAR image calibration procedure are identified.

  20. Synthetic membranes and membrane processes with counterparts in biological systems

    NASA Astrophysics Data System (ADS)

    Matson, Stephen L.

    1996-02-01

    Conventional synthetic membranes, fashioned for the most part from rather unremarkable polymeric materials, are essentially passive structures that achieve various industrial and biomedical separations through simple and selective membrane permeation processes. Indeed, simplicity of membrane material, structure, and function has long been perceived as a virtue of membranes relative to other separation processes with which they compete. The passive membrane separation processes -- exemplified by micro- and ultrafiltration, dialysis, reverse osmosis, and gas permeation -- differ from one another primarily in terms of membrane morphology or structure (e.g., porous, gel-type, and nonporous) and the permeant transport mechanism and driving force (e.g., diffusion, convection, and 'solution/diffusion'). The passive membrane separation processes have in common the fact that interaction between permeant and membrane material is typically weak and physicochemical in nature; indeed, it is frequently an objective of membrane materials design to minimize interaction between permeant and membrane polymer, since such strategies can minimize membrane fouling. As a consequence, conventional membrane processes often provide only modest separation factors or permselectivities; that is, they are more useful in performing 'group separations' (i.e., the separation of different classes of material) than they are in fractionating species within a given class. It has long been recognized within the community of membrane technologists that biological membrane structures and their components are extraordinarily sophisticated and powerful as compared to their synthetic counterparts. Moreover, biomembranes and related biological systems have been 'designed' according to a very different paradigm -- one that frequently maximizes and capitalizes on extraordinarily strong and biochemically specific interactions between components of the membrane and species interacting with them. Thus, in recent

  1. Crew and Display Concepts Evaluation for Synthetic / Enhanced Vision Systems

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Kramer, Lynda J.; Prinzel, Lawrence J., III

    2006-01-01

    NASA s Synthetic Vision Systems (SVS) project is developing technologies with practical applications that strive to eliminate low-visibility conditions as a causal factor to civil aircraft accidents and replicate the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. Enhanced Vision System (EVS) technologies are analogous and complementary in many respects to SVS, with the principle difference being that EVS is an imaging sensor presentation, as opposed to a database-derived image. The use of EVS in civil aircraft is projected to increase rapidly as the Federal Aviation Administration recently changed the aircraft operating rules under Part 91, revising the flight visibility requirements for conducting operations to civil airports. Operators conducting straight-in instrument approach procedures may now operate below the published approach minimums when using an approved EVS that shows the required visual references on the pilot s Head-Up Display. An experiment was conducted to evaluate the complementary use of SVS and EVS technologies, specifically focusing on new techniques for integration and/or fusion of synthetic and enhanced vision technologies and crew resource management while operating under the newly adopted FAA rules which provide operating credit for EVS. Overall, the experimental data showed that significant improvements in SA without concomitant increases in workload and display clutter could be provided by the integration and/or fusion of synthetic and enhanced vision technologies for the pilot-flying and the pilot-not-flying.

  2. Engineering plant metabolism into microbes: from systems biology to synthetic biology.

    PubMed

    Xu, Peng; Bhan, Namita; Koffas, Mattheos A G

    2013-04-01

    Plant metabolism represents an enormous repository of compounds that are of pharmaceutical and biotechnological importance. Engineering plant metabolism into microbes will provide sustainable solutions to produce pharmaceutical and fuel molecules that could one day replace substantial portions of the current fossil-fuel based economy. Metabolic engineering entails targeted manipulation of biosynthetic pathways to maximize yields of desired products. Recent advances in Systems Biology and the emergence of Synthetic Biology have accelerated our ability to design, construct and optimize cell factories for metabolic engineering applications. Progress in predicting and modeling genome-scale metabolic networks, versatile gene assembly platforms and delicate synthetic pathway optimization strategies has provided us exciting opportunities to exploit the full potential of cell metabolism. In this review, we will discuss how systems and synthetic biology tools can be integrated to create tailor-made cell factories for efficient production of natural products and fuel molecules in microorganisms.

  3. Engineering the Feedback Dynamics of in vitro Synthetic Biological Systems

    NASA Astrophysics Data System (ADS)

    Bishop, Joshua D.

    Building a biochemical system from scratch that rivals a living cell in ability to robustly perform many complex tasks in response to environmental signals is beyond the state-of-the- art. However, feedback is clearly a principle widely employed by cells---as it is by engineers---to enable robust dynamical behaviors, although a limited system-level understanding of feedback regulation and dynamical behavior in biochemical contexts hampers our ability to engineer such systems. Studying simple feedback systems in a rich, yet fully synthetic, biochemical context---like that provided by DNA nanotechnology---may therefore lead to a new state-of-the-art for synthetic biological systems. This thesis, in keeping with this philosophy, describes basic efforts in engineering bio- chemical feedback control systems in the form of simple, in vitro, nucleic-acid-based devices. I describe two such devices, which provide basic test-beds for engineering feedback dynamics in vitro. The first device is a DNA nanomotor, previously described in the literature, that is built from and operated by nucleic acid components, and that I modify by the introduction of a protein enzyme to improve the performance of the device in experimental tests. The second device I design and build from nucleic acid components and two protein enzymes to regulate the free quantity of an RNA molecule, which in turn can be used to dynamically drive the operation of other nucleic-acid-based systems---such as the first device---in a robust manner.

  4. Lighting system with thermal management system having point contact synthetic jets

    DOEpatents

    Arik, Mehmet; Weaver, Stanton Earl; Kuenzler, Glenn Howard; Wolfe, Jr., Charles Franklin; Sharma, Rajdeep

    2013-12-10

    Lighting system having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system includes a plurality of synthetic jets. The synthetic jets are arranged within the lighting system such that they are secured at contact points.

  5. Lighting system with thermal management system having point contact synthetic jets

    DOEpatents

    Arik, Mehmet; Weaver, Stanton Earl; Kuenzler, Glenn Howard; Wolfe, Jr., Charles Franklin; Sharma, Rajdeep

    2016-08-23

    Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system includes a plurality of synthetic jets. The synthetic jets are arranged within the lighting system such that they are secured at contact points.

  6. Lighting system with thermal management system having point contact synthetic jets

    DOEpatents

    Arik, Mehmet; Weaver, Stanton Earl; Kuenzler, Glenn Howard; Wolfe, Jr, Charles Franklin; Sharma, Rajdeep

    2016-08-30

    Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system includes a plurality of synthetic jets. The synthetic jets are arranged within the lighting system such that they are secured at contact points.

  7. Post-Stroke Depression Modulation and in Vivo Antioxidant Activity of Gallic Acid and Its Synthetic Derivatives in a Murine Model System

    PubMed Central

    Nabavi, Seyed Fazel; Habtemariam, Solomon; Di Lorenzo, Arianna; Sureda, Antoni; Khanjani, Sedigheh; Nabavi, Seyed Mohammad; Daglia, Maria

    2016-01-01

    Gallic acid (3,4,5-trihydroxybenzoic acid, GA) is a plant secondary metabolite, which shows antioxidant activity and is commonly found in many plant-based foods and beverages. Recent evidence suggests that oxidative stress contributes to the development of many human chronic diseases, including cardiovascular and neurodegenerative pathologies, metabolic syndrome, type 2 diabetes and cancer. GA and its derivative, methyl-3-O-methyl gallate (M3OMG), possess physiological and pharmacological activities closely related to their antioxidant properties. This paper describes the antidepressive-like effects of intraperitoneal administration of GA and two synthetic analogues, M3OMG and P3OMG (propyl-3-O-methylgallate), in balb/c mice with post-stroke depression, a secondary form of depression that could be due to oxidative stress occurring during cerebral ischemia and the following reperfusion. Moreover, this study determined the in vivo antioxidant activity of these compounds through the evaluation of superoxide dismutase (SOD) and catalase (Cat) activity, thiobarbituric acid-reactive substances (TBARS) and reduced glutathione (GSH) levels in mouse brain. GA and its synthetic analogues were found to be active (at doses of 25 and 50 mg/kg) in the modulation of depressive symptoms and the reduction of oxidative stress, restoring normal behavior and, at least in part, antioxidant endogenous defenses, with M3OMG being the most active of these compounds. SOD, TBARS, and GSH all showed strong correlation with behavioral parameters, suggesting that oxidative stress is tightly linked to the pathological processes involved in stroke and PSD. As a whole, the obtained results show that the administration of GA, M3OMG and P3OMG induce a reduction in depressive symptoms and oxidative stress. PMID:27136579

  8. Synthetic-gauge-field-induced Dirac semimetal state in an acoustic resonator system

    NASA Astrophysics Data System (ADS)

    Yang, Zhaoju; Gao, Fei; Shi, Xihang; Zhang, Baile

    2016-12-01

    Recently, a proposal of synthetic gauge field in reduced two-dimensional (2D) system from three-dimensional (3D) acoustic structure shows an analogue of the gapped Haldane model with fixed k z , and achieves the gapless Weyl semimetal phase in 3D momentum space. Here, extending this approach of synthetic gauge flux, we propose a reduced square lattice of acoustic resonators, which exhibits Dirac nodes with broken effective time-reversal symmetry. Protected by an additional hidden symmetry, these Dirac nodes with quantized values of topological charge are characterized by nonzero winding number and the finite structure exhibits flat edge modes that cannot be destroyed by perturbations.

  9. Nonlinear inversion for arbitrarily-oriented anisotropic models: Synthetic testing

    NASA Astrophysics Data System (ADS)

    Bremner, P. M.; Panning, M. P.

    2010-12-01

    We present an implementation of new 3-D finite-frequency kernels, based on the Born approximation, for inversion of a synthetic surface wave dataset. The kernels are formulated based on a hexagonal symmetry with an arbitrary orientation. Numerical tests are performed to achieve a robust inversion scheme. Nonlinear inversion schemes are examined for adequate recovery of three input models to include: isotropic, anisotropic, and both anisotropic and isotropic input models. Output models from inversions of calculated synthetic data are compared against these input models to test for accurate reproduction of input model features, and the resolution of those features. The focus of this study is on inverting for structure beneath western North America. The synthetic dataset consists of collected seismic waveforms of 128 earthquake mechanisms, of magnitude 6-7 from Dec 2006 to Feb 2009, from the IRIS database. Events were selected to correlate with USArray deployments, and to have as complete an azimuthal coverage as possible. The events occurred within a circular region of radius 150° centered about 44° lat, -110° lon (an arbitrary location within USArray coverage). The seismograms have been calculated within a simplified version of PREM in which the crust and 220 km discontinuity have been removed, dubbed PREM LIGHT, utilizing a spectral element code (SEM) coupled to a normal mode solution. The mesh consists of a 3-D heterogeneous outer shell, representing the upper mantle above 400 km depth, coupled to a spherically symmetric inner sphere. The SEM solves the weak formulation of the seismic wave equation in the outer shell, and uses normal mode summation methods for the inner sphere. To validate the results of the SEM, seismograms are benchmarked against seismograms calculated with a 1-D normal mode summation. From the synthetic dataset, multi-taper fundamental mode surface wave phase delay measurements are taken. The orthogonal 2.5π spheroidal wave function

  10. Synthetic-Eddy Method for Urban Atmospheric Flow Modelling

    NASA Astrophysics Data System (ADS)

    Pavlidis, D.; Gorman, G. J.; Gomes, J. L. M. A.; Pain, C. C.; Apsimon, H.

    2010-08-01

    The computational fluid dynamics code Fluidity, with anisotropic mesh adaptivity, is used as a multi-scale obstacle-accommodating meteorological model. A novel method for generating realistic inlet boundary conditions based on the view of turbulence as a superposition of synthetic eddies is adopted. It is able to reproduce prescribed first-order and second-order one-point statistics and turbulence length scales. The aim is to simulate an urban boundary layer. The model is validated against two standard benchmark tests: a plane channel flow numerical simulation and a flow past a cube physical simulation. The performed large-eddy simulations are in good agreement with both reference models giving confidence that the model can be used to successfully simulate urban atmospheric flows.

  11. Comparison of different synthetic 5-min rainfall time series regarding their suitability for urban drainage modelling

    NASA Astrophysics Data System (ADS)

    van der Heijden, Sven; Callau Poduje, Ana; Müller, Hannes; Shehu, Bora; Haberlandt, Uwe; Lorenz, Manuel; Wagner, Sven; Kunstmann, Harald; Müller, Thomas; Mosthaf, Tobias; Bárdossy, András

    2015-04-01

    For the design and operation of urban drainage systems with numerical simulation models, long, continuous precipitation time series with high temporal resolution are necessary. Suitable observed time series are rare. As a result, intelligent design concepts often use uncertain or unsuitable precipitation data, which renders them uneconomic or unsustainable. An expedient alternative to observed data is the use of long, synthetic rainfall time series as input for the simulation models. Within the project SYNOPSE, several different methods to generate synthetic precipitation data for urban drainage modelling are advanced, tested, and compared. The presented study compares four different approaches of precipitation models regarding their ability to reproduce rainfall and runoff characteristics. These include one parametric stochastic model (alternating renewal approach), one non-parametric stochastic model (resampling approach), one downscaling approach from a regional climate model, and one disaggregation approach based on daily precipitation measurements. All four models produce long precipitation time series with a temporal resolution of five minutes. The synthetic time series are first compared to observed rainfall reference time series. Comparison criteria include event based statistics like mean dry spell and wet spell duration, wet spell amount and intensity, long term means of precipitation sum and number of events, and extreme value distributions for different durations. Then they are compared regarding simulated discharge characteristics using an urban hydrological model on a fictitious sewage network. First results show a principal suitability of all rainfall models but with different strengths and weaknesses regarding the different rainfall and runoff characteristics considered.

  12. Ferritin nanocontainers that self-direct in synthetic polymer systems

    NASA Astrophysics Data System (ADS)

    Sengonul, Merih C.

    Currently, there are many approaches to introduce functionality into synthetic polymers. Among these, for example, are copolymerization, grafting, and blending methods. However, modifications made by such methods also change the thermodynamics and rheological properties of the polymer system of interest, and each new modification often requires a costly reoptimization of polymer processing. Such a reoptimalization would not be necessary if new functionality could be introduced via a container whose external surface is chemically and physically tuned to interact with the parent polymer. The contents of the container could then be changed without changing other important properties of the parent polymer. In this context this thesis project explores an innovative nanocontainer platform which can be introduced into phase-separating homopolymer blends. Ferritin is a naturally existing nanocontainer that can be used synthetically to package and selectively transport functional moieties to a particular phase that is either in the bulk or on the surface of a homopolymer blend system. The principal focus of this work centers on modifying the surface of wild ferritin to: (1) render modified ferritin soluble in a non-aqueous solvent; and (2) impart it with self-directing properties when exposed to a homopolymer blend surface or incorporated into the bulk of a homopolymer blend. Wild ferritin is water soluble, and this research project successfully modified wild ferritin by grafting either amine-functional poly(ethylene glycol) (PEG) or short-chain alkanes to carbodiimide activated carboxylate groups on ferritin's surface. Such modified ferritin is soluble in dichloromethane (DCM). Modification was confirmed by ion-exchange chromatography, zeta-potential measurements, and electrospray mass spectroscopy. FT-IR was used to quantify the extent of PEGylation of the reaction products through area ratios of the -C-O-C asymmetric stretching vibration of the grafted PEG chains to the

  13. Phase correction system for automatic focusing of synthetic aperture radar

    DOEpatents

    Eichel, Paul H.; Ghiglia, Dennis C.; Jakowatz, Jr., Charles V.

    1990-01-01

    A phase gradient autofocus system for use in synthetic aperture imaging accurately compensates for arbitrary phase errors in each imaged frame by locating highlighted areas and determining the phase disturbance or image spread associated with each of these highlight areas. An estimate of the image spread for each highlighted area in a line in the case of one dimensional processing or in a sector, in the case of two-dimensional processing, is determined. The phase error is determined using phase gradient processing. The phase error is then removed from the uncorrected image and the process is iteratively performed to substantially eliminate phase errors which can degrade the image.

  14. Quantitative statistical assessment of conditional models for synthetic aperture radar.

    PubMed

    DeVore, Michael D; O'Sullivan, Joseph A

    2004-02-01

    Many applications of object recognition in the presence of pose uncertainty rely on statistical models-conditioned on pose-for observations. The image statistics of three-dimensional (3-D) objects are often assumed to belong to a family of distributions with unknown model parameters that vary with one or more continuous-valued pose parameters. Many methods for statistical model assessment, for example the tests of Kolmogorov-Smirnov and K. Pearson, require that all model parameters be fully specified or that sample sizes be large. Assessing pose-dependent models from a finite number of observations over a variety of poses can violate these requirements. However, a large number of small samples, corresponding to unique combinations of object, pose, and pixel location, are often available. We develop methods for model testing which assume a large number of small samples and apply them to the comparison of three models for synthetic aperture radar images of 3-D objects with varying pose. Each model is directly related to the Gaussian distribution and is assessed both in terms of goodness-of-fit and underlying model assumptions, such as independence, known mean, and homoscedasticity. Test results are presented in terms of the functional relationship between a given significance level and the percentage of samples that wold fail a test at that level.

  15. Image processing in an enhanced and synthetic vision system

    NASA Astrophysics Data System (ADS)

    Mueller, Rupert M.; Palubinskas, Gintautas; Gemperlein, Hans

    2002-07-01

    'Synthetic Vision' and 'Sensor Vision' complement to an ideal system for the pilot's situation awareness. To fuse these two data sets the sensor images are first segmented by a k-means algorithm and then features are extracted by blob analysis. These image features are compared with the features of the projected airport data using fuzzy logic in order to identify the runway in the sensor image and to improve the aircraft navigation data. This process is necessary due to inaccurate input data i.e. position and attitude of the aircraft. After identifying the runway, obstacles can be detected using the sensor image. The extracted information is presented to the pilot's display system and combined with the appropriate information from the MMW radar sensor in a subsequent fusion processor. A real time image processing procedure is discussed and demonstrated with IR measurements of a FLIR system during landing approaches.

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

    PubMed

    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."

  17. Spectral classification of stars using synthetic model atmospheres

    NASA Astrophysics Data System (ADS)

    Bertone, E.; Buzzoni, A.

    2001-09-01

    We devised a straightforward procedure to derive the atmospheric fundamental parameters of stars across the different MK spectral types by comparing mid-resolution spectroscopic observations with theoretical grids of synthetic spectra. The results of a preliminary experiment, by matching the Gunn & Stryker (1983) and Jacoby et al. (1984) spectrophotometric atlases with the Kurucz (1995) models, are briefly discussed. For stars in the A-K spectral range, effective temperature is obtained within a 1-2% relative uncertainty (at 2-sigma confidence level). This value raises to 4-5% for the hottest stars in the samples (O-B spectral types). A poorer fit is obtained throughout for stars cooler than 4000 K mainly due to the limiting input physics in the Kurucz models.

  18. Synthetic clusters of massive stars to test stellar evolution models

    NASA Astrophysics Data System (ADS)

    Georgy, Cyril; Ekström, Sylvia; Granada, Anahi; Meynet, Georges; Bastian, Nate; Charbonnel, Corinne

    2015-08-01

    During the recent years, the Geneva stellar evolution group has published several sets of grids of stellar models, including the effect of rotation and with up to date input physics. These sets cover a wide range of initial masses, initial rotation rates and metallicities. In addition to these grids, we have also developed a toolbox (the SYCLIST code), allowing for the study of stellar populations as a function of time, and to build synthetic clusters of a given age.In this talk, I will present the SYCLIST code and the various effects that it is able to account for: initial distributions of rotation velocities, effect of the angle of view on the look of fast rotating stars (gravity darkening). I will show how the account for a rotation velocities distribution affects the HRD and CMD of clusters at different ages.Eventually, I will discuss how comparing our synthetic clusters with observed ones can help in understanding stellar physics. For example, I will show how the effects of rotation and of gravity darkening affects the region of the turn-off of young clusters. Rotation has also an impact on the look of the Hertzsprung gap of intermediate age clusters, by broadening the sequence of stars that lie in this region of the HRD.

  19. Synthetic event-related potentials: a computational bridge between neurolinguistic models and experiments.

    PubMed

    Barrès, Victor; Simons, Arthur; Arbib, Michael

    2013-01-01

    that mediate the relation between the brain's inputs, outputs, and internal states in executing a specific task. The neural networks used for Synthetic ERP must include neuroanatomically realistic placement and orientation of the cortical pyramidal neurons. These constraints pose exciting challenges for future work in neural network modeling that is applicable to systems and cognitive neuroscience.

  20. Optical design of a synthetic aperture ladar antenna system

    NASA Astrophysics Data System (ADS)

    Cao, Changqing; Zeng, Xiaodong; Zhao, Xiaoyan; Liu, Huanhuan; Man, Xiangkun

    2008-03-01

    The spatial resolution of a conventional imaging LADAR system is constrained by the diffraction limit of the telescope aperture. The purpose of this work is to investigate Synthetic Aperture Imaging LADAR (SAIL), which employs aperture synthesis with coherent laser radar to overcome the diffraction limit and achieve fine-resolution, long range, two-dimensional imaging with modest aperture diameters. According to the demands of the Synthetic Aperture LADAR (SAL), the key techniques are analyzed briefly. The preliminary design of the optical antenna is also introduced in this paper. We investigate the design method and relevant problems of efficient optical antenna that are required in SAL. The design is pursued on the basis of the same method as is used at microwave frequency. The method is based on numerical analysis and the error values obtained by present manufacturing technology. According to the requirement to SAL with the trial of little size, light mass, low cost and high image quality, the result by ZEMAX will result.

  1. The role of regulation in the origin and synthetic modelling of minimal cognition.

    PubMed

    Bich, Leonardo; Moreno, Alvaro

    2016-10-01

    In this paper we address the question of minimal cognition by investigating the origin of some crucial cognitive properties from the very basic organisation of biological systems. More specifically, we propose a theoretical model of how a system can distinguish between specific features of its interaction with the environment, which is a fundamental requirement for the emergence of minimal forms of cognition. We argue that the appearance of this capacity is grounded in the molecular domain, and originates from basic mechanisms of biological regulation. In doing so, our aim is to provide a theoretical account that can also work as a possible conceptual bridge between Synthetic Biology and Artificial Intelligence. In fact, we argue, Synthetic Biology can contribute to the study of minimal cognition (and therefore to a minimal AI), by providing a privileged approach to the study of these mechanisms by means of artificial systems.

  2. Literature Evidence on Live Animal Versus Synthetic Models for Training and Assessing Trauma Resuscitation Procedures.

    PubMed

    Hart, Danielle; McNeil, Mary Ann; Hegarty, Cullen; Rush, Robert; Chipman, Jeffery; Clinton, Joseph; Reihsen, Troy; Sweet, Robert

    2016-01-01

    There are many models currently used for teaching and assessing performance of trauma-related airway, breathing, and hemorrhage procedures. Although many programs use live animal (live tissue [LT]) models, there is a congressional effort to transition to the use of nonanimal- based methods (i.e., simulators, cadavers) for military trainees. We examined the existing literature and compared the efficacy, acceptability, and validity of available models with a focus on comparing LT models with synthetic systems. Literature and Internet searches were conducted to examine current models for seven core trauma procedures. We identified 185 simulator systems. Evidence on acceptability and validity of models was sparse. We found only one underpowered study comparing the performance of learners after training on LT versus simulator models for tube thoracostomy and cricothyrotomy. There is insufficient data-driven evidence to distinguish superior validity of LT or any other model for training or assessment of critical trauma procedures.

  3. Exploring the properties of the DDO system using synthetic colors

    NASA Astrophysics Data System (ADS)

    Tripicco, Michael J.; Bell, R. A.

    1991-08-01

    The properties of the David Dunlap Observatory (DDO) system (which uses bandpasses centered at about 3450, 3800, 4180, 4250, 4500, 4850, and 5150 A, referred to as 35, 38, 41, 42, 45, 48, and 51 filters) are explored by applying synthetic colors. Using DDO colors for a sample of stars for which spectrophotometric data were reported by Gunn and Stryker (1983), the correctness of the transmission profiles of the filters was established. It is shown that the presence of MgH lines in the 48 bandpass is an important reason why cool dwarfs and giants are separated in the C(45-48) vs C(42-45) diagram. It was found that including SiH lines in the spectra improved the agreement between observed and computed C(41-45) colors for dwarfs.

  4. Synthetic vision system flight test results and lessons learned

    NASA Technical Reports Server (NTRS)

    Radke, Jeffrey

    1993-01-01

    Honeywell Systems and Research Center developed and demonstrated an active 35 GHz Radar Imaging system as part of the FAA/USAF/Industry sponsored Synthetic Vision System Technology Demonstration (SVSTD) Program. The objectives of this presentation are to provide a general overview of flight test results, a system level perspective that encompasses the efforts of the SVSTD and Augmented VIsual Display (AVID) programs, and more importantly, provide the AVID workshop participants with Honeywell's perspective on the lessons that were learned from the SVS flight tests. One objective of the SVSTD program was to explore several known system issues concerning radar imaging technology. The program ultimately resolved some of these issues, left others open, and in fact created several new concerns. In some instances, the interested community has drawn improper conclusions from the program by globally attributing implementation specific issues to radar imaging technology in general. The motivation for this presentation is therefore to provide AVID researchers with a better understanding of the issues that truly remain open, and to identify the perceived issues that are either resolved or were specific to Honeywell's implementation.

  5. Capturing the Full Potential of the Synthetic Theater Operations Research Model (STORM)

    DTIC Science & Technology

    2014-09-01

    POTENTIAL OF THE SYNTHETIC THEATER OPERATIONS RESEARCH MODEL ( STORM ) by Christian N. Seymour September 2014 Thesis Co-Advisors: Thomas...SYNTHETIC THEATER OPERATIONS RESEARCH MODEL ( STORM ) 5. FUNDING NUMBERS 6. AUTHOR(S) Christian N. Seymour 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS...The Synthetic Theater Operations Research Model ( STORM ) is the primary campaign analysis tool used by the Office of the Chief of Naval Operations

  6. Modeling atmospheric precipitation impact on synthetic aperture radar imagery at X and Ka bands

    NASA Astrophysics Data System (ADS)

    Mori, Saverio; Polverari, Federica; Pulvirenti, Luca; Montopoli, Mario; Pierdicca, Nazzareno; Marzano, Frank S.

    2014-10-01

    Spaceborne synthetic aperture radars (SARs) operating at X-band and above allow observations of Earth surface at very high spatial resolution. Moreover, recent polarimetric SARs enable the complete characterization of target scattering and extinction properties. Nowadays several spaceborne X-band SAR systems are operative, and plans exist for systems operating at higher frequency bands (i.e. Ku, Ka and W). Although higher frequencies may have interesting and distinctive applications, atmospheric effects, especially in precipitating conditions, may affect the surface SAR response in both the signal amplitude and its phase, as assessed by numerous works in the last years. A valid tool to analyze and characterize the SAR response in these conditions is represented by forward modeling, where a known synthetic scenario, which is described by user-selected surface and atmospheric conditions, is considered. Thus, the SAR echoes corresponding to the synthetic scenarios are simulated using electromagnetic models. In this work a 3-D realistic polarimetric SAR response numerical simulator is presented. The proposed model framework accounts for the SAR slant observing geometry and it is able to characterize the polarimetric response both in amplitude and phase. In this work we have considered both X and Ka bands, thus exploring the atmospheric effects for the present and future polarimetric systems. The atmospheric conditions are simulated using the System for Atmospheric Modeling (SAM) which is an high-resolution mesoscale model. SAM is used to define the three-dimensional distribution of hydrometeors which are among the inputs used in the Hydrometeor Ensemble Scattering Simulator (HESS) T-Matrix which allow simulating the SAR signal due to the atmospheric component. The SAR surface component is, instead, simulated by a Semi Empirical Model (SEM) for bare-soils conditions and SEAWIND2 two-scale model for ocean surfaces. The proposed methodology has been applied in this work

  7. Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants

    PubMed Central

    Hill, Camilla Beate; Czauderna, Tobias; Klapperstück, Matthias; Roessner, Ute; Schreiber, Falk

    2015-01-01

    Life on earth depends on dynamic chemical transformations that enable cellular functions, including electron transfer reactions, as well as synthesis and degradation of biomolecules. Biochemical reactions are coordinated in metabolic pathways that interact in a complex way to allow adequate regulation. Biotechnology, food, biofuel, agricultural, and pharmaceutical industries are highly interested in metabolic engineering as an enabling technology of synthetic biology to exploit cells for the controlled production of metabolites of interest. These approaches have only recently been extended to plants due to their greater metabolic complexity (such as primary and secondary metabolism) and highly compartmentalized cellular structures and functions (including plant-specific organelles) compared with bacteria and other microorganisms. Technological advances in analytical instrumentation in combination with advances in data analysis and modeling have opened up new approaches to engineer plant metabolic pathways and allow the impact of modifications to be predicted more accurately. In this article, we review challenges in the integration and analysis of large-scale metabolic data, present an overview of current bioinformatics methods for the modeling and visualization of metabolic networks, and discuss approaches for interfacing bioinformatics approaches with metabolic models of cellular processes and flux distributions in order to predict phenotypes derived from specific genetic modifications or subjected to different environmental conditions. PMID:26557642

  8. Comparison of different synthetic 5-min rainfall time series on the results of rainfall runoff simulations in urban drainage modelling

    NASA Astrophysics Data System (ADS)

    Krämer, Stefan; Rohde, Sophia; Schröder, Kai; Belli, Aslan; Maßmann, Stefanie; Schönfeld, Martin; Henkel, Erik; Fuchs, Lothar

    2015-04-01

    The design of urban drainage systems with numerical simulation models requires long, continuous rainfall time series with high temporal resolution. However, suitable observed time series are rare. As a result, usual design concepts often use uncertain or unsuitable rainfall data, which renders them uneconomic or unsustainable. An expedient alternative to observed data is the use of long, synthetic rainfall time series as input for the simulation models. Within the project SYNOPSE, several different methods to generate synthetic rainfall data as input for urban drainage modelling are advanced, tested, and compared. Synthetic rainfall time series of three different precipitation model approaches, - one parametric stochastic model (alternating renewal approach), one non-parametric stochastic model (resampling approach), one downscaling approach from a regional climate model-, are provided for three catchments with different sewer system characteristics in different climate regions in Germany: - Hamburg (northern Germany): maritime climate, mean annual rainfall: 770 mm; combined sewer system length: 1.729 km (City center of Hamburg), storm water sewer system length (Hamburg Harburg): 168 km - Brunswick (Lower Saxony, northern Germany): transitional climate from maritime to continental, mean annual rainfall: 618 mm; sewer system length: 278 km, connected impervious area: 379 ha, height difference: 27 m - Friburg in Brisgau (southern Germany): Central European transitional climate, mean annual rainfall: 908 mm; sewer system length: 794 km, connected impervious area: 1 546 ha, height difference 284 m Hydrodynamic models are set up for each catchment to simulate rainfall runoff processes in the sewer systems. Long term event time series are extracted from the - three different synthetic rainfall time series (comprising up to 600 years continuous rainfall) provided for each catchment and - observed gauge rainfall (reference rainfall) according national hydraulic design

  9. Modeling human response errors in synthetic flight simulator domain

    NASA Technical Reports Server (NTRS)

    Ntuen, Celestine A.

    1992-01-01

    This paper presents a control theoretic approach to modeling human response errors (HRE) in the flight simulation domain. The human pilot is modeled as a supervisor of a highly automated system. The synthesis uses the theory of optimal control pilot modeling for integrating the pilot's observation error and the error due to the simulation model (experimental error). Methods for solving the HRE problem are suggested. Experimental verification of the models will be tested in a flight quality handling simulation.

  10. Investigation of Sorption Mass Transfer Models Using Synthetic Soils

    DTIC Science & Technology

    1996-12-01

    distributions of two or more materials and sizes. We tested the ability of the model to simulate the behavior of these systems and to fit system...for groundwater pollutants and improved clean-up operations are possible. New models developed for this purpose require rigorous testing using media of...be made to test model validity. Research Obiectives: The purpose of this experimental study is to test a theory that relates sorption rate to geometry

  11. EFFECTIVENESS OF THE VIDEOARTHROSCOPY LEARNING PROCESS IN SYNTHETIC SHOULDER MODELS

    PubMed Central

    Dal Molin, Fabio Farina; Mothes, Fernando Carlos; Feder, Marta Goldman

    2015-01-01

    Objectives: The authors evaluate the learning of the videoarthroscopic technique, using the video surgery simulator SAM® (Shoulder Arthroscopy Model). Methods: Twenty medical residents in Orthepaedics, without prior knowledge of the arthroscopic technique, were evaluated before and after training. The tasks consisted of positioning, in holes that simulated portals, four surgical threads attached to an anchor placed in the anatomical neck of the humerus in the synthetic model. Time, number of movements, number of attempts, amount of errors and comparison between the two phases of training before and after - were observed and noted. Results: The data was submitted to statistical analysis, and a significant difference was found in the comparison of the variables before and after the training. Conclusion: The result of this study enables us to conclude that training in the videoarthroscopic technique using the video surgery simulator SAM enables the surgeon to execute essential tasks involved in these techniques, in less time, making less mistakes, and developing the ability to deal better with the videoarthrocopic image. PMID:27027086

  12. New synthetic substrates of mammalian nucleotide excision repair system

    PubMed Central

    Evdokimov, Alexey; Petruseva, Irina; Tsidulko, Aleksandra; Koroleva, Ludmila; Serpokrylova, Inna; Silnikov, Vladimir; Lavrik, Olga

    2013-01-01

    DNA probes for the studies of damaged strand excision during the nucleotide excision repair (NER) have been designed using the novel non-nucleosidic phosphoramidite reagents that contain N-[6-(9-antracenylcarbamoyl)hexanoyl]-3-amino-1,2-propandiol (nAnt) and N-[6-(5(6)-fluoresceinylcarbamoyl)hexanoyl]-3-amino-1,2-propandiol (nFlu) moieties. New lesion-imitating adducts being inserted into DNA show good substrate properties in NER process. Modified extended linear nFlu– and nAntr–DNA are suitable for estimation of specific excision activity catalysed with mammalian whole-cell extracts. The following substrate activity range was revealed for the model 137-bp linear double-stranded DNA: nAnt–DNA ≈ nFlu–DNA > Chol–DNA (Chol–DNA—legitimate NER substrate that contains non-nucleoside fragment bearing cholesterol residue). In vitro assay shows that modified DNA can be a useful tool to study NER activity in whole-cell extracts. The developed approach should be of general use for the incorporation of NER-sensitive distortions into model DNAs. The new synthetic extended linear DNA containing bulky non-nucleoside modifications will be useful for NER mechanism study and for applications. PMID:23609543

  13. Synthetic Tumor Networks for Screening Drug Delivery Systems

    PubMed Central

    Prabhakarpandian, Balabhaskar; Shen, Ming-Che; Nichols, Joseph B.; Garson, Charles J.; Mills, Ivy R.; Matar, Majed M.; Fewell, Jason G.; Pant, Kapil

    2015-01-01

    Tumor drug delivery is a complex phenomenon affected by several elements in addition to drug or delivery vehicle’s physico-chemical properties. A key factor is tumor microvasculature with complex effects including convective transport, high interstitial pressure and enhanced vascular permeability due to the presence of “leaky vessels”. Current in vitro models of the tumor microenvironment for evaluating drug delivery are oversimplified and, as a result, show poor correlation with in vivo performance. In this study, we report on the development of a novel microfluidic platform that models the tumor microenvironment more accurately, with physiologically and morphologically realistic microvasculature including endothelial cell lined leaky capillary vessels along with 3D solid tumors. Endothelial cells and 3D spheroids of cervical tumor cells were co-cultured in the networks. Drug vehicle screening was demonstrated using GFP gene delivery by different formulations of nanopolymers. The synthetic tumor network was successful in predicting in vivo delivery efficiencies of the drug vehicles. The developed assay will have critical applications both in basic research, where it can be used to develop next generation delivery vehicles, and in drug discovery where it can be used to study drug transport and delivery efficacy in realistic tumor microenvironment, thereby enabling drug compound and/or delivery vehicle screening. PMID:25599856

  14. A Machine Reading System for Assembling Synthetic Paleontological Databases

    PubMed Central

    Peters, Shanan E.; Zhang, Ce; Livny, Miron; Ré, Christopher

    2014-01-01

    Many aspects of macroevolutionary theory and our understanding of biotic responses to global environmental change derive from literature-based compilations of paleontological data. Existing manually assembled databases are, however, incomplete and difficult to assess and enhance with new data types. Here, we develop and validate the quality of a machine reading system, PaleoDeepDive, that automatically locates and extracts data from heterogeneous text, tables, and figures in publications. PaleoDeepDive performs comparably to humans in several complex data extraction and inference tasks and generates congruent synthetic results that describe the geological history of taxonomic diversity and genus-level rates of origination and extinction. Unlike traditional databases, PaleoDeepDive produces a probabilistic database that systematically improves as information is added. We show that the system can readily accommodate sophisticated data types, such as morphological data in biological illustrations and associated textual descriptions. Our machine reading approach to scientific data integration and synthesis brings within reach many questions that are currently underdetermined and does so in ways that may stimulate entirely new modes of inquiry. PMID:25436610

  15. A machine reading system for assembling synthetic paleontological databases.

    PubMed

    Peters, Shanan E; Zhang, Ce; Livny, Miron; Ré, Christopher

    2014-01-01

    Many aspects of macroevolutionary theory and our understanding of biotic responses to global environmental change derive from literature-based compilations of paleontological data. Existing manually assembled databases are, however, incomplete and difficult to assess and enhance with new data types. Here, we develop and validate the quality of a machine reading system, PaleoDeepDive, that automatically locates and extracts data from heterogeneous text, tables, and figures in publications. PaleoDeepDive performs comparably to humans in several complex data extraction and inference tasks and generates congruent synthetic results that describe the geological history of taxonomic diversity and genus-level rates of origination and extinction. Unlike traditional databases, PaleoDeepDive produces a probabilistic database that systematically improves as information is added. We show that the system can readily accommodate sophisticated data types, such as morphological data in biological illustrations and associated textual descriptions. Our machine reading approach to scientific data integration and synthesis brings within reach many questions that are currently underdetermined and does so in ways that may stimulate entirely new modes of inquiry.

  16. Synthetic mitochondria as therapeutics against systemic aging: a hypothesis.

    PubMed

    Tang, Bor Luen

    2015-02-01

    We hypothesize herein that synthetic mitochondria, engineered, or reprogrammed to be more energetically efficient and to have mildly elevated levels of reactive oxygen species (ROS) production, would be an effective form of therapeutics against systemic aging. The free radical and mitochondria theories of aging hold that mitochondria-generated ROS underlies chronic organelle, cell and tissues damages that contribute to systemic aging. More recent findings, however, collectively suggest that while acute and massive ROS generation during events such as tissue injury is indeed detrimental, subacute stresses, and chronic elevation in ROS production may instead induce a state of mitochondrial hormesis (or "mitohormesis") that could extend lifespan. Mitohormesis appears to be a convergent mechanism for several known anti-aging signaling pathways. Importantly, mitohormetic signaling could also occur in a non-cell autonomous manner, with its induction in neurons affecting gut cells, for example. Technologies are outlined that could lead towards testing of the hypothesis, which include genetic and epigenetic engineering of the mitochondria, as well as intercellular transfer of mitochondria from transplanted helper cells to target tissues.

  17. Terahertz interferometric synthetic aperture tomography for confocal imaging systems.

    PubMed

    Heimbeck, M S; Marks, D L; Brady, D; Everitt, H O

    2012-04-15

    Terahertz (THz) interferometric synthetic aperture tomography (TISAT) for confocal imaging within extended objects is demonstrated by combining attributes of synthetic aperture radar and optical coherence tomography. Algorithms recently devised for interferometric synthetic aperture microscopy are adapted to account for the diffraction-and defocusing-induced spatially varying THz beam width characteristic of narrow depth of focus, high-resolution confocal imaging. A frequency-swept two-dimensional TISAT confocal imaging instrument rapidly achieves in-focus, diffraction-limited resolution over a depth 12 times larger than the instrument's depth of focus in a manner that may be easily extended to three dimensions and greater depths.

  18. Analytic model and frequency characteristics of plasma synthetic jet actuator

    NASA Astrophysics Data System (ADS)

    Zong, Hao-hua; Wu, Yun; Li, Ying-hong; Song, Hui-min; Zhang, Zhi-bo; Jia, Min

    2015-02-01

    This paper reports a novel analytic model of a plasma synthetic jet actuator (PSJA), considering both the heat transfer effect and the inertia of the throat gas. Both the whole cycle characteristics and the repetitive working process of PSJA can be predicted with this model. The frequency characteristics of a PSJA with 87 mm3 volume and different orifice diameters are investigated based on the analytic model combined with experiments. In the repetitive working mode, the actuator works initially in the transitional stage with 20 cycles and then in the dynamic balanced stage. During the transitional stage, major performance parameters of PSJA experience stepped growth, while during the dynamic balanced stage, these parameters are characterized by periodic variation. With a constant discharge energy of 6.9 mJ, there exists a saturated frequency of 4 kHz/6 kHz for an orifice diameter of 1 mm/1.5 mm, at which the time-averaged total pressure of the pulsed jet reaches a maximum. Between 0.5 mm and 1.5 mm, a larger orifice diameter leads to a higher saturated frequency due to the reduced jet duration time. As the actuation frequency increases, both the time-averaged cavity temperature and the peak jet velocity initially increase and then remain almost unchanged at 1600 K and 280 m/s, respectively. Besides, with increasing frequency, the mechanical energy incorporated in single pulsed jet, the expelled mass per pulse, and the time-averaged density in the cavity, decline in a stair stepping way, which is caused by the intermittent decrease of refresh stage duration in one period.

  19. Synthetic Scene Generation of Stennis Target Range for the Calibration of Remote Sensing Systems

    NASA Technical Reports Server (NTRS)

    Cao, Chang-Yong; Blonski, Slawomir; Ryan, Robert; Gasser, Gerald; Zanoni, Vicki; Jenner, Jeff

    1999-01-01

    The validation and verification (V&V) target range developed at Stennis Space Center is a useful tool for the calibration of remote sensing systems. In this paper, we present an algorithm for generating synthetic scenes or digital models of this target range. The atmospheric radiative transfer code Modtran 4 is used in simulating at-sensor radiance for a given sensor. Software is developed to generate the scene with different spatial and spectral resolutions using the at-sensor radiance values. Synthetic scenes provide a cost-effective way for in-flight validation for the spatial and radiometric accuracy of the data. Other applications include mission planning, sensor simulation, and trade-off analysis in sensor design. The radiometric and spatial accuracy of the simulation is evaluated by comparing simulated scenes with AVIRIS acquired values.

  20. Kinetics of an anaerobic moving bed reactor system treating synthetic milk wastewater.

    PubMed

    Ramakant; Satyanarayan, Shanta; Kaul, S N

    2002-10-01

    In the present study, anaerobic moving bed reactor called anaerobic rotating biological contactor treating synthetic milk wastewater operated at different organic loading rates and different hydraulic retention times, were evaluated to determine kinetic parameters for the substrate, biomass and biogas based on various models. The maximum substrate loading rate and half velocity constant were evaluated as 5.71 kgCOD/m3 x d and 1178 mg/L respectively by using Lineweaver-Burke plot. Maximum substrate removal efficiency and critical hydraulic retention time were compared with modified Young and McCarty model and the model is best fitted for the study. The complete removal of substrate cannot be expected due to presence of metabolic refractory material produced within the reactor system from influent system. Kinetic constants for maximum specific growth rate and decay coefficient were compared with the modified Monod model. Kornegay and Andrews model were used to evaluate the area capacity constant and half velocity constant. Kinetic constants for maximum specific gas production rate and proportionality constant were evaluated using Stover model. The gas production and quality are dependent on the substrate removal and substrate loading rate. The kinetic relationships derived from lab-scale experiment provided good estimates of the performance of pilot- and full-scale anaerobic rotating biological contactor packed with fibrous nylon pads and treating synthetic milk wastewater in terms of the effluent chemical oxygen demand concentrations and specific biogas production rates.

  1. EXPOSURE ANALYSIS MODELING SYSTEM (EXAMS): USER MANUAL AND SYSTEM DOCUMENTATION

    EPA Science Inventory

    The Exposure Analysis Modeling System, first published in 1982 (EPA-600/3-82-023), provides interactive computer software for formulating aquatic ecosystem models and rapidly evaluating the fate, transport, and exposure concentrations of synthetic organic chemicals - pesticides, ...

  2. Mimicry of the radical pair and triplet states in photosynthetic reaction centers with a synthetic model

    SciTech Connect

    Hasharoni, K.; Levanon, H.; Greenfield, S.R.; Gosztola, D.J.; Svec, W.A.; Wasiclewski, M.R. |

    1995-08-02

    Supramolecular systems synthesized to model the photosynthetic reaction center (RC) are designed to mimic several key properties of the RC protein. Thus far, most RC models fulfill only a subset of these criteria, with very few reports employing time-resolved electron paramagnetic resonance spectroscopy (TREPR). We now report TREPR results on a photosynthetic model system (1) in a nematic liquid crystal (LC) that does not contain the natural pigments, yet closely mimics the spin dynamics of triplet state formation found only in photosynthetic RCs. The design of supermolecule 1 follows criteria established for promoting high quantum yield charge separation in glassy media. The observation of this triplet state in 1 by TREPR demonstrates that most of the electronic states found in the primary photochemistry of photosynthetic RCs can be mimicked successfully in synthetic models interacting with LCs. 12 refs., 3 figs.

  3. Identification of line-specific strategies for improving carotenoid production in synthetic maize through data-driven mathematical modeling.

    PubMed

    Comas, Jorge; Benfeitas, Rui; Vilaprinyo, Ester; Sorribas, Albert; Solsona, Francesc; Farré, Gemma; Berman, Judit; Zorrilla, Uxue; Capell, Teresa; Sandmann, Gerhard; Zhu, Changfu; Christou, Paul; Alves, Rui

    2016-09-01

    Plant synthetic biology is still in its infancy. However, synthetic biology approaches have been used to manipulate and improve the nutritional and health value of staple food crops such as rice, potato and maize. With current technologies, production yields of the synthetic nutrients are a result of trial and error, and systematic rational strategies to optimize those yields are still lacking. Here, we present a workflow that combines gene expression and quantitative metabolomics with mathematical modeling to identify strategies for increasing production yields of nutritionally important carotenoids in the seed endosperm synthesized through alternative biosynthetic pathways in synthetic lines of white maize, which is normally devoid of carotenoids. Quantitative metabolomics and gene expression data are used to create and fit parameters of mathematical models that are specific to four independent maize lines. Sensitivity analysis and simulation of each model is used to predict which gene activities should be further engineered in order to increase production yields for carotenoid accumulation in each line. Some of these predictions (e.g. increasing Zmlycb/Gllycb will increase accumulated β-carotenes) are valid across the four maize lines and consistent with experimental observations in other systems. Other predictions are line specific. The workflow is adaptable to any other biological system for which appropriate quantitative information is available. Furthermore, we validate some of the predictions using experimental data from additional synthetic maize lines for which no models were developed.

  4. Antifouling Activity of Synthetic Alkylpyridinium Polymers Using the Barnacle Model

    PubMed Central

    Piazza, Veronica; Dragić, Ivanka; Sepčić, Kristina; Faimali, Marco; Garaventa, Francesca; Turk, Tom; Berne, Sabina

    2014-01-01

    Polymeric alkylpyridinium salts (poly-APS) isolated from the Mediterranean marine sponge, Haliclona (Rhizoniera) sarai, effectively inhibit barnacle larva settlement and natural marine biofilm formation through a non-toxic and reversible mechanism. Potential use of poly-APS-like compounds as antifouling agents led to the chemical synthesis of monomeric and oligomeric 3-alkylpyridinium analogues. However, these are less efficient in settlement assays and have greater toxicity than the natural polymers. Recently, a new chemical synthesis method enabled the production of poly-APS analogues with antibacterial, antifungal and anti-acetylcholinesterase activities. The present study examines the antifouling properties and toxicity of six of these synthetic poly-APS using the barnacle (Amphibalanus amphitrite) as a model (cyprids and II stage nauplii larvae) in settlement, acute and sub-acute toxicity assays. Two compounds, APS8 and APS12-3, show antifouling effects very similar to natural poly-APS, with an anti-settlement effective concentration that inhibits 50% of the cyprid population settlement (EC50) after 24 h of 0.32 mg/L and 0.89 mg/L, respectively. The toxicity of APS8 is negligible, while APS12-3 is three-fold more toxic (24-h LC50: nauplii, 11.60 mg/L; cyprids, 61.13 mg/L) than natural poly-APS. This toxicity of APS12-3 towards nauplii is, however, 60-fold and 1200-fold lower than that of the common co-biocides, Zn- and Cu-pyrithione, respectively. Additionally, exposure to APS12-3 for 24 and 48 h inhibits the naupliar swimming ability with respective IC50 of 4.83 and 1.86 mg/L. PMID:24699112

  5. Inclusion of sensor noise in radiometric models for generation of synthetic longwave infrared images

    NASA Astrophysics Data System (ADS)

    Schott, John R.; Salvaggio, Carl

    1987-01-01

    A radiometric model has been developed for modeling the effects of self emission, reflection of downwelled radiance, atmospheric transmission and path radiance on the radiance reaching an airborne or satellite sensing system. The model, which incorporates LOWTRAN 6, includes angular emissivity effects and will account for either specular or diffuse reflectance from targets and backgrounds. The model has been refined to facilitate its use in generating primitive synthetic images to study LWIR phenomena. In particular, various types of sensor related noise have been included in the imaging process. Images are presented simulating the effects of target-to-background contrast as a function of view angle, range, emissivity variation, and atmospheric effects. The potential for use of LWIR models in sensor and algorithm development is discussed.

  6. High-resolution imaging with a real-time synthetic aperture ultrasound system: a phantom study

    NASA Astrophysics Data System (ADS)

    Huang, Lianjie; Labyed, Yassin; Simonetti, Francesco; Williamson, Michael; Rosenberg, Robert; Heintz, Philip; Sandoval, Daniel

    2011-03-01

    It is difficult for ultrasound to image small targets such as breast microcalcifications. Synthetic aperture ultrasound imaging has recently developed as a promising tool to improve the capabilities of medical ultrasound. We use two different tissueequivalent phantoms to study the imaging capabilities of a real-time synthetic aperture ultrasound system for imaging small targets. The InnerVision ultrasound system DAS009 is an investigational system for real-time synthetic aperture ultrasound imaging. We use the system to image the two phantoms, and compare the images with those obtained from clinical scanners Acuson Sequoia 512 and Siemens S2000. Our results show that synthetic aperture ultrasound imaging produces images with higher resolution and less image artifacts than Acuson Sequoia 512 and Siemens S2000. In addition, we study the effects of sound speed on synthetic aperture ultrasound imaging and demonstrate that an accurate sound speed is very important for imaging small targets.

  7. Apparatus, systems, and methods for ultrasound synthetic aperature focusing

    DOEpatents

    Schuster, George J.; Crawford, Susan L.; Doctor, Steven R.; Harris, Robert V.

    2005-04-12

    One form of the present invention is a technique for interrogating a sample with ultrasound which includes: generating ultrasonic energy data corresponding to a volume of a sample and performing a synthetic aperture focusing technique on the ultrasonic energy data. The synthetic aperture focusing technique includes: defining a number of hyperbolic surfaces which extend through the volume at different depths and a corresponding number of multiple element accumulation vectors, performing a focused element calculation procedure for a group of vectors which are representative of the interior of a designated aperture, performing another focused element calculation procedure for vectors corresponding to the boundary of the aperture, and providing an image corresponding to features of the sample in accordance with the synthetic aperture focusing technique.

  8. A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches.

    PubMed

    Cantone, Irene; Marucci, Lucia; Iorio, Francesco; Ricci, Maria Aurelia; Belcastro, Vincenzo; Bansal, Mukesh; Santini, Stefania; di Bernardo, Mario; di Bernardo, Diego; Cosma, Maria Pia

    2009-04-03

    Systems biology approaches are extensively used to model and reverse engineer gene regulatory networks from experimental data. Conversely, synthetic biology allows "de novo" construction of a regulatory network to seed new functions in the cell. At present, the usefulness and predictive ability of modeling and reverse engineering cannot be assessed and compared rigorously. We built in the yeast Saccharomyces cerevisiae a synthetic network, IRMA, for in vivo "benchmarking" of reverse-engineering and modeling approaches. The network is composed of five genes regulating each other through a variety of regulatory interactions; it is negligibly affected by endogenous genes, and it is responsive to small molecules. We measured time series and steady-state expression data after multiple perturbations. These data were used to assess state-of-the-art modeling and reverse-engineering techniques. A semiquantitative model was able to capture and predict the behavior of the network. Reverse engineering based on differential equations and Bayesian networks correctly inferred regulatory interactions from the experimental data.

  9. A Statistical Approach For Modeling Tropical Cyclones. Synthetic Hurricanes Generator Model

    SciTech Connect

    Pasqualini, Donatella

    2016-05-11

    This manuscript brie y describes a statistical ap- proach to generate synthetic tropical cyclone tracks to be used in risk evaluations. The Synthetic Hur- ricane Generator (SynHurG) model allows model- ing hurricane risk in the United States supporting decision makers and implementations of adaptation strategies to extreme weather. In the literature there are mainly two approaches to model hurricane hazard for risk prediction: deterministic-statistical approaches, where the storm key physical parameters are calculated using physi- cal complex climate models and the tracks are usually determined statistically from historical data; and sta- tistical approaches, where both variables and tracks are estimated stochastically using historical records. SynHurG falls in the second category adopting a pure stochastic approach.

  10. Background character research for synthetical performance of thermal imaging systems

    NASA Astrophysics Data System (ADS)

    Chen, Song-lin; Wang, Ji-hui; Wang, Xiao-wei; Jin, Wei-qi

    2014-05-01

    Background is assumed to be uniform usually for evaluating the performance of thermal imaging systems, however the impact of background cannot be ignored for target acquisition in reality, background character is important research content for thermal imaging technology. A background noise parameter 𝜎 was proposed in MRTD model and used to describe background character. Background experiments were designed, and some typical backgrounds (namely lawn background, concrete pavement background, trees background and snow background) character were analyzed by 𝜎. MRTD including 𝜎 was introduced into MRTD-Channel Width (CW) model, the impact of above typical backgrounds for target information quantity were analyzed by MRTD-CW model with background character. Target information quantity for different backgrounds was calculated by MRTD-CW, and compared with that of TTP model. A target acquisition performance model based on MRTD-CW with background character will be research in the future.

  11. Functional fusion of living systems with synthetic electrode interfaces

    PubMed Central

    Staufer, Oskar; Weber, Sebastian; Bengtson, C Peter; Bading, Hilmar; Spatz, Joachim P

    2016-01-01

    Summary The functional fusion of “living” biomaterial (such as cells) with synthetic systems has developed into a principal ambition for various scientific disciplines. In particular, emerging fields such as bionics and nanomedicine integrate advanced nanomaterials with biomolecules, cells and organisms in order to develop novel strategies for applications, including energy production or real-time diagnostics utilizing biomolecular machineries “perfected” during billion years of evolution. To date, hardware–wetware interfaces that sample or modulate bioelectric potentials, such as neuroprostheses or implantable energy harvesters, are mostly based on microelectrodes brought into the closest possible contact with the targeted cells. Recently, the possibility of using electrochemical gradients of the inner ear for technical applications was demonstrated using implanted electrodes, where 1.12 nW of electrical power was harvested from the guinea pig endocochlear potential for up to 5 h (Mercier, P.; Lysaght, A.; Bandyopadhyay, S.; Chandrakasan, A.; Stankovic, K. Nat. Biotech. 2012, 30, 1240–1243). More recent approaches employ nanowires (NWs) able to penetrate the cellular membrane and to record extra- and intracellular electrical signals, in some cases with subcellular resolution (Spira, M.; Hai, A. Nat. Nano. 2013, 8, 83–94). Such techniques include nanoelectric scaffolds containing free-standing silicon NWs (Robinson, J. T.; Jorgolli, M.; Shalek, A. K.; Yoon, M. H.; Gertner, R. S.; Park, H. Nat Nanotechnol. 2012, 10, 180–184) or NW field-effect transistors (Qing, Q.; Jiang, Z.; Xu, L.; Gao, R.; Mai, L.; Lieber, C. Nat. Nano. 2013, 9, 142–147), vertically aligned gallium phosphide NWs (Hällström, W.; Mårtensson, T.; Prinz, C.; Gustavsson, P.; Montelius, L.; Samuelson, L.; Kanje, M. Nano Lett. 2007, 7, 2960–2965) or individually contacted, electrically active carbon nanofibers. The latter of these approaches is capable of recording electrical

  12. Functional fusion of living systems with synthetic electrode interfaces.

    PubMed

    Staufer, Oskar; Weber, Sebastian; Bengtson, C Peter; Bading, Hilmar; Spatz, Joachim P; Rustom, Amin

    2016-01-01

    The functional fusion of "living" biomaterial (such as cells) with synthetic systems has developed into a principal ambition for various scientific disciplines. In particular, emerging fields such as bionics and nanomedicine integrate advanced nanomaterials with biomolecules, cells and organisms in order to develop novel strategies for applications, including energy production or real-time diagnostics utilizing biomolecular machineries "perfected" during billion years of evolution. To date, hardware-wetware interfaces that sample or modulate bioelectric potentials, such as neuroprostheses or implantable energy harvesters, are mostly based on microelectrodes brought into the closest possible contact with the targeted cells. Recently, the possibility of using electrochemical gradients of the inner ear for technical applications was demonstrated using implanted electrodes, where 1.12 nW of electrical power was harvested from the guinea pig endocochlear potential for up to 5 h (Mercier, P.; Lysaght, A.; Bandyopadhyay, S.; Chandrakasan, A.; Stankovic, K. Nat. Biotech. 2012, 30, 1240-1243). More recent approaches employ nanowires (NWs) able to penetrate the cellular membrane and to record extra- and intracellular electrical signals, in some cases with subcellular resolution (Spira, M.; Hai, A. Nat. Nano. 2013, 8, 83-94). Such techniques include nanoelectric scaffolds containing free-standing silicon NWs (Robinson, J. T.; Jorgolli, M.; Shalek, A. K.; Yoon, M. H.; Gertner, R. S.; Park, H. Nat Nanotechnol. 2012, 10, 180-184) or NW field-effect transistors (Qing, Q.; Jiang, Z.; Xu, L.; Gao, R.; Mai, L.; Lieber, C. Nat. Nano. 2013, 9, 142-147), vertically aligned gallium phosphide NWs (Hällström, W.; Mårtensson, T.; Prinz, C.; Gustavsson, P.; Montelius, L.; Samuelson, L.; Kanje, M. Nano Lett. 2007, 7, 2960-2965) or individually contacted, electrically active carbon nanofibers. The latter of these approaches is capable of recording electrical responses from oxidative events

  13. Linear Frequency Modulated Signals VS Orthogonal Frequency Division Multiplexing Signals for Synthetic Aperture Radar Systems

    DTIC Science & Technology

    2014-06-01

    OFDM ) signal versus a linear frequency modulated or chirp signal on simulated synthetic aperture radar (SAR) imagery. Various parameters of the...transmitted signal, such as pulse duration, transmitted signal energy, bandwidth, and (specifically for the OFDM signal) number of subcarriers and...SAR system design cost. 14. SUBJECT TERMS Synthetic aperture radar (SAR), orthogonal frequency division multiplexing ( OFDM ), linear

  14. Millimeter Wave Synthetic Aperture Imaging System with a Unique Rotary Scanning System

    NASA Technical Reports Server (NTRS)

    Ghasr, M. T.; Pommerenke, D.; Case, J. T.; McClanahan, A. D.; Afaki-Beni, A.; Abou-Khousa, M.; Guinn, K.; DePaulis, F.; Kharkovsky, S.; Zoughi, R.

    2008-01-01

    In recent years, millimeter wave imaging techniques, using synthetic aperture focusing and holographical approaches, have shown tremendous potential for nondestructive testing applications, involving materials and structures used in space vehicles, including the space shuttle external fuel tank spray on foam insulation and its acreage heat tiles. The ability of signals at millimeter wave frequencies (30 - 300 GHz) to easily penetrate inside of low loss dielectric materials, their relatively small wavelengths, and the possibility of detecting coherent (magnitude and phase) reflections make them suitable for high resolution synthetic aperture focused imaging the interior of such materials and structures. To accommodate imaging requirements, commonly a scanning system is employed that provides for a raster scan of the desired structure. However, most such scanners, although simple in design and construction, are inherently slow primarily due to the need to stop and start at the beginning and end of each scan line. To this end, a millimeter wave synthetic aperture focusing system including a custom-designed transceiver operating at 35 - 45 GHz (Q-band) and unique and complex rotary scanner was designed and developed. The rotary scanner is capable of scanning an area with approximately 80 cm in diameter in less than 10 minutes at step sizes of 3 mm and smaller. The transceiver is capable of producing accurate magnitude and phase of reflected signal from the structure under test. Finally, a synthetic aperture focusing algorithm was developed that translates this rotary-obtained magnitude and phase into a synthetic aperture focusing image of inspected structures. This paper presents the design of the transceiver and the rotary scanning system along with showing several images obtained with this system from various complicated structures.

  15. Enhancing the Analytic Utility of the Synthetic Theater Operations Research Model (STORM)

    DTIC Science & Technology

    2014-12-01

    Operations Research Model ( STORM ) 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER...SYNTHETIC THEATER OPERATIONS RESEARCH MODEL ( STORM ) Mary L. McDonald Stephen C. Upton Christian N. Seymour Thomas W. Lucas Susan M. Sanchez...Force and Marine Corps, use the Synthetic Theater Operations Research Model ( STORM ) to assess risk in an integrated, campaign setting. Ultimately

  16. Valence tautomerism in synthetic models of cytochrome P450

    PubMed Central

    Das, Pradip Kumar; Samanta, Subhra; McQuarters, Ashley B.; Lehnert, Nicolai

    2016-01-01

    CytP450s have a cysteine-bound heme cofactor that, in its as-isolated resting (oxidized) form, can be conclusively described as a ferric thiolate species. Unlike the native enzyme, most synthetic thiolate-bound ferric porphyrins are unstable in air unless the axial thiolate ligand is sterically protected. Spectroscopic investigations on a series of synthetic mimics of cytP450 indicate that a thiolate-bound ferric porphyrin coexists in organic solutions at room temperature (RT) with a thiyl-radical bound ferrous porphyrin, i.e., its valence tautomer. The ferric thiolate state is favored by greater enthalpy and is air stable. The ferrous thiyl state is favored by entropy, populates at RT, and degrades in air. These ground states can be reversibly interchanged at RT by the addition or removal of water to the apolar medium. It is concluded that hydrogen bonding and local electrostatics protect the resting oxidized cytP450 active site from degradation in air by stabilizing the ferric thiolate ground state in contrast to its synthetic analogs. PMID:27302948

  17. A model for improving microbial biofuel production using a synthetic feedback loop

    SciTech Connect

    Dunlop, Mary; Keasling, Jay; Mukhopadhyay, Aindrila

    2011-07-14

    Cells use feedback to implement a diverse range of regulatory functions. Building synthetic feedback control systems may yield insight into the roles that feedback can play in regulation since it can be introduced independently of native regulation, and alternative control architectures can be compared. We propose a model for microbial biofuel production where a synthetic control system is used to increase cell viability and biofuel yields. Although microbes can be engineered to produce biofuels, the fuels are often toxic to cell growth, creating a negative feedback loop that limits biofuel production. These toxic effects may be mitigated by expressing efflux pumps that export biofuel from the cell. We developed a model for cell growth and biofuel production and used it to compare several genetic control strategies for their ability to improve biofuel yields. We show that controlling efflux pump expression directly with a biofuel-responsive promoter is a straight forward way of improving biofuel production. In addition, a feed forward loop controller is shown to be versatile at dealing with uncertainty in biofuel production rates.

  18. Synthetic and Enhanced Vision System for Altair Lunar Lander

    NASA Technical Reports Server (NTRS)

    Prinzell, Lawrence J., III; Kramer, Lynda J.; Norman, Robert M.; Arthur, Jarvis J., III; Williams, Steven P.; Shelton, Kevin J.; Bailey, Randall E.

    2009-01-01

    Past research has demonstrated the substantial potential of synthetic and enhanced vision (SV, EV) for aviation (e.g., Prinzel & Wickens, 2009). These augmented visual-based technologies have been shown to significantly enhance situation awareness, reduce workload, enhance aviation safety (e.g., reduced propensity for controlled flight -into-terrain accidents/incidents), and promote flight path control precision. The issues that drove the design and development of synthetic and enhanced vision have commonalities to other application domains; most notably, during entry, descent, and landing on the moon and other planetary surfaces. NASA has extended SV/EV technology for use in planetary exploration vehicles, such as the Altair Lunar Lander. This paper describes an Altair Lunar Lander SV/EV concept and associated research demonstrating the safety benefits of these technologies.

  19. Sensor fusion display evaluation using information integration models in enhanced/synthetic vision applications

    NASA Technical Reports Server (NTRS)

    Foyle, David C.

    1993-01-01

    Based on existing integration models in the psychological literature, an evaluation framework is developed to assess sensor fusion displays as might be implemented in an enhanced/synthetic vision system. The proposed evaluation framework for evaluating the operator's ability to use such systems is a normative approach: The pilot's performance with the sensor fusion image is compared to models' predictions based on the pilot's performance when viewing the original component sensor images prior to fusion. This allows for the determination as to when a sensor fusion system leads to: poorer performance than one of the original sensor displays, clearly an undesirable system in which the fused sensor system causes some distortion or interference; better performance than with either single sensor system alone, but at a sub-optimal level compared to model predictions; optimal performance compared to model predictions; or, super-optimal performance, which may occur if the operator were able to use some highly diagnostic 'emergent features' in the sensor fusion display, which were unavailable in the original sensor displays.

  20. Interferometric synthetic aperture radar and the Data Collection System Digital Terrain Elevation Demonstration

    NASA Astrophysics Data System (ADS)

    Heidelbach, Robert; Bolus, R.; Chadwick, J.

    1994-08-01

    Digital Terrain Elevations (DTE) that can be rapidly generated, and that have better fidelity and accuracy than Digital Terrain Elevation Data (DTED) Levels 1 or 2, would be extremely beneficial to Department of Defense (DOD) military operations, civil works programs, and various commercial applications. As a result, the Advanced Research Projects Agency (ARPA), along with the U.S. Army Topographic Engineering Center (TEC), are developing an Interferometric Synthetic Aperture Radar (IFSAR) elevation mapping capability. This system, the Interferometric Synthetic Aperture Radar for Digital Radar Elevations (IFSARE), is capable of collecting and providing data in all weather (reasonable), in day or night scenarios, and where obscurants are present. The IFSARE, which is currently undergoing Integration and Test, will allow for rapid on-line automatic processing of the collected digital radar data into DTE and high quality imagery. The prime contractor is the Environmental Research Institute of Michigan (ERIM). This paper addresses the proof of concept for civil works applications by analyzing a data set taken by the Wright Labs/ERIM Data Collection System (DCS). The objective was to demonstrate the capability of an IFSAR system to provide high fidelity, fine resolution DTE that can be employed in hydraulic models of the Mississippi River watershed. The demonstration was sponsored by ARPA and TEC.

  1. A synthetic ecology perspective: How well does behavior of model organisms in the laboratory predict microbial activities in natural habitats?

    SciTech Connect

    Yu, Zheng; Krause, Sascha M. B.; Beck, David A. C.; Chistoserdova, Ludmila

    2016-06-15

    In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sediment for a few decades and have identified a number of species genetically equipped for this activity. We have also identified cooccurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. Furthermore, these findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.

  2. Synthetic benchmark for modeling flow in 3D fractured media

    NASA Astrophysics Data System (ADS)

    de Dreuzy, Jean-Raynald; Pichot, Géraldine; Poirriez, Baptiste; Erhel, Jocelyne

    2013-01-01

    Intensity and localization of flows in fractured media have promoted the development of a large range of different modeling approaches including Discrete Fracture Networks, pipe networks and equivalent continuous media. While benchmarked usually within site studies, we propose an alternative numerical benchmark based on highly-resolved Discrete Fracture Networks (DFNs) and on a stochastic approach. Test cases are built on fractures of different lengths, orientations, aspect ratios and hydraulic apertures, issuing the broad ranges of topological structures and hydraulic properties classically observed. We present 18 DFN cases, with 10 random simulations by case. These 180 DFN structures are provided and fully documented. They display a representative variety of the configurations that challenge the numerical methods at the different stages of discretization, mesh generation and system solving. Using a previously assessed mixed hybrid finite element method (Erhel et al., 2009a), we systematically provide reference flow and head solutions. Because CPU and memory requirements stem mainly from system solving, we study direct and iterative sparse linear solvers. We show that the most cpu-time efficient method is a direct multifrontal method for small systems, while conjugate gradient preconditioned by algebraic multrigrid is more relevant at larger sizes. Available results can be used further as references for building up alternative numerical and physical models in both directions of improving accuracy and efficiency.

  3. Technical Challenges in the Development of a NASA Synthetic Vision System Concept

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Parrish, Russell V.; Kramer, Lynda J.; Harrah, Steve; Arthur, J. J., III

    2002-01-01

    Within NASA's Aviation Safety Program, the Synthetic Vision Systems Project is developing display system concepts to improve pilot terrain/situation awareness by providing a perspective synthetic view of the outside world through an on-board database driven by precise aircraft positioning information updating via Global Positioning System-based data. This work is aimed at eliminating visibility-induced errors and low visibility conditions as a causal factor to civil aircraft accidents, as well as replicating the operational benefits of clear day flight operations regardless of the actual outside visibility condition. Synthetic vision research and development activities at NASA Langley Research Center are focused around a series of ground simulation and flight test experiments designed to evaluate, investigate, and assess the technology which can lead to operational and certified synthetic vision systems. The technical challenges that have been encountered and that are anticipated in this research and development activity are summarized.

  4. Evaluation Digital Elevation Model Generated by Synthetic Aperture Radar Data

    NASA Astrophysics Data System (ADS)

    Makineci, H. B.; Karabörk, H.

    2016-06-01

    Digital elevation model, showing the physical and topographical situation of the earth, is defined a tree-dimensional digital model obtained from the elevation of the surface by using of selected an appropriate interpolation method. DEMs are used in many areas such as management of natural resources, engineering and infrastructure projects, disaster and risk analysis, archaeology, security, aviation, forestry, energy, topographic mapping, landslide and flood analysis, Geographic Information Systems (GIS). Digital elevation models, which are the fundamental components of cartography, is calculated by many methods. Digital elevation models can be obtained terrestrial methods or data obtained by digitization of maps by processing the digital platform in general. Today, Digital elevation model data is generated by the processing of stereo optical satellite images, radar images (radargrammetry, interferometry) and lidar data using remote sensing and photogrammetric techniques with the help of improving technology. One of the fundamental components of remote sensing radar technology is very advanced nowadays. In response to this progress it began to be used more frequently in various fields. Determining the shape of topography and creating digital elevation model comes the beginning topics of these areas. It is aimed in this work , the differences of evaluation of quality between Sentinel-1A SAR image ,which is sent by European Space Agency ESA and Interferometry Wide Swath imaging mode and C band type , and DTED-2 (Digital Terrain Elevation Data) and application between them. The application includes RMS static method for detecting precision of data. Results show us to variance of points make a high decrease from mountain area to plane area.

  5. Evaluating the Effects of Dimensionality in Advanced Avionic Display Concepts for Synthetic Vision Systems

    NASA Technical Reports Server (NTRS)

    Alexander, Amy L.; Prinzel, Lawrence J., III; Wickens, Christopher D.; Kramer, Lynda J.; Arthur, Jarvis J.; Bailey, Randall E.

    2007-01-01

    Synthetic vision systems provide an in-cockpit view of terrain and other hazards via a computer-generated display representation. Two experiments examined several display concepts for synthetic vision and evaluated how such displays modulate pilot performance. Experiment 1 (24 general aviation pilots) compared three navigational display (ND) concepts: 2D coplanar, 3D, and split-screen. Experiment 2 (12 commercial airline pilots) evaluated baseline 'blue sky/brown ground' or synthetic vision-enabled primary flight displays (PFDs) and three ND concepts: 2D coplanar with and without synthetic vision and a dynamic multi-mode rotatable exocentric format. In general, the results pointed to an overall advantage for a split-screen format, whether it be stand-alone (Experiment 1) or available via rotatable viewpoints (Experiment 2). Furthermore, Experiment 2 revealed benefits associated with utilizing synthetic vision in both the PFD and ND representations and the value of combined ego- and exocentric presentations.

  6. Prospects for Applying Synthetic Biology to Toxicology: Future Opportunities and Current Limitations for the Repurposing of Cytochrome P450 Systems.

    PubMed

    Behrendorff, James B Y H; Gillam, Elizabeth M J

    2017-01-17

    The 30 years since the inception of Chemical Research in Toxicology, game-changing advances in chemical and molecular biology, the fundamental disciplines underpinning molecular toxicology, have been made. While these have led to important advances in the study of mechanisms by which chemicals damage cells and systems, there has been less focus on applying these advances to prediction, detection, and mitigation of toxicity. Over the last ∼15 years, synthetic biology, the repurposing of biological "parts" in systems engineered for useful ends, has been explored in other areas of the biomedical and life sciences, for such applications as detecting metabolites, drug discovery and delivery, investigating disease mechanisms, improving medical treatment, and producing useful chemicals. These examples provide models for the application of synthetic biology to toxicology, which, for the most part, has not yet benefited from such approaches. In this perspective, we review the synthetic biology approaches that have been applied to date and speculate on possible short to medium term and "blue sky" aspirations for synthetic biology, particularly in clinical and environmental toxicology. Finally, we point out key hurdles that must be overcome for the full potential of synthetic biology to be realized.

  7. [System biology and synthetic biology modify drug discovery and development].

    PubMed

    Haiech, Jacques; Ranjeva, Raoul; Kilhoffer, Marie-Claude

    2012-02-01

    Life Sciences are built on observations. Right now, a more systemic approach allowing to integrate the different organizational levels in Biology is emerging. Such an approach uses a set of technologies and strategies allowing to build models that appear to be more and more predictive (omics, bioinformatics, integrative biology, computational biology…). Those models accelerate the rational development of new therapies avoiding an engineering based only on trials and errors. This approach both holistic and predictive radically modifies the discovery and development modalities used today in health industries. Moreover, because of the apparition of new jobs at the interface of disciplines, of private and public sectors and of life sciences and engineering sciences, this implies to rethink the training programs in both their contents and their pedagogical tools.

  8. ADSORPTION STUDIES IN A SYNTHETIC RUBBER LATEX-OVALBUMIN SYSTEM

    PubMed Central

    Williams, H. B.; Choppin, A. R.

    1950-01-01

    1. Adsorption of ovalbumin on the latex surface was in excess of the quantity required to produce coverage of the surface over most of the protein concentrations range which was investigated. 2. "S" shaped isothermals which probably indicated multilayer adsorption were obtained. 3. The quantity of ovalbumin required to produce a constant surface charge density on the latex particle surface was a function of the pH, and a theory of active centers on the latex particles has been suggested. 4. A shift in the isoelectric point from that of native ovalbumin has been observed for the protein when adsorbed on a synthetic latex. PMID:14824490

  9. Synthetic Quorum Sensing and Induced Aggregation in Model Microcapsule Colonies with Repressilator Feedback

    NASA Astrophysics Data System (ADS)

    Shum, Henry; Yashin, Victor; Balazs, Anna

    We model a system of synthetic microcapsules that communicate chemically by releasing nanoparticles or signaling molecules. These signaling species bind to receptors on the shells of capsules and modulate the target shell's permeability, thereby controlling nanoparticle release from the target capsule. Using the repressilator regulatory network motif, whereby three species suppress the production of the next in a cyclic fashion, we show that large amplitude oscillations in nanoparticle release can emerge when many capsules are close together. This exemplifies quorum sensing, which is the ability of cells to gauge their population density and collectively initiate a new behavior once a critical density is reached. We present a physically realizable model in which the oscillations exhibited in crowded populations induce aggregation of the microcapsules, mimicking complex biological behavior of the slime mold Dictyostelium discoideum with only simple, synthetic components. We also show that the clusters can be dispersed and reformed repeatedly and controllably by addition of chemical stimuli, demonstrating possible applications in creating reconfigurable or programmable materials.

  10. Autonomous system for initializing synthetic aperture radar seeker acquisition

    SciTech Connect

    Hamilton, P.C.

    1993-08-03

    A method is described of guiding a missile having an active seeker including a synthetic aperture radar operating in a squint mode to a target aircraft having a search radar therein the maximum range of active seeker acquisition being within said missile's maneuver capability to intercept, and the maximum range of active seeker acquisition not exceeding the capability of the active seeker, said method comprising the steps of: launching said missile in response to detection of the search radar; implementing a passive seeker mode of operation to passively guide said missile towards said target aircraft in a manner to avoid detection of said missile by said target aircraft; transferring from said passive seeker mode to an active seeker mode in response to detected shutdown of said search radar; maneuvering said missile to execute a turn angle away from said target aircraft such that the search field of said synthetic aperture radar sweeps through an entire target uncertainty volume, said turn angle being within a first preselected limit and a second preselected limit such that said target aircraft does not cross over said missile's terminal flight path; and intercepting said target aircraft within a lethal range of said missile.

  11. Neglected disease - african sleeping sickness: recent synthetic and modeling advances.

    PubMed

    Paliwal, Sarvesh K; Verma, Ankita Narayan; Paliwal, Shailendra

    2011-01-01

    Human African Trypanosomiasis (HAT) also called sleeping sickness is caused by subspecies of the parasitic hemoflagellate Trypanosoma brucei that mostly occurs in sub-Saharan Africa. The current chemotherapy of the human trypanosomiases relies on only six drugs, five of which have been developed more than 30 years ago, have undesirable toxic side effects and most of them show drug-resistance. Though development of new anti-trypanosomal drugs seems to be a priority area research in this area has lagged far behind. The given review mainly focus upon the recent synthetic and computer based approaches made by various research groups for the development of newer anti-trypanosomal analogues which may have improved efficacy and oral bioavailability than the present ones. The given paper also attempts to investigate the relationship between the various physiochemical parameters and anti-trypanosomal activity that may be helpful in development of potent anti-trypanosomal agents against sleeping sickness.

  12. Improving the Analysis Capabilities of the Synthetic Theater Operations Research Model (STORM)

    DTIC Science & Technology

    2014-09-01

    the Chief of Naval Operations, Capability Analysis and Assessment Division (OPNAV N81), along with other DOD organizations, utilizes the Synthetic...Capability Analysis and Assessment Division (OPNAV N81), along with other DOD organizations, utilizes the Synthetic Theater Operations Research Model...Navy’s Assessment Division, adopted STORM as its primary campaign analysis tool due to its stochastic nature, which provides analysts the ability to

  13. Synthetic Model of the Oxygen-Evolving Center: Photosystem II under the Spotlight.

    PubMed

    Yu, Yang; Hu, Cheng; Liu, Xiaohong; Wang, Jiangyun

    2015-09-21

    The oxygen-evolving center (OEC) in photosystem II catalyzes a water splitting reaction. Great efforts have already been made to artificially synthesize the OEC, in order to elucidate the structure-function relationship and the mechanism of the reaction. Now, a new synthetic model makes the best mimic yet of the OEC. This recent study opens up the possibility to study the mechanism of photosystem II and photosynthesis in general for applications in renewable energy and synthetic biology.

  14. Synthetic Jets for Heat Transfer Augmentation in Microelectronics Systems

    NASA Astrophysics Data System (ADS)

    Arik, Mehmet; Tamdogan, Enes

    Rapid progress in science and information technology, growing manufacturing activities and increase in globalization have boosted the demand for advanced electronics devices. Moreover, increase in microprocessor power dissipation coupled with the reduction in feature sizes due to manufacturing process improvements have resulted in continuously increasing heat fluxes. Thus, ever increasing heat fluxes have required the development of novel, reliable and affordable thermal management technologies. Although some of those proposed solutions for high flux cooling problems based on liquid cooling methods such as spray and evaporative cooling; air cooling is still commonly preferred due to its availability, reliability, easiness and low cost. Therefore, over the last decade microfluidics devices such as synthetic jets have been investigated as an alternative to conventional air moving devices, and have been shown as highly effective for cooling of electronics in compact thermal real estates...

  15. Systems-Level Synthetic Biology for Advanced Biofuel Production

    SciTech Connect

    Ruffing, Anne; Jensen, Travis J.; Strickland, Lucas Marshall; Meserole, Stephen; Tallant, David

    2015-03-01

    Cyanobacteria have been shown to be capable of producing a variety of advanced biofuels; however, product yields remain well below those necessary for large scale production. New genetic tools and high throughput metabolic engineering techniques are needed to optimize cyanobacterial metabolisms for enhanced biofuel production. Towards this goal, this project advances the development of a multiple promoter replacement technique for systems-level optimization of gene expression in a model cyanobacterial host: Synechococcus sp. PCC 7002. To realize this multiple-target approach, key capabilities were developed, including a high throughput detection method for advanced biofuels, enhanced transformation efficiency, and genetic tools for Synechococcus sp. PCC 7002. Moreover, several additional obstacles were identified for realization of this multiple promoter replacement technique. The techniques and tools developed in this project will help to enable future efforts in the advancement of cyanobacterial biofuels.

  16. Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality

    PubMed Central

    Jacunski, Alexandra; Dixon, Scott J.; Tatonetti, Nicholas P.

    2015-01-01

    Synthetic lethality is a genetic interaction wherein two otherwise nonessential genes cause cellular inviability when knocked out simultaneously. Drugs can mimic genetic knock-out effects; therefore, our understanding of promiscuous drugs, polypharmacology-related adverse drug reactions, and multi-drug therapies, especially cancer combination therapy, may be informed by a deeper understanding of synthetic lethality. However, the colossal experimental burden in humans necessitates in silico methods to guide the identification of synthetic lethal pairs. Here, we present SINaTRA (Species-INdependent TRAnslation), a network-based methodology that discovers genome-wide synthetic lethality in translation between species. SINaTRA uses connectivity homology, defined as biological connectivity patterns that persist across species, to identify synthetic lethal pairs. Importantly, our approach does not rely on genetic homology or structural and functional similarity, and it significantly outperforms models utilizing these data. We validate SINaTRA by predicting synthetic lethality in S. pombe using S. cerevisiae data, then identify over one million putative human synthetic lethal pairs to guide experimental approaches. We highlight the translational applications of our algorithm for drug discovery by identifying clusters of genes significantly enriched for single- and multi-drug cancer therapies. PMID:26451775

  17. Fast algorithm for a three-dimensional synthetic model of intermittent turbulence

    NASA Astrophysics Data System (ADS)

    Malara, Francesco; Di Mare, Francesca; Nigro, Giuseppina; Sorriso-Valvo, Luca

    2016-11-01

    Synthetic turbulence models are useful tools that provide realistic representations of turbulence, necessary to test theoretical results, to serve as background fields in some numerical simulations, and to test analysis tools. Models of one-dimensional (1D) and 3D synthetic turbulence previously developed still required large computational resources. A "wavelet-based" model of synthetic turbulence, able to produce a field with tunable spectral law, intermittency, and anisotropy, is presented here. The rapid algorithm introduced, based on the classic p -model of intermittent turbulence, allows us to reach a broad spectral range using a modest computational effort. The model has been tested against the standard diagnostics for intermittent turbulence, i.e., the spectral analysis, the scale-dependent statistics of the field increments, and the multifractal analysis, all showing an excellent response.

  18. Synthetic nanoparticles camouflaged with biomimetic erythrocyte membranes for reduced reticuloendothelial system uptake

    NASA Astrophysics Data System (ADS)

    Rao, Lang; Xu, Jun-Hua; Cai, Bo; Liu, Huiqin; Li, Ming; Jia, Yan; Xiao, Liang; Guo, Shi-Shang; Liu, Wei; Zhao, Xing-Zhong

    2016-02-01

    Suppression of the reticuloendothelial system (RES) uptake is one of the most challenging tasks in nanomedicine. Coating stratagems using polymers, such as poly(ethylene glycol) (PEG), have led to great success in this respect. Nevertheless, recent observations of immunological response toward these synthetic polymers have triggered a search for better alternatives. In this work, natural red blood cell (RBC) membranes are camouflaged on the surface of Fe3O4 nanoparticles for reducing the RES uptake. In vitro macrophage uptake, in vivo biodistribution and pharmacokinetic studies demonstrate that the RBC membrane is a superior alternative to the current gold standard PEG for nanoparticle ‘stealth’. Furthermore, we systematically investigate the in vivo potential toxicity of RBC membrane-coated nanoparticles by blood biochemistry, whole blood panel examination and histology analysis based on animal models. The combination of synthetic nanoparticles and natural cell membranes embodies a novel and biomimetic nanomaterial design strategy and presents a compelling property of functional materials for a broad range of biomedical applications.

  19. Modelling biogas production of solid waste: application of the BGP model to a synthetic landfill

    NASA Astrophysics Data System (ADS)

    Rodrigo-Ilarri, Javier; Segura-Sobrino, Francisco

    2013-04-01

    Production of biogas as a result of the decomposition of organic matter included on solid waste landfills is still an issue to be understood. Reports on this matter are rarely included on the engineering construction projects of solid waste landfills despite it can be an issue of critical importance while operating the landfill and after its closure. This paper presents an application of BGP (Bio-Gas-Production) model to a synthetic landfill. The evolution in time of the concentrations of the different chemical compounds of biogas is studied. Results obtained show the impact on the air quality of different management alternatives which are usually performed in real landfills.

  20. Using synthetic models to simulate aging of Cu contamination in soils.

    PubMed

    Proffit, S; Marin, B; Cances, B; Ponthieu, M; Sayen, S; Guillon, E

    2015-05-01

    The Bureau Commun de Référence (BCR) sequential extraction scheme and micro-synchrotron-based X-ray fluorescence (μ-SXRF) analysis were used to determine the Cu fractionation in a calcareous vineyard soil and a synthetic soil (mixture of seven constituents: calcite, birnessite, ferrihydrite, goethite, lignocellulosic residue, kaolinite, and quartz) at different Cu contamination rates (190, 1270, and 6350 mg kg(-1) of Cu) and aging times (1, 30, 92, and 181 days). The Cu distribution in the spiked vineyard and synthetic soils was different from the original vineyard one and was influenced by the loading level. The newly added Cu was preferentially present in the acid soluble fraction. Aging of the contaminated vineyard and synthetic soils during 6 months led to the redistribution of Cu from the weakly bound acid soluble fraction to the strongly bound reducible one. The evolution with time could satisfactorily be simulated by the Elovich diffusion model for the synthetic soils. It was less significant as less marked in the contaminated vineyard soil than in the synthetic one, even though the trends observed in both were similar. This study supported the hypothesis that "simple" synthetic models could be used to approach the Cu fractionation and its evolution with time in vineyard soils.

  1. Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides.

    PubMed

    Schilter, David; Camara, James M; Huynh, Mioy T; Hammes-Schiffer, Sharon; Rauchfuss, Thomas B

    2016-08-10

    Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.

  2. Reactions of Trimethylaluminium: Modelling the Chemical Degradation of Synthetic Lubricants.

    PubMed

    Slaughter, Jonathan; Peel, Andrew J; Wheatley, Andrew E H

    2017-01-01

    In investigating and seeking to mimic the reactivity of trimethylaluminium (TMA) with synthetic, ester-based lubricating oils, the reaction of methyl propionate 1 was explored with 1, 2 and 3 equivalents of the organoaluminium reagent. Spectroscopic analysis points to the formation of the adduct 1(TMA) accompanied only by the low level 1:1 production of Me2 AlOCEtMe2 2 and Me2 AlOMe 3 when an equimolar amount of TMA is applied. The deployment of excess TMA favours reaction to give 2 and 3 over 1(TMA) adduct formation and spectroscopy reveals that in hydrocarbon solution substitution product 2 traps unreacted TMA to yield 2(TMA). The (1) H NMR spectroscopic observation of two Al-Me signals not attributable to free TMA and in the ratio 1:4 suggests the formation of a previously only postulated, symmetrical metallacycle in Me4 Al2 (μ(2) -Me)(μ(2) -OCEtMe2 ). In the presence of 3, 2(TMA) undergoes thermally induced exchange to yield Me4 Al2 (μ(2) -OMe)(μ(2) -OCEtMe2 ) 4 and TMA. The reaction of methyl phenylacetate 5 with TMA allows isolation of the crystalline product Me2 AlOCBnMe2 (TMA) 6(TMA), which allows the first observation of the Me4 Al2 (μ(2) -Me)(μ(2) -OR) motif in the solid state. Distances of 2.133(3) Å (Al-Mebridging ) and 1.951 Å (mean Al-Meterminal ) are recorded. The abstraction of TMA from 6(TMA) by the introduction of Et2 O has yielded 6, which exists as a dimer.

  3. Flight test comparison between enhanced vision (FLIR) and synthetic vision systems

    NASA Astrophysics Data System (ADS)

    Arthur, Jarvis J., III; Kramer, Lynda J.; Bailey, Randall E.

    2005-05-01

    Limited visibility and reduced situational awareness have been cited as predominant causal factors for both Controlled Flight Into Terrain (CFIT) and runway incursion accidents. NASA"s Synthetic Vision Systems (SVS) project is developing practical application technologies with the goal of eliminating low visibility conditions as a causal factor to civil aircraft accidents while replicating the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. A major thrust of the SVS project involves the development/demonstration of affordable, certifiable display configurations that provide intuitive out-the-window terrain and obstacle information with advanced pathway guidance. A flight test evaluation was conducted in the summer of 2004 by NASA Langley Research Center under NASA's Aviation Safety and Security, Synthetic Vision System - Commercial and Business program. A Gulfstream G-V aircraft, modified and operated under NASA contract by the Gulfstream Aerospace Corporation, was flown over a 3-week period at the Reno/Tahoe International Airport and an additional 3-week period at the NASA Wallops Flight Facility to evaluate integrated Synthetic Vision System concepts. Flight testing was conducted to evaluate the performance, usability, and acceptance of an integrated synthetic vision concept which included advanced Synthetic Vision display concepts for a transport aircraft flight deck, a Runway Incursion Prevention System, an Enhanced Vision Systems (EVS), and real-time Database Integrity Monitoring Equipment. This paper focuses on comparing qualitative and subjective results between EVS and SVS display concepts.

  4. Flight Test Comparison Between Enhanced Vision (FLIR) and Synthetic Vision Systems

    NASA Technical Reports Server (NTRS)

    Arthur, Jarvis J., III; Kramer, Lynda J.; Bailey, Randall E.

    2005-01-01

    Limited visibility and reduced situational awareness have been cited as predominant causal factors for both Controlled Flight Into Terrain (CFIT) and runway incursion accidents. NASA s Synthetic Vision Systems (SVS) project is developing practical application technologies with the goal of eliminating low visibility conditions as a causal factor to civil aircraft accidents while replicating the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. A major thrust of the SVS project involves the development/demonstration of affordable, certifiable display configurations that provide intuitive out-the-window terrain and obstacle information with advanced pathway guidance. A flight test evaluation was conducted in the summer of 2004 by NASA Langley Research Center under NASA s Aviation Safety and Security, Synthetic Vision System - Commercial and Business program. A Gulfstream G-V aircraft, modified and operated under NASA contract by the Gulfstream Aerospace Corporation, was flown over a 3-week period at the Reno/Tahoe International Airport and an additional 3-week period at the NASA Wallops Flight Facility to evaluate integrated Synthetic Vision System concepts. Flight testing was conducted to evaluate the performance, usability, and acceptance of an integrated synthetic vision concept which included advanced Synthetic Vision display concepts for a transport aircraft flight deck, a Runway Incursion Prevention System, an Enhanced Vision Systems (EVS), and real-time Database Integrity Monitoring Equipment. This paper focuses on comparing qualitative and subjective results between EVS and SVS display concepts.

  5. Synthetic aperture LADAR at 1550 nm: system demonstration, imaging processing and experimental result

    NASA Astrophysics Data System (ADS)

    Li, Guangzuo; Wang, Ran; Wang, Peisi; Zhang, Keshu; Wu, Yirong

    2016-10-01

    In this manuscript, we propose and experimentally demonstrate our synthetic aperture LADAR (SAL) system. The system could obtain imageries in a few milliseconds with resolution of 5 cm from a long distance. Fine resolution in the range dimension was obtained by transmitting LADAR signal with large bandwidth. While in the cross-range dimension, the large synthetic aperture diameter provided fine resolution. By employing continuous translational motion of SAL system, a large aperture diameter was obtained through synthetic aperture processing. So the diffraction limit of real aperture diameter was overcome and finer resolution was achieved. Indoor and outdoor experiments were both performed and the corresponding results were showed. Results validated the feasibility of our system and processing algorithm.

  6. Frequency Response of Synthetic Vocal Fold Models with Linear and Nonlinear Material Properties

    ERIC Educational Resources Information Center

    Shaw, Stephanie M.; Thomson, Scott L.; Dromey, Christopher; Smith, Simeon

    2012-01-01

    Purpose: The purpose of this study was to create synthetic vocal fold models with nonlinear stress-strain properties and to investigate the effect of linear versus nonlinear material properties on fundamental frequency (F[subscript 0]) during anterior-posterior stretching. Method: Three materially linear and 3 materially nonlinear models were…

  7. Sonophotolytic degradation of synthetic pharmaceutical wastewater: statistical experimental design and modeling.

    PubMed

    Ghafoori, Samira; Mowla, Amir; Jahani, Ramtin; Mehrvar, Mehrab; Chan, Philip K

    2015-03-01

    The merits of the sonophotolysis as a combination of sonolysis (US) and photolysis (UV/H2O2) are investigated in a pilot-scale external loop airlift sonophotoreactor for the treatment of a synthetic pharmaceutical wastewater (SPWW). In the first part of this study, the multivariate experimental design is carried out using Box-Behnken design (BBD). The effluent is characterized by the total organic carbon (TOC) percent removal as a surrogate parameter. The results indicate that the response of the TOC percent removal is significantly affected by the synergistic effects of the linear term of H2O2 dosage and ultrasound power with the antagonistic effect of quadratic term of H2O2 dosage. The statistical analysis of the results indicates a satisfactory prediction of the system behavior by the developed model. In the second part of this study, a novel rigorous mathematical model for the sonophotolytic process is developed to predict the TOC percent removal as a function of time. The mathematical model is based on extensively accepted sonophotochemical reactions and the rate constants in advanced oxidation processes. A good agreement between the model predictions and experimental data indicates that the proposed model could successfully describe the sonophotolysis of the pharmaceutical wastewater.

  8. Development of piezoelectric-based membranes for synthetic jet actuators: experiments and modeling

    NASA Astrophysics Data System (ADS)

    Housley, Kevin W.; Clingman, Dan J.; Amitay, Michael

    2016-04-01

    A mathematical model was developed to represent the behavior of circular piezoelectric bimorphs in a synthetic jet actuator. Synthetic jet actuators are popular active flow control devices whose application is being widely explored in aerodynamics. The material properties were matched to those of PZT-5A mounted on a substrate. The actuator's geometry consisted of a cylindrical cavity of low height to diameter aspect ratio. A bimorph formed one of the cylinder's bases. The ingestion/expulsion orifice for the synthetic jet actuator was placed in the edge of the cavity so as to allow for either the present single bimorph or future dual bimorph configurations. Simply supported and rigidly supported boundary conditions were assessed around the circumference of the bimorph. The potential of alternate mode shapes occurring in the bimorphs during operation of the synthetic jet was evaluated. A limited parametric study was conducted varying the thickness of the piezoelectric wafers used in the bimorphs and the geometry of the cavity and orifice. Results were obtained for the displacement of the center of the bimorph's surface and the peak velocity of the air being ingested and expulsed through the orifice. These results were compared to values obtained through a mathematical model. Experimental data present in literature were also compared. The mathematical model was seen to have considerable potential for predicting the performance of synthetic jet actuators and their resonant frequencies but failed to capture the effects of acoustic coupling with the cavity, which is a topic of future research.

  9. A synthetic seismicity model for the Middle America Trench

    NASA Technical Reports Server (NTRS)

    Ward, Steven N.

    1991-01-01

    A novel iterative technique, based on the concept of fault segmentation and computed using 2D static dislocation theory, for building models of seismicity and fault interaction which are physically acceptable and geometrically and kinematically correct, is presented. The technique is applied in two steps to seismicity observed at the Middle America Trench. The first constructs generic models which randomly draw segment strengths and lengths from a 2D probability distribution. The second constructs predictive models in which segment lengths and strengths are adjusted to mimic the actual geography and timing of large historical earthquakes. Both types of models reproduce the statistics of seismicity over five units of magnitude and duplicate other aspects including foreshock and aftershock sequences, migration of foci, and the capacity to produce both characteristic and noncharacteristic earthquakes. Over a period of about 150 yr the complex interaction of fault segments and the nonlinear failure conditions conspire to transform an apparently deterministic model into a chaotic one.

  10. Multi-sensor Cloud Retrieval Simulator and Remote Sensing from Model Parameters . Pt. 1; Synthetic Sensor Radiance Formulation; [Synthetic Sensor Radiance Formulation

    NASA Technical Reports Server (NTRS)

    Wind, G.; DaSilva, A. M.; Norris, P. M.; Platnick, S.

    2013-01-01

    In this paper we describe a general procedure for calculating synthetic sensor radiances from variable output from a global atmospheric forecast model. In order to take proper account of the discrepancies between model resolution and sensor footprint, the algorithm takes explicit account of the model subgrid variability, in particular its description of the probability density function of total water (vapor and cloud condensate.) The simulated sensor radiances are then substituted into an operational remote sensing algorithm processing chain to produce a variety of remote sensing products that would normally be produced from actual sensor output. This output can then be used for a wide variety of purposes such as model parameter verification, remote sensing algorithm validation, testing of new retrieval methods and future sensor studies.We show a specific implementation using the GEOS-5 model, the MODIS instrument and the MODIS Adaptive Processing System (MODAPS) Data Collection 5.1 operational remote sensing cloud algorithm processing chain (including the cloud mask, cloud top properties and cloud optical and microphysical properties products). We focus on clouds because they are very important to model development and improvement.

  11. Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae

    PubMed Central

    Rantasalo, Anssi; Czeizler, Elena; Virtanen, Riitta; Rousu, Juho; Lähdesmäki, Harri; Penttilä, Merja

    2016-01-01

    This work describes the development and characterization of a modular synthetic expression system that provides a broad range of adjustable and predictable expression levels in S. cerevisiae. The system works as a fixed-gain transcription amplifier, where the input signal is transferred via a synthetic transcription factor (sTF) onto a synthetic promoter, containing a defined core promoter, generating a transcription output signal. The system activation is based on the bacterial LexA-DNA-binding domain, a set of modified, modular LexA-binding sites and a selection of transcription activation domains. We show both experimentally and computationally that the tuning of the system is achieved through the selection of three separate modules, each of which enables an adjustable output signal: 1) the transcription-activation domain of the sTF, 2) the binding-site modules in the output promoter, and 3) the core promoter modules which define the transcription initiation site in the output promoter. The system has a novel bidirectional architecture that enables generation of compact, yet versatile expression modules for multiple genes with highly diversified expression levels ranging from negligible to very strong using one synthetic transcription factor. In contrast to most existing modular gene expression regulation systems, the present system is independent from externally added compounds. Furthermore, the established system was minimally affected by the several tested growth conditions. These features suggest that it can be highly useful in large scale biotechnology applications. PMID:26901642

  12. NEMESYS: Next Generation Models of Synthetic Urban Areas

    DTIC Science & Technology

    2004-12-01

    Network of aqueducts Sewer and drainage systems Subway tunnels Utility corridors Cellars Civil defense shelters Hand-dug tunnels (older cities) Catacombs...below surface level) What Network of aqueducts Sewer and drainage systems Cellars Civil defense shelters Hand-dug tunnels (older cities) Catacombs

  13. SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs.

    PubMed

    Weeding, Emma; Houle, Jason; Kaznessis, Yiannis N

    2010-07-01

    Modeling tools can play an important role in synthetic biology the same way modeling helps in other engineering disciplines: simulations can quickly probe mechanisms and provide a clear picture of how different components influence the behavior of the whole. We present a brief review of available tools and present SynBioSS Designer. The Synthetic Biology Software Suite (SynBioSS) is used for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS consists of three distinct components: the Desktop Simulator, the Wiki, and the Designer. SynBioSS Designer takes as input molecular parts involved in gene expression and regulation (e.g. promoters, transcription factors, ribosome binding sites, etc.), and automatically generates complete networks of reactions that represent transcription, translation, regulation, induction and degradation of those parts. Effectively, Designer uses DNA sequences as input and generates networks of biomolecular reactions as output. In this paper we describe how Designer uses universal principles of molecular biology to generate models of any arbitrary synthetic biological system. These models are useful as they explain biological phenotypic complexity in mechanistic terms. In turn, such mechanistic explanations can assist in designing synthetic biological systems. We also discuss, giving practical guidance to users, how Designer interfaces with the Registry of Standard Biological Parts, the de facto compendium of parts used in synthetic biology applications.

  14. Coins as intermediate targets: reconstructive analysis with synthetic body models.

    PubMed

    Thali, Michael J; Kneubuehl, Beat P; Rodriguez, William R; Smirniotopoulos, James G; Richardson, A Charles; Fowler, David; Godwin, Michael; Jurrus, Aaron; Fletcher, Douglas; Mallak, Craig

    2009-06-01

    The phenomenon of intermediate targets is well known in wound ballistics. In forensic science, models are used to reconstruct injury patterns to answer questions regarding the dynamic formation of these unusual injuries. Soft-tissue substitutes or glycerin soap and ordnance gelatin have been well established. Recently, based on previous experiences with artificial bone, a skull-brain model was developed. The goal of this study was to create and analyze a model-supported reconstruction of a real forensic case with a coin as an intermediate target. It was possible not only to demonstrate the "bullet-coin interaction," but also to recreate the wound pattern found in the victim. This case demonstrates that by using ballistic models, gunshot cases can be reproduced simply and economically, without coming into conflict with ethical guidelines.

  15. Integration of Analytic and Synthetic Biosystem Models and Data

    DTIC Science & Technology

    2005-06-01

    environment akin to the Electrical Engineering SPICE modeling and simulation package, in which an open environment and standards-based modularity enable an...the Electrical Engineering SPICE modeling and simulation package, in which an open environment and standards-based modularity enable an enormous...was based on the following perceived requirements (excerpted from the white paper): • Heterogeneous Data Access. The Bio- SPICE DMI must support

  16. Validating high-resolution California coastal flood modeling with Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR)

    NASA Astrophysics Data System (ADS)

    O'Neill, A.

    2015-12-01

    The Coastal Storm Modeling System (CoSMoS) is a numerical modeling scheme used to predict coastal flooding due to sea level rise and storms influenced by climate change, currently in use in central California and in development for Southern California (Pt. Conception to the Mexican border). Using a framework of circulation, wave, analytical, and Bayesian models at different geographic scales, high-resolution results are translated as relevant hazards projections at the local scale that include flooding, wave heights, coastal erosion, shoreline change, and cliff failures. Ready access to accurate, high-resolution coastal flooding data is critical for further validation and refinement of CoSMoS and improved coastal hazard projections. High-resolution Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) provides an exceptional data source as appropriately-timed flights during extreme tides or storms provide a geographically-extensive method for determining areas of inundation and flooding extent along expanses of complex and varying coastline. Landward flood extents are numerically identified via edge-detection in imagery from single flights, and can also be ascertained via change detection using additional flights and imagery collected during average wave/tide conditions. The extracted flooding positions are compared against CoSMoS results for similar tide, water level, and storm-intensity conditions, allowing for robust testing and validation of CoSMoS and providing essential feedback for supporting regional and local model improvement.

  17. Liposomes containing lipid A: an effective, safe, generic adjuvant system for synthetic vaccines.

    PubMed

    Alving, Carl R; Rao, Mangala; Steers, Nicholas J; Matyas, Gary R; Mayorov, Alexander V

    2012-06-01

    Liposomes containing monophosphoryl lipid A (MPLA) have previously exhibited considerable potency and safety in human trials with a variety of candidate vaccines, including vaccines to malaria, HIV-1 and several different types of cancer. The long history of research and development of MPLA and liposomal MPLA as vaccine adjuvants reveals that there are numerous opportunities for creation and development of generic (nonproprietary) adjuvant system formulations with these materials that are not only highly potent and safe, but also readily available as native materials or as synthetic compounds. They are easily manufactured as potentially inexpensive and easy to use adjuvant systems and might be effective even with synthetic peptides as antigens.

  18. The SIR-C/X-SAR synthetic aperture radar system

    NASA Technical Reports Server (NTRS)

    Jordan, Rolando L.; Huneycutt, Bryan L.; Werner, Marian

    1991-01-01

    SIR-C/X-SAR, a three-frequency radar to be flown on the Space Shuttle in September 1993, is described. The SIR-C system is a two-frequency radar operating at 1250 MHz (L-band) and 5300 MHz (C-band), and is designed to get four-polarization radar imagery at multiple surface angles. The X-SAR system is an X-band imaging radar operating at 9600 MHz. The discussion covers the mission concept; system design; hardware; RF electronics; digital electronics; command, timing, and telemetry; and testing.

  19. Backus Effect on a Perpendicular Errors in Harmonic Models of Real vs. Synthetic Data

    NASA Technical Reports Server (NTRS)

    Voorhies, C. V.; Santana, J.; Sabaka, T.

    1999-01-01

    Measurements of geomagnetic scalar intensity on a thin spherical shell alone are not enough to separate internal from external source fields; moreover, such scalar data are not enough for accurate modeling of the vector field from internal sources because of unmodeled fields and small data errors. Spherical harmonic models of the geomagnetic potential fitted to scalar data alone therefore suffer from well-understood Backus effect and perpendicular errors. Curiously, errors in some models of simulated 'data' are very much less than those in models of real data. We analyze select Magsat vector and scalar measurements separately to illustrate Backus effect and perpendicular errors in models of real scalar data. By using a model to synthesize 'data' at the observation points, and by adding various types of 'noise', we illustrate such errors in models of synthetic 'data'. Perpendicular errors prove quite sensitive to the maximum degree in the spherical harmonic expansion of the potential field model fitted to the scalar data. Small errors in models of synthetic 'data' are found to be an artifact of matched truncation levels. For example, consider scalar synthetic 'data' computed from a degree 14 model. A degree 14 model fitted to such synthetic 'data' yields negligible error, but amplifies 4 nT (rmss) added noise into a 60 nT error (rmss); however, a degree 12 model fitted to the noisy 'data' suffers a 492 nT error (rmms through degree 12). Geomagnetic measurements remain unaware of model truncation, so the small errors indicated by some simulations cannot be realized in practice. Errors in models fitted to scalar data alone approach 1000 nT (rmss) and several thousand nT (maximum).

  20. [Hannover synthetic moulages. A singular collection of dermatologic teaching models].

    PubMed

    Schnalke, T

    1987-12-01

    Dermatological moulages rapidly lost their importance during the 1950s. The disadvantages of the classical moulage materials, plaster of Paris and wax, are pointed out. In the 1960s and 1970s modern plastics were introduced to moulage technology at the Linden Dermatological Clinic in Hannover. Silicon-caoutchouc and Vestolit-PVC were the substances used. This paper describes how the Hannover collection of plastic models was assembled and presents its current status. Wax and plastic models are set against each other in the illustrations.

  1. Comparison of model and human observer performance in FFDM, DBT, and synthetic mammography

    NASA Astrophysics Data System (ADS)

    Ikejimba, Lynda; Glick, Stephen J.; Samei, Ehsan; Lo, Joseph Y.

    2016-03-01

    Reader studies are important in assessing breast imaging systems. The purpose of this work was to assess task-based performance of full field digital mammography (FFDM), digital breast tomosynthesis (DBT), and synthetic mammography (SM) using different phantom types, and to determine an accurate observer model for human readers. Images were acquired on a Hologic Selenia Dimensions system with a uniform and anthropomorphic phantom. A contrast detail insert of small, low-contrast disks was created using an inkjet printer with iodine-doped ink and inserted in the phantoms. The disks varied in diameter from 210 to 630 μm, and in contrast from 1.1% contrast to 2.2% in regular increments. Human and model observers performed a 4-alternative forced choice experiment. The models were a non-prewhitening matched filter with eye model (NPWE) and a channelized Hotelling observer with either Gabor channels (Gabor-CHO) or Laguerre-Gauss channels (LG-CHO). With the given phantoms, reader scores were higher in FFDM and DBT than SM. The structure in the phantom background had a bigger impact on outcome for DBT than for FFDM or SM. All three model observers showed good correlation with humans in the uniform background, with ρ between 0.89 and 0.93. However, in the structured background, only the CHOs had high correlation, with ρ=0.92 for Gabor-CHO, 0.90 for LG-CHO, and 0.77 for NPWE. Because results of any analysis can depend on the phantom structure, conclusions of modality performance may need to be taken in the context of an appropriate model observer and a realistic phantom.

  2. Advanced Neural Network Modeling of Synthetic Jet Flow Fields

    DTIC Science & Technology

    2006-03-01

    The purpose of this research was to continue development of a neural network -based, lumped deterministic source term (LDST) approximation module for...main exploration involved the grid sensitivity of the neural network model. A second task was originally planned on the portability of the approach to

  3. A synthetic ecology perspective: How well does behavior of model organisms in the laboratory predict microbial activities in natural habitats?

    DOE PAGES

    Yu, Zheng; Krause, Sascha M. B.; Beck, David A. C.; ...

    2016-06-15

    In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sedimentmore » for a few decades and have identified a number of species genetically equipped for this activity. We have also identified cooccurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. Furthermore, these findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.« less

  4. Web-based software tool for constraint-based design specification of synthetic biological systems.

    PubMed

    Oberortner, Ernst; Densmore, Douglas

    2015-06-19

    miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).

  5. Co-culture systems and technologies: taking synthetic biology to the next level

    PubMed Central

    Goers, Lisa; Freemont, Paul; Polizzi, Karen M.

    2014-01-01

    Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell–cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions. PMID:24829281

  6. Co-culture systems and technologies: taking synthetic biology to the next level.

    PubMed

    Goers, Lisa; Freemont, Paul; Polizzi, Karen M

    2014-07-06

    Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions.

  7. Generating synthetic wave climates for coastal modelling: a linear mixed modelling approach

    NASA Astrophysics Data System (ADS)

    Thomas, C.; Lark, R. M.

    2013-12-01

    Numerical coastline morphological evolution models require wave climate properties to drive morphological change through time. Wave climate properties (typically wave height, period and direction) may be temporally fixed, culled from real wave buoy data, or allowed to vary in some way defined by a Gaussian or other pdf. However, to examine sensitivity of coastline morphologies to wave climate change, it seems desirable to be able to modify wave climate time series from a current to some new state along a trajectory, but in a way consistent with, or initially conditioned by, the properties of existing data, or to generate fully synthetic data sets with realistic time series properties. For example, mean or significant wave height time series may have underlying periodicities, as revealed in numerous analyses of wave data. Our motivation is to develop a simple methodology to generate synthetic wave climate time series that can change in some stochastic way through time. We wish to use such time series in a coastline evolution model to test sensitivities of coastal landforms to changes in wave climate over decadal and centennial scales. We have worked initially on time series of significant wave height, based on data from a Waverider III buoy located off the coast of Yorkshire, England. The statistical framework for the simulation is the linear mixed model. The target variable, perhaps after transformation (Box-Cox), is modelled as a multivariate Gaussian, the mean modelled as a function of a fixed effect, and two random components, one of which is independently and identically distributed (iid) and the second of which is temporally correlated. The model was fitted to the data by likelihood methods. We considered the option of a periodic mean, the period either fixed (e.g. at 12 months) or estimated from the data. We considered two possible correlation structures for the second random effect. In one the correlation decays exponentially with time. In the second

  8. The Mechanics of Neutrophils: Synthetic Modeling of Three Experiments

    PubMed Central

    Herant, Marc; Marganski, William A.; Dembo, Micah

    2003-01-01

    Much experimental data exist on the mechanical properties of neutrophils, but so far, they have mostly been approached within the framework of liquid droplet models. This has two main drawbacks: 1), It treats the cytoplasm as a single phase when in reality, it is a composite of cytosol and cytoskeleton; and 2), It does not address the problem of active neutrophil deformation and force generation. To fill these lacunae, we develop here a comprehensive continuum-mechanical paradigm of the neutrophil that includes proper treatment of the membrane, cytosol, and cytoskeleton components. We further introduce two models of active force production: a cytoskeletal swelling force and a polymerization force. Armed with these tools, we present computer simulations of three classic experiments: the passive aspiration of a neutrophil into a micropipette, the active extension of a pseudopod by a neutrophil exposed to a local stimulus, and the crawling of a neutrophil inside a micropipette toward a chemoattractant against a varying counterpressure. Principal results include: 1), Membrane cortical tension is a global property of the neutrophil that is affected by local area-increasing shape changes. We argue that there exists an area dilation viscosity caused by the work of unfurling membrane-storing wrinkles and that this viscosity is responsible for much of the regulation of neutrophil deformation. 2), If there is no swelling force of the cytoskeleton, then it must be endowed with a strong cohesive elasticity to prevent phase separation from the cytosol during vigorous suction into a capillary tube. 3), We find that both swelling and polymerization force models are able to provide a unifying fit to the experimental data for the three experiments. However, force production required in the polymerization model is beyond what is expected from a simple short-range Brownian ratchet model. 4), It appears that, in the crawling of neutrophils or other amoeboid cells inside a micropipette

  9. The mechanics of neutrophils: synthetic modeling of three experiments.

    PubMed

    Herant, Marc; Marganski, William A; Dembo, Micah

    2003-05-01

    Much experimental data exist on the mechanical properties of neutrophils, but so far, they have mostly been approached within the framework of liquid droplet models. This has two main drawbacks: 1), It treats the cytoplasm as a single phase when in reality, it is a composite of cytosol and cytoskeleton; and 2), It does not address the problem of active neutrophil deformation and force generation. To fill these lacunae, we develop here a comprehensive continuum-mechanical paradigm of the neutrophil that includes proper treatment of the membrane, cytosol, and cytoskeleton components. We further introduce two models of active force production: a cytoskeletal swelling force and a polymerization force. Armed with these tools, we present computer simulations of three classic experiments: the passive aspiration of a neutrophil into a micropipette, the active extension of a pseudopod by a neutrophil exposed to a local stimulus, and the crawling of a neutrophil inside a micropipette toward a chemoattractant against a varying counterpressure. Principal results include: 1), Membrane cortical tension is a global property of the neutrophil that is affected by local area-increasing shape changes. We argue that there exists an area dilation viscosity caused by the work of unfurling membrane-storing wrinkles and that this viscosity is responsible for much of the regulation of neutrophil deformation. 2), If there is no swelling force of the cytoskeleton, then it must be endowed with a strong cohesive elasticity to prevent phase separation from the cytosol during vigorous suction into a capillary tube. 3), We find that both swelling and polymerization force models are able to provide a unifying fit to the experimental data for the three experiments. However, force production required in the polymerization model is beyond what is expected from a simple short-range Brownian ratchet model. 4), It appears that, in the crawling of neutrophils or other amoeboid cells inside a micropipette

  10. Modeling and Simulation of Synthetic Aperture Radars in Matlab

    DTIC Science & Technology

    2013-06-01

    was done optically by utilizing Fourier optics methods including a coherent laser and a carefully positioned system of lenses to determine the... Fourier transform of the data collected and stored on film. It was the limitations posed by optical processing that prompted research into digital... Fourier Optics : Third Edition. Englewood, CO: Roberts & Company Publishers, 2005. [4] A. W. Love. In memory of Carl A. Wiley. IEEE Antennas and

  11. A synthetic model for the oxygen-evolving complex in Sr(2+)-containing photosystem II.

    PubMed

    Chen, Changhui; Zhang, Chunxi; Dong, Hongxing; Zhao, Jingquan

    2014-08-25

    A novel heterometallic MnSr complex containing the Mn3SrO4 cuboidal moiety and all types of μ-O(2-) moieties observed in the oxygen-evolving complex (OEC) in Sr(2+)-containing photosystem II (PSII) has been synthesized and characterized, which provides a new synthetic model of the OEC.

  12. Design Optimization Tool for Synthetic Jet Actuators Using Lumped Element Modeling

    NASA Technical Reports Server (NTRS)

    Gallas, Quentin; Sheplak, Mark; Cattafesta, Louis N., III; Gorton, Susan A. (Technical Monitor)

    2005-01-01

    The performance specifications of any actuator are quantified in terms of an exhaustive list of parameters such as bandwidth, output control authority, etc. Flow-control applications benefit from a known actuator frequency response function that relates the input voltage to the output property of interest (e.g., maximum velocity, volumetric flow rate, momentum flux, etc.). Clearly, the required performance metrics are application specific, and methods are needed to achieve the optimal design of these devices. Design and optimization studies have been conducted for piezoelectric cantilever-type flow control actuators, but the modeling issues are simpler compared to synthetic jets. Here, lumped element modeling (LEM) is combined with equivalent circuit representations to estimate the nonlinear dynamic response of a synthetic jet as a function of device dimensions, material properties, and external flow conditions. These models provide reasonable agreement between predicted and measured frequency response functions and thus are suitable for use as design tools. In this work, we have developed a Matlab-based design optimization tool for piezoelectric synthetic jet actuators based on the lumped element models mentioned above. Significant improvements were achieved by optimizing the piezoceramic diaphragm dimensions. Synthetic-jet actuators were fabricated and benchtop tested to fully document their behavior and validate a companion optimization effort. It is hoped that the tool developed from this investigation will assist in the design and deployment of these actuators.

  13. Comparisons of Historical versus Synthetic Weather Inputs to Watershed Models and their Effect on Pollutant Loads

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Synthetic weather generators are important for continuous-simulation of agricultural watersheds for risk analyses of downstream water quality. Many watersheds are sparsely or totally ungauged and daily weather must either be transposed or augmented. Since water quality models must recognize runoff...

  14. Dynamic visual image modeling for 3D synthetic scenes in agricultural engineering

    NASA Astrophysics Data System (ADS)

    Gao, Li; Yan, Juntao; Li, Xiaobo; Ji, Yatai; Li, Xin

    The dynamic visual image modeling for 3D synthetic scenes by using dynamic multichannel binocular visual image based on the mobile self-organizing network. Technologies of 3D modeling synthetic scenes have been widely used in kinds of industries. The main purpose of this paper is to use multiple networks of dynamic visual monitors and sensors to observe an unattended area, to use the advantages of mobile network in rural areas for improving existing mobile network information service further and providing personalized information services. The goal of displaying is to provide perfect representation of synthetic scenes. Using low-power dynamic visual monitors and temperature/humidity sensor or GPS installed in the node equipment, monitoring data will be sent at scheduled time. Then through the mobile self-organizing network, 3D model is rebuilt by synthesizing the returned images. On this basis, we formalize a novel algorithm for multichannel binocular visual 3D images based on fast 3D modeling. Taking advantage of these low prices mobile, mobile self-organizing networks can get a large number of video from where is not suitable for human observation or unable to reach, and accurately synthetic 3D scene. This application will play a great role in promoting its application in agriculture.

  15. Planetary Probe Entry Atmosphere Estimation Using Synthetic Air Data System

    NASA Technical Reports Server (NTRS)

    Karlgaard, Chris; Schoenenberger, Mark

    2017-01-01

    This paper develops an atmospheric state estimator based on inertial acceleration and angular rate measurements combined with an assumed vehicle aerodynamic model. The approach utilizes the full navigation state of the vehicle (position, velocity, and attitude) to recast the vehicle aerodynamic model to be a function solely of the atmospheric state (density, pressure, and winds). Force and moment measurements are based on vehicle sensed accelerations and angular rates. These measurements are combined with an aerodynamic model and a Kalman-Schmidt filter to estimate the atmospheric conditions. The new method is applied to data from the Mars Science Laboratory mission, which landed the Curiosity rover on the surface of Mars in August 2012. The results of the new estimation algorithm are compared with results from a Flush Air Data Sensing algorithm based on onboard pressure measurements on the vehicle forebody. The comparison indicates that the new proposed estimation method provides estimates consistent with the air data measurements, without the use of pressure measurements. Implications for future missions such as the Mars 2020 entry capsule are described.

  16. Synthetic Modeling of Autonomous Learning with a Chaotic Neural Network

    NASA Astrophysics Data System (ADS)

    Funabashi, Masatoshi

    We investigate the possible role of intermittent chaotic dynamics called chaotic itinerancy, in interaction with nonsupervised learnings that reinforce and weaken the neural connection depending on the dynamics itself. We first performed hierarchical stability analysis of the Chaotic Neural Network model (CNN) according to the structure of invariant subspaces. Irregular transition between two attractor ruins with positive maximum Lyapunov exponent was triggered by the blowout bifurcation of the attractor spaces, and was associated with riddled basins structure. We secondly modeled two autonomous learnings, Hebbian learning and spike-timing-dependent plasticity (STDP) rule, and simulated the effect on the chaotic itinerancy state of CNN. Hebbian learning increased the residence time on attractor ruins, and produced novel attractors in the minimum higher-dimensional subspace. It also augmented the neuronal synchrony and established the uniform modularity in chaotic itinerancy. STDP rule reduced the residence time on attractor ruins, and brought a wide range of periodicity in emerged attractors, possibly including strange attractors. Both learning rules selectively destroyed and preserved the specific invariant subspaces, depending on the neuron synchrony of the subspace where the orbits are situated. Computational rationale of the autonomous learning is discussed in connectionist perspective.

  17. Assessment of synthetic winds through spectral modelling, rainflow count analysis and statistics of increments

    NASA Astrophysics Data System (ADS)

    Beyer, Hans Georg; Chougule, Abhijit

    2016-04-01

    While wind energy industry growing rapidly and siting of wind turbines onshore as well as offshore is increasing, many wind engineering model tools have been developed for the assessment of loads on wind turbines due to varying wind speeds. In order to have proper wind turbine design and performance analysis, it is important to have an accurate representation of the incoming wind field. To ease the analysis, tools for the generation of synthetic wind fields have been developed, e.g the widely used TurbSim procedure. We analyse respective synthetic data sets on one hand in view of the similarity of the spectral characteristics of measured and synthetic sets. In addition, second order characteristics with direct relevance to load assessment as given by the statistics of increments and rainflow count results are inspected.

  18. Water quality assessment of the Li Canal using a functional fuzzy synthetic evaluation model.

    PubMed

    Feng, Yan; Ling, Liu

    2014-07-01

    Through introducing functional data analysis (FDA) theory into the conventional fuzzy synthetic evaluation (FSE) method, the functional fuzzy synthetic evaluation (FFSE) model is established. FFSE keeps the property of the conventional FSE that the fuzziness in the water quality condition can be suitably measured. Furthermore, compared with FSE, FFSE has the following advantages: (1) FFSE requires fewer conditions for observation, for example, pollutants can be monitored at different times, and missing data is accepted; (2) the dynamic variation of the water quality condition can be represented more comprehensively and intuitively. The procedure of FFSE is discussed and the water quality of the Li Canal in 2012 is evaluated as an illustration. The synthetic classification of the Li Canal is "II" in January, February and July, and "I" in other months, which can satisfy the requirement of the Chinese South-to-North Water Diversion Project.

  19. Comparison of Nonlinear Model Results Using Modified Recorded and Synthetic Ground Motions

    SciTech Connect

    Robert E. Spears; J. Kevin Wilkins

    2011-11-01

    A study has been performed that compares results of nonlinear model runs using two sets of earthquake ground motion time histories that have been modified to fit the same design response spectra. The time histories include applicable modified recorded earthquake ground motion time histories and synthetic ground motion time histories. The modified recorded earthquake ground motion time histories are modified from time history records that are selected based on consistent magnitude and distance. The synthetic ground motion time histories are generated using appropriate Fourier amplitude spectrums, Arias intensity, and drift correction. All of the time history modification is performed using the same algorithm to fit the design response spectra. The study provides data to demonstrate that properly managed synthetic ground motion time histories are reasonable for use in nonlinear seismic analysis.

  20. Digital computer simulation of synthetic aperture systems and images

    NASA Astrophysics Data System (ADS)

    Camporeale, Claudio; Galati, Gaspare

    1991-06-01

    Digital computer simulation is a powerful tool for the design, the mission planning and the image quality analysis of advanced SAR Systems. 'End-to-end' simulators describe the whole process of the SAR imaging including the generation of the coherent echoes and their processing and allow, unlike the 'product simulators', to evaluate the effects of the various impairments on the final image. The main disadvantage of the 'end-to-end' approach, as described in this paper, is the heavy computation burden; therefore, a new type of simulator is presented, attempting to reduce the burden but presenting a greater degree of completeness and realism than the SAR product simulators, already existing.

  1. [New polymer-drug systems based on natural and synthetic polymers].

    PubMed

    Racoviţă, Stefania; Vasiliu, Silvia; Foia, Liliana

    2010-01-01

    The great versatility of polymers makes them very useful in the biomedical and pharmaceutical fields. The combination of natural and synthetic polymers leads to new materials with tailored functional properties. The aim of this work consists in the preparation of new drug delivery system based on chitosan (natural polymer) and polybetaines (synthetic polymers), by a simple process, well known in the literature as complex coacervation methods. Also, the adsorption and release studies of two antibiotics as well as the preservation of their bactericidal capacities were performed.

  2. Synthetic Multivariate Models to Accommodate Unmodeled Interfering Components During Quantitative Spectral Analyses

    SciTech Connect

    Haaland, David M.

    1999-07-14

    The analysis precision of any multivariate calibration method will be severely degraded if unmodeled sources of spectral variation are present in the unknown sample spectra. This paper describes a synthetic method for correcting for the errors generated by the presence of unmodeled components or other sources of unmodeled spectral variation. If the spectral shape of the unmodeled component can be obtained and mathematically added to the original calibration spectra, then a new synthetic multivariate calibration model can be generated to accommodate the presence of the unmodeled source of spectral variation. This new method is demonstrated for the presence of unmodeled temperature variations in the unknown sample spectra of dilute aqueous solutions of urea, creatinine, and NaCl. When constant-temperature PLS models are applied to spectra of samples of variable temperature, the standard errors of prediction (SEP) are approximately an order of magnitude higher than that of the original cross-validated SEPs of the constant-temperature partial least squares models. Synthetic models using the classical least squares estimates of temperature from pure water or variable-temperature mixture sample spectra reduce the errors significantly for the variable temperature samples. Spectrometer drift adds additional error to the analyte determinations, but a method is demonstrated that can minimize the effect of drift on prediction errors through the measurement of the spectra of a small subset of samples during both calibration and prediction. In addition, sample temperature can be predicted with high precision with this new synthetic model without the need to recalibrate using actual variable-temperature sample data. The synthetic methods eliminate the need for expensive generation of new calibration samples and collection of their spectra. The methods are quite general and can be applied using any known source of spectral variation and can be used with any multivariate

  3. Synthetic ECG Generation and Bayesian Filtering Using a Gaussian Wave-Based Dynamical Model

    PubMed Central

    Sayadi, Omid; Shamsollahi, Mohammad B.; Clifford, Gari D.

    2011-01-01

    In this paper, we describe a Gaussian wave-based state space to model the temporal dynamics of electrocardiogram (ECG) signals. It is shown that this model may be effectively used for generating synthetic ECGs as well as separate characteristic waves (CWs) such as the atrial and ventricular complexes. The model uses separate state variables for each CW, i.e. P, QRS and T, and hence is capable of generating individual synthetic CWs as well as realistic ECG signals. The model is therefore useful for generating arrhythmias. Simulations of sinus bradycardia, sinus tachycardia, ventricular flutter, atrial fibrillation, and ventricular tachycardia are presented. In addition, discrete versions of the equations are presented for a model-based Bayesian framework for denoising. This framework, together with an extended Kalman filter (EKF) and extended Kalman smoother (EKS), were used for denoising the ECG for both normal rhythms and arrhythmias. For evaluating the denoising performance the signal-to-noise ratio (SNR) improvement of the filter outputs and clinical parameter stability were studied. The results demonstrate superiority over a wide range of input SNRs, achieving a maximum 12.7 dB improvement. Results indicate that preventing clinically relevant distortion of the ECG is sensitive to the number of model parameters. Models are presented which do not exhibit such distortions. The approach presented in this paper may therefore serve as an effective framework for synthetic ECG generation and model-based filtering of noisy ECG recordings. PMID:20720288

  4. Synthetic ECG generation and Bayesian filtering using a Gaussian wave-based dynamical model.

    PubMed

    Sayadi, Omid; Shamsollahi, Mohammad B; Clifford, Gari D

    2010-10-01

    In this paper, we describe a Gaussian wave-based state space to model the temporal dynamics of electrocardiogram (ECG) signals. It is shown that this model may be effectively used for generating synthetic ECGs as well as separate characteristic waves (CWs) such as the atrial and ventricular complexes. The model uses separate state variables for each CW, i.e. P, QRS and T, and hence is capable of generating individual synthetic CWs as well as realistic ECG signals. The model is therefore useful for generating arrhythmias. Simulations of sinus bradycardia, sinus tachycardia, ventricular flutter, atrial fibrillation and ventricular tachycardia are presented. In addition, discrete versions of the equations are presented for a model-based Bayesian framework for denoising. This framework, together with an extended Kalman filter and extended Kalman smoother, was used for denoising the ECG for both normal rhythms and arrhythmias. For evaluating the denoising performance, the signal-to-noise ratio (SNR) improvement of the filter outputs and clinical parameter stability were studied. The results demonstrate superiority over a wide range of input SNRs, achieving a maximum 12.7 dB improvement. Results indicate that preventing clinically relevant distortion of the ECG is sensitive to the number of model parameters. Models are presented which do not exhibit such distortions. The approach presented in this paper may therefore serve as an effective framework for synthetic ECG generation and model-based filtering of noisy ECG recordings.

  5. Flight Test Evaluation of Situation Awareness Benefits of Integrated Synthetic Vision System Technology f or Commercial Aircraft

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence J., III; Kramer, Lynda J.; Arthur, Jarvis J., III

    2005-01-01

    Research was conducted onboard a Gulfstream G-V aircraft to evaluate integrated Synthetic Vision System concepts during flight tests over a 6-week period at the Wallops Flight Facility and Reno/Tahoe International Airport. The NASA Synthetic Vision System incorporates database integrity monitoring, runway incursion prevention alerting, surface maps, enhanced vision sensors, and advanced pathway guidance and synthetic terrain presentation. The paper details the goals and objectives of the flight test with a focus on the situation awareness benefits of integrating synthetic vision system enabling technologies for commercial aircraft.

  6. Measurement and modeling of CO₂ solubility in natural and synthetic formation brines for CO₂ sequestration.

    PubMed

    Zhao, Haining; Dilmore, Robert; Allen, Douglas E; Hedges, Sheila W; Soong, Yee; Lvov, Serguei N

    2015-02-03

    CO2 solubility data in the natural formation brine, synthetic formation brine, and synthetic NaCl+CaCl2 brine were collected at the pressures from 100 to 200 bar, temperatures from 323 to 423 K. Experimental results demonstrate that the CO2 solubility in the synthetic formation brines can be reliably represented by that in the synthetic NaCl+CaCl2 brines. We extended our previously developed model (PSUCO2) to calculate CO2 solubility in aqueous mixed-salt solution by using the additivity rule of the Setschenow coefficients of the individual ions (Na(+), Ca(2+), Mg(2+), K(+), Cl(-), and SO4(2-)). Comparisons with previously published models against the experimental data reveal a clear improvement of the proposed PSUCO2 model. Additionally, the path of the maximum gradient of the CO2 solubility contours divides the P-T diagram into two distinct regions: in Region I, the CO2 solubility in the aqueous phase decreases monotonically in response to increased temperature; in region II, the behavior of the CO2 solubility is the opposite of that in Region I as the temperature increases.

  7. Synthetic 3D multicellular systems for drug development.

    PubMed

    Rimann, Markus; Graf-Hausner, Ursula

    2012-10-01

    Since the 1970s, the limitations of two dimensional (2D) cell culture and the relevance of appropriate three dimensional (3D) cell systems have become increasingly evident. Extensive effort has thus been made to move cells from a flat world to a 3D environment. While 3D cell culture technologies are meanwhile widely used in academia, 2D culture technologies are still entrenched in the (pharmaceutical) industry for most kind of cell-based efficacy and toxicology tests. However, 3D cell culture technologies will certainly become more applicable if biological relevance, reproducibility and high throughput can be assured at acceptable costs. Most recent innovations and developments clearly indicate that the transition from 2D to 3D cell culture for industrial purposes, for example, drug development is simply a question of time.

  8. Genome-scale engineering for systems and synthetic biology

    PubMed Central

    Esvelt, Kevin M; Wang, Harris H

    2013-01-01

    Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targeted gene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering. PMID:23340847

  9. Evolutionary adaptation of phenotypic plasticity in a synthetic microbial system

    NASA Astrophysics Data System (ADS)

    Tans, Sander

    2010-03-01

    While phenotypic plasticity -the capability to respond to the environment- is vital to organisms, tests of its adaptation have remained indecisive because constraints and selection in variable environments are unknown and entangled. We show that one can determine the phenotype-fitness landscape that specifies selection on plasticity, by uncoupling the environmental cue and stress in a genetically engineered microbial system. Evolutionary trajectories revealed genetic constraints in a regulatory protein, which imposed cross-environment trade-offs that favored specialization. However, depending on the synchronicity and amplitude of the applied cue and stress variations, adaptation could break constraints, resolve trade-offs, and evolve optimal phenotypes that exhibit qualitatively altered (inverse) responses to the cue. Our results provide a first step to explain the adaptive origins of complex behavior in heterogeneous environments.

  10. Genome-scale engineering for systems and synthetic biology.

    PubMed

    Esvelt, Kevin M; Wang, Harris H

    2013-01-01

    Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targeted gene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering.

  11. Synthetic polyion-counterion transport systems in polymersomes and gels.

    PubMed

    Montenegro, Javier; Braun, Jörg; Fischer-Onaca, Ozana; Meier, Wolfgang; Matile, Stefan

    2011-10-07

    Transport across the membranes of polymersomes remains difficult in part due to the great thickness of the polymer bilayers. Here, we report that dynamic polyion-counterion transport systems are active in fluorogenic polymersomes composed of poly(dimethylsiloxane)-b-poly(2-methyloxazoline) (PDMS-PMOXA). These results suggest that counterion-activated calf-thymus DNA can act as cation carrier that moves not only across lipid bilayer and bulk chloroform membranes but also across the "plastic" membranes of polymersomes. Compared to egg yolk phosophatidylcholine (EYPC) lipsosomes, activities and activator scope in PDMS-PMOXA polymersomes are clearly reduced. Embedded in agar gel matrices, fluorogenic PDMS-PMOXA polymersomes respond reliably to polyion-counterion transporters, with high contrast, high stability and preserved selectivity. Compared to standard EYPC liposomes, it cannot be said that PDMS-PMOXA polymersomes are better. However, they are different, and this difference could be interesting for the development of sensing devices.

  12. Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory.

    PubMed

    Nikolaev, Evgeni V; Sontag, Eduardo D

    2016-04-01

    biochemically-detailed and biologically-relevant model that we developed. Another novel feature of our approach is that our theorems on exponential stability of steady states for homogeneous or mixed populations are valid independently of the number N of cells in the population, which is usually very large (N ≫ 1) and unknown. We prove that the exponential stability depends on relative proportions of each type of state only. While monotone systems theory has been used previously for systems biology analysis, the current work illustrates its power for synthetic biology design, and thus has wider significance well beyond the application to the important problem of coordination of toggle switches.

  13. Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory

    PubMed Central

    Nikolaev, Evgeni V.

    2016-01-01

    analysis, performed for a biochemically-detailed and biologically-relevant model that we developed. Another novel feature of our approach is that our theorems on exponential stability of steady states for homogeneous or mixed populations are valid independently of the number N of cells in the population, which is usually very large (N ≫ 1) and unknown. We prove that the exponential stability depends on relative proportions of each type of state only. While monotone systems theory has been used previously for systems biology analysis, the current work illustrates its power for synthetic biology design, and thus has wider significance well beyond the application to the important problem of coordination of toggle switches. PMID:27128344

  14. Optogenetic characterization methods overcome key challenges in synthetic and systems biology.

    PubMed

    Olson, Evan J; Tabor, Jeffrey J

    2014-07-01

    Systems biologists aim to understand how organism-level processes, such as differentiation and multicellular development, are encoded in DNA. Conversely, synthetic biologists aim to program systems-level biological processes, such as engineered tissue growth, by writing artificial DNA sequences. To achieve their goals, these groups have adapted a hierarchical electrical engineering framework that can be applied in the forward direction to design complex biological systems or in the reverse direction to analyze evolved networks. Despite much progress, this framework has been limited by an inability to directly and dynamically characterize biological components in the varied contexts of living cells. Recently, two optogenetic methods for programming custom gene expression and protein localization signals have been developed and used to reveal fundamentally new information about biological components that respond to those signals. This basic dynamic characterization approach will be a major enabling technology in synthetic and systems biology.

  15. [Application of systems biology and synthetic biology in strain improvement for biofuel production].

    PubMed

    Zhao, Xinqing; Bai, Fengwu; Li, Yin

    2010-07-01

    Biofuels are renewable and environmentally friendly, but high production cost makes them economically not competitive, and the development of robust strains is thus one of the prerequisites. In this article, strain improvement studies based on the information from systems biology studies are reviewed, with a focus on their applications on stress tolerance improvement. Furthermore, the contribution of systems biology, synthetic biology and metabolic engineering in strain development for biofuel production is discussed, with an expectation for developing more robust strains for biofuel production.

  16. Assessment of synthetic winds through spectral modeling and validation using FAST

    NASA Astrophysics Data System (ADS)

    Chougule, A.; Kandukuri, S. T.; Beyer, H. G.

    2016-09-01

    In this paper, we analyse the simulated and measured wind data with respect to their spectral characteristics and their effect on wind turbine loads. The synthetic data is generated from a stochastic full-field turbulent wind simulator - TurbSim for neutral stability conditions. We first investigate a model for velocity spectra and, a coherence model, by comparing the model results with the measurements. In the second part we analyse the synthetic data via spectra and coherence for two cases; without and with adding coherent events. Finally, we compare wind turbine loads calculated by using FAST simulation of 5 MW reference wind turbine on the basis of simulated and measured data for the given mean wind speed.

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

    PubMed Central

    Aziz, Ramy K.; Monk, Jonathan M.; Lewis, Robert M.; In Loh, Suh; Mishra, Arti; Abhay Nagle, Amrita; Satyanarayana, Chitkala; Dhakshinamoorthy, Saravanakumar; Luche, Michele; Kitchen, Douglas B.; Andrews, Kathleen A.; Fong, Nicole L.; Li, Howard J.; Palsson, Bernhard O.; Charusanti, Pep

    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 and phenotype, but their ability to accurately simulate gene-gene interactions has not been investigated extensively. Here we assess how accurately a metabolic model for Escherichia coli computes one particular type of gene-gene interaction, synthetic lethality, and find that the accuracy rate is between 25% and 43%. The most common failure modes were incorrect computation of single gene essentiality and biological information that was missing from the model. Moreover, we performed virtual and biological screening against several synthetic lethal pairs to explore whether two-compound formulations could be found that inhibit the growth of Gram-negative bacteria. One set of molecules was identified that, depending on the concentrations, inhibits E. coli and S. enterica serovar Typhimurium in an additive or antagonistic manner. These findings pinpoint specific ways in which to improve the predictive ability of metabolic models, and highlight one potential application of systems biology to drug discovery and translational medicine. PMID:26531810

  18. Synthetic Botany.

    PubMed

    Boehm, Christian R; Pollak, Bernardo; Purswani, Nuri; Patron, Nicola; Haseloff, Jim

    2017-02-28

    Plants are attractive platforms for synthetic biology and metabolic engineering. Plants' modular and plastic body plans, capacity for photosynthesis, extensive secondary metabolism, and agronomic systems for large-scale production make them ideal targets for genetic reprogramming. However, efforts in this area have been constrained by slow growth, long life cycles, the requirement for specialized facilities, a paucity of efficient tools for genetic manipulation, and the complexity of multicellularity. There is a need for better experimental and theoretical frameworks to understand the way genetic networks, cellular populations, and tissue-wide physical processes interact at different scales. We highlight new approaches to the DNA-based manipulation of plants and the use of advanced quantitative imaging techniques in simple plant models such as Marchantia polymorpha. These offer the prospects of improved understanding of plant dynamics and new approaches to rational engineering of plant traits.

  19. Testing 3D landform quantification methods with synthetic drumlins in a real digital elevation model

    NASA Astrophysics Data System (ADS)

    Hillier, John K.; Smith, Mike J.

    2012-06-01

    Metrics such as height and volume quantifying the 3D morphology of landforms are important observations that reflect and constrain Earth surface processes. Errors in such measurements are, however, poorly understood. A novel approach, using statistically valid ‘synthetic' landscapes to quantify the errors is presented. The utility of the approach is illustrated using a case study of 184 drumlins observed in Scotland as quantified from a Digital Elevation Model (DEM) by the ‘cookie cutter' extraction method. To create the synthetic DEMs, observed drumlins were removed from the measured DEM and replaced by elongate 3D Gaussian ones of equivalent dimensions positioned randomly with respect to the ‘noise' (e.g. trees) and regional trends (e.g. hills) that cause the errors. Then, errors in the cookie cutter extraction method were investigated by using it to quantify these ‘synthetic' drumlins, whose location and size is known. Thus, the approach determines which key metrics are recovered accurately. For example, mean height of 6.8 m is recovered poorly at 12.5 ± 0.6 (2σ) m, but mean volume is recovered correctly. Additionally, quantification methods can be compared: A variant on the cookie cutter using an un-tensioned spline induced about twice (× 1.79) as much error. Finally, a previously reportedly statistically significant (p = 0.007) difference in mean volume between sub-populations of different ages, which may reflect formational processes, is demonstrated to be only 30-50% likely to exist in reality. Critically, the synthetic DEMs are demonstrated to realistically model parameter recovery, primarily because they are still almost entirely the original landscape. Results are insensitive to the exact method used to create the synthetic DEMs, and the approach could be readily adapted to assess a variety of landforms (e.g. craters, dunes and volcanoes).

  20. Sender–receiver systems and applying information theory for quantitative synthetic biology

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-02-01

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

  2. A synthetic vision system using directionally selective motion detectors to recognize collision.

    PubMed

    Yue, Shigang; Rind, F Claire

    2007-01-01

    Reliably recognizing objects approaching on a collision course is extremely important. A synthetic vision system is proposed to tackle the problem of collision recognition in dynamic environments. The system combines the outputs of four whole-field motion-detecting neurons, each receiving inputs from a network of neurons employing asymmetric lateral inhibition to suppress their responses to one direction of motion. An evolutionary algorithm is then used to adjust the weights between the four motion-detecting neurons to tune the system to detect collisions in two test environments. To do this, a population of agents, each representing a proposed synthetic visual system, either were shown images generated by a mobile Khepera robot navigating in a simplified laboratory environment or were shown images videoed outdoors from a moving vehicle. The agents had to cope with the local environment correctly in order to survive. After 400 generations, the best agent recognized imminent collisions reliably in the familiar environment where it had evolved. However, when the environment was swapped, only the agent evolved to cope in the robotic environment still signaled collision reliably. This study suggests that whole-field direction-selective neurons, with selectivity based on asymmetric lateral inhibition, can be organized into a synthetic vision system, which can then be adapted to play an important role in collision detection in complex dynamic scenes.

  3. Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems

    PubMed Central

    Bilitchenko, Lesia; Liu, Adam; Cheung, Sherine; Weeding, Emma; Xia, Bing; Leguia, Mariana; Anderson, J. Christopher; Densmore, Douglas

    2011-01-01

    Background Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts. Results We illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively. Conclusions Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly. PMID:21559524

  4. A synthetic gene drive system for local, reversible modification and suppression of insect populations.

    PubMed

    Akbari, Omar S; Matzen, Kelly D; Marshall, John M; Huang, Haixia; Ward, Catherine M; Hay, Bruce A

    2013-04-22

    Replacement of wild insect populations with genetically modified individuals unable to transmit disease provides a self-perpetuating method of disease prevention but requires a gene drive mechanism to spread these traits to high frequency. Drive mechanisms requiring that transgenes exceed a threshold frequency in order to spread are attractive because they bring about local but not global replacement, and transgenes can be eliminated through dilution of the population with wild-type individuals. These features are likely to be important in many social and regulatory contexts. Here we describe the first creation of a synthetic threshold-dependent gene drive system, designated maternal-effect lethal underdominance (UD(MEL)), in which two maternally expressed toxins, located on separate chromosomes, are each linked with a zygotic antidote able to rescue maternal-effect lethality of the other toxin. We demonstrate threshold-dependent replacement in single- and two-locus configurations in Drosophila. Models suggest that transgene spread can often be limited to local environments. They also show that in a population in which single-locus UD(MEL) has been carried out, repeated release of wild-type males can result in population suppression, a novel method of genetic population manipulation.

  5. A synthetic Earth Gravity Model Designed Specifically for Testing Regional Gravimetric Geoid Determination Algorithms

    NASA Astrophysics Data System (ADS)

    Baran, I.; Kuhn, M.; Claessens, S. J.; Featherstone, W. E.; Holmes, S. A.; Vaníček, P.

    2006-04-01

    A synthetic [simulated] Earth gravity model (SEGM) of the geoid, gravity and topography has been constructed over Australia specifically for validating regional gravimetric geoid determination theories, techniques and computer software. This regional high-resolution (1-arc-min by 1-arc-min) Australian SEGM (AusSEGM) is a combined source and effect model. The long-wavelength effect part (up to and including spherical harmonic degree and order 360) is taken from an assumed errorless EGM96 global geopotential model. Using forward modelling via numerical Newtonian integration, the short-wavelength source part is computed from a high-resolution (3-arc-sec by 3-arc-sec) synthetic digital elevation model (SDEM), which is a fractal surface based on the GLOBE v1 DEM. All topographic masses are modelled with a constant mass-density of 2,670 kg/m3. Based on these input data, gravity values on the synthetic topography (on a grid and at arbitrarily distributed discrete points) and consistent geoidal heights at regular 1-arc-min geographical grid nodes have been computed. The precision of the synthetic gravity and geoid data (after a first iteration) is estimated to be better than 30 μ Gal and 3 mm, respectively, which reduces to 1 μ Gal and 1 mm after a second iteration. The second iteration accounts for the changes in the geoid due to the superposed synthetic topographic mass distribution. The first iteration of AusSEGM is compared with Australian gravity and GPS-levelling data to verify that it gives a realistic representation of the Earth’s gravity field. As a by-product of this comparison, AusSEGM gives further evidence of the north south-trending error in the Australian Height Datum. The freely available AusSEGM-derived gravity and SDEM data, included as Electronic Supplementary Material (ESM) with this paper, can be used to compute a geoid model that, if correct, will agree to in 3 mm with the AusSEGM geoidal heights, thus offering independent verification of theories

  6. Cosmo Cassette: A Microfluidic Microgravity Microbial System For Synthetic Biology Unit Tests and Satellite Missions

    NASA Technical Reports Server (NTRS)

    Berliner, Aaron J.

    2013-01-01

    Although methods in the design-build-test life cycle of the synthetic biology field have grown rapidly, the expansion has been non-uniform. The design and build stages in development have seen innovations in the form of biological CAD and more efficient means for building DNA, RNA, and other biological constructs. The testing phase of the cycle remains in need of innovation. Presented will be both a theoretical abstraction of biological measurement and a practical demonstration of a microfluidics-based platform for characterizing synthetic biological phenomena. Such a platform demonstrates a design of additive manufacturing (3D printing) for construction of a microbial fuel cell (MFC) to be used in experiments carried out in space. First, the biocompatibility of the polypropylene chassis will be demonstrated. The novel MFCs will be cheaper, and faster to make and iterate through designs. The novel design will contain a manifold switchingdistribution system and an integrated in-chip set of reagent reservoirs fabricated via 3D printing. The automated nature of the 3D printing yields itself to higher resolution switching valves and leads to smaller sized payloads, lower cost, reduced power and a standardized platform for synthetic biology unit tests on Earth and in space. It will be demonstrated that the application of unit testing in synthetic biology will lead to the automatic construction and validation of desired constructs. Unit testing methodologies offer benefits of preemptive problem identification, change of facility, simplicity of integration, ease of documentation, and separation of interface from implementation, and automated design.

  7. Phenolic mediators enhance the manganese peroxidase catalyzed oxidation of recalcitrant lignin model compounds and synthetic lignin.

    PubMed

    Nousiainen, Paula; Kontro, Jussi; Manner, Helmiina; Hatakka, Annele; Sipilä, Jussi

    2014-11-01

    Fungal oxidative enzymes, such as peroxidases and laccases, are the key catalysts in lignin biodegradation in vivo, and consequently provide an important source for industrial ligninolytic biocatalysts. Recently, it has been shown that some syringyl-type phenolics have potential as industrial co-oxidants or mediators, in laccase-catalyzed modification of lignocellulosic material. We have now studied the effect of such mediators with ligninolytic peroxidases on oxidation of the most recalcitrant lignin model compounds. We found that they are able to enhance the manganese peroxidase (MnP) catalyzed oxidation reactions of small non-phenolic compounds, veratryl alcohol and veratrylglycerol β-guaiacyl ether (adlerol), which are not usually oxidized by manganese peroxidases alone. In these experiments we compared two peroxidases from white-rot fungi, MnP from Phlebia sp. Nf b19 and versatile peroxidase (VP) from Bjerkandera adusta under two oxidation conditions: (i) the Mn(III) initiated mediated oxidation by syringyl compounds and (ii) the system involving MnP-dependent lipid peroxidation, both with production of (hydrogen) peroxides in situ to maintain the peroxidase catalytic cycle. It was found that both peroxidases produced α-carbonyl oxidation product of veratryl alcohol in clearly higher yields in reactions mediated by phenoxy radicals than in lipid-peroxyl radical system. The oxidation of adlerol, on the other hand, was more efficient in lipid-peroxidation-system. VP was more efficient than MnP in the oxidation of veratryl alcohol and showed its lignin peroxidase type activity in the reaction conditions indicated by some cleavage of Cα-Cβ-bond of adlerol. Finally, the mediator assisted oxidation conditions were applied in the oxidation of synthetic lignin (DHP) and the structural analysis of the oxidized polymers showed clear modifications in the polymer outcome, e.g. the oxidation resulted in reduced amount of aliphatic hydroxyls indicated by (31)P NMR.

  8. Integrative systems and synthetic biology of cell-matrix adhesion sites

    PubMed Central

    Zamir, Eli

    2016-01-01

    ABSTRACT The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them. PMID:26853318

  9. Database Integrity Monitoring for Synthetic Vision Systems Using Machine Vision and SHADE

    NASA Technical Reports Server (NTRS)

    Cooper, Eric G.; Young, Steven D.

    2005-01-01

    In an effort to increase situational awareness, the aviation industry is investigating technologies that allow pilots to visualize what is outside of the aircraft during periods of low-visibility. One of these technologies, referred to as Synthetic Vision Systems (SVS), provides the pilot with real-time computer-generated images of obstacles, terrain features, runways, and other aircraft regardless of weather conditions. To help ensure the integrity of such systems, methods of verifying the accuracy of synthetically-derived display elements using onboard remote sensing technologies are under investigation. One such method is based on a shadow detection and extraction (SHADE) algorithm that transforms computer-generated digital elevation data into a reference domain that enables direct comparison with radar measurements. This paper describes machine vision techniques for making this comparison and discusses preliminary results from application to actual flight data.

  10. A Reduced-Order Model for Efficient Simulation of Synthetic Jet Actuators

    NASA Technical Reports Server (NTRS)

    Yamaleev, Nail K.; Carpenter, Mark H.

    2003-01-01

    A new reduced-order model of multidimensional synthetic jet actuators that combines the accuracy and conservation properties of full numerical simulation methods with the efficiency of simplified zero-order models is proposed. The multidimensional actuator is simulated by solving the time-dependent compressible quasi-1-D Euler equations, while the diaphragm is modeled as a moving boundary. The governing equations are approximated with a fourth-order finite difference scheme on a moving mesh such that one of the mesh boundaries coincides with the diaphragm. The reduced-order model of the actuator has several advantages. In contrast to the 3-D models, this approach provides conservation of mass, momentum, and energy. Furthermore, the new method is computationally much more efficient than the multidimensional Navier-Stokes simulation of the actuator cavity flow, while providing practically the same accuracy in the exterior flowfield. The most distinctive feature of the present model is its ability to predict the resonance characteristics of synthetic jet actuators; this is not practical when using the 3-D models because of the computational cost involved. Numerical results demonstrating the accuracy of the new reduced-order model and its limitations are presented.

  11. Enhanced Flight Vision Systems and Synthetic Vision Systems for NextGen Approach and Landing Operations

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Williams, Steven P.; Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Shelton, Kevin J.

    2013-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory standards and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility approach and landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O'Hare environment. Various scenarios tested the potential for using EFVS to conduct approach, landing, and roll-out operations in visibility as low as 1000 feet runway visual range (RVR). Also, SVS was tested to evaluate the potential for lowering decision heights (DH) on certain instrument approach procedures below what can be flown today. Expanding the portion of the visual segment in which EFVS can be used in lieu of natural vision from 100 feet above the touchdown zone elevation to touchdown and rollout in visibilities as low as 1000 feet RVR appears to be viable as touchdown performance was acceptable without any apparent workload penalties. A lower DH of 150 feet and/or possibly reduced visibility minima using SVS appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  12. Rewiring Cells: Synthetic biology as a tool to interrogate the organizational principles of living systems

    PubMed Central

    Bashor, Caleb J.; Horwitz, Andrew A.; Peisajovich, Sergio G.; Lim, Wendell A.

    2010-01-01

    The living cell is an incredibly complex entity, and the goal of predictively and quantitatively understanding its function is one of the next great challenges in biology. Much of what we know about the cell concerns its constituent parts, but to a great extent, we have yet to decode how these parts are organized to yield complex physiological function. Classically, we have learned about the organization of cellular networks by perturbing them through genetic or chemical means. The emerging discipline of synthetic biology offers an additional, powerful way to study systems. By rearranging the parts that comprise existing networks, we can gain valuable insight into the hierarchical logic of the networks and identify the modular building blocks that evolution uses to generate innovative function. Additionally, by building minimal “toy” networks, one can systematically explore the relationship between network space (linkages and parameters) and functional space (the system's physiological behavior). Here, we outline recent work that uses synthetic biology approaches to investigate the organization and function of cellular networks, and describe a vision for a synthetic biology toolkit that could be used to interrogate the design principles of diverse systems. PMID:20192780

  13. A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology.

    PubMed

    Grzegorczyk, Marco; Husmeier, Dirk

    2012-07-12

    An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homogeneous DBNs fail to model the non-stationarity and time-varying nature of the gene regulatory processes. Various authors have therefore recently proposed combining DBNs with multiple changepoint processes to obtain time varying dynamic Bayesian networks (TV-DBNs). However, TV-DBNs are not without problems. Gene expression time series are typically short, which leaves the model over-flexible, leading to over-fitting or inflated inference uncertainty. In the present paper, we introduce a Bayesian regularization scheme that addresses this difficulty. Our approach is based on the rationale that changes in gene regulatory processes appear gradually during an organism's life cycle or in response to a changing environment, and we have integrated this notion in the prior distribution of the TV-DBN parameters. We have extensively tested our regularized TV-DBN model on synthetic data, in which we have simulated short non-homogeneous time series produced from a system subject to gradual change. We have then applied our method to real-world gene expression time series, measured during the life cycle of Drosophila melanogaster, under artificially generated constant light condition in Arabidopsis thaliana, and from a synthetically designed strain of Saccharomyces cerevisiae exposed to a changing environment.

  14. Synthetic lethal screening in the mammalian central nervous system identifies Gpx6 as a modulator of Huntington's disease.

    PubMed

    Shema, Reut; Kulicke, Ruth; Cowley, Glenn S; Stein, Rachael; Root, David E; Heiman, Myriam

    2015-01-06

    Huntington's disease, the most common inherited neurodegenerative disease, is characterized by a dramatic loss of deep-layer cortical and striatal neurons, as well as morbidity in midlife. Human genetic studies led to the identification of the causative gene, huntingtin. Recent genomic advances have also led to the identification of hundreds of potential interacting partners for huntingtin protein and many hypotheses as to the molecular mechanisms whereby mutant huntingtin leads to cellular dysfunction and death. However, the multitude of possible interacting partners and cellular pathways affected by mutant huntingtin has complicated efforts to understand the etiology of this disease, and to date no curative therapeutic exists. To address the general problem of identifying the disease-phenotype contributing genes from a large number of correlative studies, here we develop a synthetic lethal screening methodology for the mammalian central nervous system, called SLIC, for synthetic lethal in the central nervous system. Applying SLIC to the study of Huntington's disease, we identify the age-regulated glutathione peroxidase 6 (Gpx6) gene as a modulator of mutant huntingtin toxicity and show that overexpression of Gpx6 can dramatically alleviate both behavioral and molecular phenotypes associated with a mouse model of Huntington's disease. SLIC can, in principle, be used in the study of any neurodegenerative disease for which a mouse model exists, promising to reveal modulators of neurodegenerative disease in an unbiased fashion, akin to screens in simpler model organisms.

  15. Synthetic 3D modeling of active regions and simulation of their multi-wavelength emission

    NASA Astrophysics Data System (ADS)

    Nita, Gelu M.; Fleishman, Gregory; Kuznetsov, Alexey A.; Loukitcheva, Maria A.; Viall, Nicholeen M.; Klimchuk, James A.; Gary, Dale E.

    2015-04-01

    To facilitate the study of solar active regions, we have created a synthetic modeling framework that combines 3D magnetic structures obtained from magnetic extrapolations with simplified 1D thermal models of the chromosphere, transition region, and corona. To handle, visualize, and use such synthetic data cubes to compute multi-wavelength emission maps and compare them with observations, we have undertaken a major enhancement of our simulation tools, GX_Simulator (ftp://sohoftp.nascom.nasa.gov/solarsoft/packages/gx_simulator/), developed earlier for modeling emission from flaring loops. The greatly enhanced, object-based architecture, which now runs on Windows, Mac, and UNIX platform, offers important new capabilities that include the ability to either import 3D density and temperature distribution models, or to assign to each individual voxel numerically defined coronal or chromospheric temperature and densities, or coronal Differential Emission Measure distributions. Due to these new capabilities, the GX_Simulator can now apply parametric heating models involving average properties of the magnetic field lines crossing a given voxel volume, as well as compute and investigate the spatial and spectral properties of radio (to be compared with VLA or EOVSA data), (sub-)millimeter (ALMA), EUV (AIA/SDO), and X-ray (RHESSI) emission calculated from the model. The application integrates shared-object libraries containing fast free-free, gyrosynchrotron, and gyroresonance emission codes developed in FORTRAN and C++, and soft and hard X-ray and EUV codes developed in IDL. We use this tool to model and analyze an active region and compare the synthetic emission maps obtained in different wavelengths with observations.This work was partially supported by NSF grants AGS-1250374, AGS-1262772, NASA grant NNX14AC87G, the Marie Curie International Research Staff Exchange Scheme "Radiosun" (PEOPLE-2011-IRSES-295272), RFBR grants 14-02-91157, 15-02-01089, 15-02-03717, 15

  16. Synthetic genes specifying periodic polymers modelled on the repetitive domain of wheat gliadins: conception and expression.

    PubMed

    Elmorjani, K; Thiévin, M; Michon, T; Popineau, Y; Hallet, J N; Guéguen, J

    1997-10-09

    In order to optimise new polypeptide based biomaterials, we developed a procedure for producing homoblock polypeptides using recombinant DNA technology. Synthetic genes encoding periodic polypeptides modelled on the consensus sequence of wheat gliadins (a family of wheat storage proteins) were devised to be expressed in Escherichia coli. The construction strategy followed allows the construction of three genes encoding 8, 16, and 32 copies of the PQQPY module. The optimal expression conditions in the enterobacteria were established and a convenient purification procedure was shown to be useful in recovery of sizable amounts of strictly periodic polypeptides. The identities of the synthesized polypeptides were assessed using positive cross reactions to antibodies raised against a synthetic decapeptide (PQQPYPQQPA) and amino acid composition was determined as well.

  17. Numerical modeling of the radiative transfer in a turbid medium using the synthetic iteration.

    PubMed

    Budak, Vladimir P; Kaloshin, Gennady A; Shagalov, Oleg V; Zheltov, Victor S

    2015-07-27

    In this paper we propose the fast, but the accurate algorithm for numerical modeling of light fields in the turbid media slab. For the numerical solution of the radiative transfer equation (RTE) it is required its discretization based on the elimination of the solution anisotropic part and the replacement of the scattering integral by a finite sum. The solution regular part is determined numerically. A good choice of the method of the solution anisotropic part elimination determines the high convergence of the algorithm in the mean square metric. The method of synthetic iterations can be used to improve the convergence in the uniform metric. A significant increase in the solution accuracy with the use of synthetic iterations allows applying the two-stream approximation for the regular part determination. This approach permits to generalize the proposed method in the case of an arbitrary 3D geometry of the medium.

  18. Simulation of synthetic aperture imaging ladar (SAIL) for three-dimensional target model

    NASA Astrophysics Data System (ADS)

    Yi, Ning; Wu, Zhen-Sen

    2010-11-01

    In conventional imaging laser radar, the resolution of target is constrained by the diffraction-limited, which includes the beamwidth of the laser in the target plane and the telescope's aperture. Synthetic aperture imaging Ladar (SAIL) is an imaging technique which employs aperture synthesis with coherent laser radar, the resolution is determined by the total frequency spread of the source and is independent of range, so can achieve fine resolution in long range. Ray tracing is utilized here to obtain two-dimensional scattering properties from three-dimensional geometric model of actual target, and range-doppler algorithm is used for synthetic aperture process in laser image simulation. The results show that the SAIL can support better resolution.

  19. Synthetic Genomics and Synthetic Biology Applications Between Hopes and Concerns

    PubMed Central

    König, Harald; Frank, Daniel; Heil, Reinhard; Coenen, Christopher

    2013-01-01

    New organisms and biological systems designed to satisfy human needs are among the aims of synthetic genomics and synthetic biology. Synthetic biology seeks to model and construct biological components, functions and organisms that do not exist in nature or to redesign existing biological systems to perform new functions. Synthetic genomics, on the other hand, encompasses technologies for the generation of chemically-synthesized whole genomes or larger parts of genomes, allowing to simultaneously engineer a myriad of changes to the genetic material of organisms. Engineering complex functions or new organisms in synthetic biology are thus progressively becoming dependent on and converging with synthetic genomics. While applications from both areas have been predicted to offer great benefits by making possible new drugs, renewable chemicals or clean energy, they have also given rise to concerns about new safety, environmental and socio-economic risks – stirring an increasingly polarizing debate. Here we intend to provide an overview on recent progress in biomedical and biotechnological applications of synthetic genomics and synthetic biology as well as on arguments and evidence related to their possible benefits, risks and governance implications. PMID:23997647

  20. Synthetic genomics and synthetic biology applications between hopes and concerns.

    PubMed

    König, Harald; Frank, Daniel; Heil, Reinhard; Coenen, Christopher

    2013-03-01

    New organisms and biological systems designed to satisfy human needs are among the aims of synthetic genomics and synthetic biology. Synthetic biology seeks to model and construct biological components, functions and organisms that do not exist in nature or to redesign existing biological systems to perform new functions. Synthetic genomics, on the other hand, encompasses technologies for the generation of chemically-synthesized whole genomes or larger parts of genomes, allowing to simultaneously engineer a myriad of changes to the genetic material of organisms. Engineering complex functions or new organisms in synthetic biology are thus progressively becoming dependent on and converging with synthetic genomics. While applications from both areas have been predicted to offer great benefits by making possible new drugs, renewable chemicals or clean energy, they have also given rise to concerns about new safety, environmental and socio-economic risks - stirring an increasingly polarizing debate. Here we intend to provide an overview on recent progress in biomedical and biotechnological applications of synthetic genomics and synthetic biology as well as on arguments and evidence related to their possible benefits, risks and governance implications.

  1. Analysis of Microbe-Associated Molecular Pattern-Responsive Synthetic Promoters with the Parsley Protoplast System.

    PubMed

    Kanofsky, Konstantin; Lehmeyer, Mona; Schulze, Jutta; Hehl, Reinhard

    2016-01-01

    Plants recognize pathogens by microbe-associated molecular patterns (MAMPs) and subsequently induce an immune response. The regulation of gene expression during the immune response depends largely on cis-sequences conserved in promoters of MAMP-responsive genes. These cis-sequences can be analyzed by constructing synthetic promoters linked to a reporter gene and by testing these constructs in transient expression systems. Here, the use of the parsley (Petroselinum crispum) protoplast system for analyzing MAMP-responsive synthetic promoters is described. The synthetic promoter consists of four copies of a potential MAMP-responsive cis-sequence cloned upstream of a minimal promoter and the uidA reporter gene. The reporter plasmid contains a second reporter gene, which is constitutively expressed and hence eliminates the requirement of a second plasmid used as a transformation control. The reporter plasmid is transformed into parsley protoplasts that are elicited by the MAMP Pep25. The MAMP responsiveness is validated by comparing the reporter gene activity from MAMP-treated and untreated cells and by normalizing reporter gene activity using the constitutively expressed reporter gene.

  2. Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance

    PubMed Central

    Kalluri, Udaya C; Yin, Hengfu; Yang, Xiaohan; Davison, Brian H

    2014-01-01

    Fine-tuning plant cell wall properties to render plant biomass more amenable to biofuel conversion is a colossal challenge. A deep knowledge of the biosynthesis and regulation of plant cell wall and a high-precision genome engineering toolset are the two essential pillars of efforts to alter plant cell walls and reduce biomass recalcitrance. The past decade has seen a meteoric rise in use of transcriptomics and high-resolution imaging methods resulting in fresh insights into composition, structure, formation and deconstruction of plant cell walls. Subsequent gene manipulation approaches, however, commonly include ubiquitous mis-expression of a single candidate gene in a host that carries an intact copy of the native gene. The challenges posed by pleiotropic and unintended changes resulting from such an approach are moving the field towards synthetic biology approaches. Synthetic biology builds on a systems biology knowledge base and leverages high-precision tools for high-throughput assembly of multigene constructs and pathways, precision genome editing and site-specific gene stacking, silencing and/or removal. Here, we summarize the recent breakthroughs in biosynthesis and remodelling of major secondary cell wall components, assess the impediments in obtaining a systems-level understanding and explore the potential opportunities in leveraging synthetic biology approaches to reduce biomass recalcitrance. PMID:25363806

  3. Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance.

    PubMed

    Kalluri, Udaya C; Yin, Hengfu; Yang, Xiaohan; Davison, Brian H

    2014-12-01

    Fine-tuning plant cell wall properties to render plant biomass more amenable to biofuel conversion is a colossal challenge. A deep knowledge of the biosynthesis and regulation of plant cell wall and a high-precision genome engineering toolset are the two essential pillars of efforts to alter plant cell walls and reduce biomass recalcitrance. The past decade has seen a meteoric rise in use of transcriptomics and high-resolution imaging methods resulting in fresh insights into composition, structure, formation and deconstruction of plant cell walls. Subsequent gene manipulation approaches, however, commonly include ubiquitous mis-expression of a single candidate gene in a host that carries an intact copy of the native gene. The challenges posed by pleiotropic and unintended changes resulting from such an approach are moving the field towards synthetic biology approaches. Synthetic biology builds on a systems biology knowledge base and leverages high-precision tools for high-throughput assembly of multigene constructs and pathways, precision genome editing and site-specific gene stacking, silencing and/or removal. Here, we summarize the recent breakthroughs in biosynthesis and remodelling of major secondary cell wall components, assess the impediments in obtaining a systems-level understanding and explore the potential opportunities in leveraging synthetic biology approaches to reduce biomass recalcitrance.

  4. Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems.

    PubMed

    Bashor, Caleb J; Horwitz, Andrew A; Peisajovich, Sergio G; Lim, Wendell A

    2010-01-01

    The living cell is an incredibly complex entity, and the goal of predictively and quantitatively understanding its function is one of the next great challenges in biology. Much of what we know about the cell concerns its constituent parts, but to a great extent we have yet to decode how these parts are organized to yield complex physiological function. Classically, we have learned about the organization of cellular networks by disrupting them through genetic or chemical means. The emerging discipline of synthetic biology offers an additional, powerful approach to study systems. By rearranging the parts that comprise existing networks, we can gain valuable insight into the hierarchical logic of the networks and identify the modular building blocks that evolution uses to generate innovative function. In addition, by building minimal toy networks, one can systematically explore the relationship between network structure and function. Here, we outline recent work that uses synthetic biology approaches to investigate the organization and function of cellular networks, and describe a vision for a synthetic biology toolkit that could be used to interrogate the design principles of diverse systems.

  5. Generation of topographic terrain models utilizing synthetic aperture radar and surface level data

    NASA Technical Reports Server (NTRS)

    Imhoff, Marc L. (Inventor)

    1991-01-01

    Topographical terrain models are generated by digitally delineating the boundary of the region under investigation from the data obtained from an airborne synthetic aperture radar image and surface elevation data concurrently acquired either from an airborne instrument or at ground level. A set of coregistered boundary maps thus generated are then digitally combined in three dimensional space with the acquired surface elevation data by means of image processing software stored in a digital computer. The method is particularly applicable for generating terrain models of flooded regions covered entirely or in part by foliage.

  6. Finite difference time domain electroacoustic model for synthetic jet actuators including nonlinear flow resistance.

    PubMed

    Kooijman, Gerben; Ouweltjes, Okke

    2009-04-01

    A lumped element electroacoustic model for a synthetic jet actuator is presented. The model includes the nonlinear flow resistance associated with flow separation and employs a finite difference scheme in the time domain. As opposed to more common analytical frequency domain electroacoustic models, in which the nonlinear resistance can only be considered as a constant, it allows the calculation of higher harmonics, i.e., distortion components, generated as a result of this nonlinear resistance. Model calculations for the time-averaged momentum flux of the synthetic jet as well as the radiated sound power spectrum are compared to experimental results for various configurations. It is shown that a significantly improved prediction of the momentum flux-and thus flow velocity-of the jet is obtained when including the nonlinear resistance. Here, the current model performs slightly better than an analytical model. For the power spectrum of radiated sound, a reasonable agreement is obtained when assuming a plausible slight asymmetry in the nonlinear resistance. However, results suggest that loudspeaker nonlinearities play a significant role as well in the generation of the first few higher harmonics.

  7. Gulf Coast Subsidence: Integration of Geodesy, Geophysical Modeling, and Interferometric Synthetic Aperture Radar Observations

    NASA Astrophysics Data System (ADS)

    Blom, R. G.; Chapman, B. D.; Deese, R.; Dokka, R. K.; Fielding, E. J.; Hawkins, B.; Hensley, S.; Ivins, E. R.; Jones, C. E.; Kent, J. D.; Liu, Z.; Lohman, R.; Zheng, Y.

    2012-12-01

    The vulnerability of the US Gulf Coast has received increased attention in the years since hurricanes Katrina and Rita. Agencies responsible for the long-term protection of lives and infrastructure require precise estimates of future subsidence and sea level rise. A quantitative, geophysically based methodology can provide such estimates by incorporating geological data, geodetic measurements, geophysical models of non-elastic mechanical behavior at depth, and geographically comprehensive deformation monitoring made possible with measurements from Interferometric Synthetic Aperture Radar (InSAR). To be effective, results must be available to user agencies in a format suitable for integration within existing decision-support processes. Work to date has included analysis of historical and continuing ground-based geodetic measurements. These reveal a surprising degree of complexity, including regions that are subsiding at rates faster than those considered for hurricane protection planning of New Orleans and other coastal communities (http://www.mvn.usace.army.mil/pdf/hps_verticalsettlement.pdf) as well as Louisiana's coastal restoration strategies (http://www.coast2050.gov/2050reports.htm) (Dokka, 2011, J. Geophys. Res., 116, B06403, doi:10.1029/2010JB008008). Traditional geodetic measurements provide precise information at single points, while InSAR observations provide geographically comprehensive measurements of surface deformation at lower vertical precision. Available InSAR data sources include X-, C- and L-band satellite, and NASA/JPL airborne UAVSAR L-band data. The Gulf Coast environment is very challenging for InSAR techniques, especially with systems not designed for interferometry. For example, the shorter wavelength C-band data decorrelates over short time periods requiring more elaborate time-series analysis techniques, with which we've had some success. Meanwhile, preliminary analysis of limited L-Band ALOS/PALSAR satellite data show promise

  8. Full Waveform 3D Synthetic Seismic Algorithm for 1D Layered Anelastic Models

    NASA Astrophysics Data System (ADS)

    Schwaiger, H. F.; Aldridge, D. F.; Haney, M. M.

    2007-12-01

    Numerical calculation of synthetic seismograms for 1D layered earth models remains a significant aspect of amplitude-offset investigations, surface wave studies, microseismic event location approaches, and reflection interpretation or inversion processes. Compared to 3D finite-difference algorithms, memory demand and execution time are greatly reduced, enabling rapid generation of seismic data within workstation or laptop computational environments. We have developed a frequency-wavenumber forward modeling algorithm adapted to realistic 1D geologic media, for the purpose of calculating seismograms accurately and efficiently. The earth model consists of N layers bounded by two halfspaces. Each layer/halfspace is a homogeneous and isotropic anelastic (attenuative and dispersive) solid, characterized by a rectangular relaxation spectrum of absorption mechanisms. Compressional and shear phase speeds and quality factors are specified at a particular reference frequency. Solution methodology involves 3D Fourier transforming the three coupled, second- order, integro-differential equations for particle displacements to the frequency-horizontal wavenumber domain. An analytic solution of the resulting ordinary differential system is obtained. Imposition of welded interface conditions (continuity of displacement and stress) at all interfaces, as well as radiation conditions in the two halfspaces, yields a system of 6(N+1) linear algebraic equations for the coefficients in the ODE solution. An optimized inverse 2D Fourier transform to the space domain gives the seismic wavefield on a horizontal plane. Finally, three-component seismograms are obtained by accumulating frequency spectra at designated receiver positions on this plane, followed by a 1D inverse FFT from angular frequency ω to time. Stress-free conditions may be applied at the top or bottom interfaces, and seismic waves are initiated by force or moment density sources. Examples reveal that including attenuation

  9. Synthetic Biology and Microbial Fuel Cells: Towards Self-Sustaining Life Support Systems

    NASA Technical Reports Server (NTRS)

    Hogan, John Andrew

    2014-01-01

    NASA ARC and the J. Craig Venter Institute (JCVI) collaborated to investigate the development of advanced microbial fuels cells (MFCs) for biological wastewater treatment and electricity production (electrogenesis). Synthetic biology techniques and integrated hardware advances were investigated to increase system efficiency and robustness, with the intent of increasing power self-sufficiency and potential product formation from carbon dioxide. MFCs possess numerous advantages for space missions, including rapid processing, reduced biomass and effective removal of organics, nitrogen and phosphorus. Project efforts include developing space-based MFC concepts, integration analyses, increasing energy efficiency, and investigating novel bioelectrochemical system applications

  10. Flow Physics of Synthetic Jet Interactions on a Sweptback Model with a Control Surface

    NASA Astrophysics Data System (ADS)

    Monastero, Marianne; Amitay, Michael

    2016-11-01

    Active flow control using synthetic jets can be used on aerodynamic surfaces to improve performance and increase fuel efficiency. The flowfield resulting from the interaction of the jets with a separated crossflow with a spanwise component must be understood to determine actuator spacing for aircraft integration. The current and previous work showed adjacent synthetic jets located upstream of a control surface hingeline on a sweptback model interact with each other under certain conditions. Whether these interactions are constructive or destructive is dependent on the spanwise spacing of the jets, the severity of separation over the control surface, and the magnitude of the spanwise flow. Measuring and understanding the detailed flow physics of the flow structures emanating from the synthetic jet orifices and their interactions with adjacent jets of varying spacings is the focus of this work. Wind tunnel experiments were conducted at the Rensselaer Polytechnic Institute Subsonic Wind Tunnel using stereo particle image velocimetry (SPIV) and pressure measurements to study the effect that varying the spanwise spacing has on the overall performance. Initial SPIV data gave insight into defining and understanding the mechanisms behind the beneficial or detrimental jets interactions.

  11. Evaluation of synthetic vascular grafts in a mouse carotid grafting model

    PubMed Central

    Tan, Richard P.; Michael, Praveesuda L.; Lee, Bob S. L.; Vanags, Laura Z.; Ng, Martin K. C.; Bursill, Christina A.; Wise, Steven G.

    2017-01-01

    Current animal models for the evaluation of synthetic grafts are lacking many of the molecular tools and transgenic studies available to other branches of biology. A mouse model of vascular grafting would allow for the study of molecular mechanisms of graft failure, including in the context of clinically relevant disease states. In this study, we comprehensively characterise a sutureless grafting model which facilitates the evaluation of synthetic grafts in the mouse carotid artery. Using conduits electrospun from polycaprolactone (PCL) we show the gradual development of a significant neointima within 28 days, found to be greatest at the anastomoses. Histological analysis showed temporal increases in smooth muscle cell and collagen content within the neointima, demonstrating its maturation. Endothelialisation of the PCL grafts, assessed by scanning electron microscopy (SEM) analysis and CD31 staining, was near complete within 28 days, together replicating two critical aspects of graft performance. To further demonstrate the potential of this mouse model, we used longitudinal non-invasive tracking of bone-marrow mononuclear cells from a transgenic mouse strain with a dual reporter construct encoding both luciferase and green fluorescent protein (GFP). This enabled characterisation of mononuclear cell homing and engraftment to PCL using bioluminescence imaging and histological staining over time (7, 14 and 28 days). We observed peak luminescence at 7 days post-graft implantation that persisted until sacrifice at 28 days. Collectively, we have established and characterised a high-throughput model of grafting that allows for the evaluation of key clinical drivers of graft performance. PMID:28355300

  12. Expression optimization and synthetic gene networks in cell-free systems.

    PubMed

    Karig, David K; Iyer, Sukanya; Simpson, Michael L; Doktycz, Mitchel J

    2012-04-01

    Synthetic biology offers great promise to a variety of applications through the forward engineering of biological function. Most efforts in this field have focused on employing living cells, yet cell-free approaches offer simpler and more flexible contexts. Here, we evaluate cell-free regulatory systems based on T7 promoter-driven expression by characterizing variants of TetR and LacI repressible T7 promoters in a cell-free context and examining sequence elements that determine expression efficiency. Using the resulting constructs, we then explore different approaches for composing regulatory systems, leading to the implementation of inducible negative feedback in Escherichia coli extracts and in the minimal PURE system, which consists of purified proteins necessary for transcription and translation. Despite the fact that negative feedback motifs are common and essential to many natural and engineered systems, this simple building block has not previously been implemented in a cell-free context. As a final step, we then demonstrate that the feedback systems developed using our cell-free approach can be implemented in live E. coli as well, illustrating the potential for using cell-free expression to fast track the development of live cell systems in synthetic biology. Our quantitative cell-free component characterizations and demonstration of negative feedback embody important steps on the path to harnessing biological function in a bottom-up fashion.

  13. Coherence estimation in synthetic aperture radar data based on speckle noise modeling.

    PubMed

    López-Martínez, Carlos; Pottier, Eric

    2007-02-01

    In the past we proposed a multidimensional speckle noise model to which we now include systematic phase variation effects. This extension makes it possible to define what is believed to be a novel coherence model able to identify the different sources of bias when coherence is estimated on multidimensional synthetic radar aperture (SAR) data. On the one hand, low coherence biases are basically due to the complex additive speckle noise component of the Hermitian product of two SAR images. On the other hand, the availability of the coherence model permits us to quantify the bias due to topography when multilook filtering is considered, permitting us to establish the conditions upon which information may be estimated independently of topography. Based on the coherence model, two coherence estimation approaches, aiming to reduce the different biases, are proposed. Results with simulated and experimental polarimetric and interferometric SAR data illustrate and validate both, the coherence model and the coherence estimation algorithms.

  14. Comparison of synthetic membranes in the development of an in vitro feeding system for Dermanyssus gallinae.

    PubMed

    Harrington, D W J; Guy, J H; Robinson, K; Sparagano, O A E

    2010-04-01

    Although artificial feeding models for the poultry red mite (Dermanyssus gallinae) most frequently use biological membranes consisting of day-old chick skin, there are ethical considerations associated with the use of skin. The few studies reported in the literature that have investigated the use of synthetic membranes to feed D. gallinae in vitro have reported limited success. The current study describes an investigation into the use of synthetic membranes made from either Nescofilm or rayon and silicone, used either alone or in combination with different feather or skin extracts, as well as the use of capillary tubes. In all, 12 different treatments were used, and the feeding rate of D. gallinae was compared to that of day-old chick skin. Allowing mites to feed on a membrane consisting of Nescofilm with a skin extract resulted in the highest proportion of mites feeding (32.3%), which was not significantly different to the feeding rate of mites on day-old chick skin (38.8%). This study confirms that synthetic membranes can be used to feed D. gallinae artificially. Further optimization of the membrane and mite storage conditions is still necessary, but the study demonstrates a proof of concept.

  15. Distributed and collaborative synthetic environments

    NASA Technical Reports Server (NTRS)

    Bajaj, Chandrajit L.; Bernardini, Fausto

    1995-01-01

    Fast graphics workstations and increased computing power, together with improved interface technologies, have created new and diverse possibilities for developing and interacting with synthetic environments. A synthetic environment system is generally characterized by input/output devices that constitute the interface between the human senses and the synthetic environment generated by the computer; and a computation system running a real-time simulation of the environment. A basic need of a synthetic environment system is that of giving the user a plausible reproduction of the visual aspect of the objects with which he is interacting. The goal of our Shastra research project is to provide a substrate of geometric data structures and algorithms which allow the distributed construction and modification of the environment, efficient querying of objects attributes, collaborative interaction with the environment, fast computation of collision detection and visibility information for efficient dynamic simulation and real-time scene display. In particular, we address the following issues: (1) A geometric framework for modeling and visualizing synthetic environments and interacting with them. We highlight the functions required for the geometric engine of a synthetic environment system. (2) A distribution and collaboration substrate that supports construction, modification, and interaction with synthetic environments on networked desktop machines.

  16. Fused enhanced and synthetic vision system (EVS/SVS) for low-visibility operations

    NASA Astrophysics Data System (ADS)

    Tiana, Carlo; Hennessy, Robert; Alter, Keith; Jennings, Chad

    2007-04-01

    We present an Integrated Multisensor Synthetic Imaging System (IMSIS) developed for low-visibility, low-level operations, tailored to Army rotorcraft. IMSIS optimally avails itself of a variety of image-information sources: FLIR, mm-Wave RADAR and synthetic imagery are all presented to the flying crew in real time, on a fused display. Synthetic imagery is validated in real time by a 3D terrain sensing radar, to ensure that the a priori stored database is valid, and to eliminate any possible aircraft positioning errors with respect to the database. Extensive human factor evaluations were performed on the fused display concept. All pilots agreed that IMSIS would be a valuable asset in reduced visibility conditions and that the validated SVS display was rated nearly as flyable as a good FLIR display. The pilots also indicated that the ability to select and fuse terrain information sources was an important feature. IMSIS increases situational awareness at night and in all weather conditions, while considerably reducing pilot workload compared to separately monitoring each sensor and enhancing low-level flight safety by updating the terrain in real time. While specifically designed for helicopter low-level flight and navigation, it can aid hover and touchdown and landing for both fixed and rotary wing platforms as well as aid navigation even in non-airborne domains.

  17. Aspects of Synthetic Vision Display Systems and the Best Practices of the NASA's SVS Project

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Kramer, Lynda J.; Jones, Denise R.; Young, Steven D.; Arthur, Jarvis J.; Prinzel, Lawrence J.; Glaab, Louis J.; Harrah, Steven D.; Parrish, Russell V.

    2008-01-01

    NASA s Synthetic Vision Systems (SVS) Project conducted research aimed at eliminating visibility-induced errors and low visibility conditions as causal factors in civil aircraft accidents while enabling the operational benefits of clear day flight operations regardless of actual outside visibility. SVS takes advantage of many enabling technologies to achieve this capability including, for example, the Global Positioning System (GPS), data links, radar, imaging sensors, geospatial databases, advanced display media and three dimensional video graphics processors. Integration of these technologies to achieve the SVS concept provides pilots with high-integrity information that improves situational awareness with respect to terrain, obstacles, traffic, and flight path. This paper attempts to emphasize the system aspects of SVS - true systems, rather than just terrain on a flight display - and to document from an historical viewpoint many of the best practices that evolved during the SVS Project from the perspective of some of the NASA researchers most heavily involved in its execution. The Integrated SVS Concepts are envisagements of what production-grade Synthetic Vision systems might, or perhaps should, be in order to provide the desired functional capabilities that eliminate low visibility as a causal factor to accidents and enable clear-day operational benefits regardless of visibility conditions.

  18. Characterization and three-dimensional reconstruction of synthetic bone model foams.

    PubMed

    Gómez, S; Vlad, M D; López, J; Navarro, M; Fernández, E

    2013-08-01

    Sawbones© open-cell foams with different porosity grades are being used as synthetic bone-like models for in vitro mechanical and infiltration experiments. However, a comprehensive characterization of these foams is not available and there is a lack of reliable information about them. For this reason two of these foams (Refs. 1522-505 and -507) have been characterized at the micro architectural level by scanning electron microscopy, computed tomography and image data analysis. BoneJ open software and ImageJ open software were used to obtain the characteristic histomorphometric parameters and the three dimensional virtual models of the foams. The results showed that both foams, while having different macro porosities, appeared undistinguishable at the micro scale. Moreover, the micro structural features resembled those of osteoporotic rather than healthy trabecular bone. It is concluded that Sawbones© foams behave reasonably as synthetic bone-like models. Consequently, their use is recommended for in vitro comparison purposes of both mechanical and infiltration testing performed in real vertebra. Finally, the virtual models obtained, which are available under request, can favour comparisons between future self-similar in vitro experiments and computer simulations.

  19. Development of a unique 3D interaction model of endogenous and synthetic peripheral benzodiazepine receptor ligands

    NASA Astrophysics Data System (ADS)

    Cinone, Nunzia; Höltje, Hans-Dieter; Carotti, Angelo

    2000-11-01

    Different classes of Peripheral-type Benzodiazepine Receptor (PBR) ligands were examined and common structural elements were detected and used to develop a rational binding model based on energetically allowed ligand conformations. Two lipophilic regions and one electrostatic interaction site are essential features for high affinity ligand binding, while a further lipophilic region plays an important modulator role. A comparative molecular field analysis, performed over 130 PBR ligands by means of the GRID/GOLPE methodology, led to a PLS model with both high fitting and predictive values (r2 = 0.898, Q2 = 0.761). The outcome from the 3D QSAR model and the GRID interaction fields computed on the putative endogenous PBR ligands DBI (Diazepam Binding Inhibitor) and TTN (Tetracontatetraneuropeptide) was used to identify the amino acids most probably involved in PBR binding. Three amino acids, bearing lipophilic side chains, were detected in DBI (Phe49, Leu47 and Met46) and in TTN (Phe33, Leu31 and Met30) as likely residues underlying receptor binding. Moreover, a qualitative comparison of the molecular electrostatic potentials of DBI, TTN and selected synthetic ligands indicated also similar electronic properties. Convergent results from the modeling studies of synthetic and endogenous ligands suggest a common binding mode to PBRs. This may help the rational design of new high affinity PBR ligands.

  20. Modeling and training emotional talking faces of virtual actors in synthetic movies

    NASA Astrophysics Data System (ADS)

    Karunaratne, Savant; Yan, Hong

    2000-05-01

    This paper presents an overview of a virtual actor system composed of several subsystems designed to automate some of these animation tasks. Our emphasis is on the facial animation of virtual actors. The paper specifically details the situations processor component of the framework, which is a major building block in the automatic virtual actor system. An expert system using a fuzzy knowledge-based control system is used to realize the automated system. Fuzzy linguistic rules are used to train virtual actors to know the appropriate emotions and gestures to use in different situations of a synthetic movie, the higher level parameters of which are provided by human directors. Theories of emotion, personality, dialogue, and acting, as well as empirical evidence is incorporated into our framework and knowledge bases to produce promising results.

  1. Site-Directed Mutagenesis to Improve Sensitivity of a Synthetic Two-Component Signaling System.

    PubMed

    Olshefsky, Audrey; Shehata, Laila; Kuldell, Natalie

    2016-01-01

    Two-component signaling (2CS) systems enable bacterial cells to respond to changes in their local environment, often using a membrane-bound sensor protein and a cytoplasmic responder protein to regulate gene expression. Previous work has shown that Escherichia coli's natural EnvZ/OmpR 2CS could be modified to construct a light-sensing bacterial photography system. The resulting bacterial photographs, or "coliroids," rely on a phosphotransfer reaction between Cph8, a synthetic version of EnvZ that senses red light, and OmpR. Gene expression changes can be visualized through upregulation of a LacZ reporter gene by phosphorylated OmpR. Unfortunately, basal LacZ expression leads to a detectable reporter signal even when cells are grown in the light, diminishing the contrast of the coliroids. We performed site-directed mutagenesis near the phosphotransfer site of Cph8 to isolate mutants with potentially improved image contrast. Five mutants were examined, but only one of the mutants, T541S, increased the ratio of dark/light gene expression, as measured by β-galactosidase activity. The ratio changed from 2.57 fold in the starting strain to 5.59 in the T541S mutant. The ratio decreased in the four other mutant strains we examined. The phenotype observed in the T541S mutant strain may arise because the serine sidechain is chemically similar but physically smaller than the threonine sidechain. This may minimally change the protein's local structure, but may be less sterically constrained when compared to threonine, resulting in a higher probability of a phosphotransfer event. Our initial success pairing synthetic biology and site-directed mutagenesis to optimize the bacterial photography system's performance encourages us to imagine further improvements to the performance of this and other synthetic systems, especially those based on 2CS signaling.

  2. Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking

    NASA Astrophysics Data System (ADS)

    Tsvetkov, Vladimir B.; Serbin, Alexander V.

    2014-06-01

    In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 ( HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first heptad repeat regions [ HR1]3 of viral envelope protein gp41, were pre-studied via docking in terms of newly formulated algorithm for stepwise approximation from fragments of polymeric backbone and side-group models toward real polymeric chains. In the present article the docking results were verified under molecular dynamics ( MD) modeling. In contrast with limited capabilities of the docking, the MD allowed of using much more large models of the polymeric ligands, considering flexibility of both ligand and target simultaneously. Among the synthesized polymers the dinorbornen anchors containing alternating copolymers of maleic acid were selected as the most representative ligands (possessing the top anti-HIV activity in vitro in correlation with the highest binding energy in the docking). To verify the probability of binding of the polymers with the [HR1]3 in the sites defined via docking, various starting positions of polymer chains were tried. The MD simulations confirmed the main docking-predicted priority for binding sites, and possibilities for axial and belting modes of the ligands-target interactions. Some newly MD-discovered aspects of the ligand's backbone and anchor units dynamic cooperation in binding the viral target clarify mechanisms of the synthetic polymers anti-HIV activity and drug resistance prevention.

  3. Statistical-physical model for foliage clutter in ultra-wideband synthetic aperture radar images.

    PubMed

    Banerjee, Amit; Chellappa, Rama

    2003-01-01

    Analyzing foliage-penetrating (FOPEN) ultra-wideband synthetic aperture radar (SAR) images is a challenging problem owing to the noisy and impulsive nature of foliage clutter. Indeed, many target-detection algorithms for FOPEN SAR data are characterized by high false-alarm rates. In this work, a statistical-physical model for foliage clutter is proposed that explains the presence of outliers in the data and suggests the use of symmetric alpha-stable (SalphaS) distributions for accurate clutter modeling. Furthermore, with the use of general assumptions of the noise sources and propagation conditions, the proposed model relates the parameters of the SalphaS model to physical parameters such as the attenuation coefficient and foliage density.

  4. Synthetic biology for therapeutic applications.

    PubMed

    Abil, Zhanar; Xiong, Xiong; Zhao, Huimin

    2015-02-02

    Synthetic biology is a relatively new field with the key aim of designing and constructing biological systems with novel functionalities. Today, synthetic biology devices are making their first steps in contributing new solutions to a number of biomedical challenges, such as emerging bacterial antibiotic resistance and cancer therapy. This review discusses some synthetic biology approaches and applications that were recently used in disease mechanism investigation and disease modeling, drug discovery and production, as well as vaccine development and treatment of infectious diseases, cancer, and metabolic disorders.

  5. Synthetic Biology for Therapeutic Applications

    PubMed Central

    2015-01-01

    Synthetic biology is a relatively new field with the key aim of designing and constructing biological systems with novel functionalities. Today, synthetic biology devices are making their first steps in contributing new solutions to a number of biomedical challenges, such as emerging bacterial antibiotic resistance and cancer therapy. This review discusses some synthetic biology approaches and applications that were recently used in disease mechanism investigation and disease modeling, drug discovery and production, as well as vaccine development and treatment of infectious diseases, cancer, and metabolic disorders. PMID:25098838

  6. Effects of synthetic androgens on liver function using the rabbit as a model.

    PubMed

    Hild, Sheri Ann; Attardi, Barbara J; Koduri, Sailaja; Till, Bruce A; Reel, Jerry R

    2010-01-01

    The objective of this study was to determine whether the rabbit was a suitable model to test new synthetic androgens for potential liver toxicity within a short dosing interval. Adult male rabbits were dosed orally daily on days 0-13 with 17α-methyltestosterone (MT) as a positive control and testosterone (T) as a negative control to validate this model. Synthetic androgens tested were: 7α-methyl-19-nortestosterone (MENT), dimethandrolone-undecanoate (DMAU), and 11β-methyl-19-nortestosterone-17β-dodecylcarbonate (11β-MNTDC). Serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma glutamyl transpeptidase (GGT), and sorbitol dehydrogenase (SDH), as well as clearance of intravenous injected bromsulfonphthalein (BSP) from serum on days 0, 7, and 14, were determined. As expected, T (10 mg/kg/d) did not adversely affect BSP retention or serum liver enzymes. MT (10 mg/kg/d) increased BSP retention, and AST, ALT, GGT, and SDH levels, indicating that this model could detect androgens known to be hepatotoxic. DMAU and MENT (10 mg/kg/d) increased BSP retention and all 4 serum liver enzymes as well, but the effects were less than those observed with MT at the same dose. All parameters returned to baseline 2 weeks after cessation of dosing. 11β-MNTDC at 10 mg/kg/d did not have an effect on BSP retention or liver enzymes, but a slight increase in serum GGT levels was observed in rabbits treated with 25 mg/kg/d. For the androgens that exhibited liver toxicity at 10 mg/kg/d (MT, DMAU, and MENT), a no-observed-effect level of 1 mg/kg/d was established. Overall ranking of the synthetic androgens from most to least hepatotoxic on the basis of percent BSP retention was: MT & DMAU > MENT > 11β-MNTDC. Hence, the rabbit appears to be a promising model for detection of potential liver toxicity by synthetic androgens using BSP clearance and serum liver enzyme levels as early indicators of injury.

  7. Effects of Synthetic Androgens on Liver Function Using the Rabbit as a Model*†

    PubMed Central

    Hild, Sheri Ann; Attardi, Barbara J.; Koduri, Sailaja; Till, Bruce A.; Reel, Jerry R.

    2010-01-01

    The objective of this study was to determine if the rabbit was a suitable model to test new synthetic androgens for potential liver toxicity within a short dosing interval. Adult male rabbits were dosed orally daily on days 0–13 with 17α-methyltestosterone (MT), as a positive control, and testosterone (T), as a negative control, to validate this model. Synthetic androgens tested were: 7α-methyl-19-nortestosterone (MENT), dimethandrolone-undecanoate (DMAU), and 11β-methyl-19-nortestosterone-17β-dodecylcarbonate (11β-MNTDC). Serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma glutamyl transpeptidase (GGT), and sorbitol dehydrogenase (SDH), as well as clearance of intravenous injected bromsulfonphthalein (BSP) from serum on days 0, 7 and 14, were determined. As expected, T (10 mg/kg/day) did not adversely affect BSP retention or serum liver enzymes. MT (10 mg/kg/day) increased BSP retention, and AST, ALT, GGT, and SDH levels indicating that this model could detect androgens known to be hepatotoxic. DMAU and MENT (10 mg/kg/day), increased BSP retention, and all 4 serum liver enzymes as well, but the effects were less than those observed with MT at the same dose. All parameters returned to baseline 2 weeks after cessation of dosing. 11β-MNTDC at 10 mg/kg/day did not have an effect on BSP retention or liver enzymes, but a slight increase in serum GGT levels was observed in rabbits treated with 25 mg/kg/day. For the androgens that exhibited liver toxicity at 10 mg/kg/day (MT, DMAU, and MENT), a no observed effect level (NOEL) of 1 mg/kg/day was established. Overall ranking of the synthetic androgens from most to least hepatotoxic based on %BSP retention was: MT ≫ DMAU > MENT > 11β-MNTDC. Hence, the rabbit appears to be a promising model for detection of potential liver toxicity by synthetic androgens using BSP clearance and serum liver enzyme levels as early indicators of injury. PMID:20378929

  8. Design and performance of a small-animal imaging system using synthetic collimation

    NASA Astrophysics Data System (ADS)

    Havelin, R. J.; Miller, B. W.; Barrett, H. H.; Furenlid, L. R.; Murphy, J. M.; Dwyer, R. M.; Foley, M. J.

    2013-05-01

    This work outlines the design and construction of a single-photon emission computed tomography imaging system based on the concept of synthetic collimation. A focused multi-pinhole collimator is constructed using rapid-prototyping and casting techniques. The collimator projects the centre of the field of view (FOV) through 46 pinholes when the detector is adjacent to the collimator, with the number reducing towards the edge of the FOV. The detector is then moved further from the collimator to increase the magnification of the system. The object distance remains constant, and each new detector distance is a new system configuration. The level of overlap of the pinhole projections increases as the system magnification increases, but the number of projections subtended by the detector is reduced. There is no rotation in the system; a single tomographic angle is used in each system configuration. Image reconstruction is performed using maximum-likelihood expectation-maximization and an experimentally measured system matrix. The system matrix is measured for each configuration on a coarse grid, using a point source. The pinholes are individually identified and tracked, and a Gaussian fit is made to each projection. The coefficients of these fits are used to interpolate the system matrix. The system is validated experimentally with a hot-rod phantom. The Fourier crosstalk matrix is also measured to provide an estimate of the average spatial resolution along each axis over the entire FOV. The 3D synthetic-collimator image is formed by estimating the activity distribution within the FOV and summing the activities in the voxels along the axis perpendicular to the collimator face.

  9. A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes.

    PubMed

    Gorochowski, Thomas E; Avcilar-Kucukgoze, Irem; Bovenberg, Roel A L; Roubos, Johannes A; Ignatova, Zoya

    2016-07-15

    Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular resources is dedicated to protein translation. Synthetic biology often exploits these resources in executing orthogonal genetic circuits, yet the burden this places on the cell is rarely considered. Here, we develop a minimal model of ribosome allocation dynamics capturing the demands on translation when expressing a synthetic construct together with endogenous genes required for the maintenance of cell physiology. Critically, it contains three key variables related to design parameters of the synthetic construct covering transcript abundance, translation initiation rate, and elongation time. We show that model-predicted changes in ribosome allocation closely match experimental shifts in synthetic protein expression rate and cellular growth. Intriguingly, the model is also able to accurately infer transcript levels and translation times after further exposure to additional ambient stress. Our results demonstrate that a simple model of resource allocation faithfully captures the redistribution of protein synthesis resources when faced with the burden of synthetic gene expression and environmental stress. The tractable nature of the model makes it a versatile tool for exploring the guiding principles of efficient heterologous expression and the indirect interactions that can arise between synthetic circuits and their host chassis because of competition for shared translational resources.

  10. Synthetic aperture radar image segmentation based on edge-region active contour model

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Wen, Xianbin; Xu, Haixia; Meng, Qingxia

    2016-07-01

    An energy functional is proposed based on an edge-region active contour model for synthetic aperture radar (SAR) image segmentation. The proposed energy functional not only has a desirable property to process inhomogeneous regions in SAR images, but also shows satisfactory convergence speed. Our proposed energy functional consists of two main energy terms: an edge-region term and a regularization term. The edge-region term is derived from a Gamma model and gradient term model, which can process the speckle noises and drive the motion of the curves toward desired locations. The regularization term is not only able to maintain a desired shape of the evolution curves but also has a strong smoothing curve effect and avoid the occurrence of small, isolated regions in the final segmentation. Finally, the gradient descent flow method is introduced for minimizing our energy functional. A desirable feature of the proposed method is that it is not sensitive to the contour initialization. Compared with other methods, experimental results show that the proposed approach has promising edge detection results on the synthetic and real SAR images.

  11. The nuclear uptake and retention of a synthetic progestin in the cardiovascular system of the baboon.

    PubMed

    Sheridan, P J; McGill, H C

    1984-06-01

    It has long been known that there is a sexual dimorphism in the incidence of coronary heart disease. This observation, together with more recent reports of increased cardiovascular disease associated with the use of oral contraceptives, led to a search for steroid receptors in the cardiovascular system. In this study we examined the nuclear uptake and retention of a synthetic progestin in the cardiovascular system of the baboons. Long term oophorectomized baboons were primed with estradiol benzoate for 3 days before the experiment (50 micrograms/kg, im) and adrenalectomized 2 days before the experiment. On the day of the experiment, the animals were injected under anesthesia with 2.5 micrograms/kg BW [3H]ORG 2058 (16 alpha-ethyl-21-hydroxy-19-nor-[6,7-3H]pregn-4-ene-3,20-dione) or with [3H] ORG 2058 plus a 1000-fold excess of unlabeled progesterone (control). One hour after the injection, the animals were rapidly exsanguinated, and parts of the cardiovascular system were removed and processed for autoradiography. Localization of the synthetic progestin was found in nuclei of between 25-75% of all smooth muscle cells of the media of all arteries examined and to a lesser extent in the nuclei of the fibroblasts and others cells of the adventitia. Localization of the synthetic progestin in the heart was limited to approximately 1% of the myocardial cells and less than 5% of interstitial cell nuclei. The pattern of localization found differs from that for estrogen and androgen and suggests the possible presence of estrogen-independent progesterone receptors in smooth muscle cells of the media of the aorta and coronary arteries.

  12. Nnuclear uptake and retention of a synthetic progestin in the cardiovascular system of the baboon

    SciTech Connect

    Sheridan, P.J.; McGill, H.C. Jr.

    1984-06-01

    It has long been known that there is a sexual dimorphism in the incidence of coronary heart disease. This observation, together with more recent reports of increased cardiovascular disease associated with the use of oral contraceptives, led to a search for steroid receptors in the cardiovascular system. In this study the nuclear uptake and retention of a synthetic progestin was examined in the cardiovascular system of the baboons. Long term oophorectomized baboons were primed with estradiol benzoate for 3 days before the experiment (50 micrograms/kg, im) and adrenalectomized 2 days before the experiment. On the day of the experiment, the animals were injected under anesthesia with 2.5 micrograms/kg BW (/sup 3/H)ORG 2058 (16 alpha-ethyl-21-hydroxy-19-nor-(6,7-/sup 3/H)pregn-4-ene-3,20-dione) or with (/sup 3/H) ORG 2058 plus a 1000-fold excess of unlabeled progesterone (control). One hour after the injection, the animals were rapidly exsanguinated, and parts of the cardiovascular system were removed and processed for autoradiography. Localization of the synthetic progestin was found in nuclei of between 25-75% of all smooth muscle cells of the media of all arteries examined and to a lesser extent in the nuclei of the fibroblasts and others cells of the adventitia. Localization of the synthetic progestin in the heart was limited to approximately 1% of the myocardial cells and less than 5% of interstitial cell nuclei. The pattern of localization found differs from that for estrogen and androgen and suggests the possible presence of estrogen-independent progesterone receptors in smooth muscle cells of the media of the aorta and coronary arteries.

  13. Site-Directed Mutagenesis to Improve Sensitivity of a Synthetic Two-Component Signaling System

    PubMed Central

    Kuldell, Natalie

    2016-01-01

    Two-component signaling (2CS) systems enable bacterial cells to respond to changes in their local environment, often using a membrane-bound sensor protein and a cytoplasmic responder protein to regulate gene expression. Previous work has shown that Escherichia coli’s natural EnvZ/OmpR 2CS could be modified to construct a light-sensing bacterial photography system. The resulting bacterial photographs, or “coliroids,” rely on a phosphotransfer reaction between Cph8, a synthetic version of EnvZ that senses red light, and OmpR. Gene expression changes can be visualized through upregulation of a LacZ reporter gene by phosphorylated OmpR. Unfortunately, basal LacZ expression leads to a detectable reporter signal even when cells are grown in the light, diminishing the contrast of the coliroids. We performed site-directed mutagenesis near the phosphotransfer site of Cph8 to isolate mutants with potentially improved image contrast. Five mutants were examined, but only one of the mutants, T541S, increased the ratio of dark/light gene expression, as measured by β-galactosidase activity. The ratio changed from 2.57 fold in the starting strain to 5.59 in the T541S mutant. The ratio decreased in the four other mutant strains we examined. The phenotype observed in the T541S mutant strain may arise because the serine sidechain is chemically similar but physically smaller than the threonine sidechain. This may minimally change the protein’s local structure, but may be less sterically constrained when compared to threonine, resulting in a higher probability of a phosphotransfer event. Our initial success pairing synthetic biology and site-directed mutagenesis to optimize the bacterial photography system’s performance encourages us to imagine further improvements to the performance of this and other synthetic systems, especially those based on 2CS signaling. PMID:26799494

  14. In vivo visualization of robotically implemented synthetic tracked aperture ultrasound (STRATUS) imaging system using curvilinear array

    NASA Astrophysics Data System (ADS)

    Zhang, Haichong K.; Aalamifar, Fereshteh; Boctor, Emad M.

    2016-04-01

    Synthetic aperture for ultrasound is a technique utilizing a wide aperture in both transmit and receive to enhance the ultrasound image quality. The limitation of synthetic aperture is the maximum available aperture size limit determined by the physical size of ultrasound probe. We propose Synthetic-Tracked Aperture Ultrasound (STRATUS) imaging system to overcome the limitation by extending the beamforming aperture size through ultrasound probe tracking. With a setup involving a robotic arm, the ultrasound probe is moved using the robotic arm, while the positions on a scanning trajectory are tracked in real-time. Data from each pose are synthesized to construct a high resolution image. In previous studies, we have demonstrated the feasibility through phantom experiments. However, various additional factors such as real-time data collection or motion artifacts should be taken into account when the in vivo target becomes the subject. In this work, we build a robot-based STRATUS imaging system with continuous data collection capability considering the practical implementation. A curvilinear array is used instead of a linear array to benefit from its wider capture angle. We scanned human forearms under two scenarios: one submerged the arm in the water tank under 10 cm depth, and the other directly scanned the arm from the surface. The image contrast improved 5.51 dB, and 9.96 dB for the underwater scan and the direct scan, respectively. The result indicates the practical feasibility of STRATUS imaging system, and the technique can be potentially applied to the wide range of human body.

  15. New Synthetic Biology Tools to Track Microbial Dynamics in the Earth System

    NASA Astrophysics Data System (ADS)

    Silberg, J. J.; Masiello, C. A.; Cheng, H. Y.

    2015-12-01

    Microbes drive processes in the Earth system far exceeding their physical scale, mediating significant fluxes in the global C and N cycles. The tools of synthetic biology have the potential to significantly improve our understanding of microbes' role in the Earth system; however, these tools have not yet seen wide laboratory use because synthetically "programmed" microbes typically report by fluorescing (expressing green fluorescent protein), making them challenging to deploy into many Earth materials, the majority of which are not transparent and are heterogeneous (soils, sediments, and biomass). We are developing a new suite of biosensors that report instead by releasing gases. We will provide an overview of the use of gas-reporting biosensors in biogeochemistry and will report the development of the systematics of these sensors. These sensors will make tractable the testing of gene expression hypotheses derived from metagenomics data. Examples of processes that could be tracked non-invasively with gas sensors include coordination of biofilm formation, nitrification, rhizobial infection of plant roots, and at least some forms of methanogenesis, all of which are managed by an easily-engineered cell-cell communication system. Another relatively simple process to track with gas sensors is horizontal gene transfer. Successful development of gas biosensors for Earth science applications will require addressing issues including: engineering the intensity and selectivity of microbial gas production to maximize the signal to noise using the tools of synthetic biology; normalizing the gas reporter signal to cell population size, since the number of cells and gene expression both contribute to gas production; managing gas diffusion effects on signal shape; and developing multiple gases that can be used in parallel to report on multiple biological processes in parallel. We will report on progress addressing each of these issues.

  16. Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology.

    PubMed

    Sun, Zachary Z; Hayes, Clarmyra A; Shin, Jonghyeon; Caschera, Filippo; Murray, Richard M; Noireaux, Vincent

    2013-09-16

    Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform. This is useful for expressing proteins and genetic circuits in a controlled manner as well as for providing a prototyping environment for synthetic biology. To achieve the latter goal, cell-free expression systems that preserve endogenous Escherichia coli transcription-translation mechanisms are able to more accurately reflect in vivo cellular dynamics than those based on T7 RNA polymerase transcription. We describe the preparation and execution of an efficient endogenous E. coli based transcription-translation (TX-TL) cell-free expression system that can produce equivalent amounts of protein as T7-based systems at a 98% cost reduction to similar commercial systems. The preparation of buffers and crude cell extract are described, as well as the execution of a three tube TX-TL reaction. The entire protocol takes five days to prepare and yields enough material for up to 3000 single reactions in one preparation. Once prepared, each reaction takes under 8 hr from setup to data collection and analysis. Mechanisms of regulation and transcription exogenous to E. coli, such as lac/tet repressors and T7 RNA polymerase, can be supplemented. Endogenous properties, such as mRNA and DNA degradation rates, can also be adjusted. The TX-TL cell-free expression system has been demonstrated for large-scale circuit assembly, exploring biological phenomena, and expression of proteins under both T7- and endogenous promoters. Accompanying mathematical models are available. The resulting system has unique applications in synthetic biology as a prototyping environment, or "TX-TL biomolecular breadboard."

  17. Crystal chemistry of natural and synthetic trioctahedral micas: Exploring the limits of geometric crystal chemical models

    NASA Astrophysics Data System (ADS)

    Mercier, Patrick H. J.

    Seventy-five synthetic powder trioctahedral mica samples (between Mg, Co, Ni, and Fe end members, with different degrees of oxidation, vacancy and Al/Si contents, and including an OH/F substitution series) were studied by room-temperature powder X-ray diffraction. The iron-bearing samples were studied by 57Fe Mossbauer spectroscopy. Subsets of the samples were also characterized by scanning electron microscopy combined with energy dispersive spectroscopy, optical microscopy, X-ray fluorescence spectroscopy, and gas chromatography. Lattice parameters (refined under the 1M stacking polytype, space group C2/m) were determined for all powder samples and iron site populations ([4]Fe 3+, [6]Fe2+, and [6]Fe 2+) were obtained from Mossbauer spectroscopy. The relation (c/a)cosbeta* = 113 was found to hold exactly (within experimental error) for all synthetic powders whereas it does not hold in general for synthetic and natural 1M single-crystals. The above relation is predicted to hold for geometric home-octahedral sheets (having equal M1 and M2 site bond lengths) and not to hold for geometric meso-octahedral sheets (having unequal M1 and M2 site bond lengths). The counter-rotation of the M2 site of 1M single-crystals exactly (within experimental error) follows the geometric meso-octahedral sheet model, which, assuming a uniform octahedral sheet height and site-specific M1 and M2 bond lengths, predicts site-specific flattening angles and a counter-rotation angle for the M2 site which is uniquely determined by the bond length difference between the M1 and M2 sites. A geometric meso-octahedral 2:1 layer silicate was shown to require corrugated tetrahedral sheets composed of bond-distorted tetrahedra. Key geometric meso-octahedral distortions in 1M single-crystals were identified and elucidated: (i) intra-layer top-bottom displacements within a TOT layer; and (ii) a tetrahedral bending angle between the apical bond and the pyramidal base formed by the three basal bonds. Plots

  18. Synthetic Scene Generation of the Stennis V and V Target Range for the Calibration of Remote Sensing Systems

    NASA Technical Reports Server (NTRS)

    Cao, Chang-Yong; Blonski, Slawomir; Ryan, Robert; Gasser, Jerry; Zanoni, Vicki

    1999-01-01

    The verification and validation (V&V) target range developed at Stennis Space Center is a useful test site for the calibration of remote sensing systems. In this paper, we present a simple algorithm for generating synthetic radiance scenes or digital models of this target range. The radiation propagation for the target in the solar reflective and thermal infrared spectral regions is modeled using the atmospheric radiative transfer code MODTRAN 4. The at-sensor, in-band radiance and spectral radiance for a given sensor at a given altitude is predicted. Software is developed to generate scenes with different spatial and spectral resolutions using the simulated at-sensor radiance values. The radiometric accuracy of the simulation is evaluated by comparing simulated with AVIRIS acquired radiance values. The results show that in general there is a good match between AVIRIS sensor measured and MODTRAN predicted radiance values for the target despite the fact that some anomalies exist. Synthetic scenes provide a cost-effective way for in-flight validation of the spatial and radiometric accuracy of the data. Other applications include mission planning, sensor simulation, and trade-off analysis in sensor design.

  19. Synthetic Biology and the U.S. Biotechnology Regulatory System: Challenges and Options

    SciTech Connect

    Carter, Sarah R.; Rodemeyer, Michael; Garfinkel, Michele S.; Friedman, Robert M.

    2014-05-01

    Synthetic Biology and the U.S. Biotechnology Regulatory System: Challenges and Options Sarah R. Carter, Ph.D., J. Craig Venter Institute; Michael Rodemeyer, J.D., University of Virginia; Michele S. Garfinkel, Ph.D., EMBO; Robert M. Friedman, Ph.D., J. Craig Venter Institute In recent years, a range of genetic engineering techniques referred to as “synthetic biology” has significantly expanded the tool kit available to scientists and engineers, providing them with far greater capabilities to engineer organisms than previous techniques allowed. The field of synthetic biology includes the relatively new ability to synthesize long pieces of DNA from chemicals, as well as improved methods for genetic manipulation and design of genetic pathways to achieve more precise control of biological systems. These advances will help usher in a new generation of genetically engineered microbes, plants, and animals. The JCVI Policy Center team, along with researchers at the University of Virginia and EMBO, examined how well the current U.S. regulatory system for genetically engineered products will handle the near-term introduction of organisms engineered using synthetic biology. In particular, the focus was on those organisms intended to be used or grown directly in the environment, outside of a contained facility. The study concludes that the U.S. regulatory agencies have adequate legal authority to address most, but not all, potential environmental, health and safety concerns posed by these organisms. Such near-term products are likely to represent incremental changes rather than a marked departure from previous genetically engineered organisms. However, the study also identified two key challenges for the regulatory system, which are detailed in the report. First, USDA’s authority over genetically engineered plants depends on the use of an older engineering technique that is no longer necessary for many applications. The shift to synthetic biology and other newer genetic

  20. Ion mobility-mass spectrometry strategies for untargeted systems, synthetic, and chemical biology

    PubMed Central

    May, Jody C.; Goodwin, Cody R.; McLean, John A.

    2014-01-01

    Contemporary strategies that concentrate on only one or a handful of molecular targets limits the utility of the information gained for diagnostic and predictive purposes. Recent advances in the sensitivity, speed, and precision of measurements obtained from ion mobility coupled to mass spectrometry (IM-MS) have accelerated the utility of IM-MS in untargeted, discovery-driven studies in biology. Perhaps most evident is the impact that such wide-scale discovery capabilities have yielded in the areas of systems, synthetic, and chemical biology, where the need for comprehensive, hypothesis-driving studies from multidimensional and unbiased data is required. PMID:25462629

  1. Synthetic ultrashort cationic lipopeptides induce systemic plant defense responses against bacterial and fungal pathogens.

    PubMed

    Brotman, Yariv; Makovitzki, Arik; Shai, Yechiel; Chet, Ilan; Viterbo, Ada

    2009-08-01

    A new family of synthetic, membrane-active, ultrashort lipopeptides composed of only four amino acids linked to fatty acids was tested for the ability to induce systemic resistance and defense responses in plants. We found that two peptides wherein the third residue is a d-enantiomer (italic), C16-KKKK and C16-KLLK, can induce medium alkalinization of tobacco suspension-cultured cells and expression of defense-related genes in cucumber and Arabidopsis seedlings. Moreover, these compounds can prime systemic induction of antimicrobial compounds in cucumber leaves similarly to the plant-beneficial fungus Trichoderma asperellum T203 and provide systemic protection against the phytopathogens Botrytis cinerea B05, Pseudomonas syringae pv. lachrimans, and P. syringae pv. tomato DC3000. Thus, short cationic lipopeptides are a new category of compounds with potentially high utility in the induction of systemic resistance in plants.

  2. Alaskan flight trials of a synthetic vision system for instrument landings of a piston twin aircraft

    NASA Astrophysics Data System (ADS)

    Barrows, Andrew K.; Alter, Keith W.; Jennings, Chad W.; Powell, J. D.

    1999-07-01

    Stanford University has developed a low-cost prototype synthetic vision system and flight tested it onboard general aviation aircraft. The display aids pilots by providing an 'out the window' view, making visualization of the desired flight path a simple task. Predictor symbology provides guidance on straight and curved paths presented in a 'tunnel- in-the-sky' format. Based on commodity PC hardware to achieve low cost, the Tunnel Display system uses differential GPS (typically from Stanford prototype Wide Area Augmentation System hardware) for positioning and GPS-aided inertial sensors for attitude determination. The display has been flown onboard Piper Dakota and Beechcraft Queen Air aircraft at several different locations. This paper describes the system, its development, and flight trials culminating with tests in Alaska during the summer of 1998. Operational experience demonstrated the Tunnel Display's ability to increase flight- path following accuracy and situational awareness while easing the task instrument flying.

  3. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories

    PubMed Central

    Amores, Gerardo Ruiz; Guazzaroni, María-Eugenia; Arruda, Letícia Magalhães; Silva-Rocha, Rafael

    2016-01-01

    Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant biomass and this feature has a tremendous potential for biofuel production from renewable sources. The past decades have been marked by a remarkable progress in the genetic engineering of fungi to generate industry-compatible strains needed for some biotech applications. In this sense, progress in this field has been marked by the utilization of high-throughput techniques to gain deep understanding of the molecular machinery controlling the physiology of these organisms, starting thus the Systems Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized promoters in order to construct new expression systems with enhanced performance under the conditions of interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact in the final performance of the process of interest. We expect to provide here some new directions to drive future research directed to the construction of high-performance, engineered fungal strains working as microbial cell factories. PMID:27226765

  4. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories.

    PubMed

    Amores, Gerardo Ruiz; Guazzaroni, María-Eugenia; Arruda, Letícia Magalhães; Silva-Rocha, Rafael

    2016-04-01

    Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant biomass and this feature has a tremendous potential for biofuel production from renewable sources. The past decades have been marked by a remarkable progress in the genetic engineering of fungi to generate industry-compatible strains needed for some biotech applications. In this sense, progress in this field has been marked by the utilization of high-throughput techniques to gain deep understanding of the molecular machinery controlling the physiology of these organisms, starting thus the Systems Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized promoters in order to construct new expression systems with enhanced performance under the conditions of interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact in the final performance of the process of interest. We expect to provide here some new directions to drive future research directed to the construction of high-performance, engineered fungal strains working as microbial cell factories.

  5. Evaluation of Synthetic Self-Oscillating Models of the Vocal Folds

    NASA Astrophysics Data System (ADS)

    Hubler, Elizabeth P.; Weiland, Kelley S.; Hancock, Adrienne B.; Plesniak, Michael W.

    2013-11-01

    Approximately 30% of people will suffer from a voice disorder at some point in their lives. The probability doubles for those who rely heavily on their voice, such as teachers and singers. Synthetic vocal fold (VF) models are fabricated and evaluated experimentally in a vocal tract simulator to replicate physiological conditions. Pressure measurements are acquired along the vocal tract and high-speed images are captured at varying flow rates during VF oscillation to facilitate understanding of the characteristics of healthy and damaged VFs. The images are analyzed using a videokymography line-scan technique that has been used to examine VF motion and mucosal wave dynamics in vivo. Clinically relevant parameters calculated from the volume-velocity output of a circumferentially-vented mask (Rothenberg mask) are compared to patient data. This study integrates speech science with engineering and flow physics to overcome current limitations of synthetic VF models to properly replicate normal phonation in order to advance the understanding of resulting flow features, progression of pathological conditions, and medical techniques. Supported by the GW Institute for Biomedical Engineering (GWIBE) and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  6. Awareness and Detection of Traffic and Obstacles Using Synthetic and Enhanced Vision Systems

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.

    2012-01-01

    Research literature are reviewed and summarized to evaluate the awareness and detection of traffic and obstacles when using Synthetic Vision Systems (SVS) and Enhanced Vision Systems (EVS). The study identifies the critical issues influencing the time required, accuracy, and pilot workload associated with recognizing and reacting to potential collisions or conflicts with other aircraft, vehicles and obstructions during approach, landing, and surface operations. This work considers the effect of head-down display and head-up display implementations of SVS and EVS as well as the influence of single and dual pilot operations. The influences and strategies of adding traffic information and cockpit alerting with SVS and EVS were also included. Based on this review, a knowledge gap assessment was made with recommendations for ground and flight testing to fill these gaps and hence, promote the safe and effective implementation of SVS/EVS technologies for the Next Generation Air Transportation System

  7. Synthetic Astrobiology

    NASA Technical Reports Server (NTRS)

    Rothschild, Lynn J.

    2015-01-01

    Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

  8. Synthetic Astrobiology

    NASA Technical Reports Server (NTRS)

    Rothschild, Lynn J.

    2016-01-01

    Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. And what about the limits for life? Can we create organisms that expand the envelope for life? In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

  9. Terrain Portrayal for Synthetic Vision Systems Head-Down Displays Evaluation Results: Compilation of Pilot Transcripts

    NASA Technical Reports Server (NTRS)

    Hughes, Monica F.; Glaab, Louis J.

    2007-01-01

    The Terrain Portrayal for Head-Down Displays (TP-HDD) simulation experiment addressed multiple objectives involving twelve display concepts (two baseline concepts without terrain and ten synthetic vision system (SVS) variations), four evaluation maneuvers (two en route and one approach maneuver, plus a rare-event scenario), and three pilot group classifications. The TP-HDD SVS simulation was conducted in the NASA Langley Research Center's (LaRC's) General Aviation WorkStation (GAWS) facility. The results from this simulation establish the relationship between terrain portrayal fidelity and pilot situation awareness, workload, stress, and performance and are published in the NASA TP entitled Terrain Portrayal for Synthetic Vision Systems Head-Down Displays Evaluation Results. This is a collection of pilot comments during each run of the TP-HDD simulation experiment. These comments are not the full transcripts, but a condensed version where only the salient remarks that applied to the scenario, the maneuver, or the actual research itself were compiled.

  10. Attribute Assignment to a Synthetic Population in Support of Agent-Based Disease Modeling.

    PubMed

    Cajka, James C; Cooley, Philip C; Wheaton, William D

    2010-09-01

    Communicable-disease transmission models are useful for the testing of prevention and intervention strategies. Agent-based models (ABMs) represent a new and important class of the many types of disease transmission models in use. Agent-based disease models benefit from their ability to assign disease transmission probabilities based on characteristics shared by individual agents. These shared characteristics allow ABMs to apply transmission probabilities when agents come together in geographic space. Modeling these types of social interactions requires data, and the results of the model largely depend on the quality of these input data. We initially generated a synthetic population for the United States, in support of the Models of Infectious Disease Agent Study. Subsequently, we created shared characteristics to use in ABMs. The specific goals for this task were to assign the appropriately aged populations to schools, workplaces, and public transit. Each goal presented its own challenges and problems; therefore, we used different techniques to create each type of shared characteristic. These shared characteristics have allowed disease models to more realistically predict the spread of disease, both spatially and temporally.

  11. Nuclear Test Depth Determination with Synthetic Modelling: Global Analysis from PNEs to DPRK-2016

    NASA Astrophysics Data System (ADS)

    Rozhkov, Mikhail; Stachnik, Joshua; Baker, Ben; Epiphansky, Alexey; Bobrov, Dmitry

    2016-04-01

    Seismic event depth determination is critical for the event screening process at the International Data Center, CTBTO. A thorough determination of the event depth can be conducted mostly through additional special analysis because the IDC's Event Definition Criteria is based, in particular, on depth estimation uncertainties. This causes a large number of events in the Reviewed Event Bulletin to have depth constrained to the surface making the depth screening criterion not applicable. Further it may result in a heavier workload to manually distinguish between subsurface and deeper crustal events. Since the shape of the first few seconds of signal of very shallow events is very sensitive to the depth phases, cross correlation between observed and theoretic seismograms can provide a basis for the event depth estimation, and so an expansion to the screening process. We applied this approach mostly to events at teleseismic and partially regional distances. The approach was found efficient for the seismic event screening process, with certain caveats related mostly to poorly defined source and receiver crustal models which can shift the depth estimate. An adjustable teleseismic attenuation model (t*) for synthetics was used since this characteristic is not known for most of the rays we studied. We studied a wide set of historical records of nuclear explosions, including so called Peaceful Nuclear Explosions (PNE) with presumably known depths, and recent DPRK nuclear tests. The teleseismic synthetic approach is based on the stationary phase approximation with hudson96 program, and the regional modelling was done with the generalized ray technique by Vlastislav Cerveny modified to account for the complex source topography. The software prototype is designed to be used for the Expert Technical Analysis at the IDC. With this, the design effectively reuses the NDC-in-a-Box code and can be comfortably utilized by the NDC users. The package uses Geotool as a front-end for data

  12. A model for forming airborne synthetic aperture radar images of underground targets

    SciTech Connect

    Doerry, A.W.

    1994-01-01

    Synthetic Aperture Radar (SAR) from an airborne platform has been proposed for imaging targets beneath the earth`s surface. The propagation of the radar`s energy within the ground, however, is much different than in the earth`s atmosphere. The result is signal refraction, echo delay, propagation losses, dispersion, and volumetric scattering. These all combine to make SAR image formation from an airborne platform much more challenging than a surface imaging counterpart. This report treats the ground as a lossy dispersive half-space, and presents a model for the radar echo based on measurable parameters. The model is then used to explore various imaging schemes, and image properties. Dynamic range is discussed, as is the impact of loss on dynamic range. Modified window functions are proposed to mitigate effects of sidelobes of shallow targets overwhelming deeper targets.

  13. Dynamic Changes in Local Protein Synthetic Machinery in Regenerating Central Nervous System Axons after Spinal Cord Injury.

    PubMed

    Sachdeva, Rahul; Farrell, Kaitlin; McMullen, Mary-Katharine; Twiss, Jeffery L; Houle, John D

    2016-01-01

    Intra-axonal localization of mRNAs and protein synthesis machinery (PSM) endows neurons with the capacity to generate proteins locally, allowing precise spatiotemporal regulation of the axonal response to extracellular stimuli. A number of studies suggest that this local translation is a promising target to enhance the regenerative capacity of damaged axons. Using a model of central nervous system (CNS) axons regenerating into intraspinal peripheral nerve grafts (PNGs) we established that adult regenerating CNS axons contain several different mRNAs and protein synthetic machinery (PSM) components in vivo. After lower thoracic level spinal cord transection, ascending sensory axons regenerate into intraspinal PNGs but axon growth is stalled when they reach the distal end of the PNG (3 versus 7 weeks after grafting, resp.). By immunofluorescence with optical sectioning of axons by confocal microscopy, the total and phosphorylated forms of PSMs are significantly lower in stalled compared with actively regenerating axons. Reinjury of these stalled axons increased axonal localization of the PSM proteins, indicative of possible priming for a subcellular response to axotomy. These results suggest that axons downregulate protein synthetic capacity as they cease growing, yet they retain the ability to upregulate PSM after a second injury.

  14. Dynamic Changes in Local Protein Synthetic Machinery in Regenerating Central Nervous System Axons after Spinal Cord Injury

    PubMed Central

    Sachdeva, Rahul; Farrell, Kaitlin; McMullen, Mary-Katharine; Twiss, Jeffery L.; Houle, John D.

    2016-01-01

    Intra-axonal localization of mRNAs and protein synthesis machinery (PSM) endows neurons with the capacity to generate proteins locally, allowing precise spatiotemporal regulation of the axonal response to extracellular stimuli. A number of studies suggest that this local translation is a promising target to enhance the regenerative capacity of damaged axons. Using a model of central nervous system (CNS) axons regenerating into intraspinal peripheral nerve grafts (PNGs) we established that adult regenerating CNS axons contain several different mRNAs and protein synthetic machinery (PSM) components in vivo. After lower thoracic level spinal cord transection, ascending sensory axons regenerate into intraspinal PNGs but axon growth is stalled when they reach the distal end of the PNG (3 versus 7 weeks after grafting, resp.). By immunofluorescence with optical sectioning of axons by confocal microscopy, the total and phosphorylated forms of PSMs are significantly lower in stalled compared with actively regenerating axons. Reinjury of these stalled axons increased axonal localization of the PSM proteins, indicative of possible priming for a subcellular response to axotomy. These results suggest that axons downregulate protein synthetic capacity as they cease growing, yet they retain the ability to upregulate PSM after a second injury. PMID:27375904

  15. Impact of synthetic abyssal hill roughness on resolved motions in numerical global ocean tide models

    NASA Astrophysics Data System (ADS)

    Timko, Patrick G.; Arbic, Brian K.; Goff, John A.; Ansong, Joseph K.; Smith, Walter H. F.; Melet, Angélique; Wallcraft, Alan J.

    2017-04-01

    Global models of seafloor topography have incomplete and inconsistent resolution at horizontal wavelengths less than about 10-20 km, notably due to their inability to resolve abyssal hills in areas unsurveyed by ships (that is, about 90% of the global seafloor). We investigated the impact of this unresolved bottom roughness on global numerical simulations of the HYbrid Coordinate Ocean Model (HYCOM) that are forced exclusively by the M2 and K1 internal tides. Simulations were run with horizontal resolutions of 0.08° and 0.04°, 10 isopycnal layers in the vertical direction, and two versions of bathymetry: one derived from the SRTM30_PLUS global bathymetry model, and one merging SRTM30_PLUS with a synthetic fractal surface simulating the expected roughness of abyssal hills in the 2-10 km horizontal wavelength band. Power spectra of the two bathymetry versions diverge at wavenumbers of order 4*10-4 radians/m and higher (wavelengths of order 15 km and lower), with more pronounced differences evident on the 0.04° grid, as the 0.08° grid has a more limited ability to capture bathymetric details at the abyssal hill scale. Our simulations show an increase in the amount of kinetic and potential energy in higher vertical modes, especially in the 0.04° simulation, when the synthetic roughness is added. Adding abyssal hills to the 0.04° simulation increases the M2 kinetic energy for modes 3 and 4 by 12-18% and the potential energy by 5 - 15%. Adding abyssal hills to the 0.08° simulation yields a reduced, though still measurable, impact on simulated baroclinic tidal energies. Baroclinic tidal energy conversion rates increase by up to 16% in regions of high roughness, and by up to 3.4% in the global integral. The 3.4% increase in global conversion rates in the numerical simulations is less than the 10% increase computed from a linear analysis on a 0.008° grid because of the resolution limitations of the numerical simulations. The results obtained in the present study

  16. Continuous system modeling

    NASA Technical Reports Server (NTRS)

    Cellier, Francois E.

    1991-01-01

    A comprehensive and systematic introduction is presented for the concepts associated with 'modeling', involving the transition from a physical system down to an abstract description of that system in the form of a set of differential and/or difference equations, and basing its treatment of modeling on the mathematics of dynamical systems. Attention is given to the principles of passive electrical circuit modeling, planar mechanical systems modeling, hierarchical modular modeling of continuous systems, and bond-graph modeling. Also discussed are modeling in equilibrium thermodynamics, population dynamics, and system dynamics, inductive reasoning, artificial neural networks, and automated model synthesis.

  17. Phase and extraction equilibria in water-polyethyleneglycol ethers of monoethanolamides of synthetic fatty acid-ammonium chloride systems

    NASA Astrophysics Data System (ADS)

    Lesnov, A. E.; Golovkina, A. V.; Kudryashova, O. S.; Denisova, S. A.

    2016-08-01

    Phase equilibria in layering systems of water, polyethyleneglycol ethers of monoethanolamides of synthetic fatty acids (SFAs) (synthamide-5), and ammonium chloride are studied. The possibility of using such systems for the liquid extraction of metal ions is evaluated. The effect the nature of salting-out agents has on the processes of segregation of the systems has been considered.

  18. Synthetic biology with artificially expanded genetic information systems. From personalized medicine to extraterrestrial life.

    PubMed

    Benner, Steven A; Hutter, Daniel; Sismour, A Michael

    2003-01-01

    Over 15 years ago, the Benner group noticed that the DNA alphabet need not be limited to the four standard nucleotides known in natural DNA. Rather, twelve nucleobases forming six base pairs joined by mutually exclusive hydrogen bonding patterns are possible within the geometry of the Watson-Crick pair (Fig. 1). Synthesis and studies on these compounds have brought us to the threshold of a synthetic biology, an artificial chemical system that does basic processes needed for life (in particular, Darwinian evolution), but with unnatural chemical structures. At the same time, the artificial genetic information systems (AEGIS) that we have developed have been used in FDA-approved commercial tests for managing HIV and hepatitis C infections in individual patients, and in a tool that seeks the virus for severe acute respiratory syndrome (SARS). AEGIS also supports the next generation of robotic probes to search for genetic molecules on Mars, Europa, and elsewhere where NASA probes will travel.

  19. Performance of suspended and attached growth MBR systems in treating high strength synthetic wastewater.

    PubMed

    Jamal Khan, S; Ilyas, Shazia; Javid, Sadaf; Visvanathan, C; Jegatheesan, V

    2011-05-01

    The performance of laboratory-scale attached growth (AG) and suspended growth (SG) membrane bioreactors (MBRs) was evaluated in treating synthetic wastewater simulating high strength domestic wastewater. This study investigated the influence of sponge suspended carriers in AG-MBR system, occupying 15% reactor volume, on the removal of chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP), and compared it to that of SG-MBR. Results showed that the removal efficiencies of COD, TN and TP in AG-MBR were 98%, 89% and 58%, respectively as compared to 98%, 74% and 38%, respectively in SG-MBR. Improved TN removal in AG-MBR systems was primarily based on simultaneous nitrification and denitrification (SND) process. These results infer that the presence of small bio-particles having higher microbial activity and the growth of complex biomass captured within the suspended sponge carriers resulted in improved TN and TP removal in AG-MBR.

  20. Communication-induced multistability and multirhythmicity in a synthetic multicellular system

    NASA Astrophysics Data System (ADS)

    Yi, Qizhi; Zhou, Tianshou

    2011-05-01

    Traditionally, the main role of cell-to-cell communication was thought of as synchronizing a population of cells, thereby coordinating cellular behavior. Here we show that cell density, which quantifies cellular communication, can induce multistability and multirhythmicity in a synthetic multicellular system, where individual oscillators are a combination of repressillator and hysteresis-based oscillators and are coupled through a quorum-sensing mechanism. Specifically, for moderately small cell densities, the coupled system can exhibit multistability including stable homogenous and inhomogeneous steady states. For moderately large cell densities, it has the potential to generate multirhythmicity including multimode oscillations such as an in-phase periodic solution, antiphase periodic solution, asymmetric periodic solution, mixed-mode oscillations, coexistence of periodic orbits of several different modes, and bursting oscillations such as periodic bursting, torus quasiperiodic bursting, and chaotic bursting. Such versatility of cell-to-cell communication would be beneficial for cells or organisms to live in diversely changeable environments.

  1. Study of Synthetic Vision Systems (SVS) and Velocity-vector Based Command Augmentation System (V-CAS) on Pilot Performance

    NASA Technical Reports Server (NTRS)

    Liu, Dahai; Goodric, Ken; Peak, Bob

    2006-01-01

    This study investigated the effects of synthetic vision system (SVS) concepts and advanced flight controls on single pilot performance (SPP). Specifically, we evaluated the benefits and interactions of two levels of terrain portrayal, guidance symbology, and control-system response type on SPP in the context of lower-landing minima (LLM) approaches. Performance measures consisted of flight technical error (FTE) and pilot perceived workload. In this study, pilot rating, control type, and guidance symbology were not found to significantly affect FTE or workload. It is likely that transfer from prior experience, limited scope of the evaluation task, specific implementation limitations, and limited sample size were major factors in obtaining these results.

  2. Identifying ultrasensitive HGF dose-response functions in a 3D mammalian system for synthetic morphogenesis

    PubMed Central

    Senthivel, Vivek Raj; Sturrock, Marc; Piedrafita, Gabriel; Isalan, Mark

    2016-01-01

    Nonlinear responses to signals are widespread natural phenomena that affect various cellular processes. Nonlinearity can be a desirable characteristic for engineering living organisms because it can lead to more switch-like responses, similar to those underlying the wiring in electronics. Steeper functions are described as ultrasensitive, and can be applied in synthetic biology by using various techniques including receptor decoys, multiple co-operative binding sites, and sequential positive feedbacks. Here, we explore the inherent non-linearity of a biological signaling system to identify functions that can potentially be exploited using cell genome engineering. For this, we performed genome-wide transcription profiling to identify genes with ultrasensitive response functions to Hepatocyte Growth Factor (HGF). We identified 3,527 genes that react to increasing concentrations of HGF, in Madin-Darby canine kidney (MDCK) cells, grown as cysts in 3D collagen cell culture. By fitting a generic Hill function to the dose-responses of these genes we obtained a measure of the ultrasensitivity of HGF-responsive genes, identifying a subset with higher apparent Hill coefficients (e.g. MMP1, TIMP1, SNORD75, SNORD86 and ERRFI1). The regulatory regions of these genes are potential candidates for future engineering of synthetic mammalian gene circuits requiring nonlinear responses to HGF signalling. PMID:27982133

  3. Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast

    PubMed Central

    McIsaac, R. Scott; Oakes, Benjamin L.; Wang, Xin; Dummit, Krysta A.; Botstein, David; Noyes, Marcus B.

    2013-01-01

    A general method for the dynamic control of single gene expression in eukaryotes, with no off-target effects, is a long-sought tool for molecular and systems biologists. We engineered two artificial transcription factors (ATFs) that contain Cys2His2 zinc-finger DNA-binding domains of either the mouse transcription factor Zif268 (9 bp of specificity) or a rationally designed array of four zinc fingers (12 bp of specificity). These domains were expressed as fusions to the human estrogen receptor and VP16 activation domain. The ATFs can rapidly induce a single gene driven by a synthetic promoter in response to introduction of an otherwise inert hormone with no detectable off-target effects. In the absence of inducer, the synthetic promoter is inactive and the regulated gene product is not detected. Following addition of inducer, transcripts are induced >50-fold within 15 min. We present a quantitative characterization of these ATFs and provide constructs for making their implementation straightforward. These new tools allow for the elucidation of regulatory network elements dynamically, which we demonstrate with a major metabolic regulator, Gcn4p. PMID:23275543

  4. Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.

    PubMed

    McIsaac, R Scott; Oakes, Benjamin L; Wang, Xin; Dummit, Krysta A; Botstein, David; Noyes, Marcus B

    2013-02-01

    A general method for the dynamic control of single gene expression in eukaryotes, with no off-target effects, is a long-sought tool for molecular and systems biologists. We engineered two artificial transcription factors (ATFs) that contain Cys(2)His(2) zinc-finger DNA-binding domains of either the mouse transcription factor Zif268 (9 bp of specificity) or a rationally designed array of four zinc fingers (12 bp of specificity). These domains were expressed as fusions to the human estrogen receptor and VP16 activation domain. The ATFs can rapidly induce a single gene driven by a synthetic promoter in response to introduction of an otherwise inert hormone with no detectable off-target effects. In the absence of inducer, the synthetic promoter is inactive and the regulated gene product is not detected. Following addition of inducer, transcripts are induced >50-fold within 15 min. We present a quantitative characterization of these ATFs and provide constructs for making their implementation straightforward. These new tools allow for the elucidation of regulatory network elements dynamically, which we demonstrate with a major metabolic regulator, Gcn4p.

  5. An Integrated Navigation System using GPS Carrier Phase for Real-Time Airborne Synthetic Aperture Radar (SAR)

    SciTech Connect

    Fellerhoff, J. Rick; Kim, Theodore J.; Kohler, Stewart M.

    1999-06-24

    A Synthetic Aperture Radar (SAR) requires accu- rate measurement of the motion of the imaging plat- form to produce well-focused images with minimal absolute position error. The motion measurement (MoMeas) system consists of a inertial measurement unit (IMU) and a P-code GPS receiver that outputs corrected ephemeris, L1 & L2 pseudoranges, and L1 & L2 carrier phase measurements. The unknown initial carrier phase biases to the GPS satellites are modeled as states in an extended Kalman filter and the resulting integrated navigation solution has po- sition errors that change slowly with time. Position error drifts less than 1- cm/sec have been measured from the SAR imagery for various length apertures.

  6. Effect of Synthetic Jet Actuator Spacing on the Performance Enhancement of a Vertical Tail Model

    NASA Astrophysics Data System (ADS)

    Monastero, Marianne; Rathay, Nicholas; Whalen, Edward; Amitay, Michael

    2014-11-01

    The use of synthetic-jet-based active flow control to augment the side force produced by vertical tail models through rudder separation control was experimentally investigated in the Rensselaer Polytechnic Institute Subsonic Wind Tunnel. Increasing the side force generated by the vertical tail may lead to a reduction in tail size and, therefore, less drag and fuel consumption. Stereo particle image velocimetry and aerodynamic load data were acquired with a focus on the effect of non-dimensional spacing between jets on the resulting flowfield and forces for a 1/19th scale model based on a Boeing 767 commercial airplane. For some rudder deflections, differing results with active flow control were found when force data for the 1/19th scale model were compared to force data obtained on a larger, 1/9th scale model. Actuator spacing was varied and individual jet momentum coefficient was held constant for these experiments. These results show the need for more fundamental testing to understand why jets are beneficial or detrimental to the augmented side force and how those effects scale-up. A new model was designed to enable a fundamental study of the effect on the flowfield of various jet and model parameters such as sweep angle, jets spacing, rudder chord extent, and rudder deflection.

  7. A model to estimate the methane generation rate constant in sanitary landfills using fuzzy synthetic evaluation.

    PubMed

    Garg, Anurag; Achari, Gopal; Joshi, Ramesh C

    2006-08-01

    This paper presents a model using fuzzy synthetic evaluation to estimate the methane generation rate constant, k, for landfills. Four major parameters, precipitation, temperature, waste composition and landfill depth were used as inputs to the model. Whereas, these parameters are known to impact the methane generation, mathematical relationships between them and the methane generation rate constant required to estimate methane generation in landfills, are not known. In addition, the spatial variations of k within a landfill combined with the necessity of site-specific information to estimate its value, makes k one of the most elusive parameters in the accurate prediction of methane generation within a landfill. In this paper, a fuzzy technique was used to develop a model to predict the methane generation rate constant. The model was calibrated and verified using k values from 42 locations. Data from 10 sites were used to calibrate the model and the rest were used to verify it. The model predictions are reasonably accurate. A sensitivity analysis was also conducted to investigate the effect of uncertainty in the input parameters on the generation rate constant.

  8. A novel view of modelling interactions between synthetic and biological polymers via docking

    NASA Astrophysics Data System (ADS)

    Tsvetkov, Vladimir B.; Serbin, Alexander V.

    2012-12-01

    Multipoint interactions between synthetic and natural polymers provide a promising platform for many topical applications, including therapeutic blockage of virus-specific targets. Docking may become a useful tool for modelling of such interactions. However, the rigid docking cannot be correctly applied to synthetic polymers with flexible chains. The application of flexible docking to these polymers as whole macromolecule ligands is also limited by too many possible conformations. We propose to solve this problem via stepwise flexible docking. Step 1 is docking of separate polymer components: (1) backbone units ( BU), multi-repeated along the chain, and (2) side groups ( SG) consisting of functionally active elements ( SG F ) and bridges ( SG B ) linking SG F with BU. At this step, probable binding sites locations and binding energies for the components are scored. Step 2 is docking of component-integrating models: [ BU] m , SG = SG F -SG B , BU-SG, BU-BU( SG) -BU, BU( SG) -[ BU] m -BU( SG), and [ BU var ( SG var )] m . Every modelling level yields new information, including how the linkage of various components influences on the ligand—target contacts positioning, orientation, and binding energy in step-by-step approximation to polymeric ligand motifs. Step 3 extrapolates the docking results to real-scale macromolecules. This approach has been demonstrated by studying the interactions between hetero-SG modified anionic polymers and the N-heptad repeat region tri-helix core of the human immunodeficiency virus type 1 ( HIV-1) envelope glycoprotein gp41, the key mediator of HIV-1 fusion during virus entry. The docking results are compared to real polymeric compounds, acting as HIV-1 entry inhibitors in vitro. This study clarifies the optimal macromolecular design for the viral fusion inhibition and drug resistance prevention.

  9. Constraining shallow seismic event depth via synthetic modeling for Expert Technical Analysis at the IDC

    NASA Astrophysics Data System (ADS)

    Stachnik, J.; Rozhkov, M.; Baker, B.; Bobrov, D.; Friberg, P. A.

    2015-12-01

    Depth of event is an important criterion of seismic event screening at the International Data Center, CTBTO. However, a thorough determination of the event depth can be conducted mostly through special analysis because the IDC's Event Definition Criteria is based, in particular, on depth estimation uncertainties. This causes a large number of events in the Reviewed Event Bulletin to have depth constrained to the surface. When the true origin depth is greater than that reasonable for a nuclear test (3 km based on existing observations), this may result in a heavier workload to manually distinguish between shallow and deep events. Also, IDC depth criterion is not applicable to the events with the small t(pP-P) travel time difference, which is the case of the nuclear test. Since the shape of the first few seconds of signal of very shallow events is very sensitive to the presence of the depth phase, cross correlation between observed and theoretic seismogram can provide an estimate for the depth of the event, and so provide an expansion to the screening process. We exercised this approach mostly with events at teleseismic and partially regional distances. We found that such approach can be very efficient for the seismic event screening process, with certain caveats related mostly to the poorly defined crustal models at source and receiver which can shift the depth estimate. We used adjustable t* teleseismic attenuation model for synthetics since this characteristic is not determined for most of the rays we studied. We studied a wide set of historical records of nuclear explosions, including so called Peaceful Nuclear Explosions (PNE) with presumably known depths, and recent DPRK nuclear tests. The teleseismic synthetic approach is based on the stationary phase approximation with Robert Herrmann's hudson96 program, and the regional modelling was done with the generalized ray technique by Vlastislav Cerveny modified to the complex source topography.

  10. 3-D synthetic aperture processing on high-frequency wide-beam microwave systems

    NASA Astrophysics Data System (ADS)

    Cristofani, Edison; Brook, Anna; Vandewal, Marijke

    2012-06-01

    The use of High-Frequency MicroWaves (HFMW) for high-resolution imagery has gained interest over the last years. Very promising in-depth applications can be foreseen for composite non-metal, non-polarized materials, widely used in the aeronautic and aerospace industries. Most of these materials present a high transparency in the HFMW range and, therefore, defects, delaminations or occlusions within the material can be located. This property can be exploited by applying 3-D HFMW imaging where conventional focused imaging systems are typically used but a different approach such as Synthetic Aperture (SA) radar can be addressed. This paper will present an end-to-end 3-D imagery system for short-range, non-destructive testing based on a frequency-modulated continuous-wave HFMWsensor operating at 100 GHz, implying no health concerns to the human body as well as relatively low cost and limited power requirements. The sensor scans the material while moving sequentially in every elevation plane following a 2-D grid and uses a significantly wide beam antenna for data acquisition, in contrast to focused systems. Collected data must be coherently combined using a SA algorithm to form focused images. Range-independent, synthetically improved cross-range resolutions are remarkable added values of SA processing. Such algorithms can be found in the literature and operate in the time or frequency domains, being the former computationally impractical and the latter the best option for in-depth 3-D imaging. A balanced trade-off between performance and image focusing quality is investigated for several SA algorithms.

  11. Modeling of bottom-related surface patterns imaged by synthetic aperture radar

    NASA Technical Reports Server (NTRS)

    Lyzenga, D. R.; Shuchman, R. A.; Kasischke, E. S.; Meadows, G. A.

    1983-01-01

    A hydrodynamic electromagnetic model is developed in order to provide a qualitative and quantitative description of the relationship between Seasat synthetic aperture radar (SAR) signatures and the bottom topography of the ocean in the English Channel region of the North Sea. The model is based on environmental data for winds, currents, and depth changes, and the SAR parameters of frequency polarization, incidence angle, and resolution cell size. The data are used as inputs and SAR backscatter changes are predicted for individual topographic changes on the ocean floor. It is found that the model estimates of backscatter values are in good agreement with actual Seasat SAR-observed backscatter values. A comparison of the model and actual data shows agreement to be within 1.5 dB. The model is considered to be valid for only shallow water areas (less than 50 meters in depth). It is suggested that for bottom features to be visible on SAR imagery at greater depths, a moderate-to-high velocity current of at least 0.4 m/s and a moderate wind no more than 7.5 m/sec must be present.

  12. Synthetic Aperture Radar Interferometry for Digital Elevation Model of Kuwait Desert - Analysis of Errors

    NASA Astrophysics Data System (ADS)

    Jassar, H. K. Al; Rao, K. S.

    2012-07-01

    Using different combinations of 29 Advanced Synthetic Aperture Radar (ASAR) images, 43 Digital Elevations Models (DEM) were generated adopting SAR Interferometry (InSAR) technique. Due to sand movement in desert terrain, there is a poor phase correlation between different SAR images. Therefore, suitable methodology for generating DEMs of Kuwait desert terrain using InSAR technique were worked out. Time series analysis was adopted to derive the best DEM out of 43 DEMs. The problems related to phase de-correlation over desert terrain are discussed. Various errors associated with the DEM generation are discussed which include atmospheric effects, penetration into soil medium, sand movement. The DEM of Shuttle Radar Topography Mission (SRTM) is used as a reference. The noise levels of DEM of SRTM are presented.

  13. Bose-Hubbard models with synthetic spin-orbit coupling: Mott insulators, spin textures, and superfluidity.

    PubMed

    Cole, William S; Zhang, Shizhong; Paramekanti, Arun; Trivedi, Nandini

    2012-08-24

    Motivated by the experimental realization of synthetic spin-orbit coupling for ultracold atoms, we investigate the phase diagram of the Bose-Hubbard model in a non-Abelian gauge field in two dimensions. Using a strong coupling expansion in the combined presence of spin-orbit coupling and tunable interactions, we find a variety of interesting magnetic Hamiltonians in the Mott insulator (MI), which support magnetic textures such as spin spirals and vortex and Skyrmion crystals. An inhomogeneous mean-field treatment shows that the superfluid (SF) phases inherit these exotic magnetic orders from the MI and display, in addition, unusual modulated current patterns. We present a slave-boson theory which gives insight into such intertwined spin-charge orders in the SF, and discuss signatures of these orders in Bragg scattering, in situ microscopy, and dynamic quench experiments.

  14. Active aeroelastic control aspects of an aircraft wing by using synthetic jet actuators: modeling, simulations, experiments

    NASA Astrophysics Data System (ADS)

    O'Donnell, K.; Schober, S.; Stolk, M.; Marzocca, P.; De Breuker, R.; Abdalla, M.; Nicolini, E.; Gürdal, Z.

    2007-04-01

    This paper discusses modeling, simulations and experimental aspects of active aeroelastic control on aircraft wings by using Synthetic Jet Actuators (SJAs). SJAs, a particular class of zero-net mass-flux actuators, have shown very promising results in numerous aeronautical applications, such as boundary layer control and delay of flow separation. A less recognized effect resulting from the SJAs is a momentum exchange that occurs with the flow, leading to a rearrangement of the streamlines around the airfoil modifying the aerodynamic loads. Discussions pertinent to the use of SJAs for flow and aeroelastic control and how these devices can be exploited for flutter suppression and for aerodynamic performances improvement are presented and conclusions are outlined.

  15. Toward Engineering Synthetic Microbial Metabolism

    PubMed Central

    McArthur, George H.; Fong, Stephen S.

    2010-01-01

    The generation of well-characterized parts and the formulation of biological design principles in synthetic biology are laying the foundation for more complex and advanced microbial metabolic engineering. Improvements in de novo DNA synthesis and codon-optimization alone are already contributing to the manufacturing of pathway enzymes with improved or novel function. Further development of analytical and computer-aided design tools should accelerate the forward engineering of precisely regulated synthetic pathways by providing a standard framework for the predictable design of biological systems from well-characterized parts. In this review we discuss the current state of synthetic biology within a four-stage framework (design, modeling, synthesis, analysis) and highlight areas requiring further advancement to facilitate true engineering of synthetic microbial metabolism. PMID:20037734

  16. Design and Application of an Object Oriented Graphical Database Management System for Synthetic Environments

    DTIC Science & Technology

    1991-12-01

    development of the Database Generation System was also successful. In addition to providing an excellent platform for testing GDMS funtionality , it proved to...Format Several geometries are available for modeling objects in three- space. Procedural models, fractals, grammar -based models, particle systems

  17. A constant stress-drop model for producing broadband synthetic seismograms: Comparison with the next generation attenuation relations

    USGS Publications Warehouse

    Frankel, A.

    2009-01-01

    Broadband (0.1-20 Hz) synthetic seismograms for finite-fault sources were produced for a model where stress drop is constant with seismic moment to see if they can match the magnitude dependence and distance decay of response spectral amplitudes found in the Next Generation Attenuation (NGA) relations recently developed from strong-motion data of crustal earthquakes in tectonically active regions. The broadband synthetics were constructed for earthquakes of M 5.5, 6.5, and 7.5 by combining deterministic synthetics for plane-layered models at low frequencies with stochastic synthetics at high frequencies. The stochastic portion used a source model where the Brune stress drop of 100 bars is constant with seismic moment. The deterministic synthetics were calculated using an average slip velocity, and hence, dynamic stress drop, on the fault that is uniform with magnitude. One novel aspect of this procedure is that the transition frequency between the deterministic and stochastic portions varied with magnitude, so that the transition frequency is inversely related to the rise time of slip on the fault. The spectral accelerations at 0.2, 1.0, and 3.0 sec periods from the synthetics generally agreed with those from the set of NGA relations for M 5.5-7.5 for distances of 2-100 km. At distances of 100-200 km some of the NGA relations for 0.2 sec spectral acceleration were substantially larger than the values of the synthetics for M 7.5 and M 6.5 earthquakes because these relations do not have a term accounting for Q. At 3 and 5 sec periods, the synthetics for M 7.5 earthquakes generally had larger spectral accelerations than the NGA relations, although there was large scatter in the results from the synthetics. The synthetics showed a sag in response spectra at close-in distances for M 5.5 between 0.3 and 0.7 sec that is not predicted from the NGA relations.

  18. Thiophene-Fused Nickel Dithiolenes: A Synthetic Scaffold for Highly Delocalized π-Electron Systems.

    PubMed

    Amb, Chad M; Heth, Christopher L; Evenson, Sean J; Pokhodnya, Konstantin I; Rasmussen, Seth C

    2016-11-07

    A series of thiophene-fused nickel dithiolene complexes have been prepared via synthetic methods which allow the addition of peripheral aryl groups to the fused thiophene of the dithiolene ligand, thus providing access to a range of structural and electronic modifications to the dithiolene core. X-ray structural studies of the anionic complexes show that the peripheral aryl rings lie in near-perfect coplanarity to the dithiolene core and can form π-stacked columns with N-methylpyridinium cations. Density functional theory calculations show significant delocalization of the frontier orbital electron density into the peripheral aryl rings. The complexes exhibit tunable, intense near-IR (NIR) absorption in the range of 1076-1160 nm with molar absorptivity as high as 25100 M(-1) cm(-1) in solution. The electronic tunability as well as the desirable solid-state packing arrangements of these systems suggests significant potential as NIR-absorbing materials for optoelectronic applications.

  19. Transition of Attention in Terminal Area NextGen Operations Using Synthetic Vision Systems

    NASA Technical Reports Server (NTRS)

    Ellis, Kyle K. E.; Kramer, Lynda J.; Shelton, Kevin J.; Arthur, Shelton, J. J., III; Prinzel, Lance J., III; Norman, Robert M.

    2011-01-01

    This experiment investigates the capability of Synthetic Vision Systems (SVS) to provide significant situation awareness in terminal area operations, specifically in low visibility conditions. The use of a Head-Up Display (HUD) and Head-Down Displays (HDD) with SVS is contrasted to baseline standard head down displays in terms of induced workload and pilot behavior in 1400 RVR visibility levels. Variances across performance and pilot behavior were reviewed for acceptability when using HUD or HDD with SVS under reduced minimums to acquire the necessary visual components to continue to land. The data suggest superior performance for HUD implementations. Improved attentional behavior is also suggested for HDD implementations of SVS for low-visibility approach and landing operations.

  20. Feature discrimination and detection probability in synthetic aperture radar imaging system

    NASA Technical Reports Server (NTRS)

    Lipes, R. G.; Butman, S. A.

    1977-01-01

    Images obtained using synthetic aperture radar (SAR) systems can only represent the intensities of resolution cells in the scene of interest probabilistically since radar receiver noise and Rayleigh scattering of the transmitted radiation are always present. Consequently, when features to be identified differ only by their contribution to the mean power of the radar return, discrimination can be treated by detection theory. In this paper, we develop a 'sufficient statistic' for discriminating between competing features and compare it with some suboptimal methods frequently used. Discrimination is measured by probability of detection error and depends on number of samples or 'looks', signal-to-noise ratio (SNR), and ratio of mean power returns from the competing features. Our results show discrimination and image quality rapidly saturate with SNR (very small improvement for SNR not less than 10 dB) but continue to improve with increasing number of looks.

  1. Gene brushes on a chip: From crowding and the search problem to synthetic systems

    NASA Astrophysics Data System (ADS)

    Bar-Ziv, Roy

    2009-03-01

    We assemble DNA polymer brushes coding for entire genes on a surface by means of a new photolithographic approach. The gene density can be controlled from dilute to high density where the local concentration -- Megabase pairs per micron cubed -- is comparable to that in a bacterium. The gene brush, therefore, emulates the crowded medium of the cell, allowing us to study DNA transactions in vitro under native conditions. We find that transcription/translation from these gene brushes is highly sensitive to DNA density, orientation and composition. As a step towards multi-gene synthetic systems, we integrated on a chip two spatially separated gene brushes, and implemented a two-stage transcription/translation cascade.

  2. Development of GRAS strains for nutraceutical production using systems and synthetic biology approaches: advances and prospects.

    PubMed

    Liu, Long; Guan, Ningzi; Li, Jianghua; Shin, Hyun-Dong; Du, Guocheng; Chen, Jian

    2017-03-01

    Nutraceuticals are food substances with medical and health benefits for humans. Limited by complicated procedures, high cost, low yield, insufficient raw materials, resource waste, and environment pollution, chemical synthesis and extraction are being replaced by microbial synthesis of nutraceuticals. Many microbial strains that are generally regarded as safe (GRAS) have been identified and developed for the synthesis of nutraceuticals, and significant nutraceutical production by these strains has been achieved. In this review, we systematically summarize recent advances in nutraceutical research in terms of physiological effects on health, potential applications, drawbacks of traditional production processes, characteristics of production strains, and progress in microbial fermentation. Recent advances in systems and synthetic biology techniques have enabled comprehensive understanding of GRAS strains and its wider applications. Thus, these microbial strains are promising cell factories for the commercial production of nutraceuticals.

  3. Full-color autostereoscopic 3D display system using color-dispersion-compensated synthetic phase holograms.

    PubMed

    Choi, Kyongsik; Kim, Hwi; Lee, Byoungho

    2004-10-18

    A novel full-color autostereoscopic three-dimensional (3D) display system has been developed using color-dispersion-compensated (CDC) synthetic phase holograms (SPHs) on a phase-type spatial light modulator. To design the CDC phase holograms, we used a modified iterative Fourier transform algorithm with scaling constants and phase quantization level constraints. We obtained a high diffraction efficiency (~90.04%), a large signal-to-noise ratio (~9.57dB), and a low reconstruction error (~0.0011) from our simulation results. Each optimized phase hologram was synthesized with each CDC directional hologram for red, green, and blue wavelengths for full-color autostereoscopic 3D display. The CDC SPHs were composed and modulated by only one phase-type spatial light modulator. We have demonstrated experimentally that the designed CDC SPHs are able to generate full-color autostereoscopic 3D images and video frames very well, without any use of glasses.

  4. Wavefront alignment research of segmented mirror synthetic aperture optical (SAO) system

    NASA Astrophysics Data System (ADS)

    Deng, Jian; An, Xiaoqiang; Tian, Hao

    2010-05-01

    Wavefront control technology and imaging experiment are introduced for a segmented mirror SAO system with deformable sub-mirrors. This system is a RC style with 300mm aperture, 4.5 F#, +/-0.4°FOV, 0.45~0.75μm wave band, and diffraction-limit design MTF. The primary mirror is composed by three sub-mirrors, with parabolic shape, and each deformable sub-mirror has 19 actuators to control and keep the surface shape, and 5 actuators to align sub-mirrors location in 5 degree of freedom. Interferometer is used to feed back and control exit wavefront error, and base on measurement and finite element analysis, location and quanitity of actuators are optimized, making the surface shape and misadjustment errors interact and compensate each other, and the synthetic system exit pupil wavefront error is controlled. The integrated exit pupil wavefront errors are gotten by ZYGO interferometer, and central FOV is 0.077λRMS, and edge FOV is 0.093λRMS. At the end, an imaging experiment is executed, and good results are obtained, which proves, the deformable sub-mirrors have the ability to meliorate alignment and the latter can retroact the former, and this relationship iterate make system exit pupil wavefront error convergence and improve segmented mirror SAO system imaging ability.

  5. INSYDE: a synthetic, probabilistic flood damage model based on explicit cost analysis

    NASA Astrophysics Data System (ADS)

    Dottori, Francesco; Figueiredo, Rui; Martina, Mario L. V.; Molinari, Daniela; Scorzini, Anna Rita

    2016-12-01

    Methodologies to estimate economic flood damages are increasingly important for flood risk assessment and management. In this work, we present a new synthetic flood damage model based on a component-by-component analysis of physical damage to buildings. The damage functions are designed using an expert-based approach with the support of existing scientific and technical literature, loss adjustment studies, and damage surveys carried out for past flood events in Italy. The model structure is designed to be transparent and flexible, and therefore it can be applied in different geographical contexts and adapted to the actual knowledge of hazard and vulnerability variables. The model has been tested in a recent flood event in northern Italy. Validation results provided good estimates of post-event damages, with similar or superior performances when compared with other damage models available in the literature. In addition, a local sensitivity analysis was performed in order to identify the hazard variables that have more influence on damage assessment results.

  6. Effect of the bifurcation angle on the flow within a synthetic model of lower human airways

    NASA Astrophysics Data System (ADS)

    Espinosa Moreno, Andres Santiago; Duque Daza, Carlos Alberto

    2016-11-01

    The effect of the bifurcation angle on the flow pattern developed during respiratory inhalation and exhalation processes was explored numerically using a synthetic model of lower human airways featuring three generations of a dichotomous morphology as described by a Weibel model. Laminar flow simulations were performed for six bifurcation angles and four Reynolds numbers relevant to human respiratory flow. Numerical results of the inhalation process showed a peak displacement trend of the velocity profile towards the inner walls of the model. This displacement exhibited correlation with Dean-type secondary flow patterns, as well as with the onset and location of vortices. High wall shear stress regions on the inner walls were observed for a range of bifurcation angles. Noteworthy, specific bifurcation angles produced higher values of pressure drop, compared to the average behavior, as well as changes in the volumetric flow through the branches. Results of the simulations for exhalation process showed a different picture, mainly the appearance of symmetrical velocity profiles and the change of location of the regions of high wall shear stress. The use of this modelling methodology for biomedical applications is discussed considering the validity of the obtained results. Department of Mechanical and Mechatronics Engineering, Universidad Nacional de Colombia.

  7. Can Effective Synthetic Vision System Displays be Implemented on Limited Size Display Spaces?

    NASA Technical Reports Server (NTRS)

    Comstock, J. Raymond, Jr.; Glaab, Lou J.; Prinzel, Lance J.; Elliott, Dawn M.

    2004-01-01

    The Synthetic Vision Systems (SVS) element of the NASA Aviation Safety Program is striving to eliminate poor visibility as a causal factor in aircraft accidents, and to enhance operational capabilities of all types or aircraft. To accomplish these safety and situation awareness improvements, the SVS concepts are designed to provide a clear view of the world ahead through the display of computer generated imagery derived from an onboard database of terrain, obstacle and airport information. An important issue for the SVS concept is whether useful and effective Synthetic Vision System (SVS) displays can be implemented on limited size display spaces as would be required to implement this technology on older aircraft with physically smaller instrument spaces. In this study, prototype SVS displays were put on the following display sizes: (a) size "A' (e.g. 757 EADI), (b) form factor "D" (e.g. 777 PFD), and (c) new size "X" (Rectangular flat-panel, approximately 20 x 25 cm). Testing was conducted in a high-resolution graphics simulation facility at NASA Langley Research Center. Specific issues under test included the display size as noted above, the field-of-view (FOV) to be shown on the display and directly related to FOV is the degree of minification of the displayed image or picture. Using simulated approaches with display size and FOV conditions held constant no significant differences by these factors were found. Preferred FOV based on performance was determined by using approaches during which pilots could select FOV. Mean preference ratings for FOV were in the following order: (1) 30 deg., (2) Unity, (3) 60 deg., and (4) 90 deg., and held true for all display sizes tested. Limitations of the present study and future research directions are discussed.

  8. Synthetic plant defense elicitors

    PubMed Central

    Bektas, Yasemin; Eulgem, Thomas

    2015-01-01

    To defend themselves against invading pathogens plants utilize a complex regulatory network that coordinates extensive transcriptional and metabolic reprogramming. Although many of the key players of this immunity-associated network are known, the details of its topology and dynamics are still poorly understood. As an alternative to forward and reverse genetic studies, chemical genetics-related approaches based on bioactive small molecules have gained substantial popularity in the analysis of biological pathways and networks. Use of such molecular probes can allow researchers to access biological space that was previously inaccessible to genetic analyses due to gene redundancy or lethality of mutations. Synthetic elicitors are small drug-like molecules that induce plant defense responses, but are distinct from known natural elicitors of plant immunity. While the discovery of some synthetic elicitors had already been reported in the 1970s, recent breakthroughs in combinatorial chemical synthesis now allow for inexpensive high-throughput screens for bioactive plant defense-inducing compounds. Along with powerful reverse genetics tools and resources available for model plants and crop systems, comprehensive collections of new synthetic elicitors will likely allow plant scientists to study the intricacies of plant defense signaling pathways and networks in an unparalleled fashion. As synthetic elicitors can protect crops from diseases, without the need to be directly toxic for pathogenic organisms, they may also serve as promising alternatives to conventional biocidal pesticides, which often are harmful for the environment, farmers and consumers. Here we are discussing various types of synthetic elicitors that have been used for studies on the plant immune system, their modes-of-action as well as their application in crop protection. PMID:25674095

  9. Synthetic plant defense elicitors.

    PubMed

    Bektas, Yasemin; Eulgem, Thomas

    2014-01-01

    To defend themselves against invading pathogens plants utilize a complex regulatory network that coordinates extensive transcriptional and metabolic reprogramming. Although many of the key players of this immunity-associated network are known, the details of its topology and dynamics are still poorly understood. As an alternative to forward and reverse genetic studies, chemical genetics-related approaches based on bioactive small molecules have gained substantial popularity in the analysis of biological pathways and networks. Use of such molecular probes can allow researchers to access biological space that was previously inaccessible to genetic analyses due to gene redundancy or lethality of mutations. Synthetic elicitors are small drug-like molecules that induce plant defense responses, but are distinct from known natural elicitors of plant immunity. While the discovery of some synthetic elicitors had already been reported in the 1970s, recent breakthroughs in combinatorial chemical synthesis now allow for inexpensive high-throughput screens for bioactive plant defense-inducing compounds. Along with powerful reverse genetics tools and resources available for model plants and crop systems, comprehensive collections of new synthetic elicitors will likely allow plant scientists to study the intricacies of plant defense signaling pathways and networks in an unparalleled fashion. As synthetic elicitors can protect crops from diseases, without the need to be directly toxic for pathogenic organisms, they may also serve as promising alternatives to conventional biocidal pesticides, which often are harmful for the environment, farmers and consumers. Here we are discussing various types of synthetic elicitors that have been used for studies on the plant immune system, their modes-of-action as well as their application in crop protection.

  10. Enhanced and synthetic vision system for autonomous all weather approach and landing

    NASA Astrophysics Data System (ADS)

    Korn, Bernd R.

    2007-04-01

    Within its research project ADVISE-PRO (Advanced visual system for situation awareness enhancement - prototype, 2003 - 2006) that will be presented in this contribution, DLR has combined elements of Enhanced Vision and Synthetic Vision to one integrated system to allow all low visibility operations independently from the infrastructure on ground. The core element of this system is the adequate fusion of all information that is available on-board. This fusion process is organized in a hierarchical manner. The most important subsystems are a) the sensor based navigation which determines the aircraft's position relative to the runway by automatically analyzing sensor data (MMW, IR, radar altimeter) without using neither (D)GPS nor precise knowledge about the airport geometry, b) an integrity monitoring of navigation data and terrain data which verifies on-board navigation data ((D)GPS + INS) with sensor data (MMW-Radar, IR-Sensor, Radar altimeter) and airport / terrain databases, c) an obstacle detection system and finally d) a consistent description of situation and respective HMI for the pilot.

  11. ATLAS Versus NextGen Model Atmospheres: A Combined Analysis of Synthetic Spectral Energy Distributions

    NASA Astrophysics Data System (ADS)

    Bertone, E.; Buzzoni, A.; Chávez, M.; Rodríguez-Merino, L. H.

    2004-08-01

    We carried out a critical appraisal of the two theoretical models, Kurucz' ATLAS9 and PHOENIX/NextGen, for stellar atmosphere synthesis. Our tests relied on the theoretical fit of spectral energy distributions (SEDs) for a sample of 334 target stars along the whole spectral-type sequence, from the classical optical catalogs of Gunn & Stryker and Jacoby et al. The best-fitting physical parameters (Teff, logg) of stars allowed an independent calibration of the temperature and bolometric scale versus empirical classification parameters (i.e., spectral type and MK luminosity class); in addition, the comparison of the synthetic templates from the ATLAS and NextGen grids allowed us to probe the capability of the models to match spectrophotometric properties of real stars and assess the impact of the different input physics. We can sketch the following main conclusions of our analysis: (1) Fitting accuracy of both theoretical libraries drastically degrades at low Teff at which both ATLAS and NextGen models still fail to properly account for the contribution of molecular features in the observed SED of K-M stars. (2) Compared with empirical calibrations, both ATLAS and NextGen fits tend, on average, to predict slightly warmer (by 4%-8%) Teff for both giant and dwarf stars of fixed spectral type, but ATLAS provides, in general, a sensibly better fit (a factor of 2 lower σ of flux residuals) than NextGen. (3) There is a striking tendency of NextGen to label target stars with an effective temperature and surface gravity higher than that of ATLAS. The effect is especially evident for MK I-III objects for which about one in four stars is clearly misclassified by NextGen in logg. This is a consequence of some ``degeneracy'' in the solution space, partly induced by the different input physics and geometry constraints in the computation of the integrated emerging flux (ATLAS model atmospheres assume standard plane-parallel layers, while NextGen adopts, for low-gravity stars, a

  12. Synthetic models of the active site of catechol oxidase: mechanistic studies.

    PubMed

    Koval, Iryna A; Gamez, Patrick; Belle, Catherine; Selmeczi, Katalin; Reedijk, Jan

    2006-09-01

    The ability of copper proteins to process dioxygen at ambient conditions has inspired numerous research groups to study their structural, spectroscopic and catalytic properties. Catechol oxidase is a type-3 copper enzyme usually encountered in plant tissues and in some insects and crustaceans. It catalyzes the conversion of a large number of catechols into the respective o-benzoquinones, which subsequently auto-polymerize, resulting in the formation of melanin, a dark pigment thought to protect a damaged tissue from pathogens. After the report of the X-ray crystal structure of catechol oxidase a few years earlier, a large number of publications devoted to the biomimetic modeling of its active site appeared in the literature. This critical review (citing 114 references) extensively discusses the synthetic models of this enzyme, with a particular emphasis on the different approaches used in the literature to study the mechanism of the catalytic oxidation of the substrate (catechol) by these compounds. These are the studies on the substrate binding to the model complexes, the structure-activity relationship, the kinetic studies of the catalytic oxidation of the substrate and finally the substrate interaction with (per)oxo-dicopper adducts. The general overview of the recognized types of copper proteins and the detailed description of the crystal structure of catechol oxidase, as well as the proposed mechanisms of the enzymatic cycle are also presented.

  13. Nanomechanics of nanocomposite systems: Experimental studies in bone, seashells and synthetic nanocomposites using nanoindentation and atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Mohanty, Bedabibhas

    changes along the thickness of bone. Also investigated are nanomechanical properties in synthetic nanocomposites composed of nanoclays and polymers (nylon 6). The novel experiments conducted in this work describe quantitatively the extent of the alteration zone of polymers around nanosized clays to be about 25 nm using phase imaging in atomic force microscopy. These experiments provided valuable input for the development of multiscale models of polymer clay composite systems.

  14. A New Titanium-Bearing Calcium Aluminosilicate Phase. 1; Meteoritic Occurrences and Formation in Synthetic Systems

    NASA Technical Reports Server (NTRS)

    Paque, Julie M.; Beckett, John R.; Barber, David J.; Stolper, Edward M.

    1994-01-01

    A new titanium-bearing calcium aluminosilicate mineral has been identified in coarse-grained calcium-aluminum-rich inclusions (CAIs) from carbonaceous chondrites. The formula for this phase, which we have temporarily termed "UNK," is Ca3Ti(AlTi)2(Si,Al)3O14, and it is present in at least 8 of the 20 coarse-grained CAIs from the Allende CV3 chondrite examined as part of this project. The phase occurs in Types A and B1 inclusions as small tabular crystals oriented along two mutually perpendicular planes in melilite. UNK crystallizes from melts in dynamic crystallization experiments conducted in air from four bulk compositions modeled after Types A, B1, B2 and C inclusions. Cooling rates resulting in crystallization of UNK ranged from 0.5 to 200 C/h from maximum (initial) temperatures of 1375 to 1580 C. Only below 1190 C does UNK itself begin to crystallize. To first order, the presence or absence of UNK from individual experiments can be understood in terms of the compositions of residual melts and nucleation probabilities. Compositions of synthetic and meteoritic LINK are very similar in terms of major oxides, differing only in the small amounts of trivalent Ti (7-13% of total Ti) in meteoritic samples. UNK crystallized from the Type A analog is similar texturally to that found in CAls, although glass, which is typically associated with synthetic UN& is not observed in meteoritic occurrences. A low Ti end-member of UNK ("Si-UNK") with a composition new that of Ca3Al2Si4O14 was produced in a few samples from the Type B1 analog. This phase has not been found in the meteoritic inclusions.

  15. A new titanium-bearing calcium aluminosilicate phase. 1: Meteoritic occurrences and formation in synthetic systems

    NASA Technical Reports Server (NTRS)

    Paque, Julie M.; Beckett, John R.; Barber, David J.; Stolper, Edward M.

    1994-01-01

    A new titanium-bearing calcium aluminosilicate mineral has been identified in coarse-grained calcium-aluminum-rich inclusions (CAIs) from carbonaceous chondrites. The formula for this phase, which we have temporarily termed 'UNK,' is Ca3Ti(Al,Ti)2(Si,Al)3O14, and it is present in at least 8 of the 20 coarse-grained CAIs from the Allende CV3 chondrite examined as part of this project. The phase occurs in Types A and B1 inclusions as small tabular crystal oriented along two mutually perpendicular planes in melilite. UNK crystallizes from melts in dynamic crystallization experiments conducted in air from four bulk compositions modeled after Types A, B1, B2 and C inclusions. Cooling rates resulting in crystallization of UNK ranged from 0.5 to 200 C/h from maximum (initial) temperatures of 1375 to 1580 C. Only below 1190 C does UNK itself begin to crystallize. To first order, the presence or absence of UNK from individual experiments can be understood in terms of the compositions of residual melts and nucleation probabilities. Compositions of synthetic and meteoritic UNK are very similar in terms of major oxides, differing only in the small amounts of trivalent Ti(7-13% of total Ti) in meteoritic samples. UNK crystallized from the Type A analog is similar texturally to that found in CAIs, although glass, which is typically associated with synthetic UNK, is not observed in the meteoritic occurrences. A low Ti end-member of UNK ('Si-UNK') with a composition near that of Ca3Al2Si4O14 was produced in a few samples from the Type B1 analog. This phase has not been found in the meteoritic inclusions.

  16. Loads bias genetic and signaling switches in synthetic and natural systems.

    PubMed

    Lyons, Samanthe M; Xu, Wenlong; Medford, June; Prasad, Ashok

    2014-03-01

    Biological protein interactions networks such as signal transduction or gene transcription networks are often treated as modular, allowing motifs to be analyzed in isolation from the rest of the network. Modularity is also a key assumption in synthetic biology, where it is similarly expected that when network motifs are combined together, they do not lose their essential characteristics. However, the interactions that a network module has with downstream elements change the dynamical equations describing the upstream module and thus may change the dynamic and static properties of the upstream circuit even without explicit feedback. In this work we analyze the behavior of a ubiquitous motif in gene transcription and signal transduction circuits: the switch. We show that adding an additional downstream component to the simple genetic toggle switch changes its dynamical properties by changing the underlying potential energy landscape, and skewing it in favor of the unloaded side, and in some situations adding loads to the genetic switch can also abrogate bistable behavior. We find that an additional positive feedback motif found in naturally occurring toggle switches could tune the potential energy landscape in a desirable manner. We also analyze autocatalytic signal transduction switches and show that a ubiquitous positive feedback switch can lose its switch-like properties when connected to a downstream load. Our analysis underscores the necessity of incorporating the effects of downstream components when understanding the physics of biochemical network motifs, and raises the question as to how these effects are managed in real biological systems. This analysis is particularly important when scaling synthetic networks to more complex organisms.

  17. Co-generating synthetic parts toward a self-replicating system

    DOE PAGES

    Li, Jun; Haas, Wilhelm; Jackson, Kirsten; ...

    2017-03-23

    To build replicating systems with new functions, the engineering of existing biological machineries requires a sensible strategy. Protein synthesis Using Recombinant Elements (PURE) system consists of the desired components for transcription, translation, aminoacylation and energy regeneration. PURE, might be the basis for a radically alterable, lifelike system after optimization. Here, we regenerated 54 E. coli ribosomal (r-) proteins individually from DNA templates in the PURE system. We show that using stable isotope labeling with amino acids, mass spectrometry based quantitative proteomics could detect 26 of the 33 50S and 20 of the 21 30S subunit r-proteins when co-expressed in batchmore » format PURE system. By optimizing DNA template concentrations and adapting a miniaturized Fluid Array Device with optimized feeding solution, we were able to cogenerate and detect at least 29 of the 33 50S and all of the 21 30S subunit r-proteins in one pot. The boost on yield of a single r-protein in co-expression pool varied from ~1.5 to 5-fold compared to the batch mode, with up to ~ 2.4 µM yield for a single r-protein. Reconstituted ribosomes under physiological condition from PURE system synthesized 30S r-proteins and native 16S rRNA showed ~13% activity of native 70S ribosomes, which increased to 21% when supplemented with GroEL/ES. As a result, this work also points to what is still needed to obtain self-replicating synthetic ribosomes in-situ in the PURE system.« less

  18. AER synthetic generation in hardware for bio-inspired spiking systems

    NASA Astrophysics Data System (ADS)

    Linares-Barranco, Alejandro; Linares-Barranco, Bernabe; Jimenez-Moreno, Gabriel; Civit-Balcells, Anton

    2005-06-01

    Address Event Representation (AER) is an emergent neuromorphic interchip communication protocol that allows for real-time virtual massive connectivity between huge number neurons located on different chips. By exploiting high speed digital communication circuits (with nano-seconds timings), synaptic neural connections can be time multiplexed, while neural activity signals (with mili-seconds timings) are sampled at low frequencies. Also, neurons generate 'events' according to their activity levels. More active neurons generate more events per unit time, and access the interchip communication channel more frequently, while neurons with low activity consume less communication bandwidth. When building multi-chip muti-layered AER systems it is absolutely necessary to have a computer interface that allows (a) to read AER interchip traffic into the computer and visualize it on screen, and (b) convert conventional frame-based video stream in the computer into AER and inject it at some point of the AER structure. This is necessary for test and debugging of complex AER systems. This paper addresses the problem of converting, in a computer, a conventional frame-based video stream into the spike event based representation AER. There exist several proposed software methods for synthetic generation of AER for bio-inspired systems. This paper presents a hardware implementation for one method, which is based on Linear-Feedback-Shift-Register (LFSR) pseudo-random number generation. The sequence of events generated by this hardware, which follows a Poisson distribution like a biological neuron, has been reconstructed using two AER integrator cells. The error of reconstruction for a set of images that produces different traffic loads of event in the AER bus is used as evaluation criteria. A VHDL description of the method, that includes the Xilinx PCI Core, has been implemented and tested using a general purpose PCI-AER board. This PCI-AER board has been developed by authors, and uses

  19. Chlorine partitioning between mantle minerals and aqueous fluid in synthetic and natural systems

    NASA Astrophysics Data System (ADS)

    Fabbrizio, A.; Stalder, R.; Günther, D.; Hametner, K.

    2012-12-01

    The solubility of halogens in nominally halogen-free minerals (NHFMs) and their partitioning behavior between these minerals and fluids are scarcely explored. Halogen partitioning has important consequences for the global halogen budget, the origin of high-pressure brines, the effects of halogen on mantle properties and volatile recycling in subduction zones, which in turn has consequences for the global climate. Cl partition coefficients between mantle minerals (olivine, clinopyroxene, orthopyroxene) and coexisting aqueous fluids were determined in a series of high pressure and temperature piston cylinder experiments at 2 GPa between 900 and 1300 °C both in synthetic and natural systems. Diamond aggregates were added to the experimental capsule set-up in order to separate the fluid from the solid residue and enable in situ analysis of the quenched solute by LA-ICP-MS using a Cl-bearing basaltic glass as external standard. The chlorine content of minerals was measured by EMPA (beam current: 300 nA, accelerating voltage: 15 kV, counting time: 240 s on peak), and the nature of hydrous defects was investigated by infrared spectroscopy. Partition coefficients in the synthetic system MSH ± TiO2 ± Al2O3 ± F show similar incompatibility for Cl in forsterite and enstatite, with DClfo/fl = 0.0012 ± 0.0006 , DClen/fl = 0.0018 ± 0.0008 and DClfo/en = 1.37 ± 0.71 [1]. Preliminary experiments conducted using a natural peridotite composition show that Cl content in olivine is 7 ± 2 ppm at 1300 °C and 17 ± 14 at 1200 °C. The values determined for mineral/fluid partitioning are very similar to previously determined values for mineral/melt. Applying the new mineral/fluid partition coefficients to fluids in subduction zones, a contribution between 0.05% and 4% of the total chlorine from the nominally anhydrous minerals is estimated. Infrared spectra of forsterite in the system MSH + TiO2 ± Al2O3 show absorption bands at 3,525 and 3,572 cm-1 that are characteristic for

  20. Synthetic and Enhanced Vision Systems for NextGen (SEVS) Simulation and Flight Test Performance Evaluation

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Kramer, Lynda J.; Ellis,Kyle K.; Rehfeld, Sherri A.

    2012-01-01

    The Synthetic and Enhanced Vision Systems for NextGen (SEVS) simulation and flight tests are jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA). The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SEVS operational and system-level performance capabilities. Nine test flights (38 flight hours) were conducted over the summer and fall of 2011. The evaluations were flown in Gulfstream.s G450 flight test aircraft outfitted with the SEVS technology under very low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 ft to 2400 ft visibility) into various airports from Louisiana to Maine. In-situ flight performance and subjective workload and acceptability data were collected in collaboration with ground simulation studies at LaRC.s Research Flight Deck simulator.

  1. Multi-spectrum-based enhanced synthetic vision system for aircraft DVE operations

    NASA Astrophysics Data System (ADS)

    Kashyap, Sudesh K.; Naidu, V. P. S.; Shanthakumar, N.

    2016-04-01

    This paper focus on R&D being carried out at CSIR-NAL on Enhanced Synthetic Vision System (ESVS) for Indian regional transport aircraft to enhance all weather operational capabilities with safety and pilot Situation Awareness (SA) improvements. Flight simulator has been developed to study ESVS related technologies and to develop ESVS operational concepts for all weather approach and landing and to provide quantitative and qualitative information that could be used to develop criteria for all-weather approach and landing at regional airports in India. Enhanced Vision System (EVS) hardware prototype with long wave Infrared sensor and low light CMOS camera is used to carry out few field trials on ground vehicle at airport runway at different visibility conditions. Data acquisition and playback system has been developed to capture EVS sensor data (image) in time synch with test vehicle inertial navigation data during EVS field experiments and to playback the experimental data on ESVS flight simulator for ESVS research and concept studies. Efforts are on to conduct EVS flight experiments on CSIR-NAL research aircraft HANSA in Degraded Visual Environment (DVE).

  2. Flexible end-to-end system design for synthetic aperture radar applications

    NASA Astrophysics Data System (ADS)

    Zaugg, Evan C.; Edwards, Matthew C.; Bradley, Joshua P.

    2012-06-01

    This paper presents ARTEMIS, Inc.'s approach to development of end-to-end synthetic aperture radar systems for multiple applications and platforms. The flexible design of the radar and the image processing tools facilitates their inclusion in a variety of application-specific end-to-end systems. Any given application comes with certain requirements that must be met in order to achieve success. A concept of operation is defined which states how the technology is used to meet the requirements of the application. This drives the design decisions. Key to adapting our system to multiple applications is the flexible SlimSAR radar system, which is programmable on-the-fly to meet the imaging requirements of a wide range of altitudes, swath-widths, and platform velocities. The processing software can be used for real-time imagery production or post-flight processing. The ground station is adaptable, and the radar controls can be run by an operator on the ground, on-board the aircraft, or even automated as part of the aircraft autopilot controls. System integration takes the whole operation into account, seeking to flawlessly work with data links and on-board data storage, aircraft and payload control systems, mission planning, and image processing and exploitation. Examples of applications are presented including using a small unmanned aircraft at low altitude with a line of sight data link, a long-endurance UAV maritime surveillance mission with on-board processing, and a manned ground moving target indicator application with the radar using multiple receive channels.

  3. Functional characterization and structural modeling of synthetic polyester-degrading hydrolases from Thermomonospora curvata

    PubMed Central

    2014-01-01

    Thermomonospora curvata is a thermophilic actinomycete phylogenetically related to Thermobifida fusca that produces extracellular hydrolases capable of degrading synthetic polyesters. Analysis of the genome of T. curvata DSM43183 revealed two genes coding for putative polyester hydrolases Tcur1278 and Tcur0390 sharing 61% sequence identity with the T. fusca enzymes. Mature proteins of Tcur1278 and Tcur0390 were cloned and expressed in Escherichia coli TOP10. Tcur1278 and Tcur0390 exhibited an optimal reaction temperature against p-nitrophenyl butyrate at 60°C and 55°C, respectively. The optimal pH for both enzymes was determined at pH 8.5. Tcur1278 retained more than 80% and Tcur0390 less than 10% of their initial activity following incubation for 60 min at 55°C. Tcur0390 showed a higher hydrolytic activity against poly(ε-caprolactone) and polyethylene terephthalate (PET) nanoparticles compared to Tcur1278 at reaction temperatures up to 50°C. At 55°C and 60°C, hydrolytic activity against PET nanoparticles was only detected with Tcur1278. In silico modeling of the polyester hydrolases and docking with a model substrate composed of two repeating units of PET revealed the typical fold of α/β serine hydrolases with an exposed catalytic triad. Molecular dynamics simulations confirmed the superior thermal stability of Tcur1278 considered as the main reason for its higher hydrolytic activity on PET. PMID:25405080

  4. Synthetic stratigraphy of epicontinental seas: a carbonate sedimentation model and its applications in sea level studies

    SciTech Connect

    Cisne, J.L.; Gildner, R.F.

    1984-04-01

    Carbonates from the central parts of epicontinental seas are ideal strata for detailed study of eustatic sea level change. On the basis of sedimentation model in which carbonate accumulation rate is directly proportional to water depth, we developed synthetic stratigraphies for sea level histories expected for post-glacial transgression and for constant and sinusoidally fluctuating ocean ridge volume increase. These histories give distinctly different trends for water depth as a function of stratigraphic position in the sections' bathymetric curves. In general, water depth is proportional to the rate of sea level rise. Depth-dependent sedimentation leads to a time lag between sea level fluctuation and corresponding depth fluctuation which, as examples show, can approach 10/sup 6/ years for depth fluctuations of even a few meters--a fundamental consideration for reconstructing sea level curves, time-correlating sections by bathymetric curves, and relating water depth on continents to ocean ridge volume. Bathymetric curves based on gradient analysis of fossil assemblages (coenocorrelation curves) for American Middle Ordovician sections approximate patterns expected for sinusoidally increasing sea level. The model's predictions are tested in an ''artificial experiment'' that takes advantage of differential subsidence between the craton's middle and its edge to make a difference in the bathymetric histories of sections that otherwise record the same sea level history. The depth dependence in sedimentation was that above wave base net accumulation per year was very roughly 3 x 10/sup -6/ of the water depth.

  5. A Program for Calculating and Plotting Synthetic Common-Source Seismic-Reflection Traces for Multilayered Earth Models.

    ERIC Educational Resources Information Center

    Ramananantoandro, Ramanantsoa

    1988-01-01

    Presented is a description of a BASIC program to be used on an IBM microcomputer for calculating and plotting synthetic seismic-reflection traces for multilayered earth models. Discusses finding raypaths for given source-receiver offsets using the "shooting method" and calculating the corresponding travel times. (Author/CW)

  6. MineSeis -- A MATLAB GUI program to calculate synthetic seismograms from a linear, multi-shot blast source model

    SciTech Connect

    Yang, X.

    1998-12-31

    Modeling ground motions from multi-shot, delay-fired mining blasts is important to the understanding of their source characteristics such as spectrum modulation. MineSeis is a MATLAB{reg_sign} (a computer language) Graphical User Interface (GUI) program developed for the effective modeling of these multi-shot mining explosions. The program provides a convenient and interactive tool for modeling studies. Multi-shot, delay-fired mining blasts are modeled as the time-delayed linear superposition of identical single shot sources in the program. These single shots are in turn modeled as the combination of an isotropic explosion source and a spall source. Mueller and Murphy`s (1971) model for underground nuclear explosions is used as the explosion source model. A modification of Anandakrishnan et al.`s (1997) spall model is developed as the spall source model. Delays both due to the delay-firing and due to the single-shot location differences are taken into account in calculating the time delays of the superposition. Both synthetic and observed single-shot seismograms can be used to construct the superpositions. The program uses MATLAB GUI for input and output to facilitate user interaction with the program. With user provided source and path parameters, the program calculates and displays the source time functions, the single shot synthetic seismograms and the superimposed synthetic seismograms. In addition, the program provides tools so that the user can manipulate the results, such as filtering, zooming and creating hard copies.

  7. Synthetic chloroplasts

    SciTech Connect

    Calvin, M.

    1980-06-01

    The principal function of the chloroplast is to capture solar quanta and to store them in some stable form. We are in the process of trying to construct a totally synthetic system that would simulate some of the reactions of the two photosystems which occur in natural chloroplasts. Toward this end, we have demonstrated a number of the reactions required in separated systems. We have shown that it is possible to transfer electrons across an insulating membrane barrier with a surfactant photosensitizer. Others have shown, and we have confirmed, that it is possible to collect the two electrons necessary for the generation of molecular hydrogen on a heterogeneous catalyst suspended in water and similarly to collect the four holes on another heterogeneous catalyst suspended in water for the generation of molecular oxygen. A synthesis of some of these molecular catalysts for both these purposes is underway, with some partial success. When these partial reactions are assembled in a system, the resulting synthetic chloroplasts will not resemble the natural entity in detailed construction as they will contain no protein.

  8. Detection of aquifer system compaction and land subsidence using interferometric synthetic aperture radar, Antelope Valley, Mojave Desert, California

    USGS Publications Warehouse

    Galloway, D.L.; Hudnut, K.W.; Ingebritsen, S.E.; Phillips, S.P.; Peltzer, G.; Rogez, F.; Rosen, P.A.

    1998-01-01

    Interferometric synthetic aperture radar (InSAR) has great potential to detect and quantify land subsidence caused by aquifer system compaction. InSAR maps with high spatial detail and resolution of range displacement (??10 mm in change of land surface elevation) were developed for a groundwater basin (~103 km2) in Antelope Valley, California, using radar data collected from the ERS-1 satellite. These data allow comprehensive comparison between recent (1993-1995) subsidence patterns and those detected historically (1926-1992) by more traditional methods. The changed subsidence patterns are generally compatible with recent shifts in land and water use. The InSAR-detected patterns are generally consistent with predictions based on a coupled model of groundwater flow and aquifer system compaction. The minor inconsistencies may reflect our imperfect knowledge of the distribution and properties of compressible sediments. When used in conjunction with coincident measurements of groundwater levels and other geologic information, InSAR data may be useful for constraining parameter estimates in simulations of aquifer system compaction.

  9. Mathematical circulatory system model

    NASA Technical Reports Server (NTRS)

    Lakin, William D. (Inventor); Stevens, Scott A. (Inventor)

    2010-01-01

    A system and method of modeling a circulatory system including a regulatory mechanism parameter. In one embodiment, a regulatory mechanism parameter in a lumped parameter model is represented as a logistic function. In another embodiment, the circulatory system model includes a compliant vessel, the model having a parameter representing a change in pressure due to contraction of smooth muscles of a wall of the vessel.

  10. Programmable Ligand Detection System in Plants through a Synthetic Signal Transduction Pathway

    PubMed Central

    Smith, J. Jeff; Albrecht, Kirk D.; Bowen, Tessa A.; Zdunek, Jeffrey K.; Troupe, Jared F.; Cuneo, Matthew J.; Webb, Colleen T.; Hellinga, Homme W.; Medford, June I.

    2011-01-01

    Background There is an unmet need to monitor human and natural environments for substances that are intentionally or unintentionally introduced. A long-sought goal is to adapt plants to sense and respond to specific substances for use as environmental monitors. Computationally re-designed periplasmic binding proteins (PBPs) provide a means to design highly sensitive and specific ligand sensing capabilities in receptors. Input from these proteins can be linked to gene expression through histidine kinase (HK) mediated signaling. Components of HK signaling systems are evolutionarily conserved between bacteria and plants. We previously reported that in response to cytokinin-mediated HK activation in plants, the bacterial response regulator PhoB translocates to the nucleus and activates transcription. Also, we previously described a plant visual response system, the de-greening circuit, a threshold sensitive reporter system that produces a visual response which is remotely detectable and quantifiable. Methodology/Principal Findings We describe assembly and function of a complete synthetic signal transduction pathway in plants that links input from computationally re-designed PBPs to a visual response. To sense extracellular ligands, we targeted the computational re-designed PBPs to the apoplast. PBPs bind the ligand and develop affinity for the extracellular domain of a chemotactic protein, Trg. We experimentally developed Trg fusions proteins, which bind the ligand-PBP complex, and activate intracellular PhoR, the HK cognate of PhoB. We then adapted Trg-PhoR fusions for function in plants showing that in the presence of an external ligand PhoB translocates to the nucleus and activates transcription. We linked this input to the de-greening circuit creating a detector plant. Conclusions/Significance Our system is modular and PBPs can theoretically be designed to bind most small molecules. Hence our system, with improvements, may allow plants to serve as a simple and

  11. Novel bio-synthetic hybrid materials and coculture systems for musculoskeletal tissue engineering

    NASA Astrophysics Data System (ADS)

    Lee, Hyeseung Janice

    Tissue Engineering is a truly exciting field of this age, trying to regenerate and repair impaired tissues. Unlike the old artificial implants, tissue engineering aims at making a long-term functional biological replacement. One strategy for such tissue engineering requires the following three components: cells, scaffolds, and soluble factors. Cells are cultured in a three-dimensional (3D) scaffold with medium containing various soluble factors. Once a tissue is developed in vitro, then it is implanted in vivo. The overall goal of this thesis was to develop novel bio-synthetic hybrid scaffolds and coculture system for musculoskeletal tissue engineering. The most abundant cartilage extracellular matrix (ECM) components are collagen and glycosaminoglycan (GAG), which are the natural scaffold for chondrocytes. As two different peptides, collagen mimetic peptide (CMP) and hyaluronic acid binding peptide (HABPep) were previously shown to bind to collagen and hyaluronic acid (HA) of GAG, respectively, it was hypothesized that immobilizing CMP and HABP on 3D scaffold would results in an interaction between ECM components and synthetic scaffolds via peptide-ECM bindings. CMP or HABPep-conjugated photopolymerizable poly(ethylene oxide) diacrylate (PEODA) hydrogels were synthesized and shown to retain encapsulated collagen or HA, respectively. This result supported that conjugated CMP and HABPep can interact with collagen and HA, respectively, and can serve as biological linkers in 3D synthetic hydrogels. When chondrocytes or mesenchymal stem cells (MSCs) were seeded, cells in CMP-conjugated scaffolds produced significantly more amount of type II collagen and GAG, compared to those in control scaffolds. Moreover, MSCs cultured in CMP-conjugated scaffolds exhibited lower level of hypertrophic markers, cbfa-1 and type X collagen. These results demonstrated that enhanced interaction between collagen and scaffold via CMP improves chondrogenesis of chondrocytes and MSCs and

  12. Concept of Operations for Commercial and Business Aircraft Synthetic Vision Systems. 1.0

    NASA Technical Reports Server (NTRS)

    Williams Daniel M.; Waller, Marvin C.; Koelling, John H.; Burdette, Daniel W.; Capron, William R.; Barry, John S.; Gifford, Richard B.; Doyle, Thomas M.

    2001-01-01

    A concept of operations (CONOPS) for the Commercial and Business (CaB) aircraft synthetic vision systems (SVS) is described. The CaB SVS is expected to provide increased safety and operational benefits in normal and low visibility conditions. Providing operational benefits will promote SVS implementation in the Net, improve aviation safety, and assist in meeting the national aviation safety goal. SVS will enhance safety and enable consistent gate-to-gate aircraft operations in normal and low visibility conditions. The goal for developing SVS is to support operational minima as low as Category 3b in a variety of environments. For departure and ground operations, the SVS goal is to enable operations with a runway visual range of 300 feet. The system is an integrated display concept that provides a virtual visual environment. The SVS virtual visual environment is composed of three components: an enhanced intuitive view of the flight environment, hazard and obstacle defection and display, and precision navigation guidance. The virtual visual environment will support enhanced operations procedures during all phases of flight - ground operations, departure, en route, and arrival. The applications selected for emphasis in this document include low visibility departures and arrivals including parallel runway operations, and low visibility airport surface operations. These particular applications were selected because of significant potential benefits afforded by SVS.

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

    PubMed

    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.

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

    PubMed Central

    He, Fei; Murabito, Ettore; Westerhoff, Hans 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 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. PMID:27075000

  15. Dynamic Tunnel Usability Study: Format Recommendations for Synthetic Vision System Primary Flight Displays

    NASA Technical Reports Server (NTRS)

    Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Kramer, Lynda J.; Bailey, Randall E.

    2006-01-01

    A usability study evaluating dynamic tunnel concepts has been completed under the Aviation Safety and Security Program, Synthetic Vision Systems Project. The usability study was conducted in the Visual Imaging Simulator for Transport Aircraft Systems (VISTAS) III simulator in the form of questionnaires and pilot-in-the-loop simulation sessions. Twelve commercial pilots participated in the study to determine their preferences via paired comparisons and subjective rankings regarding the color, line thickness and sensitivity of the dynamic tunnel. The results of the study showed that color was not significant in pilot preference paired comparisons or in pilot rankings. Line thickness was significant for both pilot preference paired comparisons and in pilot rankings. The preferred line/halo thickness combination was a line width of 3 pixels and a halo of 4 pixels. Finally, pilots were asked their preference for the current dynamic tunnel compared to a less sensitive dynamic tunnel. The current dynamic tunnel constantly gives feedback to the pilot with regard to path error while the less sensitive tunnel only changes as the path error approaches the edges of the tunnel. The tunnel sensitivity comparison results were not statistically significant.

  16. Using synthetic tracers as a proxy for PM2.5 air quality in physical climate models

    NASA Astrophysics Data System (ADS)

    Fang, Y.; Fiore, A. M.; Lamarque, J.; Horowitz, L. W.

    2011-12-01

    Fine particulate matter (PM2.5) adversely affects human health and is regulated as a criteria pollutant in the United States. As it is sensitive to weather, PM2.5 is expected to change with shifts in climate. Understanding the effect of climate change on PM2.5 remains inadequate. The limited availability of climate models with full chemistry complicates efforts to rigorously evaluate the uncertainties in the PM2.5 response to a warmer climate. We provide a proof-of-concept study that illustrates the potential for synthetic tracers to represent PM2.5 distributions in a climate model without interactive chemistry. The GFDL chemistry-climate model (AM3) is used to simulate current-day (1981-2000) and future (2081-2100) climate and PM2.5 distributions. We include a synthetic aerosol tracer (SAt) in our model, as adapted from the tracer experiment designed under the Hemispheric Transport of Air Pollution Task Force, with CO emissions, a 25-day lifetime and wet deposition as for sulfate. We focus on summers over the Northeastern United States. AM3 present-day simulation captures the magnitude and spatial variability of the U.S. Air Quality System (USAQS) PM2.5 observations during summer 1997-2007 (r > 0.7 with a bias of +30%). The SAt daily time series is highly correlated with that of PM2.5 (r within 0.8-0.9 in 20 summers) and the cumulative density functions of SAt resemble those of PM2.5 both at present and in the future. We develop a linear regression model to reconstruct PM2.5 from SAt that captures 75% and 80% of the simulated PM2.5 daily variability at present and in the future, respectively. This regression model also represents PM2.5 non-attainment days for the 35 ug/m3 24-h mean PM2.5 standard: 4% and 14% of all summer days are non-attainment days in AM3 present and future climate simulations, respectively; those statistics are 3% and 12% for the regression model. We further examine situations where the regression model underestimates PM2.5, and find that these

  17. Multidimensional Signal Processing Techniques for Disturbance Mitigation in Synthetic Aperture Systems

    NASA Astrophysics Data System (ADS)

    Edussooriya, Chamira Udaya Shantha

    In this thesis, multidimensional signal processing techniques to mitigate disturbances in synthetic aperture systems such as radio telescopes are investigated. Here, two computationally efficient three-dimensional (3D) spatio-temporal (ST) finite impulse response (FIR) cone filter bank structures are proposed. Furthermore, a strategy is proposed to design 3D ST FIR frustum filter banks, having double-frustum-shaped passbands oriented along the temporal axis, derived from appropriate 3D ST FIR cone filter banks. Both types of cone and frustum filter banks are almost alias free and provide near-perfect reconstruction. In the proposed cone and frustum filter banks, both temporal and spatial filtering operations can be carried out at a significantly lower rate compared to previously reported 3D ST FIR cone filter banks implying lower power consumption. Furthermore, the proposed cone and frustum filter banks require a significantly lower computational complexity than previously reported 3D ST FIR cone and frustum filter banks. Importantly, this is achieved without deteriorating the improvement in signal-to-interference-plus-noise ratio. A theoretical analysis of brightness distribution (BD) errors caused by parameter perturbations and mismatches among the transfer functions of receivers employed in synthetic aperture systems is presented. First, the BD errors caused by perturbations in the transfer functions of low noise amplifiers (LNAs) and anti-aliasing filters (AAFs) are considered, and the characteristics of the additive BD error and its effects on synthesized BDs are thoroughly analyzed. Second, the conditions that should be satisfied by the transfer functions of digital beamformers to eliminate the BD errors caused by their phase responses are examined. The sufficient condition to eliminate the BD errors is that the transfer functions are matched, and, interestingly, the phase responses are not necessary to be linear. Furthermore, the BD errors caused by typical

  18. Performance modeling of nonconcentrating solar detoxification systems

    SciTech Connect

    March, M.; Martin, A.; Saltiel, C.

    1995-03-01

    A detailed simulation model is developed for predicting the performance of solar detoxification systems. Concentration profiles are determined via a method of lines approach during sunlight hours for acquired and synthetic (simulating clear and cloudy days) ultraviolet radiation intensity data. Verification of the model is performed with comparison against indoor laboratory and outdoor field test results. Simulations are performed over a range of design parameters to examine system sensitivity. Discussions are focused on the determination of optimal sizing and operating conditions. 17 refs., 8 figs.

  19. Synthetic biology between challenges and risks: suggestions for a model of governance and a regulatory framework, based on fundamental rights.

    PubMed

    Colussi, Ilaria Anna

    2013-01-01

    This paper deals with the emerging synthetic biology, its challenges and risks, and tries to design a model for the governance and regulation of the field. The model is called of "prudent vigilance" (inspired by the report about synthetic biology, drafted by the U.S. Presidential Commission on Bioethics, 2010), and it entails (a) an ongoing and periodically revised process of assessment and management of all the risks and concerns, and (b) the adoption of policies - taken through "hard law" and "soft law" sources - that are based on the principle of proportionality (among benefits and risks), on a reasonable balancing between different interests and rights at stake, and are oriented by a constitutional frame, which is represented by the protection of fundamental human rights emerging in the field of synthetic biology (right to life, right to health, dignity, freedom of scientific research, right to environment). After the theoretical explanation of the model, its operability is "checked", by considering its application with reference to only one specific risk brought up by synthetic biology - biosecurity risk, i.e. the risk of bioterrorism.

  20. A model-based multiple-pinhole synthetic imager for stand-off range gamma-emitting objects

    NASA Astrophysics Data System (ADS)

    DeRego, Paul J.; Hecht, Adam A.; Dias da Cunha, Kenya M.; Baldez, Phoenix

    2016-09-01

    Pixelated Cadmium Zinc Telluride (CZT) detectors provide the opportunity to perform spectroscopic imaging for discriminating one radioactive material from another. Although Compton interactions provide a means for imaging high energy gamma sources, identification of materials emitting lower energy signatures are better suited to collimator imaging techniques. This paper specifically considers a multiple pinhole method for its simplicity of pinhole focusing combined with straightforward processing methods for incorporating multiple apertures to reduce photon collection time while retaining image resolution. Multiple pinhole image detections are combined using an iterative Maximum- Likelihood Expectation-Maximization (MLEM) synthetic imaging algorithm. To enable subsequent field operations, the imaging system matrix is computed using an imaging model with adjustable parameters rather than one experimentally acquired from point sources. The system model includes an object space, a multiple pinhole collimator plane, and a pixelated detection plane. The modeled object space is implemented in two dimensions to reduce image reconstruction burden since 3D imaging is not practical for single view stand-off imaging. Focusing is modeled by a function computing photon trajectory and passage through the pinhole patterned barrier plane. Results show that a MLEM processed image will achieve resolution approaching that of a single pinhole imaged onto the full detector. The multiple pinhole advantages of simple implementation with shorter focal lengths combined with the availability of portable CZT detectors would be useful in short stand-off applications. Work is currently in progress to experimentally quantify spatial resolution and imaging timelines using an eV Products D-Matrix 4x4 array of pixelated CZT modules.

  1. Deep source model for Nevado del Ruiz Volcano, Colombia, constrained by interferometric synthetic aperture radar observations

    NASA Astrophysics Data System (ADS)

    Lundgren, P.; Samsonov, S. V.; López, C. M.; Ordoñez, M.

    2015-12-01

    Nevado del Ruiz (NRV) is part of a large volcano complex in the northern Andes of Colombia with a large glacier that erupted in 1985, generating a lahar killing over 23,000 people in the city of Armero and 2,000 people in the town of Chinchina. NRV is the most active volcano in Colombia and since 2012 has generated small eruptions, with no casualties, and constant gas and ash emissions. Interferometric synthetic aperture radar (InSAR) observations from ascending and descending track RADARSAT-2 data show a large (>20 km) wide inflation pattern apparently starting in late 2011 to early 2012 and continuing to the time of this study in early 2015 at a LOS rate of over 3-4 cm/yr (Fig. 1). Volcano pressure volume models for both a point source (Mogi) and a spheroidal (Yang) source find solutions over 14 km beneath the surface, or 10 km below sea level, and centered 10 km to the SW of Nevado del Ruiz volcano. The spheroidal source has a roughly horizontal long axis oriented parallel to the Santa Isabel - Nevado del Ruiz volcanic line and perpendicular to the ambient compressive stress direction. Its solution provides a statistically significant improvement in fit compared to the point source, though consideration of spatially correlated noise sources may diminish this significance. Stress change computations do not favor one model over the other but show that propagating dikes would become trapped in sills, leading to a more complex pathway to the surface and possibly explaining the significant lateral distance between the modeled sources and Nevado del Ruiz volcano.

  2. Synthetic biology, inspired by synthetic chemistry.

    PubMed

    Malinova, V; Nallani, M; Meier, W P; Sinner, E K

    2012-07-16

    The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell.

  3. Toxicogenomic responses in rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to model chemicals and a synthetic mixture.

    PubMed

    Finne, E F; Cooper, G A; Koop, B F; Hylland, K; Tollefsen, K E

    2007-03-10

    As more salmon gene expression data has become available, the cDNA microarray platform has emerged as an appealing alternative in ecotoxicological screening of single chemicals and environmental samples relevant to the aquatic environment. This study was performed to validate biomarker gene responses of in vitro cultured rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to model chemicals, and to investigate effects of mixture toxicity in a synthetic mixture. Chemicals used for 24h single chemical- and mixture exposures were 10 nM 17alpha-ethinylestradiol (EE2), 0.75 nM 2,3,7,8-tetrachloro-di-benzodioxin (TCDD), 100 microM paraquat (PQ) and 0.75 microM 4-nitroquinoline-1-oxide (NQO). RNA was isolated from exposed cells, DNAse treated and quality controlled before cDNA synthesis, fluorescent labelling and hybridisation to a 16k salmonid microarray. The salmonid 16k cDNA array identified differential gene expression predictive of exposure, which could be verified by quantitative real time PCR. More precisely, the responses of biomarker genes such as cytochrome p4501A and UDP-glucuronosyl transferase to TCDD exposure, glutathione reductase and gammaglutamyl cysteine synthetase to paraquat exposure, as well as vitellogenin and vitelline envelope protein to EE2 exposure validated the use of microarray applied to RNA extracted from in vitro exposed hepatocytes. The mutagenic compound NQO did not result in any change in gene expression. Results from exposure to a synthetic mixture of the same four chemicals, using identical concentrations as for single chemical exposures, revealed combined effects that were not predicted by results for individual chemicals alone. In general, the response of exposure to this mixture led to an average loss of approximately 60% of the transcriptomic signature found for single chemical exposure. The present findings show that microarray analyses may contribute to our mechanistic understanding of single contaminant mode of action as well

  4. Modeling batch kinetics and thermodynamics of zinc and cadmium ions removal from waste solutions using synthetic zeolite A.

    PubMed

    El-Kamash, A M; Zaki, A A; El Geleel, M Abed

    2005-12-09

    The sorptive removal of zinc and cadmium ions from aqueous solutions using synthetic zeolite A was investigated. Experiments were carried out as a function of solute concentration and temperature (298-333 K). Several kinetic models were used to test the experimental rate data and to examine the controlling mechanism of the sorption process. Various parameters such as effective diffusion coefficient, activation energy and entropy of activation were evaluated. Equilibrium sorption data were analyzed using Langmuir, Freundlich and Dubinin-Radushkevich (D-R) isotherm models. Of the model tested, both Freundlich and D-R isotherm expressions were found to give better fit to the experimental equilibrium data compared to Langmuir model. The mean free energy is in all cases in the range corresponding to the ion exchange type of sorption. The results indicated that synthetic zeolite A can be used as an efficient ion exchange material for the removal of zinc and cadmium ions from industrial and radioactive wastewaters.

  5. Synthetic biology in plastids.

    PubMed

    Scharff, Lars B; Bock, Ralph

    2014-06-01

    Plastids (chloroplasts) harbor a small gene-dense genome that is amenable to genetic manipulation by transformation. During 1 billion years of evolution from the cyanobacterial endosymbiont to present-day chloroplasts, the plastid genome has undergone a dramatic size reduction, mainly as a result of gene losses and the large-scale transfer of genes to the nuclear genome. Thus the plastid genome can be regarded as a naturally evolved miniature genome, the gradual size reduction and compaction of which has provided a blueprint for the design of minimum genomes. Furthermore, because of the largely prokaryotic genome structure and gene expression machinery, the high transgene expression levels attainable in transgenic chloroplasts and the very low production costs in plant systems, the chloroplast lends itself to synthetic biology applications that are directed towards the efficient synthesis of green chemicals, biopharmaceuticals and other metabolites of commercial interest. This review describes recent progress with the engineering of plastid genomes with large constructs of foreign or synthetic DNA, and highlights the potential of the chloroplast as a model system in bottom-up and top-down synthetic biology approaches.

  6. Differential Multiscale Modeling of Chemically Complex Materials under Heavy Deformation: Biological, Bioinspired and Synthetic Hierarchical Materials

    DTIC Science & Technology

    2010-06-01

    biological materials such as nacre, bone and their hierarchical organization leads to: a) not following the usual banana -curve for synthetic materials of...hierarchies, a significant performance increase can be achieved. The “ Banana curve” (seen in conventional synthetic materials) is indicated in the...plot as well. 9 For more than 10,000 elements (also reported in the IJAM paper), a very interesting result is obtained. First, the banana curve

  7. BINARY STAR SYNTHETIC PHOTOMETRY AND DISTANCE DETERMINATION USING BINSYN

    SciTech Connect

    Linnell, Albert P.; DeStefano, Paul; Hubeny, Ivan E-mail: pdestefa@uw.edu

    2013-09-15

    This paper extends synthetic photometry to components of binary star systems. The paper demonstrates accurate recovery of single star photometric properties for four photometric standards, Vega, Sirius, GD153, and HD209458, ranging over the HR diagram, when their model synthetic spectra are placed in fictitious binary systems and subjected to synthetic photometry processing. Techniques for photometric distance determination have been validated for all four photometric standards.

  8. Optimal waveform-based clutter suppression algorithm for recursive synthetic aperture radar imaging systems

    NASA Astrophysics Data System (ADS)

    Zhu, Binqi; Gao, Yesheng; Wang, Kaizhi; Liu, Xingzhao

    2016-04-01

    A computational method for suppressing clutter and generating clear microwave images of targets is proposed in this paper, which combines synthetic aperture radar (SAR) principles with recursive method and waveform design theory, and it is suitable for SAR for special applications. The nonlinear recursive model is introduced into the SAR operation principle, and the cubature Kalman filter algorithm is used to estimate target and clutter responses in each azimuth position based on their previous states, which are both assumed to be Gaussian distributions. NP criteria-based optimal waveforms are designed repeatedly as the sensor flies along its azimuth path and are used as the transmitting signals. A clutter suppression filter is then designed and added to suppress the clutter response while maintaining most of the target response. Thus, with fewer disturbances from the clutter response, we can generate the SAR image with traditional azimuth matched filters. Our simulations show that the clutter suppression filter significantly reduces the clutter response, and our algorithm greatly improves the SINR of the SAR image based on different clutter suppression filter parameters. As such, this algorithm may be preferable for special target imaging when prior information on the target is available.

  9. A novel synthetic peptide vector system for optimal gene delivery to bone marrow stromal cells.

    PubMed

    Haitao, Pan; Qixin, Zheng; Xiaodong, Guo

    2007-03-01

    A 23-amino acid, bifunctional, integrin-targeted synthetic peptide was evaluated for ex vivo gene delivery to rabbit bone marrow stromal cells (BMSCs). The peptide (K)(16)GRGDSPC consists of an amino terminal domain of 16 lysines for electrostatic binding of DNA, and a 7-amino acid integrin-binding domain at the carboxyl terminal. PcDNA3-EGFP plasmids were transfected into BMSCs by (K)(16)GRGDSPC and the positive cells gave out a bright green fluorescence. High levels of gene delivery of pcDNA3-TGF-beta1 plasmids were obtained with 2 to 4 microg/ml DNA concentration, with (K)(16)GRGDSPC at an optimal peptide: DNA w/w ratio of 3:1, with a required exposure time of more than 4 h but shorter than 24 h for BMSC exposure to the peptide/DNA complexes with completely absent serum in the initial stage; with 100 microM chloroquine and at least 8 h exposure for BMSC exposure to chloroquine; with a fusogenic peptide at an optimal (K)(16)GRGDSPC/DNA/fusogenic peptide w/w ratio of 3:1:5; and with Lipofectamine 2000 at an optimal (K)(16)GRGDSPC/DNA/Lipofectamine 2000 w/w ratio of 3:1:2 at a constant DNA concentration of 2 microg/ml. Chloroquine, the fusogenic peptide and Lipofectamine 2000 all significantly promoted gene delivery, but chloroquine was more effective than the fusogenic peptide and had obvious synergistic effects with Lipofectamine 2000. Under optimal conditions, TGF-beta1 gene was transfected into BMSCs without observable toxicity, and the stable expression was examined by RT-PCR and Western blot analysis. The stable transgenic cells showed obvious bands. This novel synthetic peptide, providing a new way for the use of polylysine and RGD motif in DNA vector system, is potentially well suited to ex vivo gene delivery to BMSCs for experimental and clinical applications in the field of bone tissue engineering.

  10. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    DOEpatents

    Craig, George D.; Glass, Robert; Rupp, Bernhard

    1997-01-01

    A method for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10.sup.6 V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved.

  11. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    DOEpatents

    Craig, G.D.; Glass, R.; Rupp, B.

    1997-01-28

    A method is disclosed for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10{sup 6}V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved. 2 figs.

  12. Recent applications of a synthetic model of cytochrome c oxidase: beyond functional modeling.

    PubMed

    Collman, James P; Ghosh, Somdatta

    2010-07-05

    This account reports recent developments of a functional model for the active site of cytochrome c oxidase (CcO). This CcO mimic not only performs the selective four-electron reduction of oxygen to water but also catalytically reduces oxygen using the biological one-electron reductant, cytochrome c. This functional model has been used to understand other biological reactions of CcO, for example, the interaction between the gaseous hormone, NO, and CcO. A mechanism for inactivating NO-CcO complexes is found to involve a reaction between oxygen and Cu(B). Moreover, NO is shown to be capable of protecting CcO from toxic inhibitors such as CN(-) and CO. Finally, this functional CcO model has been used to show how H(2)S could induce hibernation by reversibly inhibiting the oxygen binding step involved in respiration.

  13. Mimicry of the radical pair and triplet states in photosynthetic reaction centers with a synthetic model

    SciTech Connect

    Wasielewski, M.R.; Greenfield, S.R.; Svec, W.A.

    1997-08-01

    Results are presented on a photosynthetic model system that closely mimics the spin dynamics of triplet state formation found in photosynthetic reaction centers. This research will make it possible to design new models to probe the mechanism of the primary events of photosynthesis.

  14. Oral Delivery of a Synthetic Sterol Reduces Axonopathy and Inflammation in a Rodent Model of Glaucoma.

    PubMed

    Lambert, Wendi S; Carlson, Brian J; Formichella, Cathryn R; Sappington, Rebecca M; Ahlem, Clarence; Calkins, David J

    2017-01-01

    Glaucoma is a group of optic neuropathies associated with aging and sensitivity to intraocular pressure (IOP). The disease is the leading cause of irreversible blindness worldwide. Early progression in glaucoma involves dysfunction of retinal ganglion cell (RGC) axons, which comprise the optic nerve. Deficits in anterograde transport along RGC axons to central visual structures precede outright degeneration, and preventing these deficits is efficacious at abating subsequent progression. HE3286 is a synthetic sterol derivative that has shown therapeutic promise in models of inflammatory disease and neurodegenerative disease. We examined the efficacy of HE3286 oral delivery in preventing loss of anterograde transport in an inducible model of glaucoma (microbead occlusion). Adult rats received HE3286 (20 or 100 mg/kg) or vehicle daily via oral gavage for 4 weeks. Microbead occlusion elevated IOP ~30% in all treatment groups, and elevation was not affected by HE3286 treatment. In the vehicle group, elevated IOP reduced anterograde axonal transport to the superior colliculus, the most distal site in the optic projection, by 43% (p = 0.003); HE3286 (100 mg/kg) prevented this reduction (p = 0.025). HE3286 increased brain-derived neurotrophic factor (BDNF) in the optic nerve head and retina, while decreasing inflammatory and pathogenic proteins associated with elevated IOP compared to vehicle treatment. Treatment with HE3286 also increased nuclear localization of the transcription factor NFκB in collicular and retinal neurons, but decreased NFκB in glial nuclei in the optic nerve head. Thus, HE3286 may have a neuroprotective influence in glaucoma, as well as other chronic neurodegenerations.

  15. Oral Delivery of a Synthetic Sterol Reduces Axonopathy and Inflammation in a Rodent Model of Glaucoma

    PubMed Central

    Lambert, Wendi S.; Carlson, Brian J.; Formichella, Cathryn R.; Sappington, Rebecca M.; Ahlem, Clarence; Calkins, David J.

    2017-01-01

    Glaucoma is a group of optic neuropathies associated with aging and sensitivity to intraocular pressure (IOP). The disease is the leading cause of irreversible blindness worldwide. Early progression in glaucoma involves dysfunction of retinal ganglion cell (RGC) axons, which comprise the optic nerve. Deficits in anterograde transport along RGC axons to central visual structures precede outright degeneration, and preventing these deficits is efficacious at abating subsequent progression. HE3286 is a synthetic sterol derivative that has shown therapeutic promise in models of inflammatory disease and neurodegenerative disease. We examined the efficacy of HE3286 oral delivery in preventing loss of anterograde transport in an inducible model of glaucoma (microbead occlusion). Adult rats received HE3286 (20 or 100 mg/kg) or vehicle daily via oral gavage for 4 weeks. Microbead occlusion elevated IOP ~30% in all treatment groups, and elevation was not affected by HE3286 treatment. In the vehicle group, elevated IOP reduced anterograde axonal transport to the superior colliculus, the most distal site in the optic projection, by 43% (p = 0.003); HE3286 (100 mg/kg) prevented this reduction (p = 0.025). HE3286 increased brain-derived neurotrophic factor (BDNF) in the optic nerve head and retina, while decreasing inflammatory and pathogenic proteins associated with elevated IOP compared to vehicle treatment. Treatment with HE3286 also increased nuclear localization of the transcription factor NFκB in collicular and retinal neurons, but decreased NFκB in glial nuclei in the optic nerve head. Thus, HE3286 may have a neuroprotective influence in glaucoma, as well as other chronic neurodegenerations. PMID:28223915

  16. Evaluation of experimental and finite element models of synthetic and cadaveric femora for pre-clinical design-analysis.

    PubMed

    McNamara, B P; Cristofolini, L; Toni, A; Taylor, D

    1994-01-01

    The aim of this study was to determine the validity with which the finite element method could model synthetic bone and thereby determine the appropriateness of such femur analogues for application in pre-clinical tests. The performance of these synthetic femora was compared with cadaveric bone when employing the same geometric and material definition protocols. A four-point bend loading configuration was selected for this analysis. Four synthetic femurs and an embalmed cadaveric bone were tested experimentally to determine the structural bending stiffness (k) for the diaphysis of these bones. A finite element (FE) model was generated and an analysis performed for each bone type to estimate the Young's modulus (E) required to obtain a model stiffness equivalent to that obtained experimentally. The estimated material elastic modulus in the FE model for the synthetic femur was found to be very similar to available data for this bone analogue. The estimated cadaveric bone modulus however was found to differ significantly from documented values for cortical bone. A theoretical analysis demonstrated the great sensitivity of the estimated modulus value to the accuracy of the geometric definition. The very low variability found in the experimental test on the synthetic bones together with their more regular geometry and the possibility of achieving greater accuracy in geometric definition was shown to enable the production of a valid FE model of this bone for an isotropic homogeneous material description. Conversely, the greater irregularity of geometry, together with the less obvious differentiation between the cortical and cancellous bone in the cadaveric specimen makes accurate geometric description of this bone very difficult. This fact, together with the uncertainty concerning the quality of the cadaveric bone and its viscoelastic response during mechanical testing, makes reproduction of its behaviour in a FE model a much more demanding task. It is suggested that

  17. Hybrid Energy System Modeling in Modelica

    SciTech Connect

    William R. Binder; Christiaan J. J. Paredis; Humberto E. Garcia

    2014-03-01

    In this paper, a Hybrid Energy System (HES) configuration is modeled in Modelica. Hybrid Energy Systems (HES) have as their defining characteristic the use of one or more energy inputs, combined with the potential for multiple energy outputs. Compared to traditional energy systems, HES provide additional operational flexibility so that high variability in both energy production and consumption levels can be absorbed more effectively. This is particularly important when including renewable energy sources, whose output levels are inherently variable, determined by nature. The specific HES configuration modeled in this paper include two energy inputs: a nuclear plant, and a series of wind turbines. In addition, the system produces two energy outputs: electricity and synthetic fuel. The models are verified through simulations of the individual components, and the system as a whole. The simulations are performed for a range of component sizes, operating conditions, and control schemes.

  18. Bergman Clusters, Multiple Bonds, and Defect Planes: Synthetic Outcomes of Chemical Frustration in Ternary Intermetallic Systems

    NASA Astrophysics Data System (ADS)

    Hadler, Amelia Beth

    Intermetallics crystallize in a variety of complex structures, many of which show unusual bonding or intriguing properties. Understanding what factors drive this structural chemistry would be a valuable step towards designing new intermetallics with specific structures or properties. One pathway towards understanding and predicting the structures of complex intermetallics is chemical frustration, a design tool which harnesses competition between incompatible bonding or packing modes to induce complexity in ternary intermetallic systems. The research outlined in this thesis focuses on developing chemical frustration through exploratory synthesis in ternary systems designed to induce frustration between the tetrahedral close packing of many intermetallics and the simple cubic packing seen for ionic salts or elemental metals. Syntheses in three systems yielded six new ternary intermetallics, four of which crystallize in novel structure types. Three were discovered in the Ca-Cu-Cd system: Ca5Cu2Cd and Ca2Cu 2Cd9, which adopt ternary variants of binary structures, and Ca10Cu2Cd27, which crystallizes in a new structure built from Bergman clusters. All three structures can be traced to electronic packing frustration induced by the similar electronegativities but different metallic radii of Cu and Cd. The Gd-Fe-C system yielded the new carbometalate Gd13Fe 10C13 and an oxycarbide derivative. These phases crystallize in structures built from Gd tricapped trigonal prisms interpenetrated by an Fe-C network. Theoretical analyses reveal that Fe-Fe and Fe-C multiple bonding is found throughout this network. A theoretical investigation of similar carbides uncovers additional metal-metal, metal-carbon, and carbon-carbon multiple bonding. This unusual bonding stabilizes the carbides by satisfying preferred electron counts for their transition metal sites. One new phase, Mg4.5Pd5Ge1.5, was found in the Mg-Pd-Ge system. Its structure is closely related to the CsCl-type structure of

  19. Synergistic Synthetic Biology: Units in Concert.

    PubMed

    Trosset, Jean-Yves; Carbonell, Pablo

    2013-01-01

    Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.

  20. The Synthetic Parasite-Derived Peptide GK1 Increases Survival in a Preclinical Mouse Melanoma Model

    PubMed Central

    Vera-Aguilera, Jesús; Hernaiz-Leonardo, Juan Carlos; Moreno-Aguilera, Eduardo; Monteverde-Suarez, Diego; Vera-Aguilera, Carlos; Estrada-Bárcenas, Daniel

    2013-01-01

    Abstract Purpose The therapeutic efficacy of a synthetic parasite-derived peptide GK1, an immune response booster, was evaluated in a mouse melanoma model. This melanoma model correlates with human stage IIb melanoma, which is treated with wide surgical excision; a parallel study employing a surgical treatment was carried out as an instructive goal. Experimental Design C57BL/6 mice were injected subcutaneously in the flank with 2×105 B16-F10 murine melanoma cells. When the tumors reached 20 mm3, mice were separated into two different groups; the GK1 group, treated weekly with peritumoral injections of GK1 (10 μg/100 μL of sterile saline solution) and the control group, treated weekly with an antiseptic peritumoral injection of 100 μL of sterile saline solution without further intervention. All mice were monitored daily for clinical appearance, tumor size, and survival. Surgical treatment was performed in parallel when the tumor size was 20 mm3 (group A), 500 mm3 (group B), and >500 mm3 (group C). Results The GK1 peptide effectively increased the mean survival time by 9.05 days, corresponding to an increase of 42.58%, and significantly delayed tumor growth from day 3 to 12 of treatment. In addition, tumor necrosis was significantly increased (p<0.05) in the treated mice. The overall survival rates obtained with surgical treatment at 6 months were 83.33% for group A, 40% for group B, and 0% for group C, with significant differences (p<0.05) among the groups. Conclusions The GK1 peptide demonstrated therapeutic properties in a mouse melanoma model, as treatment resulted in a significant increase in the mean survival time of the treated animals (42.58%). The potential for GK1 to be used as a primary or adjuvant component of chemotherapeutic cocktails for the treatment of experimental and human cancers remains to be determined, and surgical removal remains a challenge for any new experimental treatment of melanoma in mouse models. PMID:23841709

  1. MLS: Airplane system modeling

    NASA Technical Reports Server (NTRS)

    Thompson, A. D.; Stapleton, B. P.; Walen, D. B.; Rieder, P. F.; Moss, D. G.

    1981-01-01

    Analysis, modeling, and simulations were conducted as part of a multiyear investigation of the more important airplane-system-related items of the microwave landing system (MLS). Particular emphasis was placed upon the airplane RF system, including the antenna radiation distribution, the cabling options from the antenna to the receiver, and the overall impact of the airborne system gains and losses upon the direct-path signal structure. In addition, effort was expended toward determining the impact of the MLS upon the airplane flight management system and developing the initial stages of a fast-time MLS automatic control system simulation model. Results ot these studies are presented.

  2. Potential impact of synthetic biology on the development of microbial systems for the production of renewable fuels and chemicals.

    PubMed

    Picataggio, Stephen

    2009-06-01

    Synthetic biology leverages advances in computational biology, molecular biology, protein engineering, and systems biology to design, synthesize, and assemble genetic elements for manipulating cell phenotypes. This emerging field is founded on a vast amount of gene sequence data available in public databases and our ability to rapidly and inexpensively synthesize DNA fragments of sufficient length to encode full-length genes, enzymes, metabolic pathways, and even entire genomes. Several thousand genetic elements encoding enzymes, reporters, repressors, activators, promoters, terminators, ribosome binding sites, signaling devices, and measurement systems are now available for engineering microbes. In addition to facilitating rational design, these new tools allow us to create and harness genetic diversity in combinatorial approaches to rapidly optimize metabolic pathways. As such, synthetic biology holds great promise for accelerating the development of microbial systems for the production of renewable fuels and chemicals.

  3. Analysis of natural time domain entropy fluctuations of synthetic seismicity generated by a simple stick-slip system with asperities

    NASA Astrophysics Data System (ADS)

    Vargas, C. A.; Flores-Márquez, E. L.; Ramírez-Rojas, A.; Telesca, L.

    2015-02-01

    In the framework of the information theory, entropy measures the level of disorder of a system or its uncertainty. Varotsos et al. (2004) introduced the concept of entropy in natural time domain as a discriminating statistics. In this paper, we analyzed the fluctuations of entropy, δS, of synthetic seismicity produced by an experimental stick-slip system in order to investigate its Markovian behavior. Our system, whose asperities are given by sandpapers of different granularity degrees, mimics the dynamics of tectonic plates. We found that δS is able to characterize the synthetic seismic process as non-Markovian for higher threshold magnitudes and lower lengths of the time window sweeping through the dataset.

  4. Multi-spectral modulation detection of co-phasing errors for sparse-optical-synthetic-aperture systems

    NASA Astrophysics Data System (ADS)

    Dong, Li; Peng, Qi; Ma, Haotong; Xie, Zongliang; Wang, Zhipeng

    2016-10-01

    The sparse-optical-synthetic-aperture systems enlarge the aperture and increase the spatial resolution of telescope system via several sub-apertures distributed in specific way. The difficulty of its realization lies in detecting and correcting co-phase errors of the sub-apertures. This paper proposed the method of multi-spectral modulation detection of co-phasing errors for sparse-optical-synthetic-aperture systems. The method can detect the errors via phase modulation on a sub-aperture in the situation of different wavelengths. Firstly, this paper introduced the theory and implementation process of the method in detail. Then the paper analyzed the detection performance of the method and the influence of the sub-apertures structure on detection performance based on a three-sub-aperture system. These results show that the method can accurately detect the sub-apertures' co-phasing errors of the sparse-optical-synthetic-aperture systems. Compared with the current methods, the method proposed in this paper has many advantages, such as faster detection speed and wider detection range.

  5. Altered vocal fold kinematics in synthetic self-oscillating models that employ adipose tissue as a lateral boundary condition.

    NASA Astrophysics Data System (ADS)

    Saidi, Hiba; Erath, Byron D.

    2015-11-01

    The vocal folds play a major role in human communication by initiating voiced sound production. During voiced speech, the vocal folds are set into sustained vibrations. Synthetic self-oscillating vocal fold models are regularly employed to gain insight into flow-structure interactions governing the phonation process. Commonly, a fixed boundary condition is applied to the lateral, anterior, and posterior sides of the synthetic vocal fold models. However, physiological observations reveal the presence of adipose tissue on the lateral surface between the thyroid cartilage and the vocal folds. The goal of this study is to investigate the influence of including this substrate layer of adipose tissue on the dynamics of phonation. For a more realistic representation of the human vocal folds, synthetic multi-layer vocal fold models have been fabricated and tested while including a soft lateral layer representative of adipose tissue. Phonation parameters have been collected and are compared to those of the standard vocal fold models. Results show that vocal fold kinematics are affected by adding the adipose tissue layer as a new boundary condition.

  6. Integrated Workforce Modeling System

    NASA Technical Reports Server (NTRS)

    Moynihan, Gary P.

    2000-01-01

    There are several computer-based systems, currently in various phases of development at KSC, which encompass some component, aspect, or function of workforce modeling. These systems may offer redundant capabilities and/or incompatible interfaces. A systems approach to workforce modeling is necessary in order to identify and better address user requirements. This research has consisted of two primary tasks. Task 1 provided an assessment of existing and proposed KSC workforce modeling systems for their functionality and applicability to the workforce planning function. Task 2 resulted in the development of a proof-of-concept design for a systems approach to workforce modeling. The model incorporates critical aspects of workforce planning, including hires, attrition, and employee development.

  7. Coastal Modeling System

    DTIC Science & Technology

    2014-09-04

    Coastal Inlets Research Program Coastal Modeling System The work unit develops the Coastal Modeling System ( CMS ) and conducts basic research to...further understanding of sediment transport under mixed forcing from waves and currents. The CMS is a suite of coupled two- dimensional numerical...models for simulating waves, hydrodynamics, salinity and sediment transport, and morphology change. The CMS was identified by the USACE Hydraulics and

  8. The Earth System Model

    NASA Technical Reports Server (NTRS)

    Schoeberl, Mark; Rood, Richard B.; Hildebrand, Peter; Raymond, Carol

    2003-01-01

    The Earth System Model is the natural evolution of current climate models and will be the ultimate embodiment of our geophysical understanding of the planet. These models are constructed from components - atmosphere, ocean, ice, land, chemistry, solid earth, etc. models and merged together through a coupling program which is responsible for the exchange of data from the components. Climate models and future earth system models will have standardized modules, and these standards are now being developed by the ESMF project funded by NASA. The Earth System Model will have a variety of uses beyond climate prediction. The model can be used to build climate data records making it the core of an assimilation system, and it can be used in OSSE experiments to evaluate. The computing and storage requirements for the ESM appear to be daunting. However, the Japanese ES theoretical computing capability is already within 20% of the minimum requirements needed for some 2010 climate model applications. Thus it seems very possible that a focused effort to build an Earth System Model will achieve succcss.

  9. Biodegradation of perchlorate from real and synthetic effluent by Proteobacterium ARJR SMBS in a stirred tank bioreactor system.

    PubMed

    Raj, J R Anoop; Muruganandam, L

    2013-01-01

    The present work is a laboratory-scale study of perchlorate degradation using Proteobacterium ARJR SMBS in a stirred tank bioreactor (STBR). Anaerobically grown cultures of ARJR SMBS exposed to a variety of ClO4(-) levels within the range 30 to 150 mg L(-1) under anoxic conditions have been studied. The chloride released was measured and the average value found to be 43.55 mg L(-1). The average daily value of perchlorate degradation rate in this system was 17.24 mg L(-1) at optimum pH 7.5 and 0.25% NaCl salinity. The mixed liquor suspension solids of the system gradually increased from 0.025-0.156 g L(-1) during the operating period of 55 days. Mass balance indicated that the chloride produced was 0.45 mole per mole of perchlorate. The salinity of the system varied from 2.50-18.46 g L(-1), dependent primarily upon the inlet perchlorate concentration. The degradation mechanism, which obeyed a first-order substrate-utilizing kinetic model, allowed the growth rates and the half-saturation constants to be determined. The maximum observed anoxic growth rates (0.83-1.2 h(-1)) for ARJR SMBS in a synthetic effluent (SE) were considerably higher than in real effluent (RE) (0.45-0.59 h(-1)). The biomass yield of ARJR SMBS in STBR was higher in SE (1 +/- 0.4 mg L(-1)) than in RE (1 +/- 0.1 mg L(-1)). From the experimental findings, the uptake of perchlorate by the bacterium is suggested to be a non-interfacially-based mechanism. Under steady state operating condition the performance of the reactor was comparatively lower for RE than for SE but still offers significant control over the degradation of perchlorate under full-scale conditions.

  10. Applicability of cranial models in urethane resin and foam as a substitute for bone: are synthetic materials reliable?

    PubMed

    Muccino, Enrico; Porta, Davide; Magli, Francesca; Cigada, Alfredo; Sala, Remo; Gibelli, Daniele; Cattaneo, Cristina

    2013-09-01

    As literature is poor in functional synthetic cranial models, in this study, synthetic handmade models of cranial vaults were produced in two different materials (a urethane resin and a self-hardening foam), from multiple bone specimens (eight original cranial vaults: four human and four swine), in order to test their resemblance to bone structure in behavior, during fracture formation. All the vaults were mechanically tested with a 2-kg impact weight and filmed with a high-speed camera. Fracture patterns were homogeneous in all swine vaults and heterogeneous in human vaults, with resin fractures more similar to bone fractures. Mean fracture latency time extrapolated by videos were of 0.75 msec (bone), 1.5 msec (resin), 5.12 msec (foam) for human vaults and of 0.625 msec (bone), 1.87 msec (resin), 3.75 msec (foam) for swine vaults. These data showed that resin models are more similar to bone than foam reproductions, but that synthetic material may behave quite differently from bone as concerns fracture latency times.

  11. Synthetic cannabinoids: In silico prediction of the cannabinoid receptor 1 affinity by a quantitative structure-activity relationship model.

    PubMed

    Paulke, Alexander; Proschak, Ewgenij; Sommer, Kai; Achenbach, Janosch; Wunder, Cora; Toennes, Stefan W

    2016-03-14

    The number of new synthetic psychoactive compounds increase steadily. Among the group of these psychoactive compounds, the synthetic cannabinoids (SCBs) are most popular and serve as a substitute of herbal cannabis. More than 600 of these substances already exist. For some SCBs the in vitro cannabinoid receptor 1 (CB1) affinity is known, but for the majority it is unknown. A quantitative structure-activity relationship (QSAR) model was developed, which allows the determination of the SCBs affinity to CB1 (expressed as binding constant (Ki)) without reference substances. The chemically advance template search descriptor was used for vector representation of the compound structures. The similarity between two molecules was calculated using the Feature-Pair Distribution Similarity. The Ki values were calculated using the Inverse Distance Weighting method. The prediction model was validated using a cross validation procedure. The predicted Ki values of some new SCBs were in a range between 20 (considerably higher affinity to CB1 than THC) to 468 (considerably lower affinity to CB1 than THC). The present QSAR model can serve as a simple, fast and cheap tool to get a first hint of the biological activity of new synthetic cannabinoids or of other new psychoactive compounds.

  12. Model-Based Systems

    NASA Technical Reports Server (NTRS)

    Frisch, Harold P.

    2007-01-01

    Engineers, who design systems using text specification documents, focus their work upon the completed system to meet Performance, time and budget goals. Consistency and integrity is difficult to maintain within text documents for a single complex system and more difficult to maintain as several systems are combined into higher-level systems, are maintained over decades, and evolve technically and in performance through updates. This system design approach frequently results in major changes during the system integration and test phase, and in time and budget overruns. Engineers who build system specification documents within a model-based systems environment go a step further and aggregate all of the data. They interrelate all of the data to insure consistency and integrity. After the model is constructed, the various system specification documents are prepared, all from the same database. The consistency and integrity of the model is assured, therefore the consistency and integrity of the various specification documents is insured. This article attempts to define model-based systems relative to such an environment. The intent is to expose the complexity of the enabling problem by outlining what is needed, why it is needed and how needs are being addressed by international standards writing teams.

  13. Effects of Water in Synthetic Lubricant Systems and Clathrate Formation: A Literature Search and Review

    SciTech Connect

    Rohatgi, Ngoc Dung T.

    2001-08-08

    An extensive literature search and a confidential survey were critically analyzed to determine the effects of water on the stability of hydrofluorocarbon/synthetic lubricant systems and to identify key areas requiring further investigation. Following are highlights from the analysis: Clathrate hydrates are solid solutions formed when water molecules are linked through hydrogen bonding creating cavities that can enclose various guest molecules from hydrate formers, such as hydrofluorocarbons R-32, R-125, R-134a, R-407C and R-410A. The four methods for preventing clathrate formation were drying the gas, heating it, reducing its pressure, or using inhibitors. The hydrolysis of polyolester lubricants was mostly acid-catalyzed and its reaction rate constant typically followed the Arrhenius equation of an activated process. Hydrolytic stability improved with hindered molecular structures, and with the presence of acid catcher additives and desiccants. Water vapor can effect the adsorption of long-chain fatty acids and the chemistry of formation of protective oxide film. However, these effects on lubrication can be either positive or negative. Fifty to sixty percent of the moisture injected into an air-conditioning system remained in the refrigerant and the rest mixed with the compressor oil. In an automotive air-conditioning system using R-134a, ice would form at 0 C evaporating temperature when the water content in the vapor refrigerant on the low-pressure side was more than 350 ppm. Moisture would cause the embrittlement of polyethylene terephthalate and the hydrolysis of polyesters, but would reduce the effect of amine additives on fluoroelastomer rubbers. The reactions of water with refrigerants and lubricants would cause formicary and large-pit corrosion in copper tubes, as well as copper plating and sludge formation. Moreover, blockage of capillary tubes increased rapidly in the presence of water. Twenty-four companies responded to the survey. From the responses

  14. Modelling a C-Band Space Surveillance Radar using Systems Tool Kit

    DTIC Science & Technology

    2013-02-01

    Orbit LOS Line of Sight PRF Pulse Repetition Frequency PSD Power Spectral Density RCS Radar Cross Section RF Radio Frequency SAR Synthetic...Simulation of both monostatic and bistatic radar systems.  Modelling of system characteristics (e.g. transmitter power, frequency, antenna size) and...system definition, search/track modes, refraction and constraints. Synthetic aperture radar ( SAR ) and jammers can be modelled but are not applicable in

  15. Continuous wave synthetic low-coherence wind sensing Lidar: motionless measurement system with subsequent numerical range scanning.

    PubMed

    Brinkmeyer, Ernst; Waterholter, Thomas

    2013-01-28

    A continuous wave (CW) Lidar system for detection of scattering from atmospheric aerosol particles is presented which is useful in particular for remote sensing of wind velocities. It is based on a low-coherence interferometric setup powered by a synthetic broadband laser source with Gaussian power density spectrum. The laser bandwidth is electronically adjustable and determines the spatial resolution which is independent of range. The Lidar system has no moving parts. The location to be resolved can be shifted numerically after the measurement meaning that a single measurement already contains the full range information. The features of constant resolution and numerical range scanning are in sharp contrast to ordinary CW Lidar systems.

  16. The Missing Cone Problem in Computer Tomography and a Model for Interpolation in Synthetic Aperture Radar.

    NASA Astrophysics Data System (ADS)

    Hayner, David Alan

    The first part of this thesis considers the missing cone or limited view angle problem in computer tomography. In this problem only an incomplete set of projection data is available from which an image must be reconstructed. The data are limited in the sense that projections are available only over a limited view angle, a restricted perspective. The object of the algorithms presented in this thesis is to reconstruct a higher quality image than that obtainable by treating the projections as the only source of information concerning the image to be generated. This is accomplished by treating the problem in terms of spectral extrapolation. With this interpretation, various assumptions concerning the image and other forms of a priori information can be included in the data set to increase the total information content available. This larger data set allows the generation a superior image. It is shown that with data spanning over a continuous arc of only 60 degrees, that a high resolution image can be recovered; the original reconstruction, from the projection data only, is unitelligible. In order to understand the subtleties of these enhancement algorithms, the spectral extrapolation techniques employed must be well understood. The extrapolation techniques employed are those of Gerchberg and Papoulis. A result of studying these extrapolation techniques is that either can be characterized as a contraction mapping for any realizable discrete implementation. Further, it is theoretically derived and experimentally verified that these algorithms will in general obtain an optimal solution prior to converging to the unique fixed point. The norm of the error is minimized by this optimal solution, not by the fixed point. In the second part of this thesis, a nearest-neighbor interpolation scheme for image generation in spotlight mode synthetic aperture radar is analyzed. A model reflecting the effects of nearest-neighbor interpolation is derived and simulations are provided to

  17. Multiscale Cloud System Modeling

    NASA Technical Reports Server (NTRS)

    Tao, Wei-Kuo; Moncrieff, Mitchell W.

    2009-01-01

    The central theme of this paper is to describe how cloud system resolving models (CRMs) of grid spacing approximately 1 km have been applied to various important problems in atmospheric science across a wide range of spatial and temporal scales and how these applications relate to other modeling approaches. A long-standing problem concerns the representation of organized precipitating convective cloud systems in weather and climate models. Since CRMs resolve the mesoscale to large scales of motion (i.e., 10 km to global) they explicitly address the cloud system problem. By explicitly representing organized convection, CRMs bypass restrictive assumptions associated with convective parameterization such as the scale gap between cumulus and large-scale motion. Dynamical models provide insight into the physical mechanisms involved with scale interaction and convective organization. Multiscale CRMs simulate convective cloud systems in computational domains up to global and have been applied in place of contemporary convective parameterizations in global models. Multiscale CRMs pose a new challenge for model validation, which is met in an integrated approach involving CRMs, operational prediction systems, observational measurements, and dynamical models in a new international project: the Year of Tropical Convection, which has an emphasis on organized tropical convection and its global effects.

  18. Commercial Flight Crew Decision-Making during Low-Visibility Approach Operations Using Fused Synthetic/Enhanced Vision Systems

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Prinzel, Lawrence J., III

    2007-01-01

    NASA is investigating revolutionary crew-vehicle interface technologies that strive to proactively overcome aircraft safety barriers that would otherwise constrain the full realization of the next-generation air transportation system. A fixed-based piloted simulation experiment was conducted to evaluate the complementary use of Synthetic and Enhanced Vision technologies. Specific focus was placed on new techniques for integration and/or fusion of Enhanced and Synthetic Vision and its impact within a two-crew flight deck on the crew's decision-making process during low-visibility approach and landing operations. Overall, the experimental data showed that significant improvements in situation awareness, without concomitant increases in workload and display clutter, could be provided by the integration and/or fusion of synthetic and enhanced vision technologies for the pilot-flying and the pilot-not-flying. During non-normal operations, the ability of the crew to handle substantial navigational errors and runway incursions were neither improved nor adversely impacted by the display concepts. The addition of Enhanced Vision may not, unto itself, provide an improvement in runway incursion detection without being specifically tailored for this application. Existing enhanced vision system procedures were effectively used in the crew decision-making process during approach and missed approach operations but having to forcibly transition from an excellent FLIR image to natural vision by 100 ft above field level was awkward for the pilot-flying.

  19. Co-design in synthetic biology: a system-level analysis of the development of an environmental sensing device.

    PubMed

    Ball, David A; Lux, Matthew W; Graef, Russell R; Peterson, Matthew W; Valenti, Jane D; Dileo, John; Peccoud, Jean

    2010-01-01

    The concept of co-design is common in engineering, where it is necessary, for example, to determine the optimal partitioning between hardware and software of the implementation of a system features. Here we propose to adapt co-design methodologies for synthetic biology. As a test case, we have designed an environmental sensing device that detects the presence of three chemicals, and returns an output only if at least two of the three chemicals are present. We show that the logical operations can be implemented in three different design domains: (1) the transcriptional domain using synthetically designed hybrid promoters, (2) the protein domain using bi-molecular fluorescence complementation, and (3) the fluorescence domain using spectral unmixing and relying on electronic processing. We discuss how these heterogeneous design strategies could be formalized to develop co-design algorithms capable of identifying optimal designs meeting user specifications.

  20. 2D full wave modeling for a synthetic Doppler backscattering diagnostic

    SciTech Connect

    Hillesheim, J. C.; Schmitz, L.; Kubota, S.; Rhodes, T. L.; Carter, T. A.; Holland, C.

    2012-10-15

    Doppler backscattering (DBS) is a plasma diagnostic used in tokamaks and other magnetic confinement devices to measure the fluctuation level of intermediate wavenumber (k{sub {theta}}{rho}{sub s}{approx} 1) density fluctuations and the lab frame propagation velocity of turbulence. Here, a synthetic DBS diagnostic is described, which has been used for comparisons between measurements in the DIII-D tokamak and predictions from nonlinear gyrokinetic simulations. To estimate the wavenumber range to which a Gaussian beam would be sensitive, a ray tracing code and a 2D finite difference, time domain full wave code are used. Experimental density profiles and magnetic geometry are used along with the experimental antenna and beam characteristics. An example of the effect of the synthetic diagnostic on the output of a nonlinear gyrokinetic simulation is presented.

  1. Proposed data model for the next version of the synthetic biology open language.

    PubMed

    Roehner, Nicholas; Oberortner, Ernst; Pocock, Matthew; Beal, Jacob; Clancy, Kevin; Madsen, Curtis; Misirli, Goksel; Wipat, Anil; Sauro, Herbert; Myers, Chris J

    2015-01-16

    While the first version of the Synthetic Biology Open Language (SBOL) has been adopted by several academic and commercial genetic design automation (GDA) software tools, it only covers a limited number of the requirements for a standardized exchange format for synthetic biology. In particular, SBOL Version 1.1 is capable of representing DNA components and their hierarchical composition via sequence annotations. This proposal revises SBOL Version 1.1, enabling the representation of a wider range of components with and without sequences, including RNA components, protein components, small molecules, and molecular complexes. It also introduces modules to instantiate groups of components on the basis of their shared function and assert molecular interactions between components. By increasing the range of structural and functional descriptions in SBOL and allowing for their composition, the proposed improvements enable SBOL to represent and facilitate the exchange of a broader class of genetic designs.

  2. Synthetic collective intelligence.

    PubMed

    Solé, Ricard; Amor, Daniel R; Duran-Nebreda, Salva; Conde-Pueyo, Núria; Carbonell-Ballestero, Max; Montañez, Raúl

    2016-10-01

    Intelligent systems have emerged in our biosphere in different contexts and achieving different levels of complexity. The requirement of communication in a social context has been in all cases a determinant. The human brain, probably co-evolving with language, is an exceedingly successful example. Similarly, social insects complex collective decisions emerge from information exchanges between many agents. The difference is that such processing is obtained out of a limited individual cognitive power. Computational models and embodied versions using non-living systems, particularly involving robot swarms, have been used to explore the potentiality of collective intelligence. Here we suggest a novel approach to the problem grounded in the genetic engineering of unicellular systems, which can be modified in order to interact, store memories or adapt to external stimuli in collective ways. What we label as Synthetic Swarm Intelligence defines a parallel approach to the evolution of computation and swarm intelligence and allows to explore potential embodied scenarios for decision making at the microscale. Here, we consider several relevant examples of collective intelligence and their synthetic organism counterparts.

  3. Rigid-rod molecules in biomembrane models: from hydrogen-bonded chains to synthetic multifunctional pores.

    PubMed

    Sakai, Naomi; Mareda, Jiri; Matile, Stefan

    2005-02-01

    Synthetic ion channels and pores formed by rigid-rod molecules are summarized. This includes work on hydrogen-bonded chains installed along membrane-spanning rigid-rod scaffolds to transport protons. As a second topic, programmed assembly of p-septiphenyls with terminal iminodiacetate-copper complexes for potassium transport by cation-pi interactions is described. The third topic concerns rigid push-pull rods as fluorescent alpha-helix mimics to probe the importance of dipole-potential interactions for voltage gating, both on the functional and the structural level. Topic number four deals with p-octiphenyl staves as key scaffolds for the synthesis of rigid-rod beta-barrel pores. The description of internal and external design strategies for these rigid-rod beta-barrels covers a rich collection of pH-, pM-, voltage-, ligand-, and enzyme-gated synthetic multifunctional pores that can act as hosts, sensors, and catalysts. As far as practical applications are concerned, the possibility to detect chemical reactions with synthetic multifunctional pores appears most attractive. Recent molecular mechanics simulations are presented as a valuable approach to insights on the elusive suprastructures of multifunctional pores made from rigid rods.

  4. A comparative study of two statistical approaches for the analysis of real seismicity sequences and synthetic seismicity generated by a stick-slip experimental model

    NASA Astrophysics Data System (ADS)

    Flores-Marquez, Leticia Elsa; Ramirez Rojaz, Alejandro; Telesca, Luciano

    2015-04-01

    The study of two statistical approaches is analyzed for two different types of data sets, one is the seismicity generated by the subduction processes occurred at south Pacific coast of Mexico between 2005 and 2012, and the other corresponds to the synthetic seismic data generated by a stick-slip experimental model. The statistical methods used for the present study are the visibility graph in order to investigate the time dynamics of the series and the scaled probability density function in the natural time domain to investigate the critical order of the system. This comparison has the purpose to show the similarities between the dynamical behaviors of both types of data sets, from the point of view of critical systems. The observed behaviors allow us to conclude that the experimental set up globally reproduces the behavior observed in the statistical approaches used to analyses the seismicity of the subduction zone. The present study was supported by the Bilateral Project Italy-Mexico Experimental Stick-slip models of tectonic faults: innovative statistical approaches applied to synthetic seismic sequences, jointly funded by MAECI (Italy) and AMEXCID (Mexico) in the framework of the Bilateral Agreement for Scientific and Technological Cooperation PE 2014-2016.

  5. Microwave-assisted regeneration of synthetic zeolite used in tritium removal systems

    SciTech Connect

    Tanaka, M.; Takayama, S.; Sano, S.

    2015-03-15

    The regeneration process using synthetic honeycomb type 5A zeolite under microwave irradiation was experimentally investigated using a single-mode cavity at 2.46 GHz. In order to investigate the effect of electromagnetic fields, inductive heating by a magnetic field was applied to synthetic zeolite containing water. Because the microwave energy absorbed in the sample was less than 15 W, the zeolite sample was only heated to a temperature of 71 C. degrees. Water desorption was observed based on the increased temperature of the zeolite sample and the thermogravimetric curve that indicated a single step phenomenon. As a result, the regeneration process of zeolite was not complete over a period of 6000 s. A comparison of dielectric heating by an electric field with inductive heating by a magnetic field showed that the regeneration process by microwave irradiation was particularly beneficial in dielectric heating. (authors)

  6. Modeling the contribution of individual proteins to mixed skeletal muscle protein synthetic rates over increasing periods of label incorporation.

    PubMed

    Miller, Benjamin F; Wolff, Christopher A; Peelor, Fredrick F; Shipman, Patrick D; Hamilton, Karyn L

    2015-03-15

    Advances in stable isotope approaches, primarily the use of deuterium oxide ((2)H2O), allow for long-term measurements of protein synthesis, as well as the contribution of individual proteins to tissue measured protein synthesis rates. Here, we determined the influence of individual protein synthetic rates, individual protein content, and time of isotopic labeling on the measured synthesis rate of skeletal muscle proteins. To this end, we developed a mathematical model, applied the model to an established data set collected in vivo, and, to experimentally test the impact of different isotopic labeling periods, used (2)H2O to measure protein synthesis in cultured myotubes over periods of 2, 4, and 7 days. We first demonstrated the influence of both relative protein content and individual protein synthesis rates on measured synthesis rates over time. When expanded to include 286 individual proteins, the model closely approximated protein synthetic rates measured in vivo. The model revealed a 29% difference in measured synthesis rates from the slowest period of measurement (20 min) to the longest period of measurement (6 wk). In support of these findings, culturing of C2C12 myotubes with isotopic labeling periods of 2, 4, or 7 days revealed up to a doubling of the measured synthesis rate in the shorter labeling period compared with the longer period of labeling. From our model, we conclude that a 4-wk period of labeling is ideal for considering all proteins in a mixed-tissue fraction, while minimizing the slowing effect of fully turned-over proteins. In addition, we advocate that careful consideration must be paid to the period of isotopic labeling when comparing mixed protein synthetic rates between studies.

  7. Critical Infrastructure Modeling System

    SciTech Connect

    2004-10-01

    The Critical Infrastructure Modeling System (CIMS) is a 3D modeling and simulation environment designed to assist users in the analysis of dependencies within individual infrastructure and also interdependencies between multiple infrastructures. Through visual cuing and textual displays, a use can evaluate the effect of system perturbation and identify the emergent patterns that evolve. These patterns include possible outage areas from a loss of power, denial of service or access, and disruption of operations. Method of Solution: CIMS allows the user to model a system, create an overlay of information, and create 3D representative images to illustrate key infrastructure elements. A geo-referenced scene, satellite, aerial images or technical drawings can be incorporated into the scene. Scenarios of events can be scripted, and the user can also interact during run time to alter system characteristics. CIMS operates as a discrete event simulation engine feeding a 3D visualization.

  8. Studies of Cell-Mediated Immunity Against Immune Disorders Using Synthetic Peptides and Rotating Bioreactor System

    NASA Technical Reports Server (NTRS)

    Sastry, Jagannadha K.

    1997-01-01

    Our proposed experiments included: (1) immunzing mice with synthetic peptides; (2) preparing spleen and lymph node cells; (3) growing them under conventional conditions as well as in the rotatory vessel in appropriate medium reconstituting with synthetic peptides and/or cytokines as needed; and (4) comparing at regular time intervals the specific CTL activity as well as helper T-cell activity (in terms of both proliferative responses and cytokine production) using established procedures in my laboratory. We further proposed that once we demonstrated the merit of rotatory vessel technology to achieve desired results, these studies would be expanded to include immune cells from non-human primates (rhesus monkeys and chimpanzees) and also humans. We conducted a number of experiments to determine CTL induction by the synthetic peptides corresponding to antigenic proteins in HIV and HPV in different mouse strains that express MHC haplotypes H-2b or H-2d. We immunized mice with 100 ug of the synthetic peptide, suspended in sterile water, and emulsified in CFA (1:1). The immune lymph node cells obtained after 7 days were restimulated by culturing in T25 flask, HARV-10, or STLV-50, in the presence of the peptide at 20 ug/ml. The results from the 5'Cr-release assay consistently revealed complete abrogation of CTL activity of cells grown in the bioreactors (both HARV and STLV), while significant antigen-specific CTL activity was observed with cells cultured in tissue culture flasks. Thus, overall the data we generated in this study proved the usefulness of the NASA-developed developed technology for understanding the known immune deficiency during space travel. Additionally, this ex vivo microgravity technology since it mimics effectively the in vivo situation, it is also useful in understanding immune disorders in general. Thus, our proposed studies in TMC-NASA contract round II application benefit from data generated in this TMC-NASA contract round I study.

  9. Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC

    PubMed Central

    Aziz, Ramy K.; Khaw, Valerie L.; Monk, Jonathan M.; Brunk, Elizabeth; Lewis, Robert; Loh, Suh I.; Mishra, Arti; Nagle, Amrita A.; Satyanarayana, Chitkala; Dhakshinamoorthy, Saravanakumar; Luche, Michele; Kitchen, Douglas B.; Andrews, Kathleen A.; Palsson, Bernhard Ø.; Charusanti, Pep

    2015-01-01

    Mathematical models of biochemical networks form a cornerstone of bacterial systems biology. Inconsistencies between simulation output and experimental data point to gaps in knowledge about the fundamental biology of the organism. One such inconsistency centers on the gene aldA in Escherichia coli: it is essential in a computational model of E. coli metabolism, but experimentally it is not. Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA. Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100–200 μM individual concentrations. These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics. PMID:26441892

  10. Visual cues in low-level flight - Implications for pilotage, training, simulation, and enhanced/synthetic vision systems

    NASA Technical Reports Server (NTRS)

    Foyle, David C.; Kaiser, Mary K.; Johnson, Walter W.

    1992-01-01

    This paper reviews some of the sources of visual information that are available in the out-the-window scene and describes how these visual cues are important for routine pilotage and training, as well as the development of simulator visual systems and enhanced or synthetic vision systems for aircraft cockpits. It is shown how these visual cues may change or disappear under environmental or sensor conditions, and how the visual scene can be augmented by advanced displays to capitalize on the pilot's excellent ability to extract visual information from the visual scene.

  11. Modeling Sustainable Food Systems

    NASA Astrophysics Data System (ADS)

    Allen, Thomas; Prosperi, Paolo

    2016-05-01

    The processes underlying environmental, economic, and social unsustainability derive in part from the food system. Building sustainable food systems has become a predominating endeavor aiming to redirect our food systems and policies towards better-adjusted goals and improved societal welfare. Food systems are complex social-ecological systems involving multiple interactions between human and natural components. Policy needs to encourage public perception of humanity and nature as interdependent and interacting. The systemic nature of these interdependencies and interactions calls for systems approaches and integrated assessment tools. Identifying and modeling the intrinsic properties of the food system that will ensure its essential outcomes are maintained or enhanced over time and across generations, will help organizations and governmental institutions to track progress towards sustainability, and set policies that encourage positive transformations. This paper proposes a conceptual model that articulates crucial vulnerability and resilience factors to global environmental and socio-economic changes, postulating specific food and nutrition security issues as priority outcomes of food systems. By acknowledging the systemic nature of sustainability, this approach allows consideration of causal factor dynamics. In a stepwise approach, a logical application is schematized for three Mediterranean countries, namely Spain, France, and Italy.

  12. Designing synthetic biology.

    PubMed

    Agapakis, Christina M

    2014-03-21

    Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.

  13. Development of a GPS-aided motion measurement, pointing, and stabilization system for a Synthetic Aperture Radar. [Global Positioning System (GPS)

    SciTech Connect

    Fellerhoff, J.R.; Kohler, S.M.

    1991-01-01

    An advanced Synthetic Aperture Radar Motion Compensation System has been developed by Sandia National Laboratories (SNL). The system includes a miniaturized high accuracy ring laser gyro inertial measurement unit, a three axis gimbal pointing and stabilization assembly, a differential Global Positioning System (GPS) navigation aiding system, and a pilot guidance system. The system provides several improvements over previous SNL motion compensation systems and is capable of antenna stabilization to less than 0.01 degrees RMS and absolute position measurement to less than 5.0 meters RMS. These accuracies have been demonstrated in recent flight testing aboard a DHC-6-300 Twin Otter'' aircraft.

  14. Modeling of arsenic adsorption kinetics of synthetic and contaminated groundwater on natural laterite.

    PubMed

    Maiti, Abhijit; Sharma, Himanshu; Basu, Jayanta Kumar; De, Sirshendu

    2009-12-30

    A simple shrinking core model is applied to predict the adsorption kinetics of arsenite and arsenate species onto natural laterite (NL) in a stirred tank adsorber. The proposed model is a two-resistance model, in which two unknown parameters, external mass transfer coefficient (K(f)) and pore diffusion coefficient (D(e)) are estimated by comparing the simulation concentration profile with the experimental data using a nonlinear optimization technique. The model is applied under various operating conditions, e.g., initial arsenic concentration, NL dose, NL particle size, temperature, stirring speed, etc. Estimated values of D(e) and K(f) are found to be in the range of 2.2-2.6 x 10(-11)m(2)/s and 1.0-1.4 x 10(-6)m/s at 305K for different operating conditions, respectively. D(e) and K(f) values are found to be increasing with temperature and stirrer speed, respectively. Calculated values of Biot numbers indicate that both external mass transfer and pore diffusion are important during the adsorption. The model is also applied satisfactorily to predict the arsenic adsorption kinetics of arsenic contaminated groundwater-NL system and can be used to scale up.

  15. Integrated Operation of INL HYTEST System and High-Temperature Steam Electrolysis for Synthetic Natural Gas Production

    SciTech Connect

    Carl Marcel Stoots; Lee Shunn; James O'Brien

    2010-06-01

    The primary feedstock for synthetic fuel production is syngas, a mixture of carbon monoxide and hydrogen. Current hydrogen production technologies rely upon fossil fuels and produce significant quantities of greenhouse gases as a byproduct. This is not a sustainable means of satisfying future hydrogen demands, given the current projections for conventional world oil production and future targets for carbon emissions. For the past six years, the Idaho National Laboratory has been investigating the use of high-temperature steam electrolysis (HTSE) to produce the hydrogen feedstock required for synthetic fuel production. High-temperature electrolysis water-splitting technology, combined with non-carbon-emitting energy sources, can provide a sustainable, environmentally-friendly means of large-scale hydrogen production. Additionally, laboratory facilities are being developed at the INL for testing hybrid energy systems composed of several tightly-coupled chemical processes (HYTEST program). The first such test involved the coupling of HTSE, CO2 separation membrane, reverse shift reaction, and methanation reaction to demonstrate synthetic natural gas production from a feedstock of water and either CO or a simulated flue gas containing CO2. This paper will introduce the initial HTSE and HYTEST testing facilities, overall coupling of the technologies, testing results, and future plans.

  16. Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models

    PubMed Central

    Chowdhury, Ratul; Chowdhury, Anupam; Maranas, Costas D.

    2015-01-01

    Essentiality (ES) and Synthetic Lethality (SL) information identify combination of genes whose deletion inhibits cell growth. This information is important for both identifying drug targets for tumor and pathogenic bacteria suppression and for flagging and avoiding gene deletions that are non-viable in biotechnology. In this study, we performed a comprehensive ES and SL analysis of two important eukaryotic models (S. cerevisiae and CHO cells) using a bilevel optimization approach introduced earlier. Information gleaned from this study is used to propose specific model changes to remedy inconsistent with data model predictions. Even for the highly curated Yeast 7.11 model we identified 50 changes (metabolic and GPR) leading to the correct prediction of an additional 28% of essential genes and 36% of synthetic lethals along with a 53% reduction in the erroneous identification of essential genes. Due to the paucity of mutant growth phenotype data only 12 changes were made for the CHO 1.2 model leading to an additional correctly predicted 11 essential and eight non-essential genes. Overall, we find that CHO 1.2 was 76% less accurate than the Yeast 7.11 metabolic model in predicting essential genes. Based on this analysis, 14 (single and double deletion) maximally informative experiments are suggested to improve the CHO cell model by using information from a mouse metabolic model. This analysis demonstrates the importance of single and multiple knockout phenotypes in assessing and improving model reconstructions. The advent of techniques such as CRISPR opens the door for the global assessment of eukaryotic models. PMID:26426067

  17. Distributed fuzzy system modeling

    SciTech Connect

    Pedrycz, W.; Chi Fung Lam, P.; Rocha, A.F.

    1995-05-01

    The paper introduces and studies an idea of distributed modeling treating it as a new paradigm of fuzzy system modeling and analysis. This form of modeling is oriented towards developing individual (local) fuzzy models for specific modeling landmarks (expressed as fuzzy sets) and determining the essential logical relationships between these local models. The models themselves are implemented in the form of logic processors being regarded as specialized fuzzy neural networks. The interaction between the processors is developed either in an inhibitory or excitatory way. In more descriptive way, the distributed model can be sought as a collection of fuzzy finite state machines with their individual local first or higher order memories. It is also clarified how the concept of distributed modeling narrows down a gap between purely numerical (quantitative) models and the qualitative ones originated within the realm of Artificial Intelligence. The overall architecture of distributed modeling is discussed along with the detailed learning schemes. The results of extensive simulation experiments are provided as well. 17 refs.

  18. Synthetic modeling chemistry of iron-sulfur clusters in nitric oxide signaling.

    PubMed

    Fitzpatrick, Jessica; Kim, Eunsuk

    2015-08-18

    Nitric oxide (NO) is an important signaling molecule that is involved in many physiological and pathological functions. Iron-sulfur proteins are one of the main reaction targets for NO, and the [Fe-S] clusters within these proteins are converted to various iron nitrosyl species upon reaction with NO, of which dinitrosyl iron complexes (DNICs) are the most prevalent. Much progress has been made in identifying the origin of cellular DNIC generation. However, it is not well-understood which other products besides DNICs may form during [Fe-S] cluster degradation nor what effects DNICs and other degradation products can have once they are generated in cells. Even more elusive is an understanding of the manner by which cells cope with unwanted [Fe-S] modifications by NO. This Account describes our synthetic modeling efforts to identify cluster degradation products derived from the [2Fe-2S]/NO reaction in order to establish their chemical reactivity and repair chemistry. Our intent is to use the chemical knowledge that we generate to provide insight into the unknown biological consequences of cluster modification. Our recent advances in three different areas are described. First, new reaction conditions that lead to the formation of previously unrecognized products during the reaction of [Fe-S] clusters with NO are identified. Hydrogen sulfide (H2S), a gaseous signaling molecule, can be generated from the reaction between [2Fe-2S] clusters and NO in the presence of acid or formal H• (e(-)/H(+)) donors. In the presence of acid, a mononitrosyl iron complex (MNIC) can be produced as the major iron-containing product. Second, cysteine analogues can efficiently convert MNICs back to [2Fe-2S] clusters without the need for any other reagents. This reaction is possible for cysteine analogues because of their ability to labilize NO from MNICs and their capacity to undergo C-S bond cleavage, providing the necessary sulfide for [2Fe-2S] cluster formation. Lastly, unique dioxygen

  19. Stereoscopy in cinematographic synthetic imagery

    NASA Astrophysics Data System (ADS)

    Eisenmann, Jonathan; Parent, Rick

    2009-02-01

    In this paper we present experiments and results pertaining to the perception of depth in stereoscopic viewing of synthetic imagery. In computer animation, typical synthetic imagery is highly textured and uses stylized illumination of abstracted material models by abstracted light source models. While there have been numerous studies concerning stereoscopic capabilities, conventions for staging and cinematography in stereoscopic movies have not yet been well-established. Our long-term goal is to measure the effectiveness of various cinematography techniques on the human visual system in a theatrical viewing environment. We would like to identify the elements of stereoscopic cinema that are important in terms of enhancing the viewer's understanding of a scene as well as providing guidelines for the cinematographer relating to storytelling. In these experiments we isolated stereoscopic effects by eliminating as many other visual cues as is reasonable. In particular, we aim to empirically determine what types of movement in synthetic imagery affect the perceptual depth sensing capabilities of our viewers. Using synthetic imagery, we created several viewing scenarios in which the viewer is asked to locate a target object's depth in a simple environment. The scenarios were specifically designed to compare the effectiveness of stereo viewing, camera movement, and object motion in aiding depth perception. Data were collected showing the error between the choice of the user and the actual depth value, and patterns were identified that relate the test variables to the viewer's perceptual depth accuracy in our theatrical viewing environment.

  20. Synthetic approaches to the bicyclo[2.2.2]diazaoctane ring system common to the paraherquamides, stephacidins and related prenylated indole alkaloids.

    PubMed

    Miller, Kenneth A; Williams, Robert M

    2009-11-01

    The bicyclo[2.2.2]diazaoctane ring system is common to a number of highly biologically active secondary metabolites isolated from numerous species of fungi. In this tutorial review, we describe the varied synthetic approaches that have been employed to construct this ring system in the course of recent total synthesis endeavors, and this review should be of interest to synthetic organic chemists and natural product chemists. Detailed herein are a number of synthetic disconnections including intramolecular S(N)2' cyclizations, biomimetic Diels-Alder reactions, radical cyclizations, and cationic cascade reactions.

  1. Self-consistent Synthetic Mantle Discontinuities From Joint Modeling of Geodynamics and Mineral Physics and Their Effects on the 3D Global Wave Field

    NASA Astrophysics Data System (ADS)

    Schuberth, B.; Piazzoni, A.; Bunge, H.; Igel, H.; Steinle-Neumann, G.; Moder, C.; Oeser, J.

    2007-12-01

    Our current understanding of mantle structure and dynamics is to a large part based on inversion of seismic data resulting in tomographic images and on direct analysis of a wide range of seismic phases such as Pdiff, PcP, ScS SdS etc. For solving inverse problems, forward modeling is needed to obtain a synthetic dataset for a given set of model parameters. In this respect, great progress has been made over the last years in the developement of sophisticated numerical full waveform modeling tools. However, the main limitation in the application of this new class of techniques for the forward problem of seismology is the lack of accurate predictions of mantle heterogeneity that allow us to test hypotheses about Earth's mantle. Such predictive models should be based on geodynamic and mineralogical considerations and derived independently of seismological observations. Here, we demonstrate the feasibility of joining forward simulations from geodynamics, mineral physics and seismology to obtain earth-like seismograms. 3D global wave propagation is simulated for dynamically consistent thermal structures derived from 3D mantle circulation modeling (e.g. Bunge et al. 2002), for which the temperatures are converted to seismic velocities using a recently published, thermodynamically self-consistent mineral physics approach (Piazzoni et al. 2007). Assuming a certain, fixed mantle composition (e.g. pyrolite) our mineralogic modeling algorithm computes the stable phases at mantle pressures for a wide range of temperatures by system Gibbs free energy minimization. Through the same equations of state that model the Gibbs free energy, we compute elastic moduli and density for each stable phase assemblage at the same P-T conditions. One straightforward application of this approach is the study of the seismic signature of synthetic mantle discontinuities arising in such models, as the temperature dependent phase transformations occuring at around 410 Km and 660 Km depth are

  2. On modeling and controlling intelligent systems

    SciTech Connect

    Dress, W.B.

    1993-11-01

    The aim of this paper is to show how certain diverse and advanced techniques of information processing and system theory might be integrated into a model of an intelligent, complex entity capable of materially enhancing an advanced information management system. To this end, we first examine the notion of intelligence and ask whether a semblance thereof can arise in a system consisting of ensembles of finite-state automata. Our goal is to find a functional model of intelligence in an information-management setting that can be used as a tool. The purpose of this tool is to allow us to create systems of increasing complexity and utility, eventually reaching the goal of an intelligent information management system that provides and anticipates needed data and information. We base our attempt on the ideas of general system theory where the four topics of system identification, modeling, optimization, and control provide the theoretical framework for constructing a complex system that will be capable of interacting with complex systems in the real world. These four key topics are discussed within the purview of cellular automata, neural networks, and evolutionary programming. This is a report of ongoing work, and not yet a success story of a synthetic intelligent system.

  3. icpTOF: a new way for the detection of synthetic nanoparticles in environmental systems

    NASA Astrophysics Data System (ADS)

    Borovinskaya, Olga; Tanner, Martin; Böhme, Steffi; Gondikas, Andreas

    2016-04-01

    they have entered the real ecosystem. Besides, element ratios of single particles can be used as a specific merit for the identification of synthetic nanoparticles in the presence of naturally occurring particulate background [4]. In addition to higher mass resolving power, the instrument is equipped with a collision/reaction cell, which helps to improve detection limits for elements suffering from interferences (e.g. Fe, Ti, P, S). The icpTOF performance will be shown in combination with different sample introduction systems, including novel discrete microdroplet introduction. The single droplet introduction approach enables particle quantification without particulate reference materials and significantly simplifies the analysis. The advantages of fast simultaneous detection for the characterization of multi-component nanoparticles in environmental media will be demonstrated on several studies. [1] Nanoscience and Nanotechnologies: Nanoscience and nanotechnologies: opportunities and uncertainties, Final Report. Royal Society: London, 2004 [2] Degueldre et al. (2003), Coll. Surf. A, 217, 137-142. [3] Borovinskaya et al. (2014), Anal. Chem, 86, 8142-8148. [4] Von der Kammer et al. (2012), Env. Tox. and Chem., 31, 32-49.

  4. SYNTHETIC OIL,

    DTIC Science & Technology

    The patent concerns a dicarboxylate-base synthetic oil with antiwear and antioxidation additives. The oil is prepared from the esterification of 2- or 3-methylcyclohexanol and 2-ethylhexanol with adipic acid. (Author)

  5. Distributed generation systems model

    SciTech Connect

    Barklund, C.R.

    1994-12-31

    A slide presentation is given on a distributed generation systems model developed at the Idaho National Engineering Laboratory, and its application to a situation within the Idaho Power Company`s service territory. The objectives of the work were to develop a screening model for distributed generation alternatives, to develop a better understanding of distributed generation as a utility resource, and to further INEL`s understanding of utility concerns in implementing technological change.

  6. Climate system modeling program

    SciTech Connect

    1995-12-31

    The Climate System Modeling Project is a component activity of NSF's Climate Modeling, Analysis and Prediction Program, supported by the Atmospheric Sciences Program, Geosciences Directorate. Its objective is to accelerate progress toward reliable prediction of global and regional climate changes in the decades ahead. CSMP operates through workshops, support for post-docs and graduate students and other collaborative activities designed to promote interdisciplinary and strategic work in support of the overall objective (above) and specifically in three areas, (1) Causes of interdecadal variability in the climate system, (2) Interactions of regional climate forcing with global processes, and (3) Scientific needs of climate assessment.

  7. Modeling the earth system

    SciTech Connect

    Ojima, D.

    1992-12-31

    The 1990 Global Change Institute (GCI) on Earth System Modeling is the third of a series organized by the Office for Interdisciplinary Earth Studies to look in depth at particular issues critical to developing a better understanding of the earth system. The 1990 GCI on Earth System Modeling was organized around three themes: defining critical gaps in the knowledge of the earth system, developing simplified working models, and validating comprehensive system models. This book is divided into three sections that reflect these themes. Each section begins with a set of background papers offering a brief tutorial on the subject, followed by working group reports developed during the institute. These reports summarize the joint ideas and recommendations of the participants and bring to bear the interdisciplinary perspective that imbued the institute. Since the conclusion of the 1990 Global Change Institute, research programs, nationally and internationally, have moved forward to implement a number of the recommendations made at the institute, and many of the participants have maintained collegial interactions to develop research projects addressing the needs identified during the two weeks in Snowmass.

  8. Effects of CO2 on P-wave attenuation in porous media with micro-cracks: A synthetic modelling study

    NASA Astrophysics Data System (ADS)

    Ekanem, A. M.; Li, X. Y.; Chapman, M.; Main, I. G.

    2016-12-01

    The presence of CO2 in hydrocarbon reservoirs can cause significant changes in seismic wave properties. In turn these properties can be used to map CO2 saturation in hydrocarbon reservoirs or aquifers - either from natural sources or by injection from the surface. We present the results of a synthetic modelling study of the effects of supercritical CO2 saturation on P-wave attenuation in a medium consisting of four horizontal layers, including a target aquifer. The target aquifer is modelled fully by an effective medium containing pores saturated with brine and/or CO2 and randomly-aligned microcracks at different densities. The other layers are modelled solely by their bulk seismic velocities and densities. We first compute synthetic seismograms for a reference case where the third layer is completely isotropic with no cracks, no pores and no fluid saturation. We then calculate synthetic seismograms for finite crack densities of 0.01, 0.02 and 0.03 at varying degrees of CO2 saturation in the third layer. The results of our analysis indicate that attenuation is sensitive both to CO2 saturation and the crack density. For a given crack density, attenuation increases gradually with decreasing percentage of CO2 saturation and reaches a maximum at around 10% saturation. The induced attenuation increases with crack density and with offset. These observations hold out the potential of using seismic attenuation as an additional diagnostic in the characterisation of rock formations for a variety of applications, including hydrocarbon exploration and production, subsurface storage of CO2 or geothermal energy extraction.

  9. Synthetic Astrobiology

    NASA Technical Reports Server (NTRS)

    Rothschild, Lynn J.

    2017-01-01

    "Are we alone?" is one of the primary questions of astrobiology, and whose answer defines our significance in the universe. Unfortunately, this quest is hindered by the fact that we have only one confirmed example of life, that of earth. While this is enormously helpful in helping to define the minimum envelope for life, it strains credulity to imagine that life, if it arose multiple times, has not taken other routes. To help fill this gap, our lab has begun using synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - as an enabling technology. One theme, the "Hell Cell" project, focuses on creating artificial extremophiles in order to push the limits for Earth life, and to understand how difficult it is for life to evolve into extreme niches. In another project, we are re-evolving biotic functions using only the most thermodynamically stable amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids.

  10. Synthetic Astrobiology

    NASA Technical Reports Server (NTRS)

    Rothschild, Lynn J.

    2015-01-01

    'Are we alone?' is one of the primary questions of astrobiology, and whose answer defines our significance in the universe. Unfortunately, this quest is hindered by the fact that we have only one confirmed example of life, that of earth. While this is enormously helpful in helping to define the minimum envelope for life, it strains credulity to imagine that life, if it arose multiple times, has not taken other routes. To help fill this gap, our lab has begun using synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - as an enabling technology. One theme, the "Hell Cell" project, focuses on creating artificial extremophiles in order to push the limits for Earth life, and to understand how difficult it is for life to evolve into extreme niches. In another project, we are re-evolving biotic functions using only the most thermodynamically stable amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids.

  11. Synthetic oils

    NASA Technical Reports Server (NTRS)

    Hatton, R. E.

    1973-01-01

    Synthetic lubricants are discussed by chemical class and their general strengths and weaknesses in terms of lubrication properties are analyzed. Comparative ratings are given for 14 chemical classes and are used as a guide for lubricant selection. The effects of chemical structure on the properties of the lubricant are described with special emphasis on thermal stability. The diversity of synthetic lubricants which is provided by the wide range of properties permits many applications, some of which are reported.

  12. The derivation of a sub-canopy digital terrain model of a flooded forest using synthetic aperture radar

    NASA Technical Reports Server (NTRS)

    Imhoff, Marc Lee; Gesch, Dean B.

    1990-01-01

    Synthetic aperture radar data from the Shuttle Imaging Radar-B Mission were combined with the tide surface information to create a digital terrain model for a 70-km by 40-km section of the Mouths of the Ganges forests in southern Bangladesh. The dominance of the interaction phenomenon (canopy to surface or surface to canopy reflection) in flooded forests was exploited to create sub-canopy flood boundary maps for two different tide times. The boundary maps were digitally combined in x, y, z space with tide elevation models created from tide gauge data gridding the survey site and used as input to interpolation routines to create a terrain model. The end product represents a significant step in our ability to characterize the topography and hydrology of wetland ecosystems. The model derived here can be used for simulating tidal flow and nutrient transport from the forest to the marine habitat.

  13. Synthetic Aperture Ladar (SAL): Fundamental Theory, Design Equations for a Satellite System, and Laboratory Demonstration

    DTIC Science & Technology

    2007-11-02

    RICKARD Radio/IR/Optical Sensors Branch Remote Sensing Division MARK BASHKANSKY Optical Physics Branch Optical Sciences Division JONH REINTJES Optical... Wiley & Sons, New York, 1991). 5. C.V. Jakowatz, D.E. Wahl, P.H. Eichel, D.C. Ghiglia, and P.A. Thompson, Spotlight-Mode Synthetic Aperture Radar...Theory for Coherent Laser Radars,” Ap. Opt. 21(18), 3,398 – 3,407, 1982. 14. J.W. Goodman, Statistical Optics (John Wiley & Sons, New York, 1985

  14. Global mapping strategies for a synthetic aperture radar system in orbit about Venus

    NASA Technical Reports Server (NTRS)

    Kerridge, S. J.

    1980-01-01

    An analysis of the global mapping of Venus using a synthetic aperture radar (SAR) is presented. The geometry of the side-looking radar, the narrow swath width, and the slow rotation of Venus combine to constrain the methods required to produce such a map within the primary mapping mission of 121.5 days. Parametric studies indicate that multiple strategies can satisfy the requirements of the mission with reasonable assumptions for the total recording capacity, the downlink data rate, and the operating time of the SAR on each revolution.

  15. Characterization of the emergent properties of a synthetic quasi-cellular system

    PubMed Central

    2012-01-01

    Background The process of solutes entrapment during liposomes formation is interesting for the investigation of the relationship between the formation of compartments and the distribution of molecules inside them; a relevant issue in the studies of the origin of life. Theoretically, when no interactions are supposed among the chemical species to be entrapped, the entrapment is described by a standard Poisson process. But very recent experimental findings show that, for small liposomes (100 nm diameter), the distribution of entrapped molecules is best described by a power-law function. This is of a great importance, as the two random processes give rise to two completely different scenarios. Here we present an in silico stochastic simulation of the encapsulation of a cell-free molecular translation system (the PURE system), obtained following two different entrapment models: a pure Poisson process, and a power-law. The protein synthesis inside the liposomes has been studied in both cases, with the aim to highlight experimental observables that could be measured to assess which model gives a better representation of the real process. Results Firstly, a minimal model for in vitro protein synthesis, based on the PURE system molecular composition, has been formalized. Then, we have designed a reliable experimental simulation where stochastic factors affect the reaction course inside the compartment. To this end, 24 solutes, which represent the PURE system components, have been stochastically distributed among vesicles by following either a Poisson or a power-law distribution. The course of the protein synthesis within each vesicle has been consequently calculated, as a function of vesicle size. Our study can predict translation yield in a population of small liposomes down to the attoliter (10-18 L) range. Our results show that the efficiency of protein synthesis peaks at approximately 3·10-16 L (840 nm diam.) with a Poisson distribution of solutes, while a relative

  16. A female pelvic bone shape model for air/bone separation in support of synthetic CT generation for radiation therapy

    NASA Astrophysics Data System (ADS)

    Liu, Lianli; Cao, Yue; Fessler, Jeffrey A.; Jolly, Shruti; Balter, James M.

    2016-01-01

    Separating bone from air in MR data is one of the major challenges in using MR images to derive synthetic CT. The problem is further complicated when the anatomic regions filled with air are altered across scans due to air mobility, for instance, in pelvic regions, thereby the air regions estimated using an ultrashort echo time (UTE) sequence are invalid in other image series acquired for multispectral classification. This study aims to develop and investigate a female pelvic bone shape model to identify low intensity regions in MRI where air is unlikely to be present in support of synthetic CT generation without UTE imaging. CT scans of 30 patients were collected for the study, 17 of them also have corresponding MR scans. The shape model was built from the CT dataset, where the reference image was aligned to each of the training images using B-spline deformable registration. Principal component analysis was performed on B-spline coefficients for a compact model where shape variance was described by linear combination of principal modes. The model was applied to identify pelvic bone in MR images by deforming the corresponding MR data of the reference image to target MR images, where the search space of the deformation process was constrained within the subspace spanned by principal modes. The local minima in the search space were removed effectively by the shape model, thus supporting an efficient binary search for the optimal solution. We evaluated the model by its efficacy in identifying bone voxels and excluding air regions. The model was tested across the 17 patients that have corresponding MR scans using a leave-one-out cross validation. A simple model using the first leading principal mode only was found to achieve reasonable accuracy, where an averaged 87% of bone voxels were correctly identified. Finally dilation of the optimally fit bone mask by 5 mm was found to cover 96% of bone voxels while minimally impacting the overlap with air (below 0.4%).

  17. Synthetic biological networks

    NASA Astrophysics Data System (ADS)

    Archer, Eric; Süel, Gürol M.

    2013-09-01

    Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics.

  18. Autofocusing circular synthetic aperture sonar imagery using phase corrections modeled as generalized cones.

    PubMed

    Marston, Timothy M; Kennedy, Jermaine L; Marston, Philip L

    2014-08-01

    Circular synthetic aperture sonar (CSAS) is a coherent aperture synthesis technique that utilizes backscattered acoustic information from an encircled scene to generate information rich, high-resolution imagery. The aperture length required for image synthesis is much longer than in its linear synthetic aperture sonar counterpart and can result in challenging phase delay and navigation estimation constraints. Residual uncorrected phase errors manifest as focus aberrations in reconstructed CSAS imagery. This paper demonstrates that phase error in image patches can be approximated as an aspect variant linear phase shift representable as a generalized cone in wave-number space. If the geometry of the generalized cone is known, it can be applied as the spectral phase of an inverse filter for aberration correction. A method is derived for reconstructing the error cone geometry from independent estimates of its local curvatures, which are found via a series of one-dimensional line searches that maximize the focus of CSAS sub-aperture images. This approach is applied to real and simulated CSAS data containing aperture distortions, and the results successfully demonstrate estimation and correction of the underlying focus aberrations.

  19. MineSeis -- A MATLAB{reg_sign} GUI program to calculate synthetic seismograms from a linear, multi-shot blast source model

    SciTech Connect

    Yang, X.

    1998-04-01

    Large scale (up to 5 kt) chemical blasts are routinely conducted by mining and quarry industries around the world to remove overburden or to fragment rocks. Because of their ability to trigger the future International Monitoring System (IMS) of the Comprehensive Test Ban Treaty (CTBT), these blasts are monitored and studied by verification seismologists for the purpose of discriminating them from possible clandestine nuclear tests. One important component of these studies is the modeling of ground motions from these blasts with theoretical and empirical source models. The modeling exercises provide physical bases to regional discriminants and help to explain the observed signal characteristics. The program MineSeis has been developed to implement the synthetic seismogram modeling of multi-shot blast sources with the linear superposition of single shot sources. Single shot sources used in the modeling are the spherical explosion plus spall model mentioned here. Mueller and Murphy`s (1971) model is used as the spherical explosion model. A modification of Anandakrishnan et al.`s (1997) spall model is developed for the spall component. The program is implemented with the MATLAB{reg_sign} Graphical User Interface (GUI), providing the user with easy, interactive control of the calculation.

  20. A Short Review of Chemical Reaction Database Systems, Computer-Aided Synthesis Design, Reaction Prediction and Synthetic Feasibility.

    PubMed

    Warr, Wendy A

    2014-06-01

    This article is the text for a pedagogical lecture to be given at the Strasbourg Summer School in Chemoinformatics in June 2104. It covers a very wide range of reaction topics including structure and reaction representation, reaction centers, atom-to-atom mapping, reaction retrieval systems, computer-aided synthesis design, retrosynthesis, reaction prediction and synthetic feasibility. In the time available the coverage of each topic can only be cursory; the main usefulness of this article to the research community is the extensive bibliography.

  1. A framework of integrated hydrological and hydrodynamic models using synthetic rainfall for flash flood hazard mapping of ungauged catchments in tropical zones

    NASA Astrophysics Data System (ADS)

    Lohpaisankrit, Worapong; Meon, Günter; Tingsanchali, Tawatchai

    2016-05-01

    Flash flood hazard maps provide a scientific support to mitigate flash flood risk. The present study develops a practical framework with the help of integrated hydrological and hydrodynamic modelling in order to estimate the potential flash floods. We selected a small pilot catchment which has already suffered from flash floods in the past. This catchment is located in the Nan River basin, northern Thailand. Reliable meteorological and hydrometric data are missing in the catchment. Consequently, the entire upper basin of the main river was modelled with the help of the hydrological modelling system PANTA RHEI. In this basin, three monitoring stations are located along the main river. PANTA RHEI was calibrated and validated with the extreme flood events in June 2011 and July 2008, respectively. The results show a good agreement with the observed discharge data. In order to create potential flash flood scenarios, synthetic rainfall series were derived from temporal rainfall patterns based on the radar-rainfall observation and different rainfall depths from regional rainfall frequency analysis. The temporal rainfall patterns were characterized by catchment-averaged rainfall series selected from 13 rainstorms in 2008 and 2011 within the region. For regional rainfall frequency analysis, the well-known L-moments approach and related criteria were used to examine extremely climatic homogeneity of the region. According to the L-moments approach, Generalized Pareto distribution was recognized as the regional frequency distribution. The synthetic rainfall series were fed into the PANTA RHEI model. The simulated results from PANTA RHEI were provided to a 2-D hydrodynamic model (MEADFLOW), and various simulations were performed. Results from the integrated modelling framework are used in the ongoing study to regionalize and map the spatial distribution of flash flood hazards with four levels of flood severities. As an overall outcome, the presented framework can be applied in

  2. A Simple Protein Synthesis Model for the PURE System Operation.

    PubMed

    Mavelli, Fabio; Marangoni, Roberto; Stano, Pasquale

    2015-06-01

    The encapsulation of transcription-translation (TX-TL) cell-free machinery inside lipid vesicles (liposomes) is a key element in synthetic cell technology. The PURE system is a TX-TL kit composed of well-characterized parts, whose concentrations are fine tunable, which works according to a modular architecture. For these reasons, the PURE system perfectly fulfils the requirements of synthetic biology and is widely used for constructing synthetic cells. In this work, we present a simplified mathematical model to simulate the PURE system operations. Based on Michaelis-Menten kinetics and differential equations, the model describes protein synthesis dynamics by using 9 chemical species, 6 reactions and 16 kinetic parameters. The model correctly predicts the time course for messenger RNA and protein production and allows quantitative predictions. By means of this model, it is possible to foresee how the PURE system species affect the mechanism of proteins synthesis and therefore help in understanding scenarios where the concentration of the PURE system components has been modified purposely or as a result of stochastic fluctuations (for example after random encapsulation inside vesicles). The model also makes the determination of response coefficients for all species involved in the TX-TL mechanism possible and allows for scrutiny on how chemical energy is consumed by the three PURE system modules (transcription, translation and aminoacylation).

  3. Synthetic guide star generation

    DOEpatents

    Payne, Stephen A [Castro Valley, CA; Page, Ralph H [Castro Valley, CA; Ebbers, Christopher A [Livermore, CA; Beach, Raymond J [Livermore, CA

    2008-06-10

    A system for assisting in observing a celestial object and providing synthetic guide star generation. A lasing system provides radiation at a frequency at or near 938 nm and radiation at a frequency at or near 1583 nm. The lasing system includes a fiber laser operating between 880 nm and 960 nm and a fiber laser operating between 1524 nm and 1650 nm. A frequency-conversion system mixes the radiation and generates light at a frequency at or near 589 nm. A system directs the light at a frequency at or near 589 nm toward the celestial object and provides synthetic guide star generation.

  4. Synthetic guide star generation

    DOEpatents

    Payne, Stephen A.; Page, Ralph H.; Ebbers, Christopher A.; Beach, Raymond J.

    2004-03-09

    A system for assisting in observing a celestial object and providing synthetic guide star generation. A lasing system provides radiation at a frequency at or near 938 nm and radiation at a frequency at or near 1583 nm. The lasing system includes a fiber laser operating between 880 nm and 960 nm and a fiber laser operating between 1524 nm and 1650 nm. A frequency-conversion system mixes the radiation and generates light at a frequency at or near 589 nm. A system directs the light at a frequency at or near 589 nm toward the celestial object and provides synthetic guide star generation.

  5. Synthetic Generation of Myocardial Blood-Oxygen-Level-Dependent MRI Time Series via Structural Sparse Decomposition Modeling

    PubMed Central

    Rusu, Cristian; Morisi, Rita; Boschetto, Davide; Dharmakumar, Rohan; Tsaftaris, Sotirios A.

    2014-01-01

    This paper aims to identify approaches that generate appropriate synthetic data (computer generated) for Cardiac Phase-resolved Blood-Oxygen-Level-Dependent (CP–BOLD) MRI. CP–BOLD MRI is a new contrast agent- and stress-free approach for examining changes in myocardial oxygenation in response to coronary artery disease. However, since signal intensity changes are subtle, rapid visualization is not possible with the naked eye. Quantifying and visualizing the extent of disease relies on myocardial segmentation and registration to isolate the myocardium and establish temporal correspondences and ischemia detection algorithms to identify temporal differences in BOLD signal intensity patterns. If transmurality of the defect is of interest pixel-level analysis is necessary and thus a higher precision in registration is required. Such precision is currently not available affecting the design and performance of the ischemia detection algorithms. In this work, to enable algorithmic developments of ischemia detection irrespective to registration accuracy, we propose an approach that generates synthetic pixel-level myocardial time series. We do this by (a) modeling the temporal changes in BOLD signal intensity based on sparse multi-component dictionary learning, whereby segmentally derived myocardial time series are extracted from canine experimental data to learn the model; and (b) demonstrating the resemblance between real and synthetic time series for validation purposes. We envision that the proposed approach has the capacity to accelerate development of tools for ischemia detection while markedly reducing experimental costs so that cardiac BOLD MRI can be rapidly translated into the clinical arena for the noninvasive assessment of ischemic heart disease. PMID:24691119

  6. Effect of biological and adsorption interactions on removal of organic material from synthetic-fuel waste water in batch and column systems

    SciTech Connect

    Elgezawi, S.M.

    1986-01-01

    The effect of temperature on total organic carbon removal from synthetic fuel waste water by activated carbon was evaluated, at temperatures of 5, 15, 25, and 40/sup 0/C. Both batch and continuous studies were performed using granular Darco H90 activated carbon, Calgon Filtrasorb 400, carbon black 2000, and glass beads as adsorbents for organics in Run-19, Run-20, Omega-9, oil shale retort water and Hanna 1VB-02W-02U coal gasification condensate. Experimental adsorption isotherms were compared with results predicted by the Langmuir and Freundlich models. Breakthrough curves were compared with curves predicted by the Thomas model. The rate controlling mechanisms in continuous flow adsorption system including second order reversible surface kinetics, external film resistance and internal particle resistance were also evaluated. Granular activated carbons coated with a bacterial film combining physical adsorption and biological removal of organics into one unit called adsorption/biodegradation unit were also investigated. This study included determination of bacterial numbers in batch and continuous flow systems at different heights in the column ad at different temperatures. In developing a modified Thomas model, which included the bacterial activity occurring inside the fixed-packed bed system, mass transfer coefficients were evaluated to establish the relative importance of various individual mechanisms that contributed to the overall adsorption process. Biological film thickness was found to be a significant parameter in modeling the adsorption systems studied.

  7. Automated analysis of short responses in an interactive synthetic tutoring system for introductory physics

    NASA Astrophysics Data System (ADS)

    Nakamura, Christopher M.; Murphy, Sytil K.; Christel, Michael G.; Stevens, Scott M.; Zollman, Dean A.

    2016-06-01

    Computer-automated assessment of students' text responses to short-answer questions represents an important enabling technology for online learning environments. We have investigated the use of machine learning to train computer models capable of automatically classifying short-answer responses and assessed the results. Our investigations are part of a project to develop and test an interactive learning environment designed to help students learn introductory physics concepts. The system is designed around an interactive video tutoring interface. We have analyzed 9 with about 150 responses or less. We observe for 4 of the 9 automated assessment with interrater agreement of 70% or better with the human rater. This level of agreement may represent a baseline for practical utility in instruction and indicates that the method warrants further investigation for use in this type of application. Our results also suggest strategies that may be useful for writing activities and questions that are more appropriate for automated assessment. These strategies include building activities that have relatively few conceptually distinct ways of perceiving the physical behavior of relatively few physical objects. Further success in this direction may allow us to promote interactivity and better provide feedback in online learning systems. These capabilities could enable our system to function more like a real tutor.

  8. Modified ADM1 for modelling an UASB reactor laboratory plant treating starch wastewater and synthetic substrate load tests.

    PubMed

    Hinken, L; Huber, M; Weichgrebe, D; Rosenwinkel, K-H

    2014-11-01

    A laboratory plant consisting of two UASB reactors was used for the treatment of industrial wastewater from the wheat starch industry. Several load tests were carried out with starch wastewater and the synthetic substrates glucose, acetate, cellulose, butyrate and propionate to observe the impact of changing loads on gas yield and effluent quality. The measurement data sets were used for calibration and validation of the Anaerobic Digestion Model No. 1 (ADM1). For a precise simulation of the detected glucose degradation during load tests with starch wastewater and glucose, it was necessary to incorporate the complete lactic acid fermentation into the ADM1, which contains the formation and degradation of lactate and a non-competitive inhibition function. The modelling results of both reactors based on the modified ADM1 confirm an accurate calculation of the produced gas and the effluent concentrations. Especially, the modelled lactate effluent concentrations for the load cases are similar to the measurements and justified by literature.

  9. Synthetic microbial ecosystems for biotechnology.

    PubMed

    Pandhal, Jagroop; Noirel, Josselin

    2014-06-01

    Most highly controlled and specific applications of microorganisms in biotechnology involve pure cultures. Maintaining single strain cultures is important for industry as contaminants can reduce productivity and lead to longer "down-times" during sterilisation. However, microbes working together provide distinct advantages over pure cultures. They can undertake more metabolically complex tasks, improve efficiency and even expand applications to open systems. By combining rapidly advancing technologies with ecological theory, the use of microbial ecosystems in biotechnology will inevitably increase. This review provides insight into the use of synthetic microbial communities in biotechnology by applying the engineering paradigm of measure, model, manipulate and manufacture, and illustrate the emerging wider potential of the synthetic ecology field. Systems to improve biofuel production using microalgae are also discussed.

  10. Neglected Disease – African Sleeping Sickness: Recent Synthetic and Modeling Advances

    PubMed Central

    Paliwal, Sarvesh K.; Verma, Ankita Narayan; Paliwal, Shailendra

    2011-01-01

    Human African Trypanosomiasis (HAT) also called sleeping sickness is caused by subspecies of the parasitic hemoflagellate Trypanosoma brucei that mostly occurs in sub-Saharan Africa. The current chemotherapy of the human trypanosomiases relies on only six drugs, five of which have been developed more than 30 years ago, have undesirable toxic side effects and most of them show drug-resistance. Though development of new anti-trypanosomal drugs seems to be a priority area research in this area has lagged far behind. The given review mainly focus upon the recent synthetic and computer based approaches made by various research groups for the development of newer anti-trypanosomal analogues which may have improved efficacy and oral bioavailability than the present ones. The given paper also attempts to investigate the relationship between the various physiochemical parameters and anti-trypanosomal activity that may be helpful in development of potent anti-trypanosomal agents against sleeping sickness. PMID:21886894

  11. Modeling climate change impacts on combined sewer overflow using synthetic precipitation time series.

    PubMed

    Bendel, David; Beck, Ferdinand; Dittmer, Ulrich

    2013-01-01

    In the presented study climate change impacts on combined sewer overflows (CSOs) in Baden-Wuerttemberg, Southern Germany, were assessed based on continuous long-term rainfall-runoff simulations. As input data, synthetic rainfall time series were used. The applied precipitation generator NiedSim-Klima accounts for climate change effects on precipitation patterns. Time series for the past (1961-1990) and future (2041-2050) were generated for various locations. Comparing the simulated CSO activity of both periods we observe significantly higher overflow frequencies for the future. Changes in overflow volume and overflow duration depend on the type of overflow structure. Both values will increase at simple CSO structures that merely divide the flow, whereas they will decrease when the CSO structure is combined with a storage tank. However, there is a wide variation between the results of different precipitation time series (representative for different locations).

  12. Induction by lipopolysaccharide of intracellular and extracellular interleukin 1 production: analysis with synthetic models.

    PubMed

    Lasfargues, A; Ledur, A; Charon, D; Szabo, L; Chaby, R

    1987-07-15

    An attempt was made to identify the molecular structures that are present in bacterial LPS and induce the production of intracellular and extracellular pools of IL 1 by peritoneal macrophages of the mouse and by human monocytes. Activities of glycolipids and carbohydrates prepared by synthesis, and structurally related to the hydrophobic (Lipid A) and to the polysaccharide (PS) regions of LPS were compared with those induced by Bordetella pertussis endotoxin and by fragments derived therefrom. Both isolated regions of this LPS (PS and Lipid A) were able to induce IL 1 synthesis by monocytes and macrophages. Among the synthetic glycolipids employed, propyl-2-deoxy-2-[(3R)-3-hydroxytetrade-canamido]-4-O-pho sph ono-6-O-tetradecanoyl-beta-D-glucopyranoside (glycolipid M9) induced IL 1 secretion more efficiently than Lipid A and LPS, whereas the amounts of intracellular IL 1 produced upon induction by these three substances were comparable. Macrophages from C3H/HeJ mice were unresponsive to Lipid A and to glycolipid M9, but produced IL 1 when incubated with PS or with a hydrophilic fragment isolated after methanolysis of the endotoxin. However, all synthetic derivatives of 3-deoxy-D-manno-2-octulosonic acid (KDO) used in this study failed to induce IL 1 production by both mouse macrophages and human monocytes. The implications of these findings for a more precise comprehension of the molecular mechanism of LPS-induced activation of macrophages, and the relations between the molecular structures required for the induction of IL 1 production vs cytostatic activity in macrophages, are discussed.

  13. Proton and metal ion binding to natural organic polyelectrolytes-I. Studies with synthetic model compounds

    USGS Publications Warehouse

    Marinsky, J.A.; Reddy, M.M.

    1984-01-01

    A unified physico-chemical model, based on a modified Henderson-Hasselbalch equation, for the analysis of ion complexation reactions involving charged polymeric systems is presented and verified. In this model pH = pKa+p(??Ka) + log(??/1 - ??) where Ka is the intrinsic acid dissociation constant of the ionizable functional groups on the polymer, ??Ka is the deviation of the intrinsic constant due to electrostatic interaction between the hydrogen ion and the polyanion, and alpha (??) is the polyacid degree of ionization. Using this approach pKa values for repeating acidic units of polyacrylic (PAA) and polymethacrylic (PMA) acids were found to be 4.25 ?? 0.03 and 4.8 ?? 0.1, respectively. The polyion electrostatic deviation term derived from the potentiometric titration data (i.e. p(??Ka)) is used to calculate metal ion concentration at the complexation site on the surface of the polyanion. Intrinsic cobalt-polycarboxylate binding constants (7.5 for PAA and 5.6 for PMA), obtained using this procedure, are consistent with the range of published binding constants for cobalt-monomer carboxylate complexes. In two phase systems incorporation of a Donnan membrane potential term allows determination of the intrinsic pKa of a cross-linked PMA gel, pKa = 4.83, in excellent agreement with the value obtained for the linear polyelectrolyte and the monomer. Similarly, the intrinsic stability constant for cobalt ion binding to a PMA-gel (??CoPMA+ = 11) was found to be in agreement with the linear polyelectrolyte analogue and the published data for cobalt-carboxylate monodentate complexes. ?? 1984.

  14. Modelling robot construction systems

    NASA Technical Reports Server (NTRS)

    Grasso, Chris

    1990-01-01

    TROTER's are small, inexpensive robots that can work together to accomplish sophisticated construction tasks. To understand the issues involved in designing and operating a team of TROTER's, the robots and their components are being modeled. A TROTER system that features standardized component behavior is introduced. An object-oriented model implemented in the Smalltalk programming language is described and the advantages of the object-oriented approach for simulating robot and component interactions are discussed. The presentation includes preliminary results and a discussion of outstanding issues.

  15. NEP systems model

    NASA Technical Reports Server (NTRS)

    George, Jeffrey A.

    1993-01-01

    A new nuclear electric propulsion (NEP) systems analysis code is discussed. The new code is modular and consists of a driver code and various subsystem models. The code models five different subsystems: (1) reactor/shield; (2) power conversion; (3) heat rejection; (4) power management and distribution (PMAD); and (5) thrusters. The code optimizes for the following design criteria: minimum mass; minimum radiator area; and low mass/low area. The code also optimizes the following parameters: separation distance; temperature ratio; pressure ratio; and transmission frequency. The discussion is presented in vugraph form.

  16. Study on an onboard data storage system for frequency-modulated continuous-wave synthetic aperture radar

    NASA Astrophysics Data System (ADS)

    Tian, Haishan; Chang, Wenge; Li, Xiangyang; Gu, Chengfei; Liu, Zhaohe

    2016-07-01

    The airborne frequency-modulated continuous-wave synthetic aperture radar presents an enormous technical challenge on the design of data storage system due to its characteristics of high-data rate, small size, light weight, and low-power consumption. There are two main problems for the high-speed storage under the miniature requirement. One is the unpredictable response time of the flash translation layer in the CompactFlash card. The other is the relatively long response time of the file system. This paper designs a data storage system in a real-time signal processor. Two techniques called configurable buffer structure and FPFQA (FAT pre- and FDT quasiallocation) are presented to overcome these two problems. The evaluated performance indicates that the size, power consumption, and weight meet the miniature requirement, while the function of the high-speed data storage with approximately 121 MB/s storage speed and real-time file management are realized.

  17. Opportunities in plant synthetic biology.

    PubMed

    Cook, Charis; Martin, Lisa; Bastow, Ruth

    2014-05-01

    Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.

  18. Piloted Simulation of Various Synthetic Vision Systems Terrain Portrayal and Guidance Symbology Concepts for Low Altitude En-Route Scenario

    NASA Technical Reports Server (NTRS)

    Takallu, M. A.; Glaab, L. J.; Hughes, M. F.; Wong, D. T.; Bartolone, A. P.

    2008-01-01

    In support of the NASA Aviation Safety Program's Synthetic Vision Systems Project, a series of piloted simulations were conducted to explore and quantify the relationship between candidate Terrain Portrayal Concepts and Guidance Symbology Concepts, specific to General Aviation. The experiment scenario was based on a low altitude en route flight in Instrument Metrological Conditions in the central mountains of Alaska. A total of 18 general aviation pilots, with three levels of pilot experience, evaluated a test matrix of four terrain portrayal concepts and six guidance symbology concepts. Quantitative measures included various pilot/aircraft performance data, flight technical errors and flight control inputs. The qualitative measures included pilot comments and pilot responses to the structured questionnaires such as perceived workload, subjective situation awareness, pilot preferences, and the rare event recognition. There were statistically significant effects found from guidance symbology concepts and terrain portrayal concepts but no significant interactions between them. Lower flight technical errors and increased situation awareness were achieved using Synthetic Vision Systems displays, as compared to the baseline Pitch/Roll Flight Director and Blue Sky Brown Ground combination. Overall, those guidance symbology concepts that have both path based guidance cue and tunnel display performed better than the other guidance concepts.

  19. Synthetic Zeolites as Controlled-Release Delivery Systems for Anti-Inflammatory Drugs.

    PubMed

    Khodaverdi, Elham; Soleimani, Hossein Ali; Mohammadpour, Fatemeh; Hadizadeh, Farzin

    2016-06-01

    Scientists have always been trying to use artificial zeolites to make modified-release drug delivery systems in the gastrointestinal tract. An ideal carrier should have the capability to release the drug in the intestine, which is the main area of absorption. Zeolites are mineral aluminosilicate compounds with regular structure and huge porosity, which are available in natural and artificial forms. In this study, soaking, filtration and solvent evaporation methods were used to load the drugs after activation of the zeolites. Weight measurement, spectroscopy FTIR, thermogravimetry and scanning electronic microscope were used to determine drug loading on the systems. Finally, consideration of drug release was made in a simulated gastric fluid and a simulated intestinal fluid for all matrixes (zeolites containing drugs) and drugs without zeolites. Diclofenac sodium (D) and piroxicam (P) were used as the drug models, and zeolites X and Y as the carriers. Drug loading percentage showed that over 90% of drugs were loaded on zeolites. Dissolution tests in stomach pH environment showed that the control samples (drug without zeolite) released considerable amount of drugs (about 90%) within first 15 min when it was about 10-20% for the matrixes. These results are favorable as NSAIDs irritate the stomach wall and it is ideal not to release much drugs in the stomach. Furthermore, release rate of drugs from matrixes has shown slower rate in comparison with control samples in intestine pH environment.

  20. How to make a synthetic multicellular computer.

    PubMed

    Macia, Javier; Sole, Ricard

    2014-01-01

    Biological systems perform computations at multiple scales and they do so in a robust way. Engineering metaphors have often been used in order to provide a rationale for modeling cellular and molecular computing networks and as the basis for their synthetic design. However, a major constraint in this mapping between electronic and wet computational circuits is the wiring problem. Although wires are identical within electronic devices, they must be different when using synthetic biology designs. Moreover, in most cases the designed molecular systems cannot be reused for other functions. A new approximation allows us to simplify the problem by using synthetic cellular consortia where the output of the computation is distributed over multiple engineered cells. By evolving circuits in silico, we can obtain the minimal sets of Boolean units required to solve the given problem at the lowest cost using cellular consortia. Our analysis reveals that the basic set of logic units is typically non-standard. Among the most common units, the so called inverted IMPLIES (N-Implies) appears to be one of the most important elements along with the NOT and AND functions. Although NOR and NAND gates are widely used in electronics, evolved circuits based on combinations of these gates are rare, thus suggesting that the strategy of combining the same basic logic gates might be inappropriate in order to easily implement synthetic computational constructs. The implications for future synthetic designs, the general view of synthetic biology as a standard engineering domain, as well as potencial drawbacks are outlined.

  1. Synthetic earthquake catalogs simulating seismic activity in the Corynth Gulf, Greece, fault system

    NASA Astrophysics Data System (ADS)

    Console, R.; Carluccio, R.; Papadimitriou, E. E.; Karakostas, V. G.

    2014-12-01

    The characteristic earthquake hypothesis is the basis of time-dependent modeling of earthquake recurrence on major faults, using the renewal process methodology. However, the characteristic earthquake hypothesis is not strongly supported by observational data. Few fault segments have long historical or paleoseismic records of individually dated ruptures, and when data and parameter uncertainties are allowed for, the form of the recurrence-distribution is difficult to establish. This is the case, for instance, of the Corinth gulf fault system, for which documents about strong earthquakes exist for at least two thousand years, but they can be considered complete for magnitudes > 6.0 only for the latest 300 years, during which only few characteristic earthquakes are reported for single fault segments. The use of a physics-based earthquake simulator has allowed the production of catalogs lasting 100,000 years and containing more than 500,000 events of magnitudes > 4.0. The main features of our simulation algorithm are (1) the imposition of an average slip rate released by earthquakes to every single segment recognized in the investigated fault system, (2) the interaction between earthquake sources, (3) a self-organized earthquake magnitude distribution, and (4) the effect of minor earthquakes in redistributing stress. The application of our simulation algorithm to the Corinth gulf fault system has shown realistic features in time, space and magnitude behavior of the seismicity. These features include long-term periodicity of strong earthquakes, short-term clustering of both strong and smaller events, and a realistic earthquake magnitude distribution departing from the Gutenberg-Richter distribution in the higher magnitude range.

  2. YASEIS: Yet Another computer program to calculate synthetic SEISmograms for a spherically multi-layered Earth model

    NASA Astrophysics Data System (ADS)

    Ma, Yanlu

    2013-04-01

    Although most researches focus on the lateral heterogeneity of 3D Earth nowadays, a spherically multi-layered model where the parameters depend only on depth still represents a good first order approximation of real Earth. Such 1D models could be used as starting models for seismic tomographic inversion or as background model where the source mechanisms are inverted. The problem of wave propagation in a spherically layered model had been solved theoretically long time ago (Takeuchi and Saito, 1972). The existing computer programs such as Mineos (developed by G. Master, J. Woodhouse and F. Gilbert), Gemini (Friederich and Dalkolmo 1995), DSM (Kawai et. al. 2006) and QSSP (Wang 1999) tackled the computational aspects of the problem. A new simple and fast program for computing the Green's function of a stack of spherical dissipative layers is presented here. The analytical solutions within each homogeneous spherical layer are joined through the continuous boundary conditions and propagated from the center of model up to the level of source depth. Another solution is built by propagating downwardly from the free surface of model to the source level. The final solution is then constructed in frequency domain from the previous two solutions to satisfy the discontinuities of displacements and stresses at the source level which are required by the focal mechanism. The numerical instability in the propagator approach is solved by complementing the matrix propagating with an orthonormalization procedure (Wang 1999). Another unstable difficulty due to the high attenuation in the upper mantle low velocity zone is overcome by switching the bases of solutions from the spherical Bessel functions to the spherical Hankel functions when necessary. We compared the synthetic seismograms obtained from the new program YASEIS with those computed by Gemini and QSSP. In the range of near distances, the synthetics by a reflectivity code for the horizontally layers are also compared with

  3. Collective operations in a file system based execution model

    DOEpatents

    Shinde, Pravin; Van Hensbergen, Eric

    2013-02-12

    A mechanism is provided for group communications using a MULTI-PIPE synthetic file system. A master application creates a multi-pipe synthetic file in the MULTI-PIPE synthetic file system, the master application indicating a multi-pipe operation to be performed. The master application then writes a header-control block of the multi-pipe synthetic file specifying at least one of a multi-pipe synthetic file system name, a message type, a message size, a specific destination, or a specification of the multi-pipe operation. Any other application participating in the group communications then opens the same multi-pipe synthetic file. A MULTI-PIPE file system module then implements the multi-pipe operation as identified by the master application. The master application and the other applications then either read or write operation messages to the multi-pipe synthetic file and the MULTI-PIPE synthetic file system module performs appropriate actions.

  4. Collective operations in a file system based execution model

    DOEpatents

    Shinde, Pravin; Van Hensbergen, Eric

    2013-02-19

    A mechanism is provided for group communications using a MULTI-PIPE synthetic file system. A master application creates a multi-pipe synthetic file in the MULTI-PIPE synthetic file system, the master application indicating a multi-pipe operation to be performed. The master application then writes a header-control block of the multi-pipe synthetic file specifying at least one of a multi-pipe synthetic file system name, a message type, a message size, a specific destination, or a specification of the multi-pipe operation. Any other application participating in the group communications then opens the same multi-pipe synthetic file. A MULTI-PIPE file system module then implements the multi-pipe operation as identified by the master application. The master application and the other applications then either read or write operation messages to the multi-pipe synthetic file and the MULTI-PIPE synthetic file system module performs appropriate actions.

  5. Modeling stochastic noise in gene regulatory systems.

    PubMed

    Meister, Arwen; Du, Chao; Li, Ye Henry; Wong, Wing Hung

    2014-03-01

    The Master equation is considered the gold standard for modeling the stochastic mechanisms of gene regulation in molecular detail, but it is too complex to solve exactly in most cases, so approximation and simulation methods are essential. However, there is still a lack of consensus about the best way to carry these out. To help clarify the situation, we review Master equation models of gene regulation, theoretical approximations based on an expansion method due to N.G. van Kampen and R. Kubo, and simulation algorithms due to D.T. Gillespie and P. Langevin. Expansion of the Master equation shows that for systems with a single stable steady-state, the stochastic model reduces to a deterministic model in a first-order approximation. Additional theory, also due to van Kampen, describes the asymptotic behavior of multistable systems. To support and illustrate the theory and provide further insight into the complex behavior of multistable systems, we perform a detailed simulation study comparing the various approximation and simulation methods applied to synthetic gene regulatory systems with various qualitative characteristics. The simulation studies show that for large stochastic systems with a single steady-state, deterministic models are quite accurate, since the probability distribution of the solution has a single peak tracking the deterministic trajectory whose variance is inversely proportional to the system size. In multistable stochastic systems, large fluctuations can cause individual trajectories to escape from the domain of attraction of one steady-state and be attracted to another, so the system eventually reaches a multimodal probability distribution in which all stable steady-states are represented proportional to their relative stability. However, since the escape time scales exponentially with system size, this process can take a very long time in large systems.

  6. Neuroprotective Effect of a New Synthetic Aspirin-decursinol Adduct in Experimental Animal Models of Ischemic Stroke

    PubMed Central

    Shin, Bich Na; Ahn, Ji Hyeon; Kim, In Hye; Lee, Jae-Chul; Yoo, Ki-Yeon; Hwang, In Koo; Choi, Jung Hoon; Park, Jeong Ho; Lee, Yun Lyul; Suh, Hong-Won; Jun, Jong-Gab; Kwon, Young-Guen; Kim, Young-Myeong; Kwon, Seung-Hae; Her, Song; Kim, Jin Su; Hyun, Byung-Hwa; Kim, Chul-Kyu; Cho, Jun Hwi; Lee, Choong Hyun; Won, Moo-Ho

    2013-01-01

    Stroke is the second leading cause of death. Experimental animal models of cerebral ischemia are widely used for researching mechanisms of ischemic damage and developing new drugs for the prevention and treatment of stroke. The present study aimed to comparatively investigate neuroprotective effects of aspirin (ASA), decursinol (DA) and new synthetic aspirin-decursinol adduct (ASA-DA) against transient focal and global cerebral ischemic damage. We found that treatment with 20 mg/kg, not 10 mg/kg, ASA-DA protected against ischemia-induced neuronal death after transient focal and global ischemic damage, and its neuroprotective effect was much better than that of ASA or DA alone. In addition, 20 mg/kg ASA-DA treatment reduced the ischemia-induced gliosis and maintained antioxidants levels in the corresponding injury regions. In brief, ASA-DA, a new synthetic drug, dramatically protected neurons from ischemic damage, and neuroprotective effects of ASA-DA may be closely related to the attenuation of ischemia-induced gliosis and maintenance of antioxidants. PMID:24073226

  7. Synthetic Toll-like receptor 4 agonist enhances vaccine efficacy in an experimental model of toxic shock syndrome.

    PubMed

    Morefield, Garry L; Hawkins, Lynn D; Ishizaka, Sally T; Kissner, Teri L; Ulrich, Robert G

    2007-11-01

    The development of new protein subunit vaccines has stimulated the search for improved adjuvants to replace traditional aluminum-containing products. We investigated the adjuvant effects of a synthetic Toll-like receptor 4 (TLR4) agonist on vaccine efficacy in an experimental model of toxic shock syndrome. The TLR4 agonist E6020 has a simplified structure consisting of a hexa-acylated acyclic backbone. The vaccine examined is a recombinantly attenuated form of staphylococcal enterotoxin B (STEBVax). Using cells stably transfected with TLRs, E6020 transduced signals only through TLR4, suggesting monospecificity, while Escherichia coli 055:B5 lipopolysaccharide activated both the TLR2/6 heterodimer and TLR4. Coadministration of E6020 with STEBVax, by the intramuscular or intranasal route, induced significant levels of immunoglobulin G (IgG) in BALB/c mice. Further, increased IgG production resulted from the combination of E6020 with aluminum hydroxide adjuvant (AH). The antibody response to the vaccine coadministered with E6020 was a mixed Th1/Th2 response, as opposed to the Th2-biased response obtained with AH. Mice vaccinated with STEBVax coadministered with AH, TLR4 agonists, or a combination of both adjuvants were protected from toxic shock. Our data demonstrate the effectiveness of the synthetic TLR4 agonist E6020 as an alternative adjuvant for protein subunit vaccines that may also be used in combination with traditional aluminum-containing adjuvants.

  8. Improving the quality of interferometric synthetic aperture radar digital elevation models through a segmentation-based coregistration approach

    NASA Astrophysics Data System (ADS)

    Lin, Yu-Ching; Lin, Shih-Yuan; Miller, Pauline; Tsai, Ming-Da

    2016-10-01

    With the rapid development of remote sensing, multiple techniques are now capable of producing digital elevation models (DEMs), such as photogrammetry, Light Detection and Ranging (LiDAR), and interferometric synthetic aperture radar (InSAR). Satellite-derived InSAR DEMs are particularly attractive due to their advantages of large spatial extents, cost-effectiveness, and less dependence on the weather. However, several complex factors may limit the quality of derived DEMs, e.g., the inherited errors may be nonlinear and spatially variable over an entire InSAR pair scene. We propose a segmentation-based coregistration approach for generating accurate InSAR DEMs over large areas. Two matching algorithms, including least squares matching and iterative closest point, are integrated in this approach. Three Advanced Land Observing Satellite Phased Array type L-band Synthetic Aperture Radar (ALOS PALSAR) InSAR DEMs are evaluated, and their root mean square errors (RMSEs) improved from 17.87 to 9.98 m, 51.94 to 15.80 m, and 27.12 to 12.26 m. Compared to applying a single global matching strategy, the segmentation-based strategy further improved the RMSEs of the three DEMs by 3.27, 13.01, and 9.70 m, respectively. The results clearly demonstrate that the segmentation-based coregistration approach is capable of improving the geodetic quality of InSAR DEMs.

  9. Comparison of Experimental and Model Data for the Evaporation of a Synthetic Topopah Spring Tuff Pore Water, Yucca Mountain, NV

    SciTech Connect

    Alai, M; Sutton, M; Carroll, S

    2003-10-14

    The evaporation of a range of synthetic pore water solutions representative of the potential high-level-nuclear-waste repository at Yucca Mountain, NV is being investigated. The motivation of this work is to understand and predict the range of brine compositions that may contact the waste containers from evaporation of pore waters, because these brines could form corrosive thin films on the containers and impact their long-term integrity. A relatively complex synthetic Topopah Spring Tuff pore water was progressively concentrated by evaporation in a closed vessel, heated to 95 C in a series of sequential experiments. Periodic samples of the evaporating solution were taken to determine the evolving water chemistry. According to chemical divide theory at 25 C and 95 C our starting solution should evolve towards a high pH carbonate brine. Results at 95 C show that this solution evolves towards a complex brine that contains about 99 mol% Na{sup +} for the cations, and 71 mol% Cl{sup -}, 18 mol% {Sigma}CO{sub 2}(aq), 9 mol% SO{sub 4}{sup 2-} for the anions. Initial modeling of the evaporating solution indicates precipitation of aragonite, halite, silica, sulfate and fluoride phases. The experiments have been used to benchmark the use of the EQ3/6 geochemical code in predicting the evolution of carbonate-rich brines during evaporation.

  10. MISSA 2.0: an updated synthetic biology toolbox for assembly of orthogonal CRISPR/Cas systems.

    PubMed

    Zhang, Hai-Yan; Wang, Xing-Hui; Dong, Li; Wang, Zhi-Ping; Liu, Bing; Lv, Jie; Xing, Hui-Li; Han, Chun-Yan; Wang, Xue-Chen; Chen, Qi-Jun

    2017-02-03

    Efficient generation of plants carrying mutations in multiple genes remains a challenge. Using two or more orthogonal CRISPR/Cas systems can generate plants with multi-gene mutations, but assembly of these systems requires a robust, high-capacity toolkit. Here, we describe MISSA 2.0 (multiple-round in vivo site-specific assembly 2.0), an extensively updated toolkit for assembly of two or more CRISPR/Cas systems. We developed a novel suicide donor vector system based on plasmid RK2, which has much higher cloning capacity than the original, plasmid R6K-based system. We validated the utility of MISSA 2.0 by assembling multiple DNA fragments into the E. coli chromosome, and by creating transgenic Arabidopsis thaliana that constitutively or inducibly overexpress multiple genes. We then demonstrated that the higher cloning capacity of the RK2-derived MISSA 2.0 donor vectors facilitated the assembly of two orthogonal CRISPR/Cas systems including SpCas9 and SaCas9, and thus facilitated the creation of transgenic lines harboring these systems. We anticipate that MISSA 2.0 will enable substantial advancements in multiplex genome editing based on two or more orthogonal CRISPR/Cas9 systems, as well as in plant synthetic biology.

  11. MISSA 2.0: an updated synthetic biology toolbox for assembly of orthogonal CRISPR/Cas systems

    PubMed Central

    Zhang, Hai-Yan; Wang, Xing-Hui; Dong, Li; Wang, Zhi-Ping; Liu, Bing; Lv, Jie; Xing, Hui-Li; Han, Chun-Yan; Wang, Xue-Chen; Chen, Qi-Jun

    2017-01-01

    Efficient generation of plants carrying mutations in multiple genes remains a challenge. Using two or more orthogonal CRISPR/Cas systems can generate plants with multi-gene mutations, but assembly of these systems requires a robust, high-capacity toolkit. Here, we describe MISSA 2.0 (multiple-round in vivo site-specific assembly 2.0), an extensively updated toolkit for assembly of two or more CRISPR/Cas systems. We developed a novel suicide donor vector system based on plasmid RK2, which has much higher cloning capacity than the original, plasmid R6K-based system. We validated the utility of MISSA 2.0 by assembling multiple DNA fragments into the E. coli chromosome, and by creating transgenic Arabidopsis thaliana that constitutively or inducibly overexpress multiple genes. We then demonstrated that the higher cloning capacity of the RK2-derived MISSA 2.0 donor vectors facilitated the assembly of two orthogonal CRISPR/Cas systems including SpCas9 and SaCas9, and thus facilitated the creation of transgenic lines harboring these systems. We anticipate that MISSA 2.0 will enable substantial advancements in multiplex genome editing based on two or more orthogonal CRISPR/Cas9 systems, as well as in plant synthetic biology. PMID:28155921

  12. Synthetic multicellularity.

    PubMed

    Maharbiz, Michel M

    2012-12-01

    The ability to synthesize biological constructs on the scale of the organisms we observe unaided is probably one of the more outlandish, yet recurring, dreams humans have had since they began to modify genes. This review brings together recent developments in synthetic biology, cell and developmental biology, computation, and technological development to provide context and direction for the engineering of rudimentary, autonomous multicellular ensembles.

  13. Synthetic DNA

    PubMed Central

    O’ Driscoll, Aisling; Sleator, Roy D.

    2013-01-01

    With world wide data predicted to exceed 40 trillion gigabytes by 2020, big data storage is a very real and escalating problem. Herein, we discuss the utility of synthetic DNA as a robust and eco-friendly archival data storage solution of the future. PMID:23514938

  14. In vivo tissue response and durability of five novel synthetic polymers in a rabbit model.

    PubMed

    Sahin, E; Cingi, C; Eskiizmir, G; Altintoprak, N; Calli, A; Calli, C; Yilgör, I; Yilgör, E

    2016-04-01

    Alloplastic materials are frequently used in facial plastic surgeries such as rhinoplasty and nasal reconstruction. Unfortunately, the ideal alloplastic material has not been found. This experimental study evaluates the tissue response and durability of five novel polymers developed as an alloplastic material. In this experimental study involving a tertiary university hospital, six subcuticular pockets were formed at the back of 10 rabbits for the implantation of each polymer and sham group. Each pocket was excised with its adjacent tissue after three months, and collected for histopathological examination. Semi-quantitative examination including neovascularisation, inflammation, fibrosis, abscess formation, multinucleated foreign body giant cells was performed, and integrity of polymer was evaluated. A statistical comparison was performed. No statically significant difference was detected in neovascularisation, inflammation, fibrosis, abscess formation and multinucleated foreign body giant cells when a paired comparison between sham and polymer II, III and IV groups was performed individually. Nevertheless, the degree of fibrosis was less than sham group in polymer I (p = .027) and V (p = .018), although the other variables were almost similar. The integrity of polymers III (9 intact, 1 fragmented) and IV (8 intact, 2 absent) was better than the other polymers. These novel synthetic polymers could be considered as good candidates for clinical applicability. All polymers provided satisfactory results in terms of tissue response; however, fibrovascular integration was higher in polymers II, III and IV. In addition, the durability of polymer III and IV was better than the others.

  15. The Role of Galectin-1 in Cancer Progression, and Synthetic Multivalent Systems for the Study of Galectin-1

    PubMed Central

    Cousin, Jonathan M.; Cloninger, Mary J.

    2016-01-01

    This review discusses the role of galectin-1 in the tumor microenvironment. First, the structure and function of galectin-1 are discussed. Galectin-1, a member of the galectin family of lectins, is a functionally dimeric galactoside-binding protein. Although galectin-1 has both intracellular and extracellular functions, the defining carbohydrate-binding role occurs extracellularly. In this review, the extracellular roles of galectin-1 in cancer processes are discussed. In particular, the importance of multivalent interactions in galectin-1 mediated cellular processes is reviewed. Multivalent interactions involving galectin-1 in cellular adhesion, mobility and invasion, tumor-induced angiogenesis, and apoptosis are presented. Although the mechanisms of action of galectin-1 in these processes are still not well understood, the overexpression of galectin-1 in cancer progression indicates that the role of galectin-1 is significant. To conclude this review, synthetic frameworks that have been used to modulate galectin-1 processes are reviewed. Small molecule oligomers of carbohydrates, carbohydrate-functionalized pseudopolyrotaxanes, cyclodextrins, calixarenes, and glycodendrimers are presented. These synthetic multivalent systems serve as important tools for studying galectin-1 mediated cancer cellular functions. PMID:27649167

  16. An automated lung nodule detection system for CT images using synthetic minority oversampling

    NASA Astrophysics Data System (ADS)

    Mehre, Shrikant A.; Mukhopadhyay, Sudipta; Dutta, Anirvan; Harsha, Nagam Chaithan; Dhara, Ashis Kumar; Khandelwal, Niranjan

    2016-03-01

    Pulmonary nodules are a potential manifestation of lung cancer, and their early detection can remarkably enhance the survival rate of patients. This paper presents an automated pulmonary nodule detection algorithm for lung CT images. The algorithm utilizes a two-stage approach comprising nodule candidate detection followed by reduction of false positives. The nodule candidate detection involves thresholding, followed by morphological opening. The geometrical features at this stage are selected from properties of nodule size and compactness, and lead to reduced number of false positives. An SVM classifier is used with a radial basis function kernel. The data imbalance, due to uneven distribution of nodules and non-nodules as a result of the candidate detection stage, is proposed to be addressed by oversampling of minority class using Synthetic Minority Over-sampling Technique (SMOTE), and over-imposition of its misclassification penalty. Experiments were performed on 97 CT scans of a publically-available (LIDC-IDRI) database. Performance is evaluated in terms of sensitivity and false positives per scan (FP/scan). Results indicate noteworthy performance of the proposed approach (nodule detection sensitivity after 4-fold cross-validation is 92.91% with 3 FP/scan). Comparative analysis also reflects a comparable and often better performance of the proposed setup over some of the existing techniques.

  17. Multitemporal L- and C-Band Synthetic Aperture Radar To Highlight Differences in Water Status Among Boreal Forest and Wetland Systems in the Yukon Flats, Interior Alaska

    USGS Publications Warehouse

    Balser, Andrew W.; Wylie, Bruce K.

    2010-01-01

    Tracking landscape-scale water status in high-latitude boreal systems is indispensible to understanding the fate of stored and sequestered carbon in a climate change scenario. Spaceborne synthetic aperture radar (SAR) imagery provides critical information for water and moisture status in Alaskan boreal environments at the landscape scale. When combined with results from optical sensor analyses, a complementary picture of vegetation, biomass, and water status emerges. Whereas L-band SAR showed better inherent capacity to map water status, C-band had much more temporal coverage in this study. Analysis through the use of L- and C-band SARs combined with Landsat Enhanced Thematic Mapper Plus (ETM+) enables landscape stratification by vegetation and by seasonal and interannual hydrology. Resultant classifications are highly relevant to biogeochemistry at the landscape scale. These results enhance our understanding of ecosystem processes relevant to carbon balance and may be scaled up to inform regional carbon flux estimates and better parameterize general circulation models (GCMs).

  18. System of systems modeling and analysis.

    SciTech Connect

    Campbell, James E.; Anderson, Dennis James; Longsine, Dennis E.; Shirah, Donald N.

    2005-01-01

    This report documents the results of an LDRD program entitled 'System of Systems Modeling and Analysis' that was conducted during FY 2003 and FY 2004. Systems that themselves consist of multiple systems (referred to here as System of Systems or SoS) introduce a level of complexity to systems performance analysis and optimization that is not readily addressable by existing capabilities. The objective of the 'System of Systems Modeling and Analysis' project was to develop an integrated modeling and simulation environment that addresses the complex SoS modeling and analysis needs. The approach to meeting this objective involved two key efforts. First, a static analysis approach, called state modeling, has been developed that is useful for analyzing the average performance of systems over defined use conditions. The state modeling capability supports analysis and optimization of multiple systems and multiple performance measures or measures of effectiveness. The second effort involves time simulation which represents every system in the simulation using an encapsulated state model (State Model Object or SMO). The time simulation can analyze any number of systems including cross-platform dependencies and a detailed treatment of the logistics required to support the systems in a defined mission.

  19. The studies on the toxicity mechanism of environmentally hazardous natural (IAA) and synthetic (NAA) auxin--The experiments on model Arabidopsis thaliana and rat liver plasma membranes.

    PubMed

    Hąc-Wydro, Katarzyna; Flasiński, Michał

    2015-06-01

    This paper concerns the studies towards membrane-damage effect of two auxins: indole-3-acetic acid - IAA and 1-naphthaleneacetic acid - NAA on plant (Arabidopsis thaliana) and animal (rat liver) model membranes. The foregoing auxins are plant growth regulators widely used in agriculture to control the quality of the crop. However, their accumulation in the environment makes them hazardous for the living organisms. The aim of our investigations was to compare the effect of natural (IAA) vs. synthetic (NAA) auxin on the organization of plant and animal model membranes and find a possible correlation between membrane-disturbing effect of these compounds and their toxicity. The collected data evidenced that auxins cause destabilization of membranes, decrease their condensation and weakens interactions of molecules. The alterations in the morphology of model systems were also noticed. The foregoing effects of auxins are concentration-dependent and additionally NAA was found to act on animal vs. plant membranes more selectively than IAA. Interestingly, both IAA and NAA induce the strongest disordering in model lipid system at the concentration, which is frequently reported as toxic to animal and plants. Based on the above findings it was proposed that membrane-damage effect induced by IAA and NAA may be important from the point of view of the mechanism of toxicity of these compounds and cannot be ignored in further investigations in this area.

  20. On reduction of risks in UXO and mine detection using remote sensing systems and related synthetic image simulation

    NASA Astrophysics Data System (ADS)

    Bostater, Charles R., Jr.

    2005-06-01

    It is important to understand remote sensing systems and associated platforms in the context of autonomous or semi-autonomous designs for (robotic & mechatronics) that may be affect the motion control or stabilization aspects of the imagery, scan lines or fixed points scanned. This need can be most easily conceived as being related to the reduction of risks associated with false detection as well as the risks associated with hardware and software failure and risks associated with the actual operation of sensor and platform in dangerous environments. Thus safety is ultimately our concern when it comes to risk assessment. This paper will describe (a) remote sensing systems, (b) platforms (fixed and mobile, as well as to demonstrate (c) the value of thinking in terms of scalability as well as modularity in the design and application of new systems and (d) creation of synthetic signatures obtained for detection of targets in the aquatic environment. New systems - sensing systems as well as autonomous or semiautonomous robotic and mechatronic systems will be essential to secure domestic preparedness for humanitarian reasons as well as for demining and UXO detection. These same systems hold tremendous value, if thoughtfully designed for other applications which include environmental monitoring and surveillance.

  1. Engineering Ecosystems and Synthetic Ecologies#

    PubMed Central

    Mee, Michael T; Wang, Harris H

    2012-01-01

    Microbial ecosystems play an important role in nature. Engineering these systems for industrial, medical, or biotechnological purposes are important pursuits for synthetic biologists and biological engineers moving forward. Here, we provide a review of recent progress in engineering natural and synthetic microbial ecosystems. We highlight important forward engineering design principles, theoretical and quantitative models, new experimental and manipulation tools, and possible applications of microbial ecosystem engineering. We argue that simply engineering individual microbes will lead to fragile homogenous populations that are difficult to sustain, especially in highly heterogeneous and unpredictable environments. Instead, engineered microbial ecosystems are likely to be more robust and able to achieve complex tasks at the spatial and temporal resolution needed for truly programmable biology. PMID:22722235

  2. Model systems for single molecule polymer dynamics.

    PubMed

    Latinwo, Folarin; Schroeder, Charles M

    2011-01-01

    Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of "ideal" and "real" chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force-extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer-monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of "real" polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena.

  3. Model systems for single molecule polymer dynamics

    PubMed Central

    Latinwo, Folarin

    2012-01-01

    Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of “ideal” and “real” chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force–extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer–monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of “real” polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena. PMID:22956980

  4. Precipitation observations from high frequency spaceborne polarimetric synthetic aperture radar and ground-based radar: Theory and model validation

    NASA Astrophysics Data System (ADS)

    Fritz, Jason P.

    Global weather monitoring is a very useful tool to better understand the Earth's hydrological cycle and provide critical information for emergency and warning systems in severe cases. Developed countries have installed numerous ground-based radars for this purpose, but they obviously are not global in extent. To address this issue, the Tropical Rainfall Measurement Mission (TRMM) was launched in 1997 and has been quite successful. The follow-on Global Precipitation Measurement (GPM) mission will replace TRMM once it is launched. However, a single precipitation radar satellite is still limited, so it would be beneficial if additional existing satellite platforms can be used for meteorological purposes. Within the past few years, several X-band Synthetic Aperture Radar (SAR) satellites have been launched and more are planned. While the primary SAR application is surface monitoring, and they are heralded as "all weather'' systems, strong precipitation induces propagation and backscatter effects in the data. Thus, there exists a potential for weather monitoring using this technology. The process of extracting meteorological parameters from radar measurements is essentially an inversion problem that has been extensively studied for radars designed to estimate these parameters. Before attempting to solve the inverse problem for SAR data, however, the forward problem must be addressed to gain knowledge on exactly how precipitation impacts SAR imagery. This is accomplished by simulating storms in SAR data starting from real measurements of a storm by ground-based polarimetric radar. In addition, real storm observations by current SAR platforms are also quantitatively analyzed by comparison to theoretical results using simultaneous acquisitions by ground radars even in single polarization. For storm simulation, a novel approach is presented here using neural networks to accommodate the oscillations present when the particle scattering requires the Mie solution, i

  5. Phase-locked flow field analysis in a synthetic human larynx model

    NASA Astrophysics Data System (ADS)

    Lodermeyer, Alexander; Becker, Stefan; Döllinger, Michael; Kniesburges, Stefan

    2015-04-01

    The fluid flow within a human larynx plays an essential role in the fluid-structure-acoustic interaction during voice production. This study addresses the flow field downstream of aerodynamically driven, synthetic vocal folds. In order to quantitatively investigate the supraglottal formation of the flow field within one oscillation cycle of the vocal folds, a phase-locked PIV technique is introduced. The pseudo-time-resolved measurement results were averaged for each phase angle. When including a supraglottal channel, the jet was deflected from the centerline of the supraglottal channel and changed the direction of deflection in different cycles. The result is a bistable flow field. Therefore, a sorting method based on the mean cyclic supraglottal pressure difference was introduced. For both states of the flow field, a recirculation area was detected, interacting with the arising glottal jet in every oscillation cycle. This interaction could be identified as the major cause for supraglottal jet deflection, and the sense of rotation of the recirculation area defined the direction of deflection. The asymmetric structure of the flow field was caused by the geometric boundary condition, i.e., due to the present supraglottal channel. An additional key factor was found to be the contact between the two vocal folds in each oscillation cycle which interrupted the jet flow periodically. Removing the supraglottal channel resulted in a symmetric jet location. When avoiding vocal fold contact, the bistable behavior vanished and the jet was steadily deflected to one lateral side. In the present study, it cannot be confirmed that the Coanda effect is responsible for the deflection.

  6. Preparation of Silver Nanoparticles from Synthetic and Natural Sources: Remediation Model for PAHs

    NASA Astrophysics Data System (ADS)

    Abbasi, Maryam; Saeed, Fatima; Rafique, Uzaira

    2014-06-01

    The emergence of nanoscience and technology is gaining popularity with an increasing demand for metal nanoparticles applicability in various areas such as electronics, catalysis, chemistry, energy and medicine. Metallic nanoparticles are traditionally synthesized by wet chemical techniques, where the chemicals used are quite often toxic and flammable. In this work, an attempt is made to compare the efficiency of two different synthesis methods and application of each for the remediation of poly aromatic hydrocarbons (PAHs). In this regard, silver nanoparticles are prepared by green and wet chemical method using plant extract of garlic (Allium sativum). The extract is known to reduce the metal during synthesis and acts as stabilizing ligand. These synthesized silver nanoparticles (Agp) and (AgW) were applied as adsorbents in synthetic batch mode experiments at varying parameters of pH and temperature. A concentration of 0.01mg/L of Phenanthrene, Anthracene, and Pyrene were induced at fixed dosage of 1mg/Kg of adsorbent. Residual concentration of each PAH was analyzed on UV-Visible spectrophotometer. The results indicated that both adsorbents follow the sequence of Phenanthrene>Pyrene>Anthracene with optimal removal of higher than 85% in each case. A distinguishing privilege is attained by Agp adsorbent showing 3, 3 and 11 orders of magnitude higher efficiency than Agw. It may be attributed to more functional groups in the plant extract participating in binding of PAH to the surface. Each synthesized adsorbents was characterized by FTIR, SEM and EDX. The average particle size was determined to be of the order of 13-26 nm. The study concludes the use of alternate economical and green adsorbents for control of poly aromatic hydrocarbons (PAHs).

  7. Savannah woody structure modelling and mapping using multi-frequency (X-, C- and L-band) Synthetic Aperture Radar data

    NASA Astrophysics Data System (ADS)

    Naidoo, Laven; Mathieu, Renaud; Main, Russell; Kleynhans, Waldo; Wessels, Konrad; Asner, Gregory; Leblon, Brigitte

    2015-07-01

    Structural parameters of the woody component in African savannahs provide estimates of carbon stocks that are vital to the understanding of fuelwood reserves, which is the primary source of energy for 90% of households in South Africa (80% in Sub-Saharan Africa) and are at risk of over utilisation. The woody component can be characterised by various quantifiable woody structural parameters, such as tree cover, tree height, above ground biomass (AGB) or canopy volume, each been useful for different purposes. In contrast to the limited spatial coverage of ground-based approaches, remote sensing has the ability to sense the high spatio-temporal variability of e.g. woody canopy height, cover and biomass, as well as species diversity and phenological status - a defining but challenging set of characteristics typical of African savannahs. Active remote sensing systems (e.g. Light Detection and Ranging - LiDAR; Synthetic Aperture Radar - SAR), on the other hand, may be more effective in quantifying the savannah woody component because of their ability to sense within-canopy properties of the vegetation and its insensitivity to atmosphere and clouds and shadows. Additionally, the various components of a particular target's structure can be sensed differently with SAR depending on the frequency or wavelength of the sensor being utilised. This study sought to test and compare the accuracy of modelling, in a Random Forest machine learning environment, woody above ground biomass (AGB), canopy cover (CC) and total canopy volume (TCV) in South African savannahs using a combination of X-band (TerraSAR-X), C-band (RADARSAT-2) and L-band (ALOS PALSAR) radar datasets. Training and validation data were derived from airborne LiDAR data to evaluate the SAR <