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 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.

  9. 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.

  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

    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

  18. 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.

  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. 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

  6. 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.

  7. 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

  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 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

  15. 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

  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. 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.

  4. 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…

  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

    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 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

  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. 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.

  16. 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.

  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. 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

  4. 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.

  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. 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.

  16. 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

  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. 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.

  1. 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

  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. 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

  7. 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

  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. 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.

  15. 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.

  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. 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

  20. 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

  1. 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

  2. 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.

  3. 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.

  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

    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.

  2. 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

  3. 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.

  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. 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.

  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. 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

  18. 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.

  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. 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

  7. 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

  8. 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

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

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

  13. 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.

  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. 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

  17. 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.

  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. 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

  19. 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.

  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. 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.

  7. 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.

  8. 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

  9. 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

  10. 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