Science.gov

Sample records for synthetic model systems

  1. Models for synthetic biology

    PubMed Central

    Kaznessis, Yiannis N

    2007-01-01

    Synthetic biological engineering is emerging from biology as a distinct discipline based on quantification. The technologies propelling synthetic biology are not new, nor is the concept of designing novel biological molecules. What is new is the emphasis on system behavior. The objective is the design and construction of new biological devices and systems to deliver useful applications. Numerous synthetic gene circuits have been created in the past decade, including bistable switches, oscillators, and logic gates, and possible applications abound, including biofuels, detectors for biochemical and chemical weapons, disease diagnosis, and gene therapies. More than fifty years after the discovery of the molecular structure of DNA, molecular biology is mature enough for real quantification that is useful for biological engineering applications, similar to the revolution in modeling in chemistry in the 1950s. With the excitement that synthetic biology is generating, the engineering and biological science communities appear remarkably willing to cross disciplinary boundaries toward a common goal. PMID:17986347

  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. 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.

  4. 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. PMID:26525970

  5. 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.

  6. 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.

  7. Meta-stochastic simulation of biochemical models for systems and synthetic biology.

    PubMed

    Sanassy, Daven; Widera, Paweł; Krasnogor, Natalio

    2015-01-16

    Stochastic simulation algorithms (SSAs) are used to trace realistic trajectories of biochemical systems at low species concentrations. As the complexity of modeled biosystems increases, it is important to select the best performing SSA. Numerous improvements to SSAs have been introduced but they each only tend to apply to a certain class of models. This makes it difficult for a systems or synthetic biologist to decide which algorithm to employ when confronted with a new model that requires simulation. In this paper, we demonstrate that it is possible to determine which algorithm is best suited to simulate a particular model and that this can be predicted a priori to algorithm execution. We present a Web based tool ssapredict that allows scientists to upload a biochemical model and obtain a prediction of the best performing SSA. Furthermore, ssapredict gives the user the option to download our high performance simulator ngss preconfigured to perform the simulation of the queried biochemical model with the predicted fastest algorithm as the simulation engine. The ssapredict Web application is available at http://ssapredict.ico2s.org. It is free software and its source code is distributed under the terms of the GNU Affero General Public License. PMID:25152014

  8. 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. PMID:22936991

  9. 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.

  10. Online updating of synthetic vision system databases

    NASA Astrophysics Data System (ADS)

    Simard, Philippe

    In aviation, synthetic vision systems render artificial views of the world (using a database of the world and pose information) to support navigation and situational awareness in low visibility conditions. The database needs to be periodically updated to ensure its consistency with reality, since it reflects at best a nominal state of the environment. This thesis presents an approach for automatically updating the geometry of synthetic vision system databases and 3D models in general. The approach is novel in that it profits from all of the available prior information: intrinsic/extrinsic camera parameters and geometry of the world. Geometric inconsistencies (or anomalies) between the model and reality are quickly localized; this localization serves to significantly reduce the complexity of the updating problem. Given a geometric model of the world, a sample image and known camera motion, a predicted image can be generated based on a differential approach. Model locations where predictions do not match observations are assumed to be incorrect. The updating is then cast as an optimization problem where differences between observations and predictions are minimized. To cope with system uncertainties, a mechanism that automatically infers their impact on prediction validity is derived. This method not only renders the anomaly detection process robust but also prevents the overfitting of the data. The updating framework is examined at first using synthetic data and further tested in both a laboratory environment and using a helicopter in flight. Experimental results show that the algorithm is effective and robust across different operating conditions.

  11. Designing and encoding models for synthetic biology

    PubMed Central

    Endler, Lukas; Rodriguez, Nicolas; Juty, Nick; Chelliah, Vijayalakshmi; Laibe, Camille; Li, Chen; Le Novère, Nicolas

    2009-01-01

    A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis. Once a domain mostly reserved for experts, dynamical modelling of gene regulatory and reaction networks has been an area of growth over the last decade. There has been a concomitant increase in the number of software tools and standards, thereby facilitating model exchange and reuse. We give here an overview of the model creation and analysis processes as well as some software tools in common use. Using markup language to encode the model and associated annotation, we describe the mining of components, their integration in relational models, formularization and parametrization. Evaluation of simulation results and validation of the model close the systems biology ‘loop’. PMID:19364720

  12. Physiologically based synthetic models of hepatic disposition.

    PubMed

    Hunt, C Anthony; Ropella, Glen E P; Yan, Li; Hung, Daniel Y; Roberts, Michael S

    2006-12-01

    Current physiologically based pharmacokinetic (PBPK) models are inductive. We present an additional, different approach that is based on the synthetic rather than the inductive approach to modeling and simulation. It relies on object-oriented programming. A model of the referent system in its experimental context is synthesized by assembling objects that represent components such as molecules, cells, aspects of tissue architecture, catheters, etc. The single pass perfused rat liver has been well described in evaluating hepatic drug pharmacokinetics (PK) and is the system on which we focus. In silico experiments begin with administration of objects representing actual compounds. Data are collected in a manner analogous to that in the referent PK experiments. The synthetic modeling method allows for recognition and representation of discrete event and discrete time processes, as well as heterogeneity in organization, function, and spatial effects. An application is developed for sucrose and antipyrine, administered separately and together. PBPK modeling has made extensive progress in characterizing abstracted PK properties but this has also been its limitation. Now, other important questions and possible extensions emerge. How are these PK properties and the observed behaviors generated? The inherent heuristic limitations of traditional models have hindered getting meaningful, detailed answers to such questions. Synthetic models of the type described here are specifically intended to help answer such questions. Analogous to wet-lab experimental models, they retain their applicability even when broken apart into sub-components. Having and applying this new class of models along with traditional PK modeling methods is expected to increase the productivity of pharmaceutical research at all levels that make use of modeling and simulation. PMID:17051440

  13. Photocatalytic Systems with Flavinium Salts: From Photolyase Models to Synthetic Tool for Cyclobutane Ring Opening.

    PubMed

    Hartman, Tomáš; Cibulka, Radek

    2016-08-01

    Two new photocatalytic systems based on flavinium species formed in situ by protonation of riboflavin-tetraacetate (1) with triflic acid or prepared in advance via alloxazine quaternization are presented as effective tools for oxidative cyclobutane ring [2 + 2] cycloreversion using visible light. The system with 1,3-dimethyl-8-trifluoromethylalloxazinium perchlorate (2c) was found to be superior allowing an acid-free mild procedure, which results in the opening of cyclobutanes with high oxidation potential (up to 2.14 V) and/or with sensitive groups (e.g., furan) without side reactions. PMID:27415962

  14. 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.

  15. Engineering biological systems with synthetic RNA molecules

    PubMed Central

    Liang, Joe C.; Bloom, Ryan J.; Smolke, Christina D.

    2011-01-01

    RNA molecules play diverse functional roles in natural biological systems. There has been growing interest in designing synthetic RNA counterparts for programming biological function. The design of synthetic RNA molecules that exhibit diverse activities, including sensing, regulatory, information processing, and scaffolding activities, has highlighted the advantages of RNA as a programmable design substrate. Recent advances in implementing these engineered RNA molecules as key control elements in synthetic genetic networks are highlighting the functional relevance of this class of synthetic elements in programming cellular behaviors. PMID:21925380

  16. A Synthetic Model of Mass Persuasion.

    ERIC Educational Resources Information Center

    Kneupper, Charles W.; Underwood, Willard A.

    Mass persuasion involves a message production process which significantly alters or reinforces an attitude, belief, or action of the members of a large, heterogeneous audience. A synthetic communication model for mass persuasion has been constructed which incorporates aspects of several models created to describe the process of effective…

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

    PubMed Central

    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. PMID:24130532

  18. 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. PMID:24130532

  19. 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. PMID:21886680

  20. Flight testing an integrated synthetic vision system

    NASA Astrophysics Data System (ADS)

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

    2005-05-01

    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 G-V 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.

  1. 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.

  2. Miniature synthetic-aperture radar system

    NASA Astrophysics Data System (ADS)

    Stockton, Wayne; Stromfors, Richard D.

    1990-11-01

    Loral Defense Systems-Arizona has developed a high-performance synthetic-aperture radar (SAR) for small aircraft and unmanned aerial vehicle (UAV) reconnaissance applications. This miniature radar, called Miniature Synthetic-Aperture Radar (MSAR), is packaged in a small volume and has low weight. It retains key features of large SAR systems, including high-resolution imaging and all-weather operation. The operating frequency of MSAR can optionally be selected to provide foliage penetration capability. Many imaging radar configurations can be derived using this baseline system. MSAR with a data link provides an attractive UAV sensor. MSAR with a real-time image formation processor is well suited to installations where onboard processing and immediate image analysis are required. The MSAR system provides high-resolution imaging for short-to-medium range reconnaissance applications.

  3. Darwinian optimization of synthetic neural systems

    SciTech Connect

    Dress, W.B.

    1987-01-01

    This paper suggests a synthesis of computer science and artificial intelligence with the resurgent ideas of artificial neural systems and genetic algorithms cast in a classical Darwinian mold. Just as Darwin's original theory avoided the need for teleological arguments, the thrust of the approach set forth here for synthetic systems avoids the problem of programmer omniscience and the resulting brittle programs for precisely the same reasons. The price to be paid is one of many long computations on, perhaps, many parallel processors. Hardware development leading to parallel networks of RISC processors should meet the near-term needs of evolutionary parameter determination and allow the ensuring synthetic systems to function in real-time for certain tasks. In the longer term, special-purpose devices will be needed.

  4. 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.

  5. 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

  6. 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

  7. Synthetic seismograms for a complex crustal model

    NASA Astrophysics Data System (ADS)

    Sandmeier, K.-J.; Wenzel, F.

    1986-01-01

    The algorithm of the original Reflectivity Method has been vectorized and implemented on a CDC CYBER 205 computer. Calculation times are shortened by a factor of 20 to 30 compared with a general purpose computer with a capacity of several million floating point operations per second (MFLOP). The rapid calculation of synthetic seismograms for complex models, high frequency sources and all offset ranges is a provision for modeling not only particular phases but the whole observed wavefield. As an example we model refraction data of the Black Forest, Southwest Germany and are able to derive rather tight constraints on the physical properties of the lower crust.

  8. 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.

  9. Synthetic vision systems: operational considerations simulation experiment

    NASA Astrophysics Data System (ADS)

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

    2007-04-01

    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.

  10. Synthetic Microbes As Drug Delivery Systems

    PubMed Central

    2015-01-01

    Synthetic cell therapy is a field that has broad potential for future applications in human disease treatment. Next generation therapies will consist of engineered bacterial strains capable of diagnosing disease, producing and delivering therapeutics, and controlling their numbers to meet containment and safety concerns. A thorough understanding of the microbial ecology of the human body and the interaction of the microbes with the immune system will benefit the choice of an appropriate chassis that engrafts stably and interacts productively with the resident community in specific body niches. PMID:25079685

  11. 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.

  12. 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.

  13. 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

    2015-01-01

    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. PMID

  14. 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.

  15. 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.

  16. Insights Into the P-To-Q Conversion in the Catalytic Cycle of Methane Monooxygenase From a Synthetic Model System

    SciTech Connect

    Xue, G.; Fiedler, A.T.; Martinho, M.; Munck, E.; Que, L.; Jr.

    2009-05-28

    For the catalytic cycle of soluble methane monooxygenase (sMMO), it has been proposed that cleavage of the O-O bond in the ({mu}-peroxo)diiron(III) intermediate P gives rise to the diiron(IV) intermediate Q with an Fe{sub 2}({mu}-O){sub 2} diamond core, which oxidizes methane to methanol. As a model for this conversion, ({mu}-oxo) diiron(III) complex 1 ([Fe{sup III}{sub 2}({mu}-O)({mu}-O{sub 2}H{sub 3})(L){sub 2}]{sup 3+}, L = tris(3,5-dimethyl-4-methoxypyridyl-2-methyl)amine) has been treated consecutively with one eq of H{sub 2}O{sub 2} and one eq of HClO{sub 4} to form 3 ([Fe{sup IV}{sub 2}({mu}-O){sub 2}(L){sub 2}]{sup 4+}). In the course of this reaction a new species, 2, can be observed before the protonation step; 2 gives rise to a cationic peak cluster by ESI-MS at m/z 1,399, corresponding to the [Fe{sub 2}O{sub 3}L{sub 2}H](OTf){sub 2}{sup +} ion in which 1 oxygen atom derives from 1 and the other two originate from H{sub 2}O{sub 2}. Moessbauer studies of 2 reveal the presence of two distinct, exchange coupled iron(IV) centers, and EXAFS fits indicate a short Fe-O bond at 1.66 {angstrom} and an Fe-Fe distance of 3.32 {angstrom}. Taken together, the spectroscopic data point to an HO-Fe{sup IV}-O-Fe{sup IV} = O core for 2. Protonation of 2 results in the loss of H{sub 2}O and the formation of 3. Isotope labeling experiments show that the [Fe{sup IV}{sub 2}({mu}-O){sub 2}] core of 3 can incorporate both oxygen atoms from H{sub 2}O{sub 2}. The reactions described here serve as the only biomimetic precedent for the conversion of intermediates P to Q in the sMMO reaction cycle and shed light on how a peroxodiiron(III) unit can transform into an [Fe{sup IV}{sub 2}({mu}-O){sub 2}] core.

  17. 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.

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

    PubMed Central

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

    2013-01-01

    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. PMID:23822510

  19. Modeling and Experimentation on a Two-dimensional Synthetic jet

    NASA Astrophysics Data System (ADS)

    Wang, Yunfei; Mohseni, Kamran

    2007-11-01

    Hotwire anemometry is employed in order to investigate the spatial development of a two-dimensional synthetic jet. Flow velocity at various locations downstream from a slit is measured. A self similar behavior in the measured velocity is observed. An analytical model for a steady synthetic jet is developed that accurately matches the experimental data. As observed by other groups, the two-dimensional synthetic jet spreads at a rate higher than a continuous jet. This rate is accurately predicted by our model. It is identified that the main difference between a continuous jet and a synthetic jet is the higher value of the virtual viscosity (eddy viscosity) in a synthetic jet. This is attributed to the pulsate nature of a synthetic jet that makes it more susceptible to turbulence.

  20. Synthetic LISA: Simulating time delay interferometry in a model LISA

    SciTech Connect

    Vallisneri, Michele

    2005-01-15

    We report on three numerical experiments on the implementation of Time-Delay Interferometry (TDI) for LISA, performed with Synthetic LISA, a C++/Python package that we developed to simulate the LISA science process at the level of scientific and technical requirements. Specifically, we study the laser-noise residuals left by first-generation TDI when the LISA armlengths have a realistic time dependence; we characterize the armlength-measurement accuracies that are needed to have effective laser-noise cancellation in both first- and second-generation TDI; and we estimate the quantization and telemetry bitdepth needed for the phase measurements. Synthetic LISA generates synthetic time series of the LISA fundamental noises, as filtered through all the TDI observables; it also provides a streamlined module to compute the TDI responses to gravitational waves according to a full model of TDI, including the motion of the LISA array and the temporal and directional dependence of the armlengths. We discuss the theoretical model that underlies the simulation, its implementation, and its use in future investigations on system-characterization and data-analysis prototyping for LISA.

  1. 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.

  2. 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. PMID:27284029

  3. 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

  4. Multispectral Synthetic Scene Generation Using Atmospheric Propagation and Thermodynamic Models.

    NASA Astrophysics Data System (ADS)

    Salvaggio, Carl

    With today's economy and unprecedented rate of technological advancement, ideas for new remote sensing systems outpace the abilities of and funding levels for researchers and engineers to build and test these platforms. For these reasons, accurate modeling of new systems becomes a requirement. This document represents the current status of a first-principles physics-based synthetic image generation model, DIRSIG, capable of producing the radiance field reaching the front-end of an airborne or terrestrial imaging system. This model accounts for the major material interaction effect for objects in the scene in both the reflective and emissive portions of the electromagnetic spectrum, their thermodynamic behavior in a natural environment, and the propagation of energy through the atmosphere. The model is demonstrated to produce viable imagery in both the qualitative and quantitative sense. In the thermal infrared portion of the spectrum, results are demonstrated in which temperatures are shown to be modeled within truth by 5^circC in the longwave -infrared and 6^circC in the midwave-infrared regions. Many of the phenomena observed in infrared imagery are also demonstrated including background radiance effects and thermal shadows (signatures). In developing a model to work in these two thermal infrared passbands, the model naturally had the capabilities to work in the reflective regions. Example imagery from the reflective portion of the spectra is presented illustrating the qualitative fidelity of the model in this region, however, no quantitative analysis was conducted at this time.

  5. Synthetic gauge flux and Weyl points in acoustic systems

    NASA Astrophysics Data System (ADS)

    Xiao, Meng; Chen, Wen-Jie; He, Wen-Yu; Chan, C. T.

    2015-11-01

    Following the discovery of the quantum Hall effect and topological insulators, the topological properties of classical waves began to draw attention. Topologically non-trivial bands characterized by non-zero Chern numbers are realized through either the breaking of time-reversal symmetry using an external magnetic field or dynamic modulation. Owing to the absence of a Faraday-like effect, the breaking of time-reversal symmetry in an acoustic system is commonly realized with moving background fluids, which drastically increases the engineering complexity. Here we show that we can realize effective inversion symmetry breaking and create an effective gauge flux in a reduced two-dimensional system by engineering interlayer couplings, achieving an acoustic analogue of the topological Haldane model. We show that the synthetic gauge flux is closely related to Weyl points in the three-dimensional band structure and the system supports chiral edge states for fixed values of kz.

  6. 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

  7. 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

  8. 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.

  9. 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. PMID:23412545

  10. 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. PMID:26524089

  11. SIFT vehicle recognition with semi-synthetic model database

    NASA Astrophysics Data System (ADS)

    Price, Rebecca L.; Rovito, Todd V.

    2012-06-01

    Object recognition is an important problem that has many applications that are of interest to the United States Air Force (USAF). Recently the USAF released its update to Technology Horizons, a report that is designed to guide the science and technology direction of the Air Force. Technology Horizons specifically calls out for the need to use autonomous systems in essentially all aspects of Air Force operations [1]. Object recognition is a key enabler to autonomous exploitation of intelligence, surveillance, and reconnaissance (ISR) data which might make the automatic searching of millions of hours of video practical. In particular this paper focuses on vehicle recognition with Lowe's Scale-invariant feature transform (SIFT) using a model database that was generated with semi-synthetic data. To create the model database we used a desktop laser scanner to create a high resolution 3D facet model. Then the 3D facet model was imported into LuxRender, a physics accurate ray tracing tool, and several views were rendered to create a model database. SIFT was selected because the algorithm is invariant to scale, noise, and illumination making it possible to create a model database of only a hundred original viewing locations which keeps the size of the model database reasonable.

  12. Developing a synthetic signal transduction system in plants.

    PubMed

    Morey, Kevin J; Antunes, Mauricio S; Albrecht, Kirk D; Bowen, Tessa A; Troupe, Jared F; Havens, Keira L; Medford, June I

    2011-01-01

    One area of focus in the emerging field of plant synthetic biology is the manipulation of systems involved in sensing and response to environmental signals. Sensing and responding to signals, including ligands, typically involves biological signal transduction. Plants use a wide variety of signaling systems to sense and respond to their environment. One of these systems, a histidine kinase (HK) based signaling system, lends itself to manipulation using the tools of synthetic biology. Both plants and bacteria use HKs to relay signals, which in bacteria can involve as few as two proteins (two-component systems or TCS). HK proteins are evolutionarily conserved between plants and bacteria and plant HK components have been shown to be functional in bacteria. We found that this conservation also applies to bacterial HK components which can function in plants. This conservation of function led us to hypothesize that synthetic HK signaling components can be designed and rapidly tested in bacteria. These novel HK signaling components form the foundation for a synthetic signaling system in plants, but typically require modifications such as codon optimization and proper targeting to allow optimal function. We describe the process and methodology of producing a synthetic signal transduction system in plants. We discovered that the bacterial response regulator (RR) PhoB shows HK-dependent nuclear translocation in planta. Using this discovery, we engineered a partial synthetic pathway in which a synthetic promoter (PlantPho) is activated using a plant-adapted PhoB (PhoB-VP64) and the endogenous HK-based cytokinin signaling pathway. Building on this work, we adapted an input or sensing system based on bacterial chemotactic binding proteins and HKs, resulting in a complete eukaryotic signal transduction system. Input to our eukaryotic signal transduction system is provided by a periplasmic binding protein (PBP), ribose-binding protein (RBP). RBP interacts with the membrane

  13. Synthetic scene generation model (SSGM R6.0)

    NASA Astrophysics Data System (ADS)

    Wilcoxen, Bruce A.; Heckathorn, Harry M.

    1995-06-01

    The Ballistic Missile Defense Organization (BMDO) must simulate the detection, acquisition, discrimination, and tracking of anticipated targets and predict the effect of natural and man- made background phenomena on optical sensor systems designed to perform these tasks. NRL is developing such a capability using a computerized methodology to provide modeled data in the form of digital realizations of complex, dynamic scenes. The Synthetic Scene Generation Model (SSGM) is designed to integrate state-of-science knowledge, data bases, and computerized phenomenology models to simulate ballistic missile engagement scenarios and to support the design, development, and test of advanced electro-optical interceptor and surveillance systems. Multi-phenomenology scenes are produced from validated codes -- thereby serving as a traceable standard against which different BMDO concepts and designs can be tested. This paper describes the SSGM software architecture, the software modules and databases that are used to create scene elements, the synthesis of deterministic and/or stochastic structured scene elements into composite scenes, the software system to manage the various databases and digital image libraries, the ancillary software tool suite, and verification and validation by comparison with empirical data. The focus is on the functionality of the SSGM Release 6.0, and the planned development effort for subsequent SSGM releases.

  14. Synthetic biology outside the cell: linking computational tools to cell-free systems.

    PubMed

    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

  15. 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

  16. 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.

  17. Synthetic testing of the Pacific Northwest earthquake early warning system

    NASA Astrophysics Data System (ADS)

    Crowell, B. W.; Schmidt, D. A.; Bodin, P.; Vidale, J. E.; Gomberg, J. S.; Jamison, D.; Minson, S. E.; Hartog, J. R.; Kress, V. C.; Malone, S. D.; Usher, M.

    2014-12-01

    The Cascadia subduction zone poses one of the greatest risks for a megaquake in the continental United States and, because of this, the Pacific Northwest Seismic Network (PNSN) at the University of Washington is building a joint seismic and geodetic earthquake early warning system. Our two-stage approach to earthquake early warning includes: (1) detection and initial characterization using strong-motion and broadband data from the PNSN with the ElarmS package, and (2) geodetic modeling modules using GPS data from the Pacific Northwest Geodetic Array (PANGA) and combined seismogeodetic (GPS + strong-motion) data. Because of Cascadia's relatively low seismicity rate and the paucity of data from plate boundary earthquakes, we have prioritized the development of a test system and the creation of several large simulated events. The test system permits us to: (1) replay segments of actual seismic waveform data recorded from the PNSN and neighboring networks to represent both earthquakes and noise conditions, and (2) broadcast synthetic data into the system to simulate signals we anticipate from earthquakes for which we have no actual ground motion recordings. The test system lets us also simulate various error conditions (latent and/or out-of-sequence data, telemetry drop-outs, etc.) and to explore how best to mitigate them. Here, we report on the performance of the joint early warning system and the geodetic modeling modules in a simulated real-time mode using simulated 5-Hz displacements from plausible Cascadian earthquake scenarios. The simulations are created using the FK integration method for hypothetical source models for a wide array of possible faulting types and magnitudes. The results show that the geodetic modeling modules are able to properly characterize the simulated events, and we discuss the limitations with respect to latency, network architecture, and earthquake location throughout the Pacific Northwest.

  18. Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems.

    PubMed

    Cardinale, Stefano; Arkin, Adam Paul

    2012-07-01

    Despite the efforts that bioengineers have exerted in designing and constructing biological processes that function according to a predetermined set of rules, their operation remains fundamentally circumstantial. The contextual situation in which molecules and single-celled or multi-cellular organisms find themselves shapes the way they interact, respond to the environment and process external information. Since the birth of the field, synthetic biologists have had to grapple with contextual issues, particularly when the molecular and genetic devices inexplicably fail to function as designed when tested in vivo. In this review, we set out to identify and classify the sources of the unexpected divergences between design and actual function of synthetic systems and analyze possible methodologies aimed at controlling, if not preventing, unwanted contextual issues. PMID:22649052

  19. Synthetic aperture radar system design for random field classification

    NASA Technical Reports Server (NTRS)

    Harger, R. O.

    1973-01-01

    An optimum design study is carried out for synthetic aperture radar systems intended for classifying randomly reflecting areas (such as agricultural fields) characterized by a reflectivity density spectral density. The problem solution is obtained, neglecting interfield interference and assuming areas of known configuration and location, as well as a certain Gaussian signal field property. The optimum processor is nonlinear, but includes conventional matched filter processing. A set of summary design curves is plotted, and is applied to the design of a satellite synthetic aperture radar system.

  20. 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.

  1. 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.

  2. 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

  3. 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…

  4. 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.

  5. 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.

  6. Directed evolution and synthetic biology applications to microbial systems.

    PubMed

    Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

    2016-06-01

    Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. PMID:27054950

  7. 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.

  8. 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. PMID:26696234

  9. Synthetic gauge flux and Weyl points in acoustic systems

    NASA Astrophysics Data System (ADS)

    Xiao, Meng; Chen, Wen-Jie; He, Wen-Yu; Chan, C. T.

    We consider acoustic systems comprising a honeycomb lattice in the xy plane and periodic along the z direction. As kz is a good quantum number here, for each fixed kz, this system can be treated as a reduced two-dimensional system. By engineering the interlayer coupling in the z-direction, we show that we can realize effective inversion symmetry breaking and synthetic staggered gauge flux in the reduced two-dimensional system. The realizations of chiral edge states for fixed values of kz are direct consequences of the staggered gauge flux. And we then show that the synthetic gauge flux is closely related to the Weyl points in the three-dimensional band structure. This work was supported by the Hong Kong Research Grants Council (Grant No. AoE/P-02/12).

  10. 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

  11. 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

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

    PubMed

    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

  13. 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.

  14. Model annotation for synthetic biology: automating model to nucleotide sequence conversion

    PubMed Central

    Misirli, Goksel; Hallinan, Jennifer S.; Yu, Tommy; Lawson, James R.; Wimalaratne, Sarala M.; Cooling, Michael T.; Wipat, Anil

    2011-01-01

    Motivation: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models. Results: We describe a method for automatically generating DNA sequences from dynamic models implemented in CellML and Systems Biology Markup Language (SBML). We also identify the metadata needed to annotate models to facilitate automated conversion, and propose and demonstrate a method for the markup of these models using RDF. Our algorithm has been implemented in a software tool called MoSeC. Availability: The software is available from the authors' web site http://research.ncl.ac.uk/synthetic_biology/downloads.html. Contact: anil.wipat@ncl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21296753

  15. Mathematical modeling of synthetic unit hydrograph case study: Citarum watershed

    NASA Astrophysics Data System (ADS)

    Islahuddin, Muhammad; Sukrainingtyas, Adiska L. A.; Kusuma, M. Syahril B.; Soewono, Edy

    2015-09-01

    Deriving unit hydrograph is very important in analyzing watershed's hydrologic response of a rainfall event. In most cases, hourly measures of stream flow data needed in deriving unit hydrograph are not always available. Hence, one needs to develop methods for deriving unit hydrograph for ungagged watershed. Methods that have evolved are based on theoretical or empirical formulas relating hydrograph peak discharge and timing to watershed characteristics. These are usually referred to Synthetic Unit Hydrograph. In this paper, a gamma probability density function and its variant are used as mathematical approximations of a unit hydrograph for Citarum Watershed. The model is adjusted with real field condition by translation and scaling. Optimal parameters are determined by using Particle Swarm Optimization method with weighted objective function. With these models, a synthetic unit hydrograph can be developed and hydrologic parameters can be well predicted.

  16. Asymptotic modeling of synthetic aperture ladar sensor phenomenology

    NASA Astrophysics Data System (ADS)

    Neuroth, Robert M.; Rigling, Brian D.; Zelnio, Edmund G.; Watson, Edward A.; Velten, Vincent J.; Rovito, Todd V.

    2015-05-01

    Interest in the use of active electro-optical(EO) sensors for non-cooperative target identification has steadily increased as the quality and availability of EO sources and detectors have improved. A unique and recent innovation has been the development of an airborne synthetic aperture imaging capability at optical wavelengths. To effectively exploit this new data source for target identification, one must develop an understanding of target-sensor phenomenology at those wavelengths. Current high-frequency, asymptotic EM predictors are computationally intractable for such conditions, as their ray density is inversely proportional to wavelength. As a more efficient alternative, we have developed a geometric optics based simulation for synthetic aperture ladar that seeks to model the second order statistics of the diffuse scattering commonly found at those wavelengths but with much lesser ray density. Code has been developed, ported to high-performance computing environments, and tested on a variety of target models.

  17. 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. PMID:23443149

  18. EXPOSURE ANALYSIS MODELING SYSTEM (EXAMS)

    EPA Science Inventory

    The Exposure Analysis Modeling System (EXAMS), 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--pesti...

  19. 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

  20. Model Jerks: Insights from Observations and Synthetic Fields

    NASA Astrophysics Data System (ADS)

    Brown, William; Mound, Jonathan; Livermore, Philip; Gillet, Nicolas

    2015-04-01

    The geomagnetic field is generated by the constant motion of the fluid outer core and varies on timescales from months to millions of years. Geomagnetic jerks are rapid changes in the secular variation of Earth's magnetic field, attributed primarily to changing flows near the surface of the outer core. Various generation mechanisms have been suggested for these rapid changes but none have conclusively explained the phenomena. Jerks can be seen in magnetic observatory records over the last 170 years and in satellite data of the last 15 years. This data coverage, spatially limited and/or temporally restricted, makes it difficult to interpret the true character of jerks at the surface or their origins in the core. This leads us to investigate what further insight we can gain from synthetic magnetic fields such as those which are described by modelling stochastic processes. Such fields are not restricted by the temporal smoothing of most magnetic field models and can better represent rapid variations such as jerks. We compare the characteristics of the synthetic fields with those of observatory and satellite data and hence, finding great similarity, study the presence of jerks in stochastic synthetic fields. Synthetic jerks are seen which resemble observed jerks, occurring frequently with regional periodic variations in amplitudes. These synthetic jerks occur without related features in the large scale secular acceleration power at the core-mantle boundary. The flexible spatial and temporal sampling of the models creates a means of validating the robustness of observed features in the real field, which suffer from limited sampling. Results suggest that the distribution of magnetic observatories is sufficient to accurately recover the large scale features of jerks. As such comparisons between jerks seen in observatory and satellite data may be drawn. We further investigate the spectral properties of jerks in the synthetic fields using spherical harmonic analysis with a

  1. Model-Based Signal Processing: Correlation Detection With Synthetic Seismograms

    SciTech Connect

    Rodgers, A; Harris, D; Pasyanos, M; Blair, S; Matt, R

    2006-08-30

    Recent applications of correlation methods to seismological problems illustrate the power of coherent signal processing applied to seismic waveforms. Examples of these applications include detection of low amplitude signals buried in ambient noise and cross-correlation of sets of waveforms to form event clusters and accurately measure delay times for event relocation and/or earth structure. These methods rely on the exploitation of the similarity of individual waveforms and have been successfully applied to large sets of empirical observations. However, in cases with little or no empirical event data, such as aseismic regions or exotic event types, correlation methods with observed seismograms will not be possible due to the lack of previously observed similar waveforms. This study uses model-based signals computed for three-dimensional (3D) Earth models to form the basis for correlation detection. Synthetic seismograms are computed for fully 3D models estimated from the Markov Chain Monte-Carlo (MCMC) method. MCMC uses stochastic sampling to fit multiple seismological data sets. Rather than estimate a single ''optimal'' model, MCMC results in a suite of models that sample the model space and incorporates uncertainty through variability of the models. The variability reflects our ignorance of Earth structure, due to limited resolution, data and modeling errors, and produces variability in the seismic waveform response. Model-based signals are combined using a subspace method where the synthetic signals are decomposed into an orthogonal basis by singular-value decomposition (SVD) and the observed waveforms are represented with a linear combination of a sub-set of eigenvectors (signals) associated with the most significant eigenvalues. We have demonstrated the method by modeling long-period (80-10 seconds) regional seismograms for a moderate (M{approx}5) earthquake near the China-North Korea border. Synthetic seismograms are computed with the Spectral Element Method

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

    NASA Technical Reports Server (NTRS)

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

    2008-01-01

    This is the video that accompanies the "Millimeter Wave Synthetic Aperture Imaging System with a Unique Rotary Scanning System" presentation. It shows the operation of the scanning system, and reviews the results of the scanning of a sample.

  3. Processor design optimization methodology for synthetic vision systems

    NASA Astrophysics Data System (ADS)

    Wren, Bill; Tarleton, Norman G.; Symosek, Peter F.

    1997-06-01

    Architecture optimization requires numerous inputs from hardware to software specifications. The task of varying these input parameters to obtain an optimal system architecture with regard to cost, specified performance and method of upgrade considerably increases the development cost due to the infinitude of events, most of which cannot even be defined by any simple enumeration or set of inequalities. We shall address the use of a PC-based tool using genetic algorithms to optimize the architecture for an avionics synthetic vision system, specifically passive millimeter wave system implementation.

  4. A new PAMPA model proposed on the basis of a synthetic phospholipid membrane.

    PubMed

    Yu, Hui; Wang, Qi; Sun, Ying; Shen, Ming; Li, He; Duan, Yourong

    2015-01-01

    The purpose of this work was to investigate the synthetic phospholipid dependence of permeability measured by parallel artificial membrane permeability assay (PAMPA) method. Three phospholipids with hydrophobic groups of different lengths and phosphorylcholine as the hydrophilic group were concisely synthesized. Ten model drug molecules were selected because of their distinct human fraction absorbed (%FA) values and various pKa characteristics. In vitro drug permeation experiments were designed to determine the effect of the incubation time (4-20 h), pH gradient (4.6-9.32) and carbon chain length (8, 10, 12) on the drug permeability through the synthetic phospholipid membrane in the PAMPA system. The results showed that intensive and significant synthetic phospholipids dependence of permeability influenced by the length of lipid's hydrophobic carbon chain. The effective permeability constant (Pe) of each drug increased rapidly with time, then decreased slightly after reaching the maximum; the pH gradient changed the drug permeability according to the pH-partition hypothesis for drugs with diverse pKa values; and longer hydrophobic chains in the synthetic phospholipid membrane improved the drug permeability, as observed for all test drugs at almost all incubation time points. This newly proposed PAMPA model considered the synthetic phospholipid membrane and showed good Pe-%FA correlation for the passive transport of drugs, making it a helpful supplementary method for PAMPA systems. PMID:25647086

  5. Model-supported exploitation of synthetic aperture radar images

    NASA Astrophysics Data System (ADS)

    Chellappa, Rama; Kuttikkad, Shyam; Meth, Reuven; Burlina, Philippe; Shekhar, Chandra S.

    1996-02-01

    We address the application of model-supported exploitation techniques to synthetic aperture radar (SAR) imagery. The emphasis is on monitoring SAR imagery using wide area 2D and/or 3D site models along with contextual information. We consider here the following tasks useful in monitoring: (a) site model construction using segmentation and labeling techniques, (b) target detection, (c) target classification and indexing, and (d) SAR image-site model registration. The 2-D wide area site models used here for SAR image exploitation differ from typical site models developed for RADIUS applications, in that they do not model specific facilities, but constitute wide area site models of cultural features such as urban clutter areas, roads, clearings, fields, etc. These models may be derived directly from existing site models, possibly constructed from electro-optical (EO) observations. When such models are not available, a set of segmentation and labeling techniques described here can be used for the construction of 2D site models. The use of models can potentially yield critical information which can disambiguate target signatures in SAR images. We address registration of SAR and EO images to a common site model. Specific derivations are given for the case of registration within the RCDE platform. We suggest a constant false alarm rate (CFAR) detection scheme and a topographic primal sketch (TPS) based classification scheme for monitoring target occurrences in SAR images. The TPS of an observed target is matched against candidate targets TPSs synthesized for the preferred target orientation, inferred from context (e.g. road or parking lot targets). Experimental results on real and synthetic SAR images are provided.

  6. Waveform Inversion of Synthetic Ocean Models in the Laplace Domain

    NASA Astrophysics Data System (ADS)

    Rosado, H.; Blacic, T. M.; Jun, H.; Shin, C.

    2014-12-01

    In seismic oceanography, the processed images show where small temperature changes (as little as 0.03°C) occur, although they do not give absolute temperatures. To get a 2-D temperature map, the data must be inverted for sound speed, which is then converted to temperature using equations of state. Full waveform inversion requires a starting model that is iteratively updated until the residuals converge. Global search algorithms such as Genetic Algorithm do not require a starting model close to the true model, but are computationally exhausting. Local search inversion is less expensive, but requires a reasonably accurate starting model. Unfortunately, most marine seismic data has little associated hydrographic data and so it is difficult to create starting models close enough to the true model for convergence throughout the target area. In addition, the band-limited nature of seismic data makes it inherently challenging to extract the long wavelength sound speed trend directly from seismic data. Laplace domain inversion (LDI) developed by Changsoo Shin and colleagues requires only a rudimentary starting model to produce smooth background sound speed models without requiring prior information about the medium. It works by transforming input data to the Laplace domain, and then examining the zero frequency component of the damped wavefield to extract a smooth sound speed model - basically, removing higher frequency fluctuations to expose background trends. This ability to use frequencies below those effectively propagated by the seismic source is what enables LDI to produce the smooth background trend from the data. We applied LDI to five synthetic data sets based on simplified models of oceanographic features. Using LDI, we were able to recover smoothed versions of our synthetic models, showing the viability of the method for creating sound speed profiles suitable for use as starting models for other methods of inversion that output more detailed models.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

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

    PubMed

    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

  13. 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

  14. Hierarchical model-based interferometric synthetic aperture radar image registration

    NASA Astrophysics Data System (ADS)

    Wang, Yang; Huang, Haifeng; Dong, Zhen; Wu, Manqing

    2014-01-01

    With the rapid development of spaceborne interferometric synthetic aperture radar technology, classical image registration methods are incompetent for high-efficiency and high-accuracy masses of real data processing. Based on this fact, we propose a new method. This method consists of two steps: coarse registration that is realized by cross-correlation algorithm and fine registration that is realized by hierarchical model-based algorithm. Hierarchical model-based algorithm is a high-efficiency optimization algorithm. The key features of this algorithm are a global model that constrains the overall structure of the motion estimated, a local model that is used in the estimation process, and a coarse-to-fine refinement strategy. Experimental results from different kinds of simulated and real data have confirmed that the proposed method is very fast and has high accuracy. Comparing with a conventional cross-correlation method, the proposed method provides markedly improved performance.

  15. 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

  16. 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.

  17. The NASA/JPL Airborne Synthetic Aperture Radar System

    NASA Technical Reports Server (NTRS)

    Lou, Yunling; Kim,Yunjin; vanZyl, Jakob

    1996-01-01

    In this paper we will briefly describe the instrument characteristics, the evolution of various radar modes, the instrument performance and improvement in the knowledge of the positioning and attitude information of the NASA/JPL airborne synthetic aperture radar (SAR). This system operates in the fully polarimetric mode in the P, L, and C band simultaneously or in the interferometric mode in both the L and C band simultaneously. We also summarize the progress of the data processing effort, especially in the interferometry processing and we address the issue of processing and calibrating the cross-track interferometry data.

  18. 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.

  19. 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. PMID:15376934

  20. Vibratory responses of synthetic, self-oscillating vocal fold models.

    PubMed

    Murray, Preston R; Thomson, Scott L

    2012-11-01

    The flow-induced responses of four self-oscillating synthetic vocal fold models are compared. All models were life-sized and fabricated using flexible silicone compounds with material properties comparable to those of human vocal fold tissue. Three of the models had two layers of different stiffness to represent the body-cover grouping of vocal fold tissue. Two of the two-layer models were based on the "M5" geometry [Scherer et al., J. Acoust. Soc. Am. 109, 1616-1630 (2001)], while the third was based on magnetic resonance imaging data. The fourth model included several layers, including a thin epithelial layer, an exceedingly flexible superficial lamina propria layer, a ligament layer that included an anteriorly-posteriorly oriented fiber to restrict vertical motion, and a body layer. Measurements were performed with these models in full larynx and hemilarynx configurations. Data included onset pressure, vibration frequency, glottal flow rate, maximum glottal width, and medial surface motion, the latter two of which were acquired using high-speed imaging techniques. The fourth, multi-layer model exhibited onset pressure, frequency, and medial surface motion traits that are comparable to published human vocal fold data. Importantly, the model featured an alternating convergent-divergent glottal profile and mucosal wave-like motion, characteristics which are important markers of human vocal fold vibration. PMID:23145623

  1. Statistical assessment of model fit for synthetic aperture radar data

    NASA Astrophysics Data System (ADS)

    DeVore, Michael D.; O'Sullivan, Joseph A.

    2001-08-01

    Parametric approaches to problems of inference from observed data often rely on assumed probabilistic models for the data which may be based on knowledge of the physics of the data acquisition. Given a rich enough collection of sample data, the validity of those assumed models can be assessed in a statistical hypothesis testing framework using any of a number of goodness-of-fit tests developed over the last hundred years for this purpose. Such assessments can be used both to compare alternate models for observed data and to help determine the conditions under which a given model breaks down. We apply three such methods, the (chi) 2 test of Karl Pearson, Kolmogorov's goodness-of-fit test, and the D'Agostino-Pearson test for normality, to quantify how well the data fit various models for synthetic aperture radar (SAR) images. The results of these tests are used to compare a conditionally Gaussian model for complex-valued SAR pixel values, a conditionally log-normal model for SAR pixel magnitudes, and a conditionally normal model for SAR pixel quarter-power values. Sample data for these tests are drawn from the publicly released MSTAR dataset.

  2. 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.

  3. 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.

  4. Gene gymnastics: Synthetic biology for baculovirus expression vector system engineering.

    PubMed

    Vijayachandran, Lakshmi S; Thimiri Govinda Raj, Deepak B; Edelweiss, Evelina; Gupta, Kapil; Maier, Josef; Gordeliy, Valentin; Fitzgerald, Daniel J; Berger, Imre

    2013-01-01

    Most essential activities in eukaryotic cells are catalyzed by large multiprotein assemblies containing up to ten or more interlocking subunits. The vast majority of these protein complexes are not easily accessible for high resolution studies aimed at unlocking their mechanisms, due to their low cellular abundance and high heterogeneity. Recombinant overproduction can resolve this bottleneck and baculovirus expression vector systems (BEVS) have emerged as particularly powerful tools for the provision of eukaryotic multiprotein complexes in high quality and quantity. Recently, synthetic biology approaches have begun to make their mark in improving existing BEVS reagents by de novo design of streamlined transfer plasmids and by engineering the baculovirus genome. Here we present OmniBac, comprising new custom designed reagents that further facilitate the integration of heterologous genes into the baculovirus genome for multiprotein expression. Based on comparative genome analysis and data mining, we herein present a blueprint to custom design and engineer the entire baculovirus genome for optimized production properties using a bottom-up synthetic biology approach. PMID:23328086

  5. Cosmic non-TEM radiation and synthetic feed array sensor system in ASIC mixed signal technology

    NASA Astrophysics Data System (ADS)

    Centureli, F.; Scotti, G.; Tommasino, P.; Trifiletti, A.; Romano, F.; Cimmino, R.; Saitto, A.

    2014-08-01

    The paper deals with the opportunity to introduce "Not strictly TEM waves" Synthetic detection Method (NTSM), consisting in a Three Axis Digital Beam Processing (3ADBP), to enhance the performances of radio telescope and sensor systems. Current Radio Telescopes generally use the classic 3D "TEM waves" approximation Detection Method, which consists in a linear tomography process (Single or Dual axis beam forming processing) neglecting the small z component. The Synthetic FEED ARRAY three axis Sensor SYSTEM is an innovative technique using a synthetic detection of the generic "NOT strictly TEM Waves radiation coming from the Cosmo, which processes longitudinal component of Angular Momentum too. Than the simultaneous extraction from radiation of both the linear and quadratic information component, may reduce the complexity to reconstruct the Early Universe in the different requested scales. This next order approximation detection of the observed cosmologic processes, may improve the efficacy of the statistical numerical model used to elaborate the same information acquired. The present work focuses on detection of such waves at carrier frequencies in the bands ranging from LF to MMW. The work shows in further detail the new generation of on line programmable and reconfigurable Mixed Signal ASIC technology that made possible the innovative Synthetic Sensor. Furthermore the paper shows the ability of such technique to increase the Radio Telescope Array Antenna performances.

  6. Evolution of planetary nebulae. I. An improved synthetic model

    NASA Astrophysics Data System (ADS)

    Marigo, P.; Girardi, L.; Groenewegen, M. A. T.; Weiss, A.

    2001-11-01

    We present a new synthetic model to follow the evolution of a planetary nebula (PN) and its central star, starting from the onset of AGB phase up to the white dwarf cooling sequence. The model suitably combines various analytical prescriptions to account for different (but inter-related) aspects of planetary nebulae, such as: the dynamical evolution of the primary shell and surrounding ejecta, the photoionisation of H and He by the central star, the nebular emission of a few relevant optical lines (e.g. Hβ ; He II lambda 4686; [O III] lambda 5007). Particular effort has been put into the analytical description of dynamical effects such as the three-winds interaction and the shell thickening due to ionisation (i.e. the thin-shell approximation is relaxed), that are nowadays considered important aspects of the PN evolution. Predictions of the synthetic model are tested by comparison with both findings of hydrodynamical calculations, and observations of Galactic PNe. The sensitiveness of the results to the model parameters (e.g. transition time, mass of the central star, H-/He-burning tracks, etc.) is also discussed. We briefly illustrate the systematic differences that are expected in the luminosities and lifetimes of PNe with either H- or He-burning central stars, which result in different ``detection probabilities'' across the H-R diagram, in both Hβ and [OIII] lambda5007 lines. Adopting reasonable values of the model parameters, we are able to reproduce, in a satisfactory way, many general properties of PNe, like the ionised mass-nebular radius relationship, the trends of a few main nebular line ratios, and the observed ranges of nebular shell thicknesses, electron densities, and expansion velocities. The models naturally predict also the possible transitions from optically-thick to optically-thin configurations (and vice versa). In this context, our analysis indicates that the condition of optical thinness to the H continuum plays an important role in producing

  7. 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. PMID:27450602

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Design and evaluation of a gastroretentive drug delivery system for metformin HCl using synthetic and semi-synthetic polymers.

    PubMed

    Meka, Venkata Srikanth; Gorajana, Adinaravyana; Dharmanlingam, Senthil Rajan; Kolapalli, Venkata Ramana Murthy

    2013-12-01

    The aim of the present research was to prepare and evaluate a gastroretentive drug delivery system for metformin HCl, using synthetic and semi-synthetic polymers. The floating approach was applied for preparing gastroretentive tablets (GRT) and these tablets were manufactured by the direct compression method. The drug delivery system comprises of synthetic and semi-synthetic polymers such as polyethylene oxide and Carboxymethyl ethyl cellulose (CMEC) as release-retarding polymers. GRT were evaluated for physico-chemical properties like weight variation, hardness, assay friability, in vitro floating behaviour, swelling studies, in vitro dissolution studies and rate order kinetics. Based upon the drug release and floating properties, two formulations (MP04 & MC03) were selected as optimized formulations. The optimized formulations MP04 and MC03 followed zero order rate kinetics, with non-Fickian diffusion and first order rate kinetics with erosion mechanism, respectively. The optimized formulation was characterised with FTIR studies and it was observed that there was no interaction between the drug and polymers. PMID:24502177

  14. Synthetic aperture radar processing system for search and rescue

    NASA Astrophysics Data System (ADS)

    Huxtable, Barton D.; Jackson, Christopher R.; Mansfield, Arthur W.; Rais, Houra

    1997-06-01

    Synthetic aperture radar (SAR) is uniquely suited to help solve the search and rescue problem since it can be utilized either day or night and through both dense fog or thick cloud cover. This paper describes the search and rescue data processing system (SARDPS) developed at Goddard Space Flight Center. SARDPS was developed for the Search and Rescue Mission Office in order to conduct research, development, and technology demonstration of SAR to quickly locate small aircraft which have crashed in remote areas. In order to effectively apply SAR to the detection of crashed aircraft several technical challenges needed to be overcome. These include full resolution SAR image formation using low frequency radar appropriate for foliage penetration, the application of autofocusing for SAR motion compensation in the processing system, and the development of sophisticated candidate crash site detection algorithms. In addition, the need to dispatch rescue teams to specific locations requires precise SAR image georectification and map registration techniques. The final end-to-end processing system allows for raw SAR phase history data to be quickly converted to georeferenced map/image products with candidate crash site locations identified.

  15. Study on extremizing adaptive systems and applications to synthetic aperture radars

    NASA Astrophysics Data System (ADS)

    Politis, D. T.

    1983-05-01

    Klopf's work on the functioning of the neuron was studied and critically examined for engineering application possibilities. Similarly, Barto's work on the implementation of Klopf's ideas in computer simulated nets/systems was studied to determine if it could provide suitable models for physical systems. The latest learning system investigated by Barto, described as "Learning with an Adaptive Critic' was considered as the most promising for engineering applications. A functional engineering model of that system has been developed and its dynamic behavior of this system is currently being investigated in order to improve our understanding of the system operation and potential applications. In parallel with this study we are looking for possible application of such learning systems in synthetic aperture radars and data exploitation. Several potential applications have already been suggested. These suggestions will be further explored and the most promising will be proposed for full investigation and possible implementation.

  16. 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

  17. Synthetic tumor networks for screening drug delivery systems.

    PubMed

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

    2015-03-10

    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

  18. QSAR and pharmacophore modeling of natural and synthetic antimalarial prodiginines.

    PubMed

    Singh, Baljinder; Vishwakarma, Ram A; Bharate, Sandip B

    2013-09-01

    Prodiginines are a family of linear and cyclic oligopyrrole red-pigmented compounds possessing antibacterial, anticancer and immunosuppressive activities and are produced by actinomycetes and other eubacteria. Recently, prodiginines have been reported to possess potent in vitro as well as in vivo antimalarial activity against chloroquine sensitive D6 and multi-drug resistant Dd2 strains of Plasmodium falciparum. In the present paper, a QSAR and pharmacophore modeling for a series of natural and synthetic prodiginines was performed to find out structural features which are crucial for antimalarial activity against these D6 and Dd2 Plasmodium strains. The study indicated that inertia moment 2 length, Kier Chi6 (path) index, kappa 3 index and Wiener topological index plays important role in antimalarial activity against D6 strain whereas descriptors inertia moment 2 length, ADME H-bond donors, VAMP polarization XX component and VAMP quadpole XZ component play important role in antimalarial activity against Dd2 strain. Furthermore, a five-point pharmacophore (ADHRR) model with one H-bond acceptor (A), one H-bond donor (D), one hydrophobic group (H) and two aromatic rings (R) as pharmacophore features was developed for D6 strain by PHASE module of Schrodinger suite. Similarly a six-point pharmacophore AADDRR was developed for Dd2 strain activity. All developed QSAR models showed good correlation coefficient (r² > 0.7), higher F value (F >20) and excellent predictive power (Q² > 0.6). Developed models will be highly useful for predicting antimalarial activity of new compounds and could help in designing better molecules with enhanced antimalarial activity. Furthermore, calculated ADME properties indicated drug-likeness of prodiginines. PMID:24010933

  19. 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

  20. 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. PMID:25182226

  1. 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. PMID:25436610

  2. 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.

  3. Radiation-Magneto Models for Star Formation and Synthetic Observations

    NASA Astrophysics Data System (ADS)

    Commercon, Benoit; Levrier, Francois; Maury, Anaelle; Henning, Thomas; Launhardt, Ralf; Dullemond, Cornellis

    2013-07-01

    Although predicted by theoretical models, the existence of first hydrostatic cores (FHSC) has yet to be convincingly demonstrated by (sub)millimeter observations, and the multiplicity at this early stage of the star formation process is poorly constrained. We present a possible identification strategy for FHSC candidates and make predictions of ALMA dust continuum emission maps from these objects. This is done by post-processing three state-of-the-art radiation-magneto-hydrodynamic (RMHD) 3D adaptive mesh refinement calculations of first hydrostatic core models performed with the RAMSES code. We compute the dust thermal continuum emission with the 3D radiative transfer code RADMC-3D. We compute spectral energy distributions (SED) and usual evolutionary stage indicators such as bolometric luminosity and temperature, and then produce synthetic ALMA observations using the simulator included in the GILDAS software package. We show that under certain conditions, FHSCs can be identified from dust continuum emission at 24 μm and 70 μm. We also show that single SEDs cannot help in distinguishing between the formation scenarios of the FHSC, i.e., between the magnetized and non-magnetized models. We identify which combinations of the different ALMA bands and array configurations represent our best chance of solving the fragmentation issue in these objects. We thus demonstrate how ALMA will help in identifying the physical processes occurring within collapsing dense cores: If the magnetic field is playing a role, the emission pattern will show evidence of a pseudo-disk and even of a magnetically driven outflow that hydrodynamical calculations cannot reproduce.

  4. 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.

  5. Practical synthetic aperture radar image formation based on realistic spaceborne synthetic aperture radar modeling and simulation

    NASA Astrophysics Data System (ADS)

    Shim, Sang Heun; Ro, Yong Man

    2013-01-01

    This paper presents the practical spaceborne synthetic aperture radar (SAR) data focusing method based on the realistic end-to-end spaceborne SAR simulation. Our simulation reflects main factors of the satellite SAR that induce errors to degrade the focused image severely, which are related to the sensor hardware, the antenna beam pointing, the effective velocity, and the Doppler frequency. To minimize errors due to them in the spaceborne SAR image formation, we suggest and utilize the preprocessing as the internal calibration, the analysis of orbital data of an SAR satellite, the calculation of an effective velocity and the Doppler frequency utilizing the two-way slant range equation, and the usage of the phase gradient algorithm combined with the extended chirp scaling algorithm based on the azimuth signal deramping. The processing results for realistic simulated raw data of a spaceborne SAR are presented to validate the proposed methods.

  6. Height reconstruction techniques for synthetic aperture lidar systems

    NASA Technical Reports Server (NTRS)

    Chen, Curtis W.; Hensley, Scott

    2003-01-01

    The data-processing techniques and acquisition modes of a synthetic aperture lidar (SAL) instrument operating at optical wavelengths are closely related to the analogous modes of a synthetic aperture radar (SAR) instrument operating at microwave frequencies. It is consequently natural to explore the applicability of SAR processing techniques to SAL sensors. In this paper, we examine the feasibility of adopting SAR height-reconstruction techniques with SAL sensors to obtain high-resolution 3-D imagery at optical wavelengths.

  7. Synthetic fluorescent probes for studying copper in biological systems

    PubMed Central

    Cotruvo, Joseph A.; Aron, Allegra T.; Ramos-Torres, Karla M.; Chang, Christopher J.

    2015-01-01

    The potent redox activity of copper is required for sustaining life. Mismanagement of its cellular pools, however, can result in oxidative stress and damage connected to aging, neurodegenerative diseases, and metabolic disorders. Therefore, copper homeostasis is tightly regulated by cells and tissues. Whereas copper and other transition metal ions are commonly thought of as static cofactors buried within protein active sites, emerging data points to the presence of additional loosely bound, labile pools that can participate in dynamic signalling pathways. Against this backdrop, we review advances in sensing labile copper pools and understanding their functions using synthetic fluorescent indicators. Following brief introductions to cellular copper homeostasis and considerations in sensor design, we survey available fluorescent copper probes and evaluate their properties in the context of their utility as effective biological screening tools. We emphasize the need for combined chemical and biological evaluation of these reagents, as well as the value of complementing probe data with other techniques for characterizing the different pools of metal ions in biological systems. This holistic approach will maximize the exciting opportunities for these and related chemical technologies in the study and discovery of novel biology of metals. PMID:25692243

  8. Simulation assessment of synthetic vision system concepts for UAV operations

    NASA Astrophysics Data System (ADS)

    Calhoun, Gloria L.; Draper, Mark H.; Ruff, Heath A.; Nelson, Jeremy T.; Lefebvre, Austen T.

    2006-05-01

    The Air Force Research Laboratory's Human Effectiveness Directorate supports research addressing human factors associated with Unmanned Aerial Vehicle (UAV) operator control stations. One research thrust explores the value of combining synthetic vision data with live camera video presented on a UAV control station display. Information is constructed from databases (e.g., terrain, etc.), as well as numerous information updates via networked communication with other sources. This information is overlaid conformal, in real time, onto the dynamic camera video image display presented to operators. Synthetic vision overlay technology is expected to improve operator situation awareness by highlighting elements of interest within the video image. Secondly, it can assist the operator in maintaining situation awareness of an environment if the video datalink is temporarily degraded. Synthetic vision overlays can also serve to facilitate intuitive communications of spatial information between geographically separated users. This paper discusses results from a high-fidelity UAV simulation evaluation of synthetic symbology overlaid on a (simulated) live camera display. Specifically, the effects of different telemetry data update rates for synthetic visual data were examined for a representative sensor operator task. Participants controlled the zoom and orientation of the camera to find and designate targets. The results from both performance and subjective data demonstrated the potential benefit of an overlay of synthetic symbology for improving situation awareness, reducing workload, and decreasing time required to designate points of interest. Implications of symbology update rate are discussed, as well as other human factors issues.

  9. Model-Based Information Extraction From Synthetic Aperture Radar Signals

    NASA Astrophysics Data System (ADS)

    Matzner, Shari A.

    2011-07-01

    Synthetic aperture radar (SAR) is a remote sensing technology for imaging areas of the earth's surface. SAR has been successfully used for monitoring characteristics of the natural environment such as land cover type and tree density. With the advent of higher resolution sensors, it is now theoretically possible to extract information about individual structures such as buildings from SAR imagery. This information could be used for disaster response and security-related intelligence. SAR has an advantage over other remote sensing technologies for these applications because SAR data can be collected during the night and in rainy or cloudy conditions. This research presents a model-based method for extracting information about a building -- its height and roof slope -- from a single SAR image. Other methods require multiple images or ancillary data from specialized sensors, making them less practical. The model-based method uses simulation to match a hypothesized building to an observed SAR image. The degree to which a simulation matches the observed data is measured by mutual information. The success of this method depends on the accuracy of the simulation and on the reliability of the mutual information similarity measure. Electromagnetic theory was applied to relate a building's physical characteristics to the features present in a SAR image. This understanding was used to quantify the precision of building information contained in SAR data, and to identify the inputs needed for accurate simulation. A new SAR simulation technique was developed to meet the accuracy and efficiency requirements of model-based information extraction. Mutual information, a concept from information theory, has become a standard for measuring the similarity between medical images. Its performance in the context of matching a simulation image to a SAR image was evaluated in this research, and it was found to perform well under certain conditions. The factors that affect its performance

  10. Determining resolvability of mantle plumes with synthetic seismic modeling

    NASA Astrophysics Data System (ADS)

    Maguire, R.; Van Keken, P. E.; Ritsema, J.; Fichtner, A.; Goes, S. D. B.

    2014-12-01

    Hotspot volcanism in locations such as Hawaii and Iceland is commonly thought to be associated with plumes rising from the deep mantle. In theory these dynamic upwellings should be visible in seismic data due to their reduced seismic velocity and their effect on mantle transition zone thickness. Numerous studies have attempted to image plumes [1,2,3], but their deep mantle origin remains unclear. In addition, a debate continues as to whether lower mantle plumes are visible in the form of body wave travel time delays, or whether such delays will be erased due to wavefront healing. Here we combine geodynamic modeling of mantle plumes with synthetic seismic waveform modeling in order to quantitatively determine under what conditions mantle plumes should be seismically visible. We model compressible plumes with phase changes at 410 km and 670 km, and a viscosity reduction in the upper mantle. These plumes thin from greater than 600 km in diameter in the lower mantle, to 200 - 400 km in the upper mantle. Plume excess potential temperature is 375 K, which maps to seismic velocity reductions of 4 - 12 % in the upper mantle, and 2 - 4 % in the lower mantle. Previous work that was limited to an axisymmetric spherical geometry suggested that these plumes would not be visible in the lower mantle [4]. Here we extend this approach to full 3D spherical wave propagation modeling. Initial results using a simplified cylindrical plume conduit suggest that mantle plumes with a diameter of 1000 km or greater will retain a deep mantle seismic signature. References[1] Wolfe, Cecily J., et al. "Seismic structure of the Iceland mantle plume." Nature 385.6613 (1997): 245-247. [2] Montelli, Raffaella, et al. "Finite-frequency tomography reveals a variety of plumes in the mantle." Science 303.5656 (2004): 338-343. [3] Schmandt, Brandon, et al. "Hot mantle upwelling across the 660 beneath Yellowstone." Earth and Planetary Science Letters 331 (2012): 224-236. [4] Hwang, Yong Keun, et al

  11. 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, ...

  12. 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

  13. Antifouling activity of synthetic alkylpyridinium polymers using the barnacle model.

    PubMed

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

    2014-04-01

    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

  14. 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.

  15. 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.

  16. Question 7: construction of a semi-synthetic minimal cell: a model for early living cells.

    PubMed

    Murtas, Giovanni

    2007-10-01

    Using a Synthetic Biology approach we are building a semi-synthetic minimal cell. This represents an exercise to shape a minimal-cell model system recalling the simplicity of early living cells in early evolution. We have recently introduced into liposome compartments a minimal set of enzymes named "Puresystem" (PS) synthesizing EGFP proteins. To establish reproduction of the shell compartment with a minimal set of genes we have cloned the genes for the Fatty Acid Synthase (FAS) type I enzymes. These FAS genes introduced into liposomes, translated into FAS enzymes by PS and in the presence of precursors produce fatty acids. The resulting release of fatty acid molecules within liposome vesicles should promote vesicle growth and reproduction. The core reproduction of a minimal cell corresponding to the replication of the minimal genome will require a few genes for the DNA replication and the PS, and a minimum set of genes for the synthesis of t-RNAs. In future the reconstruction of a minimal ribosome will bring the number of genes for ribosomal proteins from 54 of an existing minimal genome down to 30-20 genes. A Synthetic Biology approach could bring the number of essential genes for a minimal cell down to 100 or less. PMID:17668286

  17. 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.

  18. 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

  19. 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

  20. 77 FR 2342 - Seventeenth Meeting: RTCA Special Committee 213, Enhanced Flight Vision/Synthetic Vision Systems...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-17

    ... Federal Aviation Administration Seventeenth Meeting: RTCA Special Committee 213, Enhanced Flight Vision... Transportation (DOT). ACTION: Notice of RTCA Special Committee 213, Enhanced Flight Vision/ Synthetic Vision... meeting of RTCA Special Committee 213, Enhanced Flight Vision/Synthetic Vision Systems (EFVS/SVS)....

  1. 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.

  2. Valence tautomerism in synthetic models of cytochrome P450.

    PubMed

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

    2016-06-14

    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

  3. 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.

  4. 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.

  5. Nonparaxial vector-field modeling of optical coherence tomography and interferometric synthetic aperture microscopy.

    PubMed

    Davis, Brynmor J; Schlachter, Simon C; Marks, Daniel L; Ralston, Tyler S; Boppart, Stephen A; Carney, P Scott

    2007-09-01

    A large-aperture, electromagnetic model for coherent microscopy is presented and the inverse scattering problem is solved. Approximations to the model are developed for near-focus and far-from-focus operations. These approximations result in an image-reconstruction algorithm consistent with interferometric synthetic aperture microscopy (ISAM): this validates ISAM processing of optical-coherence-tomography and optical-coherence-microscopy data in a vectorial setting. Numerical simulations confirm that diffraction-limited resolution can be achieved outside the focal plane and that depth of focus is limited only by measurement noise and/or detector dynamic range. Furthermore, the model presented is suitable for the quantitative study of polarimetric coherent microscopy systems operating within the first Born approximation. PMID:17767224

  6. 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.

  7. 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.

  8. 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.

  9. Synthetic microbial communities☆

    PubMed Central

    Großkopf, Tobias; Soyer, Orkun S

    2014-01-01

    While natural microbial communities are composed of a mix of microbes with often unknown functions, the construction of synthetic microbial communities allows for the generation of defined systems with reduced complexity. Used in a top-down approach, synthetic communities serve as model systems to ask questions about the performance and stability of microbial communities. In a second, bottom-up approach, synthetic microbial communities are used to study which conditions are necessary to generate interaction patterns like symbiosis or competition, and how higher order community structure can emerge from these. Besides their obvious value as model systems to understand the structure, function and evolution of microbial communities as complex dynamical systems, synthetic communities can also open up new avenues for biotechnological applications. PMID:24632350

  10. 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.

  11. 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.

  12. 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.

  13. Synthetic scene generation model (SSGM R7.0)

    NASA Astrophysics Data System (ADS)

    Wilcoxen, Bruce A.; Heckathorn, Harry M.

    1996-06-01

    BMDO must simulate the detection, acquisition, discrimination and tracking of anticipated targets and predict the effect of natural and man-made backgrounds and environmental phenomena on optical and radar sensor systems designed to perform these tasks. The SSGM is designed to integrate state-of-science knowledge, data bases and valid phenomenology models to simulate ballistic missile engagement scenarios for both passive and active sensors aboard surveillance system platforms and defensive interceptor missiles -- thereby serving as a traceable standard against which different BMDO concepts and designs can be evaluated. This paper concentrates on describing the current capabilities and planned development efforts for SSGM. The focus will be on the functionality of the SSGM Release 7.0 and the planned development effort for subsequent SSGM releases. We shall demonstrate the current SSGM capability (R7.0, January 1996) with sample multi-phenomenology output scenes and videos. New capabilities include realistic 6-DOF dynamics for targets, simulated target radar cross section correlated with IR information, and authorative target model data sets based on actual flight experiments.

  14. Synthetic Seismograms for Realistic 3D Earth Model with Anisotropic Inner Core

    NASA Astrophysics Data System (ADS)

    Tsuboi, S.; Tono, Y.

    2006-12-01

    We have demonstrated that we can calculate global theoretical seismograms for realistic 3D Earth models based upon the combination of a precise numerical technique (the spectral-element method) and a sufficiently fast supercomputer (the Earth Simulator) [Tsuboi et al, 2003]. Here we have calculated synthetic seismograms by using model S20RTS of the mantle (Ritsema et al., 1999), model CRUST2.0 of the crust (Basin et al., 2000), topography and bathymetry model ETOPO5, and anisotropic inner core model (Ishii 2002). The calculations are performed on 4056 processors, which require 507 out of 640 nodes of the Earth Simulator. These synthetics are computed by using SPECFEM3D(Komatitsch and Tromp, 2002) and are accurate up to 3.5 seconds. We have calculated these synthetics with aisotropic inner core model for several earthquakes and compared with the synthetics which are calculated for isotropic inner core model. Preliminary comparison shows that the travel time differences between anisotropic inner core model and isotropic core model for PKPab phases are at most a few seconds. There seems to be no significant differences in waveforms of PKP phases. These differences in travel times may help us to improve inner core fine structure by comparing these synthetics with observation.

  15. Synthetic thrombus model for in-vitro studies of laser thrombolysis

    NASA Astrophysics Data System (ADS)

    Hermes, Robert E.; Trajkovska, Keti

    1998-05-01

    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. We describe here the development of new surrogate materials based on formulations incorporating chicken 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.

  16. 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.

  17. Cotton crop spectral imaging analysis: a web-based hyperspectral synthetic imagery simulation system

    NASA Astrophysics Data System (ADS)

    Alarcon, Vladimir J.; Sassenrath, Gretchen F.

    2004-11-01

    The development of spectral libraries for specific vegetation species and soils is useful for identifying different physiological or physical-chemical characteristics. Usually, spectral libraries are provided as a data-base add-in of current commercial software used for analyzing hyperspectral imagery. The use of those databases requires installation of the software in the user"s machine for either visualizing or using the spectral libraries. There are also spectral libraries available on the web but the data is static and partitioned by spectrum of vegetation or soil because the size of the files of actual hyperspectral images precludes it"s publication on the web. In this paper, a web-based simulation environment for generating hyperspectral synthetic imagery of cotton plots is presented. The system was developed using Java and is based on a previous synthetic imagery program1. The mathematical and numerical formulation of the model is briefly sketched. The core computing components of the simulation environment were written in C for their computational efficiency. The emerging Java Native Interface (JNI) technique and standard Java techniques were used to design a user-friendly simulator. The simulation system provides interactive user control and real time visualization of the resulting hyperspectral image through standard web browsers. It shows potential for providing web-based hyperspectral libraries, in the form of images, for public use.

  18. System for synthetic vision and augmented reality in future flight decks

    NASA Astrophysics Data System (ADS)

    Behringer, Reinhold; Tam, Clement K.; McGee, Joshua H.; Sundareswaran, Venkataraman; Vassiliou, Marius S.

    2000-06-01

    Rockwell Science Center is investigating novel human-computer interface techniques for enhancing the situational awareness in future flight decks. One aspect is to provide intuitive displays which provide the vital information and the spatial awareness by augmenting the real world with an overlay of relevant information registered to the real world. Such Augmented Reality (AR) techniques can be employed during bad weather scenarios to permit flying in Visual Flight Rules (VFR) in conditions which would normally require Instrumental Flight Rules (IFR). These systems could easily be implemented on heads-up displays (HUD). The advantage of AR systems vs. purely synthetic vision (SV) systems is that the pilot can relate the information overlay to real objects in the world, whereas SV systems provide a constant virtual view, where inconsistencies can hardly be detected. The development of components for such a system led to a demonstrator implemented on a PC. A camera grabs video images which are overlaid with registered information, Orientation of the camera is obtained from an inclinometer and a magnetometer, position is acquired from GPS. In a possible implementation in an airplane, the on-board attitude information can be used for obtaining correct registration. If visibility is sufficient, computer vision modules can be used to fine-tune the registration by matching visual clues with database features. Such technology would be especially useful for landing approaches. The current demonstrator provides a frame-rate of 15 fps, using a live video feed as background and an overlay of avionics symbology in the foreground. In addition, terrain rendering from a 1 arc sec. digital elevation model database can be overlaid to provide synthetic vision in case of limited visibility. For true outdoor testing (on ground level), the system has been implemented on a wearable computer.

  19. 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.

  20. Synthetic biodegradable hydrogel delivery of demineralized bone matrix for bone augmentation in a rat model

    PubMed Central

    Kinard, Lucas A.; Dahlin, Rebecca L.; Lam, Johnny; Lu, Steven; Lee, Esther J.; Kasper, F. Kurtis; Mikos, Antonios G.

    2014-01-01

    There exists a strong clinical need for a more capable and robust method to achieve bone augmentation, and a system with fine-tuned delivery of demineralized bone matrix (DBM) has potential to meet that need. As such, the objective of the present study was to investigate a synthetic biodegradable hydrogel for the delivery of DBM for bone augmentation in a rat model. Oligo(poly(ethylene glycol) fumarate) (OPF) constructs were designed and fabricated by varying the content of rat-derived DBM particles (either 1:3, 1:1, or 3:1 DBM:OPF weight ratio on a dry basis) and using two DBM particle size ranges (50–150 or 150–250 μm). The physical properties of the constructs and the bioactivity of the DBM were evaluated. Select formulations (1:1 and 3:1 with 50–150 μm DBM) were evaluated in vivo compared to an empty control to investigate the effect of DBM dose and construct properties on bone augmentation. Overall, 3:1 constructs with higher DBM content achieved the greatest volume of bone augmentation exceeding 1:1 constructs and empty implants by 3-fold and 5-fold, respectively. As such, we have established that a synthetic, biodegradable hydrogel can function as a carrier for DBM, and that the volume of bone augmentation achieved by the constructs correlated directly to DBM dose. PMID:25046637

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

    PubMed

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

    2016-02-26

    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. PMID:26820630

  2. Multi-frequency synthetic-aperture imaging with a lightweight ground penetrating radar system

    NASA Astrophysics Data System (ADS)

    Koppenjan, Steven K.; Allen, Curt M.; Gardner, Duane; Wong, Howard R.; Lee, Hua; Lockwood, Stephanie J.

    2000-03-01

    The detection of buried objects, particularly hazardous waste containers and unexploded ordnance (UXO), has gained significant interest in the Unites States in the late 1990s. The desire to remediate the thousands of sites worldwide has become an increasing concern and the application of radar to this problem has received renewed attention. The US Department of Energy's Special Technologies Laboratory (STL), operated by Bechtel Nevada, has developed several frequency-modulated, continuous-wave (FM-CW) ground penetrating radar (GPR) units. To meet technical requirements for higher-resolution data, STL and the University of California, Santa Barbara (UCSB) is investigating advanced GPR hardware, signal processing, and synthetic-aperture imaging with the development of an innovative system. The goal is to design and fabricate a lightweight, battery-operated unit that does not require surface contact, can be operated by a novice user, and can achieve improved resolution. The latter is accomplished by using synthetic-aperture imaging, which forms the subsurface images by fully utilizing the data sequences collectively along a scan path. We also present the backward propagation algorithm as the basic structure of the multiple-frequency tomographic imaging technique, and the conventional fast Fourier transform (FFT) method which can be described as a degenerated case of the model where the computation procedure is approximated under the narrow-beam assumption.

  3. 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.

  4. 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.

  5. 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. PMID:25801368

  6. 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. PMID:27353631

  7. Resonance-based low-frequency synthetic jet actuator modeling, design, and testing

    NASA Astrophysics Data System (ADS)

    Gravatt, Lynn; Flatau, Alison

    2006-03-01

    Synthetic Jet Actuators have been the topic of extensive study in the aerospace industry because of their ability to actively control flow over aerodynamic surfaces without discrete control surfaces such as a flap. One challenge has been to develop a low frequency, lightweight actuator that can provide large displacements. This study will discuss the modeling, design, manufacture, and testing of a bimorph piezo-composite actuator that will provide such displacements at low frequencies. The design employs two opposing benders that provide a piston-type motion. The initial goals of this study were to achieve 30 m/s out of the slot while maintaining the mechanical resonant frequency of the system at about 100 Hz.

  8. Synthetic Feedback Loop Model for Increasing Microbial Biofuel Production Using a Biosensor

    PubMed Central

    Harrison, Mary E.; Dunlop, Mary J.

    2012-01-01

    Current biofuel production methods use engineered bacteria to break down cellulose and convert it to biofuel. A major challenge in microbial fuel production is that increasing biofuel yields can be limited by the toxicity of the biofuel to the organism that is producing it. Previous research has demonstrated that efflux pumps are effective at increasing tolerance to various biofuels. However, when overexpressed, efflux pumps burden cells, which hinders growth and slows biofuel production. Therefore, the toxicity of the biofuel must be balanced with the toxicity of pump overexpression. We have developed a mathematical model for cell growth and biofuel production that implements a synthetic feedback loop using a biosensor to control efflux pump expression. In this way, the production rate will be maximal when the concentration of biofuel is low because the cell does not expend energy expressing efflux pumps when they are not needed. Additionally, the microbe is able to adapt to toxic conditions by triggering the expression of efflux pumps, which allow it to continue biofuel production. Sensitivity analysis indicates that the feedback sensor model is insensitive to many system parameters, but a few key parameters can influence growth and production. In comparison to systems that express efflux pumps at a constant level, the feedback sensor increases overall biofuel production by delaying pump expression until it is needed. This result is more pronounced when model parameters are variable because the system can use feedback to adjust to the actual rate of biofuel production. PMID:23112794

  9. 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.

  10. 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.

  11. 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…

  12. 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. PMID:25460426

  13. 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.

  14. 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.

  15. Waveform error analysis for bistatic synthetic aperture radar systems

    NASA Astrophysics Data System (ADS)

    Adams, J. W.; Schifani, T. M.

    The signal phase histories at the transmitter, receiver, and radar signal processor in bistatic SAR systems are described. The fundamental problem of mismatches in the waveform generators for the illuminating and receiving radar systems is analyzed. The effects of errors in carrier frequency and chirp slope are analyzed for bistatic radar systems which use linear FM waveforms. It is shown that the primary effect of a mismatch in carrier frequencies is an azimuth displacement of the image.

  16. 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

  17. Investigation of the synthetic experiment system of machine equipment fault diagnosis

    NASA Astrophysics Data System (ADS)

    Liu, Hongyu; Xu, Zening; Yu, Xiaoguang

    2008-12-01

    The invention and manufacturing of the synthetic experiment system of machine equipment fault diagnosis filled in the blank of this kind of experiment equipment in China and obtained national practical new type patent. By the motor speed regulation system, machine equipment fault imitation system, measuring and monitoring system and analysis and diagnosis system of the synthetic experiment system, students can regulate motor speed arbitrarily, imitate multi-kinds of machine equipment parts fault, collect the signals of acceleration, speed, displacement, force and temperature and make multi-kinds of time field, frequency field and figure analysis. The application of the synthetic experiment system in our university's teaching practice has obtained good effect on fostering professional eligibility in measuring, monitoring and fault diagnosis of machine equipment. The synthetic experiment system has the advantages of short training time, quick desirable result and low test cost etc. It suits for spreading in university extraordinarily. If the systematic software was installed in portable computer, user can fulfill measuring, monitoring, signal processing and fault diagnosis on multi-kinds of field machine equipment conveniently. Its market foreground is very good.

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

    PubMed

    Rantasalo, Anssi; Czeizler, Elena; Virtanen, Riitta; Rousu, Juho; Lähdesmäki, Harri; Penttilä, Merja; Jäntti, Jussi; Mojzita, Dominik

    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

  19. Development of a Synthetic Adaptive Neuro-Fuzzy Prediction Model for Tumor Motion Tracking in External Radiotherapy by Evaluating Various Data Clustering Algorithms.

    PubMed

    Ghorbanzadeh, Leila; Torshabi, Ahmad Esmaili; Nabipour, Jamshid Soltani; Arbatan, Moslem Ahmadi

    2016-04-01

    In image guided radiotherapy, in order to reach a prescribed uniform dose in dynamic tumors at thorax region while minimizing the amount of additional dose received by the surrounding healthy tissues, tumor motion must be tracked in real-time. Several correlation models have been proposed in recent years to provide tumor position information as a function of time in radiotherapy with external surrogates. However, developing an accurate correlation model is still a challenge. In this study, we proposed an adaptive neuro-fuzzy based correlation model that employs several data clustering algorithms for antecedent parameters construction to avoid over-fitting and to achieve an appropriate performance in tumor motion tracking compared with the conventional models. To begin, a comparative assessment is done between seven nuero-fuzzy correlation models each constructed using a unique data clustering algorithm. Then, each of the constructed models are combined within an adaptive sevenfold synthetic model since our tumor motion database has high degrees of variability and that each model has its intrinsic properties at motion tracking. In the proposed sevenfold synthetic model, best model is selected adaptively at pre-treatment. The model also updates the steps for each patient using an automatic model selectivity subroutine. We tested the efficacy of the proposed synthetic model on twenty patients (divided equally into two control and worst groups) treated with CyberKnife synchrony system. Compared to Cyberknife model, the proposed synthetic model resulted in 61.2% and 49.3% reduction in tumor tracking error in worst and control group, respectively. These results suggest that the proposed model selection program in our synthetic neuro-fuzzy model can significantly reduce tumor tracking errors. Numerical assessments confirmed that the proposed synthetic model is able to track tumor motion in real time with high accuracy during treatment. PMID:25765021

  20. 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.

  1. Generating a dynamic synthetic population--using an age-structured two-sex model for household dynamics.

    PubMed

    Namazi-Rad, M; Namazi-Rad, Mohammad-Reza; Mokhtarian, P; Mokhtarian, Payam; Perez, P; Perez, Pascal

    2014-01-01

    Generating a reliable computer-simulated synthetic population is necessary for knowledge processing and decision-making analysis in agent-based systems in order to measure, interpret and describe each target area and the human activity patterns within it. In this paper, both synthetic reconstruction (SR) and combinatorial optimisation (CO) techniques are discussed for generating a reliable synthetic population for a certain geographic region (in Australia) using aggregated- and disaggregated-level information available for such an area. A CO algorithm using the quadratic function of population estimators is presented in this paper in order to generate a synthetic population while considering a two-fold nested structure for the individuals and households within the target areas. The baseline population in this study is generated from the confidentialised unit record files (CURFs) and 2006 Australian census tables. The dynamics of the created population is then projected over five years using a dynamic micro-simulation model for individual- and household-level demographic transitions. This projection is then compared with the 2011 Australian census. A prediction interval is provided for the population estimates obtained by the bootstrapping method, by which the variability structure of a predictor can be replicated in a bootstrap distribution. PMID:24733522

  2. 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.

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

    DOE PAGESBeta

    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 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. A Synthetic Ecology Perspective: How Well Does Behavior of Model Organisms in the Laboratory Predict Microbial Activities in Natural Habitats?

    PubMed Central

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

    2016-01-01

    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 co-occurring 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. These findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities. PMID:27379075

  5. 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 ). PMID:25426642

  6. 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

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

    PubMed

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

    2014-07-01

    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

  8. Current Challenges for Modeling Enzyme Active Sites by Biomimetic Synthetic Diiron Complexes

    PubMed Central

    Friedle, Simone; Reisner, Erwin; Lippard, Stephen J.

    2010-01-01

    This tutorial review describes recent progress in modeling the active sites of carboxylate-rich non-heme diiron enzymes that activate dioxygen to carry out several key reactions in nature. The chemistry of soluble methane monooxygenase, which catalyzes the selective oxidation of methane to methanol, is of particular interest for (bio)technological applications. Novel synthetic diiron complexes that mimic structural, and, to a lesser extent, functional features of these diiron enzymes are discussed. The chemistry of the enzymes is also briefly summarized. A particular focus of this review is on models that mimic characteristics of the diiron systems that were previously not emphasized, including systems that contain (i) aqua ligands, (ii) different substrates tethered to the ligand framework, (iii) dendrimers attached to carboxylates to mimic the protein environment, (iv) two N-donors in a syn-orientation with respect to the iron-iron vector, and (v) a N-rich ligand environment capable of accessing oxygenated high-valent diiron intermediates. PMID:20485834

  9. 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

  10. 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

  11. Combined influence of cholesterol and synthetic amphiphillic peptides upon bilayer thickness in model membranes.

    PubMed Central

    Nezil, F A; Bloom, M

    1992-01-01

    Deuterium (2H) NMR was used to study bilayer hydrophobic thickness and mechanical properties when cholesterol and/or synthetic amphiphillic polypeptides were added to deuterated POPC lipid bilayer membranes in the liquid-crystalline (fluid) phase. Smoothed acyl chain orientational order profiles were used to calculate bilayer hydrophobic thickness. Addition of 30 mol% cholesterol to POPC at 25 degrees C increased the bilayer thickness from 2.58 to 2.99 nm. The peptides were chosen to span the bilayers with more or less mismatch between the hydrophobic peptide length and membrane hydrophobic thickness. The average thickness of the pure lipid bilayers was significantly perturbed upon addition of peptide only in cases of large mismatch, being increased (decreased) when the peptide hydrophobic length was greater (less) than that of the pure bilayer, consistent with the "mattress" model of protein lipid interactions (Mouritsen, O.G., and M. Bloom. 1984. Biophys. J. 46:141-153). The experimental results were also used to examine the combined influence of the polypeptides and cholesterol on the orientational order profile and thickness expansivity of the membranes. A detailed model for the spatial distribution of POPC and cholesterol molecules in the bilayers was proposed to reconcile the general features of these measurements with micromechanical measurements of area expansivity in closely related systems. Experiments to test the model were proposed. PMID:1600079

  12. 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.

  13. 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.

  14. 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...

  15. 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.

  16. The NASA/JPL Airborne Synthetic Aperture Radar System

    NASA Technical Reports Server (NTRS)

    Kim, Yun-Jin; Lou, Yun-Ling; vanZyl, Jakob

    1996-01-01

    The NASA/JPL airborne SAR (AIRSAR) system operates in the fully polarimetric mode at P-, L- and C-band simultaneously or in the interferometric mode in both L- and C-band simultaneously. The system became operational in late 1987 and flew its first mission aboard a DC-8 aircraft operated by NASA's Ames Research Center in Mountain View, California. Since then, the AIRSAR has flown missions every year and acquired images in North, Central and South America, Europe and Australia. In this paper, we will briefly describe the instrument characteristics, the evolution of the various radar modes, the instrument performance, and improvement in the knowledge of the positioning and attitude information of the radar. In addition, we will summarize the progress of the data processing effort especially in the interferometry processing. Finally, we will address the issue of processing and calibrating the cross-track interferometry (XTI) data.

  17. 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. PMID:24835844

  18. 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.

  19. Glottal jet measurements in synthetic, MRI-based human vocal fold models

    NASA Astrophysics Data System (ADS)

    Thomson, Scott; Pickup, Brian; Gollnick, Paul

    2007-11-01

    Human vocal fold vibration generates a time-varying elliptically-shaped glottal jet that produces sound in speech. Improved understanding of glottal jet dynamics can yield insight into voice production mechanisms and improve the diagnosis and treatment of voice disorders. Experiments using recently developed life-sized synthetic models of the vocal folds are presented. The fabrication process of converting MRI images to synthetic models is described. The process allows for varying the Young's modulus of the models, allowing for asymmetric conditions to be created by casting opposing vocal folds using materials of different stiffness. The models are shown to oscillate at frequencies, pressures, and flow rates typical of human speech. Phase-locked particle image velocimetry (PIV) results are presented which characterize the glottal jet, including jet direction, vortical structures, and turbulence levels. Results are shown for symmetric and asymmetric vocal fold models. The degree of material asymmetry required to cause significant asymmetry in the glottal jet is reported.

  20. Discussions About “Synthetic Intelligence" in Dissociated Culture System

    NASA Astrophysics Data System (ADS)

    Kudoh, Suguru N.; Kiyohara, Ai; Taguchi, Takahisa

    The fundamental frameworks for possessing qualia are “embodiment” and the network structures of the relationships between internal modules. We proposed “Anaplastic cognitive agent (ACA)” composed by interactions between sub modules with hierarchical history functions and network structures. A dissociated culture system can discriminate several distinct spatiotemporal patterns of action potentials evoked by current inputs, and possesses kinds of history function; a history properties of network dynamics, synaptic plasticity, and so on. These features are fundamental for parts to compose ACA.

  1. 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

  2. [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. PMID:20700991

  3. 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

    2015-02-01

    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. PMID:25558883

  4. Advanced synthetic image generation models and their application to multi/hyperspectral algorithm development

    NASA Astrophysics Data System (ADS)

    Schott, John R.; Brown, Scott D.; Raqueno, Rolando V.; Gross, Harry N.; Robinson, Gary

    1999-01-01

    The need for robust image data sets for algorithm development and testing has prompted the consideration of synthetic imagery as a supplement to real imagery. The unique ability of synthetic image generation (SIG) tools to supply per-pixel truth allows algorithm writers to test difficult scenarios that would require expensive collection and instrumentation efforts. In addition, SIG data products can supply the user with `actual' truth measurements of the entire image area that are not subject to measurement error thereby allowing the user to more accurately evaluate the performance of their algorithm. Advanced algorithms place a high demand on synthetic imagery to reproduce both the spectro-radiometric and spatial character observed in real imagery. This paper describes a synthetic image generation model that strives to include the radiometric processes that affect spectral image formation and capture. In particular, it addresses recent advances in SIG modeling that attempt to capture the spatial/spectral correlation inherent in real images. The model is capable of simultaneously generating imagery from a wide range of sensors allowing it to generate daylight, low-light-level and thermal image inputs for broadband, multi- and hyper-spectral exploitation algorithms.

  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. 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.

  7. Instrumentation and procedures for validation of synthetic infrared image generation models

    NASA Astrophysics Data System (ADS)

    Rankin-Parobek, Donna; Salvaggio, Carl; Gallagher, Timothy W.; Schott, John R.

    1993-01-01

    This paper describes an experimental approach to validation of the radiometric integrity of an end-to-end thermal infrared SIG model. The approach attempts to break down the overall SIG model into a set of submodels with measurable input and output parameters. A scene is then instrumented and imaged in a time lapse fashion over an extended period. This scene is also synthetically produced so that the actual and synthetic scenes can be compared. The experimental approach includes acquisition of meteorological data, object data, atmospheric data, and image data. Error propagation models are used in conjunction with the experimental data to determine the source and relative importance of errors in the modeling process.

  8. Optimisation of synthetic medium composition for levorin biosynthesis by Streptomyces levoris 99/23 and investigation of its accumulation dynamics using mathematical modelling methods.

    PubMed

    Stanchev, Veselin S; Kozhuharova, Lubka Y; Zhekova, Boriana Y; Gochev, Velizar K

    2010-01-01

    The composition of a synthetic culture medium for levorin biosynthesis by Streptomyces levoris 99/23 was optimised using mathematical modelling methods. The optimal concentrations of the medium components were established by means of an optimum composition design at three factor variation levels. An adequate regression model was obtained. Levorin biosynthesis by Streptomyces levoris 99/23 in the optimised synthetic medium was over 38% higher than in the initial medium. The antibiotic biosynthesis dynamics in the optimised culture medium was studied by means of a non-linear differential equation system. The resultant model was valid. PMID:21033581

  9. 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. PMID:27128344

  10. 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

  11. A synthetic GMPE based on deterministic simulated ground motion data obtained from dynamic rupture models

    NASA Astrophysics Data System (ADS)

    Dalguer, L. A.; Baumann, C.; Cauzzi, C.

    2013-12-01

    Empirical ground motion prediction in the very near-field and for large magnitudes is often based on extrapolation of ground motion prediction equations (GMPEs) outside the range where they are well constrained by recorded data. With empirical GMPEs it is also difficult to capture source-dominated ground motion patterns, such as the effects of velocity pulses induced by subshear and supershear rupture directivity, buried and surface-rupturing, hanging-wall and foot-wall, weak shallow layers, complex geometry faults and stress drop. A way to cope at least in part with these shortcomings is to augment the calibration datasets with synthetic ground motions. To this aim, physics-based dynamic rupture models - where the physical bases involved in the fault rupture are explicitly considered - appear to be a suitable approach to produce synthetic ground motions. In this contribution, we first perform an assessment of a database of synthetic ground motions generated by a suite of dynamic rupture simulations to verify compatibility of the peak ground amplitudes with current GMPEs. The synthetic data-set is composed by 360 earthquake scenarios with moment magnitudes in the range of 5.5-7, for three mechanisms of faulting (reverse, normal and strike-slip) and for both buried faults and surface rupturing faults. Second, we parameterise the synthetic dataset through a GMPE. For this purpose, we identify the basic functional forms by analyzing the variation of the synthetic peak ground motions and spectral ordinates as a function of different explanatory variables related to the earthquake source characteristics, in order to account for some of the source effects listed above. We argue that this study provides basic guidelines for the developments of future GMPEs including data from physics-based numerical simulations.

  12. A synthetic biology approach to the development of transcriptional regulatory models and custom enhancer design.

    PubMed

    Martinez, Carlos A; Barr, Kenneth A; Kim, Ah-Ram; Reinitz, John

    2013-07-15

    Synthetic biology offers novel opportunities for elucidating transcriptional regulatory mechanisms and enhancer logic. Complex cis-regulatory sequences--like the ones driving expression of the Drosophila even-skipped gene--have proven difficult to design from existing knowledge, presumably due to the large number of protein-protein interactions needed to drive the correct expression patterns of genes in multicellular organisms. This work discusses two novel computational methods for the custom design of enhancers that employ a sophisticated, empirically validated transcriptional model, optimization algorithms, and synthetic biology. These synthetic elements have both utilitarian and academic value, including improving existing regulatory models as well as evolutionary questions. The first method involves the use of simulated annealing to explore the sequence space for synthetic enhancers whose expression output fit a given search criterion. The second method uses a novel optimization algorithm to find functionally accessible pathways between two enhancer sequences. These paths describe a set of mutations wherein the predicted expression pattern does not significantly vary at any point along the path. Both methods rely on a predictive mathematical framework that maps the enhancer sequence space to functional output. PMID:23732772

  13. Robust model matching design methodology for a stochastic synthetic gene network.

    PubMed

    Chen, Bor-Sen; Chang, Chia-Hung; Wang, Yu-Chao; Wu, Chih-Hung; Lee, Hsiao-Ching

    2011-03-01

    Synthetic biology has shown its potential and promising applications in the last decade. However, many synthetic gene networks cannot work properly and maintain their desired behaviors due to intrinsic parameter variations and extrinsic disturbances. In this study, the intrinsic parameter uncertainties and external disturbances are modeled in a non-linear stochastic gene network to mimic the real environment in the host cell. Then a non-linear stochastic robust matching design methodology is introduced to withstand the intrinsic parameter fluctuations and to attenuate the extrinsic disturbances in order to achieve a desired reference matching purpose. To avoid solving the Hamilton-Jacobi inequality (HJI) in the non-linear stochastic robust matching design, global linearization technique is used to simplify the design procedure by solving a set of linear matrix inequalities (LMIs). As a result, the proposed matching design methodology of the robust synthetic gene network can be efficiently designed with the help of LMI toolbox in Matlab. Finally, two in silico design examples of the robust synthetic gene network are given to illustrate the design procedure and to confirm the robust model matching performance to achieve the desired behavior in spite of stochastic parameter fluctuations and environmental disturbances in the host cell. PMID:21215760

  14. Broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria

    PubMed Central

    Taton, Arnaud; Unglaub, Federico; Wright, Nicole E.; Zeng, Wei Yue; Paz-Yepes, Javier; Brahamsha, Bianca; Palenik, Brian; Peterson, Todd C.; Haerizadeh, Farzad; Golden, Susan S.; Golden, James W.

    2014-01-01

    Inspired by the developments of synthetic biology and the need for improved genetic tools to exploit cyanobacteria for the production of renewable bioproducts, we developed a versatile platform for the construction of broad-host-range vector systems. This platform includes the following features: (i) an efficient assembly strategy in which modules released from 3 to 4 donor plasmids or produced by polymerase chain reaction are assembled by isothermal assembly guided by short GC-rich overlap sequences. (ii) A growing library of molecular devices categorized in three major groups: (a) replication and chromosomal integration; (b) antibiotic resistance; (c) functional modules. These modules can be assembled in different combinations to construct a variety of autonomously replicating plasmids and suicide plasmids for gene knockout and knockin. (iii) A web service, the CYANO-VECTOR assembly portal, which was built to organize the various modules, facilitate the in silico construction of plasmids, and encourage the use of this system. This work also resulted in the construction of an improved broad-host-range replicon derived from RSF1010, which replicates in several phylogenetically distinct strains including a new experimental model strain Synechocystis sp. WHSyn, and the characterization of nine antibiotic cassettes, four reporter genes, four promoters, and a ribozyme-based insulator in several diverse cyanobacterial strains. PMID:25074377

  15. Synthetic cell division system: Controlling equal vs. unequal divisions by design

    PubMed Central

    Sato, Yoichi; Yasuhara, Kazuma; Kikuchi, Jun-ichi; Sato, Thomas N.

    2013-01-01

    Cell division is one of the most fundamental and evolutionarily conserved biological processes. Here, we report a synthetic system where we can control by design equal vs. unequal divisions. We synthesized a micro-scale inverse amphipathic droplet of which division is triggered by the increase of surface to volume ratio. Using this system, we succeeded in selectively inducing equal vs. unequal divisions of the droplet cells by adjusting the temperature or the viscosity of the solvent outside the droplet cell accordingly. Our synthetic division system may provide a platform for further development to a system where intracellular contents of the parent droplet cell could be divided into various ratios between the two daughter droplet cells to control their functions and fates. PMID:24327069

  16. Parametric Study of Synthetic-Jet-Based Flow Control on a Vertical Tail Model

    NASA Astrophysics Data System (ADS)

    Monastero, Marianne; Lindstrom, Annika; Beyar, Michael; Amitay, Michael

    2015-11-01

    Separation control over the rudder of the vertical tail of a commercial airplane using synthetic-jet-based flow control can lead to a reduction in tail size, with an associated decrease in drag and increase in fuel savings. A parametric, experimental study was undertaken using an array of finite span synthetic jets to investigate the sensitivity of the enhanced vertical tail side force to jet parameters, such as jet spanwise spacing and jet momentum coefficient. A generic wind tunnel model was designed and fabricated to fundamentally study the effects of the jet parameters at varying rudder deflection and model sideslip angles. Wind tunnel results obtained from pressure measurements and tuft flow visualization in the Rensselaer Polytechnic Subsonic Wind Tunnel show a decrease in separation severity and increase in model performance in comparison to the baseline, non-actuated case. The sensitivity to various parameters will be presented.

  17. Synthetic cellularity based on non-lipid micro-compartments and protocell models.

    PubMed

    Li, Mei; Huang, Xin; Tang, T-Y Dora; Mann, Stephen

    2014-10-01

    This review discusses recent advances in the design and construction of protocell models based on the self-assembly or microphase separation of non-lipid building blocks. We focus on strategies involving partially hydrophobic inorganic nanoparticles (colloidosomes), protein-polymer globular nano-conjugates (proteinosomes), amphiphilic block copolymers (polymersomes), and stoichiometric mixtures of oppositely charged biomolecules and polyelectrolytes (coacervates). Developments in the engineering of membrane functionality to produce synthetic protocells with gated responses and control over multi-step reactions are described. New routes to protocells comprising molecularly crowded, cytoskeletal-like hydrogel interiors, as well as to the construction of hybrid protocell models are also highlighted. Together, these strategies enable a wide range of biomolecular and synthetic components to be encapsulated, regulated and processed within the micro-compartmentalized volume, and suggest that the development of non-lipid micro-ensembles offers an approach that is complementary to protocell models based on phospholipid or fatty acid vesicles. PMID:24952153

  18. 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

  19. Synthetic vision in the cockpit: 3D systems for general aviation

    NASA Astrophysics Data System (ADS)

    Hansen, Andrew J.; Rybacki, Richard M.; Smith, W. Garth

    2001-08-01

    Synthetic vision has the potential to improve safety in aviation through better pilot situational awareness and enhanced navigational guidance. The technological advances enabling synthetic vision are GPS based navigation (position and attitude) systems and efficient graphical systems for rendering 3D displays in the cockpit. A benefit for military, commercial, and general aviation platforms alike is the relentless drive to miniaturize computer subsystems. Processors, data storage, graphical and digital signal processing chips, RF circuitry, and bus architectures are at or out-pacing Moore's Law with the transition to mobile computing and embedded systems. The tandem of fundamental GPS navigation services such as the US FAA's Wide Area and Local Area Augmentation Systems (WAAS) and commercially viable mobile rendering systems puts synthetic vision well with the the technological reach of general aviation. Given the appropriate navigational inputs, low cost and power efficient graphics solutions are capable of rendering a pilot's out-the-window view into visual databases with photo-specific imagery and geo-specific elevation and feature content. Looking beyond the single airframe, proposed aviation technologies such as ADS-B would provide a communication channel for bringing traffic information on-board and into the cockpit visually via the 3D display for additional pilot awareness. This paper gives a view of current 3D graphics system capability suitable for general aviation and presents a potential road map following the current trends.

  20. 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).

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

    PubMed Central

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

    2014-01-01

    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 during anterior-posterior stretching. Method Three materially linear and three materially nonlinear models were created and stretched up to 10 mm in 1 mm increments. Phonation onset pressure (Pon) and fundamental frequency (F0) at Pon were recorded for each length. Measurements were repeated as the models were relaxed in 1 mm increments back to their resting lengths, and tensile tests were conducted to determine the stress-strain responses of linear versus nonlinear models. Results Nonlinear models demonstrated a more substantial frequency response than did linear models and a more predictable pattern of F0 increase with respect to increasing length (although range was inconsistent across models). Pon generally increased with increasing vocal fold length for nonlinear models, whereas for linear models, Pon decreased with increasing length. Conclusions Nonlinear synthetic models appear to more accurately represent the human vocal folds than linear models, especially with respect to F0 response. PMID:22271874

  2. A Synthetic Self-Oscillating Vocal Fold Model Platform for Studying Augmentation Injection

    PubMed Central

    Murray, Preston R.; Thomson, Scott L.; Smith, Marshall E.

    2013-01-01

    Objective Design and evaluate a platform for studying the mechanical effects of augmentation injections using synthetic self-oscillating vocal fold models. Study Design Basic science. Methods Life-sized, synthetic, multi-layer, self-oscillating vocal fold models were created that simulated bowing via volumetric reduction of the body layer relative to that of a normal, unbowed model. Material properties of the layers were unchanged. Models with varying degrees of bowing were created and paired with normal models. Following initial acquisition of data (onset pressure, vibration frequency, flow rate, and high-speed image sequences), bowed models were injected with silicone that had material properties similar to those used in augmentation procedures. Three different silicone injection quantities were tested: sufficient to close the glottal gap, insufficient to close the glottal gap, and excess silicone to create convex bowing of the bowed model. The above-mentioned metrics were again taken and compared. Pre- and post-injection high-speed image sequences were acquired using a hemilarynx setup, from which medial surface dynamics were quantified. Results The models vibrated with mucosal wave-like motion and at onset pressures and frequencies typical of human phonation. The models successfully exhibited various degrees of bowing which were then mitigated by injecting filler material. The models showed general pre- to post-injection decreases in onset pressure, flow rate, and open quotient, and a corresponding increase in vibration frequency. Conclusion The model may be useful in further explorations of the mechanical consequences of augmentation injections. PMID:24476985

  3. 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. PMID:25282688

  4. 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

  5. The G-FAST Geodetic Earthquake Early Warning System: Operational Performance and Synthetic Testing

    NASA Astrophysics Data System (ADS)

    Crowell, B. W.; Schmidt, D. A.; Bodin, P.; Vidale, J. E.; Melbourne, T. I.; Santillan, V. M.

    2015-12-01

    The G-FAST (Geodetic First Approximation of Size and TIming) earthquake early warning module is part of a joint seismic and geodetic earthquake early warning system currently under development at the Pacific Northwest Seismic Network (PNSN). Our two-stage approach to earthquake early warning includes: (1) initial detection and characterization from PNSN strong-motion and broadband data with the ElarmS package within ShakeAlert, and then (2) modeling of GPS data from the Pacific Northwest Geodetic Array (PANGA). The two geodetic modeling modules are (1) a fast peak-ground-displacement magnitude and depth estimate and (2) a CMT-based finite fault inversion that utilizes coseismic offsets to compute earthquake extent, slip and magnitude. The seismic and geodetic source estimates are then combined in a decision module currently under development. In this presentation, we first report on the operational performance during the first several months that G-FAST has been live with respect to magnitude estimates, timing information, and stability. Secondly, we report on the performance of the G-FAST test system using simulated displacements from plausible Cascadian earthquake scenarios. The test system permits us to: (1) replay segments of actual seismic waveform data recorded from the PNSN and neighboring networks to investigate both earthquakes and noise conditions, and (2) broadcast synthetic data into the system to simulate signals we anticipate from earthquakes for which we have no actual ground motion recordings. The test system lets us also simulate various error conditions (latent and/or out-of-sequence data, telemetry drop-outs, etc.) in order to explore how best to mitigate them. For example, we show for a replay of the 2001 M6.8 Nisqually earthquake that telemetry drop-outs create the largest variability and biases in magnitude and depth estimates whereas latency only causes some variability towards the beginning of the recordings before quickly stabilizing

  6. Therapeutic Effect of a Synthetic RORα/γ Agonist in an Animal Model of Autism.

    PubMed

    Wang, Yongjun; Billon, Cyrielle; Walker, John K; Burris, Thomas P

    2016-02-17

    Autism is a developmental disorder of the nervous system associated with impaired social communication and interactions as well excessive repetitive behaviors. There are no drug therapies that directly target the pathology of this disease. The retinoic acid receptor-related orphan receptor α (RORα) is a nuclear receptor that has been demonstrated to have reduced expression in many individuals with autism spectrum disorder (ASD). Several genes that have been shown to be downregulated in individuals with ASD have also been identified as putative RORα target genes. Utilizing a synthetic RORα/γ agonist, SR1078, that we identified previously, we demonstrate that treatment of BTBR mice (a model of autism) with SR1078 results in reduced repetitive behavior. Furthermore, these mice display increased expression of ASD-associated RORα target genes in both the brains of the BTBR mice and in a human neuroblastoma cell line treated with SR1078. These data suggest that pharmacological activation of RORα may be a method for treatment of autism. PMID:26625251

  7. Therapeutic Effect of a Synthetic RORα/γ Agonist in an Animal Model of Autism

    PubMed Central

    2015-01-01

    Autism is a developmental disorder of the nervous system associated with impaired social communication and interactions as well excessive repetitive behaviors. There are no drug therapies that directly target the pathology of this disease. The retinoic acid receptor-related orphan receptor α (RORα) is a nuclear receptor that has been demonstrated to have reduced expression in many individuals with autism spectrum disorder (ASD). Several genes that have been shown to be downregulated in individuals with ASD have also been identified as putative RORα target genes. Utilizing a synthetic RORα/γ agonist, SR1078, that we identified previously, we demonstrate that treatment of BTBR mice (a model of autism) with SR1078 results in reduced repetitive behavior. Furthermore, these mice display increased expression of ASD-associated RORα target genes in both the brains of the BTBR mice and in a human neuroblastoma cell line treated with SR1078. These data suggest that pharmacological activation of RORα may be a method for treatment of autism. PMID:26625251

  8. 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

  9. 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.

  10. Synthetic environments

    NASA Astrophysics Data System (ADS)

    Lukes, George E.; Cain, Joel M.

    1996-02-01

    The Advanced Distributed Simulation (ADS) Synthetic Environments Program seeks to create robust virtual worlds from operational terrain and environmental data sources of sufficient fidelity and currency to interact with the real world. While some applications can be met by direct exploitation of standard digital terrain data, more demanding applications -- particularly those support operations 'close to the ground' -- are well-served by emerging capabilities for 'value-adding' by the user working with controlled imagery. For users to rigorously refine and exploit controlled imagery within functionally different workstations they must have a shared framework to allow interoperability within and between these environments in terms of passing image and object coordinates and other information using a variety of validated sensor models. The Synthetic Environments Program is now being expanded to address rapid construction of virtual worlds with research initiatives in digital mapping, softcopy workstations, and cartographic image understanding. The Synthetic Environments Program is also participating in a joint initiative for a sensor model applications programer's interface (API) to ensure that a common controlled imagery exploitation framework is available to all researchers, developers and users. This presentation provides an introduction to ADS and the associated requirements for synthetic environments to support synthetic theaters of war. It provides a technical rationale for exploring applications of image understanding technology to automated cartography in support of ADS and related programs benefitting from automated analysis of mapping, earth resources and reconnaissance imagery. And it provides an overview and status of the joint initiative for a sensor model API.

  11. 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. PMID

  12. Quantification of synthetic lens surface characteristics by an optical measurement system as stylus instrument

    NASA Astrophysics Data System (ADS)

    Schäfer, Patrick; Wünsche, Christine; Rascher, Rolf

    2015-01-01

    A measurement system to monitor the turning tool achieves a reduction in production rejects by decreasing the delay time between tool wear detection and quality control of the surface, which usually takes place after the time-intensive polishing process. In highly automated production of lucent synthetic lenses the standardized polishing process turns out to be inefficient if there is an insufficient surface quality caused by outrunning tool wear limits of the undergone turning process. The possibility to indicate the tool's wear will be demonstrated by checking the surface characteristics of synthetic lenses. For that research an experimental measurement setup is shown. This optical measurement system detects the surface's roughness, which is indicative of tool wear.

  13. 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.

  14. Can we build synthetic, multicellular systems by controlling developmental signaling in space and time?

    PubMed Central

    Ismagilov, Rustem F.; Maharbiz, Michel M.

    2008-01-01

    Using biological machinery to make new, functional molecules is an exciting area in chemical biology. Complex molecules containing both “natural” and “unnatural” components are made by processes ranging from enzymatic catalysis to the combination of molecular biology with chemical tools. Here, we discuss applying this approach to the next level of biological complexity—building synthetic, functional biotic systems by manipulating biological machinery responsible for development of multicellular organisms. We describe recent advances enabling this approach, including: i) recent developmental biology progress unraveling the pathways and molecules involved in development and pattern formation, ii) emergence of microfluidic tools for delivering stimuli to a developing organism with exceptional control in space and time, iii) the development of molecular and synthetic biology toolsets for redesigning or de novo engineering of signaling networks, and iv) biological systems that are especially amendable to this approach. PMID:17967432

  15. 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.

  16. 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.

  17. 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

  18. A Hybrid Synthetic Vision System for the Tele-operation of Unmanned Vehicles

    NASA Technical Reports Server (NTRS)

    Delgado, Frank; Abernathy, Mike

    2004-01-01

    A system called SmartCam3D (SC3D) has been developed to provide enhanced situational awareness for operators of a remotely piloted vehicle. SC3D is a Hybrid Synthetic Vision System (HSVS) that combines live sensor data with information from a Synthetic Vision System (SVS). By combining the dual information sources, the operators are afforded the advantages of each approach. The live sensor system provides real-time information for the region of interest. The SVS provides information rich visuals that will function under all weather and visibility conditions. Additionally, the combination of technologies allows the system to circumvent some of the limitations from each approach. Video sensor systems are not very useful when visibility conditions are hampered by rain, snow, sand, fog, and smoke, while a SVS can suffer from data freshness problems. Typically, an aircraft or satellite flying overhead collects the data used to create the SVS visuals. The SVS data could have been collected weeks, months, or even years ago. To that extent, the information from an SVS visual could be outdated and possibly inaccurate. SC3D was used in the remote cockpit during flight tests of the X-38 132 and 131R vehicles at the NASA Dryden Flight Research Center. SC3D was also used during the operation of military Unmanned Aerial Vehicles. This presentation will provide an overview of the system, the evolution of the system, the results of flight tests, and future plans. Furthermore, the safety benefits of the SC3D over traditional and pure synthetic vision systems will be discussed.

  19. 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

  20. 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.

  1. Synthetic, Multi-Layer, Self-Oscillating Vocal Fold Model Fabrication

    PubMed Central

    Murray, Preston R.; Thomson, Scott L.

    2011-01-01

    Sound for the human voice is produced via flow-induced vocal fold vibration. The vocal folds consist of several layers of tissue, each with differing material properties 1. Normal voice production relies on healthy tissue and vocal folds, and occurs as a result of complex coupling between aerodynamic, structural dynamic, and acoustic physical phenomena. Voice disorders affect up to 7.5 million annually in the United States alone 2 and often result in significant financial, social, and other quality-of-life difficulties. Understanding the physics of voice production has the potential to significantly benefit voice care, including clinical prevention, diagnosis, and treatment of voice disorders. Existing methods for studying voice production include in vivo experimentation using human and animal subjects, in vitro experimentation using excised larynges and synthetic models, and computational modeling. Owing to hazardous and difficult instrument access, in vivo experiments are severely limited in scope. Excised larynx experiments have the benefit of anatomical and some physiological realism, but parametric studies involving geometric and material property variables are limited. Further, they are typically only able to be vibrated for relatively short periods of time (typically on the order of minutes). Overcoming some of the limitations of excised larynx experiments, synthetic vocal fold models are emerging as a complementary tool for studying voice production. Synthetic models can be fabricated with systematic changes to geometry and material properties, allowing for the study of healthy and unhealthy human phonatory aerodynamics, structural dynamics, and acoustics. For example, they have been used to study left-right vocal fold asymmetry 3,4, clinical instrument development 5, laryngeal aerodynamics 6-9, vocal fold contact pressure 10, and subglottal acoustics 11 (a more comprehensive list can be found in Kniesburges et al. 12) Existing synthetic vocal fold models

  2. Synthetic, multi-layer, self-oscillating vocal fold model fabrication.

    PubMed

    Murray, Preston R; Thomson, Scott L

    2011-01-01

    Sound for the human voice is produced via flow-induced vocal fold vibration. The vocal folds consist of several layers of tissue, each with differing material properties. Normal voice production relies on healthy tissue and vocal folds, and occurs as a result of complex coupling between aerodynamic, structural dynamic, and acoustic physical phenomena. Voice disorders affect up to 7.5 million annually in the United States alone and often result in significant financial, social, and other quality-of-life difficulties. Understanding the physics of voice production has the potential to significantly benefit voice care, including clinical prevention, diagnosis, and treatment of voice disorders. Existing methods for studying voice production include in vivo experimentation using human and animal subjects, in vitro experimentation using excised larynges and synthetic models, and computational modeling. Owing to hazardous and difficult instrument access, in vivo experiments are severely limited in scope. Excised larynx experiments have the benefit of anatomical and some physiological realism, but parametric studies involving geometric and material property variables are limited. Further, they are typically only able to be vibrated for relatively short periods of time (typically on the order of minutes). Overcoming some of the limitations of excised larynx experiments, synthetic vocal fold models are emerging as a complementary tool for studying voice production. Synthetic models can be fabricated with systematic changes to geometry and material properties, allowing for the study of healthy and unhealthy human phonatory aerodynamics, structural dynamics, and acoustics. For example, they have been used to study left-right vocal fold asymmetry, clinical instrument development, laryngeal aerodynamics, vocal fold contact pressure, and subglottal acoustics (a more comprehensive list can be found in Kniesburges et al.) Existing synthetic vocal fold models, however, have either

  3. Observations and modeling of the current deformation in Afar using Synthetic Aperture Radar Interferometry

    NASA Astrophysics Data System (ADS)

    Tomic, Jelena

    The Afar system is a unique place on Earth where a triple rift junction may be emerging. As the three rifts separating Arabia, Nubia and Somalia plates have not achieved a complete connection at present, I observe a 200 km wide area of complex surface deformation. A variety of extensional structures including a network of faults, fissures, dikes, and volcanic centers are collectively accommodating far field movement of the surrounding plates. Understanding the nature and distribution of the deformation over this vast region is critical since here I observe the transition between established oceanic ridges (the Red Sea and the Aden-Goubbet ridges) and continental deformation. In this study I use the technique of Synthetic Aperture Radar Interferometry (InSAR) to analyze radar data of the Afar region, and to construct a 10 yr timeline of surface displacement over a 200 km by 400 km area. By combining data acquired from ascending and descending passes I construct a two-dimensional velocity maps of the region. The maps show localized extensional deformation across the Asal-Ghoubbet rift segment accommodating the diverging motion of the Arabia-Somalia plates, as well as regional uplift asymmetrically distributed north and south of the Asal Rift area. The vertical velocity map in the rift indicates subsidence of the rift floor with respect to the rift shoulders, accommodated by fault creep. To interpret the observed velocity across the Asal rift I develop a 2-dimensional and a 3-dimensional dislocation model using a combination of dikes, sill and faults embedded in an elastic half space. The forward modeling allows me to place the overall geometry of sub-surface structures and estimate rates of dike and sill inflation, and fault movement. Then I construct a 3-dimensional model to perform a least-squares inversion of the radar-derived velocity maps. The results show an inflating body centered under the Fieale volcano expanding at a rate of 2 106 m3/yr. Faults bordering

  4. 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

  5. Maritime surveillance with synthetic aperture radar (SAR) and automatic identification system (AIS) onboard a microsatellite constellation

    NASA Astrophysics Data System (ADS)

    Peterson, E. H.; Zee, R. E.; Fotopoulos, G.

    2012-11-01

    New developments in small spacecraft capabilities will soon enable formation-flying constellations of small satellites, performing cooperative distributed remote sensing at a fraction of the cost of traditional large spacecraft missions. As part of ongoing research into applications of formation-flight technology, recent work has developed a mission concept based on combining synthetic aperture radar (SAR) with automatic identification system (AIS) data. Two or more microsatellites would trail a large SAR transmitter in orbit, each carrying a SAR receiver antenna and one carrying an AIS antenna. Spaceborne AIS can receive and decode AIS data from a large area, but accurate decoding is limited in high traffic areas, and the technology relies on voluntary vessel compliance. Furthermore, vessel detection amidst speckle in SAR imagery can be challenging. In this constellation, AIS broadcasts of position and velocity are received and decoded, and used in combination with SAR observations to form a more complete picture of maritime traffic and identify potentially non-cooperative vessels. Due to the limited transmit power and ground station downlink time of the microsatellite platform, data will be processed onboard the spacecraft. Herein we present the onboard data processing portion of the mission concept, including methods for automated SAR image registration, vessel detection, and fusion with AIS data. Georeferencing in combination with a spatial frequency domain method is used for image registration. Wavelet-based speckle reduction facilitates vessel detection using a standard CFAR algorithm, while leaving sufficient detail for registration of the filtered and compressed imagery. Moving targets appear displaced from their actual position in SAR imagery, depending on their velocity and the image acquisition geometry; multiple SAR images acquired from different locations are used to determine the actual positions of these targets. Finally, a probabilistic inference

  6. Generating synthetic time series from Bak Sneppen co-evolution model mixtures

    NASA Astrophysics Data System (ADS)

    Petroni, F.; Ausloos, M.; Rotundo, G.

    2007-10-01

    The Bak-Sneppen model of co-evolution is used to derive synthetic time series with a priori specified fractal dimension (or Hurst exponent) through a mixing of processes in various lattice dimensions. Both theoretical and numerical analyses concern the avalanches at the critical threshold and provide a model for time series reconstruction that can be tested as an alternative to the classical fractional Brownian motion (fBm) because of differences in properties. New results on critical threshold and avalanche structure are obtained up to Euclidean dimension d=6. The method involves a lattice-based structure and therefore is suitable for the application of parallel computing.

  7. 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.

  8. 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

  9. Crew and display concepts evaluation for synthetic/enhanced vision systems

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

    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.

  10. 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. PMID:27557767

  11. Solubilization of naphthalene in the presence of plant-synthetic mixed surfactant systems.

    PubMed

    Rao, K Jagajjanani; Paria, Santanu

    2009-01-15

    Solubilization efficiencies of naphthalene by micellar solution of a plant-based surfactant extracted from fruit of Sapindus mukorossi (reetha) and the synthetic surfactants like nonionic (Triton X-100 or TX-100), cationic (cetyltrimethylammonium bromide or CTAB), and anionic (sodium dodecylbenzenesulfonate or SDBS; dioctyl sodium sulfosuccinate or AOT; sodium octanesulfonate or SOS) in their single and as well as binary mixed (plant-synthetic) systems were measured and compared. The solubilization efficiency of single surfactants shows that reetha is less effective than TX-100, similar to SDBS, and more than AOT and SOS. The mixed surfactant systems show negative deviation in molar solubilization ratio (MSR) from ideality. The ascending order of percent change in MSR (Delta(MSR)) is TX-100-reetha < CTAB-reetha < SDBS-reetha < AOT-reetha < SOS-reetha. The mixed micellar solution for a particular combination also shows that Delta(MSR) is more negative when the interaction parameter for the mixed micelle (beta) is more negative. The results of this study may be useful for the applications of natural or natural-synthetic mixed surfactants in surfactant-enhanced remediation or detergency. PMID:19099430

  12. 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

  13. 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

  14. 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

  15. A digital system to produce imagery from SAR data. [Synthetic Aperture Radar

    NASA Technical Reports Server (NTRS)

    Wu, C.

    1976-01-01

    This paper describes a digital processing algorithm and its associated system design for producing images from Synthetic Aperture Radar (SAR) data. The proposed system uses the Fast Fourier Transform (FFT) approach to perform the two-dimensional correlation process. The range migration problem, which is often a major obstacle to efficient processing, can be alleviated by approximating the locus of echoes from a point target by several linear segments. SAR data corresponding to each segment is correlated separately, and the results are coherently summed to produce full-resolution images. This processing approach exhibits greatly improved computation efficiency relative to conventional digital processing methods.

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

    PubMed Central

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

    2012-01-01

    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. PMID:22180537

  17. 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. PMID:17230249

  18. 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. PMID:19413915

  19. 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.

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

    EPA Science Inventory

    The Exposure Analysis Modeling System (EXAMS) was designed for rapid evaluation of the behavior of synthetic organic chemicals in aquatic ecosystems. From the chemistry of a compound and the relevant transport and physical/chemical characteristics of the ecosystem, EXAMS computes...

  1. 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.

  2. 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.

  3. 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. PMID:26799494

  4. Flow-induced vibratory response of idealized versus magnetic resonance imaging-based synthetic vocal fold models.

    PubMed

    Pickup, Brian A; Thomson, Scott L

    2010-09-01

    Recent vocal fold vibration studies have used models defined using idealized geometry. Although these models exhibit important similarities with human vocal fold vibration, some aspects of their motion are less than realistic. In this report it is demonstrated that more realistic motion may be obtained when using geometry derived from magnetic resonance imaging (MRI) data. The dynamic response of both idealized and MRI-based synthetic vocal fold models are presented. MRI-based model improvements include evidence of mucosal wave-like motion and less vertical movement. Limitations of the MRI-based model are discussed and suggestions for further synthetic model development are offered. PMID:20815428

  5. EXPOSURE ANALYSIS MODELING SYSTEM: REFERENCE MANUAL FOR EXAMS 2

    EPA Science Inventory

    The Exposure Analysis Modeling System (EXAMS), published in 1982 (EPA-600/3-82-023), provides rapid evaluations of the behavior of synthetic organic chemicals in aquatic ecosystems. EXAMS combines laboratory data describing reactivity and thermodynamic properties of chemicals wit...

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

    NASA Astrophysics Data System (ADS)

    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 (SαS) 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 SαS model to physical parameters such as the attenuation coefficient and foliage density.

  7. 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. PMID:12542316

  8. 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

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

    PubMed

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

    2013-05-21

    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. PMID:23618819

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

    PubMed Central

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

    2015-01-01

    This work outlines the design and construction of a single-photon emission computed tomography (SPECT) 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 forty-six 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 (MLEM), 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. PMID:23618819

  11. 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. PMID:27112032

  12. 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

  13. 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.

  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. 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

  16. 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.

  17. 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

  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. Computational approaches to metabolic engineering utilizing systems biology and synthetic biology

    PubMed Central

    Fong, Stephen S.

    2014-01-01

    Metabolic engineering modifies cellular function to address various biochemical applications. Underlying metabolic engineering efforts are a host of tools and knowledge that are integrated to enable successful outcomes. Concurrent development of computational and experimental tools has enabled different approaches to metabolic engineering. One approach is to leverage knowledge and computational tools to prospectively predict designs to achieve the desired outcome. An alternative approach is to utilize combinatorial experimental tools to empirically explore the range of cellular function and to screen for desired traits. This mini-review focuses on computational systems biology and synthetic biology tools that can be used in combination for prospective in silico strain design. PMID:25379141

  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. 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.

  2. Synthetic Ultrashort Cationic Lipopeptides Induce Systemic Plant Defense Responses against Bacterial and Fungal Pathogens ▿

    PubMed Central

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

    2009-01-01

    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. PMID:19542326

  3. 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. PMID:27226765

  4. Spectral hole burning and flourescence studies of a synthetic chlorophyll dimer, a bacterial antenna system and a bacterial reaction center

    SciTech Connect

    Johnson, S.G.

    1990-06-13

    Hole burning and fluorescence spectroscopy are applied to a synthetic chlorophyll dimer, an antenna system from the bacterium Prosthecochloris aestuarii and a reaction center from the bacterium Rhodobacter sphaeroides. Information concerning the strength of the linear electron-phonon (exciton-phonon) coupling, inhomogeneous broadening, energy transfer times, nature or structure of the excited states (S{sub 1}), the excited state decay times and the vibrational levels of S{sub 1} for these three systems are reported and discussed. A theory for modelling the hole shape and absorption profile for a single transition which is inhomogeneously broadened and coupled to two low frequency modes, with arbitrary coupling strength, is presented and applied to photochemical hole spectra and the absorption profile of the bacterial RC from Rhodobacter sphaeroides. 122 refs., 29 figs.

  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. 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.

  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. 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

  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. 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

  11. 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.

  12. Natural and synthetic podolactones with potential use as natural herbicide models.

    PubMed

    Macías, F A; Simonet, A M; Pacheco, P C; Barrero, A F; Cabrera, E; Jiménez-González, D

    2000-07-01

    A collection of 11 natural and synthetic podolactones have been tested as allelochemicals in a range between 10(-4) and 10(-9) M, and their potential use as natural herbicide models is discussed. Their effects on the germination and growth of the dicots Lactuca sativa (cv. Nigra and cv. Roman), Lepidium sativum, and Lycopersicon esculentum and the monocots Allium cepa, Hordeum vulgare, and Triticum aestivum as standard target species have been studied. An important inhibitory effect on the germination and growth of all tested species (average = 90%) was produced by compounds 9-11 at 10(-4) M. The specific structural requirements related to their activities are studied. On the basis of these results, their use as potential natural herbicide models is proposed. PMID:10898656

  13. Forward induced seismic hazard assessment: application to a synthetic seismicity catalogue from hydraulic stimulation modelling

    NASA Astrophysics Data System (ADS)

    Hakimhashemi, Amir Hossein; Yoon, Jeoung Seok; Heidbach, Oliver; Zang, Arno; Grünthal, Gottfried

    2014-07-01

    The M w 3.2-induced seismic event in 2006 due to fluid injection at the Basel geothermal site in Switzerland was the starting point for an ongoing discussion in Europe on the potential risk of hydraulic stimulation in general. In particular, further development of mitigation strategies of induced seismic events of economic concern became a hot topic in geosciences and geoengineering. Here, we present a workflow to assess the hazard of induced seismicity in terms of occurrence rate of induced seismic events. The workflow is called Forward Induced Seismic Hazard Assessment (FISHA) as it combines the results of forward hydromechanical-numerical models with methods of time-dependent probabilistic seismic hazard assessment. To exemplify FISHA, we use simulations of four different fluid injection types with various injection parameters, i.e. injection rate, duration and style of injection. The hydromechanical-numerical model applied in this study represents a geothermal reservoir with preexisting fractures where a routine of viscous fluid flow in porous media is implemented from which flow and pressure driven failures of rock matrix and preexisting fractures are simulated, and corresponding seismic moment magnitudes are computed. The resulting synthetic catalogues of induced seismicity, including event location, occurrence time and magnitude, are used to calibrate the magnitude completeness M c and the parameters a and b of the frequency-magnitude relation. These are used to estimate the time-dependent occurrence rate of induced seismic events for each fluid injection scenario. In contrast to other mitigation strategies that rely on real-time data or already obtained catalogues, we can perform various synthetic experiments with the same initial conditions. Thus, the advantage of FISHA is that it can quantify hazard from numerical experiments and recommend a priori a stimulation type that lowers the occurrence rate of induced seismic events. The FISHA workflow is rather

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

    PubMed

    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. PMID:21728571

  16. 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.

  17. Comparison of Two Synthetic Bone Graft Products in a Rabbit Posterolateral Fusion Model

    PubMed Central

    Fredericks, Douglas; Petersen, Emily B.; Watson, Nicole; Grosland, Nicole; Gibson-Corley, Katherine; Smucker, Joseph

    2016-01-01

    Background The drawbacks of iliac crest autograft as graft material for spine fusion are well reported. Despite continued modifications to improve bone healing capacity, the efficacy of synthetic graft materials as stand-alone replacements remains uncertain. The rabbit posterolateral fusion model is an established environment for testing of fusion concepts. It offers the opportunity to obtain radiographic, biomechanical and histological data on novel fusion materials. The objective of this study was to compare the spine fusion capability of two synthetic bone graft products in an established rabbit posterolateral spine fusion (PLF) model: Signafuse® Bioactive Bone Graft Putty and Actifuse® ABX. Methods Bilateral intertransverse spine fusion was performed at the L5-L6 transverse processes (TPs) of New Zealand White rabbits using either Signafuse or Actifuse ABX as the bone graft material. Bone remodeling and spine fusion were assessed at 6 and 12 weeks using radiographic, biomechanical and histological endpoints. Results Fusion rate by manual palpation at 6 weeks was greater for Signafuse (33%) compared to Actifuse ABX (0%), and equivalent in both groups at 12 weeks (50%). Biomechanical fusion rate based on flexion-extension data was 80% in Signafuse group and 44% for Actifuse ABX. Histology revealed a normal healing response in both groups. MicroCT and histomorphometric data at 6 weeks showed greater new bone formation in the Signafuse group compared to Actifuse ABX (p <0.05), with no differences detected at 12 weeks. Histological fusion scores were greater in the Signafuse group at 6 and 12 weeks, indicated by higher degree structural remodeling and tendency towards complete bridging of the fusion bed compared to the Actifuse ABX group. Conclusion Confirmed by several metrics, Signafuse outperformed Actifuse ABX as a standalone synthetic bone graft in an established PLF model, demonstrating greater rates of bone remodeling and spine fusion. The combination of 45

  18. 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.

  19. 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.

  20. 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; Goodrich, 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.

  1. 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.

  2. Precise estimation of pressure-temperature paths from zoned minerals using Markov random field modeling: theory and synthetic inversion

    NASA Astrophysics Data System (ADS)

    Kuwatani, Tatsu; Nagata, Kenji; Okada, Masato; Toriumi, Mitsuhiro

    2012-03-01

    The chemical zoning profile in metamorphic minerals is often used to deduce the pressure-temperature ( P- T) history of rock. However, it remains difficult to restore detailed paths from zoned minerals because thermobarometric evaluation of metamorphic conditions involves several uncertainties, including measurement errors and geological noise. We propose a new stochastic framework for estimating precise P- T paths from a chemical zoning structure using the Markov random field (MRF) model, which is a type of Bayesian stochastic method that is often applied to image analysis. The continuity of pressure and temperature during mineral growth is incorporated by Gaussian Markov chains as prior probabilities in order to apply the MRF model to the P- T path inversion. The most probable P- T path can be obtained by maximizing the posterior probability of the sequential set of P and T given the observed compositions of zoned minerals. Synthetic P- T inversion tests were conducted in order to investigate the effectiveness and validity of the proposed model from zoned Mg-Fe-Ca garnet in the divariant KNCFMASH system. In the present study, the steepest descent method was implemented in order to maximize the posterior probability using the Markov chain Monte Carlo algorithm. The proposed method successfully reproduced the detailed shape of the synthetic P- T path by eliminating appropriately the statistical compositional noises without operator's subjectivity and prior knowledge. It was also used to simultaneously evaluate the uncertainty of pressure, temperature, and mineral compositions for all measurement points. The MRF method may have potential to deal with several geological uncertainties, which cause cumbersome systematic errors, by its Bayesian approach and flexible formalism, so that it comprises potentially powerful tools for various inverse problems in petrology.

  3. 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.

  4. Prediction of Antimicrobial Activity of Synthetic Peptides by a Decision Tree Model

    PubMed Central

    Lira, Felipe; Perez, Pedro S.; Baranauskas, José A.

    2013-01-01

    Antimicrobial resistance is a persistent problem in the public health sphere. However, recent attempts to find effective substitutes to combat infections have been directed at identifying natural antimicrobial peptides in order to circumvent resistance to commercial antibiotics. This study describes the development of synthetic peptides with antimicrobial activity, created in silico by site-directed mutation modeling using wild-type peptides as scaffolds for these mutations. Fragments of antimicrobial peptides were used for modeling with molecular modeling computational tools. To analyze these peptides, a decision tree model, which indicated the action range of peptides on the types of microorganisms on which they can exercise biological activity, was created. The decision tree model was processed using physicochemistry properties from known antimicrobial peptides available at the Antimicrobial Peptide Database (APD). The two most promising peptides were synthesized, and antimicrobial assays showed inhibitory activity against Gram-positive and Gram-negative bacteria. Colossomin C and colossomin D were the most inhibitory peptides at 5 μg/ml against Staphylococcus aureus and Escherichia coli. The methods described in this work and the results obtained are useful for the identification and development of new compounds with antimicrobial activity through the use of computational tools. PMID:23455341

  5. 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.

  6. Towards a compendium of essential genes – From model organisms to synthetic lethality in cancer cells

    PubMed Central

    Zhan, Tianzuo; Boutros, Michael

    2016-01-01

    Abstract Essential genes are defined by their requirement to sustain life in cells or whole organisms. The systematic identification of essential gene sets not only allows insights into the fundamental building blocks of life, but may also provide novel therapeutic targets in oncology. The discovery of essential genes has been tightly linked to the development and deployment of various screening technologies. Here, we describe how gene essentiality was addressed in different eukaryotic model organisms, covering a range of organisms from yeast to mouse. We describe how increasing knowledge of evolutionarily divergent genomes facilitate identification of gene essentiality across species. Finally, the impact of gene essentiality and synthetic lethality on cancer research and the clinical translation of screening results are highlighted. PMID:26627871

  7. Iron-sulfur clusters—new features in enzymes and synthetic models

    NASA Astrophysics Data System (ADS)

    Bill, Eckhard

    2012-03-01

    Mössbauer spectroscopy is very important for the characterization of iron sulfur clusters in biological and synthetic molecules. The electric and magnetic hyperfine parameters obtained for 57Fe provide valuable information about the electronic structure of the different iron sites occurring in Fe:S clusters. Although known since more than four decades, research in this field is very active, revealing unexpected functions, structures and redox states. In this overview, new aspects of double exchange and vibronic coupling in a structurally well-characterized two-iron model compound are discussed, the electronic structure of extremely reduced clusters with all iron in ferrous or even in iron(I) state is elucidated, and an exciting new type of cubane cluster occurring in oxygen-insensitive hydrogenases is presented. The latter cluster involves structural changes during function and it supports more than one redox transition, which may be essential for oxygen protection of the enzymes.

  8. Deep source model for Nevado del Ruiz Volcano, Colombia, constrained by interferometric synthetic aperture radar observations

    NASA Astrophysics Data System (ADS)

    Lundgren, Paul; Samsonov, Sergey V.; López Velez, Cristian Mauricio; Ordoñez, Milton

    2015-06-01

    Nevado del Ruiz is part of a large volcano complex in the northern Andes of Colombia. Interferometric synthetic aperture radar observations from the RADARSAT-2 satellite since 2011 show steady inflation of the volcano since 2012 at 3-4 cm/yr. The broad (>20 km) deformation pattern from both ascending and descending track data constrain source models for either point or spheroidal sources, both located at >14 km beneath the surface (mean elevation 4.2 km) and 10 km SW of Nevado del Ruiz, below nearby Santa Isabel Volcano. Stress change computations for both sources in the context of a compressive regional stress indicate that dikes propagating from the source should become trapped in sills, possibly leading to a more complex pathway to the surface and explaining the significant lateral separation of the source and Nevado del Ruiz Volcano.

  9. 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

  10. 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.

  11. Polymerase Interactions with Wobble Mismatches in Synthetic Genetic Systems and Their Evolutionary Implications.

    PubMed

    Winiger, Christian B; Kim, Myong-Jung; Hoshika, Shuichi; Shaw, Ryan W; Moses, Jennifer D; Matsuura, Mariko F; Gerloff, Dietlind L; Benner, Steven A

    2016-07-19

    In addition to completing the Watson-Crick nucleobase matching "concept" (big pairs with small, hydrogen bond donors pair with hydrogen bond acceptors), artificially expanded genetic information systems (AEGIS) also challenge DNA polymerases with a complete set of mismatches, including wobble mismatches. Here, we explore wobble mismatches with AEGIS with DNA polymerase 1 from Escherichia coli. Remarkably, we find that the polymerase tolerates an AEGIS:standard wobble that has the same geometry as the G:T wobble that polymerases have evolved to exclude but excludes a wobble geometry that polymerases have never encountered in natural history. These results suggest certain limits to "structural analogy" and "evolutionary guidance" as tools to help synthetic biologists expand DNA alphabets. PMID:27347689

  12. 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.

  13. Modulation of endothelial cell adhesion to synthetic vascular grafts using biotinylated fibronectin in a dual ligand protein system

    NASA Astrophysics Data System (ADS)

    Anamelechi, Charles Chibuzor

    Over half a million coronary artery bypass operations are performed annually in the US yielding an annual health care cost of over 16 billion dollars. Only five percent of bypasses are repeat operations in spite of the procedures prevalence. Patients facing repeat coronary artery bypass operations often lack transplantable autologous arteries or veins, necessitating the use of substitutes. Unfortunately, synthetic small diameter vascular grafts have unacceptable patency rates, primarily due to lumenal thrombus formation and intimal thickening. Endothelial cells (EC) mediate the anti-thrombotic activity in healthy blood vessels, and due to the scarcity of suitable autologous vascular replacement, EC-seeded small diameter synthetic vascular grafts represent a clear, immediate, and practical solution. The fundamental goal of this project was to optimize the dual ligand (DL) system on synthetic vascular graft (SVG) surrogates to show enhanced cell adhesion, retention, and native functionality compared to fibronectin alone. Initially, two SVG surrogates were identified through characterization by x-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and 125I radiolabeling. The first modification to the DL system involved direct biotinylation of fibronectin (bFN) as a replacement for co-adsorption of FN with biotinylated bovine serum albumin (bBSA). This was analyzed with a Langmuir model using surface plasmon resonance (SPR) spectroscopy to verify the binding affinity of bFN and ELISA to detect the availability of the RGD binding motif post biotinylation. The second major change in this project examined cell binding and formation of focal adhesion after shifting from direct incubation of HUVECs with RGD-SA to sequentially adsorbing bFN(9) and RGD-SA prior to introducing unmodified HUVECs. These experiments were conducted under static seeding conditions. Next, dynamic cell seeding onto the sequentially adsorbed protein surface was examined as a function

  14. Synthetic spectral analysis of a kinetic model for slow-magnetosonic waves in solar corona

    NASA Astrophysics Data System (ADS)

    Ruan, Wenzhi; He, Jiansen; Zhang, Lei; Vocks, Christian; Marsch, Eckart; Tu, Chuanyi; Peter, Hardi; Wang, Linghua

    2016-03-01

    We propose a kinetic model of slow-magnetosonic waves to explain various observational features associated with the propagating intensity disturbances (PIDs) occurring in the solar corona. The characteristics of slow mode waves, e.g, inphase oscillations of density, velocity, and thermal speed, are reproduced in this kinetic model. Moreover, the red-blue (R-B) asymmetry of the velocity distribution as self-consistently generated in the model is found to be contributed from the beam component, as a result of the competition between Landau resonance and Coulomb collisions. Furthermore, we synthesize the spectral lines and make the spectral analysis, based on the kinetic simulation data of the flux tube plasmas and the hypothesis of the surrounding background plasmas. It is found that the fluctuations of parameters of the synthetic spectral lines are basically consistent with the observations: (1) the line intensity, Doppler shift, and line width are fluctuating in phase; (2) the R-B asymmetry usually oscillate out of phase with the former three parameters; (3) the blueward asymmetry is more evident than the redward asymmetry in the R-B fluctuations. The oscillations of line parameters become weakened for the case with denser surrounding background plasmas. Similar to the observations, there is no doubled-frequency oscillation of the line width for the case with flux-tube plasmas flowing bulkly upward among the static background plasmas. Therefore, we suggest that the "wave + beam flow" kinetic model may be a viable interpretation for the PIDs observed in the solar corona.

  15. Modeling Parallel System Workloads with Temporal Locality

    NASA Astrophysics Data System (ADS)

    Minh, Tran Ngoc; Wolters, Lex

    In parallel systems, similar jobs tend to arrive within bursty periods. This fact leads to the existence of the locality phenomenon, a persistent similarity between nearby jobs, in real parallel computer workloads. This important phenomenon deserves to be taken into account and used as a characteristic of any workload model. Regrettably, this property has received little if any attention of researchers and synthetic workloads used for performance evaluation to date often do not have locality. With respect to this research trend, Feitelson has suggested a general repetition approach to model locality in synthetic workloads [6]. Using this approach, Li et al. recently introduced a new method for modeling temporal locality in workload attributes such as run time and memory [14]. However, with the assumption that each job in the synthetic workload requires a single processor, the parallelism has not been taken into account in their study. In this paper, we propose a new model for parallel computer workloads based on their result. In our research, we firstly improve their model to control locality of a run time process better and then model the parallelism. The key idea for modeling the parallelism is to control the cross-correlation between the run time and the number of processors. Experimental results show that not only the cross-correlation is controlled well by our model, but also the marginal distribution can be fitted nicely. Furthermore, the locality feature is also obtained in our model.

  16. Modeling Water Flow in the Everglades Wetlands Using Interferometric Synthetic Aperture Radar (InSAR)Observations

    NASA Astrophysics Data System (ADS)

    Garcia-Martinez, R.; Miralles-Wilhelm, F.; Wdowinski, S.

    2005-05-01

    New space-based Interferometric Synthetic Aperture Radar (InSAR) observations of the Everglades wetlands provide high spatial resolution maps of water level changes that are essential for improved modeling efforts of surface water sheetflow. In this study, we model the Everglades' Water Conservation Area 1 (WCA-1), which is used to restore, protect, and preserve water resources and wildlife in southern Florida. We use a 2-D surface flow finite element model that considers the vegetation cover as a spatially roughness variable, topography data and influence of peripheral canals. The model provides the water elevation and velocity field throughout the conservation areas, based on rainfall record, discharge inputs and outflows through managed hydraulic structures. Our study focuses on two InSAR observed water level change patterns in WCA-1 acquired during two seasons and different weather conditions. The first pattern describes water level changes in the spring of 1998, showing a radial change caused mainly due to flow along the peripheral canals. The second pattern describes longitudinal change occurring in the fall of 2004, in the peak of hurricanes season, which caused abrupt flow income into the conservation areas. In order to improve the model results, we use a two-step procedure to calculate the vegetation roughness coefficient, which varies both in space and time. The first step includes a Supervised Image Analysis classification of WCA-1 according to remotely sensed determined vegetation maps. The estimated values are assigned to the model for the initial run. In the second step, we use an iterative procedure adjusting the vegetation roughness coefficients until the modeled water level changes agree with the InSAR observations. This technique of coupling high spatial resolution InSAR images with numerical modeling allows improved predictive abilities in the WCA under different weather scenarios, thus helping water resources managers and operators in their

  17. 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.

  18. 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

  19. Gamma irradiated micro system for long-term parenteral contraception: An alternative to synthetic polymers.

    PubMed

    Puthli, S; Vavia, P

    2008-11-15

    An injectable system of levonorgestrel (LNG) was developed using biodegradable polymer of natural origin. The parenteral system was optimized for particle size and higher drug loading. The microparticulate system was characterised by scanning electron microscopy, encapsulation efficiency, moisture content, IR, DSC, XRD, residual solvent content, sterility testing, test of abnormal toxicity and test for pyrogens. The microparticles were sterilised by gamma irradiation (2.5Mrad). The system was injected intramuscularly in rabbits and the blood levels of LNG were determined using radioimmunoassay technique. An optimized drug to polymer ratio of 0.3-1.0 (w/w ratio) gave improved drug loading of about 52%. In vivo studies in rabbits showed that the drug was released in a sustained manner for a period of 1 month. The AUC(0-t) was found to be 9363.6+/-2340pg/mLday(-1) with MRT calculated to be about 16 days and Kel of 0.01day(-1). LNG levels were maintained between 200 and 400pg/mL. In vivo release exhibited an initial burst effect which was not observed in the in vitro dissolution. This promising "Progestin-only" long-term contraceptive with improved user compliance is an alternative to the synthetic expensive polymeric carriers. PMID:18760352

  20. 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

  1. 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.

  2. 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.

  3. 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. PMID:24676102

  4. Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems

    PubMed Central

    Medford, June; Prasad, Ashok

    2014-01-01

    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. PMID:24676102

  5. Distance-dependent Ground motion variability from source models of the 1992 Landers earthquake and synthetic rupture models.

    NASA Astrophysics Data System (ADS)

    Vyas, J. C.; Mai, P. M.; Galis, M.

    2014-12-01

    We investigate near field ground motion variability due to five different kinematic rupture models for 1992 Landers earthquake. The ground motion simulations are accomplished by solving the elasto-dynamic equations of motion using a generalized finite-difference method (Ely et al., 2008). Simulated waveforms are calibrated against near-field strong-motion recordings. We then analyze a large data-set of ground-motions from 2000 sites, binned with respect to distance and azimuth to compute mean and standard deviation of peak ground velocity (PGV). We consider 1D-velocity structures as used in the source inversions, and honor the geometrical complexity due to fault segmentation. Our simulations reveal that ground motion variability is reduced as the distance from the fault increases. Variability in the kinematic sources has considerable impact on the resulting shaking variability, although the five source models considered are derived by inversion of seismic and/or geodetic data. Simulated mean PGV and its standard deviation are comparable to empirical estimates using the ground-motion prediction equation (GMPE) of Boore and Atkinson (2008). In addition, we find that intra-event ground motion variability is large in fault-parallel and small in fault-normal direction. We also compare our simulations with and without Spudich and Chiou (2008) directivity corrections, applied to Boore and Atkinson (2008), which shows that slip heterogeneity controls near-field ground-motion variability. We further investigate the effect of slip heterogeneity by considering eleven (ten heterogeneous and one uniform) synthetic rupture models. Heterogeneous slip models are generated following the algorithm of Mai and Beroza (2002) for different correlation lengths and Hurst exponents. We then examine synthetic seismograms calculated at 1500 stations for the eleven rupture models, confirming that the distance decay of ground motion variability is due to slip heterogeneity.

  6. Analysis of properties of synthetic mineral microparticles for retention and drainage system

    NASA Astrophysics Data System (ADS)

    Lee, Sa Yong

    Over the past 20 years there has been a revolution involving the use of nano- or macro-sized particles as a component of drainage and retention systems during the manufacture of paper. More recently a group of patented technologies called Synthetic Mineral Microparticles (SMM) has been invented and developed. This system has potential to further promote the drainage of water and retention of fine particles during papermaking. Prior research, as well as our own preliminary research showed that the SMM system has advantages in both of drainage and retention, compared with montmorillonite (bentonite), which is one of the most popular materials presently used in this kind of application. In spite of the demonstrated advantages of this SMM system, the properties and activity of SMM particles in the aqueous state have not been elucidated yet. To help understand the molecular mechanisms involved in SMM technology, streaming current and potentiometric titration were employed to characterize the charge behavior of SMM, depending on the synthetic conditions, which included variation of the Al/Si ratio, partial neutralization of Al species, salt addition and shear rate. Surface area of SMM and the distribution of SMM particle size were investigated with scanning electron microscopy in order to elucidate the relationship between the morphology and coagulation behavior of SMM, versus the pre-stated synthetic conditions, as well as to estimate the optimal conditions to produce SMM as a retention and drainage aid for use during papermaking. Through the streaming current titration experiments it was found that pH variation, caused by the change of Al/Si ratio and partial neutralization of aluminum's acidity, profoundly affects the charge properties of SMM. These effects can be attributed to the variation of Al-ion speciation and the influence ionizable groups on the Si-containing particle surfaces. The relationship between Al/Si ratio and isoelectric pH, measured by potentiometric

  7. Large Hybrid Energy Systems for Making Low CO2 Load-Following Power and Synthetic Fuel

    SciTech Connect

    Robert S. Cherry; Richard D. Boardman; Steven Aumeier

    2012-02-01

    Hybrid energy systems using nuclear heat sources can economically produce load-following electrical power by exploiting the surplus generation capacity available at night or seasonally to make synthetic fuel. Vehicle fuel is the only current energy use large enough to absorb all the energy capacity that might be diverted from the power industry, and its ease of storage obviates problems with discontinuous synfuel production. The potential benefits and challenges of synfuels integration are illustrated by the production of methanol from natural gas (as a source of carbon) using steam from a light water nuclear power reactor which is assumed to be available in accord with a year's worth of power demand data. Methanol's synthesis process is easily adapted to using 300 C heat from a light water reactor and this simple compound can be further processed into gasoline, biodiesel, or dimethyl ether, fuels which can be used with the current vehicle fleet. A supplemental feed to the methanol process of natural gas (for energy) allows operation at constant full rate when the nuclear heat is being used to produce electrical power. The higher capital costs of such a system are offset by a lower cost of heat and power production from a large base load type of plant and by reduced costs associated with much lower CO2 emissions. Other less tangible economic benefits of this and similar hybrid systems include better use of natural resource for fuels and greater energy services security from the domestic production of vehicle fuel.

  8. 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.

  9. Gravity and Seismic Tomography Joint Inversion: A synthetic study modelling magmatic massive sulphide type bodies

    NASA Astrophysics Data System (ADS)

    Carter-McAuslan, Angela; Lelievre, Peter; Farquharson, Colin

    2013-04-01

    Gravity methods have long been used in mineral exploration. However, gravity methods have difficulty resolving small details. Seismic methods provide high resolving potential for use in mineral exploration. However, complicated hard-rock geology can make seismic data processing and interpretation difficult. By jointly inverting seismic tomography data with gravity data these difficulty may be overcome. We investigated the viability of deterministic minimum-structure style joint inversion of seismic traveltime and gravity data for the delineation of magmatic massive sulphide type geological targets. These tests also assessed the potential of employing borehole gravity. A number of synthetic Earth models were created. These models were built on triangular unstructured meshes, allowing for efficient generation of complicated, realistic geological structures. 2D models were based on conceptualized models of the magmatic massive sulphide body similar to the Eastern Deeps of the Voisey's Bay, Labrador, Canada. Single property and joint inversions were performed with seismic traveltimes and both ground-based and borehole gravity. There is a known relationship between seismic velocity and density for both silicate rocks and sulphide minerals for the models constructed; this lithological relationship was used to design an appropriate coupling strategy in the joint inversions. Joint inversions were able to successfully locate a buried high contrast target with a variety of survey designs. 2D inversions results provided guidance to 3D inversion. Experimentation with noise levels, mesh design, and various inversion parameters has led to a better understanding of how to practically apply joint inversion of traveltimes and gravity data to this and similar exploration problems.

  10. Ultra-wide-band model-based synthetic aperture radar imaging through complex media

    NASA Astrophysics Data System (ADS)

    Cai, Lixin

    2000-10-01

    It is known that electromagnetic signals can penetrate into non-metallic barriers such as building walls and soil. A portable Synthetic Aperture Radar (SAR) unit capable of transmitting and receiving such signals is desirable in various non-intrusive (proximity or remote) sensing applications. Theoretical and experimental issues associated with Ultra-Wide-Band (UWB) SAR imaging through complex media are studied. The complex media of interest include building walls, underground and foliage. It may be inconvenient and impractical for a hand-held unit to collect data at uniformly spaced positions. A back-projection algorithm is developed for the case where spatial sampling is not uniform. In addition, a spherical wavefront (as opposed to a uniformly planar wavefront) is assumed in the algorithm to account for the proximity of a radar unit relative to a target scene. Imaging results from simulated point target data and measurements of various real targets are obtained. Defocusing and other image defects associated with imaging through complex media using the free space (or dielectric full space) assumption are addressed. Refocusing techniques based on a dielectric wall model and a dielectric half-space model are formulated and imaging results are compared with those generated using the free space assumption.

  11. 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

  12. 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.

  13. Synthetic Output by Simulation. An Introductory Paper.

    ERIC Educational Resources Information Center

    Mason, Thomas R.

    Simulation is the process of synthetically manipulating the variables in a model of a system for the purpose of understanding, experimenting with, and predicting the behavior of that system. Many different models are now being developed by university administrators to aid them in making decisions. Simulation models have been developed for…

  14. Communication system modeling

    NASA Technical Reports Server (NTRS)

    Holland, L. D.; Walsh, J. R., Jr.; Wetherington, R. D.

    1971-01-01

    This report presents the results of work on communications systems modeling and covers three different areas of modeling. The first of these deals with the modeling of signals in communication systems in the frequency domain and the calculation of spectra for various modulations. These techniques are applied in determining the frequency spectra produced by a unified carrier system, the down-link portion of the Command and Communications System (CCS). The second modeling area covers the modeling of portions of a communication system on a block basis. A detailed analysis and modeling effort based on control theory is presented along with its application to modeling of the automatic frequency control system of an FM transmitter. A third topic discussed is a method for approximate modeling of stiff systems using state variable techniques.

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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. PMID:27075000

  1. 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.

  2. Using the Wiener estimator to determine optimal imaging parameters in a synthetic-collimator SPECT system used for small animal imaging

    NASA Astrophysics Data System (ADS)

    Lin, Alexander; Johnson, Lindsay C.; Shokouhi, Sepideh; Peterson, Todd E.; Kupinski, Matthew A.

    2015-03-01

    In synthetic-collimator SPECT imaging, two detectors are placed at different distances behind a multi-pinhole aperture. This configuration allows for image detection at different magnifications and photon energies, resulting in higher overall sensitivity while maintaining high resolution. Image multiplexing the undesired overlapping between images due to photon origin uncertainty may occur in both detector planes and is often present in the second detector plane due to greater magnification. However, artifact-free image reconstruction is possible by combining data from both the front detector (little to no multiplexing) and the back detector (noticeable multiplexing). When the two detectors are used in tandem, spatial resolution is increased, allowing for a higher sensitivity-to-detector-area ratio. Due to variability in detector distances and pinhole spacings found in synthetic-collimator SPECT systems, a large parameter space must be examined to determine optimal imaging configurations. We chose to assess image quality based on the task of estimating activity in various regions of a mouse brain. Phantom objects were simulated using mouse brain data from the Magnetic Resonance Microimaging Neurological Atlas (MRM NeAt) and projected at different angles through models of a synthetic-collimator SPECT system, which was developed by collaborators at Vanderbilt University. Uptake in the different brain regions was modeled as being normally distributed about predetermined means and variances. We computed the performance of the Wiener estimator for the task of estimating activity in different regions of the mouse brain. Our results demonstrate the utility of the method for optimizing synthetic-collimator system design.

  3. Predicting the performance of system for the co-production of Fischer-Tropsch synthetic liquid and power from coal

    SciTech Connect

    Wang, X.; Xiao, Y.; Xu, S.; Guo, Z.

    2008-01-15

    A co-production system based on Fischer-Tropsch (FT) synthesis reactor and gas turbine was simulated and analyzed. Syngas from entrained bed coal gasification was used as feedstock of the low-temperature slurry phase Fischer-Tropsch reactor. Raw synthetic liquid produced was fractioned and upgraded to diesel, gasoline, and liquid petrol gas (LPG). Tail gas composed of unconverted syngas and FT light components was fed to the gas turbine. Supplemental fuel (NG, or refinery mine gas) might be necessary, which was dependent on gas turbine capacity expander through flow capacity, etc. FT yield information was important to the simulation of this co-production system. A correlation model based on Mobil's two step pilot plant was applied. User models that can predict product yields and cooperate with other units were embedded into Aspen plus simulation. Performance prediction of syngas fired gas turbine was the other key of this system. The increase in mass flow through the turbine affects the match between compressor and turbine operating conditions. The calculation was carried out by GS software developed by Politecnico Di Milano and Princeton University. Various cases were investigated to match the FT synthesis island, power island, and gasification island in co-production systems. Effects of CO{sub 2} removal/LPG recovery, co-firing, and CH{sub 4} content variation were studied. Simulation results indicated that more than 50% of input energy was converted to electricity and FT products. Total yield of gasoline, diesel, and LPG was 136-155 g/N m{sup 3} (CO+H{sub 2}). At coal feed of 21.9 kg/s, net electricity exported to the grid was higher than 100 MW. Total production of diesel and gasoline (and LPG) was 118,000 t (134,000 t)/year. Under the economic analysis conditions assumed in this paper the co-production system was economically feasible.

  4. 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

  5. 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. PMID:24340832

  6. 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.

  7. Modeling of babesipain-1 and identification of natural and synthetic leads for bovine babesiosis drug development.

    PubMed

    Meetei, Potshangbam Angamba; Rathore, R S; Prabhu, N Prakash; Vindal, Vaibhav

    2016-04-01

    Babesiosis is a tick-borne, zoonotic disease caused by species of the intraerythrocytic protozoan Babesia. It is distributed all around the world and affects various domestic and wild animals, mainly cattle. Recently, the cysteine protease enzyme, babesipain-1 from Babesia bigemina has been identified as a potential target for designing new anti-babesiosis drugs. In the present study, a three-dimensional structural model of babesipain-1 was developed. An active site with three pockets (S1, S2, and S3), which is congruent with its homolog, falcipain-3, was also identified. Moreover, the conservation of active site residues was consistent with the cysteine protease family. In order to identify potential inhibitors, a virtual screening workflow was employed with a chemical library containing natural and synthetic compounds. Potential inhibitors interacting with all the three subsites were identified. Further, molecular dynamic simulations were carried out to assess the interactions and stability of the inhibitors. The informatics approach, and the findings presented in this study will assist researchers in further development of potential anti-babesiosis molecules. PMID:26969677

  8. Induction of hypospadias in a murine model by maternal exposure to synthetic estrogens.

    PubMed

    Kim, Kun Suk; Torres, Carlos R; Yucel, Selcuk; Raimondo, Kamakshi; Cunha, Gerald R; Baskin, Laurence S

    2004-03-01

    We tested the hypothesis that maternal exposure to synthetic estrogen can cause hypospadias in male offspring and defined the morphological changes in the disrupted urethral seam. Timed pregnant C57/6 mice were exposed to synthetic estrogens. The genital tubercles were examined for the presence of hypospadias using histology, three-dimensional computer reconstruction, and plastic cast injection molds of the urethra. Microscopic serial analysis confirmed the presence of hypospadias, which occurred in approximately 50% of the synthetic-estrogen-treated male fetuses. No effect was seen in the female embryos. Plastic cast injection showed that affected males had a shorter total urethral length and loss of male anatomic features such as the prostatic utricle. Exposure to synthetic estrogens during pregnancy affects the normal development of the urethra in the mouse. We conclude that endocrine disrupters play an important role in genital tubercle anomalies. PMID:15016594

  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. Synthetic photometry for M and K giants and stellar evolution: hydrostatic dust-free model atmospheres and chemical abundances

    NASA Astrophysics Data System (ADS)

    Aringer, B.; Girardi, L.; Nowotny, W.; Marigo, P.; Bressan, A.

    2016-04-01

    Based on a grid of hydrostatic spherical COMARCS models for cool stars, we have calculated observable properties of these objects, which will be mainly used in combination with stellar evolution tracks and population synthesis tools. The high-resolution opacity sampling and low-resolution convolved spectra as well as bolometric corrections for a large number of filter systems are made electronically available. We exploit those data to study the effect of mass, C/O ratio and nitrogen abundance on the photometry of K and M giants. Depending on effective temperature, surface gravity and the chosen wavelength ranges, variations of the investigated parameters cause very weak to moderate and, in the case of C/O values close to 1, even strong shifts of the colours. For the usage with stellar evolution calculations, they will be treated as correction factors applied to the results of an interpolation in the main quantities. When we compare the synthetic photometry to observed relations and to data from the Galactic bulge, we find in general a good agreement. Deviations appear for the coolest giants showing pulsations, mass-loss and dust shells, which cannot be described by hydrostatic models.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. A synthetic sex ratio distortion system for the control of the human malaria mosquito.

    PubMed

    Galizi, Roberto; Doyle, Lindsey A; Menichelli, Miriam; Bernardini, Federica; Deredec, Anne; Burt, Austin; Stoddard, Barry L; Windbichler, Nikolai; Crisanti, Andrea

    2014-01-01

    It has been theorized that inducing extreme reproductive sex ratios could be a method to suppress or eliminate pest populations. Limited knowledge about the genetic makeup and mode of action of naturally occurring sex distorters and the prevalence of co-evolving suppressors has hampered their use for control. Here we generate a synthetic sex distortion system by exploiting the specificity of the homing endonuclease I-PpoI, which is able to selectively cleave ribosomal gene sequences of the malaria vector Anopheles gambiae that are located exclusively on the mosquito's X chromosome. We combine structure-based protein engineering and molecular genetics to restrict the activity of the potentially toxic endonuclease to spermatogenesis. Shredding of the paternal X chromosome prevents it from being transmitted to the next generation, resulting in fully fertile mosquito strains that produce >95% male offspring. We demonstrate that distorter male mosquitoes can efficiently suppress caged wild-type mosquito populations, providing the foundation for a new class of genetic vector control strategies. PMID:24915045

  17. A synthetic sex ratio distortion system for the control of the human malaria mosquito

    PubMed Central

    Galizi, Roberto; Doyle, Lindsey A.; Menichelli, Miriam; Bernardini, Federica; Deredec, Anne; Burt, Austin; Stoddard, Barry L.; Windbichler, Nikolai; Crisanti, Andrea

    2014-01-01

    It has been theorized that inducing extreme reproductive sex ratios could be a method to suppress or eliminate pest populations. Limited knowledge about the genetic makeup and mode of action of naturally occurring sex distorters and the prevalence of co-evolving suppressors has hampered their use for control. Here we generate a synthetic sex distortion system by exploiting the specificity of the homing endonuclease I-PpoI, which is able to selectively cleave ribosomal gene sequences of the malaria vector Anopheles gambiae that are located exclusively on the mosquito’s X chromosome. We combine structure-based protein engineering and molecular genetics to restrict the activity of the potentially toxic endonuclease to spermatogenesis. Shredding of the paternal X chromosome prevents it from being transmitted to the next generation, resulting in fully fertile mosquito strains that produce >95% male offspring. We demonstrate that distorter male mosquitoes can efficiently suppress caged wild-type mosquito populations, providing the foundation for a new class of genetic vector control strategies. PMID:24915045

  18. Multiple-input multiple-output synthetic aperture ladar system for wide-range swath with high azimuth resolution.

    PubMed

    Tang, Yu; Qin, Bao; Yan, Yun; Xing, Mengdao

    2016-02-20

    For the trade-off between the high azimuth resolution and the wide-range swath in the single-input single-output synthetic aperture ladar (SAL) system, the range swath of the SAL system is restricted to a narrow range, this paper proposes a multiple-input multiple-output (MIMO) synthetic aperture ladar system. The MIMO system adopts a low pulse repetition frequency (PRF) to avoid a range ambiguity for the wide-range swath and in azimuth adopts the multi-channel method to achieve azimuth high resolution from the unambiguous azimuth wide-spectrum signal, processed through adaptive digital beam-forming technology. Simulations and analytical results are presented. PMID:26906593

  19. 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

  20. Synergistic Synthetic Biology: Units in Concert

    PubMed Central

    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. PMID:25022769

  1. Synthetic polyspermine imidazole-4, 5-amide as an efficient and cytotoxicity-free gene delivery system

    PubMed Central

    Duan, Shi-Yue; Ge, Xue-Mei; Lu, Nan; Wu, Fei; Yuan, Weien; Jin, Tuo

    2012-01-01

    A chemically dynamic spermine-based polymer: polyspermine imidazole-4, 5-amide (PSIA, Mw > 7 kDa) was designed, synthesized, and evaluated in terms of its ability to deliver nucleic acids. This polymer was made from an endogenous monomer professionally condensing genes in sperms, spermine, and a known safety drug metabolite, imidazole-4, 5-dicarboxylic acid, through a bis-amide bond conjugated with the imidazole ring. This polymer can condense pDNA at a W/W ratio above 10 to form polyplexes (100–200 nm in diameter), which is consistent with the observation by transmission electron microscopy (TEM), and the zeta potential was in the range of 10–20 mV. The pDNA packaged polymer was stable in phosphate buffer solution (PBS) at pH 7.4 (simulated body fluid) while the polyplexes were releasing pDNA into the solution at pH 5.8 (simulated endo-lysosomes) due to the degradation of the bis-amide linkages in response to changes in pH values. PSIA-polyplexes were able to achieve efficient cellular uptake and luciferase gene silencing by co-transfection of pDNA and siRNA in COS-7 cells and HepG2 cells with negligible cytotoxicity. Biodistribution of Rhodamine B-labeled PSIA-polyplexes after being systemically injected in BALB/c nude-mice showed that the polyplexes circulated throughout the body, accumulated mainly in the kidney at 4 hours of sample administration, and moved to the liver and spleen after 24 hours. All the results suggested that PSIA offered a promising example to balance the transfection efficiency and toxicity of a synthetic carrier system for the delivery of therapeutic nucleic acids. PMID:22888236

  2. 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

  3. DOUBLE-DETONATION SUB-CHANDRASEKHAR SUPERNOVAE: SYNTHETIC OBSERVABLES FOR MINIMUM HELIUM SHELL MASS MODELS

    SciTech Connect

    Kromer, M.; Sim, S. A.; Fink, M.; Roepke, F. K.; Seitenzahl, I. R.; Hillebrandt, W.

    2010-08-20

    In the double-detonation scenario for Type Ia supernovae, it is suggested that a detonation initiates in a shell of helium-rich material accreted from a companion star by a sub-Chandrasekhar-mass white dwarf. This shell detonation drives a shock front into the carbon-oxygen white dwarf that triggers a secondary detonation in the core. The core detonation results in a complete disruption of the white dwarf. Earlier studies concluded that this scenario has difficulties in accounting for the observed properties of Type Ia supernovae since the explosion ejecta are surrounded by the products of explosive helium burning in the shell. Recently, however, it was proposed that detonations might be possible for much less massive helium shells than previously assumed (Bildsten et al.). Moreover, it was shown that even detonations of these minimum helium shell masses robustly trigger detonations of the carbon-oxygen core (Fink et al.). Therefore, it is possible that the impact of the helium layer on observables is less than previously thought. Here, we present time-dependent multi-wavelength radiative transfer calculations for models with minimum helium shell mass and derive synthetic observables for both the optical and {gamma}-ray spectral regions. These differ strongly from those found in earlier simulations of sub-Chandrasekhar-mass explosions in which more massive helium shells were considered. Our models predict light curves that cover both the range of brightnesses and the rise and decline times of observed Type Ia supernovae. However, their colors and spectra do not match the observations. In particular, their B - V colors are generally too red. We show that this discrepancy is mainly due to the composition of the burning products of the helium shell of the Fink et al. models which contain significant amounts of titanium and chromium. Using a toy model, we also show that the burning products of the helium shell depend crucially on its initial composition. This leads us

  4. System Advisor Model

    Energy Science and Technology Software Center (ESTSC)

    2010-03-01

    The System Advisor Model (SAM) is a performance and economic model designed to facilitate decision making for people involved in the renewable energy industry, ranging from project managers and engineers to incentive program designers, technology developers, and researchers.

  5. Model for Planning Water-Energy Systems

    NASA Astrophysics Data System (ADS)

    Lall, Upmanu; Mays, Larry W.

    1981-08-01

    A mathematical programing model which has a nonlinear objective function and linear constraints is developed for the planning of composite regional water-energy systems and is solved using the largescale generalized reduced-gradient technique. Three interacting subsystems (the water subsystem, the power generation subsystem, and the coal and synthetic natural gas subsystem) are modeled to define the interlinked water-energy system. The objective of the model is to minimize the sum of the capital, operating, and distribution costs incurred in meeting future water, gas, coal and power demands within a region. The nonlinear objective function represents an improvement over existing models, as it permits analysis of nonlinear system response and economies of scale. The model is applied to a region located in northeastern Texas.

  6. 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.

  7. Synthetic Active Site Model of the [NiFeSe] Hydrogenase

    PubMed Central

    Wombwell, Claire; Reisner, Erwin

    2015-01-01

    A dinuclear synthetic model of the [NiFeSe] hydrogenase active site and a structural, spectroscopic and electrochemical analysis of this complex is reported. [NiFe(‘S2Se2’)(CO)3] (H2‘S2Se2’=1,2-bis(2-thiabutyl-3,3-dimethyl-4-selenol)benzene) has been synthesized by reacting the nickel selenolate complex [Ni(‘S2Se2’)] with [Fe(CO)3bda] (bda=benzylideneacetone). X-ray crystal structure analysis confirms that [NiFe(‘S2Se2’)(CO)3] mimics the key structural features of the enzyme active site, including a doubly bridged heterobimetallic nickel and iron center with a selenolate terminally coordinated to the nickel center. Comparison of [NiFe(‘S2Se2’)(CO)3] with the previously reported thiolate analogue [NiFe(‘S4’)(CO)3] (H2‘S4’=H2xbsms=1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) showed that the selenolate groups in [NiFe(‘S2Se2’)(CO)3] give lower carbonyl stretching frequencies in the IR spectrum. Electrochemical studies of [NiFe(‘S2Se2’)(CO)3] and [NiFe(‘S4’)(CO)3] demonstrated that both complexes do not operate as homogenous H2 evolution catalysts, but are precursors to a solid deposit on an electrode surface for H2 evolution catalysis in organic and aqueous solution. PMID:25847470

  8. 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.

  9. A comparison of spatial sampling techniques enabling first principles modeling of a synthetic aperture RADAR imaging platform

    NASA Astrophysics Data System (ADS)

    Gartley, Michael; Goodenough, Adam; Brown, Scott; Kauffman, Russel P.

    2010-04-01

    Simulation of synthetic aperture radar (SAR) imagery may be approached in many different ways. One method treats a scene as a radar cross section (RCS) map and simply evaluates the radar equation, convolved with a system impulse response to generate simulated SAR imagery. Another approach treats a scene as a series of primitive geometric shapes, for which a closed form solution for the RCS exists (such as boxes, spheres and cylinders), and sums their contribution at the antenna level by again solving the radar equation. We present a ray-tracing approach to SAR image simulation that treats a scene as a series of arbitrarily shaped facetized objects, each facet potentially having a unique radio frequency optical property and time-varying location and orientation. A particle based approach, as compared to a wave based approach, presents a challenge for maintaining coherency of sampled scene points between pulses that allows the reconstruction of an exploitable image from the modeled complex phase history. We present a series of spatial sampling techniques and their relative success at producing accurate phase history data for simulations of spotlight, stripmap and SAR-GMTI collection scenarios.

  10. Prefiltering synthetic images for projection in hardware-in-the-loop systems

    NASA Astrophysics Data System (ADS)

    Flynn, David S.; Sieglinger, Breck A.; Coker, Charles F.

    1997-07-01

    A challenging problem associated with performing hardware- in-the-loop tests of imaging infrared seekers is projecting images that are spatially realistic. The problem is complicated by the fact that the targets may be small and unresolved at acquisition and grow to fill the field of view during the final guidance updates. Although characteristics of the projection system are usually thought of as determining the spatial realism, the imagery used to drive the projector is also important. For a pixelized projector, the driving imagery must be sampled at a rate determined by the sample spacing of the pixels in the projector. If the scenes contain important information that is small compared to the projector pixel spacing (that is, if they have important information at high spatial frequencies), then information may be lost in the sampling process if the images are not adequately bandlimited. This bandlimiting can be accomplished by prefiltering the scenes. At acquisition, targets are usually small; thus, prefiltering is necessary to preserve information about the target. Without such prefiltering, for example, infinitesimally small targets would never be seen unless they just happened to be at the exact location where the scene is sampled for a projector pixel. This paper reports the results of a study of various filters that might be used for prefiltering synthetic imagery generated to drive projectors in the KHILS facility. Projector and seeker characteristics typical of the KHILS facility were adopted for the study. Since the radiance produced by projectors is always positive, filters that can produce negative values were not considered. Figures of merit were defined based on the sensor-measured quantities such as radiant intensity, centroid, and spot size. The performance of prefilters of various shapes and sizes and for typical projector and seeker characteristics will be reported.

  11. Modeling and experimental analysis of phased array synthetic jet cross-flow interactions

    NASA Astrophysics Data System (ADS)

    Hasnain, Zohaib

    Synthetic Jet Actuators (SJAs) are fluidic devices capable of adding momentum to static or non-static bodies of fluid without adding mass. They are therefore categorized as zero-net-mass-flux (ZNMF) momentum source. In its simplest compact form a SJA consists of an oscillatory surface connected to a cavity with a single exit orifice through which the fluid enters and exits. SJA technology has been utilized in applications ranging from boundary layer control over aerodynamic surfaces to fluidic mixing in dispersion applications. The ZNMF nature of the technology means it is not subject to constraints experienced by traditional momentum sources that require the addition of mass in order to impart momentum. The momentum that can be added by a single SJA is limited by the energy transfer capabilities of the oscillating surface. In modern SJAs this surface usually is a piezoceramic/metal composite subjected to a high voltage AC signal. For applications such as flow control over aerodynamic surfaces, modern SJAs are used in an array configuration and are capable of altering the flow momentum by values ranging from 0.01-10%. While it is possible to build larger actuators to increase this value the benefits associated with the compact size would be lost. It is therefore desirable to tune other parameters associated with SJA arrays to increase this value. The specific motivation for this study comes from the desire to control the momentum addition capacity of a specific SJA array, without having to alter any geometric parameters. In a broader sense this study focuses on understanding the physics of SJA interaction in array configuration through experiments which are then used to guide in the design of modeling technique that predicts SJA array behavior in cross-flows. The first half of the project focused on understanding SJA behavior through modeling. Numerical techniques were initially used to model SJA and SJA arrays in cross-flows. Reduced numerical models were then

  12. 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.

  13. Synthetic fuels

    SciTech Connect

    Sammons, V.O.

    1980-01-01

    This guide is designed for those who wish to learn more about the science and technology of synthetic fuels by reviewing materials in the collections of the Library of Congress. This is not a comprehensive bibliography, it is designed to put the reader on target. Subject headings used by the Library of Congress under which books on synthetic fuels can be located are: oil-shale industry; oil-shales; shale oils; synthetic fuels; synthetic fuels industry; coal gasification; coal liquefaction; fossil fuels; hydrogen as fuel; oil sands; petroleum, synthesis gas; biomass energy; pyrolysis; and thermal oil recovery. Basic texts, handbooks, government publications, journals, etc. were included. (DP)

  14. 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. PMID:26795018

  15. 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. PMID:23865474

  16. 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.

  17. A Synthetic Quorum Sensing System Reveals a Potential Private Benefit for Public Good Production in a Biofilm

    PubMed Central

    Zhang, Fang; Kwan, Anna; Xu, Amy; Süel, Gürol M.

    2015-01-01

    Bacteria predominantly reside in microbial communities known as biofilms, where cells are encapsulated and protected by the extracellular matrix (ECM). While all biofilm cells benefit from the ECM, only a subgroup of cells carries the burden of producing this public good. This dilemma provokes the question of how these cells balance the cost of ECM production. Here we show that ECM producing cells have a higher gene expression response to quorum sensing (QS) signals, which can lead to a private benefit. Specifically, we constructed a synthetic quorum-sensing system with designated “Sender” and “Receiver” cells in Bacillus subtilis. This synthetic QS system allowed us to uncouple and independently investigate ECM production and QS in both biofilms and single cells. Results revealed that ECM production directly enhances the response to QS signals, which may offset the cost of ECM production. PMID:26196509

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

    PubMed

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

    2016-01-01

    In this review, we address recent advances made in pathway engineering, directed evolution, and systems/synthetic biology approaches employed in the production and modification of flavonoids from microbial cells. The review is divided into two major parts. In the first, various metabolic engineering and system/synthetic biology approaches used for production of flavonoids and derivatives are discussed broadly. All the manipulations/engineering accomplished on the microorganisms since 2000 are described in detail along with the biosynthetic pathway enzymes, their sources, structures of the compounds, and yield of each product. In the second part of the review, post-modifications of flavonoids by four major reactions, namely glycosylations, methylations, hydroxylations and prenylations using recombinant strains are described. PMID:26946281

  19. 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

  20. Shuttle Imaging Radar-C mission operations - Technology test bed for Earth Observing System synthetic aperture radar

    NASA Technical Reports Server (NTRS)

    Trimble, J. P.; Collins, C. E.

    1992-01-01

    The mission operations for the Space Radar Lab (SRL), particularly in the areas of real-time replanning and science activity coordination, are presented. The two main components of SRL are the Shuttle Imaging Radar-C and the X-Band Synthetic Aperture Radar. The Earth Observing System SAR will be a multispectral, multipolarization radar satellite that will provide information over an entire decade, permitting scientists to monitor large-scale changes in the earth's environment over a long period of time.

  1. 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.

  2. 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.

  3. A constructed wetland model for synthetic reactive dye wastewater treatment by narrow-leaved cattails (Typha angustifolia Linn.).

    PubMed

    Nilratnisakorn, S; Thiravetyan, P; Nakbanpote, W

    2009-01-01

    Textile wastewater is contaminated by reactive dye causing unattractive levels of wastewater color, high pH and high salt content when discharged into public water systems. Decolorization of textile wastewater by plant, phytoremediation, is an alternative, sustainable method which is suitable for long term operation. Narrow-leaved cattails are one species of wetland plant with efficiency for decolorizing and remediating textile wastewater. In addition, chemical oxygen demand (COD) can be lowered and dye residue can be removed. The plant also showed a good salt tolerance even after being exposed to a salt solution for 15 days. The narrow-leaved cattails were set up in a constructed wetland model with a vertical flow system operating from bottom to top for synthetic reactive dye wastewater (SRDW) removal. Narrow-leaved cattails could achieve the removal of SRDW at approximately 0.8 g(SRDW) m(-2) day(-1). Decolorization of SRDW by this plant was approximately 60%. The advantage of this method is that it is suitable for textile wastewater management and improvement of wetland. These plants could lower COD, remove dye, sodium and total dissolved solids (TDS) whereas other biological and chemical methods could not remove TDS and dye in the same time. These results suggested that the spongy cell structure of this plant has the ability to absorb large amounts of water and nutrients. Physico-chemical analysis revealed increasing amounts of sulfur, silicon, iron and calcium in the plant leafs and roots after exposure to wastewater. Proteins or amide groups in the plant might help in textile dye removal. Regarding decolorization, this plant accumulates dye in the intercellular space and still grows in this SRDW condition. Hence, it can be noted here that narrow-leaved cattails are efficient for textile dye wastewater treatment. PMID:19759459

  4. Use of biodegradable PLGA microspheres as a slow release delivery system for the Boophilus microplus synthetic vaccine SBm7462.

    PubMed

    Sales-Junior, P A; Guzman, F; Vargas, M I; Sossai, S; Patarroyo V, A M; González, C Z L; Patarroyo, J H

    2005-09-15

    The synthetic anti-Boophilus microplus vaccine SBm7462 derived from the tick intestinal protein, Bm86, induced a protective immune response when emulsified in saponin and used in cattle. Using a mice model, and with the objective of improving the vaccine by continual peptide release, it was encapsulated in PLGA 50:50 microspheres and inoculated in BALB/c mice to assess the immunological response by detection of anti-peptide IgGs. Comparative studies were made with the peptide emulsified in saponin and with another synthetic vaccine, and the microsphere/peptide was characterized for efficiency of encapsulation, in vitro release profile, morphology, size, peptide integrity after encapsulation and stability in different pHs. The findings showed that saponin enhances a better immune response from SBm7462 and that the PLGA 50:50 microspheres are suitable for use with this peptide. PMID:16002149

  5. 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.

  6. 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.

  7. Natural-Synthetic Hybrid Polymers Developed via Electrospinning: The Effect of PET in Chitosan/Starch System

    PubMed Central

    Espíndola-González, Adolfo; Martínez-Hernández, Ana Laura; Fernández-Escobar, Francisco; Castaño, Victor Manuel; Brostow, Witold; Datashvili, Tea; Velasco-Santos, Carlos

    2011-01-01

    Chitosan is an amino polysaccharide found in nature, which is biodegradable, nontoxic and biocompatible. It has versatile features and can be used in a variety of applications including films, packaging, and also in medical surgery. Recently a possibility to diversify chitosan properties has emerged by combining it with synthetic materials to produce novel natural-synthetic hybrid polymers. We have studied structural and thermophysical properties of chitosan + starch + poly(ethylene terephthalate) (Ch + S + PET) fibers developed via electrospinning. Properties of these hybrids polymers are compared with extant chitosan containing hybrids synthesized by electrospinning. Molecular interactions and orientation in the fibers are analyzed by infrared and Raman spectroscopies respectively, morphology by scanning electron microscopy and thermophysical properties by thermogravimetric analysis and differential scanning calorimetry. Addition of PET to Ch + S systems results in improved thermal stability at elevated temperatures. PMID:21673930

  8. Finding realistic dike models from interferometric synthetic aperture radar data: The February 2000 eruption at Piton de la Fournaise

    NASA Astrophysics Data System (ADS)

    Fukushima, Y.; Cayol, V.; Durand, P.

    2005-03-01

    Dike intrusions often cause complex ground displacements that are not sufficiently explained by simple analytical models. We develop a method to find complex and realistic dike geometries and overpressures from interferometric synthetic aperture radar (InSAR) data. This method is based on a combination of a boundary element method with realistic topography and a neighborhood algorithm inversion. Dike model geometry is roughly a quadrangle with its top reaching the ground. The inversion has two stages: search and appraisal. The appraisal stage involves calculations of model marginal probability density functions using misfit values calculated during the search stage. The misfit function takes into account the variance and correlation of data noise. Synthetic tests show that a model is successfully retrieved within predicted narrow confidence intervals. We apply the method on InSAR data of the February 2000 flank eruption at Piton de la Fournaise and get a trapezoid dike dipping seaward (61.0°-67.3°) with its bottom passing 800-1000 m beneath the summit. A model with a basal slip plane does not better explain observed asymmetric displacements, and thus this asymmetry is solely attributed to the dipping dike. The dike lies above a narrow band of preeruption seismicity, suggesting that lateral magma propagation occurred. Neglecting topography results in poor modeling at depth and in overestimations of overpressure (or opening), height (both about 30%), and volume (about 20%).

  9. Building synthetic memory

    PubMed Central

    Inniss, Mara C.; Silver, Pamela A.

    2013-01-01

    Synopsis Cellular memory – conversion of a transient signal into a sustained response – is a common feature of biological systems. Synthetic biologists aim to understand and reengineer such systems in a reliable and predictable manner. Synthetic memory circuits have been designed and built in vitro and in vivo based on diverse mechanisms such as oligonucleotide hybridization, recombination, transcription, phosphorylation, and RNA editing. Thus far, building these circuits has helped us explore the basic principles required for stable memory and ask novel biological questions. Here we discuss strategies for building synthetic memory circuits, their use as research tools, and future applications of these devices in medicine and industry. PMID:24028965

  10. Building synthetic memory.

    PubMed

    Inniss, Mara C; Silver, Pamela A

    2013-09-01

    Cellular memory - conversion of a transient signal into a sustained response - is a common feature of biological systems. Synthetic biologists aim to understand and re-engineer such systems in a reliable and predictable manner. Synthetic memory circuits have been designed and built in vitro and in vivo based on diverse mechanisms, such as oligonucleotide hybridization, recombination, transcription, phosphorylation, and RNA editing. Thus far, building these circuits has helped us explore the basic principles required for stable memory and ask novel biological questions. Here we discuss strategies for building synthetic memory circuits, their use as research tools, and future applications of these devices in medicine and industry. PMID:24028965

  11. 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)

  12. Modeling the contribution of individual proteins to mixed skeletal muscle protein synthetic rates over increasing periods of label incorporation

    PubMed Central

    Wolff, Christopher A.; Peelor, Fredrick F.; Shipman, Patrick D.; Hamilton, Karyn L.

    2015-01-01

    Advances in stable isotope approaches, primarily the use of deuterium oxide (2H2O), 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 2H2O 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. PMID:25593288

  13. Comparison of photoelectrochemical water oxidation activity of a synthetic photocatalyst system with photosystem II.

    PubMed

    Lai, Yi-Hsuan; Kato, Masaru; Mersch, Dirk; Reisner, Erwin

    2014-01-01

    This discussion describes a direct comparison of photoelectrochemical (PEC) water oxidation activity between a photosystem II (PSII)-functionalised photoanode and a synthetic nanocomposite photoanode. The semi-biological photoanode is composed of PSII from the thermophilic cyanobacterium Thermosynechococcus elongatus on a mesoporous indium tin oxide electrode (mesoITO|PSII). PSII embeds all of the required functionalities for light absorption, charge separation and water oxidation and ITO serves solely as the electron collector. The synthetic photoanode consists of a TiO(2) and NiO(x) coated nanosheet-structured WO(3) electrode (nanoWO(3)|TiO(2)|NiO(x)). The composite structure of the synthetic electrode allows mimicry of the functional key features in PSII: visible light is absorbed by WO(3), TiO(2) serves as a protection and charge separation layer and NiO(x) serves as the water oxidation electrocatalyst. MesoITO|PSII uses low energy red light, whereas nanoWO(3)|TiO(2)|NiO(x) requires high energy photons of blue-end visible and UV regions to oxidise water. The electrodes have a comparable onset potential at approximately 0.6 V vs. reversible hydrogen electrode (RHE). MesoITO|PSII reaches its saturation photocurrent at 0.84 V vs. RHE, whereas nanoWO(3)|TiO(2)NiO(x) requires more than 1.34 V vs. RHE. This suggests that mesoITO|PSII suffers from fewer limitations from charge recombination and slow water oxidation catalysis than the synthetic electrode. MesoITO|PSII displays a higher 'per active' site activity, but is less photostable and displays a much lower photocurrent per geometrical surface area and incident photon to current conversion efficiency (IPCE) than nanoWO(3)|TiO(2)|NiO(x_. PMID:25434986

  14. 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.

  15. 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.

  16. A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism

    PubMed Central

    2011-01-01

    Background FeFe-hydrogenases are the most active class of H2-producing enzymes known in nature and may have important applications in clean H2 energy production. Many potential uses are currently complicated by a crucial weakness: the active sites of all known FeFe-hydrogenases are irreversibly inactivated by O2. Results We have developed a synthetic metabolic pathway in E. coli that links FeFe-hydrogenase activity to the production of the essential amino acid cysteine. Our design includes a complementary host strain whose endogenous redox pool is insulated from the synthetic metabolic pathway. Host viability on a selective medium requires hydrogenase expression, and moderate O2 levels eliminate growth. This pathway forms the basis for a genetic selection for O2 tolerance. Genetically selected hydrogenases did not show improved stability in O2 and in many cases had lost H2 production activity. The isolated mutations cluster significantly on charged surface residues, suggesting the evolution of binding surfaces that may accelerate hydrogenase electron transfer. Conclusions Rational design can optimize a fully heterologous three-component pathway to provide an essential metabolic flux while remaining insulated from the endogenous redox pool. We have developed a number of convenient in vivo assays to aid in the engineering of synthetic H2 metabolism. Our results also indicate a H2-independent redox activity in three different FeFe-hydrogenases, with implications for the future directed evolution of H2-activating catalysts. PMID:21615937

  17. Canister Model, Systems Analysis

    Energy Science and Technology Software Center (ESTSC)

    1993-09-29

    This packges provides a computer simulation of a systems model for packaging nuclear waste and spent nuclear fuel in canisters. The canister model calculates overall programmatic cost, number of canisters, and fuel and waste inventories for the Idaho Chemical Processing Plant (other initial conditions can be entered).

  18. 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

  19. 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. PMID:24156739

  20. A Preclinical Evaluation of Alternative Synthetic Biomaterials for Fascial Defect Repair Using a Rat Abdominal Hernia Model

    PubMed Central

    Ulrich, Daniela; Edwards, Sharon L.; White, Jacinta F.; Supit, Tommy; Ramshaw, John A. M.; Lo, Camden; Rosamilia, Anna; Werkmeister, Jerome A.; Gargett, Caroline E.

    2012-01-01

    Introduction Fascial defects are a common problem in the abdominal wall and in the vagina leading to hernia or pelvic organ prolapse that requires mesh enhancement to reduce operation failure. However, the long-term outcome of synthetic mesh surgery may be unsatisfactory due to post-surgical complications. We hypothesized that mesh fabricated from alternative synthetic polymers may evoke a different tissue response, and provide more appropriate mechanical properties for hernia repair. Our aim was to compare the in vivo biocompatibility of new synthetic meshes with a commercial mesh. Methods We have fabricated 3 new warp-knitted synthetic meshes from different polymers with different tensile properties polyetheretherketone (PEEK), polyamide (PA) and a composite, gelatin coated PA (PA+G). The rat abdominal hernia model was used to implant the meshes (25×35 mm, n = 24/ group). After 7, 30, 60, 90 days tissues were explanted for immunohistochemical assessment of foreign body reaction and tissue integration, using CD31, CD45, CD68, alpha-SMA antibodies. The images were analysed using an image analysis software program. Biomechanical properties were uniaxially evaluated using an Instron Tensile® Tester. Results This study showed that the new meshes induced complex differences in the type of foreign body reaction over the time course of implantation. The PA, and particularly the composite PA+G meshes, evoked a milder early inflammatory response, and macrophages were apparent throughout the time course. Our meshes led to better tissue integration and new collagen deposition, particularly with the PA+G meshes, as well as greater and sustained neovascularisation compared with the PP meshes. Conclusion PA, PA+G and PEEK appear to be well tolerated and are biocompatible, evoking an overlapping and different host tissue response with time that might convey mechanical variations in the healing tissue. These new meshes comprising different polymers may provide an

  1. 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. PMID:19717233

  2. The validity of the one-dimensional fluid model of electrical breakdown in synthetic air at low pressure

    NASA Astrophysics Data System (ADS)

    Jovanović, A. P.; Stankov, M. N.; Marković, V. Lj.; Stamenković, S. N.

    2013-12-01

    In this letter the validity of the fluid model used to simulate the electrical breakdown in air at low pressure is discussed. The new method for the determination of the ionization source term for the mixed gases is proposed. Paschen's curve obtained by the fluid model is compared to the available experimental data. The electron and ions density profiles calculated by the fluid model are presented. Based on Ohm's law, the current and voltage waveforms are calculated and compared to the ones measured by the oscilloscope in the synthetic-air filled tube with stainless-steel electrodes. It is shown that the one-dimensional fluid model can be used for modeling the electrical breakdown at pd values higher than Paschen's minimum and to determine stationary values of electron and ions densities.

  3. Time-domain inflow boundary condition for turbulence-airfoil interaction noise prediction using synthetic turbulence modeling

    NASA Astrophysics Data System (ADS)

    Kim, Daehwan; Heo, Seung; Cheong, Cheolung

    2015-03-01

    The present paper deals with development of the synthetic turbulence inflow boundary condition (STIBC) to predict inflow broadband noise generated by interaction between turbulence and an airfoil/a cascade of airfoils in the time-domain. The STIBC is derived by combining inflow boundary conditions that have been successfully applied in external and internal computational aeroacoustics (CAA) simulations with a synthetic turbulence model. The random particle mesh (RPM) method based on a digital filter is used as the synthetic turbulence model. Gaussian and Liepmann spectra are used to define the filters for turbulence energy spectra. The linearized Euler equations are used as governing equations to evaluate the suitability of the STIBC in time-domain CAA simulations. First, the velocity correlations and energy spectra of the synthesized turbulent velocities are compared with analytic ones. The comparison results reveal that the STIBC can reproduce a turbulent velocity field satisfying the required statistical characteristics of turbulence. Particularly, the Liepmann filter representing a non-Gaussian filter is shown to be effectively described by superposing the Gaussian filters. Each Gaussian filter has a different turbulent kinetic energy and integral length scale. Second, two inflow noise problems are numerically solved using the STIBC: the turbulence-airfoil interaction and the turbulence-a cascade of airfoils interaction problems. The power spectrum of noise due to an isolated flat plate airfoil interacting with incident turbulence is predicted, and its result is successfully validated against Amiet's analytic model (Amiet, 1975) [4]. The prediction results of the upstream and downstream acoustic power spectra from a cascade of flat plates are then compared with Cheong's analytic model (Cheong et al., 2006) [30]. These comparisons are also in excellent agreement. On the basis of these illustrative computation results, the STIBC is expected to be applied to

  4. Detection of partial melt in continental collision zones using different magnetotelluric tensor relationships: Results from synthetic models and real data

    NASA Astrophysics Data System (ADS)

    LLovet, Joan Campanya i.; Ledo, Juanjo; Jones, Alan G.; Queralt, Pilar; Marcuello, Alex; Liesa, Montserrat; Antón Muñoz, Josep

    2014-05-01

    Three magnetotelluric (MT) tensor relationships - the single-station MT impedance tensor (Z), the single-station vertical geomagnetic transfer function (GTF) and the multiple-station horizontal geomagnetic transfer function (HGTF) - were investigated for their effectiveness in detecting the presence of partial melt in continental collision zones. Realistic synthetic models, based on prior field studies, were used to characterize the sensitivity of each tensor relationship constraining the presence of partial melt at lower-crustal and upper-mantle depths. From the MT response of the synthetic models, each type of data was inverted separately and jointly with the others, thus determining the properties and advantages of each when modeling the subsurface. Non-linear sensitivity tests were carried out to determine the resolution that can be expected in constraining electrical resistivity anomalies associated with the presence of partial melt. Results obtained show which configuration of the HGTF is more sensitive to partial melt. The analysis of partial melt sensitivity was also performed using real data from a MT survey carried out in the Pyrenees. The data comprise a total of 82 broadband MT sites and 29 long period MT sites distributed along four profiles across the Pyrenean mountain range between the Atlantic Ocean and the Mediterranean Sea. Using the results from the synthetic models, real MT data in the Eastern Pyrenees were used to constrain if the partial melting area associated with the Iberian subducted lower crust observed below the Western, the West-central and the Central Pyrenees continues to the East. A non-linear sensitivity test was undertaken to determine the boundary to the east of this geoelectrical anomaly associated with partial melt.

  5. 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.

  6. Using Two-Component Systems and other Bacterial Regulatory Factors for the Fabrication of Synthetic Genetic Devices

    PubMed Central

    Ninfa, Alexander J.; Selinsky, Stephen; Perry, Nicolas; Atkins, Stephen; Song, Qi Xiu; Mayo, Avi; Arps, David; Woolf, Peter; Atkinson, Mariette R.

    2011-01-01

    Synthetic biology is an emerging field in which the procedures and methods of engineering are extended to living organisms, with the long-term goal of producing novel cell types that aid human society. For example, engineered cell types may sense a particular environment and express gene products that serve as an indicator of that environment, or effect a change in that environment. While we are still some way from producing cells with significant practical applications, the immediate goals of synthetic biology are to develop a quantitative understanding of genetic circuitry and its interactions with the environment and to develop modular genetic circuitry derived from standard, interoperable, parts, that can be introduced into cells and results in some desired input/output function. Using an engineering approach, the input/output function of each modular element is characterized independently, providing a toolkit of elements that can be linked in different ways to provide various circuit topologies. The principle of modularity, yet largely unproven for biological systems, suggests that modules will function appropriately based on their design characteristics when combined into larger synthetic genetic devices. This modularity concept is similar to that used to develop large computer programs, where inpendent software modules can be independently developed and later combined into the final program. PMID:17628156

  7. A fast and inexpensive procedure for the isolation of synthetic cannabinoids from 'Spice' products using a flash chromatography system.

    PubMed

    Moosmann, Bjoern; Kneisel, Stefan; Wohlfarth, Ariane; Brecht, Volker; Auwärter, Volker

    2013-05-01

    In the age of the Internet, the variety of drugs offered online is constantly increasing, and new drugs emerge every month. One group of drugs showing such an enormous increase is that of synthetic cannabinoids. Since their first identification in 'herbal mixtures', new structural modifications continue to appear on the market. In order to keep up with this process, toxicological screening methods need to be up to date. This can become extremely difficult if no reference material is available. In this article, a fast and effective way to extract and purify synthetic cannabinoids from 'herbal mixtures' is presented. This method opens a new opportunity for a timely reaction by obtaining reference material straight out of the 'herbal mixtures' ordered via the Internet. Isolation was carried out on a flash chromatography system with gradient elution on a C18 column using methanol and 0.55 % formic acid as mobile phases. The obtained purity of all compounds exceeded 99 %. In addition to the isolation of single compounds, the method proved to be suitable for the separation of various synthetic cannabinoids in one mixture, including the diastereomers cis- and trans-CP-47,497-C8. This approach for obtaining pure standards of new drugs proved to be effective, inexpensive and much quicker than waiting for the substances to be commercially available as reference material. PMID:23064708

  8. 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.

  9. 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

  10. 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

  11. Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models.

    PubMed

    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

  12. Test of simultaneous synthetic DNA tracer injections for the estimation of the englacial and subglacial drainage system structure of Storglaciären, northern Sweden

    NASA Astrophysics Data System (ADS)

    Dahlke, H. E.; Leung, S.; Lyon, S. W.; Sharma, A. N.; Walter, M. T.; Williamson, A.

    2013-12-01

    Storglaciären glacier, located in the sub-arctic Tarfala catchment, in northern Sweden is one of the world's longest continuously monitored glaciers which provides a unique research platform for the long-term assessment of glacier and ice sheet processes. For example, small mountain glacier hydrological knowledge of the subglacial water distribution at the ice-bed interface has been applied to ice sheets to predict basal sliding processes. Basal sliding promoted by hydraulic jacking is an important glacial-velocity control that is dependent on the subglacial flow pathways' morphology. Thus, understanding subglacial water distribution and drainage system structure and morphology is crucial for modeling ice masses' flow. In order to estimate subglacial drainage system structure and morphology dye tracing experiments are widely employed. Tracer experiments provide quantitative parameters for any input location including tracer transit velocity, dispersivity, recovery and storage. However, spatial data coverage is limited by the finite number of tracers available for simultaneous tracing. In the presented study we test the use of synthetic DNA tracers for the assessment of the englacial and subglacial drainage system structure of Storglaciären. The synthetic DNA tracer is composed of polylactic acid (PLA) microspheres into which short strands of synthetic DNA and paramagnetic iron oxide nanoparticles are incorporated (Sharma et al., 2012, Environmental Science & Technology). Because the DNA sequences can be randomly combined the synthetic DNA tracer provides an enormous number of unique tracers (approximately 1.61 x 1060). Thus, these synthetic tracers have the advantage that multiple (>10) experiments can be conducted simultaneously, allowing a greater information gain within a shorter measurement period. Quantities of a certain DNA strand can be detected using biotechnology tools such as polymerase chain reaction (PCR) and quantitative PCR (qPCR). During the 2013

  13. Critical Infrastructure Modeling System

    Energy Science and Technology Software Center (ESTSC)

    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 ofmore » 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.« less

  14. 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.

  15. Using state-of-the-art hydrodynamic models to generate synthetic data cubes for imaging spectral sensing applications

    NASA Astrophysics Data System (ADS)

    Kao, Jim; Smith, William S.; Smith, Barham W.; Borel, Christoph C.

    2002-01-01

    An airborne IR hyperspectral imaging sensor based on the Fourier transform spectrometer technique has been used for studying atmospheric gaseous plumes under the auspice of U.S. Department of Energy. Model generated synthetic data of spectral intensity associated withe the plume and the surface background is useful in terms of performing trade studies as well as testing new algorithms. To cope with the highly turbulent and transient atmospheric boundary layer where plume emissions and evolution are embedded, we have used a high-resolution (at the scale of 1 m) time-dependent Napier-Stoke atmospheric hydrodynamic code, HIGRAD, to replace the Gaussian/multi-fractal approach in the original package of the Los Alamos End-to-End Modeling of Imaging Spectral Sensing Applications (EMISSA). The output from HIGRAD is then used for calculations of radiance reaching the sensor through the Fast Atmospheric Signature Code (FASCODE) with a spectral resolution of 1 cm-1 or less. The modeled plume structure in concentrations and associated plume images in radiance bear great resemblance to the contrast model for its capability in quantifying the column densities of chemical species. The synthetic data produced through our approach proves to be effective in evaluation our understanding of the thermal infrared imaging process.

  16. 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. PMID:19847349

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. Modeling Sustainable Food Systems.

    PubMed

    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. PMID:26932834

  2. 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.

  3. Hybrid PET/CT for noninvasive pharmacokinetic evaluation of dynamic PolyConjugates, a synthetic siRNA delivery system.

    PubMed

    Mudd, Sarah R; Trubetskoy, Vladimir S; Blokhin, Andrei V; Weichert, Jamey P; Wolff, Jon A

    2010-07-21

    Positron emission tomography/computed tomography (PET/CT) hybrid imaging can be used to gain insights into a synthetic siRNA delivery system targeted to the liver. Either siRNA or the delivery vehicle was labeled with (64)Cu via 1, 4, 7, 10- tetraazacyclododecane- 1, 4, 7, 10- tetraacetic acid (DOTA) chelation. This study confirmed that the siRNA delivery system was successfully targeted to the liver. Incorporation of the siRNA into the delivery system protected the siRNA from renal filtration long enough so that the siRNA could be delivered to the liver. PET/CT imaging was important for confirming biodistribution and for determining differences in the distribution of labeled siRNA, siRNA incorporated into the delivery system, and the delivery system without siRNA. PMID:20552976

  4. 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%).

  5. The mechanisms of subharmonic tone generation in a synthetic larynx model.

    PubMed

    Kniesburges, Stefan; Lodermeyer, Alexander; Becker, Stefan; Traxdorf, Maximilian; Döllinger, Michael

    2016-06-01

    The sound spectra obtained in a synthetic larynx exhibited subharmonic tones that are characteristic for diplophonia. Although the generation of subharmonics is commonly associated with asymmetrically oscillating vocal folds, the synthetic elastic vocal folds showed symmetrical oscillations. The amplitudes of the subharmonics decreased with an increasing lateral diameter of the supraglottal channel, which indicates a strong dependence of the supraglottal boundary conditions. Investigations of the supraglottal flow field revealed small cycle-to-cycle variations of the static pressure in the region of the pulsatile glottal jet as the origin of the first subharmonic tone. It is located at half the fundamental frequency of the vocal fold oscillation. A principle component analysis of the supraglottal flow field with the fully developed glottal jet revealed a large recirculation area in the second spatial eigenvector which deflected the glottal jet slightly in a perpendicular direction of the jet axis. The rotation direction of the recirculation area changed with different oscillation cycles between clockwise and counterclockwise. As both directions were uniformly distributed across all acquired oscillation cycles, a cycle-wise change can be assumed. It is concluded that acoustic subharmonics are generated by small fluctuations of the glottal jet location favored by small lateral diameters of the supraglottal channel. PMID:27369142

  6. 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

  7. Optical systems integrated modeling

    NASA Technical Reports Server (NTRS)

    Shannon, Robert R.; Laskin, Robert A.; Brewer, SI; Burrows, Chris; Epps, Harlan; Illingworth, Garth; Korsch, Dietrich; Levine, B. Martin; Mahajan, Vini; Rimmer, Chuck

    1992-01-01

    An integrated modeling capability that provides the tools by which entire optical systems and instruments can be simulated and optimized is a key technology development, applicable to all mission classes, especially astrophysics. Many of the future missions require optical systems that are physically much larger than anything flown before and yet must retain the characteristic sub-micron diffraction limited wavefront accuracy of their smaller precursors. It is no longer feasible to follow the path of 'cut and test' development; the sheer scale of these systems precludes many of the older techniques that rely upon ground evaluation of full size engineering units. The ability to accurately model (by computer) and optimize the entire flight system's integrated structural, thermal, and dynamic characteristics is essential. Two distinct integrated modeling capabilities are required. These are an initial design capability and a detailed design and optimization system. The content of an initial design package is shown. It would be a modular, workstation based code which allows preliminary integrated system analysis and trade studies to be carried out quickly by a single engineer or a small design team. A simple concept for a detailed design and optimization system is shown. This is a linkage of interface architecture that allows efficient interchange of information between existing large specialized optical, control, thermal, and structural design codes. The computing environment would be a network of large mainframe machines and its users would be project level design teams. More advanced concepts for detailed design systems would support interaction between modules and automated optimization of the entire system. Technology assessment and development plans for integrated package for initial design, interface development for detailed optimization, validation, and modeling research are presented.

  8. 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.

  9. 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.

  10. 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.

  11. A synthetic system for expression of components of a bacterial microcompartment

    PubMed Central

    Kelly, Ciarán L.; Binny, Rachelle; Christodoulides, Natasha; Gibson, David; Johansson, Emelie; Kozyrska, Katarzyna; Lado, Lucia Licandro; MacCallum, Jane; Montague, Rachel; Ortmann, Brian; Owen, Richard; Coulthurst, Sarah J.; Dupuy, Lionel; Prescott, Alan R.; Palmer, Tracy

    2013-01-01

    In general, prokaryotes are considered to be single-celled organisms that lack internal membrane-bound organelles. However, many bacteria produce proteinaceous microcompartments that serve a similar purpose, i.e. to concentrate specific enzymic reactions together or to shield the wider cytoplasm from toxic metabolic intermediates. In this paper, a synthetic operon encoding the key structural components of a microcompartment was designed based on the genes for the Salmonella propanediol utilization (Pdu) microcompartment. The genes chosen included pduA, -B, -J, -K, -N, -T and -U, and each was shown to produce protein in an Escherichia coli chassis. In parallel, a set of compatible vectors designed to express non-native cargo proteins was also designed and tested. Engineered hexa-His tags allowed isolation of the components of the microcompartments together with co-expressed, untagged, cargo proteins. Finally, an in vivo protease accessibility assay suggested that a PduD–GFP fusion could be protected from proteolysis when co-expressed with the synthetic microcompartment operon. This work gives encouragement that it may be possible to harness the genes encoding a non-native microcompartment for future biotechnological applications. PMID:24014666

  12. A synthetic system for expression of components of a bacterial microcompartment.

    PubMed

    Sargent, Frank; Davidson, Fordyce A; Kelly, Ciarán L; Binny, Rachelle; Christodoulides, Natasha; Gibson, David; Johansson, Emelie; Kozyrska, Katarzyna; Lado, Lucia Licandro; Maccallum, Jane; Montague, Rachel; Ortmann, Brian; Owen, Richard; Coulthurst, Sarah J; Dupuy, Lionel; Prescott, Alan R; Palmer, Tracy

    2013-11-01

    In general, prokaryotes are considered to be single-celled organisms that lack internal membrane-bound organelles. However, many bacteria produce proteinaceous microcompartments that serve a similar purpose, i.e. to concentrate specific enzymic reactions together or to shield the wider cytoplasm from toxic metabolic intermediates. In this paper, a synthetic operon encoding the key structural components of a microcompartment was designed based on the genes for the Salmonella propanediol utilization (Pdu) microcompartment. The genes chosen included pduA, -B, -J, -K, -N, -T and -U, and each was shown to produce protein in an Escherichia coli chassis. In parallel, a set of compatible vectors designed to express non-native cargo proteins was also designed and tested. Engineered hexa-His tags allowed isolation of the components of the microcompartments together with co-expressed, untagged, cargo proteins. Finally, an in vivo protease accessibility assay suggested that a PduD-GFP fusion could be protected from proteolysis when co-expressed with the synthetic microcompartment operon. This work gives encouragement that it may be possible to harness the genes encoding a non-native microcompartment for future biotechnological applications. PMID:24014666

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. A game-of-life like simulator for design-oriented modeling of BioBricks in synthetic biology.

    PubMed

    Madec, Morgan; Gendrault, Yves; Lallement, Christophe; Haiech, Jacques

    2012-01-01

    This paper deals with the development of a new simulator that will be very helpful to establish new accurate and predictive design-oriented models for the BioBricks used in synthetic biology. The simulator uses the principle of the game-of-life: molecules can move on a grid and, at every iteration, binding and dissociation rules are applied when two molecules are on same node. The principle is elementary but it can highlight interesting biological phenomenon. Those can be modeled by mathematical equations to achieve design-oriented models. In this case, the simulator also helps to make to link between mathematical parameters and the microscopic parameters. A first version of the software has been implemented in MATLAB. It permits to retrieve very interesting results, such as the Hill's equation and the properties of Hill's coefficient. PMID:23367165

  20. 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. PMID:25043796

  1. 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.

  2. 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). PMID:23823552

  3. 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

  4. Anisotropic organization and microscopic manipulation of self-assembling synthetic porphyrin microrods that mimic chlorosomes: bacterial light-harvesting systems.

    PubMed

    Chappaz-Gillot, Cyril; Marek, Peter L; Blaive, Bruno J; Canard, Gabriel; Bürck, Jochen; Garab, Gyozo; Hahn, Horst; Jávorfi, Tamás; Kelemen, Loránd; Krupke, Ralph; Mössinger, Dennis; Ormos, Pál; Reddy, Chilla Malla; Roussel, Christian; Steinbach, Gábor; Szabó, Milán; Ulrich, Anne S; Vanthuyne, Nicolas; Vijayaraghavan, Aravind; Zupcanova, Anita; Balaban, Teodor Silviu

    2012-01-18

    Being able to control in time and space the positioning, orientation, movement, and sense of rotation of nano- to microscale objects is currently an active research area in nanoscience, having diverse nanotechnological applications. In this paper, we demonstrate unprecedented control and maneuvering of rod-shaped or tubular nanostructures with high aspect ratios which are formed by self-assembling synthetic porphyrins. The self-assembly algorithm, encoded by appended chemical-recognition groups on the periphery of these porphyrins, is the same as the one operating for chlorosomal bacteriochlorophylls (BChl's). Chlorosomes, rod-shaped organelles with relatively long-range molecular order, are the most efficient naturally occurring light-harvesting systems. They are used by green photosynthetic bacteria to trap visible and infrared light of minute intensities even at great depths, e.g., 100 m below water surface or in volcanic vents in the absence of solar radiation. In contrast to most other natural light-harvesting systems, the chlorosomal antennae are devoid of a protein scaffold to orient the BChl's; thus, they are an attractive goal for mimicry by synthetic chemists, who are able to engineer more robust chromophores to self-assemble. Functional devices with environmentally friendly chromophores-which should be able to act as photosensitizers within hybrid solar cells, leading to high photon-to-current conversion efficiencies even under low illumination conditions-have yet to be fabricated. The orderly manner in which the BChl's and their synthetic counterparts self-assemble imparts strong diamagnetic and optical anisotropies and flow/shear characteristics to their nanostructured assemblies, allowing them to be manipulated by electrical, magnetic, or tribomechanical forces. PMID:22148684

  5. Electronic Education System Model.

    ERIC Educational Resources Information Center

    Cloete, Elsabe

    2001-01-01

    Discusses electronic learning efforts and problems in implementing computers in schools. Defines and describes an electronic educational system model that was developed to assist the designers of different electronic learning settings to plan and successfully implement a specific learning situation, with the focus on the individual requirements of…

  6. 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.

  7. Synthetic Jets

    NASA Technical Reports Server (NTRS)

    Milanovic, Ivana M.

    2003-01-01

    Current investigation of synthetic jets and synthetic jets in cross-flow examined the effects of orifice geometry and dimensions, momentum-flux ratio, cluster of orifices, pitch and yaw angles as well as streamwise development of the flow field. This comprehensive study provided much needed experimental information related to the various control strategies. The results of the current investigation on isolated and clustered synthetic jets with and without cross-flow will be further analyzed and documented in detail. Presentations at national conferences and publication of peer- reviewed journal articles are also expected. Projected publications will present both the mean and turbulent properties of the flow field, comparisons made with the data available in an open literature, as well as recommendations for the future work.

  8. Synthetic Catalysts for CO2 Storage: Catalytic Improvement of Solvent Capture Systems

    SciTech Connect

    2010-08-15

    IMPACCT Project: LLNL is designing a process to pull CO2 out of the exhaust gas of coal-fired power plants so it can be transported, stored, or utilized elsewhere. Human lungs rely on an enzyme known as carbonic anhydrase to help separate CO2 from our blood and tissue as part of the normal breathing process. LLNL is designing a synthetic catalyst with the same function as this enzyme. The catalyst can be used to quickly capture CO2 from coal exhaust, just as the natural enzyme does in our lungs. LLNL is also developing a method of encapsulating chemical solvents in permeable microspheres that will greatly increase the speed of binding of CO2. The goal of the project is an industry-ready chemical vehicle that can withstand the harsh environments found in exhaust gas and enable new, simple process designs requiring less capital investment.

  9. The antioxidative response system in Glycine max (L.) Merr. exposed to Deltamethrin, a synthetic pyrethroid insecticide.

    PubMed

    Bashir, Fozia; Mahmooduzzafar; Siddiqi, T O; Iqbal, Muhammad

    2007-05-01

    Forty-five-day-old plants of Glycine max (soybean) were exposed to several Deltamethrin (synthetic pyrethroid insecticide) concentrations (0.00%, 0.05%, 0.10%, 0.15% and 0.20%) through foliar spray in the field conditions. In the treated plants, as observed at the pre-flowering (10 DAT), flowering (45 DAT) and post-flowering (70 DAT) stages, lipid peroxidation, proline content and total glutathione content increased, whereas the total ascorbate content decreased, as compared with the control. Among the enzymatic antioxidants, activity of superoxide dismutase, ascorbate peroxidase and glutathione reductase increased significantly whereas that of catalase declined markedly in relation to increasing concentration of Deltamethrin applied. The changes observed were dose-dependent, showing a strong correlation with the degree of treatment. PMID:17055627

  10. 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. PMID:23389172

  11. Modelling resonant planetary systems

    NASA Astrophysics Data System (ADS)

    Emel'yanenko, V.

    2012-09-01

    Many discovered multi-planet systems are in meanmotion resonances. The aim of this work is to study dynamical processes leading to the formation of resonant configurations on the basis of a unified model described earlier [1]. The model includes gravitational interactions of planets and migration of planets due to the presence of a gas disc. For the observed systems 24 Sex, HD 37124, HD 73526, HD 82943, HD 128311, HD 160691, Kepler 9, NN Ser with planets moving in the 2:1 resonance, it is shown that the capture in this resonance occurs at very wide ranges of parameters of both type I and type II migration. Conditions of migration leading to the formation of the resonant systems HD 45364 и HD 200964 (3:2 and 4:3, respectively) are obtained. Formation scenarios are studied for the systems HD 102272, HD 108874, HD 181433, HD 202206 with planets in high order resonances. We discuss also how gravitational interactions of planets and planetesimal discs lead to the breakup of resonant configurations and the formation of systems similar to the 47 UMa system.

  12. Numerical modeling on the source parameter scaling relations and synthetic surface deformation of episodic slow slip events in subduction zones

    NASA Astrophysics Data System (ADS)

    Liu, Y.

    2013-12-01

    moment-duration relation may be dependent on friction parameters and pore pressure condition. We also compute the resulted surface deformation (synthetic GPS time series) due to the spatiotemporal evolution of slip velocity on the subduction fault. Preliminary modeling results show that the along-strike segmentation in Cascadia SSEs may result from the slip velocity variation as SSEs propagate along the trench. Comparison between the spectra of modeled synthetic displacement and the Plate Boundary Observatory GPS time series along Cascadia will be conducted, to determine the detection threshold of the synthetic signal.

  13. 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.

  14. Development of a Synthetic Oxytetracycline-Inducible Expression System for Streptomycetes Using de Novo Characterized Genetic Parts.

    PubMed

    Wang, Weishan; Yang, Tongjian; Li, Yihong; Li, Shanshan; Yin, Shouliang; Styles, Kathryn; Corre, Christophe; Yang, Keqian

    2016-07-15

    Precise control of gene expression using exogenous factors is of great significance. To develop ideal inducible expression systems for streptomycetes, new genetic parts, oxytetracycline responsive repressor OtrR, operator otrO, and promoter otrBp from Streptomyces rimosus, were selected de novo and characterized in vivo and in vitro. OtrR showed strong affinity to otrO (KD = 1.7 × 10(-10) M) and oxytetracycline induced dissociation of the OtrR/DNA complex in a concentration-dependent manner. On the basis of these genetic parts, a synthetic inducible expression system Potr* was optimized. Induction of Potr* with 0.01-4 μM of oxytetracycline triggered a wide-range expression level of gfp reporter gene in different Streptomyces species. Benchmarking Potr* against the widely used constitutive promoters ermE* and kasOp* revealed greatly enhanced levels of expression when Potr* was fully induced. Finally, Potr* was used as a tool to activate and optimize the expression of the silent jadomycin biosynthetic gene cluster in Streptomyces venezuelae. Altogether, the synthetic Potr* presents a new versatile tool for fine-tuning gene expression in streptomycetes. PMID:27100123

  15. 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. PMID:26705687

  16. 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.

  17. Tuning the dials of Synthetic Biology

    PubMed Central

    Arpino, James A. J.; Hancock, Edward J.; Anderson, James; Barahona, Mauricio; Stan, Guy-Bart V.; Polizzi, Karen

    2013-01-01

    Synthetic Biology is the ‘Engineering of Biology’ – it aims to use a forward-engineering design cycle based on specifications, modelling, analysis, experimental implementation, testing and validation to modify natural or design new, synthetic biology systems so that they behave in a predictable fashion. Motivated by the need for truly plug-and-play synthetic biological components, we present a comprehensive review of ways in which the various parts of a biological system can be modified systematically. In particular, we review the list of ‘dials’ that are available to the designer and discuss how they can be modelled, tuned and implemented. The dials are categorized according to whether they operate at the global, transcriptional, translational or post-translational level and the resolution that they operate at. We end this review with a discussion on the relative advantages and disadvantages of some dials over others. PMID:23704788

  18. 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

  19. 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.

  20. An In Vitro Model for Oral Mixed Biofilms of Candida albicans and Streptococcus gordonii in Synthetic Saliva

    PubMed Central

    Montelongo-Jauregui, Daniel; Srinivasan, Anand; Ramasubramanian, Anand K.; Lopez-Ribot, Jose L.

    2016-01-01

    As a member of the normal human oral microbiota, the fungus Candida albicans is often found in association with Streptococcus gordonii, a member of dental plaque forming bacteria. Evidence suggests that S. gordonii serves as a facilitator of C. albicans adherence to dental tissues, which represents a clinically relevant problem, particularly for immunocompromised individuals that could subsequently develop fungal infections. In this study we describe the development of a relatively simple and economical in vitro model that allows for the growth of mixed bacterial/fungal biofilms in 96-well microtiter plates. We have applied this method to test and compare the growth characteristics of single and dual species biofilms in traditional microbiological media versus a synthetic saliva medium (basal medium mucin, BMM) that more closely resembles physiological conditions within the oral cavity. Results indicated a synergistic effect for the formation of biofilms when both microorganisms were seeded together under all conditions tested. The structural and architectural features of the resulting biofilms were further characterized using scanning electron microscopy and confocal scanning laser microscopy. We also performed drug susceptibility assays against single and mixed species biofilms using commonly used antifungals and antibacterial antibiotics, both in monotherapy and in combination therapy, for a direct comparison of resistance against antimicrobial treatment. As expected, mixed species biofilms displayed higher levels of resistance to antimicrobial treatment at every dose tested in both traditional media and BMM synthetic saliva, as compared to single-species biofilms. PMID:27242712

  1. 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.

  2. 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.

  3. 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.

  4. Synthetic earthquake catalogs simulating seismic activity in the Corinth Gulf, Greece, fault system

    NASA Astrophysics Data System (ADS)

    Console, Rodolfo; Carluccio, Roberto; Papadimitriou, Eleftheria; Karakostas, Vassilis

    2015-01-01

    The characteristic earthquake hypothesis is the basis of time-dependent modeling of earthquake recurrence on major faults. 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 (CGFS), for which documents about strong earthquakes exist for at least 2000 years, although they can be considered complete for M ≥ 6.0 only for the latest 300 years, during which only few characteristic earthquakes are reported for individual 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) an average slip rate released by earthquakes for every single segment in the investigated fault system, (2) heuristic procedures for rupture growth and stop, leading to a self-organized earthquake magnitude distribution, (3) the interaction between earthquake sources, and (4) the effect of minor earthquakes in redistributing stress. The application of our simulation algorithm to the CGFS 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.

  5. On the Prediction of Tropical Cyclones over the Indian Region Using a Synthetic Vortex Scheme in a Mesoscale Model

    NASA Astrophysics Data System (ADS)

    Sandeep, S.; Chandrasekar, A.; Dash, S. K.

    2007-09-01

    The tropical cyclones form over the oceanic regions where conventional meteorological observations are not available. This contributes to a poor initial analysis of the cyclonic vortex and hence inadequate forecast. One way of overcoming the above problem is to modify the initial analysis by replacing the weak and ill-defined vortex in the initial analysis with a synthetic vortex having the correct size and intensity at the correct location. In this study we are investigating the effect of inclusion of a synthetic vortex based on Rankine as well as on Holland wind profiles, using NCAR-AFWA bogussing scheme for the prediction of four tropical cyclones, which formed over the Bay of Bengal during November 2002 and 2005, December 2005 and over the Arabian Sea during May 2004, using the MM5 model. Two numerical experiments are designed in this study for each of the above four cyclones. In the first experiment the model is integrated with a synthetic vortex based on Rankine wind profile while in the second experiment we utilize the Holland wind profile. For the November 2002 cyclone, in both the experiments the model is integrated from 10 November 2002 18 UTC to 12 November, 2002 12 UTC with the synthetic vortex inserted at the initial time. The results of the study for the November 2002 cyclone show that the model simulation with the Holland vortex has produced a stronger cyclone in terms of minimum sea-level pressure and maximum wind speed. Also, the results for the November 2002 cyclone with the Holland vortex showed a better longitudinal height section of the horizontal wind speed across the center of the cyclone. The track error of the cyclone for the November 2002 cyclone is less in the model simulation with the Holland vortex at the initial time and at 24 hours of forecast. The results for the November 2002 cyclone with the Rankine vortex showed greater vertical wind speed as compared to the Holland vortex. However, for the November 2002 cyclone there were no

  6. Efficient Enzymatic Preparation of (13) N-Labelled Amino Acids: Towards Multipurpose Synthetic Systems.

    PubMed

    da Silva, Eunice S; Gómez-Vallejo, Vanessa; Baz, Zuriñe; Llop, Jordi; López-Gallego, Fernando

    2016-09-12

    Nitrogen-13 can be efficiently produced in biomedical cyclotrons in different chemical forms, and its stable isotopes are present in the majority of biologically active molecules. Hence, it may constitute a convenient alternative to Fluorine-18 and Carbon-11 for the preparation of positron-emitter-labelled radiotracers; however, its short half-life demands for the development of simple, fast, and efficient synthetic processes. Herein, we report the one-pot, enzymatic and non-carrier-added synthesis of the (13) N-labelled amino acids l-[(13) N]alanine, [(13) N]glycine, and l-[(13) N]serine by using l-alanine dehydrogenase from Bacillus subtilis, an enzyme that catalyses the reductive amination of α-keto acids by using nicotinamide adenine dinucleotide (NADH) as the redox cofactor and ammonia as the amine source. The integration of both l-alanine dehydrogenase and formate dehydrogenase from Candida boidinii in the same reaction vessel to facilitate the in situ regeneration of NADH during the radiochemical synthesis of the amino acids allowed a 50-fold decrease in the concentration of the cofactor without compromising reaction yields. After optimization of the experimental conditions, radiochemical yields were sufficient to carry out in vivo imaging studies in small rodents. PMID:27515007

  7. Leachability of chemical constituents in soil–plant systems irrigated with synthetic graywater.

    PubMed

    Negahban-Azar, Masoud; Sharvelle, Sybil E; Qian, Yaling; Shogbon, Alicia

    2013-04-01

    Over recent years, reuse of graywater for irrigation has become increasingly widespread internationally. While this practice is rapidly growing, there remain unanswered questions with respect to impacts to environmental quality and human health. The objective of this research was to determine the leachability of graywater constituents after applied to soil through a set of controlled greenhouse experiments. Four plant species including bermudagrass, tall fescue, Meyer Lemon and Emerald Gaiety Euonymus were included in the study. Three replicate columns for each species were set up and irrigated either with synthetic graywater or potable water for a 17 month duration. Leachate quality was assessed for dissolved organic carbon, nitrate, ammonium, total phosphorous, boron, sodium adsorption ratio, conductivity, surfactants, and total dissolved solids. The same constituents and also organic matter were measured in soil samples collected at the end of experiments. Phosphorus did not leach through the 50 cm deep soil columns. Salts, including boron, showed potential to leach through graywater irrigated soil. A portion of the applied nitrogen was assimilated by plants, but leaching of nitrogen was still observed as documented by statistically higher nitrogen in leachate collected from graywater-irrigated columns compared to potable water-irrigated columns (P ≤ 0.05). A low percentage of surfactants added to columns leached through (7 ± 6% on average) and a mass balance on surfactant parent compounds showed that 92–96% of added surfactants were biodegraded. PMID:23653909

  8. Numerical modeling of separated flows in three-dimensional diffusers and application of synthetic jets for separation control

    NASA Astrophysics Data System (ADS)

    Krasheninnikov, S. Yu.; Pudovikov, D. E.; Torohov, S. A.

    2012-01-01

    Solving the problem of creating an environmentally friendly "green plane" implies development and implementation of several actions aimed at increasing airplane performance and reducing environmental contamination. One possible way to solve this problem is to reduce the powerplant weight, in particular, by decreasing its length. The airplane engine flowpath comprises transition ducts: those between the low- and high-pressure compressors, between the compressor and combustor, and between the high- and low-pressure turbines. In a modern high-bypass turbofan, the flowpath varies in the streamwise direction. Shorter transition ducts have greater curvature. Because of this, intensive separation may occur, which leads to increased losses in the flowpath and to significant growth of nonuniformity of flow parameters. Vast experience of numerical and experimental studies of unsteady separated flows has been accumulated by now. In many cases, however, these investigations are performed in a two-dimensional (2D) formulation, which is primarily caused by the high cost of three-dimensional (3D) unsteady calculations. The numerical and experimental work [1] shows that flows in diffuser ducts can have an essentially unsteady 3D structure. This is valid even for ducts modeling 2D configurations. This paper describes the results of a numerical study of the flow structure and its features in model S-shaped transition ducts, as well as the results of using a synthetic jet generator for flow control and for reduction of total pressure losses. Three-dimensional flows are numerically modeled by the unsteady Reynolds-averaged Navier-Stokes (URANS) / RANS methods. The calculations show that the use of the synthetic jet generator can lead to duct loss reduction by 45%.

  9. 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).

  10. 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

  11. A female pelvic bone shape model for air/bone separation in support of synthetic CT generation for radiation therapy.

    PubMed

    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%). PMID

  12. 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.

  13. 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).

  14. 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.

  15. 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

  16. 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 modelling accuracies. It was concluded that the L-band SAR frequency was more effective in the modelling of the CC (coefficient of determination or R2 of 0.77), TCV (R2 of 0.79) and AGB (R2 of 0.78) metrics in Southern African

  17. Towards a Data-Optimized Coronal Magnetic Field Model (DOC-FM): Synthetic Test Beds and Multiwavelength Forward Modeling

    NASA Astrophysics Data System (ADS)

    Gibson, S. E.; Dalmasse, K.; Fan, Y.; Fineschi, S.; MacKay, D.; Rempel, M.; White, S. M.

    2015-12-01

    Understanding the physical state of the solar corona is key to deciphering the origins of space weather as well as to realistically representing the environment to be navigated by missions such as Solar Orbiter and Solar Probe Plus. However, inverting solar coronal observations to reconstruct this physical state -- and in particular the three-dimensional coronal magnetic field - is complicated by limited lines of sight and by projection effects. On the other hand, the sensitivity of multiwavelength observations to different physical mechanisms implies a potential for simultaneous probing of different parts of the coronal plasma. In order to study this complementarity, and to ultimately establish an optimal set of observations for constraining the three-dimensional coronal magnetic field, we are developing a suite of representative simulations to act as diagnostic test beds. We will present three such test beds: a coronal active region, a quiescent prominence, and a global corona. Each fully define the physical state of density, temperature, and vector magnetic field in three dimensions throughout the simulation domain. From these test beds, and using the FORWARD SolarSoft IDL codes, we will create a broad range of synthetic data. Radio observables will include intensity and circular polarization (including gyroresonance effects) and Faraday rotation for a range of frequencies. Infrared and visible forbidden line diagnostics of Zeeman and saturated Hanle effects will yield full Stokes vector (I, Q, U, V) synthetic data, and UV permitted line Hanle diagnostics will yield intensity and linear polarization. In addition, we will synthesize UV and SXR imager data, UV/EUV spectrometric data, and white light brightness and polarized brightness. All of these synthetic data, along with the "ground truth" physical state of the simulations from which they are derived, will be made available to the community for the purpose of testing coronal inversion techniques.

  18. Influence of supraglottal structures on the glottal jet exiting a two-layer synthetic, self-oscillating vocal fold model

    PubMed Central

    Drechsel, James S.; Thomson, Scott L.

    2008-01-01

    A synthetic two-layer, self-oscillating, life-size vocal fold model was used to study the influence of the vocal tract and false folds on the glottal jet. The model vibrated at frequencies, pressures, flow rates, and amplitudes consistent with human phonation, although some differences in behavior between the model and the human vocal folds are noted. High-speed images of model motion and flow visualization were acquired. Phase-locked ensemble-averaged glottal jet velocity measurements using particle image velocimetry (PIV) were acquired with and without an idealized vocal tract, with and without false folds. PIV data were obtained with varying degrees of lateral asymmetric model positioning. Glottal jet velocity magnitudes were consistent with those measured using excised larynges. A starting vortex was observed in all test cases. The false folds interfered with the starting vortex, and in some cases vortex shedding from the false folds was observed. In asymmetric cases without false folds, the glottal jet tended to skew toward the nearest wall; with the false folds, the opposite trend was observed. rms velocity calculations showed the jet shear layer and laminar core. The rms velocities were higher in the vocal tract cases compared to the open jet and false fold cases. PMID:18537394

  19. Synthetic chromosomes.

    PubMed

    Schindler, Daniel; Waldminghaus, Torsten

    2015-11-01

    What a living organism looks like and how it works and what are its components-all this is encoded on DNA, the genetic blueprint. Consequently, the way to change an organism is to change its genetic information. Since the first pieces of recombinant DNA have been used to transform cells in the 1970s, this approach has been enormously extended. Bigger and bigger parts of the genetic information have been exchanged or added over the years. Now we are at a point where the construction of entire chromosomes becomes a reachable goal and first examples appear. This development leads to fundamental new questions, for example, about what is possible and desirable to build or what construction rules one needs to follow when building synthetic chromosomes. Here we review the recent progress in the field, discuss current challenges and speculate on the appearance of future synthetic chromosomes. PMID:26111960

  20. The iron-related molecular toxicity mechanism of synthetic asbestos nanofibres: a model study for high-aspect-ratio nanoparticles.

    PubMed

    Turci, Francesco; Tomatis, Maura; Lesci, Isidoro G; Roveri, Norberto; Fubini, Bice

    2011-01-01

    Asbestos shares with carbon nanotubes some morphological and physico-chemical features. An asbestos-like behaviour has been recently reported by some authors, though the mechanism of toxicity may be very different. To identify at the atomic level the source of toxicity in asbestos, the effect of progressive iron loading on a synthetic iron-free model nanofibre previously found non-toxic in cellular tests was studied. A set of five synthetic chrysotile nanofibres [(Mg,Fe)3(Si2O5)(OH)4] has been prepared with Fe ranging from 0 to 1.78 wt %. The relationship between fibre-induced free-radical generation and the physico-chemical characteristics of iron active sites was investigated with spin-trapping techniques on an aqueous suspension of the fibres and Mössbauer and EPR spectroscopies on the solids, respectively. The fully iron-free fibre was inert, whereas radical activity arose with even the smallest amount of iron. Surprisingly, such activity decreased upon increasing iron loading. Mössbauer and EPR revealed isolated iron ions in octahedral sites that undergo both axial and rhombic distortion and the occurrence of aggregated iron ions and/or extra-framework clustering. The isolated ions largely prevailed at the lowest loadings. Upon increasing the loading, the amount of isolated iron was reduced and the aggregation increased. A linear relationship between the formation of carbon-centred radicals and the amount of rhombic-distorted isolated iron sites was found. Even the smallest iron contamination imparts radical reactivity, hence toxicity, to any chrysotile outcrop, thereby discouraging the search for non-toxic chrysotile. The use of model solids that only differ in one property at a time appears to be the most successful approach for a molecular understanding of the physico-chemical determinants of toxicity. Such findings could also be useful in the design of safer nanofibres. PMID:21207631

  1. 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.

  2. Synthetic battery cycling techniques

    NASA Technical Reports Server (NTRS)

    Leibecki, H. F.; Thaller, L. H.

    1982-01-01

    Synthetic battery cycling makes use of the fast growing capability of computer graphics to illustrate some of the basic characteristics of operation of individual electrodes within an operating electrochemical cell. It can also simulate the operation of an entire string of cells that are used as the energy storage subsystem of a power system. The group of techniques that as a class have been referred to as Synthetic Battery Cycling is developed in part to try to bridge the gap of understanding that exists between single cell characteristics and battery system behavior.

  3. Waveform modelling using locked-mode synthetic and differential seismograms: application to determination of the structure of Mexico

    USGS Publications Warehouse

    Gomberg, J.S.; Masters, T. Guy

    1988-01-01

    We have developed algorithms for modelling seismic waveforms to constrain regional Earth structure. The seismogram is represented as a sum of locked-mode travelling waves in a layered medium. This representation is convenient as it allows us to model structures with slowly varying heterogeneity and to construct differential seismograms. Describes the techniques we have implemented that enable us to compute