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Sample records for synthetic genetic oscillators

  1. Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation.

    Tomazou, Marios; Barahona, Mauricio; Polizzi, Karen M; Stan, Guy-Bart

    2018-04-25

    To perform well in biotechnology applications, synthetic genetic oscillators must be engineered to allow independent modulation of amplitude and period. This need is currently unmet. Here, we demonstrate computationally how two classic genetic oscillators, the dual-feedback oscillator and the repressilator, can be re-designed to provide independent control of amplitude and period and improve tunability-that is, a broad dynamic range of periods and amplitudes accessible through the input "dials." Our approach decouples frequency and amplitude modulation by incorporating an orthogonal "sink module" where the key molecular species are channeled for enzymatic degradation. This sink module maintains fast oscillation cycles while alleviating the translational coupling between the oscillator's transcription factors and output. We characterize the behavior of our re-designed oscillators over a broad range of physiologically reasonable parameters, explain why this facilitates broader function and control, and provide general design principles for building synthetic genetic oscillators that are more precisely controllable. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  2. How to turn a genetic circuit into a synthetic tunable oscillator, or a bistable switch.

    Lucia Marucci

    2009-12-01

    Full Text Available Systems and Synthetic Biology use computational models of biological pathways in order to study in silico the behaviour of biological pathways. Mathematical models allow to verify biological hypotheses and to predict new possible dynamical behaviours. Here we use the tools of non-linear analysis to understand how to change the dynamics of the genes composing a novel synthetic network recently constructed in the yeast Saccharomyces cerevisiae for In-vivo Reverse-engineering and Modelling Assessment (IRMA. Guided by previous theoretical results that make the dynamics of a biological network depend on its topological properties, through the use of simulation and continuation techniques, we found that the network can be easily turned into a robust and tunable synthetic oscillator or a bistable switch. Our results provide guidelines to properly re-engineering in vivo the network in order to tune its dynamics.

  3. Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing.

    Chen, Bor-Sen; Hsu, Chih-Yuan

    2012-10-26

    Collective rhythms of gene regulatory networks have been a subject of considerable interest for biologists and theoreticians, in particular the synchronization of dynamic cells mediated by intercellular communication. Synchronization of a population of synthetic genetic oscillators is an important design in practical applications, because such a population distributed over different host cells needs to exploit molecular phenomena simultaneously in order to emerge a biological phenomenon. However, this synchronization may be corrupted by intrinsic kinetic parameter fluctuations and extrinsic environmental molecular noise. Therefore, robust synchronization is an important design topic in nonlinear stochastic coupled synthetic genetic oscillators with intrinsic kinetic parameter fluctuations and extrinsic molecular noise. Initially, the condition for robust synchronization of synthetic genetic oscillators was derived based on Hamilton Jacobi inequality (HJI). We found that if the synchronization robustness can confer enough intrinsic robustness to tolerate intrinsic parameter fluctuation and extrinsic robustness to filter the environmental noise, then robust synchronization of coupled synthetic genetic oscillators is guaranteed. If the synchronization robustness of a population of nonlinear stochastic coupled synthetic genetic oscillators distributed over different host cells could not be maintained, then robust synchronization could be enhanced by external control input through quorum sensing molecules. In order to simplify the analysis and design of robust synchronization of nonlinear stochastic synthetic genetic oscillators, the fuzzy interpolation method was employed to interpolate several local linear stochastic coupled systems to approximate the nonlinear stochastic coupled system so that the HJI-based synchronization design problem could be replaced by a simple linear matrix inequality (LMI)-based design problem, which could be solved with the help of LMI

  4. Synchronous long-term oscillations in a synthetic gene circuit.

    Potvin-Trottier, Laurent; Lord, Nathan D; Vinnicombe, Glenn; Paulsson, Johan

    2016-10-27

    Synthetically engineered genetic circuits can perform a wide variety of tasks but are generally less accurate than natural systems. Here we revisit the first synthetic genetic oscillator, the repressilator, and modify it using principles from stochastic chemistry in single cells. Specifically, we sought to reduce error propagation and information losses, not by adding control loops, but by simply removing existing features. We show that this modification created highly regular and robust oscillations. Furthermore, some streamlined circuits kept 14 generation periods over a range of growth conditions and kept phase for hundreds of generations in single cells, allowing cells in flasks and colonies to oscillate synchronously without any coupling between them. Our results suggest that even the simplest synthetic genetic networks can achieve a precision that rivals natural systems, and emphasize the importance of noise analyses for circuit design in synthetic biology.

  5. Strategy revealing phenotypic differences among synthetic oscillator designs.

    Lomnitz, Jason G; Savageau, Michael A

    2014-09-19

    Considerable progress has been made in identifying and characterizing the component parts of genetic oscillators, which play central roles in all organisms. Nonlinear interaction among components is sufficiently complex that mathematical models are required to elucidate their elusive integrated behavior. Although natural and synthetic oscillators exhibit common architectures, there are numerous differences that are poorly understood. Utilizing synthetic biology to uncover basic principles of simpler circuits is a way to advance understanding of natural circadian clocks and rhythms. Following this strategy, we address the following questions: What are the implications of different architectures and molecular modes of transcriptional control for the phenotypic repertoire of genetic oscillators? Are there designs that are more realizable or robust? We compare synthetic oscillators involving one of three architectures and various combinations of the two modes of transcriptional control using a methodology that provides three innovations: a rigorous definition of phenotype, a procedure for deconstructing complex systems into qualitatively distinct phenotypes, and a graphical representation for illuminating the relationship between genotype, environment, and the qualitatively distinct phenotypes of a system. These methods provide a global perspective on the behavioral repertoire, facilitate comparisons of alternatives, and assist the rational design of synthetic gene circuitry. In particular, the results of their application here reveal distinctive phenotypes for several designs that have been studied experimentally as well as a best design among the alternatives that has yet to be constructed and tested.

  6. Queueing-Based Synchronization and Entrainment for Synthetic Gene Oscillators

    Mather, William; Butzin, Nicholas; Hochendoner, Philip; Ogle, Curtis

    Synthetic gene oscillators have been a major focus of synthetic biology research since the beginning of the field 15 years ago. They have proven to be useful both for biotechnological applications as well as a testing ground to significantly develop our understanding of the design principles behind synthetic and native gene oscillators. In particular, the principles governing synchronization and entrainment of biological oscillators have been explored using a synthetic biology approach. Our work combines experimental and theoretical approaches to specifically investigate how a bottleneck for protein degradation, which is present in most if not all existing synthetic oscillators, can be leveraged to robustly synchronize and entrain biological oscillators. We use both the terminology and mathematical tools of queueing theory to intuitively explain the role of this bottleneck in both synchronization and entrainment, which extends prior work demonstrating the usefulness of queueing theory in synthetic and native gene circuits. We conclude with an investigation of how synchronization and entrainment may be sensitive to the presence of multiple proteolytic pathways in a cell that couple weakly through crosstalk. This work was supported by NSF Grant #1330180.

  7. Growth-rate-dependent dynamics of a bacterial genetic oscillator

    Osella, Matteo; Lagomarsino, Marco Cosentino

    2013-01-01

    Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available analyses generally neglect the coupling of regulatory circuits with the cellular “chassis” in which the circuits are embedded. For example, the intracellular macromolecular composition of fast-growing bacteria changes with growth rate. As a consequence, important parameters of gene expression, such as ribosome concentration or cell volume, are growth-rate dependent, ultimately coupling the dynamics of genetic circuits with cell physiology. This work addresses the effects of growth rate on the dynamics of a paradigmatic example of genetic oscillator, the repressilator. Making use of empirical growth-rate dependencies of parameters in bacteria, we show that the repressilator dynamics can switch between oscillations and convergence to a fixed point depending on the cellular state of growth, and thus on the nutrients it is fed. The physical support of the circuit (type of plasmid or gene positions on the chromosome) also plays an important role in determining the oscillation stability and the growth-rate dependence of period and amplitude. This analysis has potential application in the field of synthetic biology, and suggests that the coupling between endogenous genetic oscillators and cell physiology can have substantial consequences for their functionality.

  8. [Synthetic biology and rearrangements of microbial genetic material].

    Liang, Quan-Feng; Wang, Qian; Qi, Qing-Sheng

    2011-10-01

    As an emerging discipline, synthetic biology has shown great scientific values and application prospects. Although there have been many reviews of various aspects on synthetic biology over the last years, this article, for the first time, attempted to discuss the relationship and difference between microbial genetics and synthetic biology. We summarized the recent development of synthetic biology in rearranging microbial genetic materials, including synthesis, design and reduction of genetic materials, standardization of genetic parts and modularization of genetic circuits. The relationship between synthetic biology and microbial genetic engineering was also discussed in the paper.

  9. Alternative Watson-Crick Synthetic Genetic Systems.

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

    2016-11-01

    In its "grand challenge" format in chemistry, "synthesis" as an activity sets out a goal that is substantially beyond current theoretical and technological capabilities. In pursuit of this goal, scientists are forced across uncharted territory, where they must answer unscripted questions and solve unscripted problems, creating new theories and new technologies in ways that would not be created by hypothesis-directed research. Thus, synthesis drives discovery and paradigm changes in ways that analysis cannot. Described here are the products that have arisen so far through the pursuit of one grand challenge in synthetic biology: Recreate the genetics, catalysis, evolution, and adaptation that we value in life, but using genetic and catalytic biopolymers different from those that have been delivered to us by natural history on Earth. The outcomes in technology include new diagnostic tools that have helped personalize the care of hundreds of thousands of patients worldwide. In science, the effort has generated a fundamentally different view of DNA, RNA, and how they work. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

  10. Chemical event chain model of coupled genetic oscillators.

    Jörg, David J; Morelli, Luis G; Jülicher, Frank

    2018-03-01

    We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their frequency, their quality factor, and their synchrony by the oscillator cross correlation. The steady state is determined by coupling and exhibits stochastic transitions between different modes. The interplay of stochasticity and nonlinearity leads to isolated regions in parameter space in which the coupled system works best as a biological pacemaker. Key features of the stochastic oscillations can be captured by an effective model for phase oscillators that are coupled by signals with distributed delays.

  11. Chemical event chain model of coupled genetic oscillators

    Jörg, David J.; Morelli, Luis G.; Jülicher, Frank

    2018-03-01

    We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their frequency, their quality factor, and their synchrony by the oscillator cross correlation. The steady state is determined by coupling and exhibits stochastic transitions between different modes. The interplay of stochasticity and nonlinearity leads to isolated regions in parameter space in which the coupled system works best as a biological pacemaker. Key features of the stochastic oscillations can be captured by an effective model for phase oscillators that are coupled by signals with distributed delays.

  12. Modularization of genetic elements promotes synthetic metabolic engineering.

    Qi, Hao; Li, Bing-Zhi; Zhang, Wen-Qian; Liu, Duo; Yuan, Ying-Jin

    2015-11-15

    In the context of emerging synthetic biology, metabolic engineering is moving to the next stage powered by new technologies. Systematical modularization of genetic elements makes it more convenient to engineer biological systems for chemical production or other desired purposes. In the past few years, progresses were made in engineering metabolic pathway using synthetic biology tools. Here, we spotlighted the topic of implementation of modularized genetic elements in metabolic engineering. First, we overviewed the principle developed for modularizing genetic elements and then discussed how the genetic modules advanced metabolic engineering studies. Next, we picked up some milestones of engineered metabolic pathway achieved in the past few years. Last, we discussed the rapid raised synthetic biology field of "building a genome" and the potential in metabolic engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Engineering genetic circuit interactions within and between synthetic minimal cells

    Adamala, Katarzyna P.; Martin-Alarcon, Daniel A.; Guthrie-Honea, Katriona R.; Boyden, Edward S.

    2017-05-01

    Genetic circuits and reaction cascades are of great importance for synthetic biology, biochemistry and bioengineering. An open question is how to maximize the modularity of their design to enable the integration of different reaction networks and to optimize their scalability and flexibility. One option is encapsulation within liposomes, which enables chemical reactions to proceed in well-isolated environments. Here we adapt liposome encapsulation to enable the modular, controlled compartmentalization of genetic circuits and cascades. We demonstrate that it is possible to engineer genetic circuit-containing synthetic minimal cells (synells) to contain multiple-part genetic cascades, and that these cascades can be controlled by external signals as well as inter-liposomal communication without crosstalk. We also show that liposomes that contain different cascades can be fused in a controlled way so that the products of incompatible reactions can be brought together. Synells thus enable a more modular creation of synthetic biology cascades, an essential step towards their ultimate programmability.

  14. Synthetic Genetic Targeting of Genome Instability in Cancer

    Sajesh, Babu V.; Guppy, Brent J.; McManus, Kirk J.

    2013-01-01

    Cancer is a leading cause of death throughout the World. A limitation of many current chemotherapeutic approaches is that their cytotoxic effects are not restricted to cancer cells, and adverse side effects can occur within normal tissues. Consequently, novel strategies are urgently needed to better target cancer cells. As we approach the era of personalized medicine, targeting the specific molecular defect(s) within a given patient’s tumor will become a more effective treatment strategy than traditional approaches that often target a given cancer type or sub-type. Synthetic genetic interactions are now being examined for their therapeutic potential and are designed to target the specific genetic and epigenetic phenomena associated with tumor formation, and thus are predicted to be highly selective. In general, two complementary approaches have been employed, including synthetic lethality and synthetic dosage lethality, to target aberrant expression and/or function associated with tumor suppressor genes and oncogenes, respectively. Here we discuss the concepts of synthetic lethality and synthetic dosage lethality, and explain three general experimental approaches designed to identify novel genetic interactors. We present examples and discuss the merits and caveats of each approach. Finally, we provide insight into the subsequent pre-clinical work required to validate novel candidate drug targets

  15. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    The present study was conducted to assess the genetic diversity of Elite-II synthetic hexaploid (SH) wheat by genome DNA fingerprinting as revealed by random amplified polymorphic DNA (RAPD) analysis. Ten decamer RAPD primers (OPG-1, OPG-2, OPG-3, OPG-4, OPG-5, OPA-3, OPA-4, OPA-5, OPA-8, and OPA-15) ...

  16. Biocontainment of genetically modified organisms by synthetic protein design

    Mandell, Daniel J.; Lajoie, Marc J.; Mee, Michael T.; Takeuchi, Ryo; Kuznetsov, Gleb; Norville, Julie E.; Gregg, Christopher J.; Stoddard, Barry L.; Church, George M.

    2015-02-01

    Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.

  17. Robust Nonlinear Regulation of Limit Cycle Oscillations in UAVs Using Synthetic Jet Actuators

    Natalie Ramos Pedroza

    2014-09-01

    Full Text Available In this paper, a synthetic jet actuators (SJA-based nonlinear robust controller is developed, which is capable of completely suppressing limit cycle oscillations (LCO in UAV systems with parametric uncertainty in the SJA dynamics and unmodeled external disturbances. Specifically, the control law compensates for uncertainty in an input gain matrix, which results from the unknown airflow dynamics generated by the SJA. Challenges in the control design include compensation for input-multiplicative parametric uncertainty in the actuator dynamic model. The result was achieved via innovative algebraic manipulation in the error system development, along with a Lyapunov-based robust control law. A rigorous Lyapunov-based stability analysis is utilized to prove asymptotic LCO suppression, considering a detailed dynamic model of the pitching and plunging dynamics. Numerical simulation results are provided to demonstrate the robustness and practical performance of the proposed control law.

  18. Fractional dynamics of globally slow transcription and its impact on deterministic genetic oscillation.

    Kun Wei

    Full Text Available In dynamical systems theory, a system which can be described by differential equations is called a continuous dynamical system. In studies on genetic oscillation, most deterministic models at early stage are usually built on ordinary differential equations (ODE. Therefore, gene transcription which is a vital part in genetic oscillation is presupposed to be a continuous dynamical system by default. However, recent studies argued that discontinuous transcription might be more common than continuous transcription. In this paper, by appending the inserted silent interval lying between two neighboring transcriptional events to the end of the preceding event, we established that the running time for an intact transcriptional event increases and gene transcription thus shows slow dynamics. By globally replacing the original time increment for each state increment by a larger one, we introduced fractional differential equations (FDE to describe such globally slow transcription. The impact of fractionization on genetic oscillation was then studied in two early stage models--the Goodwin oscillator and the Rössler oscillator. By constructing a "dual memory" oscillator--the fractional delay Goodwin oscillator, we suggested that four general requirements for generating genetic oscillation should be revised to be negative feedback, sufficient nonlinearity, sufficient memory and proper balancing of timescale. The numerical study of the fractional Rössler oscillator implied that the globally slow transcription tends to lower the chance of a coupled or more complex nonlinear genetic oscillatory system behaving chaotically.

  19. Fractional dynamics of globally slow transcription and its impact on deterministic genetic oscillation.

    Wei, Kun; Gao, Shilong; Zhong, Suchuan; Ma, Hong

    2012-01-01

    In dynamical systems theory, a system which can be described by differential equations is called a continuous dynamical system. In studies on genetic oscillation, most deterministic models at early stage are usually built on ordinary differential equations (ODE). Therefore, gene transcription which is a vital part in genetic oscillation is presupposed to be a continuous dynamical system by default. However, recent studies argued that discontinuous transcription might be more common than continuous transcription. In this paper, by appending the inserted silent interval lying between two neighboring transcriptional events to the end of the preceding event, we established that the running time for an intact transcriptional event increases and gene transcription thus shows slow dynamics. By globally replacing the original time increment for each state increment by a larger one, we introduced fractional differential equations (FDE) to describe such globally slow transcription. The impact of fractionization on genetic oscillation was then studied in two early stage models--the Goodwin oscillator and the Rössler oscillator. By constructing a "dual memory" oscillator--the fractional delay Goodwin oscillator, we suggested that four general requirements for generating genetic oscillation should be revised to be negative feedback, sufficient nonlinearity, sufficient memory and proper balancing of timescale. The numerical study of the fractional Rössler oscillator implied that the globally slow transcription tends to lower the chance of a coupled or more complex nonlinear genetic oscillatory system behaving chaotically.

  20. Synthetic multicellular oscillatory systems: controlling protein dynamics with genetic circuits

    Koseska, Aneta; Volkov, Evgenii; Kurths, Juergen

    2011-01-01

    Synthetic biology is a relatively new research discipline that combines standard biology approaches with the constructive nature of engineering. Thus, recent efforts in the field of synthetic biology have given a perspective to consider cells as 'programmable matter'. Here, we address the possibility of using synthetic circuits to control protein dynamics. In particular, we show how intercellular communication and stochasticity can be used to manipulate the dynamical behavior of a population of coupled synthetic units and, in this manner, finely tune the expression of specific proteins of interest, e.g. in large bioreactors.

  1. GABAergic synapse properties may explain genetic variation in hippocampal network oscillations in mice

    Tim S Heistek

    2010-06-01

    Full Text Available Cognitive ability and the properties of brain oscillation are highly heritable in humans. Genetic variation underlying oscillatory activity might give rise to differences in cognition and behavior. How genetic diversity translates into altered properties of oscillations and synchronization of neuronal activity is unknown. To address this issue, we investigated cellular and synaptic mechanisms of hippocampal fast network oscillations in eight genetically distinct inbred mouse strains. The frequency of carbachol-induced oscillations differed substantially between mouse strains. Since GABAergic inhibition sets oscillation frequency, we studied the properties of inhibitory synaptic inputs (IPSCs received by CA3 and CA1 pyramidal cells of three mouse strains that showed the highest, lowest and intermediate frequencies of oscillations. In CA3 pyramidal cells, the frequency of rhythmic IPSC input showed the same strain differences as the frequency of field oscillations. Furthermore, IPSC decay times in both CA1 and CA3 pyramidal cells were faster in mouse strains with higher oscillation frequencies than in mouse strains with lower oscillation frequency, suggesting that differences in GABAA-receptor subunit composition exist between these strains. Indeed, gene expression of GABAA-receptor β2 (Gabrb2 and β3 (Gabrb2 subunits was higher in mouse strains with faster decay kinetics compared with mouse strains with slower decay kinetics. Hippocampal pyramidal neurons in mouse strains with higher oscillation frequencies and faster decay kinetics fired action potential at higher frequencies. These data indicate that differences in genetic background may result in different GABAA-receptor subunit expression, which affects the rhythm of pyramidal neuron firing and fast network activity through GABA synapse kinetics.

  2. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    STORAGESEVER

    2009-07-20

    Jul 20, 2009 ... The presence of sufficient genetic diversity in the germplam is an important ..... Figure 1. PCR amplification profile of Elite-II SH Wheat using the primer OPG-2. .... genetic relationships among cowpea breeding lines and local.

  3. Genetic analyses of agronomic and seed quality traits of synthetic ...

    As for protein content, similar results were found in the F2 plants and their maternal parents. ... doubled haploid; genetic analysis; gene interaction; agronomic traits; seed ..... Han J. Q. and Liu H. L. 1993 Principal component analysis for main.

  4. Synthetic review on the genetic relatedness between North Africa ...

    ... genetic markers are associated with certain aspects of human culture like languages, ... In the Middle East, the predominant categories of Y chromosomes are ... less frequency than the Middle Eastern ones, showing an important paternal ...

  5. Altered vocal fold kinematics in synthetic self-oscillating models that employ adipose tissue as a lateral boundary condition.

    Saidi, Hiba; Erath, Byron D.

    2015-11-01

    The vocal folds play a major role in human communication by initiating voiced sound production. During voiced speech, the vocal folds are set into sustained vibrations. Synthetic self-oscillating vocal fold models are regularly employed to gain insight into flow-structure interactions governing the phonation process. Commonly, a fixed boundary condition is applied to the lateral, anterior, and posterior sides of the synthetic vocal fold models. However, physiological observations reveal the presence of adipose tissue on the lateral surface between the thyroid cartilage and the vocal folds. The goal of this study is to investigate the influence of including this substrate layer of adipose tissue on the dynamics of phonation. For a more realistic representation of the human vocal folds, synthetic multi-layer vocal fold models have been fabricated and tested while including a soft lateral layer representative of adipose tissue. Phonation parameters have been collected and are compared to those of the standard vocal fold models. Results show that vocal fold kinematics are affected by adding the adipose tissue layer as a new boundary condition.

  6. Synthetic genetic polymers capable of heredity and evolution

    Pinheiro, Vitor B; Taylor, Alexander I; Cozens, Christopher

    2012-01-01

    in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity......Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored...... for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage....

  7. Improving microalgae for biotechnology - From genetics to synthetic biology

    Hlavová, Monika; Turóczy, Zoltán; Bišová, Kateřina

    2015-01-01

    Roč. 33, č. 6 (2015), s. 1194-1203 ISSN 0734-9750 R&D Projects: GA MŠk EE2.3.30.0059; GA MŠk ED2.1.00/03.0110 Institutional support: RVO:61388971 Keywords : Microalgae * Genetics * Mutagenesis Subject RIV: EE - Microbiology, Virology Impact factor: 9.848, year: 2015

  8. Reverse engineering large-scale genetic networks: synthetic versus ...

    2010-04-19

    Apr 19, 2010 ... process computationally to describe the structure of the sys- tem and ... to the different mathematical formalisms used to model net-. Keywords. gene ..... All the algorithms were implemented in MATLAB 7.0 and run on all the 'gold ..... De Jong H. 2002 Medeling and simulation of genetic regulatory systems: a ...

  9. SYNTHETIC HYDROGEN SPECTRA OF OSCILLATING PROMINENCE SLABS IMMERSED IN THE SOLAR CORONA

    Zapiór, M.; Heinzel, P.; Oliver, R.; Ballester, J. L.

    2016-01-01

    We study the behavior of H α and H β spectral lines and their spectral indicators in an oscillating solar prominence slab surrounded by the solar corona, using an MHD model combined with a 1D radiative transfer code taken in the line of sight perpendicular to the slab. We calculate the time variation of the Doppler shift, half-width, and maximum intensity of the H α and H β spectral lines for different modes of oscillation. We find a non-sinusoidal time dependence of some spectral parameters with time. Because H α and H β spectral indicators have different behavior for different modes, caused by differing optical depths of formation and different plasma parameter variations in time and along the slab, they may be used for prominence seismology, especially to derive the internal velocity field in prominences.

  10. SYNTHETIC HYDROGEN SPECTRA OF OSCILLATING PROMINENCE SLABS IMMERSED IN THE SOLAR CORONA

    Zapiór, M.; Heinzel, P. [Astronomical Institute, The Czech Academy of Sciences, 25165 Ondřejov, The Czech Republic (Czech Republic); Oliver, R.; Ballester, J. L. [Universitat de les Illes Balears. Cra. de Valldemossa, km 7.5. Palma (Illes Balears), E-07122 (Spain)

    2016-08-20

    We study the behavior of H α and H β spectral lines and their spectral indicators in an oscillating solar prominence slab surrounded by the solar corona, using an MHD model combined with a 1D radiative transfer code taken in the line of sight perpendicular to the slab. We calculate the time variation of the Doppler shift, half-width, and maximum intensity of the H α and H β spectral lines for different modes of oscillation. We find a non-sinusoidal time dependence of some spectral parameters with time. Because H α and H β spectral indicators have different behavior for different modes, caused by differing optical depths of formation and different plasma parameter variations in time and along the slab, they may be used for prominence seismology, especially to derive the internal velocity field in prominences.

  11. Investigation into the efficacy of generating synthetic pathological oscillations for domain adaptation

    Lewis, Rory; Ellenberger, James; Williams, Colton; White, Andrew M.

    2013-11-01

    In the ongoing investigation of integrating Knowledge Discovery in Databases (KDD) into neuroscience, we present a paper that facilitates overcoming the two challenges preventing this integration. Pathological oscillations found in the human brain are difficult to evaluate because 1) there is often no time to learn and train off of the same distribution in the fatally sick, and 2) sinusoidal signals found in the human brain are complex and transient in nature requiring large data sets to work with which are costly and often very expensive or impossible to acquire. Overcoming these challenges in today's neuro-intensive-care unit (ICU) requires insurmountable resources. For these reasons, optimizing KDD for pathological oscillations so machine learning systems can predict neuropathological states would be of immense value. Domain adaptation, which allows a way of predicting on a separate set of data than the training data, can theoretically overcome the first challenge. However, the challenge of acquiring large data sets that show whether domain adaptation is a good candidate to test in a live neuro ICU remains a challenge. To solve this conundrum, we present a methodology for generating synthesized neuropathological oscillations for domain adaptation.

  12. Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances.

    Wagner, James M; Alper, Hal S

    2016-04-01

    Coupling the tools of synthetic biology with traditional molecular genetic techniques can enable the rapid prototyping and optimization of yeast strains. While the era of yeast synthetic biology began in the well-characterized model organism Saccharomyces cerevisiae, it is swiftly expanding to include non-conventional yeast production systems such as Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. These yeasts already have roles in the manufacture of vaccines, therapeutic proteins, food additives, and biorenewable chemicals, but recent synthetic biology advances have the potential to greatly expand and diversify their impact on biotechnology. In this review, we summarize the development of synthetic biological tools (including promoters and terminators) and enabling molecular genetics approaches that have been applied in these four promising alternative biomanufacturing platforms. An emphasis is placed on synthetic parts and genome editing tools. Finally, we discuss examples of synthetic tools developed in other organisms that can be adapted or optimized for these hosts in the near future. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. The population genetics of X-autosome synthetic lethals and steriles.

    Lachance, Joseph; Johnson, Norman A; True, John R

    2011-11-01

    Epistatic interactions are widespread, and many of these interactions involve combinations of alleles at different loci that are deleterious when present in the same individual. The average genetic environment of sex-linked genes differs from that of autosomal genes, suggesting that the population genetics of interacting X-linked and autosomal alleles may be complex. Using both analytical theory and computer simulations, we analyzed the evolutionary trajectories and mutation-selection balance conditions for X-autosome synthetic lethals and steriles. Allele frequencies follow a set of fundamental trajectories, and incompatible alleles are able to segregate at much higher frequencies than single-locus expectations. Equilibria exist, and they can involve fixation of either autosomal or X-linked alleles. The exact equilibrium depends on whether synthetic alleles are dominant or recessive and whether fitness effects are seen in males, females, or both sexes. When single-locus fitness effects and synthetic incompatibilities are both present, population dynamics depend on the dominance of alleles and historical contingency (i.e., whether X-linked or autosomal mutations occur first). Recessive synthetic lethality can result in high-frequency X-linked alleles, and dominant synthetic lethality can result in high-frequency autosomal alleles. Many X-autosome incompatibilities in natural populations may be cryptic, appearing to be single-locus effects because one locus is fixed. We also discuss the implications of these findings with respect to standing genetic variation and the origins of Haldane's rule.

  14. Synthetic alienation of microbial organisms by using genetic code engineering: Why and how?

    Kubyshkin, Vladimir; Budisa, Nediljko

    2017-08-01

    The main goal of synthetic biology (SB) is the creation of biodiversity applicable for biotechnological needs, while xenobiology (XB) aims to expand the framework of natural chemistries with the non-natural building blocks in living cells to accomplish artificial biodiversity. Protein and proteome engineering, which overcome limitation of the canonical amino acid repertoire of 20 (+2) prescribed by the genetic code by using non-canonic amino acids (ncAAs), is one of the main focuses of XB research. Ideally, estranging the genetic code from its current form via systematic introduction of ncAAs should enable the development of bio-containment mechanisms in synthetic cells potentially endowing them with a "genetic firewall" i.e. orthogonality which prevents genetic information transfer to natural systems. Despite rapid progress over the past two decades, it is not yet possible to completely alienate an organism that would use and maintain different genetic code associations permanently. In order to engineer robust bio-contained life forms, the chemical logic behind the amino acid repertoire establishment should be considered. Starting from recent proposal of Hartman and Smith about the genetic code establishment in the RNA world, here the authors mapped possible biotechnological invasion points for engineering of bio-contained synthetic cells equipped with non-canonical functionalities. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Adaptive logical stochastic resonance in time-delayed synthetic genetic networks

    Zhang, Lei; Zheng, Wenbin; Song, Aiguo

    2018-04-01

    In the paper, the concept of logical stochastic resonance is applied to implement logic operation and latch operation in time-delayed synthetic genetic networks derived from a bacteriophage λ. Clear logic operation and latch operation can be obtained when the network is tuned by modulated periodic force and time-delay. In contrast with the previous synthetic genetic networks based on logical stochastic resonance, the proposed system has two advantages. On one hand, adding modulated periodic force to the background noise can increase the length of the optimal noise plateau of obtaining desired logic response and make the system adapt to varying noise intensity. On the other hand, tuning time-delay can extend the optimal noise plateau to larger range. The result provides possible help for designing new genetic regulatory networks paradigm based on logical stochastic resonance.

  16. Synthetic

    Anna Maria Manferdini

    2010-06-01

    Full Text Available Traditionally materials have been associated with a series of physical properties that can be used as inputs to production and manufacturing. Recently we witnessed an interest in materials considered not only as ‘true matter’, but also as new breeds where geometry, texture, tooling and finish are able to provoke new sensations when they are applied to a substance. These artificial materials can be described as synthetic because they are the outcome of various qualities that are not necessarily true to the original matter, but they are the combination of two or more parts, whether by design or by natural processes. The aim of this paper is to investigate the potential of architectural surfaces to produce effects through the invention of new breeds of artificial matter, using micro-scale details derived from Nature as an inspiration.

  17. Genetic influences on phase synchrony of brain oscillations supporting response inhibition.

    Müller, Viktor; Anokhin, Andrey P; Lindenberger, Ulman

    2017-05-01

    Phase synchronization of neuronal oscillations is a fundamental mechanism underlying cognitive processing and behavior, including context-dependent response production and inhibition. Abnormalities in neural synchrony can lead to abnormal information processing and contribute to cognitive and behavioral deficits in neuropsychiatric disorders. However, little is known about genetic and environmental contributions to individual differences in cortical oscillatory dynamics underlying response inhibition. This study examined heritability of event-related phase synchronization of brain oscillations in 302 young female twins including 94 MZ and 57 DZ pairs performing a cued Go/No-Go version of the Continuous Performance Test (CPT). We used the Phase Locking Index (PLI) to assess inter-trial phase clustering (synchrony) in several frequency bands in two time intervals after stimulus onset (0-300 and 301-600ms). Response inhibition (i.e., successful response suppression in No-Go trials) was characterized by a transient increase in phase synchronization of delta- and theta-band oscillations in the fronto-central midline region. Genetic analysis showed significant heritability of the phase locking measures related to response inhibition, with 30 to 49% of inter-individual variability being accounted for by genetic factors. This is the first study providing evidence for heritability of task-related neural synchrony. The present results suggest that PLI can serve as an indicator of genetically transmitted individual differences in neural substrates of response inhibition. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Persistency of Prediction Accuracy and Genetic Gain in Synthetic Populations Under Recurrent Genomic Selection.

    Müller, Dominik; Schopp, Pascal; Melchinger, Albrecht E

    2017-03-10

    Recurrent selection (RS) has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents [Formula: see text] but little is known about how [Formula: see text] affects genomic selection (GS) in RS, especially the persistency of prediction accuracy ([Formula: see text]) and genetic gain. Synthetics were simulated by intermating [Formula: see text]= 2-32 parent lines from an ancestral population with short- or long-range linkage disequilibrium ([Formula: see text]) and subjected to multiple cycles of GS. We determined [Formula: see text] and genetic gain across 30 cycles for different training set ( TS ) sizes, marker densities, and generations of recombination before model training. Contributions to [Formula: see text] and genetic gain from pedigree relationships, as well as from cosegregation and [Formula: see text] between QTL and markers, were analyzed via four scenarios differing in (i) the relatedness between TS and selection candidates and (ii) whether selection was based on markers or pedigree records. Persistency of [Formula: see text] was high for small [Formula: see text] where predominantly cosegregation contributed to [Formula: see text], but also for large [Formula: see text] where [Formula: see text] replaced cosegregation as the dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing [Formula: see text] > 4, given long-range LD A in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed to [Formula: see text] for only very few generations in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS size ([Formula: see text]) and higher marker density improved persistency of

  19. Persistency of Prediction Accuracy and Genetic Gain in Synthetic Populations Under Recurrent Genomic Selection

    Dominik Müller

    2017-03-01

    Full Text Available Recurrent selection (RS has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents ( Np , but little is known about how Np affects genomic selection (GS in RS, especially the persistency of prediction accuracy (rg , g ^ and genetic gain. Synthetics were simulated by intermating Np= 2–32 parent lines from an ancestral population with short- or long-range linkage disequilibrium (LDA and subjected to multiple cycles of GS. We determined rg , g ^ and genetic gain across 30 cycles for different training set (TS sizes, marker densities, and generations of recombination before model training. Contributions to rg , g ^ and genetic gain from pedigree relationships, as well as from cosegregation and LDA between QTL and markers, were analyzed via four scenarios differing in (i the relatedness between TS and selection candidates and (ii whether selection was based on markers or pedigree records. Persistency of rg , g ^ was high for small Np , where predominantly cosegregation contributed to rg , g ^ , but also for large Np , where LDA replaced cosegregation as the dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing Np > 4, given long-range LDA in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed to rg , g ^ for only very few generations in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS size (NTS and higher marker density improved persistency of rg , g ^ and hence genetic gain, but additional recombinations could not increase genetic gain.

  20. Synthetic biology approaches in cancer immunotherapy, genetic network engineering, and genome editing.

    Chakravarti, Deboki; Cho, Jang Hwan; Weinberg, Benjamin H; Wong, Nicole M; Wong, Wilson W

    2016-04-18

    Investigations into cells and their contents have provided evolving insight into the emergence of complex biological behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. In this review, we will highlight the broad and vital role that the synthetic biology approach has played in applying fundamental biological discoveries in receptors, genetic circuits, and genome-editing systems towards translation in the fields of immunotherapy, biosensors, disease models and gene therapy. These examples are evidence of the strength of synthetic approaches, while also illustrating considerations that must be addressed when developing systems around living cells.

  1. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems

    Chen, Yvonne Y.; Jensen, Michael C.; Smolke, Christina D.

    2010-01-01

    RNA molecules perform diverse regulatory functions in natural biological systems, and numerous synthetic RNA-based control devices that integrate sensing and gene-regulatory functions have been demonstrated, predominantly in bacteria and yeast. Despite potential advantages of RNA-based genetic control strategies in clinical applications, there has been limited success in extending engineered RNA devices to mammalian gene-expression control and no example of their application to functional res...

  2. An optimization method of relativistic backward wave oscillator using particle simulation and genetic algorithms

    Chen, Zaigao; Wang, Jianguo [Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi' an Jiaotong University, Xi' an, Shaanxi 710049 (China); Northwest Institute of Nuclear Technology, P.O. Box 69-12, Xi' an, Shaanxi 710024 (China); Wang, Yue; Qiao, Hailiang; Zhang, Dianhui [Northwest Institute of Nuclear Technology, P.O. Box 69-12, Xi' an, Shaanxi 710024 (China); Guo, Weijie [Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi' an Jiaotong University, Xi' an, Shaanxi 710049 (China)

    2013-11-15

    Optimal design method of high-power microwave source using particle simulation and parallel genetic algorithms is presented in this paper. The output power, simulated by the fully electromagnetic particle simulation code UNIPIC, of the high-power microwave device is given as the fitness function, and the float-encoding genetic algorithms are used to optimize the high-power microwave devices. Using this method, we encode the heights of non-uniform slow wave structure in the relativistic backward wave oscillators (RBWO), and optimize the parameters on massively parallel processors. Simulation results demonstrate that we can obtain the optimal parameters of non-uniform slow wave structure in the RBWO, and the output microwave power enhances 52.6% after the device is optimized.

  3. Genetic interaction motif finding by expectation maximization – a novel statistical model for inferring gene modules from synthetic lethality

    Ye Ping

    2005-12-01

    Full Text Available Abstract Background Synthetic lethality experiments identify pairs of genes with complementary function. More direct functional associations (for example greater probability of membership in a single protein complex may be inferred between genes that share synthetic lethal interaction partners than genes that are directly synthetic lethal. Probabilistic algorithms that identify gene modules based on motif discovery are highly appropriate for the analysis of synthetic lethal genetic interaction data and have great potential in integrative analysis of heterogeneous datasets. Results We have developed Genetic Interaction Motif Finding (GIMF, an algorithm for unsupervised motif discovery from synthetic lethal interaction data. Interaction motifs are characterized by position weight matrices and optimized through expectation maximization. Given a seed gene, GIMF performs a nonlinear transform on the input genetic interaction data and automatically assigns genes to the motif or non-motif category. We demonstrate the capacity to extract known and novel pathways for Saccharomyces cerevisiae (budding yeast. Annotations suggested for several uncharacterized genes are supported by recent experimental evidence. GIMF is efficient in computation, requires no training and automatically down-weights promiscuous genes with high degrees. Conclusion GIMF effectively identifies pathways from synthetic lethality data with several unique features. It is mostly suitable for building gene modules around seed genes. Optimal choice of one single model parameter allows construction of gene networks with different levels of confidence. The impact of hub genes the generic probabilistic framework of GIMF may be used to group other types of biological entities such as proteins based on stochastic motifs. Analysis of the strongest motifs discovered by the algorithm indicates that synthetic lethal interactions are depleted between genes within a motif, suggesting that synthetic

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

    Medford, June; Prasad, Ashok

    2014-01-01

    Biological protein interactions networks such as signal transduction or gene transcription networks are often treated as modular, allowing motifs to be analyzed in isolation from the rest of the network. Modularity is also a key assumption in synthetic biology, where it is similarly expected that when network motifs are combined together, they do not lose their essential characteristics. However, the interactions that a network module has with downstream elements change the dynamical equations describing the upstream module and thus may change the dynamic and static properties of the upstream circuit even without explicit feedback. In this work we analyze the behavior of a ubiquitous motif in gene transcription and signal transduction circuits: the switch. We show that adding an additional downstream component to the simple genetic toggle switch changes its dynamical properties by changing the underlying potential energy landscape, and skewing it in favor of the unloaded side, and in some situations adding loads to the genetic switch can also abrogate bistable behavior. We find that an additional positive feedback motif found in naturally occurring toggle switches could tune the potential energy landscape in a desirable manner. We also analyze autocatalytic signal transduction switches and show that a ubiquitous positive feedback switch can lose its switch-like properties when connected to a downstream load. Our analysis underscores the necessity of incorporating the effects of downstream components when understanding the physics of biochemical network motifs, and raises the question as to how these effects are managed in real biological systems. This analysis is particularly important when scaling synthetic networks to more complex organisms. PMID:24676102

  5. Synthetic Biology Parts for the Storage of Increased Genetic Information in Cells.

    Morris, Sydney E; Feldman, Aaron W; Romesberg, Floyd E

    2017-10-20

    To bestow cells with novel forms and functions, the goal of synthetic biology, we have developed the unnatural nucleoside triphosphates dNaMTP and dTPT3TP, which form an unnatural base pair (UBP) and expand the genetic alphabet. While the UBP may be retained in the DNA of a living cell, its retention is sequence-dependent. We now report a steady-state kinetic characterization of the rate with which the Klenow fragment of E. coli DNA polymerase I synthesizes the UBP and its mispairs in a variety of sequence contexts. Correct UBP synthesis is as efficient as for a natural base pair, except in one sequence context, and in vitro performance is correlated with in vivo performance. The data elucidate the determinants of efficient UBP synthesis, show that the dNaM-dTPT3 UBP is the first generally recognized natural-like base pair, and importantly, demonstrate that dNaMTP and dTPT3TP are well optimized and standardized parts for the expansion of the genetic alphabet.

  6. The influence of climatic oscillations during the Quaternary Era on the genetic structure of Asian black bears in Japan.

    Ohnishi, N; Uno, R; Ishibashi, Y; Tamate, H B; Oi, T

    2009-06-01

    The Asian black bear (Ursus thibetanus) inhabits two of the main islands, Honshu and Shikoku, in Japan. To determine how climatic oscillations during the Quaternary Era affected the genetic structure of the black bear populations in Japan, we examined their phylogeographic relationships and compared their genetic structure. We analysed an approximately 700-bp sequence in the D-loop region of mitochondrial DNA collected from 589 bears in this study with 108 bears from a previous study. We observed a total of 57 haplotypes and categorized them into three clusters (Eastern, Western and Southern) based on the spatial distribution of the haplotypes. All but 2 of the 41 haplotypes in the Eastern cluster were distributed locally. Genetic diversity was generally low in northern Japan and high in central Japan. Demographic tests rejected the expansion model in northern populations. Haplotypes of the Western and Southern clusters were unique to local populations. We conclude that the extant genetic structure of the Asian black bear populations arose as follows: first, populations became small and genetic drift decreased genetic diversity in the northern area during the last glacial period, whereas large continuous populations existed in the southern part of central Japan. These patterns were essentially maintained until the present time. In western and southern Japan, the effects of climatic oscillations were smaller, and thus, local structure was maintained.

  7. A Blueprint for a Synthetic Genetic Feedback Controller to Reprogram Cell Fate.

    Del Vecchio, Domitilla; Abdallah, Hussein; Qian, Yili; Collins, James J

    2017-01-25

    To artificially reprogram cell fate, experimentalists manipulate the gene regulatory networks (GRNs) that maintain a cell's phenotype. In practice, reprogramming is often performed by constant overexpression of specific transcription factors (TFs). This process can be unreliable and inefficient. Here, we address this problem by introducing a new approach to reprogramming based on mathematical analysis. We demonstrate that reprogramming GRNs using constant overexpression may not succeed in general. Instead, we propose an alternative reprogramming strategy: a synthetic genetic feedback controller that dynamically steers the concentration of a GRN's key TFs to any desired value. The controller works by adjusting TF expression based on the discrepancy between desired and actual TF concentrations. Theory predicts that this reprogramming strategy is guaranteed to succeed, and its performance is independent of the GRN's structure and parameters, provided that feedback gain is sufficiently high. As a case study, we apply the controller to a model of induced pluripotency in stem cells. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  8. A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-offs on Phenotype Robustness in Biological Networks. Part III: Synthetic Gene Networks in Synthetic Biology

    Chen, Bor-Sen; Lin, Ying-Po

    2013-01-01

    Robust stabilization and environmental disturbance attenuation are ubiquitous systematic properties that are observed in biological systems at many different levels. The underlying principles for robust stabilization and environmental disturbance attenuation are universal to both complex biological systems and sophisticated engineering systems. In many biological networks, network robustness should be large enough to confer: intrinsic robustness for tolerating intrinsic parameter fluctuations; genetic robustness for buffering genetic variations; and environmental robustness for resisting environmental disturbances. Network robustness is needed so phenotype stability of biological network can be maintained, guaranteeing phenotype robustness. Synthetic biology is foreseen to have important applications in biotechnology and medicine; it is expected to contribute significantly to a better understanding of functioning of complex biological systems. This paper presents a unifying mathematical framework for investigating the principles of both robust stabilization and environmental disturbance attenuation for synthetic gene networks in synthetic biology. Further, from the unifying mathematical framework, we found that the phenotype robustness criterion for synthetic gene networks is the following: if intrinsic robustness + genetic robustness + environmental robustness ≦ network robustness, then the phenotype robustness can be maintained in spite of intrinsic parameter fluctuations, genetic variations, and environmental disturbances. Therefore, the trade-offs between intrinsic robustness, genetic robustness, environmental robustness, and network robustness in synthetic biology can also be investigated through corresponding phenotype robustness criteria from the systematic point of view. Finally, a robust synthetic design that involves network evolution algorithms with desired behavior under intrinsic parameter fluctuations, genetic variations, and environmental

  9. Decomposing Additive Genetic Variance Revealed Novel Insights into Trait Evolution in Synthetic Hexaploid Wheat

    Abdulqader Jighly

    2018-02-01

    Full Text Available Whole genome duplication (WGD is an evolutionary phenomenon, which causes significant changes to genomic structure and trait architecture. In recent years, a number of studies decomposed the additive genetic variance explained by different sets of variants. However, they investigated diploid populations only and none of the studies examined any polyploid organism. In this research, we extended the application of this approach to polyploids, to differentiate the additive variance explained by the three subgenomes and seven sets of homoeologous chromosomes in synthetic allohexaploid wheat (SHW to gain a better understanding of trait evolution after WGD. Our SHW population was generated by crossing improved durum parents (Triticum turgidum; 2n = 4x = 28, AABB subgenomes with the progenitor species Aegilops tauschii (syn Ae. squarrosa, T. tauschii; 2n = 2x = 14, DD subgenome. The population was phenotyped for 10 fungal/nematode resistance traits as well as two abiotic stresses. We showed that the wild D subgenome dominated the additive effect and this dominance affected the A more than the B subgenome. We provide evidence that this dominance was not inflated by population structure, relatedness among individuals or by longer linkage disequilibrium blocks observed in the D subgenome within the population used for this study. The cumulative size of the three homoeologs of the seven chromosomal groups showed a weak but significant positive correlation with their cumulative explained additive variance. Furthermore, an average of 69% for each chromosomal group's cumulative additive variance came from one homoeolog that had the highest explained variance within the group across all 12 traits. We hypothesize that structural and functional changes during diploidization may explain chromosomal group relations as allopolyploids keep balanced dosage for many genes. Our results contribute to a better understanding of trait evolution mechanisms in polyploidy

  10. Improved Alkane Production in Nitrogen-Fixing and Halotolerant Cyanobacteria via Abiotic Stresses and Genetic Manipulation of Alkane Synthetic Genes.

    Kageyama, Hakuto; Waditee-Sirisattha, Rungaroon; Sirisattha, Sophon; Tanaka, Yoshito; Mahakhant, Aparat; Takabe, Teruhiro

    2015-07-01

    Cyanobacteria possess the unique capacity to produce alkane. In this study, effects of nitrogen deficiency and salt stress on biosynthesis of alkanes were investigated in three kinds of cyanobacteria. Intracellular alkane accumulation was increased in nitrogen-fixing cyanobacterium Anabaena sp. PCC7120, but decreased in non-diazotrophic cyanobacterium Synechococcus elongatus PCC7942 and constant in a halotolerant cyanobacterium Aphanothece halophytica under nitrogen-deficient condition. We also found that salt stress increased alkane accumulation in Anabaena sp. PCC7120 and A. halophytica. The expression levels of two alkane synthetic genes were not upregulated significantly under nitrogen deficiency or salt stress in Anabaena sp. PCC7120. The transformant Anabaena sp. PCC7120 cells with additional alkane synthetic gene set from A. halophytica increased intracellular alkane accumulation level compared to control cells. These results provide a prospect to improve bioproduction of alkanes in nitrogen-fixing halotolerant cyanobacteria via abiotic stresses and genetic engineering.

  11. Novel synthetic Medea selfish genetic elements drive population replacement in Drosophila; a theoretical exploration of Medea-dependent population suppression.

    Akbari, Omar S; Chen, Chun-Hong; Marshall, John M; Huang, Haixia; Antoshechkin, Igor; Hay, Bruce A

    2014-12-19

    Insects act as vectors for diseases of plants, animals, and humans. Replacement of wild insect populations with genetically modified individuals unable to transmit disease provides a potentially self-perpetuating method of disease prevention. Population replacement requires a gene drive mechanism in order to spread linked genes mediating disease refractoriness through wild populations. We previously reported the creation of synthetic Medea selfish genetic elements able to drive population replacement in Drosophila. These elements use microRNA-mediated silencing of myd88, a maternally expressed gene required for embryonic dorso-ventral pattern formation, coupled with early zygotic expression of a rescuing transgene, to bring about gene drive. Medea elements that work through additional mechanisms are needed in order to be able to carry out cycles of population replacement and/or remove existing transgenes from the population, using second-generation elements that spread while driving first-generation elements out of the population. Here we report the synthesis and population genetic behavior of two new synthetic Medea elements that drive population replacement through manipulation of signaling pathways involved in cellular blastoderm formation or Notch signaling, demonstrating that in Drosophila Medea elements can be generated through manipulation of diverse signaling pathways. We also describe the mRNA and small RNA changes in ovaries and early embryos associated from Medea-bearing females. Finally, we use modeling to illustrate how Medea elements carrying genes that result in diapause-dependent female lethality could be used to bring about population suppression.

  12. A novel optogenetically tunable frequency modulating oscillator.

    Tarun Mahajan

    Full Text Available Synthetic biology has enabled the creation of biological reconfigurable circuits, which perform multiple functions monopolizing a single biological machine; Such a system can switch between different behaviours in response to environmental cues. Previous work has demonstrated switchable dynamical behaviour employing reconfigurable logic gate genetic networks. Here we describe a computational framework for reconfigurable circuits in E.coli using combinations of logic gates, and also propose the biological implementation. The proposed system is an oscillator that can exhibit tunability of frequency and amplitude of oscillations. Further, the frequency of operation can be changed optogenetically. Insilico analysis revealed that two-component light systems, in response to light within a frequency range, can be used for modulating the frequency of the oscillator or stopping the oscillations altogether. Computational modelling reveals that mixing two colonies of E.coli oscillating at different frequencies generates spatial beat patterns. Further, we show that these oscillations more robustly respond to input perturbations compared to the base oscillator, to which the proposed oscillator is a modification. Compared to the base oscillator, the proposed system shows faster synchronization in a colony of cells for a larger region of the parameter space. Additionally, the proposed oscillator also exhibits lesser synchronization error in the transient period after input perturbations. This provides a strong basis for the construction of synthetic reconfigurable circuits in bacteria and other organisms, which can be scaled up to perform functions in the field of time dependent drug delivery with tunable dosages, and sets the stage for further development of circuits with synchronized population level behaviour.

  13. Parallel responses of species and genetic diversity to El Nino Southern Oscillation-induced environmental destruction

    Cleary, D.F.R.; Fauvelot, C.Y.; Genner, J.; Menken, S.B.J.; Mooers, A.O.

    2006-01-01

    Species diversity within communities and genetic diversity within species are two fundamental levels of biodiversity. Positive relationships between species richness and within-species genetic diversity have recently been documented across natural and semi-natural habitat islands, leading Vellend to

  14. pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes

    Arévalo-Rodríguez Miguel

    2011-02-01

    Full Text Available Abstract Background Since publication in 1977 of plasmid pBR322, many breakthroughs in Biology have depended on increasingly sophisticated vector platforms for analysis and engineering of given bacterial strains. Although restriction sites impose a certain format in the procedures for assembling cloned genes, every attempt thus far to standardize vector architecture and nomenclature has ended up in failure. While this state of affairs may still be tolerable for traditional one-at-a-time studies of single genes, the onset of systems and synthetic biology calls for a simplification -along with an optimization- of the currently unwieldy pool of genetic tools. Results The functional DNA sequences present in the natural bacterial transposon Tn5 have been methodically edited and refactored for the production of a multi-purpose genetic tool named pBAM1, which allows a range of manipulations in the genome of Gram-negative bacteria. This all-synthetic construct enhances the power of mini-transposon vectors for either de-construction or re-construction of phenotypes á la carte by incorporating features inspired in systems engineering: modularity, re-usability, minimization, and compatibility with other genetic tools. pBAM1 bears an streamlined, restriction site-freed and narrow-host range replication frame bearing the sequences of R6K oriV, oriT and an ampicillin resistance marker. These go along with a business module that contains a host-independent and hyperactive transposition platform for in vivo or in vitro insertion of desired DNA into the genome of the target bacterium. All functional sequences were standardized for a straightforward replacement by equivalent counterparts, if required. pBAM1 can be delivered into recipient cells by either mating or electroporation, producing transposon insertion frequencies of 1.8 × 10-3 and 1.02 × 10-7, respectively in the soil bacterium Pseudomonas putida. Analyses of the resulting clones revealed a 100% of

  15. Genetically transformed tobacco plants expressing synthetic EPSPS gene confer tolerance against glyphosate herbicide.

    Imran, Muhammad; Asad, Shaheen; Barboza, Andre Luiz; Galeano, Esteban; Carrer, Helaine; Mukhtar, Zahid

    2017-04-01

    Glyphosate quashes the synthesis of 5-enolpyruvylshikimate-3- phosphate synthase (EPSPS) enzyme which intercedes the functioning of shikimate pathway for the production of aromatic amino acids. Herbicide resistant crops are developed using glyphosate insensitive EPSPS gene isolated from Agrobacterium sp. strain CP4, which give farmers a sustainable weed control option. Intentions behind this study were to design and characterize the synthetic herbicide resistant CP4 - EPSPS gene in a model plant system and check the effectiveness of transformed tobacco against application of glyphosate. Putative transgenic plants were obtained from independent transformation events, and stable plant transformation, transgene expression and integration were demonstrated respectively by PCR, qRT-PCR and Southern hybridization. Gene transcript level and gene copy number (1-4) varied among the tested transgenic tobacco lines. Herbicide assays showed that transgenic plants were resistant to glyphosate after 12 days of spraying with glyphosate, and EPSPS activity remained at sufficient level to withstand the spray at 1000 ppm of the chemical. T 1 plants analyzed through immunoblot strips and PCR showed that the gene was being translated into protein and transmitted to the next generation successfully. This codon optimized synthetic CP4 - EPSPS gene is functionally equivalent to the gene for glyphosate resistance available in the commercial crops and hence we recommend this gene for transformation into commercial crops.

  16. A synthetic maternal-effect selfish genetic element drives population replacement in Drosophila.

    Chen, Chun-Hong; Huang, Haixia; Ward, Catherine M; Su, Jessica T; Schaeffer, Lorian V; Guo, Ming; Hay, Bruce A

    2007-04-27

    One proposed strategy for controlling the transmission of insect-borne pathogens uses a drive mechanism to ensure the rapid spread of transgenes conferring disease refractoriness throughout wild populations. Here, we report the creation of maternal-effect selfish genetic elements in Drosophila that drive population replacement and are resistant to recombination-mediated dissociation of drive and disease refractoriness functions. These selfish elements use microRNA-mediated silencing of a maternally expressed gene essential for embryogenesis, which is coupled with early zygotic expression of a rescuing transgene.

  17. GENETIC VARIATION IN RED RASPBERRIES (RUBUS IDAEUS L.; ROSACEAE) FROM SITES DIFFERING IN ORGANIC POLLUTANTS COMPARED WITH SYNTHETIC TANDEM REPEAT DNA PROBES

    Two synthetic tandem repetitive DNA probes were used to compare genetic variation at variable-number-tandem-repeat (VNTR) loci among Rubus idaeus L. var. strigosus (Michx.) Maxim. (Rosaceae) individuals sampled at eight sites contaminated by pollutants (N = 39) and eight adjacent...

  18. Synthetic Botany.

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

    2017-07-05

    Plants are attractive platforms for synthetic biology and metabolic engineering. Plants' modular and plastic body plans, capacity for photosynthesis, extensive secondary metabolism, and agronomic systems for large-scale production make them ideal targets for genetic reprogramming. However, efforts in this area have been constrained by slow growth, long life cycles, the requirement for specialized facilities, a paucity of efficient tools for genetic manipulation, and the complexity of multicellularity. There is a need for better experimental and theoretical frameworks to understand the way genetic networks, cellular populations, and tissue-wide physical processes interact at different scales. We highlight new approaches to the DNA-based manipulation of plants and the use of advanced quantitative imaging techniques in simple plant models such as Marchantia polymorpha. These offer the prospects of improved understanding of plant dynamics and new approaches to rational engineering of plant traits. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  19. Plant synthetic biology.

    Liu, Wusheng; Stewart, C Neal

    2015-05-01

    Plant synthetic biology is an emerging field that combines engineering principles with plant biology toward the design and production of new devices. This emerging field should play an important role in future agriculture for traditional crop improvement, but also in enabling novel bioproduction in plants. In this review we discuss the design cycles of synthetic biology as well as key engineering principles, genetic parts, and computational tools that can be utilized in plant synthetic biology. Some pioneering examples are offered as a demonstration of how synthetic biology can be used to modify plants for specific purposes. These include synthetic sensors, synthetic metabolic pathways, and synthetic genomes. We also speculate about the future of synthetic biology of plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Genetic influences on functional connectivity associated with feedback processing and prediction error: Phase coupling of theta-band oscillations in twins.

    Demiral, Şükrü Barış; Golosheykin, Simon; Anokhin, Andrey P

    2017-05-01

    Detection and evaluation of the mismatch between the intended and actually obtained result of an action (reward prediction error) is an integral component of adaptive self-regulation of behavior. Extensive human and animal research has shown that evaluation of action outcome is supported by a distributed network of brain regions in which the anterior cingulate cortex (ACC) plays a central role, and the integration of distant brain regions into a unified feedback-processing network is enabled by long-range phase synchronization of cortical oscillations in the theta band. Neural correlates of feedback processing are associated with individual differences in normal and abnormal behavior, however, little is known about the role of genetic factors in the cerebral mechanisms of feedback processing. Here we examined genetic influences on functional cortical connectivity related to prediction error in young adult twins (age 18, n=399) using event-related EEG phase coherence analysis in a monetary gambling task. To identify prediction error-specific connectivity pattern, we compared responses to loss and gain feedback. Monetary loss produced a significant increase of theta-band synchronization between the frontal midline region and widespread areas of the scalp, particularly parietal areas, whereas gain resulted in increased synchrony primarily within the posterior regions. Genetic analyses showed significant heritability of frontoparietal theta phase synchronization (24 to 46%), suggesting that individual differences in large-scale network dynamics are under substantial genetic control. We conclude that theta-band synchronization of brain oscillations related to negative feedback reflects genetically transmitted differences in the neural mechanisms of feedback processing. To our knowledge, this is the first evidence for genetic influences on task-related functional brain connectivity assessed using direct real-time measures of neuronal synchronization. Copyright © 2016

  1. Synthetic virus seeds for improved vaccine safety: Genetic reconstruction of poliovirus seeds for a PER.C6 cell based inactivated poliovirus vaccine.

    Sanders, Barbara P; Edo-Matas, Diana; Papic, Natasa; Schuitemaker, Hanneke; Custers, Jerome H H V

    2015-10-13

    Safety of vaccines can be compromised by contamination with adventitious agents. One potential source of adventitious agents is a vaccine seed, typically derived from historic clinical isolates with poorly defined origins. Here we generated synthetic poliovirus seeds derived from chemically synthesized DNA plasmids encoding the sequence of wild-type poliovirus strains used in marketed inactivated poliovirus vaccines. The synthetic strains were phenotypically identical to wild-type polioviruses as shown by equivalent infectious titers in culture supernatant and antigenic content, even when infection cultures are scaled up to 10-25L bioreactors. Moreover, the synthetic seeds were genetically stable upon extended passaging on the PER.C6 cell culture platform. Use of synthetic seeds produced on the serum-free PER.C6 cell platform ensures a perfectly documented seed history and maximum control over starting materials. It provides an opportunity to maximize vaccine safety which increases the prospect of a vaccine end product that is free from adventitious agents. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network

    Han Kyungsook

    2010-06-01

    Full Text Available Abstract Background Genetic interaction profiles are highly informative and helpful for understanding the functional linkages between genes, and therefore have been extensively exploited for annotating gene functions and dissecting specific pathway structures. However, our understanding is rather limited to the relationship between double concurrent perturbation and various higher level phenotypic changes, e.g. those in cells, tissues or organs. Modifier screens, such as synthetic genetic arrays (SGA can help us to understand the phenotype caused by combined gene mutations. Unfortunately, exhaustive tests on all possible combined mutations in any genome are vulnerable to combinatorial explosion and are infeasible either technically or financially. Therefore, an accurate computational approach to predict genetic interaction is highly desirable, and such methods have the potential of alleviating the bottleneck on experiment design. Results In this work, we introduce a computational systems biology approach for the accurate prediction of pairwise synthetic genetic interactions (SGI. First, a high-coverage and high-precision functional gene network (FGN is constructed by integrating protein-protein interaction (PPI, protein complex and gene expression data; then, a graph-based semi-supervised learning (SSL classifier is utilized to identify SGI, where the topological properties of protein pairs in weighted FGN is used as input features of the classifier. We compare the proposed SSL method with the state-of-the-art supervised classifier, the support vector machines (SVM, on a benchmark dataset in S. cerevisiae to validate our method's ability to distinguish synthetic genetic interactions from non-interaction gene pairs. Experimental results show that the proposed method can accurately predict genetic interactions in S. cerevisiae (with a sensitivity of 92% and specificity of 91%. Noticeably, the SSL method is more efficient than SVM, especially for

  3. Molecular Cloning Designer Simulator (MCDS: All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects

    Zhenyu Shi

    2016-12-01

    Full Text Available Molecular Cloning Designer Simulator (MCDS is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1 it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2 it can perform a user-defined workflow of cloning steps in a single execution of the software; (3 it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4 it includes experimental information to conveniently guide wet lab work; and (5 it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. Keywords: BioCAD, Genetic engineering software, Molecular cloning software, Synthetic biology, Workflow simulation and management

  4. Novel Synthetic Medea selfish genetic elements drive population replacement in Drosophila, and a theoretical exploration of Medea-dependent population suppression

    Akbari, Omar S.; Chen, Chun-Hong; Marshall, John M.; Huang, Haixia; Antoshechkin, Igor; Hay, Bruce A.

    2013-01-01

    Insects act as vectors for diseases of plants, animals and humans. Replacement of wild insect populations with genetically modified individuals unable to transmit disease provides a potentially self-perpetuating method of disease prevention. Population replacement requires a gene drive mechanism in order to spread linked genes mediating disease refractoriness through wild populations. We previously reported the creation of synthetic Medea selfish genetic elements able to drive population replacement in Drosophila. These elements use microRNA-mediated silencing of myd88, a maternally expressed gene required for embryonic dorso-ventral pattern formation, coupled with early zygotic expression of a rescuing transgene, to bring about gene drive. Medea elements that work through additional mechanisms are needed in order to be able to carry out cycles of population replacement and/or remove existing transgenes from the population, using second-generation elements that spread while driving first-generation elements out of the population. Here we report the synthesis and population genetic behavior of two new synthetic Medea elements that drive population replacement through manipulation of signaling pathways involved in cellular blastoderm formation or Notch signaling, demonstrating that in Drosophila Medea elements can be generated through manipulation of diverse signaling pathways. We also describe the mRNA and small RNA changes in ovaries and early embryos associated from Medea-bearing females. Finally, we use modeling to illustrate how Medea elements carrying genes that result in diapause-dependent female lethality could be used to bring about population suppression. PMID:23654248

  5. Assessment of genetic fidelity in Rauvolfia serpentina plantlets grown from synthetic (encapsulated) seeds following in vitro storage at 4 °C.

    Faisal, Mohammad; Alatar, Abdulrahman A; Ahmad, Naseem; Anis, Mohammad; Hegazy, Ahmad K

    2012-05-03

    An efficient method was developed for plant regeneration and establishment from alginate encapsulated synthetic seeds of Rauvolfia serpentina. Synthetic seeds were produced using in vitro proliferated microshoots upon complexation of 3% sodium alginate prepared in Llyod and McCown woody plant medium (WPM) and 100 mM calcium chloride. Re-growth ability of encapsulated nodal segments was evaluated after storage at 4 °C for 0, 1, 2, 4, 6 and 8 weeks and compared with non-encapsulated buds. Effects of different media viz; Murashige and Skoog medium; Lloyd and McCown woody Plant medium, Gamborg’s B5 medium and Schenk and Hildebrandt medium was also investigated for conversion into plantlets. The maximum frequency of conversion into plantlets from encapsulated nodal segments stored at 4 °C for 4 weeks was achieved on woody plant medium supplement with 5.0 μM BA and 1.0 μM NAA. Rooting in plantlets was achieved in half-strength Murashige and Skoog liquid medium containing 0.5 μM indole-3-acetic acid (IAA) on filter paper bridges. Plantlets obtained from stored synseeds were hardened, established successfully ex vitro and were morphologically similar to each other as well as their mother plant. The genetic fidelity of Rauvolfia clones raised from synthetic seeds following four weeks of storage at 4 °C were assessed by using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. All the RAPD and ISSR profiles from generated plantlets were monomorphic and comparable to the mother plant, which confirms the genetic stability among the clones. This synseed protocol could be useful for establishing a particular system for conservation, short-term storage and production of genetically identical and stable plants before it is released for commercial purposes.

  6. Pleistocene climatic oscillations rather than recent human disturbance influence genetic diversity in one of the world's highest treeline species.

    Peng, Yanling; Lachmuth, Susanne; Gallegos, Silvia C; Kessler, Michael; Ramsay, Paul M; Renison, Daniel; Suarez, Ricardo; Hensen, Isabell

    2015-10-01

    Biological responses to climatic change usually leave imprints on the genetic diversity and structure of plants. Information on the current genetic diversity and structure of dominant tree species has facilitated our general understanding of phylogeographical patterns. Using amplified fragment length polymorphism (AFLPs), we compared genetic diversity and structure of 384 adults of P. tarapacana with those of 384 seedlings across 32 forest sites spanning a latitudinal gradient of 600 km occurring between 4100 m and 5000 m a.s.l. in Polylepis tarapacana (Rosaceae), one of the world's highest treeline species endemic to the central Andes. Moderate to high levels of genetic diversity and low genetic differentiation were detected in both adults and seedlings, with levels of genetic diversity and differentiation being almost identical. Four slightly genetically divergent clusters were identified that accorded to differing geographical regions. Genetic diversity decreased from south to north and with increasing precipitation for adults and seedlings, but there was no relationship to elevation. Our study shows that, unlike the case for other Andean treeline species, recent human activities have not affected the genetic structure of P. tarapacana, possibly because its inhospitable habitat is unsuitable for agriculture. The current genetic pattern of P. tarapacana points to a historically more widespread distribution at lower altitudes, which allowed considerable gene flow possibly during the glacial periods of the Pleistocene epoch, and also suggests that the northern Argentinean Andes may have served as a refugium for historical populations. © 2015 Botanical Society of America.

  7. The influence of oscillating electromagnetic fields on membrane structure and function: Synthetic liposome and natural membrane bilayer systems with direct application to the controlled delivery of chemical agents

    Liburdy, R.P.; de Manincor, D.; Fingado, B.

    1989-09-01

    Investigations have been conducted to determine if an imposed electromagnetic field can influence membrane transport, and ion and drug permeability in both synthetic and natural cell membrane systems. Microwave fields enhance accumulation of sodium in the lymphocyte and induce protein shedding at Tc. Microwaves also trigger membrane permeability of liposome systems under specific field exposure conditions. Sensitivity varies in a defined way in bilayers displaying a membrane structural phase transition temperature, Tc; maximal release was observed at or near Tc. Significantly, liposome systems without a membrane phase transition were also found to experience permeability increases but, in contrast, this response was temperature independent. The above results indicate that field-enhanced drug release occurs in liposome vesicles that possess a Tc as well as non-Tc liposomes. Additional studies extend non-Tc liposome responses to the in vivo case in which microwaves trigger Gentamicin release from a liposome ''depot'' placed subcutaneously in the rat hind leg. In addition, evidence is provided that cell surface sequestered liposomes can be triggered by microwave fields to release drugs directly into target cells. 24 refs., 6 figs

  8. Models for synthetic biology.

    Kaznessis, Yiannis N

    2007-11-06

    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.

  9. Synthetic Brainbows

    Wan, Y.

    2013-06-01

    Brainbow is a genetic engineering technique that randomly colorizes cells. Biological samples processed with this technique and imaged with confocal microscopy have distinctive colors for individual cells. Complex cellular structures can then be easily visualized. However, the complexity of the Brainbow technique limits its applications. In practice, most confocal microscopy scans use different florescence staining with typically at most three distinct cellular structures. These structures are often packed and obscure each other in rendered images making analysis difficult. In this paper, we leverage a process known as GPU framebuffer feedback loops to synthesize Brainbow-like images. In addition, we incorporate ID shuffing and Monte-Carlo sampling into our technique, so that it can be applied to single-channel confocal microscopy data. The synthesized Brainbow images are presented to domain experts with positive feedback. A user survey demonstrates that our synthetic Brainbow technique improves visualizations of volume data with complex structures for biologists.

  10. Reporter-Based Synthetic Genetic Array Analysis: A Functional Genomics Approach for Investigating Transcript or Protein Abundance Using Fluorescent Proteins in Saccharomyces cerevisiae.

    Göttert, Hendrikje; Mattiazzi Usaj, Mojca; Rosebrock, Adam P; Andrews, Brenda J

    2018-01-01

    Fluorescent reporter genes have long been used to quantify various cell features such as transcript and protein abundance. Here, we describe a method, reporter synthetic genetic array (R-SGA) analysis, which allows for the simultaneous quantification of any fluorescent protein readout in thousands of yeast strains using an automated pipeline. R-SGA combines a fluorescent reporter system with standard SGA analysis and can be used to examine any array-based strain collection available to the yeast community. This protocol describes the R-SGA methodology for screening different arrays of yeast mutants including the deletion collection, a collection of temperature-sensitive strains for the assessment of essential yeast genes and a collection of inducible overexpression strains. We also present an alternative pipeline for the analysis of R-SGA output strains using flow cytometry of cells in liquid culture. Data normalization for both pipelines is discussed.

  11. Small molecule inhibitors uncover synthetic genetic interactions of human flap endonuclease 1 (FEN1 with DNA damage response genes.

    Thomas A Ward

    Full Text Available Flap endonuclease 1 (FEN1 is a structure selective endonuclease required for proficient DNA replication and the repair of DNA damage. Cellularly active inhibitors of this enzyme have previously been shown to induce a DNA damage response and, ultimately, cell death. High-throughput screens of human cancer cell-lines identify colorectal and gastric cell-lines with microsatellite instability (MSI as enriched for cellular sensitivity to N-hydroxyurea series inhibitors of FEN1, but not the PARP inhibitor olaparib or other inhibitors of the DNA damage response. This sensitivity is due to a synthetic lethal interaction between FEN1 and MRE11A, which is often mutated in MSI cancers through instabilities at a poly(T microsatellite repeat. Disruption of ATM is similarly synthetic lethal with FEN1 inhibition, suggesting that disruption of FEN1 function leads to the accumulation of DNA double-strand breaks. These are likely a result of the accumulation of aberrant replication forks, that accumulate as a consequence of a failure in Okazaki fragment maturation, as inhibition of FEN1 is toxic in cells disrupted for the Fanconi anemia pathway and post-replication repair. Furthermore, RAD51 foci accumulate as a consequence of FEN1 inhibition and the toxicity of FEN1 inhibitors increases in cells disrupted for the homologous recombination pathway, suggesting a role for homologous recombination in the resolution of damage induced by FEN1 inhibition. Finally, FEN1 appears to be required for the repair of damage induced by olaparib and cisplatin within the Fanconi anemia pathway, and may play a role in the repair of damage associated with its own disruption.

  12. Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects.

    Shi, Zhenyu; Vickers, Claudia E

    2016-12-01

    Molecular Cloning Designer Simulator (MCDS) is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2) it can perform a user-defined workflow of cloning steps in a single execution of the software; (3) it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and (5) it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com.

  13. Novel genetic diversity of the alien D-genome synthetic hexaploid wheat (2n=6x=42, Aabbdd) germplasm for various phenology traits

    Masood, R.M.; Bibi, K.; Jamil, M.

    2016-01-01

    The current study evaluates genetic penetrance and expressivity of an alien genome introgression in a set of 117 primary synthetic hexaploid wheat (SHW) accessions. These SHW have originated from durum wheat /accessions with three sets of durum wheat cultivars ALTAR 84, D67.2 and CERCETA as the female and diverse Ae. tauschii accessions as the pollen parents. Diversity of the 12 important traits (Growth habit, pigmentation, chlorophyll content, leaf area index, crop digital ground cover, awn size, awn length, and several seed digital imaging parameters)revealed significant variation for the respective traits, leading to the conclusion that Ae. tauschii accessions have tremendous diversity than the durum controls. Further, the value deviations within each attribute had a range of being lower or higher than their durum wheat female parents and these observations allowed us to use the variations as selective sieves and narrow down the desirable SHW that would be advantageous to exploit for wheat breeding and cultivar improvement programs. Selections were made and a group of 41SHW accessions were identified that will after an intermediate DNA diversity evaluation form a crisper final set for user friendly utilization. The range of selections shows multiple trait advantages for exploitation in both irrigated and rain-fed conditions. This pivotal study sets the foundation to better define the D genome SHW for efficient utilization in future research investigations. Our results have implications in widening the genetic base of hexaploid bread wheat and may facilitate the development of agronomically desirable wheat cultivars. (author)

  14. Complex and unexpected dynamics in simple genetic regulatory networks

    Borg, Yanika; Ullner, Ekkehard; Alagha, Afnan; Alsaedi, Ahmed; Nesbeth, Darren; Zaikin, Alexey

    2014-03-01

    One aim of synthetic biology is to construct increasingly complex genetic networks from interconnected simpler ones to address challenges in medicine and biotechnology. However, as systems increase in size and complexity, emergent properties lead to unexpected and complex dynamics due to nonlinear and nonequilibrium properties from component interactions. We focus on four different studies of biological systems which exhibit complex and unexpected dynamics. Using simple synthetic genetic networks, small and large populations of phase-coupled quorum sensing repressilators, Goodwin oscillators, and bistable switches, we review how coupled and stochastic components can result in clustering, chaos, noise-induced coherence and speed-dependent decision making. A system of repressilators exhibits oscillations, limit cycles, steady states or chaos depending on the nature and strength of the coupling mechanism. In large repressilator networks, rich dynamics can also be exhibited, such as clustering and chaos. In populations of Goodwin oscillators, noise can induce coherent oscillations. In bistable systems, the speed with which incoming external signals reach steady state can bias the network towards particular attractors. These studies showcase the range of dynamical behavior that simple synthetic genetic networks can exhibit. In addition, they demonstrate the ability of mathematical modeling to analyze nonlinearity and inhomogeneity within these systems.

  15. Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America.

    Sproul, John S; Houston, Derek D; Nelson, C Riley; Evans, R Paul; Crandall, Keith A; Shiozawa, Dennis K

    2015-12-12

    Phylogeographic studies of aquatic insects provide valuable insights into mechanisms that shape the genetic structure of communities, yet studies that include broad geographic areas are uncommon for this group. We conducted a broad scale phylogeographic analysis of the least salmonfly Pteronarcella badia (Plecoptera) across western North America. We tested hypotheses related to mode of dispersal and the influence of historic climate oscillations on population genetic structure. In order to generate a larger mitochondrial data set, we used 454 sequencing to reconstruct the complete mitochondrial genome in the early stages of the project. Our analysis revealed high levels of population structure with several deeply divergent clades present across the sample area. Evidence from five mitochondrial genes and one nuclear locus identified a potentially cryptic lineage in the Pacific Northwest. Gene flow estimates and geographic clade distributions suggest that overland flight during the winged adult stage is an important dispersal mechanism for this taxon. We found evidence of multiple glacial refugia across the species distribution and signs of secondary contact within and among major clades. This study provides a basis for future studies of aquatic insect phylogeography at the inter-basin scale in western North America. Our findings add to an understanding of the role of historical climate isolations in shaping assemblages of aquatic insects in this region. We identified several geographic areas that may have historical importance for other aquatic organisms with similar distributions and dispersal strategies as P. badia. This work adds to the ever-growing list of studies that highlight the potential of next-generation DNA sequencing in a phylogenetic context to improve molecular data sets from understudied groups.

  16. Oscillator monitor

    McNeill, G.A.

    1981-01-01

    Present high-speed data acquisition systems in nuclear diagnostics use high-frequency oscillators to provide timing references for signals recorded on fast, traveling-wave oscilloscopes. An oscillator's sinusoidal wave shape is superimposed on the recorded signal with each cycle representing a fixed time increment. During data analysis the sinusoid is stripped from the signal, leaving a clean signal shape with known timing. Since all signal/time relationships are totally dependant upon working oscillators, these critical devices must have remote verification of proper operation. This manual presents the newly-developed oscillator monitor which will provide the required verification

  17. Chromospheric oscillations

    Lites, B.W.; Rutten, R.J.; Thomas, J.H.

    1995-01-01

    We show results from SO/Sacramento Peak data to discuss three issues: (i)--the spatial occurrence of chromospheric 3--min oscillations; (ii)--the validity of Ca II H&K line-center Doppler Shift measurements; (iii)--the signi ?cance of oscillation power and phase at frequencies above 10 mHz.

  18. Inverted oscillator

    Yuce, C [Physics Department, Anadolu University, Eskisehir (Turkey); Kilic, A [Physics Department, Anadolu University, Eskisehir (Turkey); Coruh, A [Physics Department, Sakarya University, Sakarya (Turkey)

    2006-07-15

    The inverted harmonic oscillator problem is investigated quantum mechanically. The exact wavefunction for the confined inverted oscillator is obtained and it is shown that the associated energy eigenvalues are discrete, and the energy is given as a linear function of the quantum number n.

  19. Synthetic Cannabinoids

    Aslihan Okan Ibiloglu

    2017-09-01

    Full Text Available Synthetic cannabinoids which is a subgroup of cannabinoids are commonly used for recreational drug use throughout the whole world. Although both marijuana and synthetic cannabinoids stimulate the same receptors, cannabinoid receptor 1 (CB1 and cannabinoid receptor 2 (CB2, studies have shown that synthetic cannabinoids are much more potent than marijuana. The longer use of synthetic cannabinoids can cause severe physical and psychological symptoms that might even result in death, similar to many known illicit drugs. Main treatment options mostly involve symptom management and supportive care. The aim of this article is to discuss clinical and pharmacological properties of the increasingly used synthetic cannabinoids. [Psikiyatride Guncel Yaklasimlar - Current Approaches in Psychiatry 2017; 9(3.000: 317-328

  20. Chemical Oscillations

    IMTECH),. Chandigarh. Praveen Kumar is pursuing his PhD in chemical dynamics at. Panjab University,. Chandigarh. Keywords. Chemical oscillations, autoca-. talYSis, Lotka-Volterra model, bistability, hysteresis, Briggs-. Rauscher reaction.

  1. Chemical Oscillations

    the law of mass-action that every simple reaction approaches ... from thermodynamic equilibrium. Such oscillating systems cor- respond to thermodynamically open systems. .... experimentally observable, and the third is always unstable.

  2. Synthetic biology and metabolic engineering.

    Stephanopoulos, Gregory

    2012-11-16

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

  3. Synthetic environments

    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.

  4. Nonlinear oscillations

    Nayfeh, Ali Hasan

    1995-01-01

    Nonlinear Oscillations is a self-contained and thorough treatment of the vigorous research that has occurred in nonlinear mechanics since 1970. The book begins with fundamental concepts and techniques of analysis and progresses through recent developments and provides an overview that abstracts and introduces main nonlinear phenomena. It treats systems having a single degree of freedom, introducing basic concepts and analytical methods, and extends concepts and methods to systems having degrees of freedom. Most of this material cannot be found in any other text. Nonlinear Oscillations uses sim

  5. BNN-20, a synthetic microneurotrophin, strongly protects dopaminergic neurons in the "weaver" mouse, a genetic model of dopamine-denervation, acting through the TrkB neurotrophin receptor.

    Botsakis, Konstantinos; Mourtzi, Theodora; Panagiotakopoulou, Vasiliki; Vreka, Malamati; Stathopoulos, Georgios T; Pediaditakis, Iosif; Charalampopoulos, Ioannis; Gravanis, Achilleas; Delis, Foteini; Antoniou, Katerina; Zisimopoulos, Dimitrios; Georgiou, Christos D; Panagopoulos, Nikolaos T; Matsokis, Nikolaos; Angelatou, Fevronia

    2017-07-15

    Neurotrophic factors are among the most promising treatments aiming at slowing or stopping and even reversing Parkinson's disease (PD). However, in most cases, they cannot readily cross the human blood-brain-barrier (BBB). Herein, we propose as a therapeutic for PD the small molecule 17-beta-spiro-[5-androsten-17,2'-oxiran]-3beta-ol (BNN-20), a synthetic analogue of DHEA, which crosses the BBB and is deprived of endocrine side-effects. Using the "weaver" mouse, a genetic model of PD, which exhibits progressive dopaminergic neurodegeneration in the Substantia Nigra (SN), we have shown that long-term administration (P1-P21) of BNN-20 almost fully protected the dopaminergic neurons and their terminals, via i) a strong anti-apoptotic effect, probably mediated through the Tropomyosin receptor kinase B (TrkB) neurotrophin receptor's PI3K-Akt-NF-κB signaling pathway, ii) by exerting an efficient antioxidant effect, iii) by inducing significant anti-inflammatory activity and iv) by restoring Brain-Derived Neurotrophic Factor (BDNF) levels. By intercrossing "weaver" with NGL mice (dual GFP/luciferase-NF-κΒ reporter mice, NF-κΒ.GFP.Luc), we obtained Weaver/NGL mice that express the NF-κB reporter in all somatic cells. Acute BNN-20 administration to Weaver/NGL mice induced a strong NF-κB-dependent transcriptional response in the brain as detected by bioluminescence imaging, which was abolished by co-administration of the TrkB inhibitor ANA-12. This indicates that BNN-20 exerts its beneficial action (at least in part) through the TrkB-PI3K-Akt-NF-κB signaling pathway. These results could be of clinical relevance, as they suggest BNN-20 as an important neuroprotective agent acting through the TrkB neurotrophin receptor pathway, mimicking the action of the endogenous neurotrophin BDNF. Thus BNN-20 could be proposed for treatment of PD. Copyright © 2017. Published by Elsevier Ltd.

  6. Synthetic Rutile

    Burastero, J.

    1975-01-01

    This work is about the laboratory scale investigation of the conditions in the rutile synthetic production from one me nita in Aguas Dulces reservoir. The iron mineral is chlorinated and volatilized selectively leaving a residue enriched in titanium dioxide which can be used as a substitute of rutile mineral

  7. A Simple Negative Interaction in the Positive Transcriptional Feedback of a Single Gene Is Sufficient to Produce Reliable Oscillations

    Miró-Bueno, Jesús M.; Rodríguez-Patón, Alfonso

    2011-01-01

    Negative and positive transcriptional feedback loops are present in natural and synthetic genetic oscillators. A single gene with negative transcriptional feedback needs a time delay and sufficiently strong nonlinearity in the transmission of the feedback signal in order to produce biochemical rhythms. A single gene with only positive transcriptional feedback does not produce oscillations. Here, we demonstrate that this single-gene network in conjunction with a simple negative interaction can also easily produce rhythms. We examine a model comprised of two well-differentiated parts. The first is a positive feedback created by a protein that binds to the promoter of its own gene and activates the transcription. The second is a negative interaction in which a repressor molecule prevents this protein from binding to its promoter. A stochastic study shows that the system is robust to noise. A deterministic study identifies that the dynamics of the oscillator are mainly driven by two types of biomolecules: the protein, and the complex formed by the repressor and this protein. The main conclusion of this paper is that a simple and usual negative interaction, such as degradation, sequestration or inhibition, acting on the positive transcriptional feedback of a single gene is a sufficient condition to produce reliable oscillations. One gene is enough and the positive transcriptional feedback signal does not need to activate a second repressor gene. This means that at the genetic level an explicit negative feedback loop is not necessary. The model needs neither cooperative binding reactions nor the formation of protein multimers. Therefore, our findings could help to clarify the design principles of cellular clocks and constitute a new efficient tool for engineering synthetic genetic oscillators. PMID:22205920

  8. Synthetic Brainbows

    Wan, Y.; Otsuna, H.; Hansen, C.

    2013-01-01

    Brainbow is a genetic engineering technique that randomly colorizes cells. Biological samples processed with this technique and imaged with confocal microscopy have distinctive colors for individual cells. Complex cellular structures can

  9. Genetics

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  10. Genetics

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  11. Oscillator circuits

    Graf, Rudolf F

    1996-01-01

    This series of circuits provides designers with a quick source for oscillator circuits. Why waste time paging through huge encyclopedias when you can choose the topic you need and select any of the specialized circuits sorted by application?This book in the series has 250-300 practical, ready-to-use circuit designs, with schematics and brief explanations of circuit operation. The original source for each circuit is listed in an appendix, making it easy to obtain additional information.Ready-to-use circuits.Grouped by application for easy look-up.Circuit source listing

  12. Approaches to chemical synthetic biology.

    Chiarabelli, Cristiano; Stano, Pasquale; Anella, Fabrizio; Carrara, Paolo; Luisi, Pier Luigi

    2012-07-16

    Synthetic biology is first represented in terms of two complementary aspects, the bio-engineering one, based on the genetic manipulation of extant microbial forms in order to obtain forms of life which do not exist in nature; and the chemical synthetic biology, an approach mostly based on chemical manipulation for the laboratory synthesis of biological structures that do not exist in nature. The paper is mostly devoted to shortly review chemical synthetic biology projects currently carried out in our laboratory. In particular, we describe: the minimal cell project, then the "Never Born Proteins" and lastly the Never Born RNAs. We describe and critically analyze the main results, emphasizing the possible relevance of chemical synthetic biology for the progress in basic science and biotechnology. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  13. Natural - synthetic - artificial!

    Nielsen, Peter E

    2010-01-01

    The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life.......The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life....

  14. Synthetic Cannabinoids.

    Mills, Brooke; Yepes, Andres; Nugent, Kenneth

    2015-07-01

    Synthetic cannabinoids (SCBs), also known under the brand names of "Spice," "K2," "herbal incense," "Cloud 9," "Mojo" and many others, are becoming a large public health concern due not only to their increasing use but also to their unpredictable toxicity and abuse potential. There are many types of SCBs, each having a unique binding affinity for cannabinoid receptors. Although both Δ-tetrahydrocannabinol (THC) and SCBs stimulate the same receptors, cannabinoid receptor 1 (CB1) and cannabinoid receptor 2 (CB2), studies have shown that SCBs are associated with higher rates of toxicity and hospital admissions than is natural cannabis. This is likely due to SCBs being direct agonists of the cannabinoid receptors, whereas THC is a partial agonist. Furthermore, the different chemical structures of SCBs found in Spice or K2 may interact in unpredictable ways to elicit previously unknown, and the commercial products may have unknown contaminants. The largest group of users is men in their 20s who participate in polydrug use. The most common reported toxicities with SCB use based on studies using Texas Poison Control records are tachycardia, agitation and irritability, drowsiness, hallucinations, delusions, hypertension, nausea, confusion, dizziness, vertigo and chest pain. Acute kidney injury has also been strongly associated with SCB use. Treatment mostly involves symptom management and supportive care. More research is needed to identify which contaminants are typically found in synthetic marijuana and to understand the interactions between different SBCs to better predict adverse health outcomes.

  15. Synthetic Biology and Personalized Medicine

    Jain, K.K.

    2013-01-01

    Synthetic biology, application of synthetic chemistry to biology, is a broad term that covers the engineering of biological systems with structures and functions not found in nature to process information, manipulate chemicals, produce energy, maintain cell environment and enhance human health. Synthetic biology devices contribute not only to improve our understanding of disease mechanisms, but also provide novel diagnostic tools. Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs. The potential of synthetic genome, using an expanded genetic code that is designed for specific drug synthesis as well as delivery and activation of the drug in vivo by a pathological signal, was already pointed out during a lecture delivered at Kuwait University in 2005. Of two approaches to synthetic biology, top-down and bottom-up, the latter is more relevant to the development of personalized medicines as it provides more flexibility in constructing a partially synthetic cell from basic building blocks for a desired task. PMID:22907209

  16. Mammalian synthetic biology: emerging medical applications.

    Kis, Zoltán; Pereira, Hugo Sant'Ana; Homma, Takayuki; Pedrigi, Ryan M; Krams, Rob

    2015-05-06

    In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON-OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and toggle switches will be described. Several synthetic gene networks are further reviewed in the medical applications section, including cancer therapy gene circuits, immuno-regulatory networks, among others. The final sections focus on the applicability of synthetic gene networks to drug discovery, drug delivery, receptor-activating gene circuits and mammalian biomanufacturing processes. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  17. Synthetic biology: Emerging bioengineering in Indonesia

    Suhandono, Sony

    2017-05-01

    The development of synthetic biology will shape the new era of science and technology. It is an emerging bioengineering technique involving genetic engineering which can alter the phenotype and behavior of the cell or the new product. Synthetic biology may produce biomaterials, drugs, vaccines, biosensors, and even a recombinant secondary metabolite used in herbal and complementary medicine, such as artemisinin, a malaria drug which is usually extracted from the plant Artemisia annua. The power of synthetic biology has encouraged scientists in Indonesia, and is still in early development. This paper also covers some research from an Indonesian research institute in synthetic biology such as observing the production of bio surfactants and the enhanced production of artemisinin using a transient expression system. Synthetic biology development in Indonesia may also be related to the iGEM competition, a large synthetic biology research competition which was attended by several universities in Indonesia. The application of synthetic biology for drug discovery will be discussed.

  18. Modular design of artificial tissue homeostasis: robust control through synthetic cellular heterogeneity.

    Miles Miller

    Full Text Available Synthetic biology efforts have largely focused on small engineered gene networks, yet understanding how to integrate multiple synthetic modules and interface them with endogenous pathways remains a challenge. Here we present the design, system integration, and analysis of several large scale synthetic gene circuits for artificial tissue homeostasis. Diabetes therapy represents a possible application for engineered homeostasis, where genetically programmed stem cells maintain a steady population of β-cells despite continuous turnover. We develop a new iterative process that incorporates modular design principles with hierarchical performance optimization targeted for environments with uncertainty and incomplete information. We employ theoretical analysis and computational simulations of multicellular reaction/diffusion models to design and understand system behavior, and find that certain features often associated with robustness (e.g., multicellular synchronization and noise attenuation are actually detrimental for tissue homeostasis. We overcome these problems by engineering a new class of genetic modules for 'synthetic cellular heterogeneity' that function to generate beneficial population diversity. We design two such modules (an asynchronous genetic oscillator and a signaling throttle mechanism, demonstrate their capacity for enhancing robust control, and provide guidance for experimental implementation with various computational techniques. We found that designing modules for synthetic heterogeneity can be complex, and in general requires a framework for non-linear and multifactorial analysis. Consequently, we adapt a 'phenotypic sensitivity analysis' method to determine how functional module behaviors combine to achieve optimal system performance. We ultimately combine this analysis with Bayesian network inference to extract critical, causal relationships between a module's biochemical rate-constants, its high level functional behavior in

  19. Modular design of artificial tissue homeostasis: robust control through synthetic cellular heterogeneity.

    Miller, Miles; Hafner, Marc; Sontag, Eduardo; Davidsohn, Noah; Subramanian, Sairam; Purnick, Priscilla E M; Lauffenburger, Douglas; Weiss, Ron

    2012-01-01

    Synthetic biology efforts have largely focused on small engineered gene networks, yet understanding how to integrate multiple synthetic modules and interface them with endogenous pathways remains a challenge. Here we present the design, system integration, and analysis of several large scale synthetic gene circuits for artificial tissue homeostasis. Diabetes therapy represents a possible application for engineered homeostasis, where genetically programmed stem cells maintain a steady population of β-cells despite continuous turnover. We develop a new iterative process that incorporates modular design principles with hierarchical performance optimization targeted for environments with uncertainty and incomplete information. We employ theoretical analysis and computational simulations of multicellular reaction/diffusion models to design and understand system behavior, and find that certain features often associated with robustness (e.g., multicellular synchronization and noise attenuation) are actually detrimental for tissue homeostasis. We overcome these problems by engineering a new class of genetic modules for 'synthetic cellular heterogeneity' that function to generate beneficial population diversity. We design two such modules (an asynchronous genetic oscillator and a signaling throttle mechanism), demonstrate their capacity for enhancing robust control, and provide guidance for experimental implementation with various computational techniques. We found that designing modules for synthetic heterogeneity can be complex, and in general requires a framework for non-linear and multifactorial analysis. Consequently, we adapt a 'phenotypic sensitivity analysis' method to determine how functional module behaviors combine to achieve optimal system performance. We ultimately combine this analysis with Bayesian network inference to extract critical, causal relationships between a module's biochemical rate-constants, its high level functional behavior in isolation, and

  20. One dimension harmonic oscillator

    Cohen-Tannoudji, Claude; Diu, Bernard; Laloe, Franck.

    1977-01-01

    The importance of harmonic oscillator in classical and quantum physics, eigenvalues and eigenstates of hamiltonian operator are discussed. In complement are presented: study of some physical examples of harmonic oscillators; study of stationnary states in the /x> representation; Hermite polynomials; resolution of eigenvalue equation of harmonic oscillator by polynomial method; isotope harmonic oscillator with three dimensions; charged harmonic oscillator in uniform electric field; quasi classical coherent states of harmonic oscillator; eigenmodes of vibration of two coupled harmonic oscillators; vibration modus of a continuous physical system (application to radiation: photons); vibration modus of indefinite linear chain of coupled harmonic oscillators (phonons); one-dimensional harmonic oscillator in thermodynamic equilibrium at temperature T [fr

  1. Power oscillation damping controller

    2012-01-01

    A power oscillation damping controller is provided for a power generation device such as a wind turbine device. The power oscillation damping controller receives an oscillation indicating signal indicative of a power oscillation in an electricity network and provides an oscillation damping control...

  2. Oscillations of void lattices

    Akhiezer, A.I.; Davydov, L.N.; Spol'nik, Z.A.

    1976-01-01

    Oscillations of a nonideal crystal are studied, in which macroscopic defects (pores) form a hyperlattice. It is shown that alongside with acoustic and optical phonons (relative to the hyperlattice), in such a crystal oscillations of the third type are possible which are a hydridization of sound oscillations of atoms and surface oscillations of a pore. Oscillation spectra of all three types were obtained

  3. Assessment of Genetic Fidelity in Rauvolfia serpentina Plantlets Grown from Synthetic (Encapsulated Seeds Following in Vitro Storage at 4 °C

    Mohammad Anis

    2012-05-01

    Full Text Available An efficient method was developed for plant regeneration and establishment from alginate encapsulated synthetic seeds of Rauvolfia serpentina. Synthetic seeds were produced using in vitro proliferated microshoots upon complexation of 3% sodium alginate prepared in Llyod and McCown woody plant medium (WPM and 100 mM calcium chloride. Re-growth ability of encapsulated nodal segments was evaluated after storage at 4 °C for 0, 1, 2, 4, 6 and 8 weeks and compared with non-encapsulated buds. Effects of different media viz; Murashige and Skoog medium; Lloyd and McCown woody Plant medium, Gamborg’s B5 medium and Schenk and Hildebrandt medium was also investigated for conversion into plantlets. The maximum frequency of conversion into plantlets from encapsulated nodal segments stored at 4 °C for 4 weeks was achieved on woody plant medium supplement with 5.0 μM BA and 1.0 μM NAA. Rooting in plantlets was achieved in half-strength Murashige and Skoog liquid medium containing 0.5 μM indole-3-acetic acid (IAA on filter paper bridges. Plantlets obtained from stored synseeds were hardened, established successfully ex vitro and were morphologically similar to each other as well as their mother plant. The genetic fidelity of Rauvolfia clones raised from synthetic seeds following four weeks of storage at 4 °C were assessed by using random amplified polymorphic DNA (RAPD and inter-simple sequence repeat (ISSR markers. All the RAPD and ISSR profiles from generated plantlets were monomorphic and comparable to the mother plant, which confirms the genetic stability among the clones. This synseed protocol could be useful for establishing a particular system for conservation, short-term storage and production of genetically identical and stable plants before it is released for commercial purposes.

  4. Oscillators - a simple introduction

    Lindberg, Erik

    2013-01-01

    Oscillators are kernel components of electrical and electronic circuits. Discussion of history, mechanisms and design based on Barkhausens observation. Discussion of a Wien Bridge oscillator based on the question: Why does this circuit oscillate ?......Oscillators are kernel components of electrical and electronic circuits. Discussion of history, mechanisms and design based on Barkhausens observation. Discussion of a Wien Bridge oscillator based on the question: Why does this circuit oscillate ?...

  5. Oscillators and Eigenvalues

    Lindberg, Erik

    1997-01-01

    In order to obtain insight in the nature of nonlinear oscillators the eigenvalues of the linearized Jacobian of the differential equations describing the oscillator are found and displayed as functions of time. A number of oscillators are studied including Dewey's oscillator (piecewise linear wit...... with negative resistance), Kennedy's Colpitts-oscillator (with and without chaos) and a new 4'th order oscillator with hyper-chaos....

  6. Synthetic Phage for Tissue Regeneration

    So Young Yoo

    2014-01-01

    Full Text Available Controlling structural organization and signaling motif display is of great importance to design the functional tissue regenerating materials. Synthetic phage, genetically engineered M13 bacteriophage has been recently introduced as novel tissue regeneration materials to display a high density of cell-signaling peptides on their major coat proteins for tissue regeneration purposes. Structural advantages of their long-rod shape and monodispersity can be taken together to construct nanofibrous scaffolds which support cell proliferation and differentiation as well as direct orientation of their growth in two or three dimensions. This review demonstrated how functional synthetic phage is designed and subsequently utilized for tissue regeneration that offers potential cell therapy.

  7. A standard-enabled workflow for synthetic biology

    Myers, Chris J.; Beal, Jacob; Gorochowski, Thomas E.; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Gö ksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach

    2017-01-01

    A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select

  8. Synthetic Astrobiology

    Rothschild, Lynn J.

    2017-01-01

    "Are we alone?" is one of the primary questions of astrobiology, and whose answer defines our significance in the universe. Unfortunately, this quest is hindered by the fact that we have only one confirmed example of life, that of earth. While this is enormously helpful in helping to define the minimum envelope for life, it strains credulity to imagine that life, if it arose multiple times, has not taken other routes. To help fill this gap, our lab has begun using synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - as an enabling technology. One theme, the "Hell Cell" project, focuses on creating artificial extremophiles in order to push the limits for Earth life, and to understand how difficult it is for life to evolve into extreme niches. In another project, we are re-evolving biotic functions using only the most thermodynamically stable amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids.

  9. Space Synthetic Biology Project

    Howard, David; Roman, Monsi; Mansell, James (Matt)

    2015-01-01

    Synthetic biology is an effort to make genetic engineering more useful by standardizing sections of genetic code. By standardizing genetic components, biological engineering will become much more similar to traditional fields of engineering, in which well-defined components and subsystems are readily available in markets. Specifications of the behavior of those components and subsystems can be used to model a system which incorporates them. Then, the behavior of the novel system can be simulated and optimized. Finally, the components and subsystems can be purchased and assembled to create the optimized system, which most often will exhibit behavior similar to that indicated by the model. The Space Synthetic Biology project began in 2012 as a multi-Center effort. The purpose of this project was to harness Synthetic Biology principals to enable NASA's missions. A central target for application was to Environmental Control & Life Support (ECLS). Engineers from NASA Marshall Space Flight Center's (MSFC's) ECLS Systems Development Branch (ES62) were brought into the project to contribute expertise in operational ECLS systems. Project lead scientists chose to pursue the development of bioelectrochemical technologies to spacecraft life support. Therefore, the ECLS element of the project became essentially an effort to develop a bioelectrochemical ECLS subsystem. Bioelectrochemical systems exploit the ability of many microorganisms to drive their metabolisms by direct or indirect utilization of electrical potential gradients. Whereas many microorganisms are capable of deriving the energy required for the processes of interest (such as carbon dioxide (CO2) fixation) from sunlight, it is believed that subsystems utilizing electrotrophs will exhibit smaller mass, volume, and power requirements than those that derive their energy from sunlight. In the first 2 years of the project, MSFC personnel conducted modeling, simulation, and conceptual design efforts to assist the

  10. Benchmarking of TALE- and CRISPR/dCas9-Based Transcriptional Regulators in Mammalian Cells for the Construction of Synthetic Genetic Circuits.

    Lebar, Tina; Jerala, Roman

    2016-10-21

    Transcriptional activator-like effector (TALE)- and CRISPR/Cas9-based designable recognition domains represent a technological breakthrough not only for genome editing but also for building designed genetic circuits. Both platforms are able to target rarely occurring DNA segments, even within complex genomes. TALE and dCas9 domains, genetically fused to transcriptional regulatory domains, can be used for the construction of engineered logic circuits. Here we benchmarked the performance of the two platforms, targeting the same DNA sequences, to compare their advantages for the construction of designed circuits in mammalian cells. Optimal targeting strands for repression and activation of dCas9-based designed transcription factors were identified; both platforms exhibited good orthogonality and were used to construct functionally complete NOR gates. Although the CRISPR/dCas9 system is clearly easier to construct, TALE-based activators were significantly stronger, and the TALE-based platform performed better, especially for the construction of layered circuits.

  11. Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project.

    Sliva, Anna; Yang, Huanming; Boeke, Jef D; Mathews, Debra J H

    2015-08-01

    First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) PROJECT is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with this field of research and operate under a common set of principles. In this commentary, we survey the current ethics and regulatory landscape of synthetic biology and present the Sc2.0 Statement of Ethics and Governance to which all members of the project adhere. This statement focuses on four aspects of the Sc2.0 PROJECT: societal benefit, intellectual property, safety, and self-governance. We propose that such project-level agreements are an important, valuable, and flexible model of self-regulation for similar global, large-scale synthetic biology projects in order to maximize the benefits and minimize potential harms. Copyright © 2015 by the Genetics Society of America.

  12. Control theory meets synthetic biology.

    Del Vecchio, Domitilla; Dy, Aaron J; Qian, Yili

    2016-07-01

    The past several years have witnessed an increased presence of control theoretic concepts in synthetic biology. This review presents an organized summary of how these control design concepts have been applied to tackle a variety of problems faced when building synthetic biomolecular circuits in living cells. In particular, we describe success stories that demonstrate how simple or more elaborate control design methods can be used to make the behaviour of synthetic genetic circuits within a single cell or across a cell population more reliable, predictable and robust to perturbations. The description especially highlights technical challenges that uniquely arise from the need to implement control designs within a new hardware setting, along with implemented or proposed solutions. Some engineering solutions employing complex feedback control schemes are also described, which, however, still require a deeper theoretical analysis of stability, performance and robustness properties. Overall, this paper should help synthetic biologists become familiar with feedback control concepts as they can be used in their application area. At the same time, it should provide some domain knowledge to control theorists who wish to enter the rising and exciting field of synthetic biology. © 2016 The Author(s).

  13. Protocols for In Vitro Propagation, Conservation, Synthetic Seed Production, Embryo Rescue, Microrhizome Production, Molecular Profiling, and Genetic Transformation in Ginger (Zingiber officinale Roscoe.).

    Nirmal Babu, K; Samsudeen, K; Divakaran, Minoo; Pillai, Geetha S; Sumathi, V; Praveen, K; Ravindran, P N; Peter, K V

    2016-01-01

    Ginger is a rhizomatous plant that belongs to the family Zingiberaceae. It is a herbaceous perennial but cultivated as annual, with crop duration of 7-10 months. Ginger is native to India and Tropical South Asia. The tuberous rhizomes or underground stems of ginger are used as condiment, an aromatic stimulant, and food preservative as well as in traditional medicine. Ginger is propagated vegetatively with rhizome bits as seed material. Cultivation of ginger is plagued by rhizome rot diseases, most of which are mainly spread through infected seed rhizomes. Micropropagation will help in production of disease-free planting material. Sexual reproduction is absent in ginger, making recombinant breeding very impossible. In vitro technology can thus become the preferred choice as it can be utilized for multiplication, conservation of genetic resources, generating variability, gene transfer, molecular tagging, and their utility in crop improvement of these crops.

  14. Programmed Nanomaterial Assemblies in Large Scales: Applications of Synthetic and Genetically- Engineered Peptides to Bridge Nano-Assemblies and Macro-Assemblies

    Matsui, Hiroshi

    2014-09-09

    Work is reported in these areas: Large-scale & reconfigurable 3D structures of precise nanoparticle assemblies in self-assembled collagen peptide grids; Binary QD-Au NP 3D superlattices assembled with collagen-like peptides and energy transfer between QD and Au NP in 3D peptide frameworks; Catalytic peptides discovered by new hydrogel-based combinatorial phage display approach and their enzyme-mimicking 2D assembly; New autonomous motors of metal-organic frameworks (MOFs) powered by reorganization of self-assembled peptides at interfaces; Biomimetic assembly of proteins into microcapsules on oil-in-water droplets with structural reinforcement via biomolecular recognition-based cross-linking of surface peptides; and Biomimetic fabrication of strong freestanding genetically-engineered collagen peptide films reinforced by quantum dot joints. We gained the broad knowledge about biomimetic material assembly from nanoscale to microscale ranges by coassembling peptides and NPs via biomolecular recognition. We discovered: Genetically-engineered collagen-like peptides can be self-assembled with Au NPs to generate 3D superlattices in large volumes (> μm{sup 3}); The assembly of the 3D peptide-Au NP superstructures is dynamic and the interparticle distance changes with assembly time as the reconfiguration of structure is triggered by pH change; QDs/NPs can be assembled with the peptide frameworks to generate 3D superlattices and these QDs/NPs can be electronically coupled for the efficient energy transfer; The controlled assembly of catalytic peptides mimicking the catalytic pocket of enzymes can catalyze chemical reactions with high selectivity; and, For the bacteria-mimicking swimmer fabrication, peptide-MOF superlattices can power translational and propellant motions by the reconfiguration of peptide assembly at the MOF-liquid interface.

  15. Potencial genético de um sintético de milho de grãos duros para formação de híbridos Genetic potential of a flint maize synthetic for hybrid production

    Elto Eugenio Gomes e Gama

    2003-08-01

    Full Text Available O objetivo deste estudo foi determinar através das estimativas de parâmetros genéticos o potencial de um sintético de milho de grãos duros e de ciclo semiprecoce, para a formação de híbridos e/ou melhoramento intrapopulacional. Foram utilizadas 142 progênies endogâmicas S2 do Sin EEL Flint, em cruzamentos topcrosses com um Sintético heteroticamente contrastante. Essas progênies topcrosses foram avaliadas utilizando-se o delineamento em látice simples 12 x 12, e em dois locais de teste. Os maiores valores médios para PED foram observados para os topcrosses n.º 101 (12069kg ha-1 e nº 72 (11068Kg ha-1, tendo o primeiro apresentado comportamento específico para Londrina, e o segunda demonstrado comportamento superior nos dois ambientes. Os valores das estimativas dos parâmetros estudados foram semelhantes aos encontrados em alguns estudos conduzidos em condições tropicais. O grupo de progênies S2 da Sin EEL Flint conduziu a valores médios de , CVg e h² similares aos encontrados na literatura para outros genótipos. Observa-se que esse Sintético possui suficiente variabilidade genética e potencial para extração de linhagens para formação de híbridos e como germoplasma em programas de melhoramento.The objective of this study was to determine the genetic potential of a semi-early maize synthetic with flint type kernel (Sin EEL Flint. The estimation of genetic parameters was obtained with S2 progenies, and the performance of the progenies in hybrid combinations were evaluated. One hundred fourty-two S2 progenies of Sin EEL Flint were used. They were obtained by top crossings with a contrasting heterotic synthetic of dent type kernel. These topcross progenies were tested in a lattice design 12 x 12 with two replications in two locations, Sete Lagoas and Londrina. The selected topcross nº 101, with specific adaptation for Londrina. and nº72, being adapted to both locations, were the best yieldings (PED with 12069Kg ha-1 and

  16. Mammalian synthetic biology for studying the cell.

    Mathur, Melina; Xiang, Joy S; Smolke, Christina D

    2017-01-02

    Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology. © 2017 Mathur et al.

  17. Oscillating heat pipes

    Ma, Hongbin

    2015-01-01

    This book presents the fundamental fluid flow and heat transfer principles occurring in oscillating heat pipes and also provides updated developments and recent innovations in research and applications of heat pipes. Starting with fundamental presentation of heat pipes, the focus is on oscillating motions and its heat transfer enhancement in a two-phase heat transfer system. The book covers thermodynamic analysis, interfacial phenomenon, thin film evaporation,  theoretical models of oscillating motion and heat transfer of single phase and two-phase flows, primary  factors affecting oscillating motions and heat transfer,  neutron imaging study of oscillating motions in an oscillating heat pipes, and nanofluid’s effect on the heat transfer performance in oscillating heat pipes.  The importance of thermally-excited oscillating motion combined with phase change heat transfer to a wide variety of applications is emphasized. This book is an essential resource and learning tool for senior undergraduate, gradua...

  18. US Competitiveness in Synthetic Biology.

    Gronvall, Gigi Kwik

    2015-01-01

    Synthetic biology is an emerging technical field that aims to make biology easier to engineer; the field has applications in strategically important sectors for the US economy. While the United States currently leads in synthetic biology R&D, other nations are heavily investing in order to boost their economies, which will inevitably diminish the US leadership position. This outcome is not entirely negative--additional investments will expand markets--but it is critical that the US government take steps to remain competitive: There are applications from which the US population and economy may benefit; there are specific applications with importance for national defense; and US technical leadership will ensure that US experts have a leading role in synthetic biology governance, regulation, and oversight. Measures to increase competitiveness in S&T generally are broadly applicable for synthetic biology and should be pursued. However, the US government will also need to take action on fundamental issues that will affect the field's development, such as countering anti-GMO (genetically modified organism) sentiments and anti-GMO legislation. The United States should maintain its regulatory approach so that it is the product that is regulated, not the method used to create a product. At the same time, the United States needs to ensure that the regulatory framework is updated so that synthetic biology products do not fall into regulatory gaps. Finally, the United States needs to pay close attention to how synthetic biology applications may be governed internationally, such as through the Nagoya Protocol of the Convention on Biological Diversity, so that beneficial applications may be realized.

  19. Synthetic biology, inspired by synthetic chemistry.

    Malinova, V; Nallani, M; Meier, W P; Sinner, E K

    2012-07-16

    The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  20. Automatic Oscillating Turret.

    1981-03-01

    Final Report: February 1978 ZAUTOMATIC OSCILLATING TURRET SYSTEM September 1980 * 6. PERFORMING 01G. REPORT NUMBER .J7. AUTHOR(S) S. CONTRACT OR GRANT...o....e.... *24 APPENDIX P-4 OSCILLATING BUMPER TURRET ...................... 25 A. DESCRIPTION 1. Turret Controls ...Other criteria requirements were: 1. Turret controls inside cab. 2. Automatic oscillation with fixed elevation to range from 20* below the horizontal to

  1. Neutrino oscillations in matter

    Mikheyev, S.P.; Smirnov, A.Yu.

    1986-01-01

    In this paper we describe united formalism of ν-oscillations for different regimes, which is immediate generalization of vacuum oscillations theory. Adequate graphical representation of this formalism is given. We summarize main properties of ν-oscillations for different density distributions. (orig./BBOE)

  2. The colpitts oscillator family

    Lindberg, Erik; Murali, K.; Tamasevicius, A.

    A tutorial study of the Colpitts oscillator family defined as all oscillators based on a nonlinear amplifier and a three- terminal linear resonance circuit with one coil and two capacitors. The original patents are investigated. The eigenvalues of the linearized Jacobian for oscillators based...

  3. Synthetic Cathinones ("Bath Salts")

    ... Alcohol Club Drugs Cocaine Fentanyl Hallucinogens Inhalants Heroin Marijuana MDMA (Ecstasy/Molly) Methamphetamine Opioids Over-the-Counter Medicines Prescription Medicines Steroids (Anabolic) Synthetic Cannabinoids (K2/Spice) Synthetic Cathinones (Bath Salts) Tobacco/ ...

  4. Synergistic Synthetic Biology: Units in Concert

    Trosset, Jean-Yves; Carbonell, Pablo

    2013-01-01

    Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.

  5. Synergistic Synthetic Biology: Units in Concert

    Trosset, Jean-Yves; Carbonell, Pablo

    2013-01-01

    Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications. PMID:25022769

  6. Nature's Autonomous Oscillators

    Mayr, H. G.; Yee, J.-H.; Mayr, M.; Schnetzler, R.

    2012-01-01

    Nonlinearity is required to produce autonomous oscillations without external time dependent source, and an example is the pendulum clock. The escapement mechanism of the clock imparts an impulse for each swing direction, which keeps the pendulum oscillating at the resonance frequency. Among nature's observed autonomous oscillators, examples are the quasi-biennial oscillation and bimonthly oscillation of the Earth atmosphere, and the 22-year solar oscillation. The oscillations have been simulated in numerical models without external time dependent source, and in Section 2 we summarize the results. Specifically, we shall discuss the nonlinearities that are involved in generating the oscillations, and the processes that produce the periodicities. In biology, insects have flight muscles, which function autonomously with wing frequencies that far exceed the animals' neural capacity; Stretch-activation of muscle contraction is the mechanism that produces the high frequency oscillation of insect flight, discussed in Section 3. The same mechanism is also invoked to explain the functioning of the cardiac muscle. In Section 4, we present a tutorial review of the cardio-vascular system, heart anatomy, and muscle cell physiology, leading up to Starling's Law of the Heart, which supports our notion that the human heart is also a nonlinear oscillator. In Section 5, we offer a broad perspective of the tenuous links between the fluid dynamical oscillators and the human heart physiology.

  7. Design Automation in Synthetic Biology.

    Appleton, Evan; Madsen, Curtis; Roehner, Nicholas; Densmore, Douglas

    2017-04-03

    Design automation refers to a category of software tools for designing systems that work together in a workflow for designing, building, testing, and analyzing systems with a target behavior. In synthetic biology, these tools are called bio-design automation (BDA) tools. In this review, we discuss the BDA tools areas-specify, design, build, test, and learn-and introduce the existing software tools designed to solve problems in these areas. We then detail the functionality of some of these tools and show how they can be used together to create the desired behavior of two types of modern synthetic genetic regulatory networks. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  8. A memristor-based third-order oscillator: beyond oscillation

    Talukdar, Abdul Hafiz Ibne

    2012-10-06

    This paper demonstrates the first third-order autonomous linear time variant circuit realization that enhances parametric oscillation through the usage of memristor in conventional oscillators. Although the output has sustained oscillation, the linear features of the conventional oscillators become time dependent. The poles oscillate in nonlinear behavior due to the oscillation of memristor resistance. The mathematical formulas as well as SPICE simulations are introduced for the memristor-based phase shift oscillator showing a great matching.

  9. A memristor-based third-order oscillator: beyond oscillation

    Talukdar, Abdul Hafiz Ibne; Radwan, Ahmed G.; Salama, Khaled N.

    2012-01-01

    This paper demonstrates the first third-order autonomous linear time variant circuit realization that enhances parametric oscillation through the usage of memristor in conventional oscillators. Although the output has sustained oscillation, the linear features of the conventional oscillators become time dependent. The poles oscillate in nonlinear behavior due to the oscillation of memristor resistance. The mathematical formulas as well as SPICE simulations are introduced for the memristor-based phase shift oscillator showing a great matching.

  10. The emerging age of cell-free synthetic biology.

    Smith, Mark Thomas; Wilding, Kristen M; Hunt, Jeremy M; Bennett, Anthony M; Bundy, Bradley C

    2014-08-25

    The engineering of and mastery over biological parts has catalyzed the emergence of synthetic biology. This field has grown exponentially in the past decade. As increasingly more applications of synthetic biology are pursued, more challenges are encountered, such as delivering genetic material into cells and optimizing genetic circuits in vivo. An in vitro or cell-free approach to synthetic biology simplifies and avoids many of the pitfalls of in vivo synthetic biology. In this review, we describe some of the innate features that make cell-free systems compelling platforms for synthetic biology and discuss emerging improvements of cell-free technologies. We also select and highlight recent and emerging applications of cell-free synthetic biology. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  11. Oscillations of disks

    Kato, Shoji

    2016-01-01

    This book presents the current state of research on disk oscillation theory, focusing on relativistic disks and tidally deformed disks. Since the launch of the Rossi X-ray Timing Explorer (RXTE) in 1996, many high-frequency quasiperiodic oscillations (HFQPOs) have been observed in X-ray binaries. Subsequently, similar quasi-periodic oscillations have been found in such relativistic objects as microquasars, ultra-luminous X-ray sources, and galactic nuclei. One of the most promising explanations of their origin is based on oscillations in relativistic disks, and a new field called discoseismology is currently developing. After reviewing observational aspects, the book presents the basic characteristics of disk oscillations, especially focusing on those in relativistic disks. Relativistic disks are essentially different from Newtonian disks in terms of several basic characteristics of their disk oscillations, including the radial distributions of epicyclic frequencies. In order to understand the basic processes...

  12. Philosophy of Systems and Synthetic Biology

    Green, Sara

    2017-01-01

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

  13. Oscillations in stellar atmospheres

    Costa, A.; Ringuelet, A.E.; Fontenla, J.M.

    1989-01-01

    Atmospheric excitation and propagation of oscillations are analyzed for typical pulsating stars. The linear, plane-parallel approach for the pulsating atmosphere gives a local description of the phenomenon. From the local analysis of oscillations, the minimum frequencies are obtained for radially propagating waves. The comparison of the minimum frequencies obtained for a variety of stellar types is in good agreement with the observed periods of the oscillations. The role of the atmosphere in the globar stellar pulsations is thus emphasized. 7 refs

  14. Synchronization of coupled stochastic oscillators: The effect of ...

    as an approximate means of accounting for a separation of time-scales between ... phase relationships between coupled oscillator systems as well as to effect a variety ... ations are often termed as internal noise since their origin is in the very ..... design and control of synthetic biological networks where synchronous ...

  15. Rewiring protein synthesis: From natural to synthetic amino acids.

    Fan, Yongqiang; Evans, Christopher R; Ling, Jiqiang

    2017-11-01

    The protein synthesis machinery uses 22 natural amino acids as building blocks that faithfully decode the genetic information. Such fidelity is controlled at multiple steps and can be compromised in nature and in the laboratory to rewire protein synthesis with natural and synthetic amino acids. This review summarizes the major quality control mechanisms during protein synthesis, including aminoacyl-tRNA synthetases, elongation factors, and the ribosome. We will discuss evolution and engineering of such components that allow incorporation of natural and synthetic amino acids at positions that deviate from the standard genetic code. The protein synthesis machinery is highly selective, yet not fixed, for the correct amino acids that match the mRNA codons. Ambiguous translation of a codon with multiple amino acids or complete reassignment of a codon with a synthetic amino acid diversifies the proteome. Expanding the genetic code with synthetic amino acids through rewiring protein synthesis has broad applications in synthetic biology and chemical biology. Biochemical, structural, and genetic studies of the translational quality control mechanisms are not only crucial to understand the physiological role of translational fidelity and evolution of the genetic code, but also enable us to better design biological parts to expand the proteomes of synthetic organisms. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Evolvable synthetic neural system

    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.

  17. The Oscillator Principle of Nature

    Lindberg, Erik

    2012-01-01

    Oscillators are found on all levels in Nature. The general oscillator concept is defined and investigated. Oscillators may synchronize into fractal patterns. Apparently oscillators are the basic principle in Nature. The concepts of zero and infinite are discussed. Electronic manmade oscillators...

  18. [From synthetic biology to synthetic humankind].

    Nouvel, Pascal

    2015-01-01

    In this paper, we propose an historical survey of the expression "synthetic biology" in order to identify its main philosophical components. The result of the analysis is then used to investigate the meaning of the notion of "synthetic man". It is shown that both notions share a common philosophical background that can be summed up by the short but meaningful assertion: "biology is technology". The analysis allows us to distinguish two notions that are often confused in transhumanist literature: the notion of synthetic man and the notion of renewed man. The consequences of this crucial distinction are discussed. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  19. On the Dirac oscillator

    Rodrigues, R. de Lima

    2007-01-01

    In the present work we obtain a new representation for the Dirac oscillator based on the Clifford algebra C 7. The symmetry breaking and the energy eigenvalues for our model of the Dirac oscillator are studied in the non-relativistic limit. (author)

  20. A Conspiracy of Oscillators

    Hjorth, Poul G.

    2008-01-01

    We discuss nonlinear mechanical systems containing several oscillators whose frequecies are all much higher than frequencies associated with the remaining degrees of freedom. In this situation a near constant of the motion, an adiabatic invariant, exists which is the sum of all the oscillator...... actions. The phenomenon is illustrated, and calculations of the small change of the adiabatic invariant is outlined....

  1. Synchronization of hyperchaotic oscillators

    Tamasevicius, A.; Cenys, A.; Mykolaitis, G.

    1997-01-01

    Synchronization of chaotic oscillators is believed to have promising applications in secure communications. Hyperchaotic systems with multiple positive Lyapunov exponents (LEs) have an advantage over common chaotic systems with only one positive LE. Three different types of hyperchaotic electronic...... oscillators are investigated demonstrating synchronization by means of only one properly selected variable....

  2. Design and construction of "synthetic species".

    Eduardo Moreno

    Full Text Available Synthetic biology is an area of biological research that combines science and engineering. Here, I merge the principles of synthetic biology and regulatory evolution to create a new species with a minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic population arises with small eyes and a different venation pattern that fulfils the criteria of a new species according to Mayr's Biological Species Concept. The population described here is the first transgenic organism that cannot hybridize with the original wild type population but remains fertile when crossed with other identical transgenic animals. I therefore propose the term "synthetic species" to distinguish it from "natural species", not only because it has been created by genetic manipulation, but also because it may never be able to survive outside the laboratory environment. The use of genetic engineering to design artificial species barriers could help us understand natural speciation and may have practical applications. For instance, the transition from transgenic organisms towards synthetic species could constitute a safety mechanism to avoid the hybridization of genetically modified animals with wild type populations, preserving biodiversity.

  3. Designing synthetic biology.

    Agapakis, Christina M

    2014-03-21

    Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.

  4. Observation of Quasichanneling Oscillations

    Wistisen, T. N.; Mikkelsen, R. E.; Uggerhoj, University I.; Wienands, University; Markiewicz, T. W.

    2017-01-01

    Here, we report on the first experimental observations of quasichanneling oscillations, recently seen in simulations and described theoretically. Although above-barrier particles penetrating a single crystal are generally seen as behaving almost as in an amorphous substance, distinct oscillation peaks nevertheless appear for particles in that category. The quasichanneling oscillations were observed at SLAC National Accelerator Laboratory by aiming 20.35 GeV positrons and electrons at a thin silicon crystal bent to a radius of R = 0.15 m, exploiting the quasimosaic effect. For electrons, two relatively faint quasichanneling peaks were observed, while for positrons, seven quasichanneling peaks were clearly identified.

  5. LSND neutrino oscillation results

    Louis, W.C.

    1996-01-01

    In the past several years, a number of experiments have searched for neutrino oscillations, where a neutrino of one type (say bar ν μ ) spontaneously transforms into a neutrino of another type (say bar ν e ). For this phenomenon to occur, neutrinos must be massive and the apparent conservation law of lepton families must be violated. In 1995 the LSND experiment published data showing candidate events that are consistent with bar ν μ oscillations. Additional data are reported here which provide stronger evidence for neutrino oscillations

  6. Neutrino Oscillation Physics

    Kayser, Boris

    2014-01-01

    To complement the neutrino-physics lectures given at the 2011 International School on Astro Particle Physics devoted to Neutrino Physics and Astrophysics (ISAPP 2011; Varenna, Italy), at the 2011 European School of High Energy Physics (ESHEP 2011; Cheila Gradistei, Romania), and, in modified form, at other summer schools, we present here a written description of the physics of neutrino oscillation. This description is centered on a new way of deriving the oscillation probability. We also provide a brief guide to references relevant to topics other than neutrino oscillation that were covered in the lectures

  7. Neutrino Oscillation Physics

    Kayser, Boris [Fermilab (United States)

    2014-07-01

    To complement the neutrino-physics lectures given at the 2011 International School on Astro Particle Physics devoted to Neutrino Physics and Astrophysics (ISAPP 2011; Varenna, Italy), at the 2011 European School of High Energy Physics (ESHEP 2011; Cheila Gradistei, Romania), and, in modified form, at other summer schools, we present here a written description of the physics of neutrino oscillation. This description is centered on a new way of deriving the oscillation probability. We also provide a brief guide to references relevant to topics other than neutrino oscillation that were covered in the lectures.

  8. Oscillator, neutron modulator

    Agaisse, R.; Leguen, R.; Ombredane, D.

    1960-01-01

    The authors present a mechanical device and an electronic control circuit which have been designed to sinusoidally modulate the reactivity of the Proserpine atomic pile. The mechanical device comprises an oscillator and a mechanism assembly. The oscillator is made of cadmium blades which generate the reactivity oscillation. The mechanism assembly comprises a pulse generator for cycle splitting, a gearbox and an engine. The electronic device comprises or performs pulse detection, an on-off device, cycle pulse shaping, phase separation, a dephasing amplifier, electronic switches, counting scales, and control devices. All these elements are briefly presented

  9. OSCILLATING FILAMENTS. I. OSCILLATION AND GEOMETRICAL FRAGMENTATION

    Gritschneder, Matthias; Heigl, Stefan; Burkert, Andreas, E-mail: gritschm@usm.uni-muenchen.de [University Observatory Munich, LMU Munich, Scheinerstrasse 1, D-81679 Munich (Germany)

    2017-01-10

    We study the stability of filaments in equilibrium between gravity and internal as well as external pressure using the grid-based AMR code RAMSES. A homogeneous, straight cylinder below a critical line mass is marginally stable. However, if the cylinder is bent, such as with a slight sinusoidal perturbation, an otherwise stable configuration starts to oscillate, is triggered into fragmentation, and collapses. This previously unstudied behavior allows a filament to fragment at any given scale, as long as it has slight bends. We call this process “geometrical fragmentation.” In our realization, the spacing between the cores matches the wavelength of the sinusoidal perturbation, whereas up to now, filaments were thought to be only fragmenting on the characteristic scale set by the mass-to-line ratio. Using first principles, we derive the oscillation period as well as the collapse timescale analytically. To enable a direct comparison with observations, we study the line-of-sight velocity for different inclinations. We show that the overall oscillation pattern can hide the infall signature of cores.

  10. Modelling emergence of oscillations in communicating bacteria: a structured approach from one to many cells.

    Mina, Petros; di Bernardo, Mario; Savery, Nigel J; Tsaneva-Atanasova, Krasimira

    2013-01-06

    Population-level measurements of phenotypic behaviour in biological systems may not necessarily reflect individual cell behaviour. To assess qualitative changes in the behaviour of a single cell, when alone and when part of a community, we developed an agent-based model describing the metabolic states of a population of quorum-coupled cells. The modelling is motivated by published experimental work of a synthetic genetic regulatory network (GRN) used in Escherichia coli cells that exhibit oscillatory behaviour across the population. To decipher the mechanisms underlying oscillations in the system, we investigate the behaviour of the model via numerical simulation and bifurcation analysis. In particular, we study the effect of an increase in population size as well as the spatio-temporal behaviour of the model. Our results demonstrate that oscillations are possible only in the presence of a high concentration of the coupling chemical and are due to a time scale separation in key regulatory components of the system. The model suggests that the population establishes oscillatory behaviour as the system's preferred stable state. This is achieved via an effective increase in coupling across the population. We conclude that population effects in GRN design need to be taken into consideration and be part of the design process. This is important in planning intervention strategies or designing specific cell behaviours.

  11. Synthetic Defects for Vibrothermography

    Renshaw, Jeremy; Holland, Stephen D.; Thompson, R. Bruce; Eisenmann, David J.

    2010-02-01

    Synthetic defects are an important tool used for characterizing the performance of nondestructive evaluation techniques. Viscous material-filled synthetic defects were developed for use in vibrothermography (also known as sonic IR) as a tool to improve inspection accuracy and reliability. This paper describes how the heat-generation response of these VMF synthetic defects is similar to the response of real defects. It also shows how VMF defects can be applied to improve inspection accuracy for complex industrial parts and presents a study of their application in an aircraft engine stator vane.

  12. Synthetic biological networks

    Archer, Eric; Süel, Gürol M

    2013-01-01

    Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics. (review article)

  13. Again on neutrino oscillations

    Bilenky, S.M.; Pontecorvo, B.

    1976-01-01

    The general case is treated of a weak interaction theory in which a term violating lepton charges is present. In such a scheme the particles with definite masses are Majorana neutrinos (2N if in the weak interaction participate N four-component neutrinos). Neutrino oscillations are discussed and it is shown that the minimum average intensity at the earth of solar neutrinos is 1/2N of the intensity expected when oscillations are absent

  14. Density-wave oscillations

    Belblidia, L.A.; Bratianu, C.

    1979-01-01

    Boiling flow in a steam generator, a water-cooled reactor, and other multiphase processes can be subject to instabilities. It appears that the most predominant instabilities are the so-called density-wave oscillations. They can cause difficulties for three main reasons; they may induce burnout; they may cause mechanical vibrations of components; and they create system control problems. A comprehensive review is presented of experimental and theoretical studies concerning density-wave oscillations. (author)

  15. Oscillators and operational amplifiers

    Lindberg, Erik

    2005-01-01

    A generalized approach to the design of oscillators using operational amplifiers as active elements is presented. A piecewise-linear model of the amplifier is used so that it make sense to investigate the eigenvalues of the Jacobian of the differential equations. The characteristic equation of the general circuit is derived. The dynamic nonlinear transfer characteristic of the amplifier is investigated. Examples of negative resistance oscillators are discussed.

  16. Chaotic solar oscillations

    Blacher, S; Perdang, J [Institut d' Astrophysique, B-4200 Cointe-Ougree (Belgium)

    1981-09-01

    A numerical experiment on Hamiltonian oscillations demonstrates the existence of chaotic motions which satisfy the property of phase coherence. It is observed that the low-frequency end of the power spectrum of such motions is remarkably similar in structure to the low-frequency SCLERA spectra. Since the smallness of the observed solar amplitudes is not a sufficient mathematical ground for inefficiency of non-linear effects the possibility of chaos among solar oscillations cannot be discarded a priori.

  17. Case for neutrino oscillations

    Ramond, P.

    1982-01-01

    The building of a machine capable of producing an intense, well-calibrated beam of muon neutrinos is regarded by particle physicists with keen interest because of its ability of studying neutrino oscillations. The possibility of neutrino oscillations has long been recognized, but it was not made necessary on theoretical or experimental grounds; one knew that oscillations could be avoided if neutrinos were massless, and this was easily done by the conservation of lepton number. The idea of grand unification has led physicists to question the existence (at higher energies) of global conservation laws. The prime examples are baryon-number conservation, which prevents proton decay, and lepton-number conservation, which keeps neutrinos massless, and therefore free of oscillations. The detection of proton decay and neutrino oscillations would therefore be an indirect indication of the idea of Grand Unification, and therefore of paramount importance. Neutrino oscillations occur when neutrinos acquire mass in such a way that the neutrino mass eigenstates do not match the (neutrino) eigenstates produced by the weak interactions. We shall study the ways in which neutrinos can get mass, first at the level of the standard SU 2 x U 1 model, then at the level of its Grand Unification Generalizations

  18. Designing synthetic networks in silico: a generalised evolutionary algorithm approach.

    Smith, Robert W; van Sluijs, Bob; Fleck, Christian

    2017-12-02

    Evolution has led to the development of biological networks that are shaped by environmental signals. Elucidating, understanding and then reconstructing important network motifs is one of the principal aims of Systems & Synthetic Biology. Consequently, previous research has focused on finding optimal network structures and reaction rates that respond to pulses or produce stable oscillations. In this work we present a generalised in silico evolutionary algorithm that simultaneously finds network structures and reaction rates (genotypes) that can satisfy multiple defined objectives (phenotypes). The key step to our approach is to translate a schema/binary-based description of biological networks into systems of ordinary differential equations (ODEs). The ODEs can then be solved numerically to provide dynamic information about an evolved networks functionality. Initially we benchmark algorithm performance by finding optimal networks that can recapitulate concentration time-series data and perform parameter optimisation on oscillatory dynamics of the Repressilator. We go on to show the utility of our algorithm by finding new designs for robust synthetic oscillators, and by performing multi-objective optimisation to find a set of oscillators and feed-forward loops that are optimal at balancing different system properties. In sum, our results not only confirm and build on previous observations but we also provide new designs of synthetic oscillators for experimental construction. In this work we have presented and tested an evolutionary algorithm that can design a biological network to produce desired output. Given that previous designs of synthetic networks have been limited to subregions of network- and parameter-space, the use of our evolutionary optimisation algorithm will enable Synthetic Biologists to construct new systems with the potential to display a wider range of complex responses.

  19. Technical Assessment: Synthetic Biology

    2015-01-01

    Pfizer, Bausch & Lomb, Coca - Cola , and other Fortune 500 companies 8 Data estimated by the... financial prize for ideas to drive forward the production of a sensor relying on synthetic organisms that can detect exposure to 500 specific chemicals

  20. Synthetic Biology: Applications in the Food Sector.

    Tyagi, Ashish; Kumar, Ashwani; Aparna, S V; Mallappa, Rashmi H; Grover, Sunita; Batish, Virender Kumar

    2016-08-17

    Synthetic biology also termed as "genomic alchemy" represents a powerful area of science that is based on the convergence of biological sciences with systems engineering. It has been fittingly described as "moving from reading the genetic code to writing it" as it focuses on building, modeling, designing and fabricating novel biological systems using customized gene components that result in artificially created genetic circuitry. The scientifically compelling idea of the technological manipulation of life has been advocated since long time. Realization of this idea has gained momentum with development of high speed automation and the falling cost of gene sequencing and synthesis following the completion of the human genome project. Synthetic biology will certainly be instrumental in shaping the development of varying areas ranging from biomedicine, biopharmaceuticals, chemical production, food and dairy quality monitoring, packaging, and storage of food and dairy products, bioremediation and bioenergy production, etc. However, potential dangers of using synthetic life forms have to be acknowledged and adoption of policies by the scientific community to ensure safe practice while making important advancements in the ever expanding field of synthetic biology is to be fully supported and implemented.

  1. Synthetic Biology to Engineer Bacteriophage Genomes.

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

    2018-01-01

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

  2. Do muons oscillate?

    Dolgov, A.D.; Morozov, A.Yu.; Okun, L.B.; Schepkin, M.G.

    1997-01-01

    We develop a theory of the EPR-like effects due to neutrino oscillations in the π→μν decays. Its experimental implications are space-time correlations of the neutrino and muon when they are both detected, while the pion decay point is not fixed. However, the more radical possibility of μ-oscillations in experiments where only muons are detected (as suggested in hep-ph/9509261), is ruled out. We start by discussing decays of monochromatic pions, and point out a few ''paradoxes''. Then we consider pion wave packets, solve the ''paradoxes'', and show that the formulas for μν correlations can be transformed into the usual expressions, describing neutrino oscillations, as soon as the pion decay point is fixed. (orig.)

  3. Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.

    Gilad, Assaf A; Shapiro, Mikhail G

    2017-06-01

    Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.

  4. Oscillations in neutron stars

    Hoeye, Gudrun Kristine

    1999-01-01

    We have studied radial and nonradial oscillations in neutron stars, both in a general relativistic and non-relativistic frame, for several different equilibrium models. Different equations of state were combined, and our results show that it is possible to distinguish between the models based on their oscillation periods. We have particularly focused on the p-, f-, and g-modes. We find oscillation periods of II approx. 0.1 ms for the p-modes, II approx. 0.1 - 0.8 ms for the f-modes and II approx. 10 - 400 ms for the g-modes. For high-order (l → 4) f-modes we were also able to derive a formula that determines II l+1 from II l and II l-1 to an accuracy of 0.1%. Further, for the radial f-mode we find that the oscillation period goes to infinity as the maximum mass of the star is approached. Both p-, f-, and g-modes are sensitive to changes in the central baryon number density n c , while the g-modes are also sensitive to variations in the surface temperature. The g-modes are concentrated in the surface layer, while p- and f-modes can be found in all parts of the star. The effects of general relativity were studied, and we find that these are important at high central baryon number densities, especially for the p- and f-modes. General relativistic effects can therefore not be neglected when studying oscillations in neutron stars. We have further developed an improved Cowling approximation in the non-relativistic frame, which eliminates about half of the gap in the oscillation periods that results from use of the ordinary Cowling approximation. We suggest to develop an improved Cowling approximation also in the general relativistic frame. (Author)

  5. Oscillations in neutron stars

    Hoeye, Gudrun Kristine

    1999-07-01

    We have studied radial and nonradial oscillations in neutron stars, both in a general relativistic and non-relativistic frame, for several different equilibrium models. Different equations of state were combined, and our results show that it is possible to distinguish between the models based on their oscillation periods. We have particularly focused on the p-, f-, and g-modes. We find oscillation periods of II approx. 0.1 ms for the p-modes, II approx. 0.1 - 0.8 ms for the f-modes and II approx. 10 - 400 ms for the g-modes. For high-order (l (>{sub )} 4) f-modes we were also able to derive a formula that determines II{sub l+1} from II{sub l} and II{sub l-1} to an accuracy of 0.1%. Further, for the radial f-mode we find that the oscillation period goes to infinity as the maximum mass of the star is approached. Both p-, f-, and g-modes are sensitive to changes in the central baryon number density n{sub c}, while the g-modes are also sensitive to variations in the surface temperature. The g-modes are concentrated in the surface layer, while p- and f-modes can be found in all parts of the star. The effects of general relativity were studied, and we find that these are important at high central baryon number densities, especially for the p- and f-modes. General relativistic effects can therefore not be neglected when studying oscillations in neutron stars. We have further developed an improved Cowling approximation in the non-relativistic frame, which eliminates about half of the gap in the oscillation periods that results from use of the ordinary Cowling approximation. We suggest to develop an improved Cowling approximation also in the general relativistic frame. (Author)

  6. Oscillating acoustic streaming jet

    Moudjed, Brahim; Botton, Valery; Henry, Daniel; Millet, Severine; Ben Hadid, Hamda; Garandet, Jean-Paul

    2014-01-01

    The present paper provides the first experimental investigation of an oscillating acoustic streaming jet. The observations are performed in the far field of a 2 MHz circular plane ultrasound transducer introduced in a rectangular cavity filled with water. Measurements are made by Particle Image Velocimetry (PIV) in horizontal and vertical planes near the end of the cavity. Oscillations of the jet appear in this zone, for a sufficiently high Reynolds number, as an intermittent phenomenon on an otherwise straight jet fluctuating in intensity. The observed perturbation pattern is similar to that of former theoretical studies. This intermittently oscillatory behavior is the first step to the transition to turbulence. (authors)

  7. Oscillating Finite Sums

    Alabdulmohsin, Ibrahim M.

    2018-03-07

    In this chapter, we use the theory of summability of divergent series, presented earlier in Chap. 4, to derive the analogs of the Euler-Maclaurin summation formula for oscillating sums. These formulas will, in turn, be used to perform many remarkable deeds with ease. For instance, they can be used to derive analytic expressions for summable divergent series, obtain asymptotic expressions of oscillating series, and even accelerate the convergence of series by several orders of magnitude. Moreover, we will prove the notable fact that, as far as the foundational rules of summability calculus are concerned, summable divergent series behave exactly as if they were convergent.

  8. Brownian parametric oscillators

    Zerbe, Christine; Jung, Peter; Hänggi, Peter

    1994-05-01

    We discuss the stochastic dynamics of dissipative, white-noise-driven Floquet oscillators, characterized by a time-periodic stiffness. Thus far, little attention has been paid to these exactly solvable nonstationary systems, although they carry a rich potential for several experimental applications. Here, we calculate and discuss the mean values and variances, as well as the correlation functions and the Floquet spectrum. As one main result, we find for certain parameter values that the fluctuations of the position coordinate are suppressed as compared to the equilibrium value of a harmonic oscillator (parametric squeezing).

  9. Friedel oscillations in graphene

    Lawlor, J. A.; Power, S. R.; Ferreira, M.S.

    2013-01-01

    Symmetry breaking perturbations in an electronically conducting medium are known to produce Friedel oscillations in various physical quantities of an otherwise pristine material. Here we show in a mathematically transparent fashion that Friedel oscillations in graphene have a strong sublattice...... asymmetry. As a result, the presence of impurities and/or defects may impact the distinct graphene sublattices very differently. Furthermore, such an asymmetry can be used to explain the recent observations that nitrogen atoms and dimers are not randomly distributed in graphene but prefer to occupy one...

  10. Proprioceptive evoked gamma oscillations

    Arnfred, S.M.; Hansen, Lars Kai; Parnas, J.

    2007-01-01

    A proprioceptive stimulus consisting of a weight change of a handheld load has recently been shown to elicit an evoked potential. Previously, somatosensory gamma oscillations have only been evoked by electrical stimuli. We conjectured that a natural proprioceptive stimulus also would be able...... to evoke gamma oscillations. EEG was recorded using 64 channels in 14 healthy subjects. In each of three runs a stimulus of 100 g load increment in each hand was presented in 120 trials. Data were wavelet transformed and runs collapsed. Inter-trial phase coherence (ITPC) was computed as the best measure...

  11. Oscillating Finite Sums

    Alabdulmohsin, Ibrahim M.

    2018-01-01

    In this chapter, we use the theory of summability of divergent series, presented earlier in Chap. 4, to derive the analogs of the Euler-Maclaurin summation formula for oscillating sums. These formulas will, in turn, be used to perform many remarkable deeds with ease. For instance, they can be used to derive analytic expressions for summable divergent series, obtain asymptotic expressions of oscillating series, and even accelerate the convergence of series by several orders of magnitude. Moreover, we will prove the notable fact that, as far as the foundational rules of summability calculus are concerned, summable divergent series behave exactly as if they were convergent.

  12. Oscillators from nonlinear realizations

    Kozyrev, N.; Krivonos, S.

    2018-02-01

    We construct the systems of the harmonic and Pais-Uhlenbeck oscillators, which are invariant with respect to arbitrary noncompact Lie algebras. The equations of motion of these systems can be obtained with the help of the formalism of nonlinear realizations. We prove that it is always possible to choose time and the fields within this formalism in such a way that the equations of motion become linear and, therefore, reduce to ones of ordinary harmonic and Pais-Uhlenbeck oscillators. The first-order actions, that produce these equations, can also be provided. As particular examples of this construction, we discuss the so(2, 3) and G 2(2) algebras.

  13. Oscillation Baselining and Analysis Tool

    2017-03-27

    PNNL developed a new tool for oscillation analysis and baselining. This tool has been developed under a new DOE Grid Modernization Laboratory Consortium (GMLC) Project (GM0072 - “Suite of open-source applications and models for advanced synchrophasor analysis”) and it is based on the open platform for PMU analysis. The Oscillation Baselining and Analysis Tool (OBAT) performs the oscillation analysis and identifies modes of oscillations (frequency, damping, energy, and shape). The tool also does oscillation event baselining (fining correlation between oscillations characteristics and system operating conditions).

  14. Synthetic biology approaches: Towards sustainable exploitation of marine bioactive molecules.

    Seghal Kiran, G; Ramasamy, Pasiyappazham; Sekar, Sivasankari; Ramu, Meenatchi; Hassan, Saqib; Ninawe, A S; Selvin, Joseph

    2018-06-01

    The discovery of genes responsible for the production of bioactive metabolites via metabolic pathways combined with the advances in synthetic biology tools, has allowed the establishment of numerous microbial cell factories, for instance the yeast cell factories, for the manufacture of highly useful metabolites from renewable biomass. Genome mining and metagenomics are two platforms provide base-line data for reconstruction of genomes and metabolomes which is based in the development of synthetic/semi-synthetic genomes for marine natural products discovery. Engineered biofilms are being innovated on synthetic biology platform using genetic circuits and cell signalling systems as represillators controlling biofilm formation. Recombineering is a process of homologous recombination mediated genetic engineering, includes insertion, deletion or modification of any sequence specifically. Although this discipline considered new to the scientific domain, this field has now developed as promising endeavor on the accomplishment of sustainable exploitation of marine natural products. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Synthetic biology for pharmaceutical drug discovery

    Trosset JY

    2015-12-01

    Full Text Available Jean-Yves Trosset,1 Pablo Carbonell2,3 1Bioinformation Research Laboratory, Sup’Biotech, Villejuif, France; 2Faculty of Life Sciences, SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK; 3Department of Experimental and Health Sciences (DCEXS, Research Programme on Biomedical Informatics (GRIB, Hospital del Mar Medical Research Institute (IMIM, Universitat Pompeu Fabra (UPF, Barcelona, Spain Abstract: Synthetic biology (SB is an emerging discipline, which is slowly reorienting the field of drug discovery. For thousands of years, living organisms such as plants were the major source of human medicines. The difficulty in resynthesizing natural products, however, often turned pharmaceutical industries away from this rich source for human medicine. More recently, progress on transformation through genetic manipulation of biosynthetic units in microorganisms has opened the possibility of in-depth exploration of the large chemical space of natural products derivatives. Success of SB in drug synthesis culminated with the bioproduction of artemisinin by microorganisms, a tour de force in protein and metabolic engineering. Today, synthetic cells are not only used as biofactories but also used as cell-based screening platforms for both target-based and phenotypic-based approaches. Engineered genetic circuits in synthetic cells are also used to decipher disease mechanisms or drug mechanism of actions and to study cell–cell communication within bacteria consortia. This review presents latest developments of SB in the field of drug discovery, including some challenging issues such as drug resistance and drug toxicity. Keywords: metabolic engineering, plant synthetic biology, natural products, synthetic quorum sensing, drug resistance

  16. From excitability to oscillations

    Postnov, D. E.; Neganova, A. Y.; Jacobsen, J. C. B.

    2013-01-01

    One consequence of cell-to-cell communication is the appearance of synchronized behavior, where many cells cooperate to generate new dynamical patterns. We present a simple functional model of vasomotion based on the concept of a two-mode oscillator with dual interactions: via relatively slow dif...

  17. Neutrino oscillation experiments

    Camilleri, L.

    1996-01-01

    Neutrino oscillation experiments (ν μ →ν e and ν μ →ν τ ) currently being performed at accelerators are reviewed. Future plans for short and long base-line experiments are summarized. (author) 10 figs., 2 tabs., 29 refs

  18. A simple violin oscillator

    Jones, R. T.

    1976-01-01

    For acoustic tests the violin is driven laterally at the bridge by a small speaker of the type commonly found in pocket transistor radios. An audio oscillator excites the tone which is picked up by a sound level meter. Gross patterns of vibration modes are obtained by the Chladni method.

  19. Nonlinearity in oscillating bridges

    Filippo Gazzola

    2013-09-01

    Full Text Available We first recall several historical oscillating bridges that, in some cases, led to collapses. Some of them are quite recent and show that, nowadays, oscillations in suspension bridges are not yet well understood. Next, we survey some attempts to model bridges with differential equations. Although these equations arise from quite different scientific communities, they display some common features. One of them, which we believe to be incorrect, is the acceptance of the linear Hooke law in elasticity. This law should be used only in presence of small deviations from equilibrium, a situation which does not occur in widely oscillating bridges. Then we discuss a couple of recent models whose solutions exhibit self-excited oscillations, the phenomenon visible in real bridges. This suggests a different point of view in modeling equations and gives a strong hint how to modify the existing models in order to obtain a reliable theory. The purpose of this paper is precisely to highlight the necessity of revisiting the classical models, to introduce reliable models, and to indicate the steps we believe necessary to reach this target.

  20. Integrated optoelectronic oscillator.

    Tang, Jian; Hao, Tengfei; Li, Wei; Domenech, David; Baños, Rocio; Muñoz, Pascual; Zhu, Ninghua; Capmany, José; Li, Ming

    2018-04-30

    With the rapid development of the modern communication systems, radar and wireless services, microwave signal with high-frequency, high-spectral-purity and frequency tunability as well as microwave generator with light weight, compact size, power-efficient and low cost are increasingly demanded. Integrated microwave photonics (IMWP) is regarded as a prospective way to meet these demands by hybridizing the microwave circuits and the photonics circuits on chip. In this article, we propose and experimentally demonstrate an integrated optoelectronic oscillator (IOEO). All of the devices needed in the optoelectronic oscillation loop circuit are monolithically integrated on chip within size of 5×6cm 2 . By tuning the injection current to 44 mA, the output frequency of the proposed IOEO is located at 7.30 GHz with phase noise value of -91 dBc/Hz@1MHz. When the injection current is increased to 65 mA, the output frequency can be changed to 8.87 GHz with phase noise value of -92 dBc/Hz@1MHz. Both of the oscillation frequency can be slightly tuned within 20 MHz around the center oscillation frequency by tuning the injection current. The method about improving the performance of IOEO is carefully discussed at the end of in this article.

  1. The variational spiked oscillator

    Aguilera-Navarro, V.C.; Ullah, N.

    1992-08-01

    A variational analysis of the spiked harmonic oscillator Hamiltonian -d 2 / d x 2 + x 2 + δ/ x 5/2 , δ > 0, is reported in this work. A trial function satisfying Dirichlet boundary conditions is suggested. The results are excellent for a large range of values of the coupling parameter. (author)

  2. Neutrino oscillation experiments

    Camilleri, L [European Organization for Nuclear Research, Geneva (Switzerland)

    1996-11-01

    Neutrino oscillation experiments ({nu}{sub {mu}}{yields}{nu}{sub e} and {nu}{sub {mu}}{yields}{nu}{sub {tau}}) currently being performed at accelerators are reviewed. Future plans for short and long base-line experiments are summarized. (author) 10 figs., 2 tabs., 29 refs.

  3. Mammalian Synthetic Biology: Time for Big MACs.

    Martella, Andrea; Pollard, Steven M; Dai, Junbiao; Cai, Yizhi

    2016-10-21

    The enabling technologies of synthetic biology are opening up new opportunities for engineering and enhancement of mammalian cells. This will stimulate diverse applications in many life science sectors such as regenerative medicine, development of biosensing cell lines, therapeutic protein production, and generation of new synthetic genetic regulatory circuits. Harnessing the full potential of these new engineering-based approaches requires the design and assembly of large DNA constructs-potentially up to chromosome scale-and the effective delivery of these large DNA payloads to the host cell. Random integration of large transgenes, encoding therapeutic proteins or genetic circuits into host chromosomes, has several drawbacks such as risks of insertional mutagenesis, lack of control over transgene copy-number and position-specific effects; these can compromise the intended functioning of genetic circuits. The development of a system orthogonal to the endogenous genome is therefore beneficial. Mammalian artificial chromosomes (MACs) are functional, add-on chromosomal elements, which behave as normal chromosomes-being replicating and portioned to daughter cells at each cell division. They are deployed as useful gene expression vectors as they remain independent from the host genome. MACs are maintained as a single-copy and can accommodate multiple gene expression cassettes of, in theory, unlimited DNA size (MACs up to 10 megabases have been constructed). MACs therefore enabled control over ectopic gene expression and represent an excellent platform to rapidly prototype and characterize novel synthetic gene circuits without recourse to engineering the host genome. This review describes the obstacles synthetic biologists face when working with mammalian systems and how the development of improved MACs can overcome these-particularly given the spectacular advances in DNA synthesis and assembly that are fuelling this research area.

  4. A standard-enabled workflow for synthetic biology

    Myers, Chris J.

    2017-06-15

    A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

  5. What Are Synthetic Cannabinoids?

    ... years, synthetic cannabinoid mixtures have been easy to buy in drug paraphernalia shops, novelty stores, gas stations, and over ... abuse, authorities have made it illegal to sell, buy, or possess some of ... use is that standard drug tests cannot easily detect many of the chemicals ...

  6. Synthetic Aperture Sequential Beamforming

    Kortbek, Jacob; Jensen, Jørgen Arendt; Gammelmark, Kim Løkke

    2008-01-01

    A synthetic aperture focusing (SAF) technique denoted Synthetic Aperture Sequential Beamforming (SASB) suitable for 2D and 3D imaging is presented. The technique differ from prior art of SAF in the sense that SAF is performed on pre-beamformed data contrary to channel data. The objective is to im......A synthetic aperture focusing (SAF) technique denoted Synthetic Aperture Sequential Beamforming (SASB) suitable for 2D and 3D imaging is presented. The technique differ from prior art of SAF in the sense that SAF is performed on pre-beamformed data contrary to channel data. The objective...... is to improve and obtain a more range independent lateral resolution compared to conventional dynamic receive focusing (DRF) without compromising frame rate. SASB is a two-stage procedure using two separate beamformers. First a set of Bmode image lines using a single focal point in both transmit and receive...... is stored. The second stage applies the focused image lines from the first stage as input data. The SASB method has been investigated using simulations in Field II and by off-line processing of data acquired with a commercial scanner. The performance of SASB with a static image object is compared with DRF...

  7. Building synthetic cellular organization

    Polka, Jessica K.; Silver, Pamela A.

    2013-01-01

    The elaborate spatial organization of cells enhances, restricts, and regulates protein–protein interactions. However, the biological significance of this organization has been difficult to study without ways of directly perturbing it. We highlight synthetic biology tools for engineering novel cellular organization, describing how they have been, and can be, used to advance cell biology.

  8. Towards a synthetic chloroplast.

    Christina M Agapakis

    2011-04-01

    Full Text Available The evolution of eukaryotic cells is widely agreed to have proceeded through a series of endosymbiotic events between larger cells and proteobacteria or cyanobacteria, leading to the formation of mitochondria or chloroplasts, respectively. Engineered endosymbiotic relationships between different species of cells are a valuable tool for synthetic biology, where engineered pathways based on two species could take advantage of the unique abilities of each mutualistic partner.We explored the possibility of using the photosynthetic bacterium Synechococcus elongatus PCC 7942 as a platform for studying evolutionary dynamics and for designing two-species synthetic biological systems. We observed that the cyanobacteria were relatively harmless to eukaryotic host cells compared to Escherichia coli when injected into the embryos of zebrafish, Danio rerio, or taken up by mammalian macrophages. In addition, when engineered with invasin from Yersinia pestis and listeriolysin O from Listeria monocytogenes, S. elongatus was able to invade cultured mammalian cells and divide inside macrophages.Our results show that it is possible to engineer photosynthetic bacteria to invade the cytoplasm of mammalian cells for further engineering and applications in synthetic biology. Engineered invasive but non-pathogenic or immunogenic photosynthetic bacteria have great potential as synthetic biological devices.

  9. Synthetic Metabolic Pathways

    topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Synthetic Metabolic Pathways: Methods and Protocols aims to ensure successful results in the further study...

  10. Anharmonic oscillator and Bogoliubov transformation

    Pattnayak, G.C.; Torasia, S.; Rath, B.

    1990-01-01

    The anharmonic oscillator occupies a cornerstone in many problems in physics. It was observed that none of the authors have tested Bogoliubov transformation to study anharmonic oscillator. The groundstate energy of the anharmonic oscillator is studied using Bogoliubov transformation and the results presented. (author)

  11. Bimodal oscillations in nephron autoregulation

    Sosnovtseva, Olga; Pavlov, A.N.; Mosekilde, Erik

    2002-01-01

    The individual functional unit of the kidney (the nephron) displays oscillations in its pressure and flow regulation at two different time scales: fast oscillations associated with a myogenic dynamics of the afferent arteriole, and slower oscillations arising from a delay in the tubuloglomerular ...

  12. Observation and analysis of oscillations in linear accelerators

    Seeman, J.T.

    1991-11-01

    This report discusses the following on oscillation in linear accelerators: Betatron Oscillations; Betatron Oscillations at High Currents; Transverse Profile Oscillations; Transverse Profile Oscillations at High Currents.; Oscillation and Profile Transient Jitter; and Feedback on Transverse Oscillations

  13. Microorganism Utilization for Synthetic Milk

    Morford, Megan A.; Khodadad, Christina L.; Caro, Janicce I.; Spencer, LaShelle E.; Richards, Jeffery T.; Strayer, Richard F.; Birmele, Michele N.; Wheeler, Raymond M.

    2014-01-01

    A desired architecture for long duration spaceflight, like aboard the International Space Station or for future missions to Mars, is to provide a supply of fresh food crops for the astronauts. However, some crops can create a high proportion of inedible plant waste. The main goal of the Synthetic Biology project, Cow in a Column, was to produce the components of milk (sugar, lipid, protein) from inedible plant waste by utilizing microorganisms (fungi, yeast, bacteria). Of particular interest was utilizing the valuable polysaccharide, cellulose, found in plant waste, to naturally fuel-through microorganism cellular metabolism- the creation of sugar (glucose), lipid (milk fat), and protein (casein) in order to produce a synthetic edible food product. Environmental conditions such as pH, temperature, carbon source, aeration, and choice microorganisms were optimized in the laboratory and the desired end-products, sugars and lipids, were analyzed. Trichoderma reesei, a known cellulolytic fungus, was utilized to drive the production of glucose, with the intent that the produced glucose would serve as the carbon source for milk fat production and be a substitute for the milk sugar lactose. Lipid production would be carried out by Rhodosporidium toruloides, yeast known to accumulate those lipids that are typically found in milk fat. Results showed that glucose and total lipid content were below what was expected during this phase of experimentation. In addition, individual analysis of six fatty acids revealed that the percentage of each fatty acid was lower than naturally produced bovine milk. Overall, this research indicates that microorganisms could be utilized to breakdown inedible solid waste to produce useable products. For future work, the production of the casein protein for milk would require the development of a genetically modified organism, which was beyond the scope of the original project. Additional trials would be needed to further refine the required

  14. Reactor oscillator - Proposal of the organisation for oscillator operation; Reaktorski oscilator - Predlog organizacije rada na oscilatoru

    Lolic, B; Loloc, B [Institute of Nuclear Sciences Boris Kidric, Laboratorija za fiziku reaktora, Vinca, Beograd (Serbia and Montenegro)

    1961-12-15

    The organizational structure for operating the reactor with the reactor oscillator describes the duties of the reactor operators; staff responsible for operating the oscillator who are responsible for measurements, preparation of the samples and further treatment of the obtained results.

  15. Quenching oscillating behaviors in fractional coupled Stuart-Landau oscillators

    Sun, Zhongkui; Xiao, Rui; Yang, Xiaoli; Xu, Wei

    2018-03-01

    Oscillation quenching has been widely studied during the past several decades in fields ranging from natural sciences to engineering, but investigations have so far been restricted to oscillators with an integer-order derivative. Here, we report the first study of amplitude death (AD) in fractional coupled Stuart-Landau oscillators with partial and/or complete conjugate couplings to explore oscillation quenching patterns and dynamics. It has been found that the fractional-order derivative impacts the AD state crucially. The area of the AD state increases along with the decrease of the fractional-order derivative. Furthermore, by introducing and adjusting a limiting feedback factor in coupling links, the AD state can be well tamed in fractional coupled oscillators. Hence, it provides one an effective approach to analyze and control the oscillating behaviors in fractional coupled oscillators.

  16. Pattern formation in arrays of chemical oscillators

    Chemical oscillators; phase flip; oscillation death. PACS No. 05.45 .... array oscillate (with varying amplitudes and frequencies), while the others experience oscillation death .... Barring the boundary cells, one observes near phase flip and near ...

  17. Synthetic biology: Novel approaches for microbiology.

    Padilla-Vaca, Felipe; Anaya-Velázquez, Fernando; Franco, Bernardo

    2015-06-01

    In the past twenty years, molecular genetics has created powerful tools for genetic manipulation of living organisms. Whole genome sequencing has provided necessary information to assess knowledge on gene function and protein networks. In addition, new tools permit to modify organisms to perform desired tasks. Gene function analysis is speed up by novel approaches that couple both high throughput data generation and mining. Synthetic biology is an emerging field that uses tools for generating novel gene networks, whole genome synthesis and engineering. New applications in biotechnological, pharmaceutical and biomedical research are envisioned for synthetic biology. In recent years these new strategies have opened up the possibilities to study gene and genome editing, creation of novel tools for functional studies in virus, parasites and pathogenic bacteria. There is also the possibility to re-design organisms to generate vaccine subunits or produce new pharmaceuticals to combat multi-drug resistant pathogens. In this review we provide our opinion on the applicability of synthetic biology strategies for functional studies of pathogenic organisms and some applications such as genome editing and gene network studies to further comprehend virulence factors and determinants in pathogenic organisms. We also discuss what we consider important ethical issues for this field of molecular biology, especially for potential misuse of the new technologies. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

  18. Synthetic biology for microbial heavy metal biosensors.

    Kim, Hyun Ju; Jeong, Haeyoung; Lee, Sang Jun

    2018-02-01

    Using recombinant DNA technology, various whole-cell biosensors have been developed for detection of environmental pollutants, including heavy metal ions. Whole-cell biosensors have several advantages: easy and inexpensive cultivation, multiple assays, and no requirement of any special techniques for analysis. In the era of synthetic biology, cutting-edge DNA sequencing and gene synthesis technologies have accelerated the development of cell-based biosensors. Here, we summarize current technological advances in whole-cell heavy metal biosensors, including the synthetic biological components (bioparts), sensing and reporter modules, genetic circuits, and chassis cells. We discuss several opportunities for improvement of synthetic cell-based biosensors. First, new functional modules must be discovered in genome databases, and this knowledge must be used to upgrade specific bioparts through molecular engineering. Second, modules must be assembled into functional biosystems in chassis cells. Third, heterogeneity of individual cells in the microbial population must be eliminated. In the perspectives, the development of whole-cell biosensors is also discussed in the aspects of cultivation methods and synthetic cells.

  19. Entanglement in neutrino oscillations

    Blasone, M.; Dell' Anno, F.; De Siena, S.; Illuminati, F. [Universita degli Studi di Salerno Via Ponte don Melillon, Dipt. di Matematica e Informatica, Fisciano SA (Italy); INFN Sezione di Napoli, Gruppo collegato di Salerno - Baronissi SA (Italy); Dell' Anno, F.; De Siena, S.; Illuminati, F. [CNR-INFM Coherentia - Napoli (Italy); Blasone, M. [ISI Foundation for Scientific Interchange, Torino (Italy)

    2009-03-15

    Flavor oscillations in elementary particle physics are related to multimode entanglement of single-particle states. We show that mode entanglement can be expressed in terms of flavor transition probabilities, and therefore that single-particle entangled states acquire a precise operational characterization in the context of particle mixing. We treat in detail the physically relevant cases of two- and three-flavor neutrino oscillations, including the effective measure of CP violation. We discuss experimental schemes for the transfer of the quantum information encoded in single-neutrino states to spatially delocalized two-flavor charged-lepton states, thus showing, at least in principle, that single-particle entangled states of neutrino mixing are legitimate physical resources for quantum information tasks. (authors)

  20. Nonlinear (Anharmonic Casimir Oscillator

    Habibollah Razmi

    2011-01-01

    Full Text Available We want to study the dynamics of a simple linear harmonic micro spring which is under the influence of the quantum Casimir force/pressure and thus behaves as a (an nonlinear (anharmonic Casimir oscillator. Generally, the equation of motion of this nonlinear micromechanical Casimir oscillator has no exact solvable (analytical solution and the turning point(s of the system has (have no fixed position(s; however, for particular values of the stiffness of the micro spring and at appropriately well-chosen distance scales and conditions, there is (are approximately sinusoidal solution(s for the problem (the variable turning points are collected in a very small interval of positions. This, as a simple and elementary plan, may be useful in controlling the Casimir stiction problem in micromechanical devices.

  1. Entanglement in neutrino oscillations

    Blasone, M.; Dell'Anno, F.; De Siena, S.; Illuminati, F.; Dell'Anno, F.; De Siena, S.; Illuminati, F.; Blasone, M.

    2009-01-01

    Flavor oscillations in elementary particle physics are related to multimode entanglement of single-particle states. We show that mode entanglement can be expressed in terms of flavor transition probabilities, and therefore that single-particle entangled states acquire a precise operational characterization in the context of particle mixing. We treat in detail the physically relevant cases of two- and three-flavor neutrino oscillations, including the effective measure of CP violation. We discuss experimental schemes for the transfer of the quantum information encoded in single-neutrino states to spatially delocalized two-flavor charged-lepton states, thus showing, at least in principle, that single-particle entangled states of neutrino mixing are legitimate physical resources for quantum information tasks. (authors)

  2. Acoustics waves and oscillations

    Sen, S.N.

    2013-01-01

    Parameters of acoustics presented in a logical and lucid style Physical principles discussed with mathematical formulations Importance of ultrasonic waves highlighted Dispersion of ultrasonic waves in viscous liquids explained This book presents the theory of waves and oscillations and various applications of acoustics in a logical and simple form. The physical principles have been explained with necessary mathematical formulation and supported by experimental layout wherever possible. Incorporating the classical view point all aspects of acoustic waves and oscillations have been discussed together with detailed elaboration of modern technological applications of sound. A separate chapter on ultrasonics emphasizes the importance of this branch of science in fundamental and applied research. In this edition a new chapter ''Hypersonic Velocity in Viscous Liquids as revealed from Brillouin Spectra'' has been added. The book is expected to present to its readers a comprehensive presentation of the subject matter...

  3. Discrete repulsive oscillator wavefunctions

    Munoz, Carlos A; Rueda-Paz, Juvenal; Wolf, Kurt Bernardo

    2009-01-01

    For the study of infinite discrete systems on phase space, the three-dimensional Lorentz algebra and group, so(2,1) and SO(2,1), provide a discrete model of the repulsive oscillator. Its eigenfunctions are found in the principal irreducible representation series, where the compact generator-that we identify with the position operator-has the infinite discrete spectrum of the integers Z, while the spectrum of energies is a double continuum. The right- and left-moving wavefunctions are given by hypergeometric functions that form a Dirac basis for l 2 (Z). Under contraction, the discrete system limits to the well-known quantum repulsive oscillator. Numerical computations of finite approximations raise further questions on the use of Dirac bases for infinite discrete systems.

  4. Neutrino Masses and Oscillations

    CERN. Geneva. Audiovisual Unit; Treille, Daniel

    2002-01-01

    This course will not cover its subject in the customary way. The emphasis will be on the simple theoretical concepts (helicity, handedness, chirality, Majorana masses) which are obscure in most of the literature, and on the quantum mechanics of oscillations, that ALL books get wrong. Which, hopefully, will not deter me from discussing some of the most interesting results from the labs and from the cosmos.

  5. Oscillations in quasineutral plasmas

    Grenier, E.

    1996-01-01

    The purpose of this article is to describe the limit, as the vacuum electric permittivity goes to zero, of a plasma physics system, deduced from the Vlasov-Poisson system for special initial data (distribution functions which are analytic in the space variable, with compact support in velocity), a limit also called open-quotes quasineutral regimeclose quotes of the plasma, and the related oscillations of the electric field, with high frequency in time. 20 refs

  6. Density oscillations within hadrons

    Arnold, R.; Barshay, S.

    1976-01-01

    In models of extended hadrons, in which small bits of matter carrying charge and effective mass exist confined within a medium, oscillations in the matter density may occur. A way of investigating this possibility experimentally in high-energy hadron-hadron elastic diffraction scattering is suggested, and the effect is illustrated by examining some existing data which might be relevant to the question [fr

  7. Neutrino Oscillations Physics

    Fogli, Gianluigi

    2005-06-01

    We review the status of the neutrino oscillations physics, with a particular emphasis on the present knowledge of the neutrino mass-mixing parameters. We consider first the νμ → ντ flavor transitions of atmospheric neutrinos. It is found that standard oscillations provide the best description of the SK+K2K data, and that the associated mass-mixing parameters are determined at ±1σ (and NDF = 1) as: Δm2 = (2.6 ± 0.4) × 10-3 eV2 and sin 2 2θ = 1.00{ - 0.05}{ + 0.00} . Such indications, presently dominated by SK, could be strengthened by further K2K data. Then we point out that the recent data from the Sudbury Neutrino Observatory, together with other relevant measurements from solar and reactor neutrino experiments, in particular the KamLAND data, convincingly show that the flavor transitions of solar neutrinos are affected by Mikheyev-Smirnov-Wolfenstein (MSW) effects. Finally, we perform an updated analysis of two-family active oscillations of solar and reactor neutrinos in the standard MSW case.

  8. Synthetic Electric Microbial Biosensors

    2017-06-10

    domains and DNA-binding domains into a single protein for deregulation of down stream genes of have been favored [10]. Initially experiments with... Germany DISTRIBUTION A. Approved for public release: distribution unlimited.   Talk title: “Synthetic biology based microbial biosensors for the...toolbox” in Heidelberg, Germany Poster title: “Anaerobic whole cell microbial biosensors” Link: http://phdsymposium.embl.org/#home   September, 2014

  9. Preparing Synthetic Biology for the World

    Gerd H.G. Moe-Behrens

    2013-01-01

    Full Text Available Synthetic Biology promises low-cost, exponentially scalable products and global health solutions in the form of self-replicating organisms, or living devices. As these promises are realized, proof-of-concept systems will gradually migrate from tightly regulated laboratory or industrial environments into private spaces as, for instance, probiotic health products, food, and even do-it-yourself bioengineered systems. What additional steps, if any, should be taken before releasing engineered self-replicating organisms into a broader user space? In this review, we explain how studies of genetically modified organisms lay groundwork for the future landscape of biosafety. Early in the design process, biological engineers are anticipating potential hazards and developing innovative tools to mitigate risk. Here, we survey lessons learned, ongoing efforts to engineer intrinsic biocontainment, and how different stakeholders in synthetic biology can act to accomplish best practices for biosafety.

  10. Misconceptions of Synthetic Biology: Lessons from an Interdisciplinary Summer School

    Verseux, Cyprien; Acevedo-Rocha, Carlos G.; Chizzolini, Fabio; Rothschild, Lynn J.

    2016-01-01

    In 2014, an international group of scholars from various fields analysed the "societal dimensions" of synthetic biology in an interdisciplinary summer school. Here, we report and discuss the biologists' observations on the general perception of synthetic biology by non-biologists who took part in this event. Most attendees mainly associated synthetic biology with contributions from the best-known public figures of the field, rarely mentioning other scientists. Media extrapolations of those contributions appeared to have created unrealistic expectations and irrelevant fears that were widely disconnected from the current research in synthetic biology. Another observation was that when debating developments in synthetic biology, semantics strongly mattered: depending on the terms used to present an application of synthetic biology, attendees reacted in radically different ways. For example, using the term "GMOs" (genetically modified organisms) rather than the term "genetic engineering" led to very different reactions. Stimulating debates also happened with participants having unanticipated points of view, for instance biocentrist ethicists who argued that engineered microbes should not be used for human purposes. Another communication challenge emerged from the connotations and inaccuracies surrounding the word "life", which impaired constructive debates, thus leading to misconceptions about the abilities of scientists to engineer or even create living organisms. Finally, it appeared that synthetic biologists tend to overestimate the knowledge of non-biologists, further affecting communication. The motivation and ability of synthetic biologists to communicate their work outside their research field needs to be fostered, notably towards policymakers who need a more accurate and technical understanding of the field to make informed decisions. Interdisciplinary events gathering scholars working in and around synthetic biology are an effective tool in addressing those

  11. Opportunities in plant synthetic biology.

    Cook, Charis; Martin, Lisa; Bastow, Ruth

    2014-05-01

    Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.

  12. Synthetic quorum sensing in model microcapsule colonies

    Shum, Henry; Balazs, Anna C.

    2017-08-01

    Biological quorum sensing refers to the ability of cells to gauge their population density and collectively initiate a new behavior once a critical density is reached. Designing synthetic materials systems that exhibit quorum sensing-like behavior could enable the fabrication of devices with both self-recognition and self-regulating functionality. Herein, we develop models for a colony of synthetic microcapsules that communicate by producing and releasing signaling molecules. Production of the chemicals is regulated by a biomimetic negative feedback loop, the “repressilator” network. Through theory and simulation, we show that the chemical behavior of such capsules is sensitive to both the density and number of capsules in the colony. For example, decreasing the spacing between a fixed number of capsules can trigger a transition in chemical activity from the steady, repressed state to large-amplitude oscillations in chemical production. Alternatively, for a fixed density, an increase in the number of capsules in the colony can also promote a transition into the oscillatory state. This configuration-dependent behavior of the capsule colony exemplifies quorum-sensing behavior. Using our theoretical model, we predict the transitions from the steady state to oscillatory behavior as a function of the colony size and capsule density.

  13. Quasioptical Josephson oscillator

    Wengler, M.J.; Pance, A.; Liu, B.

    1991-01-01

    This paper discusses the authors' work with large 2-dimensional arrays of Josephson junctions for submillimeter power generation. The basic design of the Quasioptical Josephson Oscillator (QJO) is presented. The reasons for each design decision are discussed. Superconducting devices have not yet been fabricated, but scale models and computer simulations have been done. A method for characterizing array rf coupling structures is described, and initial results with this method are presented. Microwave scale models of the radiation structure are built and a series of measurements are made with a network analyzer

  14. Modeling microtubule oscillations

    Jobs, E.; Wolf, D.E.; Flyvbjerg, H.

    1997-01-01

    Synchronization of molecular reactions in a macroscopic volume may cause the volume's physical properties to change dynamically and thus reveal much about the reactions. As an example, experimental time series for so-called microtubule oscillations are analyzed in terms of a minimal model...... for this complex polymerization-depolymerization cycle. The model reproduces well the qualitatively different time series that result from different experimental conditions, and illuminates the role and importance of individual processes in the cycle. Simple experiments are suggested that can further test...... and define the model and the polymer's reaction cycle....

  15. Oscillations in nonlinear systems

    Hale, Jack K

    2015-01-01

    By focusing on ordinary differential equations that contain a small parameter, this concise graduate-level introduction to the theory of nonlinear oscillations provides a unified approach to obtaining periodic solutions to nonautonomous and autonomous differential equations. It also indicates key relationships with other related procedures and probes the consequences of the methods of averaging and integral manifolds.Part I of the text features introductory material, including discussions of matrices, linear systems of differential equations, and stability of solutions of nonlinear systems. Pa

  16. Neutrino oscillations at LAMPF

    Carlini, R.; Choi, C.; Donohue, J.

    1985-01-01

    Work at Argonne continues on the construction of the neutrino oscillation experiment (E645). Construction of detector supports and active shield components were completed at the Provo plant of the principal contractor for the project (the Pittsburgh-Des Moines Corporation). Erection of the major experimental components was completed at the LAMPF experimental site in mid-March 1985. Work continues on the tunnel which will house the detector. Construction of detector components (scintillators and proportional drift tubes) is proceeding at Ohio State University and Louisiana State University. Consolidation of these components into the 20-ton neutrino detector is beginning at LAMPF

  17. Theory of oscillators

    Andronov, Aleksandr Aleksandrovich; Vitt, Aleksandr Adolfovich

    1966-01-01

    Theory of Oscillators presents the applications and exposition of the qualitative theory of differential equations. This book discusses the idea of a discontinuous transition in a dynamic process. Organized into 11 chapters, this book begins with an overview of the simplest type of oscillatory system in which the motion is described by a linear differential equation. This text then examines the character of the motion of the representative point along the hyperbola. Other chapters consider examples of two basic types of non-linear non-conservative systems, namely, dissipative systems and self-

  18. Solar and stellar oscillations

    Fossat, E.

    1981-01-01

    We try to explain in simple words what a stellar oscillation is, what kind of restoring forces and excitation mechanisms can be responsible for its occurence, what kind of questions the theoretician asks to the observer and what kind of tools the latter is using to look for the answers. A selected review of the most striking results obtained in the last few years in solar seismology and the present status of their consequences on solar models is presented. A brief discussion on the expected extension towards stellar seismology will end the paper. A selected bibliography on theory as well as observations and recent papers is also included. (orig.)

  19. Coupled nonlinear oscillators

    Chandra, J; Scott, A C

    1983-01-01

    Topics discussed include transitions in weakly coupled nonlinear oscillators, singularly perturbed delay-differential equations, and chaos in simple laser systems. Papers are presented on truncated Navier-Stokes equations in a two-dimensional torus, on frequency locking in Josephson point contacts, and on soliton excitations in Josephson tunnel junctions. Attention is also given to the nonlinear coupling of radiation pulses to absorbing anharmonic molecular media, to aspects of interrupted coarse-graining in stimulated excitation, and to a statistical analysis of long-term dynamic irregularity in an exactly soluble quantum mechanical model.

  20. Synthetic staggered architecture composites

    Dutta, Abhishek; Tekalur, Srinivasan Arjun

    2013-01-01

    Highlights: ► Composite design inspired by nature. ► Tuning microstructure via changing ceramic content and aspect ratio. ► Experimental display of structure–property correlationship in synthetic composites. - Abstract: Structural biocomposites (for example, nacre in seashells, bone, etc.) are designed according to the functional role they are delegated for. For instance, bone is primarily designed for withstanding time-dependent loading (for example, withstanding stresses while running, jumping, accidental fall) and hence the microstructure is designed primarily from enhanced toughness and moderate stiffness point of view. On the contrary, seashells (which lie in the abyss of oceans) apart from providing defense to the organism (it is hosting) against predatory attacks, are subjected to static loading (for example, enormous hydrostatic pressure). Hence, emphasis on the shell structure evolution is directed primarily towards providing enhanced stiffness. In order to conform between stiffness and toughness, nature precisely employs a staggered arrangement of inorganic bricks in a biopolymer matrix (at its most elementary level of architecture). Aspect ratio and content of ceramic bricks are meticulously used by nature to synthesize composites having varying degrees of stiffness, strength and toughness. Such an amazing capability of structure–property correlationship has rarely been demonstrated in synthetic composites. Therefore, in order to better understand the mechanical behavior of synthetic staggered composites, the problem becomes two-pronged: (a) synthesize composites with varying brick size and contents and (b) experimental investigation of the material response. In this article, an attempt has been made to synthesize and characterize staggered ceramic–polymer composites having varying aspect ratio and ceramic content using freeze-casting technique. This will in-turn help us in custom-design manufacture of hybrid bio-inspired composite materials

  1. Synthetic Aperture Ultrasound Imaging

    Jensen, Jørgen Arendt; Nikolov, Svetoslav; Gammelmark, Kim Løkke

    2006-01-01

    The paper describes the use of synthetic aperture (SA) imaging in medical ultrasound. SA imaging is a radical break with today's commercial systems, where the image is acquired sequentially one image line at a time. This puts a strict limit on the frame rate and the possibility of acquiring...... a sufficient amount of data for high precision flow estimation. These constrictions can be lifted by employing SA imaging. Here data is acquired simultaneously from all directions over a number of emissions, and the full image can be reconstructed from this data. The talk will demonstrate the many benefits...

  2. Transition in synthetic jets

    Tesař, Václav; Kordík, Jozef

    2012-01-01

    Roč. 187, NOV 2012 (2012), s. 105-117 ISSN 0924-4247 R&D Projects: GA TA ČR(CZ) TA02020795; GA ČR(CZ) GPP101/12/P556; GA ČR(CZ) GCP101/11/J019 Institutional research plan: CEZ:AV0Z20760514 Keywords : turbulence * synthetic jet * transition * velocity spectra Subject RIV: BK - Fluid Dynamics Impact factor: 1.841, year: 2012 http://www. science direct.com/ science /article/pii/S0924424712005031

  3. Brain Oscillations, Hypnosis, and Hypnotizability.

    Jensen, Mark P; Adachi, Tomonori; Hakimian, Shahin

    2015-01-01

    This article summarizes the state-of-science knowledge regarding the associations between hypnosis and brain oscillations. Brain oscillations represent the combined electrical activity of neuronal assemblies, usually measured as specific frequencies representing slower (delta, theta, alpha) and faster (beta, gamma) oscillations. Hypnosis has been most closely linked to power in the theta band and changes in gamma activity. These oscillations are thought to play a critical role in both the recording and recall of declarative memory and emotional limbic circuits. The authors propose that this role may be the mechanistic link between theta (and perhaps gamma) oscillations and hypnosis, specifically, that the increases in theta oscillations and changes in gamma activity observed with hypnosis may underlie some hypnotic responses. If these hypotheses are supported, they have important implications for both understanding the effects of hypnosis and for enhancing response to hypnotic treatments.

  4. Bounded-oscillation Pushdown Automata

    Pierre Ganty

    2016-09-01

    Full Text Available We present an underapproximation for context-free languages by filtering out runs of the underlying pushdown automaton depending on how the stack height evolves over time. In particular, we assign to each run a number quantifying the oscillating behavior of the stack along the run. We study languages accepted by pushdown automata restricted to k-oscillating runs. We relate oscillation on pushdown automata with a counterpart restriction on context-free grammars. We also provide a way to filter all but the k-oscillating runs from a given PDA by annotating stack symbols with information about the oscillation. Finally, we study closure properties of the defined class of languages and the complexity of the k-emptiness problem asking, given a pushdown automaton P and k >= 0, whether P has a k-oscillating run. We show that, when k is not part of the input, the k-emptiness problem is NLOGSPACE-complete.

  5. Single ICCII Sinusoidal Oscillators Employing Grounded Capacitors

    J. W. Horng

    2011-09-01

    Full Text Available Two inverting second-generation current conveyors (ICCII based sinusoidal oscillators are presented. The first sinusoidal oscillator is composed of one ICCII, two grounded capacitors and two resistors. The oscillation condition and oscillation frequency can be orthogonally controllable. The second sinusoidal oscillator is composed of one ICCII, two grounded capacitors and three resistors. The oscillation condition and oscillation frequency can be independently controllable through different resistors.

  6. Stable And Oscillating Acoustic Levitation

    Barmatz, Martin B.; Garrett, Steven L.

    1988-01-01

    Sample stability or instability determined by levitating frequency. Degree of oscillation of acoustically levitated object along axis of levitation chamber controlled by varying frequency of acoustic driver for axis above or below frequency of corresponding chamber resonance. Stabilization/oscillation technique applied in normal Earth gravity, or in absence of gravity to bring object quickly to rest at nominal levitation position or make object oscillate in desired range about that position.

  7. Isotropic oscillator: spheroidal wave functions

    Mardoyan, L.G.; Pogosyan, G.S.; Ter-Antonyan, V.M.; Sisakyan, A.N.

    1985-01-01

    Solutions of the Schroedinger equation are found for an isotropic oscillator (10) in prolate and oblate spheroidal coordinates. It is shown that the obtained solutions turn into spherical and cylindrical bases of the isotropic oscillator at R→0 and R→ infinity (R is the dimensional parameter entering into the definition of prolate and oblate spheroidal coordinates). The explicit form is given for both prolate and oblate basis of the isotropic oscillator for the lowest quantum states

  8. Neutrino oscillations. Theory and experiment

    Beshtoev, Kh.M.

    2001-01-01

    Theoretical schemes on neutrino oscillations are considered. The experimental data on neutrino oscillations obtained in the Super-Kamiokande (Japan) and SNO (Canada) experiments are given. Comparison of these data with the predictions obtained in the theoretical schemes is done. Conclusion is made that the experimental data confirm only the scheme with transitions (oscillations) between aromatic ν e -, ν μ -, ν τ - neutrinos with maximal angle mixings. (author)

  9. Biosynthesis of therapeutic natural products using synthetic biology.

    Awan, Ali R; Shaw, William M; Ellis, Tom

    2016-10-01

    Natural products are a group of bioactive structurally diverse chemicals produced by microorganisms and plants. These molecules and their derivatives have contributed to over a third of the therapeutic drugs produced in the last century. However, over the last few decades traditional drug discovery pipelines from natural products have become far less productive and far more expensive. One recent development with promise to combat this trend is the application of synthetic biology to therapeutic natural product biosynthesis. Synthetic biology is a young discipline with roots in systems biology, genetic engineering, and metabolic engineering. In this review, we discuss the use of synthetic biology to engineer improved yields of existing therapeutic natural products. We further describe the use of synthetic biology to combine and express natural product biosynthetic genes in unprecedented ways, and how this holds promise for opening up completely new avenues for drug discovery and production. Copyright © 2016 Elsevier B.V. All rights reserved.

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

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

    2017-06-15

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

  11. Synthetic Biology and the Argument from Continuity with Established Technologies

    Christiansen, Andreas

    2015-01-01

    ) that it ignores the distinction between what reasons we have and what we should do all things considered. I then illustrate the Continuity Argument and its problems in the case where human manipulation of organisms’ genetic makeup is a suggested reason for finding synthetic biology problematic. Finally, I suggest......Defenders of synthetic biology commonly make reference to the fact that established technologies, such as domestication or selective breeding, share some of the features of synthetic biology that critics argue make it ethically problematic. In this chapter, I reconstruct such references...... as instances of a type of argument which I dub the Continuity Argument. Roughly, the Continuity Argument seeks to show that if we are not disposed to reject the established technology, then features that this technology share with synthetic biology cannot provide reasons to find it ethically problematic. I...

  12. Antiangiogenic effects of synthetic analogs of curcumin in vivo ...

    The active compound curcumin is isolated from the spice turmeric. Curcumin, curcuminoids and their synthetic analogs have been shown to inhibit the progression of cancer in animal models. In colon and skin carcinogenesis the genetic changes engross different genes, but curcumin is effective in preventing ...

  13. Breeding value of primary synthetic wheat genotypes for grain yield

    To introduce new genetic diversity into the bread wheat gene pool from its progenitor, Aegilops tauschii (Coss.) Schmalh, 33 primary synthetic hexaploid wheat genotypes (SYN) were crossed to 20 spring bread wheat (BW) cultivars at the International Wheat and Maize Improvement Center. Modified single...

  14. BISRU: Synthetic Microbes for Moon, Mars and Beyond

    Cumbers, J.; Rothchild, L.

    2010-04-01

    Synthetic biology and genomics will bring a new range of designer organisms into being and give us new tools for the manipulation and control of these organisms. BISRU or biological in situ resource utilization is the use of such genetically modified organisms in space.

  15. The Next Generation of Synthetic Biology Chassis: Moving Synthetic Biology from the Laboratory to the Field.

    Adams, Bryn L

    2016-12-16

    Escherichia coli (E. coli) has played a pivotal role in the development of genetics and molecular biology as scientific fields. It is therefore not surprising that synthetic biology (SB) was built upon E. coli and continues to dominate the field. However, scientific capabilities have advanced from simple gene mutations to the insertion of rationally designed, complex synthetic circuits and creation of entirely synthetic genomes. The point is rapidly approaching where E. coli is no longer an adequate host for the increasingly sophisticated genetic designs of SB. It is time to develop the next generation of SB chassis; robust organisms that can provide the advanced physiology novel synthetic circuits will require to move SB from the laboratory into fieldable technologies. This can be accomplished by developing chassis-specific genetic toolkits that are as extensive as those for E. coli. However, the holy grail of SB would be the development of a universal toolkit that can be ported into any chassis. This viewpoint article underscores the need for new bacterial chassis, as well as discusses some of the important considerations in their selection. It also highlights a few examples of robust, tractable bacterial species that can meet the demands of tomorrow's state-of-the-art in SB. Significant advances have been made in the first 15 years since this field has emerged. However, the advances over the next 15 years will occur not in laboratory organisms, but in fieldable species where the potential of SB can be fully realized in game changing technology.

  16. Chemotaxis and Actin Oscillations

    Bodenschatz, Eberhard; Hsu, Hsin-Fang; Negrete, Jose; Beta, Carsten; Pumir, Alain; Gholami, Azam; Tarantola, Marco; Westendorf, Christian; Zykov, Vladimir

    Recently, self-oscillations of the cytoskeletal actin have been observed in Dictyostelium, a model system for studying chemotaxis. Here we report experimental results on the self-oscillation mechanism and the role of regulatory proteins and myosin II. We stimulate cells rapidly and periodically by using photo un-caging of the chemoattractant in a micro-fluidic device and measured the cellular responses. We found that the response amplitude grows with stimulation strength only in a very narrow region of stimulation, after which the response amplitude reaches a plateau. Moreover, the frequency-response is not constant but rather varies with the strength of external stimuli. To understand the underlying mechanism, we analyzed the polymerization and de-polymerization time in the single cell level. Despite of the large cell-to-cell variability, we found that the polymerization time is independent of external stimuli and the de-polymerization time is prolonged as the stimulation strength increases. Our conclusions will be summarized and the role of noise in the signaling network will be discussed. German Science Foundation CRC 937.

  17. The Wien Bridge Oscillator Family

    Lindberg, Erik

    2006-01-01

    A tutorial in which the Wien bridge family of oscillators is defined and investigated. Oscillators which do not fit into the Barkhausen criterion topology may be designed. A design procedure based on initial complex pole quality factor is reported. The dynamic transfer characteristic of the ampli......A tutorial in which the Wien bridge family of oscillators is defined and investigated. Oscillators which do not fit into the Barkhausen criterion topology may be designed. A design procedure based on initial complex pole quality factor is reported. The dynamic transfer characteristic...

  18. Unstable oscillators based hyperchaotic circuit

    Murali, K.; Tamasevicius, A.; G. Mykolaitis, A.

    1999-01-01

    A simple 4th order hyperchaotic circuit with unstable oscillators is described. The circuit contains two negative impedance converters, two inductors, two capacitors, a linear resistor and a diode. The Lyapunov exponents are presented to confirm hyperchaotic nature of the oscillations in the circ...... in the circuit. The performance of the circuit is investigated by means of numerical integration of appropriate differential equations, PSPICE simulations, and hardware experiment.......A simple 4th order hyperchaotic circuit with unstable oscillators is described. The circuit contains two negative impedance converters, two inductors, two capacitors, a linear resistor and a diode. The Lyapunov exponents are presented to confirm hyperchaotic nature of the oscillations...

  19. Heat exchanger with oscillating flow

    Scotti, Stephen J. (Inventor); Blosser, Max L. (Inventor); Camarda, Charles J. (Inventor)

    1993-01-01

    Various heat exchange apparatuses are described in which an oscillating flow of primary coolant is used to dissipate an incident heat flux. The oscillating flow may be imparted by a reciprocating piston, a double action twin reciprocating piston, fluidic oscillators or electromagnetic pumps. The oscillating fluid flows through at least one conduit in either an open loop or a closed loop. A secondary flow of coolant may be used to flow over the outer walls of at least one conduit to remove heat transferred from the primary coolant to the walls of the conduit.

  20. Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project

    Sliva, Anna; Yang, Huanming; Boeke, Jef D.; Mathews, Debra J. H.

    2015-01-01

    First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) Project is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with...

  1. Analog synthetic biology.

    Sarpeshkar, R

    2014-03-28

    We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog-digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA-protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in Escherichia coli using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations.

  2. Synthetic lubricating oils

    Rodriguez Jurado, J

    1953-01-01

    A yellow solid petroleum paraffin d/sup 60/ 0.808, I number 3.5, average molecular weight 350, chlorinated and condensed with benzene, xylene, or naphthalene by the Friedel and Crafts reaction, in the presence of anhydrous AlCl/sub 3/ or activated Al, gave synthetic lubricating oils. Xylene was the preferred aromatic compound, naphthalene required the use of less completely chlorinated paraffin, benzene produced resins difficult to remove and gave darker oils with excessive green fluorescence. Activated Al rather than anhydrous AlCl/sub 3/ gave darker oils with higher viscosity and Conradson C values. Tar from the low-temperature distillation of lignite, used as a source of a paraffin fraction melting 40/sup 0/ to 48/sup 0/ (chlorinated to 26.5 percent Cl) and an aromatic fraction, 45 percent aromatic compounds by volume (mainly polysubstituted benzenes), I number 10, was converted to a similar synthetic lubricant with the following properties: Kinematic viscosity at 210/sup 0/ F., 50.4 centistokes; viscosity index, 92; Conradson C, 1.5 percent; solidification point, 9/sup 0/; S, 0.41 percent.

  3. Coloring of synthetic fluorite

    Birsoy, R.

    1980-01-01

    A synthetic fluorite of the Harshaw Chemical Company is analyzed for rare earth elements, yttrium, and sodium. Samples of this fluorite are irradiated with X-rays, γ-rays, neutrons, electrons, protons, and α-particles at different energies, and their absorption spectra are analyzed. Analyzing the thermal bleaching of these radiation-coloured fluorites shows that both, impurities and radiation play a part in the coloration of synthetic fluorite. However, the main contribution comes from the radiation induced lattice defects. In the visible region spectra, the colour centre of the 5800 to 5900 A absorption band is probably mainly related with large aggregates of F-centres. The 5450 and the 5300 A absorption bands are mainly related to monovalent and divalent ion impurities and their association with lattice defects. The 3800 A absorption band seems to be related with F-centre aggregates. However, the contribution from the rare earth elements related complex color centres also plays some part for the production of this absorption band. These results indicate that the color centres of different origin can absorb light at the same wavelength. (author)

  4. Synthesizing genetic sequential logic circuit with clock pulse generator.

    Chuang, Chia-Hua; Lin, Chun-Liang

    2014-05-28

    Rhythmic clock widely occurs in biological systems which controls several aspects of cell physiology. For the different cell types, it is supplied with various rhythmic frequencies. How to synthesize a specific clock signal is a preliminary but a necessary step to further development of a biological computer in the future. This paper presents a genetic sequential logic circuit with a clock pulse generator based on a synthesized genetic oscillator, which generates a consecutive clock signal whose frequency is an inverse integer multiple to that of the genetic oscillator. An analogous electronic waveform-shaping circuit is constructed by a series of genetic buffers to shape logic high/low levels of an oscillation input in a basic sinusoidal cycle and generate a pulse-width-modulated (PWM) output with various duty cycles. By controlling the threshold level of the genetic buffer, a genetic clock pulse signal with its frequency consistent to the genetic oscillator is synthesized. A synchronous genetic counter circuit based on the topology of the digital sequential logic circuit is triggered by the clock pulse to synthesize the clock signal with an inverse multiple frequency to the genetic oscillator. The function acts like a frequency divider in electronic circuits which plays a key role in the sequential logic circuit with specific operational frequency. A cascaded genetic logic circuit generating clock pulse signals is proposed. Based on analogous implement of digital sequential logic circuits, genetic sequential logic circuits can be constructed by the proposed approach to generate various clock signals from an oscillation signal.

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

    Knuuttila, Tarja; Loettgers, Andrea

    2013-06-01

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

  6. EEG simulation by 2D interconnected chaotic oscillators

    Kubany, Adam; Mhabary, Ziv; Gontar, Vladimir

    2011-01-01

    Research highlights: → ANN of 2D interconnected chaotic oscillators is explored for EEG simulation. → An inverse problem solution (PRCGA) is proposed. → Good matching between the simulated and experimental EEG signals has been achieved. - Abstract: An artificial neuronal network composed by 2D interconnected chaotic oscillators is explored for brain waves (EEG) simulation. For the inverse problem solution a parallel real-coded genetic algorithm (PRCGA) is proposed. In order to conduct thorough comparison between the simulated and target signal characteristics, a spectrum analysis of the signals is undertaken. A good matching between the theoretical and experimental EEG signals has been achieved. Numerical results of calculations are presented and discussed.

  7. EEG simulation by 2D interconnected chaotic oscillators

    Kubany, Adam, E-mail: adamku@bgu.ac.i [Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105 (Israel); Mhabary, Ziv; Gontar, Vladimir [Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105 (Israel)

    2011-01-15

    Research highlights: ANN of 2D interconnected chaotic oscillators is explored for EEG simulation. An inverse problem solution (PRCGA) is proposed. Good matching between the simulated and experimental EEG signals has been achieved. - Abstract: An artificial neuronal network composed by 2D interconnected chaotic oscillators is explored for brain waves (EEG) simulation. For the inverse problem solution a parallel real-coded genetic algorithm (PRCGA) is proposed. In order to conduct thorough comparison between the simulated and target signal characteristics, a spectrum analysis of the signals is undertaken. A good matching between the theoretical and experimental EEG signals has been achieved. Numerical results of calculations are presented and discussed.

  8. Paper-based synthetic gene networks.

    Pardee, Keith; Green, Alexander A; Ferrante, Tom; Cameron, D Ewen; DaleyKeyser, Ajay; Yin, Peng; Collins, James J

    2014-11-06

    Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides an alternate, versatile venue for synthetic biologists to operate and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze dried onto paper, enabling the inexpensive, sterile, and abiotic distribution of synthetic-biology-based technologies for the clinic, global health, industry, research, and education. For field use, we create circuits with colorimetric outputs for detection by eye and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small-molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors.

  9. Paper-based Synthetic Gene Networks

    Pardee, Keith; Green, Alexander A.; Ferrante, Tom; Cameron, D. Ewen; DaleyKeyser, Ajay; Yin, Peng; Collins, James J.

    2014-01-01

    Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides a new venue for synthetic biologists to operate, and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze-dried onto paper, enabling the inexpensive, sterile and abiotic distribution of synthetic biology-based technologies for the clinic, global health, industry, research and education. For field use, we create circuits with colorimetric outputs for detection by eye, and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors. PMID:25417167

  10. Evaluation of cytoplasmic genetic effects for production and ...

    uvp

    2014-12-03

    Dec 3, 2014 ... Cytoplasmic genetic effects are transmitted directly only from mother to offspring through mitochondrial DNA. Normal genetic .... inheritance in three synthetic lines of beef cattle differing in mature size. J. Anim. Sci. 69, 745.

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

    Thomas E Gorochowski

    Full Text Available 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.

  12. Reactor oscillator - I - III, Part I

    Lolic, B.

    1961-12-01

    Project 'Reactor oscillator' covers the following activities: designing reactor oscillators for reactors RA and RB with detailed engineering drawings; constructing and mounting of the oscillator; designing and constructing the appropriate electronic equipment for the oscillator; measurements at the RA and RB reactors needed for completing the oscillator construction

  13. Time domain oscillating poles: Stability redefined in Memristor based Wien-oscillators

    Talukdar, Abdul Hafiz Ibne; Radwan, Ahmed G.; Salama, Khaled N.

    2012-01-01

    poles. The idea is verified using a Memristor based Wien oscillator. Sustained oscillations are observed without having the poles of the system fixed on the imaginary axis and the oscillating behavior of the system poles is reported. The oscillating

  14. Current status of synthetic epikeratoplasty.

    Thompson, K P; Hanna, K; Waring, G O; Gipson, I; Liu, Y; Gailitis, R P; Johnson-Wint, B; Green, K

    1991-01-01

    Many of the deficiencies with human tissue epikeratoplasty might be improved by the use of a suitable synthetic lenticule. Potential biomaterials for epikeratoplasty include collagen (types I, III, or IV), collagen-hydrogel copolymers, bioactive synthetics, and coated hydrogels. The biomaterial must be engineered to achieve strict specifications of optical clarity, support of epithelial migration and adhesion, permeability to solutes, and stability to corneal proteases. Attaching synthetic lenticules to the cornea without cutting Bowman's layer by adhesives, laser welding, or direct adhesion may also improve the efficacy of synthetic epikeratoplasty.

  15. Synthetic biology and occupational risk.

    Howard, John; Murashov, Vladimir; Schulte, Paul

    2017-03-01

    Synthetic biology is an emerging interdisciplinary field of biotechnology that involves applying the principles of engineering and chemical design to biological systems. Biosafety professionals have done an excellent job in addressing research laboratory safety as synthetic biology and gene editing have emerged from the larger field of biotechnology. Despite these efforts, risks posed by synthetic biology are of increasing concern as research procedures scale up to industrial processes in the larger bioeconomy. A greater number and variety of workers will be exposed to commercial synthetic biology risks in the future, including risks to a variety of workers from the use of lentiviral vectors as gene transfer devices. There is a need to review and enhance current protection measures in the field of synthetic biology, whether in experimental laboratories where new advances are being researched, in health care settings where treatments using viral vectors as gene delivery systems are increasingly being used, or in the industrial bioeconomy. Enhanced worker protection measures should include increased injury and illness surveillance of the synthetic biology workforce; proactive risk assessment and management of synthetic biology products; research on the relative effectiveness of extrinsic and intrinsic biocontainment methods; specific safety guidance for synthetic biology industrial processes; determination of appropriate medical mitigation measures for lentiviral vector exposure incidents; and greater awareness and involvement in synthetic biology safety by the general occupational safety and health community as well as by government occupational safety and health research and regulatory agencies.

  16. Finding Hope in Synthetic Biology.

    Takala, Tuija

    2017-04-01

    For some, synthetic biology represents great hope in offering possible solutions to many of the world's biggest problems, from hunger to sustainable development. Others remain fearful of the harmful uses, such as bioweapons, that synthetic biology can lend itself to, and most hold that issues of biosafety are of utmost importance. In this article, I will evaluate these points of view and conclude that although the biggest promises of synthetic biology are unlikely to become reality, and the probability of accidents is fairly substantial, synthetic biology could still be seen to benefit humanity by enhancing our ethical understanding and by offering a boost to world economy.

  17. Tissue Harmonic Synthetic Aperture Imaging

    Rasmussen, Joachim

    The main purpose of this PhD project is to develop an ultrasonic method for tissue harmonic synthetic aperture imaging. The motivation is to advance the field of synthetic aperture imaging in ultrasound, which has shown great potentials in the clinic. Suggestions for synthetic aperture tissue...... system complexity compared to conventional synthetic aperture techniques. In this project, SASB is sought combined with a pulse inversion technique for 2nd harmonic tissue harmonic imaging. The advantages in tissue harmonic imaging (THI) are expected to further improve the image quality of SASB...

  18. Life after the synthetic cell

    Rasmussen, Steen

    2010-01-01

    Nature asked eight synthetic-biology experts about the implications for science and society of the “synthetic cell” made by the J. Craig Venter Institute (JCVI). The institute's team assembled, modified and implanted a synthesized genome into a DNA-free bacterial shell to make a self-replicating ......Nature asked eight synthetic-biology experts about the implications for science and society of the “synthetic cell” made by the J. Craig Venter Institute (JCVI). The institute's team assembled, modified and implanted a synthesized genome into a DNA-free bacterial shell to make a self...

  19. [How to be prudent with synthetic biology. Synthetic Biology and the precautionary principle].

    Rodríguez López, Blanca

    2014-01-01

    Synthetic biology is a new discipline that is twofold: firstly it offers the promise to pay benefits that can alleviate some of the ills that plague mankind; On the other hand, like all technologies, holds risks. Given these, the most critical and concerned about the risks, invoke the application of the precautionary principle, common in cases where an activity or new technology creates risks to the environment and/or human health, but far from universally accepted happens to be currently one of the most controversial principles. In this paper the question of the risks and benefits of synthetic biology and the relevance of applying the precautionary principle are analyzed. To do this we proceed as follows. The first part focuses on synthetic biology. At first, this discipline is characterized, with special attention to what is novel compared to the known as "genetic engineering". In the second stage both the benefits and the risks associated with it are discussed. The first part concludes with a review of the efforts currently being made to control or minimize the risks. The second part aims to analyze the precautionary principle and its possible relevance to the case of Synthetic Biology. At first, the different versions and interpretations of the principle and the various criticisms of which has been the subject are reviewed. Finally, after discarding the Precautionary Principle as an useful tool, it is seen as more appropriate some recent proposals to treat technologies that take into account not only risks but also their benefits.

  20. Damping of Coherent oscillations

    Vos, L

    1996-01-01

    Damping of coherent oscillations by feedback is straightforward in principle. It has been a vital ingredient for the safe operation of accelerators since a long time. The increasing dimensions and beam intensities of the new generation of hadron colliders impose unprecedented demands on the performance of future systems. The arguments leading to the specification of a transverse feedback system for the CERN SPS in its role as LHC injector and the LHC collider itself are developped to illustrate this. The preservation of the transverse emittance is the guiding principle during this exercise keeping in mind the hostile environment which comprises: transverse impedance bent on developping coupled bunch instabilities, injection errors, unwanted transverse excitation, unavoidable tune spreads and noise in the damping loop.

  1. Convection and stellar oscillations

    Aarslev, Magnus Johan

    2017-01-01

    for asteroseismology, because of the challenges inherent in modelling turbulent convection in 1D stellar models. As a result of oversimplifying the physics near the surface, theoretical calculations systematically overestimate the oscillation frequencies. This has become known as the asteroseismic surface effect. Due...... to lacking better options, this frequency difference is typically corrected for with ad-hoc formulae. The topic of this thesis is the improvement of 1D stellar convection models and the effects this has on asteroseismic properties. The source of improvements is 3D simulations of radiation...... atmospheres to replace the outer layers of stellar models. The additional turbulent pressure and asymmetrical opacity effects in the atmosphere model, compared to convection in stellar evolution models, serve to expand the atmosphere. The enlarged acoustic cavity lowers the pulsation frequencies bringing them...

  2. Photospheric oscillations. Pt. 1

    Fossat, E.; Ricort, G.

    1975-01-01

    Intensity fluctuations in the wings of the Fraunhofer line Na D 1 5896 have been recorded for about two hundred hours at the focus of the Nice coude refractor, using a sodium optical resonance device. Because of the large beam aperture available, records have been made on circular apertures from 22'' up to 32' diameter (the whole sun). The principal results from the analysis of these date are: As shown by White and Cha, the five-minute oscillation has a gaussian random character with a mean lifetime of about 20 min. Its two-dimensional spatial power spectrum is roughly gaussian for every temporal frequency between 2 and 6 MHz. The width of this gaussian spectrum is near 5 x 10 -5 km -1 (i.e. π = 20,000 km). (orig./BJ) [de

  3. Coronal Waves and Oscillations

    Nakariakov Valery M.

    2005-07-01

    Full Text Available Wave and oscillatory activity of the solar corona is confidently observed with modern imaging and spectral instruments in the visible light, EUV, X-ray and radio bands, and interpreted in terms of magnetohydrodynamic (MHD wave theory. The review reflects the current trends in the observational study of coronal waves and oscillations (standing kink, sausage and longitudinal modes, propagating slow waves and fast wave trains, the search for torsional waves, theoretical modelling of interaction of MHD waves with plasma structures, and implementation of the theoretical results for the mode identification. Also the use of MHD waves for remote diagnostics of coronal plasma - MHD coronal seismology - is discussed and the applicability of this method for the estimation of coronal magnetic field, transport coefficients, fine structuring and heating function is demonstrated.

  4. Computational synthetic geometry

    Bokowski, Jürgen

    1989-01-01

    Computational synthetic geometry deals with methods for realizing abstract geometric objects in concrete vector spaces. This research monograph considers a large class of problems from convexity and discrete geometry including constructing convex polytopes from simplicial complexes, vector geometries from incidence structures and hyperplane arrangements from oriented matroids. It turns out that algorithms for these constructions exist if and only if arbitrary polynomial equations are decidable with respect to the underlying field. Besides such complexity theorems a variety of symbolic algorithms are discussed, and the methods are applied to obtain new mathematical results on convex polytopes, projective configurations and the combinatorics of Grassmann varieties. Finally algebraic varieties characterizing matroids and oriented matroids are introduced providing a new basis for applying computer algebra methods in this field. The necessary background knowledge is reviewed briefly. The text is accessible to stud...

  5. Synthetic Aperture Compound Imaging

    Hansen, Jens Munk

    and the limiting factor is the amount of memory IO resources available. An equally high demand for memory throughput is found in the computer gaming industry, where a large part of the processing takes place on the graphics processing unit (GPU). Using the GPU, a framework for synthetic aperture imaging......Medical ultrasound imaging is used for many purposes, e.g. for localizing and classifying cysts, lesions, and other processes. Almost any mass is first observed using B-mode imaging and later classified using e.g. color flow, strain, or attenuation imaging. It is therefore important that the B......-mode images have high contrast. Like all imaging modalities, ultrasound is subject to a number of inherent artifacts that compromise image quality. The most prominent artifact is the degradation by coherent wave interference, known as “speckle”, which gives a granular appearance to an otherwise homogeneous...

  6. Transionospheric synthetic aperture imaging

    Gilman, Mikhail; Tsynkov, Semyon

    2017-01-01

    This landmark monograph presents the most recent mathematical developments in the analysis of ionospheric distortions of SAR images and offers innovative new strategies for their mitigation. As a prerequisite to addressing these topics, the book also discusses the radar ambiguity theory as it applies to synthetic aperture imaging and the propagation of radio waves through the ionospheric plasma, including the anisotropic and turbulent cases. In addition, it covers a host of related subjects, such as the mathematical modeling of extended radar targets (as opposed to point-wise targets) and the scattering of radio waves off those targets, as well as the theoretical analysis of the start-stop approximation, which is used routinely in SAR signal processing but often without proper justification. The mathematics in this volume is clean and rigorous – no assumptions are hidden or ambiguously stated. The resulting work is truly interdisciplinary, providing both a comprehensive and thorough exposition of the field,...

  7. Radioimmunoassay of synthetic steroids

    Raynaud, J -P; Bucourt, R; Salmon, J

    1975-12-01

    The sensitivity of a radioimmunoassay depends on the intrinsic association constant of the interaction between ligand and antibody. Its specificity depends on the position of the chain which forms the link with the antigen. Thus, an antibody specific of estradiol has been obtained by coupling estradiol to albumin via a chain at position 7. For synthetic steroids the structure of which is sufficiency different from that of natural hormones, the requirements for a sensitive assay method not involving chromatography are simply maximum affinity and positioning of the couple at a site which does not undergo metabolic attack. These criteria were used to develop assays for R 2858 and R 2453 which obviate the need to administer radioactive product in clinical pharmacology. Cross-reaction with structural analogs may be used to assay competitors. Thus, R 2323 antibody, highly specific for endogenous steroids, may be used to assay other trienes such as R 1697 (trenbolone) and R 2010 (norgestrienone).

  8. Synthetic fuels and fusion

    Fillo, J A; Powell, J; Steinberg, M [Brookhaven National Lab., Upton, NY (USA)

    1981-03-01

    The decreasing availability of fossil fuels emphasizes the need to develop systems which will produce synthetic fuel to substitute for and supplement the natural supply. An important first step in the synthesis of liquid and gaseous fuels is the production of hydrogen. Thermonuclear fusion offers an inexhaustible source of energy for the production of hydrogen from water. Depending on design, electric generation efficiencies of approx. equal to 40-60% and hydrogen production efficiencies by high temperature electrolysis of approx. equal to 50-70% are projected for fusion reactors using high temperature blankets. Fusion/coal symbiotic systems appear economically promising for the first generation of commercial fusion synfuels plants. Coal production requirements and the environmental effects of large-scale coal usage would be greatly reduced by a fusion/coal system. In the long-term, there could be a gradual transition to an inexhaustible energy system based solely on fusion.

  9. Oscillator strengths for neutral technetium

    Garstang, R.H.

    1981-01-01

    Oscillator strengths have been calculated for most of the spectral lines of TcI which are of interest in the study of stars of spectral type S. Oscillator strengths have been computed for the corresponding transitions in MnI as a partial check of the technetium calculations

  10. Hyperchaos in coupled Colpitts oscillators

    Cenys, Antanas; Tamasevicius, Arunas; Baziliauskas, Antanas

    2003-01-01

    The paper suggests a simple solution of building a hyperchaotic oscillator. Two chaotic Colpitts oscillators, either identical or non-identical ones are coupled by means of two linear resistors R-k. The hyperchaotic output signal v(t) is a linear combination, specifically the mean of the individual...

  11. Stochastic and Chaotic Relaxation Oscillations

    Grasman, J.; Roerdink, J.B.T.M.

    1988-01-01

    For relaxation oscillators stochastic and chaotic dynamics are investigated. The effect of random perturbations upon the period is computed. For an extended system with additional state variables chaotic behavior can be expected. As an example, the Van der Pol oscillator is changed into a

  12. Oscillating solitons in nonlinear optics

    ... are derived, and the relevant properties and features of oscillating solitons are illustrated. Oscillating solitons are controlled by the reciprocal of the group velocity and Kerr nonlinearity. Results of this paper will be valuable to the study of dispersion-managed optical communication system and mode-locked fibre lasers.

  13. Augmenting cognition by neuronal oscillations

    Horschig, J.M.; Zumer, J.; Bahramisharif, A.

    2014-01-01

    Cortical oscillations have been shown to represent fundamental functions of a working brain, e.g., communication, stimulus binding, error monitoring, and inhibition, and are directly linked to behavior. Recent studies intervening with these oscillations have demonstrated effective modulation of both

  14. Mammalian Synthetic Biology: Engineering Biological Systems.

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

    2017-06-21

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

  15. Oscillating universe with quintom matter

    Xiong Huahui; Cai Yifu; Qiu Taotao; Piao Yunsong; Zhang Xinmin

    2008-01-01

    In this Letter, we study the possibility of building a model of the oscillating universe with quintom matter in the framework of 4-dimensional Friedmann-Robertson-Walker background. Taking the two-scalar-field quintom model as an example, we find in the model parameter space there are five different types of solutions which correspond to: (I) a cyclic universe with the minimal and maximal values of the scale factor remaining the same in every cycle, (II) an oscillating universe with its minimal and maximal values of the scale factor increasing cycle by cycle, (III) an oscillating universe with its scale factor always increasing, (IV) an oscillating universe with its minimal and maximal values of the scale factor decreasing cycle by cycle, and (V) an oscillating universe with its scale factor always decreasing

  16. Free oscillation of the Earth

    Y. Abedini

    2000-06-01

    Full Text Available   This work is a study of the Earths free oscillations considering a merge of solid and liquid model. At the turn of 19th century Geophysicists presented the theory of the free oscillations for a self-gravitating, isotropic and compressible sphere. Assuming a steel structure for an Earth size sphere, they predicted a period of oscillation of about 1 hour. About 50 years later, the free oscillations of stars was studied by Cowling and others. They classified the oscillation modes of the stars into acoustic and gravity modes on the basis of their driving forces. These are pressure and buoyancy forces respectively. The earliest measurements for the period of the free oscillations of the Earth was made by Benyove from a study of Kamchathca earthquake. Since then, the Geophysicists have been trying to provide a theoretical basis for these measurements. Recently, the theory concerning oscillations of celestial fluids is extended by Sobouti to include the possible oscillations of the Earthlike bodies. Using the same technique, we study the free oscillations of a spherically symmetric, non-rotating and elastic model for the Earth.   We used the actual data of the Earths interior structure in our numerical calculations. Numerical results show that there exist three distinct oscillation modes namely acoustic, gravity and toroidal modes. These modes are driven by pressure, buoyancy and shear forces respectively. The shear force is due to the elastic properties of the solid part of the Earth. Our numerical results are consistent with the seismic data recorded from earthquake measurements.

  17. Synthetic Biology of Cyanobacteria: Unique Challenges and Opportunities

    Bertram M Berla

    2013-08-01

    Full Text Available Photosynthetic organisms, and especially cyanobacteria, hold great promise as sources of renewably-produced fuels, bulk and specialty chemicals, and nutritional products. Synthetic biology tools can help unlock cyanobacteria’s potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli. While these organisms may in many cases be more difficult to work with as ‘chassis’ strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a ‘green E. coli’. In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria. We review classical and recently developed methods for constructing targeted mutants in various cyanobacterial strains, and offer perspective on what genetic tools might most greatly expand the ability to engineer new functions in such strains. Similarly, we review what genetic parts are most needed for the development of cyanobacterial synthetic biology. Finally, we highlight recent methods to construct genome-scale models of cyanobacterial metabolism and to use those models to measure properties of autotrophic metabolism. Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.

  18. Genetic improvement of vegetables

    Jaramillo Vasquez, J.G.

    2001-01-01

    Some genetic bases of the improvement of vegetables are given. The objectives of the genetic improvement and the fundamental stages of this process are done. The sources of genetic variation are indicated and they are related the reproduction systems of the main horticultural species. It is analyzed the concept of genetic inheritance like base to determine the procedures more appropriate of improvement. The approaches are discussed, has more than enough phenotypic value, genetic action and genotypic variance; Equally the heredability concepts and value of improvement. The conventional methods of improvement are described, like they are: the introduction of species or varieties, the selection, the pure line, the pedigree method, the selection for families, the recurrent selection, the selection for unique seed, the haploids method, the selection for heterosis and the synthetic varieties

  19. Imaging with Synthetic Aperture Radar

    Massonnet, Didier

    2008-01-01

    Describing a field that has been transformed by the recent availability of data from a new generation of space and airborne systems, the authors offer a synthetic geometrical approach to the description of synthetic aperture radar, one that addresses physicists, radar specialists, as well as experts in image processing.  

  20. Synthetic peptides for antibody production

    Zegers, N.D.

    1995-01-01

    Synthetic peptides are useful tools for the generation of antibodies. The use of antibodies as specific reagents in inununochemical assays is widely applied. In this chapter, the application of synthetic peptides for the generation of antibodies is described. The different steps that lead to the

  1. Synthetic peptides for antibody production

    N.D. Zegers (Netty)

    1995-01-01

    textabstractSynthetic peptides are useful tools for the generation of antibodies. The use of antibodies as specific reagents in inununochemical assays is widely applied. In this chapter, the application of synthetic peptides for the generation of antibodies is described. The different steps

  2. The Ethics of Synthetic Biology

    Christiansen, Andreas

    The dissertation analyses and discusses a number of ethical issues that have been raised in connection with the development of synthetic biology. Synthetic biology is a set of new techniques for DNA-level design and construction of living beings with useful properties. The dissertation especially...

  3. Synthetic biology of polyketide synthases

    Yuzawa, Satoshi; Backman, Tyler W.H.; Keasling, Jay D.

    2018-01-01

    ). The modules are composed of enzymatic domains that share sequence and functional similarity across all known PKSs. We have used the nomenclature of synthetic biology to classify the enzymatic domains and modules as parts and devices, respectively, and have generated detailed lists of both. In addition, we...... realize the potential that synthetic biology approaches bring to this class of molecules....

  4. A theory of generalized Bloch oscillations

    Duggen, Lars; Lassen, Benny; Lew Yan Voon, L C; Willatzen, Morten

    2016-01-01

    Bloch oscillations of electrons are shown to occur for cases when the energy spectrum does not consist of the traditional evenly-spaced ladders and the potential gradient does not result from an external electric field. A theory of such generalized Bloch oscillations is presented and an exact calculation is given to confirm this phenomenon. Our results allow for a greater freedom of design for experimentally observing Bloch oscillations. For strongly coupled oscillator systems displaying Bloch oscillations, it is further demonstrated that reordering of oscillators leads to destruction of Bloch oscillations. We stipulate that the presented theory of generalized Bloch oscillations can be extended to other systems such as acoustics and photonics. (paper)

  5. Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality.

    Otero-Muras, Irene; Banga, Julio R

    2017-07-21

    In this work we consider Pareto optimality for automated design in synthetic biology. We present a generalized framework based on a mixed-integer dynamic optimization formulation that, given design specifications, allows the computation of Pareto optimal sets of designs, that is, the set of best trade-offs for the metrics of interest. We show how this framework can be used for (i) forward design, that is, finding the Pareto optimal set of synthetic designs for implementation, and (ii) reverse design, that is, analyzing and inferring motifs and/or design principles of gene regulatory networks from the Pareto set of optimal circuits. Finally, we illustrate the capabilities and performance of this framework considering four case studies. In the first problem we consider the forward design of an oscillator. In the remaining problems, we illustrate how to apply the reverse design approach to find motifs for stripe formation, rapid adaption, and fold-change detection, respectively.

  6. Computing with synthetic protocells.

    Courbet, Alexis; Molina, Franck; Amar, Patrick

    2015-09-01

    In this article we present a new kind of computing device that uses biochemical reactions networks as building blocks to implement logic gates. The architecture of a computing machine relies on these generic and composable building blocks, computation units, that can be used in multiple instances to perform complex boolean functions. Standard logical operations are implemented by biochemical networks, encapsulated and insulated within synthetic vesicles called protocells. These protocells are capable of exchanging energy and information with each other through transmembrane electron transfer. In the paradigm of computation we propose, protoputing, a machine can solve only one problem and therefore has to be built specifically. Thus, the programming phase in the standard computing paradigm is represented in our approach by the set of assembly instructions (specific attachments) that directs the wiring of the protocells that constitute the machine itself. To demonstrate the computing power of protocellular machines, we apply it to solve a NP-complete problem, known to be very demanding in computing power, the 3-SAT problem. We show how to program the assembly of a machine that can verify the satisfiability of a given boolean formula. Then we show how to use the massive parallelism of these machines to verify in less than 20 min all the valuations of the input variables and output a fluorescent signal when the formula is satisfiable or no signal at all otherwise.

  7. Neutrino oscillation: status and outlooks

    Nedelec, P.

    1994-01-01

    Whether the neutrinos are massive or not is one of the most puzzling question of physics today. If they are massive, they can contribute significantly to the Dark Matter of the Universe. An other consequence of a non-zero mass of neutrinos is that they might oscillate from one flavor to another. This oscillation process is by now the only way to detect a neutrino with a mass in the few eV range. Several neutrino experiments are currently looking for such an oscillation, in different modes, using different techniques. An overview of the experimental situation for neutrino experiments at accelerators is given. (author). 9 refs., 5 figs., 5 tabs

  8. Synchronous Oscillations in Microtubule Polymerization

    Carlier, M. F.; Melki, R.; Pantaloni, D.; Hill, T. L.; Chen, Y.

    1987-08-01

    Under conditions where microtubule nucleation and growth are fast (i.e., high magnesium ion and tubulin concentrations and absence of glycerol), microtubule assembly in vitro exhibits an oscillatory regime preceding the establishment of steady state. The amplitude of the oscillations can represent >50% of the maximum turbidity change and oscillations persist for up to 20 periods of 80 s each. Oscillations are accompanied by extensive length redistribution of microtubules. Preliminary work suggests that the oscillatory kinetics can be simulated using a model in which many microtubules undergo synchronous transitions between growing and rapidly depolymerizing phases, complicated by the kinetically limiting rate of nucleotide exchange on free tubulin.

  9. Rabi oscillation between states of a coupled harmonic oscillator

    Park, Tae Jun

    2003-01-01

    Rabi oscillation between bound states of a single potential is well known. However the corresponding formula between the states of two different potentials has not been obtained yet. In this work, we derive Rabi formula between the states of a coupled harmonic oscillator which may be used as a simple model for the electron transfer. The expression is similar to typical Rabi formula for a single potential. This result may be used to describe transitions between coupled diabatic potential curves

  10. Oscillations in Mathematical Biology

    1983-01-01

    The papers in this volume are based on talks given at a one day conference held on the campus of Adelphi University in April 1982. The conference was organized with the title "Oscillations in Mathematical Biology;" however the speakers were allowed considerable latitutde in their choice of topics. In the event, the talks all concerned the dynamics of non-linear systems arising in biology so that the conference achieved a good measure of cohesion. Some of the speakers cho~e not to submit a manuscript for these proceedings, feeling that their material was too conjectural to be committed to print. Also the paper of Rinzel and Troy is a distillation of the two separate talks that the authors gave. Otherwise the material reproduces the conference proceedings. The conference was made possible by the generous support of the Office of the Dean of the College of Arts and Sciences at Adelphi. The bulk of the organization of the conference was carried out by Dr. Ronald Grisell whose energy was in large measure responsib...

  11. Principal oscillation patterns

    Storch, H. von; Buerger, G.; Storch, J.S. von

    1993-01-01

    The Principal Oscillation Pattern (POP) analysis is a technique which is used to simultaneously infer the characteristic patterns and time scales of a vector time series. The POPs may be seen as the normal modes of a linearized system whose system matrix is estimated from data. The concept of POP analysis is reviewed. Examples are used to illustrate the potential of the POP technique. The best defined POPs of tropospheric day-to-day variability coincide with the most unstable modes derived from linearized theory. POPs can be derived even from a space-time subset of data. POPs are successful in identifying two independent modes with similar time scales in the same data set. The POP method can also produce forecasts which may potentially be used as a reference for other forecast models. The conventional POP analysis technique has been generalized in various ways. In the cyclostationary POP analysis, the estimated system matrix is allowed to vary deterministically with an externally forced cycle. In the complex POP analysis not only the state of the system but also its ''momentum'' is modeled. Associated correlation patterns are a useful tool to describe the appearance of a signal previously identified by a POP analysis in other parameters. (orig.)

  12. Synthetic Biology Open Language (SBOL Version 2.2.0

    Cox Robert Sidney

    2018-04-01

    Full Text Available Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year’s JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

  13. Synthetic Biology Open Language (SBOL) Version 2.2.0

    Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James Alastair; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Beal, Jacob; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Grunberg, Raik; Macklin, Chris; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H.; Myers, Chris; Sauro, Herbert; Wipat, Anil

    2018-01-01

    Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year's JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

  14. Synthetic Biology Open Language (SBOL) Version 2.2.0.

    Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James Alastair; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Beal, Jacob; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Grünberg, Raik; Macklin, Chris; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H; Myers, Chris; Sauro, Herbert; Wipat, Anil

    2018-04-02

    Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year's JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

  15. Synthetic Biology Open Language (SBOL) Version 2.2.0

    Cox, Robert Sidney

    2018-04-04

    Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year\\'s JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

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

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

    2012-01-01

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

  17. The Duffing oscillator with damping

    Johannessen, Kim

    2015-01-01

    An analytical solution to the differential equation describing the Duffing oscillator with damping is presented. The damping term of the differential equation and the initial conditions satisfy an algebraic equation, and thus the solution is specific for this type of damping. The nonlinear term...... of the differential equation is allowed to be considerable compared to the linear term. The solution is expressed in terms of the Jacobi elliptic functions by including a parameter-dependent elliptic modulus. The analytical solution is compared to the numerical solution, and the agreement is found to be very good....... It is established that the period of oscillation is shorter compared to that of a linearized model but increasing with time and asymptotically approaching the period of oscillation of the linear damped model. An explicit expression for the period of oscillation has been derived, and it is found to be very accurate....

  18. Electronically tunable RC sinusoidal oscillators

    Florescu, Valeriu

    2008-01-01

    This paper presents two types of active configurations for realizing electronically tunable RC sinusoidal oscillators. The type-1 network employs two grounded scaled resistances KR 1 and KR 2 , where K is scaling factor. The frequency of oscillation W 0 is controlled conveniently by adjusting K, since W 0 appears in the form W 0 =1/K √ R 1 C 1 R 2 C 2 . For realizing the scaled resistances, an active configuration is proposed, which realizes KR 1 =R 1 /(1+f(V B )), where f(V B ) denotes a function of a controlling voltage V B . Thus the frequency tuning can be effected by controlling a voltage V B . The type-2 oscillator uses two periodically switched conductances. It is shown that the tuning of oscillation frequency can be done by varying the pulse width-to-period ratio (t/T) of the periodically switched conductances. (author)

  19. Thermoelastic Loss in Microscale Oscillators

    Houston, B. H; Photiadis, D. M; Marcus, M. H; Bucaro, J. A; Liu, Xiao; Vignola, J. F

    2001-01-01

    ...) and nanoelectromechanical (NEMS) oscillators. The theory defines a flexural modal participation factor, the fraction of potential energy stored in flexure, and approximates the internal friction by assuming the energy loss to occur solely via...

  20. Oscillating nonlinear acoustic shock waves

    Gaididei, Yuri; Rasmussen, Anders Rønne; Christiansen, Peter Leth

    2016-01-01

    We investigate oscillating shock waves in a tube using a higher order weakly nonlinear acoustic model. The model includes thermoviscous effects and is non isentropic. The oscillating shock waves are generated at one end of the tube by a sinusoidal driver. Numerical simulations show that at resona......We investigate oscillating shock waves in a tube using a higher order weakly nonlinear acoustic model. The model includes thermoviscous effects and is non isentropic. The oscillating shock waves are generated at one end of the tube by a sinusoidal driver. Numerical simulations show...... polynomial in the space and time variables, we find analytical approximations to the observed single shock waves in an infinitely long tube. Using perturbation theory for the driven acoustic system approximative analytical solutions for the off resonant case are determined....

  1. Transient voltage oscillations in coils

    Chowdhuri, P.

    1985-01-01

    Magnet coils may be excited into internal voltage oscillations by transient voltages. Such oscillations may electrically stress the magnet's dielectric components to many times its normal stress. This may precipitate a dielectric failure, and the attendant prolonged loss of service and costly repair work. Therefore, it is important to know the natural frequencies of oscillations of a magnet during the design stage, and to determine whether the expected switching transient voltages can excite the magnet into high-voltage internal oscillations. The series capacitance of a winding significantly affects its natural frequencies. However, the series capacitance is difficult to calculate, because it may comprise complex capacitance network, consisting of intra- and inter-coil turn-to-turn capacitances of the coil sections. A method of calculating the series capacitance of a winding is proposed. This method is rigorous but simple to execute. The time-varying transient voltages along the winding are also calculated

  2. Modelling solar-like oscillators

    Eggenberger, P; Miglio, A [Institut d' Astrophysique et de Geophysique de l' Universite de Liege, 17 Allee du 6 Aout, B-4000 Liege (Belgium); Carrier, F [Institute of Astronomy, University of Leuven, Celestijnenlaan 200 D, B-3001 Leuven (Belgium); Mathis, S [CEA/DSM/DAPNIA/Service d' Astrophysique, CEA/Saclay, AIM-Unite Mixte de Recherche CEA-CNRS-Universite Paris VII, UMR 7158, 91191 Gif-sur-Yvette Cedex (France)], E-mail: eggenberger@Qastro.ulg.ac.be

    2008-10-15

    The computation of models of stars for which solar-like oscillations have been observed is discussed. After a brief intoduction on the observations of solar-like oscillations, the modelling of isolated stars and of stars belonging to a binary system is presented with specific examples of recent theoretical calibrations. Finally the input physics introduced in stellar evolution codes for the computation of solar-type stars is discussed with a peculiar emphasis on the modelling of rotation for these stars.

  3. Modeling nonlinearities in MEMS oscillators.

    Agrawal, Deepak K; Woodhouse, Jim; Seshia, Ashwin A

    2013-08-01

    We present a mathematical model of a microelectromechanical system (MEMS) oscillator that integrates the nonlinearities of the MEMS resonator and the oscillator circuitry in a single numerical modeling environment. This is achieved by transforming the conventional nonlinear mechanical model into the electrical domain while simultaneously considering the prominent nonlinearities of the resonator. The proposed nonlinear electrical model is validated by comparing the simulated amplitude-frequency response with measurements on an open-loop electrically addressed flexural silicon MEMS resonator driven to large motional amplitudes. Next, the essential nonlinearities in the oscillator circuit are investigated and a mathematical model of a MEMS oscillator is proposed that integrates the nonlinearities of the resonator. The concept is illustrated for MEMS transimpedance-amplifier- based square-wave and sine-wave oscillators. Closed-form expressions of steady-state output power and output frequency are derived for both oscillator models and compared with experimental and simulation results, with a good match in the predicted trends in all three cases.

  4. On the nonlinear modeling of ring oscillators

    Elwakil, Ahmed S.

    2009-06-01

    We develop higher-order nonlinear models of three-stage and five-stage ring oscillators based on a novel inverter model. The oscillation condition and oscillation frequency are derived and compared to classical linear model analysis. Two important special cases for five-stage ring oscillators are also studied. Numerical simulations are shown. © 2009 World Scientific Publishing Company.

  5. Some comparison of two fractional oscillators

    Kang Yonggang; Zhang Xiu'e

    2010-01-01

    The other form of fractional oscillator equation comparing to the widely discussed one is ushered in. The properties of vibration of two fractional oscillators are discussed under the influence of different initial conditions. The interpretation of the characteristics of the fractional oscillators using different method is illustrated. Based on two fractional oscillator equations, two linked bodies and the continuous system are studied.

  6. Magnetically Coupled Magnet-Spring Oscillators

    Donoso, G.; Ladera, C. L.; Martin, P.

    2010-01-01

    A system of two magnets hung from two vertical springs and oscillating in the hollows of a pair of coils connected in series is a new, interesting and useful example of coupled oscillators. The electromagnetically coupled oscillations of these oscillators are experimentally and theoretically studied. Its coupling is electromagnetic instead of…

  7. On the nonlinear modeling of ring oscillators

    Elwakil, Ahmed S.; Salama, Khaled N.

    2009-01-01

    We develop higher-order nonlinear models of three-stage and five-stage ring oscillators based on a novel inverter model. The oscillation condition and oscillation frequency are derived and compared to classical linear model analysis. Two important special cases for five-stage ring oscillators are also studied. Numerical simulations are shown. © 2009 World Scientific Publishing Company.

  8. Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces.

    Alexander, William G; Peris, David; Pfannenstiel, Brandon T; Opulente, Dana A; Kuang, Meihua; Hittinger, Chris Todd

    2016-04-01

    Saccharomyces interspecies hybrids are critical biocatalysts in the fermented beverage industry, including in the production of lager beers, Belgian ales, ciders, and cold-fermented wines. Current methods for making synthetic interspecies hybrids are cumbersome and/or require genome modifications. We have developed a simple, robust, and efficient method for generating allotetraploid strains of prototrophic Saccharomyces without sporulation or nuclear genome manipulation. S. cerevisiae×S. eubayanus, S. cerevisiae×S. kudriavzevii, and S. cerevisiae×S. uvarum designer hybrid strains were created as synthetic lager, Belgian, and cider strains, respectively. The ploidy and hybrid nature of the strains were confirmed using flow cytometry and PCR-RFLP analysis, respectively. This method provides an efficient means for producing novel synthetic hybrids for beverage and biofuel production, as well as for constructing tetraploids to be used for basic research in evolutionary genetics and genome stability. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Cell-free synthetic biology for environmental sensing and remediation.

    Karig, David K

    2017-06-01

    The fields of biosensing and bioremediation leverage the phenomenal array of sensing and metabolic capabilities offered by natural microbes. Synthetic biology provides tools for transforming these fields through complex integration of natural and novel biological components to achieve sophisticated sensing, regulation, and metabolic function. However, the majority of synthetic biology efforts are conducted in living cells, and concerns over releasing genetically modified organisms constitute a key barrier to environmental applications. Cell-free protein expression systems offer a path towards leveraging synthetic biology, while preventing the spread of engineered organisms in nature. Recent efforts in the areas of cell-free approaches for sensing, regulation, and metabolic pathway implementation, as well as for preserving and deploying cell-free expression components, embody key steps towards realizing the potential of cell-free systems for environmental sensing and remediation. Copyright © 2017 The Author. Published by Elsevier Ltd.. All rights reserved.

  10. Synthetic Biology for Specialty Chemicals.

    Markham, Kelly A; Alper, Hal S

    2015-01-01

    In this review, we address recent advances in the field of synthetic biology and describe how those tools have been applied to produce a wide variety of chemicals in microorganisms. Here we classify the expansion of the synthetic biology toolbox into three different categories based on their primary function in strain engineering-for design, for construction, and for optimization. Next, focusing on recent years, we look at how chemicals have been produced using these new synthetic biology tools. Advances in producing fuels are briefly described, followed by a more thorough treatment of commodity chemicals, specialty chemicals, pharmaceuticals, and nutraceuticals. Throughout this review, an emphasis is placed on how synthetic biology tools are applied to strain engineering. Finally, we discuss organism and host strain diversity and provide a future outlook in the field.

  11. Is synthetic biology mechanical biology?

    Holm, Sune

    2015-12-01

    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  12. Adaptive Synthetic Forces: Situation Awareness

    Hill, Randall

    2001-01-01

    ...: perception, comprehension, and prediction. Building on these ideas, we developed techniques for improving the situation awareness in synthetic helicopter pilots for the ModSAF military simulation by giving them more human-like perception...

  13. Programming languages for synthetic biology.

    Umesh, P; Naveen, F; Rao, Chanchala Uma Maheswara; Nair, Achuthsankar S

    2010-12-01

    In the backdrop of accelerated efforts for creating synthetic organisms, the nature and scope of an ideal programming language for scripting synthetic organism in-silico has been receiving increasing attention. A few programming languages for synthetic biology capable of defining, constructing, networking, editing and delivering genome scale models of cellular processes have been recently attempted. All these represent important points in a spectrum of possibilities. This paper introduces Kera, a state of the art programming language for synthetic biology which is arguably ahead of similar languages or tools such as GEC, Antimony and GenoCAD. Kera is a full-fledged object oriented programming language which is tempered by biopart rule library named Samhita which captures the knowledge regarding the interaction of genome components and catalytic molecules. Prominent feature of the language are demonstrated through a toy example and the road map for the future development of Kera is also presented.

  14. On the mechanism of oscillations in neutrophils

    Brasen, Jens Christian; Barington, Torben; Olsen, Lars Folke

    2010-01-01

    We have investigated the regulation of the oscillatory generation of H(2)O(2) and oscillations in shape and size in neutrophils in suspension. The oscillations are independent of cell density and hence do not represent a collective phenomena. Furthermore, the oscillations are independent...... of the external glucose concentration and the oscillations in H(2)O(2) production are 180 degrees out of phase with the oscillations in NAD(P)H. Cytochalasin B blocked the oscillations in shape and size whereas it increased the period of the oscillations in H(2)O(2) production. 1- and 2-butanol also blocked...... the oscillations in shape and size, but only 1-butanol inhibited the oscillations in H(2)O(2) production. We conjecture that the oscillations are likely to be due to feedback regulations in the signal transduction cascade involving phosphoinositide 3-kinases (PI3K). We have tested this using a simple mathematical...

  15. Digital signal processing reveals circadian baseline oscillation in majority of mammalian genes.

    Andrey A Ptitsyn

    2007-06-01

    Full Text Available In mammals, circadian periodicity has been described for gene expression in the hypothalamus and multiple peripheral tissues. It is accepted that 10%-15% of all genes oscillate in a daily rhythm, regulated by an intrinsic molecular clock. Statistical analyses of periodicity are limited by the small size of datasets and high levels of stochastic noise. Here, we propose a new approach applying digital signal processing algorithms separately to each group of genes oscillating in the same phase. Combined with the statistical tests for periodicity, this method identifies circadian baseline oscillation in almost 100% of all expressed genes. Consequently, circadian oscillation in gene expression should be evaluated in any study related to biological pathways. Changes in gene expression caused by mutations or regulation of environmental factors (such as photic stimuli or feeding should be considered in the context of changes in the amplitude and phase of genetic oscillations.

  16. Reactor oscillator - I - III, Part I; Reaktorski oscilator - I-III, I Deo

    Lolic, B [Institute of Nuclear Sciences Boris Kidric, Laboratorija za fiziku reaktora, Vinca, Beograd (Serbia and Montenegro)

    1961-12-15

    Project 'Reactor oscillator' covers the following activities: designing reactor oscillators for reactors RA and RB with detailed engineering drawings; constructing and mounting of the oscillator; designing and constructing the appropriate electronic equipment for the oscillator; measurements at the RA and RB reactors needed for completing the oscillator construction.

  17. Plant synthetic biology: a new platform for industrial biotechnology.

    Fesenko, Elena; Edwards, Robert

    2014-05-01

    Thirty years after the production of the first generation of genetically modified plants we are now set to move into a new era of recombinant crop technology through the application of synthetic biology to engineer new and complex input and output traits. The use of synthetic biology technologies will represent more than incremental additions of transgenes, but rather the directed design of completely new metabolic pathways, physiological traits, and developmental control strategies. The need to enhance our ability to improve crops through new engineering capability is now increasingly pressing as we turn to plants not just for food, but as a source of renewable feedstocks for industry. These accelerating and diversifying demands for new output traits coincide with a need to reduce inputs and improve agricultural sustainability. Faced with such challenges, existing technologies will need to be supplemented with new and far-more-directed approaches to turn valuable resources more efficiently into usable agricultural products. While these objectives are challenging enough, the use of synthetic biology in crop improvement will face public acceptance issues as a legacy of genetically modified technologies in many countries. Here we review some of the potential benefits of adopting synthetic biology approaches in improving plant input and output traits for their use as industrial chemical feedstocks, as linked to the rapidly developing biorefining industry. Several promising technologies and biotechnological targets are identified along with some of the key regulatory and societal challenges in the safe and acceptable introduction of such technology.

  18. Pareto Optimal Design for Synthetic Biology.

    Patanè, Andrea; Santoro, Andrea; Costanza, Jole; Carapezza, Giovanni; Nicosia, Giuseppe

    2015-08-01

    Recent advances in synthetic biology call for robust, flexible and efficient in silico optimization methodologies. We present a Pareto design approach for the bi-level optimization problem associated to the overproduction of specific metabolites in Escherichia coli. Our method efficiently explores the high dimensional genetic manipulation space, finding a number of trade-offs between synthetic and biological objectives, hence furnishing a deeper biological insight to the addressed problem and important results for industrial purposes. We demonstrate the computational capabilities of our Pareto-oriented approach comparing it with state-of-the-art heuristics in the overproduction problems of i) 1,4-butanediol, ii) myristoyl-CoA, i ii) malonyl-CoA , iv) acetate and v) succinate. We show that our algorithms are able to gracefully adapt and scale to more complex models and more biologically-relevant simulations of the genetic manipulations allowed. The Results obtained for 1,4-butanediol overproduction significantly outperform results previously obtained, in terms of 1,4-butanediol to biomass formation ratio and knock-out costs. In particular overproduction percentage is of +662.7%, from 1.425 mmolh⁻¹gDW⁻¹ (wild type) to 10.869 mmolh⁻¹gDW⁻¹, with a knockout cost of 6. Whereas, Pareto-optimal designs we have found in fatty acid optimizations strictly dominate the ones obtained by the other methodologies, e.g., biomass and myristoyl-CoA exportation improvement of +21.43% (0.17 h⁻¹) and +5.19% (1.62 mmolh⁻¹gDW⁻¹), respectively. Furthermore CPU time required by our heuristic approach is more than halved. Finally we implement pathway oriented sensitivity analysis, epsilon-dominance analysis and robustness analysis to enhance our biological understanding of the problem and to improve the optimization algorithm capabilities.

  19. Synthetic Biology and Ethics: Past, Present, and Future.

    Häyry, Matti

    2017-04-01

    This article explores the ethical issues that have been identified in emerging technologies, from early genetic engineering to synthetic biology. The scientific advances in the field form a continuum, and some ethical considerations can be raised time and again when new developments occur. An underlying concern is the cumulative effect of scientific advances and ensuing technological innovation that can change our understanding of life and humanity.

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

    Voigt, Christopher [Massachusetts Institute of Technology

    2014-07-01

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

  1. Nanomotor dynamics in a chemically oscillating medium

    Robertson, Bryan, E-mail: bryan.robertson@mail.utoronto.ca; Kapral, Raymond, E-mail: rkapral@chem.utoronto.ca [Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 (Canada)

    2015-04-21

    Synthetic nanomotors powered by chemical reactions have potential uses as cargo transport vehicles in both in vivo and in vitro applications. In many situations, motors will have to operate in out-of-equilibrium complex chemically reacting media, which supply fuel to the motors and remove the products they produce. Using molecular simulation and mean-field theory, this paper describes some of the new features that arise when a chemically powered nanomotor, operating through a diffusiophoretic mechanism, moves in an environment that supports an oscillatory chemical reaction network. It is shown how oscillations in the concentrations in chemical species in the environment give rise to oscillatory motor dynamics. More importantly, since the catalytic reactions on the motor that are responsible for its propulsion couple to the bulk phase reaction network, the motor can change its local environment. This process can give rise to distinctive spatiotemporal structures in reaction-diffusion media that occur as a result of active motor motion. Such locally induced nonequilibrium structure will play an important role in applications that involve motor dynamics in complex chemical media.

  2. Nanomotor dynamics in a chemically oscillating medium

    Robertson, Bryan; Kapral, Raymond

    2015-01-01

    Synthetic nanomotors powered by chemical reactions have potential uses as cargo transport vehicles in both in vivo and in vitro applications. In many situations, motors will have to operate in out-of-equilibrium complex chemically reacting media, which supply fuel to the motors and remove the products they produce. Using molecular simulation and mean-field theory, this paper describes some of the new features that arise when a chemically powered nanomotor, operating through a diffusiophoretic mechanism, moves in an environment that supports an oscillatory chemical reaction network. It is shown how oscillations in the concentrations in chemical species in the environment give rise to oscillatory motor dynamics. More importantly, since the catalytic reactions on the motor that are responsible for its propulsion couple to the bulk phase reaction network, the motor can change its local environment. This process can give rise to distinctive spatiotemporal structures in reaction-diffusion media that occur as a result of active motor motion. Such locally induced nonequilibrium structure will play an important role in applications that involve motor dynamics in complex chemical media

  3. Flashing oscillation in pool water

    Takamasa, Tomoji; Kondo, Koichi; Hazuku, Tatsuya

    1996-01-01

    This paper presents an experimental study of high-pressure saturated water discharging into the pool water. The purpose of the experiment is to clarify the phenomena that occur in blow-down of high-pressure saturated water from the pressure vessel into the water-filled containment in the case of a wall-crack accident or a LOCA in an advanced reactor. The results revealed that a flashing oscillation (FO) occurs when high-pressure saturated water discharges into the pool water, under specified experimental settings. The range of the flashing oscillates between a point very close to and some distance from the vent hole. The pressures in the vent tube and pool water vary according to the flashing oscillation. The pressure oscillation and frequency of flashing position might be caused by the balancing action between the supply of saturated water, flashing at the control volume and its condensation on the steam-water interface. A linear analysis was conducted using a spherical flashing bubble model. The period of the flashing oscillation in the experiments can be explained by theoretical analysis

  4. Neutrino oscillations at proton accelerators

    Michael, Douglas

    2002-01-01

    Data from many different experiments have started to build a first glimpse of the phenomenology associated with neutrino oscillations. Results on atmospheric and solar neutrinos are particularly clear while a third result from LSND suggests a possibly very complex oscillation phenomenology. As impressive as the results from current experiments are, it is clear that we are just getting started on a long-term experimental program to understand neutrino masses, mixings and the physics which produce them. A number of exciting fundamental physics possibilities exist, including that neutrino oscillations could demonstrate CP or CPT violation and could be tied to exotic high-energy phenomena including strings and extra dimensions. A complete exploration of oscillation phenomena demands many experiments, including those possible using neutrino beams produced at high energy proton accelerators. Most existing neutrino experiments are statistics limited even though they use gigantic detectors. High intensity proton beams are essential for producing the intense neutrino beams which we need for next generation neutrino oscillation experiments

  5. Neutrino Oscillations at Proton Accelerators

    Michael, Douglas

    2002-12-01

    Data from many different experiments have started to build a first glimpse of the phenomenology associated with neutrino oscillations. Results on atmospheric and solar neutrinos are particularly clear while a third result from LSND suggests a possibly very complex oscillation phenomenology. As impressive as the results from current experiments are, it is clear that we are just getting started on a long-term experimental program to understand neutrino masses, mixings and the physics which produce them. A number of exciting fundamental physics possibilities exist, including that neutrino oscillations could demonstrate CP or CPT violation and could be tied to exotic high-energy phenomena including strings and extra dimensions. A complete exploration of oscillation phenomena demands many experiments, including those possible using neutrino beams produced at high energy proton accelerators. Most existing neutrino experiments are statistics limited even though they use gigantic detectors. High intensity proton beams are essential for producing the intense neutrino beams which we need for next generation neutrino oscillation experiments.

  6. A standard-enabled workflow for synthetic biology.

    Myers, Chris J; Beal, Jacob; Gorochowski, Thomas E; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach

    2017-06-15

    A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  7. Restoration of oscillation in network of oscillators in presence of direct and indirect interactions

    Majhi, Soumen; Bera, Bidesh K. [Physics and Applied Mathematics Unit, Indian Statistical Institute, Kolkata-700108 (India); Bhowmick, Sourav K. [Department of Electronics, Asutosh College, Kolkata-700026 (India); Ghosh, Dibakar, E-mail: diba.ghosh@gmail.com [Physics and Applied Mathematics Unit, Indian Statistical Institute, Kolkata-700108 (India)

    2016-10-23

    The suppression of oscillations in coupled systems may lead to several unwanted situations, which requires a suitable treatment to overcome the suppression. In this paper, we show that the environmental coupling in the presence of direct interaction, which can suppress oscillation even in a network of identical oscillators, can be modified by introducing a feedback factor in the coupling scheme in order to restore the oscillation. We inspect how the introduction of the feedback factor helps to resurrect oscillation from various kinds of death states. We numerically verify the resurrection of oscillations for two paradigmatic limit cycle systems, namely Landau–Stuart and Van der Pol oscillators and also in generic chaotic Lorenz oscillator. We also study the effect of parameter mismatch in the process of restoring oscillation for coupled oscillators. - Highlights: • Amplitude death is observed using direct and indirect coupling. • Revival of oscillation using feedback parameter is discussed. • Restoration of oscillation is observed in limit cycle and chaotic systems.

  8. Meeting Report: Synthetic Biology Jamboree for Undergraduates

    Campbell, A. Malcolm

    2005-01-01

    The field of synthetic biology (the name is derived from an analogy to synthetic chemistry) has recognized itself as a "field" only since about 2002. Synthetic biology has gotten some high-profile attention recently, but most people are not aware the field even exists. Synthetic biologists apply engineering principles to genomic circuits to…

  9. Nonstationary oscillations in gyrotrons revisited

    Dumbrajs, O.; Kalis, H.

    2015-01-01

    Development of gyrotrons requires careful understanding of different regimes of gyrotron oscillations. It is known that in the planes of the generalized gyrotron variables: cyclotron resonance mismatch and dimensionless current or cyclotron resonance mismatch and dimensionless interaction length complicated alternating sequences of regions of stationary, periodic, automodulation, and chaotic oscillations exist. In the past, these regions were investigated on the supposition that the transit time of electrons through the interaction space is much shorter than the cavity decay time. This assumption is valid for short and/or high diffraction quality resonators. However, in the case of long and/or low diffraction quality resonators, which are often utilized, this assumption is no longer valid. In such a case, a different mathematical formalism has to be used for studying nonstationary oscillations. One example of such a formalism is described in the present paper

  10. Prediction of pilot induced oscillations

    Valentin PANĂ

    2011-03-01

    Full Text Available An important problem in the design of flight-control systems for aircraft under pilotedcontrol is the determination of handling qualities and pilot-induced oscillations (PIO tendencieswhen significant nonlinearities exist in the vehicle description. The paper presents a method to detectpossible pilot-induced oscillations of Category II (with rate and position limiting, a phenomenonusually due to a misadaptation between the pilot and the aircraft response during some tasks in whichtight closed loop control of the aircraft is required from the pilot. For the analysis of Pilot in the LoopOscillations an approach, based on robust stability analysis of a system subject to uncertainparameters, is proposed. In this analysis the nonlinear elements are substituted by linear uncertainparameters. This approach assumes that PIO are characterized by a limit cycle behavior.

  11. Magnetically insulated transmission line oscillator

    Bacon, L.D.; Ballard, W.P.; Clark, M.C.; Marder, B.M.

    1987-05-19

    A magnetically insulated transmission line oscillator employs self-generated magnetic fields to generate microwave energy. An anode of the oscillator includes slow-wave structures which are formed of a plurality of thin conductive vanes defining cavities therebetween, and a gap is formed between the anode and a cathode of the oscillator. In response to a pulsed voltage applied to the anode and cathode, self-generated magnetic fields are produced in a cross-field orientation with respect to the orientation of the electric field between the anode and the cathode. The cross-field magnetic fields insulate the flow of electrons in the gap and confine the flow of electrons within the gap. 11 figs.

  12. Synthetic biology, metaphors and responsibility.

    McLeod, Carmen; Nerlich, Brigitte

    2017-08-29

    Metaphors are not just decorative rhetorical devices that make speech pretty. They are fundamental tools for thinking about the world and acting on the world. The language we use to make a better world matters; words matter; metaphors matter. Words have consequences - ethical, social and legal ones, as well as political and economic ones. They need to be used 'responsibly'. They also need to be studied carefully - this is what we want to do through this editorial and the related thematic collection. In the context of synthetic biology, natural and social scientists have become increasingly interested in metaphors, a wave of interest that we want to exploit and amplify. We want to build on emerging articles and books on synthetic biology, metaphors of life and the ethical and moral implications of such metaphors. This editorial provides a brief introduction to synthetic biology and responsible innovation, as well as a comprehensive review of literature on the social, cultural and ethical impacts of metaphor use in genomics and synthetic biology. Our aim is to stimulate an interdisciplinary and international discussion on the impact that metaphors can have on science, policy and publics in the context of synthetic biology.

  13. Content metamorphosis in synthetic holography

    Desbiens, Jacques

    2013-01-01

    A synthetic hologram is an optical system made of hundreds of images amalgamated in a structure of holographic cells. Each of these images represents a point of view on a three-dimensional space which makes us consider synthetic holography as a multiple points of view perspective system. In the composition of a computer graphics scene for a synthetic hologram, the field of view of the holographic image can be divided into several viewing zones. We can attribute these divisions to any object or image feature independently and operate different transformations on image content. In computer generated holography, we tend to consider content variations as a continuous animation much like a short movie. However, by composing sequential variations of image features in relation with spatial divisions, we can build new narrative forms distinct from linear cinematographic narration. When observers move freely and change their viewing positions, they travel from one field of view division to another. In synthetic holography, metamorphoses of image content are within the observer's path. In all imaging Medias, the transformation of image features in synchronisation with the observer's position is a rare occurrence. However, this is a predominant characteristic of synthetic holography. This paper describes some of my experimental works in the development of metamorphic holographic images.

  14. Spontaneous oscillations in microfluidic networks

    Case, Daniel; Angilella, Jean-Regis; Motter, Adilson

    2017-11-01

    Precisely controlling flows within microfluidic systems is often difficult which typically results in systems being heavily reliant on numerous external pumps and computers. Here, I present a simple microfluidic network that exhibits flow rate switching, bistablity, and spontaneous oscillations controlled by a single pressure. That is, by solely changing the driving pressure, it is possible to switch between an oscillating and steady flow state. Such functionality does not rely on external hardware and may even serve as an on-chip memory or timing mechanism. I use an analytic model and rigorous fluid dynamics simulations to show these results.

  15. Oscillating liquid flow ICF Reactor

    Petzoldt, R.W.

    1990-01-01

    Oscillating liquid flow in a falling molten salt inertial confinement fusion reactor is predicted to rapidly clear driver beam paths of residual liquid droplets. Oscillating flow will also provide adequate neutron and x-ray protection for the reactor structure with a short (2-m) fall distance permitting an 8 Hz repetition rate. A reactor chamber configuration is presented with specific features to clear the entire heavy-ion beam path of splashed molten salt. The structural components, including the structure between beam ports, are shielded. 3 refs., 12 figs

  16. Neutrino oscillation measurements with reactors

    McKeown, R.D. [W. K. Kellogg Radiation Laboratory, California Institute of Technology, Pasadena, CA 91125 (United States)

    2010-11-01

    Since the first direct observations of antineutrino events by Reines and Cowan in the 1950's, nuclear reactors have been an important tool in the study of neutrino properties. More recently, the study of neutrino oscillations has been a very active area of research. The pioneering observation of oscillations by the KamLAND experiment has provided important information on the neutrino masses and the neutrino mixing matrix. New experiments to study the remaining unknown mixing angle are currently under development. These recent studies and potential future developments will be discussed.

  17. ALG-2 oscillates in subcellular localization, unitemporally with calcium oscillations

    la Cour, Jonas Marstrand; Mollerup, Jens; Berchtold, Martin Werner

    2007-01-01

    discovered that the subcellular distribution of a tagged version of ALG-2 could be directed by physiological external stimuli (including ATP, EGF, prostaglandin, histamine), which provoke intracellular Ca2+ oscillations. Cellular stimulation led to a redistribution of ALG-2 from the cytosol to a punctate...

  18. TOWARDS THRESHOLD FREQUENCY IN CHAOTIC COLPITTS OSCILLATOR

    Lindberg, Erik; Tamasevicius, Arunas; Mykolaitis, Gytis

    2007-01-01

    A novel version of chaotic Colpitts oscillator is described. Instead of a linear loss resistor, it includes an extra inductor and diode in the collector circuit of the transistor. The modified circuit in comparison with the common Colpitts oscillator may generate chaotic oscillations at the funda......A novel version of chaotic Colpitts oscillator is described. Instead of a linear loss resistor, it includes an extra inductor and diode in the collector circuit of the transistor. The modified circuit in comparison with the common Colpitts oscillator may generate chaotic oscillations...

  19. Microfluidic Technologies for Synthetic Biology

    Sung Kuk Lee

    2011-06-01

    Full Text Available Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.

  20. Synthetic neurosteroids on brain protection

    Mariana Rey

    2015-01-01

    Full Text Available Neurosteroids, like allopregnanolone and pregnanolone, are endogenous regulators of neuronal excitability. Inside the brain, they are highly selective and potent modulators of GABA A receptor activity. Their anticonvulsant, anesthetics and anxiolytic properties are useful for the treatments of several neurological and psychiatric disorders via reducing the risks of side effects obtained with the commercial drugs. The principal disadvantages of endogenous neurosteroids administration are their rapid metabolism and their low oral bioavailability. Synthetic steroids analogues with major stability or endogenous neurosteroids stimulation synthesis might constitute promising novel strategies for the treatment of several disorders. Numerous studies indicate that the 3α-hydroxyl configuration is the key for binding and activity, but modifications in the steroid nucleus may emphasize different pharmacophores. So far, several synthetic steroids have been developed with successful neurosteroid-like effects. In this work, we summarize the properties of various synthetic steroids probed in trials throughout the analysis of several neurosteroids-like actions.

  1. Synthetic Microwave Imaging Reflectometry diagnostic using 3D FDTD Simulations

    Kruger, Scott; Jenkins, Thomas; Smithe, David; King, Jacob; Nimrod Team Team

    2017-10-01

    Microwave Imaging Reflectometry (MIR) has become a standard diagnostic for understanding tokamak edge perturbations, including the edge harmonic oscillations in QH mode operation. These long-wavelength perturbations are larger than the normal turbulent fluctuation levels and thus normal analysis of synthetic signals become more difficult. To investigate, we construct a synthetic MIR diagnostic for exploring density fluctuation amplitudes in the tokamak plasma edge by using the three-dimensional, full-wave FDTD code Vorpal. The source microwave beam for the diagnostic is generated and refelected at the cutoff surface that is distorted by 2D density fluctuations in the edge plasma. Synthetic imaging optics at the detector can be used to understand the fluctuation and background density profiles. We apply the diagnostic to understand the fluctuations in edge plasma density during QH-mode activity in the DIII-D tokamak, as modeled by the NIMROD code. This work was funded under DOE Grant Number DE-FC02-08ER54972.

  2. Synthetic biology devices and circuits for RNA-based 'smart vaccines': a propositional review.

    Andries, Oliwia; Kitada, Tasuku; Bodner, Katie; Sanders, Niek N; Weiss, Ron

    2015-02-01

    Nucleic acid vaccines have been gaining attention as an alternative to the standard attenuated pathogen or protein based vaccine. However, an unrealized advantage of using such DNA or RNA based vaccination modalities is the ability to program within these nucleic acids regulatory devices that would provide an immunologist with the power to control the production of antigens and adjuvants in a desirable manner by administering small molecule drugs as chemical triggers. Advances in synthetic biology have resulted in the creation of highly predictable and modular genetic parts and devices that can be composed into synthetic gene circuits with complex behaviors. With the recent advent of modified RNA gene delivery methods and developments in the RNA replicon platform, we foresee a future in which mammalian synthetic biologists will create genetic circuits encoded exclusively on RNA. Here, we review the current repertoire of devices used in RNA synthetic biology and propose how programmable 'smart vaccines' will revolutionize the field of RNA vaccination.

  3. Synthetic biology as red herring.

    Preston, Beth

    2013-12-01

    It has become commonplace to say that with the advent of technologies like synthetic biology the line between artifacts and living organisms, policed by metaphysicians since antiquity, is beginning to blur. But that line began to blur 10,000 years ago when plants and animals were first domesticated; and has been thoroughly blurred at least since agriculture became the dominant human subsistence pattern many millennia ago. Synthetic biology is ultimately only a late and unexceptional offshoot of this prehistoric development. From this perspective, then, synthetic biology is a red herring, distracting us from more thorough philosophical consideration of the most truly revolutionary human practice-agriculture. In the first section of this paper I will make this case with regard to ontology, arguing that synthetic biology crosses no ontological lines that were not crossed already in the Neolithic. In the second section I will construct a parallel case with regard to cognition, arguing that synthetic biology as biological engineering represents no cognitive advance over what was required for domestication and the new agricultural subsistence pattern it grounds. In the final section I will make the case with regard to human existence, arguing that synthetic biology, even if wildly successful, is not in a position to cause significant existential change in what it is to be human over and above the massive existential change caused by the transition to agriculture. I conclude that a longer historical perspective casts new light on some important issues in philosophy of technology and environmental philosophy. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. Synthetic biology and its promises

    José Manuel De Cózar Escalante

    2016-12-01

    Full Text Available Synthetic biology is a new science and emerging technology, or rather a technoscience, which converges with others such as nanotechnology, information technology, robotics, artificial intelligence and neuroscience. All have common features that could have highly concerning social and environmental impacts. With its ambitious goals of controlling complexity, redesigning and creating new living entities, synthetic biology perfectly exemplifies the new bioeconomic reality. This requires expanding the focus of the discussion beyond the limited comparative analysis of risks and benefits, to address uncertainties, reassign responsibilities and initiate a thorough social assessment of what is at stake.

  5. Annotating novel genes by integrating synthetic lethals and genomic information

    Faty Mahamadou

    2008-01-01

    Full Text Available Abstract Background Large scale screening for synthetic lethality serves as a common tool in yeast genetics to systematically search for genes that play a role in specific biological processes. Often the amounts of data resulting from a single large scale screen far exceed the capacities of experimental characterization of every identified target. Thus, there is need for computational tools that select promising candidate genes in order to reduce the number of follow-up experiments to a manageable size. Results We analyze synthetic lethality data for arp1 and jnm1, two spindle migration genes, in order to identify novel members in this process. To this end, we use an unsupervised statistical method that integrates additional information from biological data sources, such as gene expression, phenotypic profiling, RNA degradation and sequence similarity. Different from existing methods that require large amounts of synthetic lethal data, our method merely relies on synthetic lethality information from two single screens. Using a Multivariate Gaussian Mixture Model, we determine the best subset of features that assign the target genes to two groups. The approach identifies a small group of genes as candidates involved in spindle migration. Experimental testing confirms the majority of our candidates and we present she1 (YBL031W as a novel gene involved in spindle migration. We applied the statistical methodology also to TOR2 signaling as another example. Conclusion We demonstrate the general use of Multivariate Gaussian Mixture Modeling for selecting candidate genes for experimental characterization from synthetic lethality data sets. For the given example, integration of different data sources contributes to the identification of genetic interaction partners of arp1 and jnm1 that play a role in the same biological process.

  6. Neutrino masses and neutrino oscillations

    Di Lella, L

    2000-01-01

    These lectures review direct measurements of neutrino masses and the status of neutrino oscillation searches using both natural neutrino sources (the Sun and cosmic rays interacting in the Earth atmosphere) and artificial neutrinos (produced by nuclear reactors and accelerators). Finally, future experiments and plans are presented. (68 refs).

  7. Harmonic oscillator in Snyder space

    The harmonic oscillator in Snyder space is investigated in its classical and quantum versions. The classical trajectory is obtained and the semiclassical quantization from the phase space trajectories is discussed. An effective cut-off to high frequencies is found. The quantum version is developed and an equivalent usual ...

  8. Compressible flow in fluidic oscillators

    Graff, Emilio; Hirsch, Damian; Gharib, Mory

    2013-11-01

    We present qualitative observations on the internal flow characteristics of fluidic oscillator geometries commonly referred to as sweeping jets in active flow control applications. We also discuss the effect of the geometry on the output jet in conditions from startup to supersonic exit velocity. Supported by the Boeing Company.

  9. Ellipsoidal basis for isotropic oscillator

    Kallies, W.; Lukac, I.; Pogosyan, G.S.; Sisakyan, A.N.

    1994-01-01

    The solutions of the Schroedinger equation are derived for the isotropic oscillator potential in the ellipsoidal coordinate system. The explicit expression is obtained for the ellipsoidal integrals of motion through the components of the orbital moment and Demkov's tensor. The explicit form of the ellipsoidal basis is given for the lowest quantum numbers. 10 refs.; 1 tab. (author)

  10. The relativistic harmonic oscillator reconsidered

    Hofsaess, T.

    1978-01-01

    The bound states of scalar quarks interacting through a scalar harmonic oscillator are investigated. In the presence of this interaction the dressed quark propagator differs substantially from the free one. This leads to a Bethe Salpeter equation which does not allow for any stable bound states of positive mass. (orig.) [de

  11. Inverse problem of solar oscillations

    Sekii, T.; Shibahashi, H.

    1987-01-01

    The authors present some preliminary results of numerical simulation to infer the sound velocity distribution in the solar interior from the oscillation data of the Sun as the inverse problem. They analyze the acoustic potential itself by taking account of some factors other than the sound velocity, and infer the sound velocity distribution in the deep interior of the Sun

  12. Sum rules for neutrino oscillations

    Kobzarev, I.Yu.; Martemyanov, B.V.; Okun, L.B.; Schepkin, M.G.

    1981-01-01

    Sum rules for neutrino oscillations are obtained. The derivation of the general form of the s matrix for two stage process lsub(i)sup(-)→ν→lsub(k)sup(+-) (where lsub(i)sup(-)e, μ, tau, ... are initial leptons with flavor i and lsub(k)sup(+-) is final lepton) is presented. The consideration of two stage process lsub(i)sup(-)→ν→lsub(k)sup(+-) gives the possibility to take into account neutrino masses and to obtain the expressions for the oscillating cross sections. In the case of Dirac and left-handed Majorana neutrino is obtained the sum rule for the quantities 1/Vsub(K)σ(lsub(i)sup(-)→lsub(K)sup(+-)), (where Vsub(K) is a velocity of lsub(K)). In the left-handed Majorana neutrino case there is an additional antineutrino admixture leading to lsub(i)sup(-)→lsub(K)sup(+) process. Both components (neutrino and antineutrino) oscillate independently. The sums Σsub(K)1/Vsub(k)σ(lsub(i)sup(-) - lsub(K)sup(+-) then oscillate due to the presence of left-handed antineutrinos and right-handed neutrinos which do not take part in weak interactions. If right-handed currents are added sum rules analogous to considered above may be obtained. All conclusions are valid in the general case when CP is not conserved [ru

  13. Oscillating solitons in nonlinear optics

    The study of solitons in those physical systems reveals some exciting .... With the following power series expansions for g(z,t) and f(z,t): g(z,t) = εg1(z,t) + ... If nonlinearity γ (z) is also taken as a function in figure 1b, the periodic and oscillation.

  14. Low-Vibration Oscillating Compressor

    Studer, P. A.

    1984-01-01

    Oscillating compressor momentum compensated: produces little vibration in its supporting structure. Compressure requires no lubrication and virtually free of wear. Compresses working fluids such as helium, nitrogen or chlorfluorocarbons for Stirling-cycle refrigeration or other purposes. Compressor includes two mutually opposed ferromagnetic pistons of same shape and mass. Electromagnetic flux links both pistons, causing magnetic attraction between them.

  15. Matter effects in neutrino oscillations

    Dass, G.V.

    1989-01-01

    After a review of the relevant aspects of neutrino oscillations for propagation in vacuum and in material media, this paper discuss the Mikheyev-Smirnov-Wolfenstein mechanism and its application to a solution of the solar neutrino puzzle. The elementary level of the talk is suitable to people not working in neutrino physics

  16. Mesino oscillation in MFV SUSY

    Berger, Joshua [Cornell University, Department of Physics, LEPP, Ithaca, NY (United States); SLAC National Accelerator Laboratory, Menlo Park, CA (United States); Csaki, Csaba; Grossman, Yuval; Heidenreich, Ben [Cornell University, Department of Physics, LEPP, Ithaca, NY (United States)

    2013-04-15

    R-parity violating supersymmetry in a Minimal Flavor Violation paradigm can produce same-sign dilepton signals via direct sbottom-LSP pair production. Such signals arise when the sbottom hadronizes and the resulting mesino oscillates into an antimesino. The first bounds on the sbottom mass are placed in this scenario using current LHC results. (orig.)

  17. Chimera States in Neural Oscillators

    Bahar, Sonya; Glaze, Tera

    2014-03-01

    Chimera states have recently been explored both theoretically and experimentally, in various coupled nonlinear oscillators, ranging from phase-oscillator models to coupled chemical reactions. In a chimera state, both coherent and incoherent (or synchronized and desynchronized) states occur simultaneously in populations of identical oscillators. We investigate chimera behavior in a population of neural oscillators using the Huber-Braun model, a Hodgkin-Huxley-like model originally developed to characterize the temperature-dependent bursting behavior of mammalian cold receptors. One population of neurons is allowed to synchronize, with each neuron receiving input from all the others in its group (global within-group coupling). Subsequently, a second population of identical neurons is placed under an identical global within-group coupling, and the two populations are also coupled to each other (between-group coupling). For certain values of the coupling constants, the neurons in the two populations exhibit radically different synchronization behavior. We will discuss the range of chimera activity in the model, and discuss its implications for actual neural activity, such as unihemispheric sleep.

  18. Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students†

    Beach, Dale L.; Alvarez, Consuelo J.

    2015-01-01

    Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniq...

  19. Definition of natural T cell antigens with mimicry epitopes obtained from dedicated synthetic peptide libraries.

    Hiemstra, H S; van Veelen, P A; Schloot, N C; Geluk, A; van Meijgaarden, K E; Willemen, S J; Leunissen, J A; Benckhuijsen, W E; Amons, R; de Vries, R R; Roep, B O; Ottenhoff, T H; Drijfhout, J W

    1998-10-15

    Progress has recently been made in the use of synthetic peptide libraries for the identification of T cell-stimulating ligands. T cell epitopes identified from synthetic libraries are mimics of natural epitopes. Here we show how the mimicry epitopes obtained from synthetic peptide libraries enable unambiguous identification of natural T cell Ags. Synthetic peptide libraries were screened with Mycobacterium tuberculosis-reactive and -autoreactive T cell clones. In two cases, database homology searches with mimicry epitopes isolated from a dedicated synthetic peptide library allowed immediate identification of the natural antigenic protein. In two other cases, an amino acid pattern that reflected the epitope requirements of the T cell was determined by substitution and omission mixture analysis. Subsequently, the natural Ag was identified from databases using this refined pattern. This approach opens new perspectives for rapid and reliable Ag definition, representing a feasible alternative to the biochemical and genetic approaches described thus far.

  20. Synthetic review on the genetic relatedness between North Africa ...

    Soumaya

    the Horn of Africa and the Indian Ocean in the southeast. ... threatened until the Islamic Arabs expanded their religion and culture to the Maghreb, ... decline from the Middle East toward Central Asia, Caucasus, North Africa and Europe.

  1. Reverse engineering large-scale genetic networks: synthetic versus

    Development of microarray technology has resulted in an exponential rise in gene expression data. Linear computational methods are of great assistance in identifying molecular interactions, and elucidating the functional properties of gene networks. It overcomes the weaknesses of in vivo experiments including high cost, ...

  2. Generalized oscillator systems and their parabosonic interpretation

    Macfarlane, A J [Cambridge Univ. (United Kingdom). Dept. of Applied Mathematics and Theoretical Physics

    1994-12-31

    The Fock space description of various bosonic oscillator systems are carried out. All descriptions are based on a single creation - annihilation pair. Special attention is paid to the q-deformed Calogero-Vasiliev oscillator. 23 refs.

  3. Analytic Neutrino Oscillation Probabilities in Matter: Revisited

    Parke, Stephen J. [Fermilab; Denton, Peter B. [Copenhagen U.; Minakata, Hisakazu [Madrid, IFT

    2018-01-02

    We summarize our recent paper on neutrino oscillation probabilities in matter, explaining the importance, relevance and need for simple, highly accurate approximations to the neutrino oscillation probabilities in matter.

  4. Characterizing brain oscillations in cognition and disease

    Jiang, H.

    2016-01-01

    It has been suggested that neuronal oscillations play a fundamental role for shaping the functional architecture of the working brain. This thesis investigates brain oscillations in rat, human healthy population and major depressive disorder (MDD) patients. A novel measurement termed

  5. Solar atmosphere wave dynamics generated by solar global oscillating eigenmodes

    Griffiths, M. K.; Fedun, V.; Erdélyi, R.; Zheng, R.

    2018-01-01

    The solar atmosphere exhibits a diverse range of wave phenomena, where one of the earliest discovered was the five-minute global acoustic oscillation, also referred to as the p-mode. The analysis of wave propagation in the solar atmosphere may be used as a diagnostic tool to estimate accurately the physical characteristics of the Sun's atmospheric layers. In this paper, we investigate the dynamics and upward propagation of waves which are generated by the solar global eigenmodes. We report on a series of hydrodynamic simulations of a realistically stratified model of the solar atmosphere representing its lower region from the photosphere to low corona. With the objective of modelling atmospheric perturbations, propagating from the photosphere into the chromosphere, transition region and low corona, generated by the photospheric global oscillations the simulations use photospheric drivers mimicking the solar p-modes. The drivers are spatially structured harmonics across the computational box parallel to the solar surface. The drivers perturb the atmosphere at 0.5 Mm above the bottom boundary of the model and are placed coincident with the location of the temperature minimum. A combination of the VALIIIC and McWhirter solar atmospheres are used as the background equilibrium model. We report how synthetic photospheric oscillations may manifest in a magnetic field free model of the quiet Sun. To carry out the simulations, we employed the magnetohydrodynamics code, SMAUG (Sheffield MHD Accelerated Using GPUs). Our results show that the amount of energy propagating into the solar atmosphere is consistent with a model of solar global oscillations described by Taroyan and Erdélyi (2008) using the Klein-Gordon equation. The computed results indicate a power law which is compared to observations reported by Ireland et al. (2015) using data from the Solar Dynamics Observatory/Atmospheric Imaging Assembly.

  6. Where Synthetic Biology Meets ET

    Rothschild, Lynn J.

    2016-01-01

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

  7. Stereoscopy in cinematographic synthetic imagery

    Eisenmann, Jonathan; Parent, Rick

    2009-02-01

    In this paper we present experiments and results pertaining to the perception of depth in stereoscopic viewing of synthetic imagery. In computer animation, typical synthetic imagery is highly textured and uses stylized illumination of abstracted material models by abstracted light source models. While there have been numerous studies concerning stereoscopic capabilities, conventions for staging and cinematography in stereoscopic movies have not yet been well-established. Our long-term goal is to measure the effectiveness of various cinematography techniques on the human visual system in a theatrical viewing environment. We would like to identify the elements of stereoscopic cinema that are important in terms of enhancing the viewer's understanding of a scene as well as providing guidelines for the cinematographer relating to storytelling. In these experiments we isolated stereoscopic effects by eliminating as many other visual cues as is reasonable. In particular, we aim to empirically determine what types of movement in synthetic imagery affect the perceptual depth sensing capabilities of our viewers. Using synthetic imagery, we created several viewing scenarios in which the viewer is asked to locate a target object's depth in a simple environment. The scenarios were specifically designed to compare the effectiveness of stereo viewing, camera movement, and object motion in aiding depth perception. Data were collected showing the error between the choice of the user and the actual depth value, and patterns were identified that relate the test variables to the viewer's perceptual depth accuracy in our theatrical viewing environment.

  8. Synthetic biology meets tissue engineering.

    Davies, Jamie A; Cachat, Elise

    2016-06-15

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

  9. Shock compression of synthetic opal

    Inoue, A; Okuno, M; Okudera, H; Mashimo, T; Omurzak, E; Katayama, S; Koyano, M

    2010-01-01

    Structural change of synthetic opal by shock-wave compression up to 38.1 GPa has been investigated by using SEM, X-ray diffraction method (XRD), Infrared (IR) and Raman spectroscopies. Obtained information may indicate that the dehydration and polymerization of surface silanole due to high shock and residual temperature are very important factors in the structural evolution of synthetic opal by shock compression. Synthetic opal loses opalescence by 10.9 and 18.4 GPa of shock pressures. At 18.4 GPa, dehydration and polymerization of surface silanole and transformation of network structure may occur simultaneously. The 4-membered ring of TO 4 tetrahedrons in as synthetic opal may be relaxed to larger ring such as 6-membered ring by high residual temperature. Therefore, the residual temperature may be significantly high at even 18.4 GPa of shock compression. At 23.9 GPa, opal sample recovered the opalescence. Origin of this opalescence may be its layer structure by shock compression. Finally, sample fuse by very high residual temperature at 38.1 GPa and the structure closes to that of fused SiO 2 glass. However, internal silanole groups still remain even at 38.1 GPa.

  10. Assessment of synthetic image fidelity

    Mitchell, Kevin D.; Moorhead, Ian R.; Gilmore, Marilyn A.; Watson, Graham H.; Thomson, Mitch; Yates, T.; Troscianko, Tomasz; Tolhurst, David J.

    2000-07-01

    Computer generated imagery is increasingly used for a wide variety of purposes ranging from computer games to flight simulators to camouflage and sensor assessment. The fidelity required for this imagery is dependent on the anticipated use - for example when used for camouflage design it must be physically correct spectrally and spatially. The rendering techniques used will also depend upon the waveband being simulated, spatial resolution of the sensor and the required frame rate. Rendering of natural outdoor scenes is particularly demanding, because of the statistical variation in materials and illumination, atmospheric effects and the complex geometric structures of objects such as trees. The accuracy of the simulated imagery has tended to be assessed subjectively in the past. First and second order statistics do not capture many of the essential characteristics of natural scenes. Direct pixel comparison would impose an unachievable demand on the synthetic imagery. For many applications, such as camouflage design, it is important that nay metrics used will work in both visible and infrared wavebands. We are investigating a variety of different methods of comparing real and synthetic imagery and comparing synthetic imagery rendered to different levels of fidelity. These techniques will include neural networks (ICA), higher order statistics and models of human contrast perception. This paper will present an overview of the analyses we have carried out and some initial results along with some preliminary conclusions regarding the fidelity of synthetic imagery.

  11. Shock compression of synthetic opal

    Inoue, A.; Okuno, M.; Okudera, H.; Mashimo, T.; Omurzak, E.; Katayama, S.; Koyano, M.

    2010-03-01

    Structural change of synthetic opal by shock-wave compression up to 38.1 GPa has been investigated by using SEM, X-ray diffraction method (XRD), Infrared (IR) and Raman spectroscopies. Obtained information may indicate that the dehydration and polymerization of surface silanole due to high shock and residual temperature are very important factors in the structural evolution of synthetic opal by shock compression. Synthetic opal loses opalescence by 10.9 and 18.4 GPa of shock pressures. At 18.4 GPa, dehydration and polymerization of surface silanole and transformation of network structure may occur simultaneously. The 4-membered ring of TO4 tetrahedrons in as synthetic opal may be relaxed to larger ring such as 6-membered ring by high residual temperature. Therefore, the residual temperature may be significantly high at even 18.4 GPa of shock compression. At 23.9 GPa, opal sample recovered the opalescence. Origin of this opalescence may be its layer structure by shock compression. Finally, sample fuse by very high residual temperature at 38.1 GPa and the structure closes to that of fused SiO2 glass. However, internal silanole groups still remain even at 38.1 GPa.

  12. Shock compression of synthetic opal

    Inoue, A; Okuno, M; Okudera, H [Department of Earth Sciences, Kanazawa University Kanazawa, Ishikawa, 920-1192 (Japan); Mashimo, T; Omurzak, E [Shock Wave and Condensed Matter Research Center, Kumamoto University, Kumamoto, 860-8555 (Japan); Katayama, S; Koyano, M, E-mail: okuno@kenroku.kanazawa-u.ac.j [JAIST, Nomi, Ishikawa, 923-1297 (Japan)

    2010-03-01

    Structural change of synthetic opal by shock-wave compression up to 38.1 GPa has been investigated by using SEM, X-ray diffraction method (XRD), Infrared (IR) and Raman spectroscopies. Obtained information may indicate that the dehydration and polymerization of surface silanole due to high shock and residual temperature are very important factors in the structural evolution of synthetic opal by shock compression. Synthetic opal loses opalescence by 10.9 and 18.4 GPa of shock pressures. At 18.4 GPa, dehydration and polymerization of surface silanole and transformation of network structure may occur simultaneously. The 4-membered ring of TO{sub 4} tetrahedrons in as synthetic opal may be relaxed to larger ring such as 6-membered ring by high residual temperature. Therefore, the residual temperature may be significantly high at even 18.4 GPa of shock compression. At 23.9 GPa, opal sample recovered the opalescence. Origin of this opalescence may be its layer structure by shock compression. Finally, sample fuse by very high residual temperature at 38.1 GPa and the structure closes to that of fused SiO{sub 2} glass. However, internal silanole groups still remain even at 38.1 GPa.

  13. Methods for preparing synthetic freshwaters.

    Smith, E J; Davison, W; Hamilton-Taylor, J

    2002-03-01

    Synthetic solutions that emulate the major ion compositions of natural waters are useful in experiments aimed at understanding biogeochemical processes. Standard recipes exist for preparing synthetic analogues of seawater, with its relatively constant composition, but, due to the diversity of freshwaters, a range of compositions and recipes is required. Generic protocols are developed for preparing synthetic freshwaters of any desired composition. The major problems encountered in preparing hard and soft waters include dissolving sparingly soluble calcium carbonate, ensuring that the ionic components of each concentrated stock solution cannot form an insoluble salt and dealing with the supersaturation of calcium carbonate in many hard waters. For acidic waters the poor solubility of aluminium salts requires attention. These problems are overcome by preparing concentrated stock solutions according to carefully designed reaction paths that were tested using a combination of experiment and equilibrium modeling. These stock solutions must then be added in a prescribed order to prepare a final solution that is brought into equilibrium with the atmosphere. The example calculations for preparing hard, soft and acidic freshwater surrogates with major ion compositions the same as published analyses, are presented in a generalized fashion that should allow preparation of any synthetic freshwater according to its known analysis.

  14. Two particle states, lepton mixing and oscillations

    Kachelriess, M; Schönert, S

    2000-01-01

    Discussions of lepton mixing and oscillations consider generally only flavor oscillations of neutrinos and neglect the accompanying charged leptons. In cases of experimental interest like pion or nuclear beta decay an oscillation pattern is expected indeed only for neutrinos if only one of the two produced particles is observed. We argue that flavor oscillations of neutrinos without detecting the accompanying lepton is a peculiarity of the two-particle states $|l\

  15. A theory of generalized Bloch oscillations

    Duggen, Lars; Lew Yan Voon, L. C.; Lassen, Benny

    2016-01-01

    Bloch oscillations of electrons are shown to occur for cases when the energy spectrum does not consist of the traditional evenly-spaced ladders and the potential gradient does not result from an external electric field. A theory of such generalized Bloch oscillations is presented and an exact...... oscillations. We stipulate that the presented theory of generalized Bloch oscillations can be extended to other systems such as acoustics and photonics....

  16. Pile oscillator ROB-1, cooperation NPY

    Petrovic, M; Markovic, V; Obradovic, D; Kocic, A; Velickovic, LJ; Jovanovic, S [Boris Kidric Institute of nuclear sciences Vinca, Belgrade (Yugoslavia)

    1965-11-15

    The present paper explains the purpose of the work on reactor kinetics and separately deals with the region for which the ROB-1 reactor oscillator is constructed. The theoretical part concerns the basic principles on which the oscillator operates. the paper also discusses the details of the oscillator, the procedure for preparation and measurement, and analyzes the source of errors. In addition several examples of the use of oscillator are given. (author)

  17. Nonlinear analysis of ring oscillator circuits

    Ge, Xiaoqing

    2010-06-01

    Using nonlinear systems techniques, we analyze the stability properties and synchronization conditions for ring oscillator circuits, which are essential building blocks in digital systems. By making use of its cyclic structure, we investigate local and global stability properties of an n-stage ring oscillator. We present a sufficient condition for global asymptotic stability of the origin and obtain necessity if the ring oscillator consists of identical inverter elements. We then give a synchronization condition for identical interconnected ring oscillators.

  18. Comparison of Methods for Oscillation Detection

    Odgaard, Peter Fogh; Trangbæk, Klaus

    2006-01-01

    This paper compares a selection of methods for detecting oscillations in control loops. The methods are tested on measurement data from a coal-fired power plant, where some oscillations are occurring. Emphasis is put on being able to detect oscillations without having a system model and without...... using process knowledge. The tested methods show potential for detecting the oscillations, however, transient components in the signals cause false detections as well, motivating usage of models in order to remove the expected signals behavior....

  19. Pile oscillator ROB-1, cooperation NPY

    Petrovic, M.; Markovic, V.; Obradovic, D.; Kocic, A.; Velickovic, LJ.; Jovanovic, S.

    1965-11-01

    The present paper explains the purpose of the work on reactor kinetics and separately deals with the region for which the ROB-1 reactor oscillator is constructed. The theoretical part concerns the basic principles on which the oscillator operates. the paper also discusses the details of the oscillator, the procedure for preparation and measurement, and analyzes the source of errors. In addition several examples of the use of oscillator are given. (author)

  20. Nonlinear analysis of ring oscillator circuits

    Ge, Xiaoqing; Arcak, Murat; Salama, Khaled N.

    2010-01-01

    Using nonlinear systems techniques, we analyze the stability properties and synchronization conditions for ring oscillator circuits, which are essential building blocks in digital systems. By making use of its cyclic structure, we investigate local and global stability properties of an n-stage ring oscillator. We present a sufficient condition for global asymptotic stability of the origin and obtain necessity if the ring oscillator consists of identical inverter elements. We then give a synchronization condition for identical interconnected ring oscillators.

  1. Understanding Synchrony and Stochasticity in Coupled Neuronal and Genetic Oscillators

    2015-09-01

    SCN),  the  central  circadian  pacemakers  in   mammals ,   comprise  a  multiscale  neuronal  system  that  times...across  North  America  to  their  over  wintering  sites  in  a   small  region  of   Mexico .  The  ability  of  an

  2. Protease-sensitive synthetic prions.

    David W Colby

    2010-01-01

    Full Text Available Prions arise when the cellular prion protein (PrP(C undergoes a self-propagating conformational change; the resulting infectious conformer is designated PrP(Sc. Frequently, PrP(Sc is protease-resistant but protease-sensitive (s prions have been isolated in humans and other animals. We report here that protease-sensitive, synthetic prions were generated in vitro during polymerization of recombinant (rec PrP into amyloid fibers. In 22 independent experiments, recPrP amyloid preparations, but not recPrP monomers or oligomers, transmitted disease to transgenic mice (n = 164, denoted Tg9949 mice, that overexpress N-terminally truncated PrP. Tg9949 control mice (n = 174 did not spontaneously generate prions although they were prone to late-onset spontaneous neurological dysfunction. When synthetic prion isolates from infected Tg9949 mice were serially transmitted in the same line of mice, they exhibited sPrP(Sc and caused neurodegeneration. Interestingly, these protease-sensitive prions did not shorten the life span of Tg9949 mice despite causing extensive neurodegeneration. We inoculated three synthetic prion isolates into Tg4053 mice that overexpress full-length PrP; Tg4053 mice are not prone to developing spontaneous neurological dysfunction. The synthetic prion isolates caused disease in 600-750 days in Tg4053 mice, which exhibited sPrP(Sc. These novel synthetic prions demonstrate that conformational changes in wild-type PrP can produce mouse prions composed exclusively of sPrP(Sc.

  3. NOx Emission Reduction by Oscillating Combustion

    None

    2005-09-01

    This project focuses on a new technology that reduces NOx emissions while increasing furnace efficiency for both air- and oxygen-fired furnaces. Oscillating combustion is a retrofit technology that involves the forced oscillation of the fuel flow rate to a furnace. These oscillations create successive, fuel-rich and fuel-lean zones within the furnace.

  4. Neutrino oscillations: present status and outlook

    Schwetz, T.

    2005-01-01

    In this talk the present status of neutrino oscillations is reviewed, based on a global analysis of world neutrino oscillation data from solar, atmospheric, reactor, and accelerator neutrino experiments. Furthermore, I discuss the expected improvements in the determination of neutrino parameters by future oscillation experiments within a timescale of 10 years. (author)

  5. Neutrino oscillations in the early universe

    Enqvist, K.

    1990-01-01

    The oscillations of electron neutrinos into inert neutrinos may have resonant behaviour in the heat bath of the early Universe. It is shown that any initial neutrino asymmetry will be washed away by the oscillations. Neutrino oscillations would affect also primordial helium production, which implies stringent limits on the neutrino mixing parameters. (orig.)

  6. The supersymmetric Pegg-Barnett oscillator

    Shen, Jian Qi

    2005-01-01

    The su(n) Lie algebraic structure of the Pegg-Barnett oscillator that possesses a finite-dimensional number-state space is demonstrated. The supersymmetric generalization of the Pegg-Barnett oscillator is suggested. it is shown that such a supersymmetric Pegg-Barnett oscillator may have some potential applications, e.g., the mass spectrum of the charged leptons

  7. Three flavour oscillation interpretation of neutrino data

    To explain the atmospheric neutrino problem in terms of neutrino oscillations, ЖС¾ of about 10-¿. eV. ¾. [8] is needed whereas the neutrino oscil- lation solution to the solar neutrino problem requires ЖС¾ ~10- eV. ¾ . Hence both solar and atmospheric neutrino problems cannot be explained in terms of e ° μ oscillations.

  8. A survey of Wien bridge-based chaotic oscillators: Design and experimental issues

    Kilic, Recai [Erciyes University, Department of Electrical and Electronic Engineering, 38039 Kayseri (Turkey)], E-mail: kilic@erciyes.edu.tr; Yildirim, Fatma [Erciyes University, Civil Aviation School, 38039 Kayseri (Turkey)

    2008-12-15

    This paper presents a comparative study on design and implementation of Wien type chaotic oscillators. By making a collection of almost all Wien bridge-based chaotic circuits, we have investigated these oscillators in terms of chaotic dynamics, circuit structures, active building blocks, nonlinear element structures and operating frequency by using PSpice simulations and laboratory experiments. In addition to this comparative investigation, we present our two basic experimental contributions to referred implementations. While the first of our experimental contributions consists of the experimentally implementation of CFOA-based Chua's circuit modified for very high chaotic oscillations, the scope of the second is to experimentally implement a Wien type high frequency chaos generator, which has the diode-inductor composite, in the inductorless form by using CFOA-based synthetic inductor.

  9. A survey of Wien bridge-based chaotic oscillators: Design and experimental issues

    Kilic, Recai; Yildirim, Fatma

    2008-01-01

    This paper presents a comparative study on design and implementation of Wien type chaotic oscillators. By making a collection of almost all Wien bridge-based chaotic circuits, we have investigated these oscillators in terms of chaotic dynamics, circuit structures, active building blocks, nonlinear element structures and operating frequency by using PSpice simulations and laboratory experiments. In addition to this comparative investigation, we present our two basic experimental contributions to referred implementations. While the first of our experimental contributions consists of the experimentally implementation of CFOA-based Chua's circuit modified for very high chaotic oscillations, the scope of the second is to experimentally implement a Wien type high frequency chaos generator, which has the diode-inductor composite, in the inductorless form by using CFOA-based synthetic inductor

  10. Design of synthetic biological logic circuits based on evolutionary algorithm.

    Chuang, Chia-Hua; Lin, Chun-Liang; Chang, Yen-Chang; Jennawasin, Tanagorn; Chen, Po-Kuei

    2013-08-01

    The construction of an artificial biological logic circuit using systematic strategy is recognised as one of the most important topics for the development of synthetic biology. In this study, a real-structured genetic algorithm (RSGA), which combines general advantages of the traditional real genetic algorithm with those of the structured genetic algorithm, is proposed to deal with the biological logic circuit design problem. A general model with the cis-regulatory input function and appropriate promoter activity functions is proposed to synthesise a wide variety of fundamental logic gates such as NOT, Buffer, AND, OR, NAND, NOR and XOR. The results obtained can be extended to synthesise advanced combinational and sequential logic circuits by topologically distinct connections. The resulting optimal design of these logic gates and circuits are established via the RSGA. The in silico computer-based modelling technology has been verified showing its great advantages in the purpose.

  11. Slow oscillations orchestrating fast oscillations and memory consolidation.

    Mölle, Matthias; Born, Jan

    2011-01-01

    Slow-wave sleep (SWS) facilitates the consolidation of hippocampus-dependent declarative memory. Based on the standard two-stage memory model, we propose that memory consolidation during SWS represents a process of system consolidation which is orchestrated by the neocortical memory. The slow oscillations temporally group neuronal activity into up-states of strongly enhanced neuronal activity and down-states of neuronal silence. In a feed-forward efferent action, this grouping is induced not only in the neocortex but also in other structures relevant to consolidation, namely the thalamus generating 10-15Hz spindles, and the hippocampus generating sharp wave-ripples, with the latter well known to accompany a replay of newly encoded memories taking place in hippocampal circuitries. The feed-forward synchronizing effect of the slow oscillation enables the formation of spindle-ripple events where ripples and accompanying reactivated hippocampal memory information become nested into the single troughs of spindles. Spindle-ripple events thus enable reactivated memory-related hippocampal information to be fed back to neocortical networks in the excitable slow oscillation up-state where they can induce enduring plastic synaptic changes underlying the effective formation of long-term memories. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. Measuring neutrino oscillation parameters using $\

    Backhouse, Christopher James [Oriel College, Oxford (United Kingdom)

    2011-01-01

    MINOS is a long-baseline neutrino oscillation experiment. It consists of two large steel-scintillator tracking calorimeters. The near detector is situated at Fermilab, close to the production point of the NuMI muon-neutrino beam. The far detector is 735 km away, 716m underground in the Soudan mine, Northern Minnesota. The primary purpose of the MINOS experiment is to make precise measurements of the 'atmospheric' neutrino oscillation parameters (Δmatm2 and sin2atm). The oscillation signal consists of an energy-dependent deficit of vμ interactions in the far detector. The near detector is used to characterize the properties of the beam before oscillations develop. The two-detector design allows many potential sources of systematic error in the far detector to be mitigated by the near detector observations. This thesis describes the details of the vμ-disappearance analysis, and presents a new technique to estimate the hadronic energy of neutrino interactions. This estimator achieves a significant improvement in the energy resolution of the neutrino spectrum, and in the sensitivity of the neutrino oscillation fit. The systematic uncertainty on the hadronic energy scale was re-evaluated and found to be comparable to that of the energy estimator previously in use. The best-fit oscillation parameters of the vμ-disappearance analysis, incorporating this new estimator were: Δm2 = 2.32-0.08+0.12 x 10-3 eV2, sin 2 2θ > 0.90 (90% C.L.). A similar analysis, using data from a period of running where the NuMI beam was operated in a configuration producing a predominantly $\\bar{v}$μ beam, yielded somewhat different best-fit parameters Δ$\\bar{m}${sup 2} = (3.36-0.40+0.46(stat.) ± 0.06(syst.)) x 10-3eV2, sin2 2$\\bar{θ}$ = 0.86-0.12_0

  13. Time domain oscillating poles: Stability redefined in Memristor based Wien-oscillators

    Talukdar, Abdul Hafiz Ibne

    2012-07-28

    Traditionally, the necessary and sufficient condition for any system to be oscillating is that its poles are located on the imaginary (jω) axis. In this paper, for the first time, we have shown that systems can oscillate with time-domain oscillating poles. The idea is verified using a Memristor based Wien oscillator. Sustained oscillations are observed without having the poles of the system fixed on the imaginary axis and the oscillating behavior of the system poles is reported. The oscillating resistance and triangular shape of FFT are also demonstrated with mathematical reasoning and simulation results to support the unusual and surprising characteristics. © 2009 IEEE.

  14. Artificial intelligence: Collective behaviors of synthetic micromachines

    Duan, Wentao

    Synthetic nano- and micromotors function through the conversion of chemical free energy or forms of energy into mechanical motion. Ever since the first reports, such motors have been the subject of growing interest. In addition to motility in response to gradients, these motors interact with each other, resulting in emergent collective behavior like schooling, exclusion, and predator-prey. However, most of these systems only exhibit a single type of collective behavior in response to a certain stimuli. The research projects in the disseratation aim at designing synthetic micromotors that can exhibit transition between various collective behaviors in response to different stimuli, as well as quantitative understanding on the pairwise interaction and propulsion mechanism of such motors. Chapter 1 offers an overview on development of synthetic micromachines. Interactions and collective behaviors of micromotors are also summarized and included. Chapter 2 presents a silver orthophosphate microparticle system that exhibits collective behaviors. Transition between two collective patterns, clustering and dispersion, can be triggered by shift in chemical equilibrium upon the addition or removal of ammonia, in response to UV light, or under two orthogonal stimuli (UV and acoustic field) and powering mechanisms. The transitions can be explained by the self-diffusiophoresis mechanism resulting from either ionic or neutral solute gradients. Potential applications of the reported system in logic gates, microscale pumping, and hierarchical assembly have been demonstrated. Chapter 3 introduces a self-powered oscillatory micromotor system in which active colloids form clusters whose size changes periodically. The system consists of an aqueous suspension of silver orthophosphate particles under UV radiation, in the presence of a mixture of glucose and hydrogen peroxide. The colloid particles first attract with each other to form clusters. After a lag time of around 5min, chemical

  15. Selection platforms for directed evolution in synthetic biology.

    Tizei, Pedro A G; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B

    2016-08-15

    Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. © 2016 The Author(s).

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

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

    2015-08-21

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

  17. A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

    Khalil, Ahmad S.; Lu, Timothy K.; Bashor, Caleb J.; Ramirez, Cherie L.; Pyenson, Nora C.; Joung, J. Keith; Collins, James J.

    2013-01-01

    SUMMARY Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks. PMID:22863014

  18. RAPD and SSR based genetic diversity analysis of elite-2 set of ...

    Background: Synthetic hexaploid wheats are artificially reconstituted hexaploid wheats that possess high genetic variation which could be utilized for the development of new improved wheat varieties. One such group of synthetic wheats is called the Elite-II set of synthetic wheats that are derived from crossing durum wheat ...

  19. Genetic algorithms

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  20. Accelerator studies of neutrino oscillations

    Ereditato, A

    2000-01-01

    The question of whether the neutrino has a non-vanishing mass plays acrucial role in particle physics. A massive neutrino would unambiguously reveal the existence of new physics beyond the Standard Model. In addition, it could have profound implications on astrophysics and cosmology, with effects on the evolution of the Universe. Experiments aiming at direct neutrino-mass measurements based on kinematics have not been able, so far, to measure the very small neutrino mass. Indirect measurements can be performed by exploiting reactions which may only occur for massive neutrinos. Neutrino oscillation is one of those processes. The mass difference between neutrino mass-eigenstates can be inferred from a phase measurement. This feature allows for high sensitivity experiments. Neutrinos from different sources can be used to search for oscillations: solar neutrinos, neutrinos produced in the interaction of cosmic rays with the atmosphere and artificially produced neutrinos from nuclear reactors and particle accelera...

  1. Oscillators that sync and swarm.

    O'Keeffe, Kevin P; Hong, Hyunsuk; Strogatz, Steven H

    2017-11-15

    Synchronization occurs in many natural and technological systems, from cardiac pacemaker cells to coupled lasers. In the synchronized state, the individual cells or lasers coordinate the timing of their oscillations, but they do not move through space. A complementary form of self-organization occurs among swarming insects, flocking birds, or schooling fish; now the individuals move through space, but without conspicuously altering their internal states. Here we explore systems in which both synchronization and swarming occur together. Specifically, we consider oscillators whose phase dynamics and spatial dynamics are coupled. We call them swarmalators, to highlight their dual character. A case study of a generalized Kuramoto model predicts five collective states as possible long-term modes of organization. These states may be observable in groups of sperm, Japanese tree frogs, colloidal suspensions of magnetic particles, and other biological and physical systems in which self-assembly and synchronization interact.

  2. Experimental studies of neutrino oscillations

    Kajita, Takaaki

    2016-01-01

    The 2015 Nobel Prize in physics has been awarded to Takaaki Kajita and Arthur McDonald "for the discovery of neutrino oscillations, which shows that neutrinos have mass". Takaaki Kajita of Tokyo University is a Japanese physicist, known for neutrino experiments at the Kamiokande and its successor, Super-Kamiokande. This volume of collected works of Kajita on neutrino oscillations provides a good glimpse into as well as a record of the rise and the role of Asian research in the frontiers of neutrino physics. Japan is now a major force in the study of the 3 families of neutrinos. Much remains to be done to clarify the Dirac vs. Majorana nature of the neutrino, and the cosmological implications of the neutrino. The collected works of Kajita and his Super-Kamiokande group will leave an indelible foot-print in the history of big and better science.

  3. Torsional oscillations of the sun

    Snodgrass, H.B.; Howard, R.; National Solar Observatory, Tucson, AZ)

    1985-01-01

    The sun's differential rotation has a cyclic pattern of change that is tightly correlated with the sunspot, or magnetic activity, cycle. This pattern can be described as a torsional oscillation, in which the solar rotation is periodically sped up or slowed down in certain zones of latitude while elsewhere the rotation remains essentially steady. The zones of anomalous rotation move on the sun in wavelike fashion, keeping pace with and flanking the zones of magnetic activity. It is uncertain whether this torsional oscillation is a globally coherent ringing of the sun or whether it is a local pattern caused by and causing local changes in the magnetic fields. In either case, it may be an important link in the connection between the rotation and the cycle that is widely believed to exist but is not yet understood. 46 references

  4. Cubication of conservative nonlinear oscillators

    Belendez, Augusto; Alvarez, Mariela L; Fernandez, Elena; Pascual, Inmaculada

    2009-01-01

    A cubication procedure of the nonlinear differential equation for conservative nonlinear oscillators is analysed and discussed. This scheme is based on the Chebyshev series expansion of the restoring force, and this allows us to approximate the original nonlinear differential equation by a Duffing equation in which the coefficients for the linear and cubic terms depend on the initial amplitude, A, while in a Taylor expansion of the restoring force these coefficients are independent of A. The replacement of the original nonlinear equation by an approximate Duffing equation allows us to obtain an approximate frequency-amplitude relation as a function of the complete elliptic integral of the first kind. Some conservative nonlinear oscillators are analysed to illustrate the usefulness and effectiveness of this scheme.

  5. Coding of Information in Limit Cycle Oscillators

    Schleimer, Jan-Hendrik; Stemmler, Martin

    2009-12-01

    Starting from a general description of noisy limit cycle oscillators, we derive from the Fokker-Planck equations the linear response of the instantaneous oscillator frequency to a time-varying external force. We consider the time series of zero crossings of the oscillator’s phase and compute the mutual information between it and the driving force. A direct link is established between the phase response curve summarizing the oscillator dynamics and the ability of a limit cycle oscillator, such as a heart cell or neuron, to encode information in the timing of peaks in the oscillation.

  6. Quantum oscillations of conductivity in bismuth wires

    Condrea, Elena

    2011-01-01

    Measurements of the resistance of bismuth nanowires with several diameters and different quality reveal oscillations on the dependence of resistance under uniaxial strain at T = 4.2 K. Amplitude of oscillations is significant (38 %) at helium temperature and becomes smearing at T = 77 K. Observed oscillations originate from quantum size effect. A simple evaluation of period of oscillations allows us to identify the groups of carriers involved in transport. Calculated periods of 42.2 and 25.9 nm satisfy approximately the ratio 2:1 for two experimentally observed sets of oscillations from light and heavy electrons.

  7. Memristor-based reactance-less oscillator

    Zidan, Mohammed A.

    2012-10-02

    The first reactance-less oscillator is introduced. By using a memristor, the oscillator can be fully implemented on-chip without the need for any capacitors or inductors, which results in an area-efficient fully integrated solution. The concept of operation of the proposed oscillator is explained and detailed mathematical analysis is introduced. Closed-form expressions for the oscillation frequency and oscillation conditions are derived. Finally, the derived equations are verified with circuit simulations showing excellent agreement. © 2011 The Institution of Engineering and Technology.

  8. Low-frequency oscillations in Hall thrusters

    Wei Li-Qiu; Han Liang; Yu Da-Ren; Guo Ning

    2015-01-01

    In this paper, we summarize the research development of low-frequency oscillations in the last few decades. The findings of physical mechanism, characteristics and stabilizing methods of low-frequency oscillations are discussed. It shows that it is unreasonable and incomplete to model an ionization region separately to analyze the physical mechanism of low-frequency oscillations. Electro-dynamics as well as the formation conditions of ionization distribution play an important role in characteristics and stabilizing of low-frequency oscillations. Understanding the physical mechanism and characteristics of low- frequency oscillations thoroughly and developing a feasible method stabilizing this instability are still important research subjects. (review)

  9. Memristor-based reactance-less oscillator

    Zidan, Mohammed A.; Omran, Hesham; Radwan, Ahmed G.; Salama, Khaled N.

    2012-01-01

    The first reactance-less oscillator is introduced. By using a memristor, the oscillator can be fully implemented on-chip without the need for any capacitors or inductors, which results in an area-efficient fully integrated solution. The concept of operation of the proposed oscillator is explained and detailed mathematical analysis is introduced. Closed-form expressions for the oscillation frequency and oscillation conditions are derived. Finally, the derived equations are verified with circuit simulations showing excellent agreement. © 2011 The Institution of Engineering and Technology.

  10. Harmonic oscillator on a lattice

    Ader, J.P.; Bonnier, B.; Hontebeyrie, M.; Meyers, C.

    1983-01-01

    The continuum limit of the ground state energy for the harmonic oscillator with discrete time is derived for all possible choices of the lattice derivative. The occurrence of unphysical values is shown to arise whenever the lattice laplacian is not strictly positive on its Brillouin zone. These undesirable limits can either be finite and arbitrary (multiple spectrum) or infinite (overlapping sublattices with multiple spectrum). (orig.)

  11. Multipartite entanglement in neutrino oscillations

    Blasone, Massimo; Dell'Anno, Fabio; De Siena, Silvio; Illuminati, Fabrizio

    2009-01-01

    Particle mixing is related to multi-mode entanglement of single-particle states The occupation number of both flavor eigenstates and mass eigenstates can be used to define a multiqubit space. In such a framework, flavor neutrino states can be interpreted as multipartite mode-entangled states. By using two different entanglement measures, we analyze the behavior of multipartite entanglement in the phenomenon of neutrino oscillations.

  12. Multipartite entanglement in neutrino oscillations

    Blasone, Massimo; Dell' Anno, Fabio; De Siena, Silvio; Illuminati, Fabrizio, E-mail: blasone@sa.infn.i [Dipartimento di Matematica e Informatica, Universita degli Studi di Salerno, Via Ponte don Melillo, I-84084 Fisciano (Italy)

    2009-06-01

    Particle mixing is related to multi-mode entanglement of single-particle states The occupation number of both flavor eigenstates and mass eigenstates can be used to define a multiqubit space. In such a framework, flavor neutrino states can be interpreted as multipartite mode-entangled states. By using two different entanglement measures, we analyze the behavior of multipartite entanglement in the phenomenon of neutrino oscillations.

  13. Invariants of collective neutrino oscillations

    Pehlivan, Y.; Balantekin, A. B.; Kajino, Toshitaka; Yoshida, Takashi

    2011-01-01

    We consider the flavor evolution of a dense neutrino gas by taking into account both vacuum oscillations and self-interactions of neutrinos. We examine the system from a many-body perspective as well as from the point of view of an effective one-body description formulated in terms of the neutrino polarization vectors. We show that, in the single angle approximation, both the many-body picture and the effective one-particle picture possess several constants of motion. We write down these constants of motion explicitly in terms of the neutrino isospin operators for the many-body case and in terms of the polarization vectors for the effective one-body case. The existence of these constants of motion is a direct consequence of the fact that the collective neutrino oscillation Hamiltonian belongs to the class of Gaudin Hamiltonians. This class of Hamiltonians also includes the (reduced) BCS pairing Hamiltonian describing superconductivity. We point out the similarity between the collective neutrino oscillation Hamiltonian and the BCS pairing Hamiltonian. The constants of motion manifest the exact solvability of the system. Borrowing the well established techniques of calculating the exact BCS spectrum, we present exact eigenstates and eigenvalues of both the many-body and the effective one-particle Hamiltonians describing the collective neutrino oscillations. For the effective one-body case, we show that spectral splits of neutrinos can be understood in terms of the adiabatic evolution of some quasiparticle degrees of freedom from a high-density region where they coincide with flavor eigenstates to the vacuum where they coincide with mass eigenstates. We write down the most general consistency equations which should be satisfied by the effective one-body eigenstates and show that they reduce to the spectral split consistency equations for the appropriate initial conditions.

  14. Oscillations and Waves in Sunspots

    Elena Khomenko

    2015-11-01

    Full Text Available A magnetic field modifies the properties of waves in a complex way. Significant advances have been made recently in our understanding of the physics of sunspot waves with the help of high-resolution observations, analytical theories, as well as numerical simulations. We review the current ideas in the field, providing the most coherent picture of sunspot oscillations as by present understanding.

  15. Automatic oscillator frequency control system

    Smith, S. F. (Inventor)

    1985-01-01

    A frequency control system makes an initial correction of the frequency of its own timing circuit after comparison against a frequency of known accuracy and then sequentially checks and corrects the frequencies of several voltage controlled local oscillator circuits. The timing circuit initiates the machine cycles of a central processing unit which applies a frequency index to an input register in a modulo-sum frequency divider stage and enables a multiplexer to clock an accumulator register in the divider stage with a cyclical signal derived from the oscillator circuit being checked. Upon expiration of the interval, the processing unit compares the remainder held as the contents of the accumulator against a stored zero error constant and applies an appropriate correction word to a correction stage to shift the frequency of the oscillator being checked. A signal from the accumulator register may be used to drive a phase plane ROM and, with periodic shifts in the applied frequency index, to provide frequency shift keying of the resultant output signal. Interposition of a phase adder between the accumulator register and phase plane ROM permits phase shift keying of the output signal by periodic variation in the value of a phase index applied to one input of the phase adder.

  16. Micro-machined resonator oscillator

    Koehler, Dale R.; Sniegowski, Jeffry J.; Bivens, Hugh M.; Wessendorf, Kurt O.

    1994-01-01

    A micro-miniature resonator-oscillator is disclosed. Due to the miniaturization of the resonator-oscillator, oscillation frequencies of one MHz and higher are utilized. A thickness-mode quartz resonator housed in a micro-machined silicon package and operated as a "telemetered sensor beacon" that is, a digital, self-powered, remote, parameter measuring-transmitter in the FM-band. The resonator design uses trapped energy principles and temperature dependence methodology through crystal orientation control, with operation in the 20-100 MHz range. High volume batch-processing manufacturing is utilized, with package and resonator assembly at the wafer level. Unique design features include squeeze-film damping for robust vibration and shock performance, capacitive coupling through micro-machined diaphragms allowing resonator excitation at the package exterior, circuit integration and extremely small (0.1 in. square) dimensioning. A family of micro-miniature sensor beacons is also disclosed with widespread applications as bio-medical sensors, vehicle status monitors and high-volume animal identification and health sensors. The sensor family allows measurement of temperatures, chemicals, acceleration and pressure. A microphone and clock realization is also available.

  17. Drifting oscillations in axion monodromy

    Flauger, Raphael [Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213 (United States); McAllister, Liam [Department of Physics, Cornell University, Ithaca, NY 14853 (United States); Silverstein, Eva [Stanford Institute for Theoretical Physics, Stanford University, Stanford, CA 94305 (United States); Westphal, Alexander, E-mail: flauger@physics.ucsd.edu, E-mail: mcallister@cornell.edu, E-mail: evas@stanford.edu, E-mail: alexander.westphal@desy.de [Theory Group, Deutsches Elektronen-Synchrotron DESY, D-22603 Hamburg (Germany)

    2017-10-01

    We study the pattern of oscillations in the primordial power spectrum in axion monodromy inflation, accounting for drifts in the oscillation period that can be important for comparing to cosmological data. In these models the potential energy has a monomial form over a super-Planckian field range, with superimposed modulations whose size is model-dependent. The amplitude and frequency of the modulations are set by the expectation values of moduli fields. We show that during the course of inflation, the diminishing energy density can induce slow adjustments of the moduli, changing the modulations. We provide templates capturing the effects of drifting moduli, as well as drifts arising in effective field theory models based on softly broken discrete shift symmetries, and we estimate the precision required to detect a drifting period. A non-drifting template suffices over a wide range of parameters, but for the highest frequencies of interest, or for sufficiently strong drift, it is necessary to include parameters characterizing the change in frequency over the e-folds visible in the CMB. We use these templates to perform a preliminary search for drifting oscillations in a part of the parameter space in the Planck nominal mission data.

  18. Neutrino Oscillation Experiment at JHF

    2002-01-01

    T2K is a long baseline neutrino experiment designed to investigate how neutrinos change from one flavor to another as they travel (neutrino oscillations). An intense beam of muon neutrinos is generated at the J-PARC nuclear physics site on the East coast of Japan and directed across the country to the Super-Kamiokande neutrino detector in the mountains of western Japan. The beam is measured once before it leaves the J-PARC site, using the near detector ND280, and again at Super-K, 295 km away: the change in the measured intensity and composition of the beam is used to provide information on the properties of neutrinos. The high intensity neutrino beam is produced in an off-axis configuration. The peak neutrino energy is tuned to the oscillation maximum of ∼ 0.6 GeV to maximize the sensitivity to neutrino oscillations. The science goals of T2K can be summarized as follows: •\tsearch for CP violation in the neutrino sector •\tdiscovery of νμ → νe ( i.e. the confirmation that θ13 > 0 ) •\tprecision ...

  19. Superconducting low-noise oscillator

    Riebman, L.

    1992-01-01

    This patent describes a cryogenic oscillator having low phase noise and low noise. It comprises resonant circuit means formed of superconducting material for generating a signal at a desired frequency; linear amplifier means electrically connected to the resonant circuit means at first and second locations thereon; limiter means electrically connected to the resonant circuit means at a third location thereon; and buffer amplifier means for applying the signal generated by the resonant circuit means to a load and electrically connected to the resonant circuit means at a fourth location thereon. This patent also describes a method of minimizing phase noise and 1/f noise in an oscillator circuit of the type having a resonant circuit driving a load and at least a linear amplifier connected to the resonant circuit defining a closed loop having a loop gain greater than unity, and having a limiter for stabilizing the oscillator. It comprises connecting between the resonant circuit and the load a buffer amplifier and connecting the linear amplifier and the buffer amplifier to the resonant circuit

  20. Boltzmann map for quantum oscillators

    Streater, R.F.

    1987-01-01

    The authors define a map tau on the space of quasifree states of the CCR or CAR of more than one harmonic oscillator which increases entropy except at fixed points of tau. The map tau is the composition of a double stochastic map T*, and the quasifree reduction Q. Under mixing conditions on T, iterates of tau take any initial state to the Gibbs states, provided that the oscillator frequencies are mutually rational. They give an example of a system with three degrees of freedom with energies omega 1 , omega 2 , and omega 3 mutually irrational, but obeying a relation n 1 omega 1 + n 2 omega 2 = n 3 omega 3 , n/sub i/epsilon Z. The iterated Boltzmann map converges from an initial state rho to independent Gibbs states of the three oscillators at betas (inverse temperatures) β 1 , β 2 , β 3 obeying the equation n 1 omega 1 β 1 + n 2 omega 3 β 1 number. The equilibrium state can be rewritten as a grand canonical state. They show that for two, three, or four fermions we can get the usual rate equations as a special case

  1. Neutrino Oscillations:. a Phenomenological Approach

    Fogli, G. L.; Lisi, E.; Marrone, A.; Palazzo, A.; Rotunno, A. M.; Montanino, D.

    We review the status of the neutrino oscillations physics, with a particular emphasis on the present knowledge of the neutrino mass-mixing parameters. We consider first the νμ → ντ flavor transitions of atmospheric neutrinos. It is found that standard oscillations provide the best description of the SK+K2K data, and that the associated mass-mixing parameters are determined at ±1σ (and NDF = 1) as: Δm2 = (2.6 ± 0.4) × 10-3 eV2 and sin 2 2θ = 1.00{ - 0.05}{ + 0.00} . Such indications, presently dominated by SK, could be strengthened by further K2K data. Then we point out that the recent data from the Sudbury Neutrino Observatory, together with other relevant measurements from solar and reactor neutrino experiments, in particular the KamLAND data, convincingly show that the flavor transitions of solar neutrinos are affected by Mikheyev-Smirnov-Wolfenstein (MSW) effects. Finally, we perform an updated analysis of two-family active oscillations of solar and reactor neutrinos in the standard MSW case.

  2. Drifting oscillations in axion monodromy

    Flauger, Raphael; Westphal, Alexander

    2014-12-01

    We study the pattern of oscillations in the primordial power spectrum in axion monodromy inflation, accounting for drifts in the oscillation period that can be important for comparing to cosmological data. In these models the potential energy has a monomial form over a super-Planckian field range, with superimposed modulations whose size is model-dependent. The amplitude and frequency of the modulations are set by the expectation values of moduli fields. We show that during the course of inflation, the diminishing energy density can induce slow adjustments of the moduli, changing the modulations. We provide templates capturing the effects of drifting moduli, as well as drifts arising in effective field theory models based on softly broken discrete shift symmetries, and we estimate the precision required to detect a drifting period. A non-drifting template suffices over a wide range of parameters, but for the highest frequencies of interest, or for sufficiently strong drift, it is necessary to include parameters characterizing the change in frequency over the e-folds visible in the CMB. We use these templates to perform a preliminary search for drifting oscillations in a part of the parameter space in the Planck nominal mission data.

  3. Nonlinearity induced synchronization enhancement in mechanical oscillators

    Czaplewski, David A.; Lopez, Omar; Guest, Jeffrey R.; Antonio, Dario; Arroyo, Sebastian I.; Zanette, Damian H.

    2018-05-08

    An autonomous oscillator synchronizes to an external harmonic force only when the forcing frequency lies within a certain interval, known as the synchronization range, around the oscillator's natural frequency. Under ordinary conditions, the width of the synchronization range decreases when the oscillation amplitude grows, which constrains synchronized motion of micro- and nano-mechanical resonators to narrow frequency and amplitude bounds. The present invention shows that nonlinearity in the oscillator can be exploited to manifest a regime where the synchronization range increases with an increasing oscillation amplitude. The present invention shows that nonlinearities in specific configurations of oscillator systems, as described herein, are the key determinants of the effect. The present invention presents a new configuration and operation regime that enhances the synchronization of micro- and nano-mechanical oscillators by capitalizing on their intrinsic nonlinear dynamics.

  4. Nonlocal synchronization in nearest neighbour coupled oscillators

    El-Nashar, H.F.; Elgazzar, A.S.; Cerdeira, H.A.

    2002-02-01

    We investigate a system of nearest neighbour coupled oscillators. We show that the nonlocal frequency synchronization, that might appear in such a system, occurs as a consequence of the nearest neighbour coupling. The power spectra of nonadjacent oscillators shows that there is no complete coincidence between all frequency peaks of the oscillators in the nonlocal cluster, while the peaks for neighbouring oscillators approximately coincide even if they are not yet in a cluster. It is shown that nonadjacent oscillators closer in frequencies, share slow modes with their adjacent oscillators which are neighbours in space. It is also shown that when a direct coupling between non-neighbours oscillators is introduced explicitly, the peaks of the spectra of the frequencies of those non-neighbours coincide. (author)

  5. Applications of cell-free protein synthesis in synthetic biology: Interfacing bio-machinery with synthetic environments.

    Lee, Kyung-Ho; Kim, Dong-Myung

    2013-11-01

    Synthetic biology is built on the synthesis, engineering, and assembly of biological parts. Proteins are the first components considered for the construction of systems with designed biological functions because proteins carry out most of the biological functions and chemical reactions inside cells. Protein synthesis is considered to comprise the most basic levels of the hierarchical structure of synthetic biology. Cell-free protein synthesis has emerged as a powerful technology that can potentially transform the concept of bioprocesses. With the ability to harness the synthetic power of biology without many of the constraints of cell-based systems, cell-free protein synthesis enables the rapid creation of protein molecules from diverse sources of genetic information. Cell-free protein synthesis is virtually free from the intrinsic constraints of cell-based methods and offers greater flexibility in system design and manipulability of biological synthetic machinery. Among its potential applications, cell-free protein synthesis can be combined with various man-made devices for rapid functional analysis of genomic sequences. This review covers recent efforts to integrate cell-free protein synthesis with various reaction devices and analytical platforms. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Catalysts for synthetic liquid fuels

    Bruce, L.A.; Turney, T.W.

    1987-12-01

    Fischer-Tropsch catalysts have been designed, characterized and tested for the selective production of hydrocarbons suitable as synthetic liquid transport fuels from synthesis gas (i.e., by the reduction of carbon monoxide with hydrogen). It was found that hydrocarbons in the middle distillate range, or suitable for conversion to that range, could be produced over several of the new catalyst systems. The various catalysts examined included: (1) synthetic cobalt clays, mainly cobalt chlorites; (2) cobalt hydrotalcites; (3) ruthenium metal supported on rare earth oxides of high surface area; and (4) a novel promoted cobalt catalyst. Active and selective catalysts have been obtained, in each category. With the exception of the clays, reproducibility of catalyst performance has been good. Catalysts in groups 2 and 4 have exhibited very high activity, with long lifetimes and easy regeneration.

  7. Synthetic biology character and impact

    Pade, Christian; Wigger, Henning; Gleich, Arnim

    2015-01-01

    Synthetic Biology is already an object of intensive debate. However, to a great extent the discussion to date has been concerned with fundamental ethical, religious and philosophical questions. By contrast, based on an investigation of the field’s scientific and technological character, this book focuses on new functionalities provided by synthetic biology and explores the associated opportunities and risks. Following an introduction to the subject and a discussion of the most central paradigms and methodologies, the book provides an overview of the structure of this field of science and technology. It informs the reader about the current stage of development, as well as topical problems and potential opportunities in important fields of application. But not only the science itself is in focus. In order to investigate its broader impact, ecological as well as ethical implications will be considered, paving the way for a discussion of responsibilities in the context of a field at a transitional crossroads be...

  8. Synthetic greenhouse gases under control

    Horisberger, B.; Karlaganis, G.

    2003-01-01

    This article discusses new Swiss regulations on the use of synthetic materials that posses a considerable greenhouse-warming potential. Synthetic materials such as hydro-chlorofluorocarbons HCFCs, perfluoride-hydrocarbons and sulphur hexafluoride have, in recent years, replaced chlorofluorocarbons CFCs, which were banned on account of their ozone depletion characteristics. The use of these persistent substances is now being limited to applications where more environment-friendly alternatives are not available. The measures decreed in the legislation, which include a general ban on HCFCs as of 2004 and a ban on the export of installations and equipment that use ozone-depleting refrigerants are described. Details on the legislation's effects on the Swiss refrigeration industry are listed and discussed

  9. Synthetic LDL as targeted drug delivery vehicle

    Forte, Trudy M [Berkeley, CA; Nikanjam, Mina [Richmond, CA

    2012-08-28

    The present invention provides a synthetic LDL nanoparticle comprising a lipid moiety and a synthetic chimeric peptide so as to be capable of binding the LDL receptor. The synthetic LDL nanoparticle of the present invention is capable of incorporating and targeting therapeutics to cells expressing the LDL receptor for diseases associated with the expression of the LDL receptor such as central nervous system diseases. The invention further provides methods of using such synthetic LDL nanoparticles.

  10. Vibrational spectrum of synthetic carnotite

    Baran, E J; Botto, I L [La Plata Univ. Nacional (Argentina). Facultad de Ciencias Exactas

    1976-05-01

    The infrared and laser-Raman spectra of synthetic carnotite, K/sub 2/((UO/sub 2/)/sub 2/V/sub 2/O/sub 8/), are reported and discussed. Force constants for the terminal V-O bonds as well as for the UO/sub 2//sup 2 +/ ions are evaluated. From the spectroscopic data, a U-O bond length of 1.81 A is estimated for the uranyl ion in this compound.

  11. Designer Drugs: A Synthetic Catastrophe

    Fratantonio, James; Andrade, Lawrence; Febo, Marcelo

    2015-01-01

    Synthetic stimulants can cause hallucinations, aggressive behaviors, death and are sometimes legal. These substances are sold as plant food and bath salts that are "Not for Human Consumption", therefore skirting the 1986 Federal Analogue Act and giving a false pretense of safety. Studies have proved that these substances are toxic, have a high abuse potential, and are becoming extremely prevalent in the United States. This creates a dilemma for law enforcement agents, hospitals, and substance...

  12. Genetic Mapping

    ... greatly advanced genetics research. The improved quality of genetic data has reduced the time required to identify a ... cases, a matter of months or even weeks. Genetic mapping data generated by the HGP's laboratories is freely accessible ...

  13. Hydrogen speciation in synthetic quartz

    Aines, R.D.; Kirby, S.H.; Rossman, G.R.

    1984-01-01

    The dominant hydrogen impurity in synthetic quartz is molecular H2O. H-OH groups also occur, but there is no direct evidence for the hydrolysis of Si-O-Si bonds to yield Si-OH HO-Si groups. Molecular H2O concentrations in the synthetic quartz crystals studied range from less than 10 to 3,300 ppm (H/Si), and decrease smoothly by up to an order of magnitude with distance away from the seed. OH- concentrations range from 96 to 715 ppm, and rise smoothly with distance away from the seed by up to a factor of three. The observed OH- is probably all associated with cationic impurities, as in natural quartz. Molecular H2O is the dominant initial hydrogen impurity in weak quartz. The hydrolytic weakening of quartz may be caused by the transformation H2O + Si-O-Si ??? 2SiOH, but this may be a transitory change with the SiOH groups recombining to form H2O, and the average SiOH concentration remaining very low. Synthetic quartz is strengthened when the H2O is accumulated into fluid inclusions and cannot react with the quartz framework. ?? 1984 Springer-Verlag.

  14. Dysrhythmias of the respiratory oscillator

    Paydarfar, David; Buerkel, Daniel M.

    1995-03-01

    Breathing is regulated by a central neural oscillator that produces rhythmic output to the respiratory muscles. Pathological disturbances in rhythm (dysrhythmias) are observed in the breathing pattern of children and adults with neurological and cardiopulmonary diseases. The mechanisms responsible for genesis of respiratory dysrhythmias are poorly understood. The present studies take a novel approach to this problem. The basic postulate is that the rhythm of the respiratory oscillator can be altered by a variety of stimuli. When the oscillator recovers its rhythm after such perturbations, its phase may be reset relative to the original rhythm. The amount of phase resetting is dependent upon stimulus parameters and the level of respiratory drive. The long-range hypothesis is that respiratory dysrhythmias can be induced by stimuli that impinge upon or arise within the respiratory oscillator with certain combinations of strength and timing relative to the respiratory cycle. Animal studies were performed in anesthetized or decerebrate preparations. Neural respiratory rhythmicity is represented by phrenic nerve activity, allowing use of open-loop experimental conditions which avoid negative chemical feedback associated with changes in ventilation. In animal experiments, respiratory dysrhythmias can be induced by stimuli having specific combinations of strength and timing. Newborn animals readily exhibit spontaneous dysrhythmias which become more prominent at lower respiratory drives. In human subjects, swallowing was studied as a physiological perturbation of respiratory rhythm, causing a pattern of phase resetting that is characterized topologically as type 0. Computational studies of the Bonhoeffer-van der Pol (BvP) equations, whose qualitative behavior is representative of many excitable systems, supports a unified interpretation of these experimental findings. Rhythmicity is observed when the BvP model exhibits recurrent periods of excitation alternating with

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

    Nemhauser, Jennifer L; Torii, Keiko U

    2016-03-02

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

  16. Synthetic biology in cell-based cancer immunotherapy.

    Chakravarti, Deboki; Wong, Wilson W

    2015-08-01

    The adoptive transfer of genetically engineered T cells with cancer-targeting receptors has shown tremendous promise for eradicating tumors in clinical trials. This form of cellular immunotherapy presents a unique opportunity to incorporate advanced systems and synthetic biology approaches to create cancer therapeutics with novel functions. We first review the development of synthetic receptors, switches, and circuits to control the location, duration, and strength of T cell activity against tumors. In addition, we discuss the cellular engineering and genome editing of host cells (or the chassis) to improve the efficacy of cell-based cancer therapeutics, and to reduce the time and cost of manufacturing. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Characterization of synthetic peptides by mass spectrometry

    Prabhala, Bala Krishna; Mirza, Osman Asghar; Højrup, Peter

    2015-01-01

    Mass spectrometry (MS) is well suited for analysis of the identity and purity of synthetic peptides. The sequence of a synthetic peptide is most often known, so the analysis is mainly used to confirm the identity and purity of the peptide. Here, simple procedures are described for MALDI......-TOF-MS and LC-MS of synthetic peptides....

  18. Synthetic Hydrogen Spectra of Oscillating Prominence Slabs Immersed in the Solar Corona

    Zapiór, Maciej; Oliver, R.; Ballester, J.L.; Heinzel, Petr

    2016-01-01

    Roč. 827, č. 2 (2016), 131/1-131/7 ISSN 0004-637X R&D Projects: GA ČR(CZ) GA16-18495S Institutional support: RVO:67985815 Keywords : Sun * filaments * prominences Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 5.533, year: 2016

  19. Genetic privacy.

    Sankar, Pamela

    2003-01-01

    During the past 10 years, the number of genetic tests performed more than tripled, and public concern about genetic privacy emerged. The majority of states and the U.S. government have passed regulations protecting genetic information. However, research has shown that concerns about genetic privacy are disproportionate to known instances of information misuse. Beliefs in genetic determinacy explain some of the heightened concern about genetic privacy. Discussion of the debate over genetic testing within families illustrates the most recent response to genetic privacy concerns.

  20. Rational design of functional and tunable oscillating enzymatic networks

    Semenov, Sergey N.; Wong, Albert S. Y.; van der Made, R. Martijn; Postma, Sjoerd G. J.; Groen, Joost; van Roekel, Hendrik W. H.; de Greef, Tom F. A.; Huck, Wilhelm T. S.

    2015-02-01

    Life is sustained by complex systems operating far from equilibrium and consisting of a multitude of enzymatic reaction networks. The operating principles of biology's regulatory networks are known, but the in vitro assembly of out-of-equilibrium enzymatic reaction networks has proved challenging, limiting the development of synthetic systems showing autonomous behaviour. Here, we present a strategy for the rational design of programmable functional reaction networks that exhibit dynamic behaviour. We demonstrate that a network built around autoactivation and delayed negative feedback of the enzyme trypsin is capable of producing sustained oscillating concentrations of active trypsin for over 65 h. Other functions, such as amplification, analog-to-digital conversion and periodic control over equilibrium systems, are obtained by linking multiple network modules in microfluidic flow reactors. The methodology developed here provides a general framework to construct dissipative, tunable and robust (bio)chemical reaction networks.

  1. Separation control with fluidic oscillators in water

    Schmidt, H.-J.; Woszidlo, R.; Nayeri, C. N.; Paschereit, C. O.

    2017-08-01

    The present study assesses the applicability of fluidic oscillators for separation control in water. The first part of this work evaluates the properties of the fluidic oscillators including frequency, cavitation effects, and exerted thrust. Derived from the governing internal dynamics, the oscillation frequency is found to scale directly with the jet's exit velocity and the size of the fluidic oscillator independent of the working fluid. Frequency data from various experiments collapse onto a single curve. The occurrence of cavitation is examined by visual inspection and hydrophone measurements. The oscillation frequency is not affected by cavitation because it does not occur inside the oscillators. The spectral information obtained with the hydrophone provide a reliable indicator for the onset of cavitation at the exit. The performance of the fluidic oscillators for separation control on a bluff body does not seem to be affected by the presence of cavitation. The thrust exerted by an array of fluidic oscillators with water as the working fluid is measured to be even larger than theoretically estimated values. The second part of the presented work compares the performance of fluidic oscillators for separation control in water with previous results in air. The array of fluidic oscillators is installed into the rear end of a bluff body model. The drag improvements based on force balance measurements agree well with previous wind tunnel experiments on the same model. The flow field is examined by pressure measurements and with particle image velocimetry. Similar performance and flow field characteristics are observed in both water and air.

  2. Statistics for Learning Genetics

    Charles, Abigail Sheena

    , although the necessity for infusing these quantitative subjects with genetics and, overall, the biological sciences is growing (topics including synthetic biology, molecular systems biology and phylogenetics) there remains little time in the semester to be dedicated to the consolidation of learning and understanding.

  3. Synthetic circuit designs for earth terraformation.

    Solé, Ricard V; Montañez, Raúl; Duran-Nebreda, Salva

    2015-07-18

    Mounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation scenarios capable of counterbalancing these effects involve geoengineering, sustainable practices and carbon sequestration, among others. None of these scenarios seems powerful enough to achieve the desired restoration of safe boundaries. We hypothesize that synthetic organisms with the appropriate engineering design could be used to safely prevent declines in some stressed ecosystems and help improving carbon sequestration. Such schemes would include engineering mutualistic dependencies preventing undesired evolutionary processes. We hypothesize that some particular design principles introduce unescapable constraints to the engineered organisms that act as effective firewalls. Testing this designed organisms can be achieved by using controlled bioreactor models, with single and heterogeneous populations, and accurate computational models including different scales (from genetic constructs and metabolic pathways to population dynamics). Our hypothesis heads towards a future anthropogenic action that should effectively act as Terraforming processes. It also implies a major challenge in the existing biosafety policies, since we suggest release of modified organisms as potentially necessary strategy for success.

  4. Karhunen-Loève (PCA) based detection of multiple oscillations in multiple measurement signals from large-scale process plants

    Odgaard, Peter Fogh; Wickerhauser, M.V.

    2007-01-01

     In the perspective of optimizing the control and operation of large scale process plants, it is important to detect and to locate oscillations in the plants. This paper presents a scheme for detecting and localizing multiple oscillations in multiple measurements from such a large-scale power plant....... The scheme is based on a Karhunen-Lo\\`{e}ve analysis of the data from the plant. The proposed scheme is subsequently tested on two sets of data: a set of synthetic data and a set of data from a coal-fired power plant. In both cases the scheme detects the beginning of the oscillation within only a few samples....... In addition the oscillation localization has also shown its potential by localizing the oscillations in both data sets....

  5. A Canadian refiner's perspective of synthetic crudes

    Halford, T.L.; McIntosh, A.P.; Rasmussen

    1997-01-01

    Some of the factors affecting a refiner's choice of crude oil include refinery hardware, particularly gas oil crackers, products slate and product specifications, crude availability, relative crude price and crude quality. An overview of synthetic crude, the use of synthetic crude combined with other crudes and a comparison of synthetic crude with conventional crude oil was given. The two main users of synthetic crude are basically two groups of refiners, those large groups who use synthetic crude combined with other crudes, and a smaller group who run synthetic crude on specially designed units as a sole feed. The effects of changes in fuel legislation were reviewed. It was predicted that the changes will have a mixed impact on the value of synthetic crude, but low sulphur diesel regulations and gasoline sulphur regulations will make current synthetic crudes attractive. The big future change with a negative impact will be diesel cetane increases to reduce engine emissions. This will reduce synthetic crude attractiveness due to distillate yields and quality and high gas oil yields. Similarly, any legislation limiting aromatics in diesel fuel will also make synthetic crudes less attractive. Problems experienced by refiners with hardware dedicated to synthetic crude (salt, naphthenic acid, fouling, quality variations) were also reviewed. 3 tabs

  6. A Powerful Toolkit for Synthetic Biology: Over 3.8 Billion Years of Evolution

    Rothschild, Lynn J.

    2010-01-01

    The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested

  7. Printability of Synthetic Papers by Electrophotography

    Rozália Szentgyörgyvölgyi

    2010-04-01

    Full Text Available This paper deals with the printability of synthetic papers by the electrophotography technique. Prints of cmyk colour fields from 20% to 100% raster tone values were printed on three types of synthetic papers (one film synthetic paper and two fiber synthetic papers. The investigation of the appearance included densitometric measurement of the cmyk prints. The results have shown differences in the optical density and optical tone value between cmyk prints made on various synthetic papers. The highest optical density and the increase of the optical tone value were observed on the film synthetic paper, where cmyk prints were more saturated. The highest abrasion resistance of cmyk prints was obtained from the fibre synthetic paper.

  8. Bifurcation and category learning in network models of oscillating cortex

    Baird, Bill

    1990-06-01

    A genetic model of oscillating cortex, which assumes “minimal” coupling justified by known anatomy, is shown to function as an associative memory, using previously developed theory. The network has explicit excitatory neurons with local inhibitory interneuron feedback that forms a set of nonlinear oscillators coupled only by long-range excitatory connections. Using a local Hebb-like learning rule for primary and higher-order synapses at the ends of the long-range connections, the system learns to store the kinds of oscillation amplitude patterns observed in olfactory and visual cortex. In olfaction, these patterns “emerge” during respiration by a pattern forming phase transition which we characterize in the model as a multiple Hopf bifurcation. We argue that these bifurcations play an important role in the operation of real digital computers and neural networks, and we use bifurcation theory to derive learning rules which analytically guarantee CAM storage of continuous periodic sequences-capacity: N/2 Fourier components for an N-node network-no “spurious” attractors.

  9. Clusters in nonsmooth oscillator networks

    Nicks, Rachel; Chambon, Lucie; Coombes, Stephen

    2018-03-01

    For coupled oscillator networks with Laplacian coupling, the master stability function (MSF) has proven a particularly powerful tool for assessing the stability of the synchronous state. Using tools from group theory, this approach has recently been extended to treat more general cluster states. However, the MSF and its generalizations require the determination of a set of Floquet multipliers from variational equations obtained by linearization around a periodic orbit. Since closed form solutions for periodic orbits are invariably hard to come by, the framework is often explored using numerical techniques. Here, we show that further insight into network dynamics can be obtained by focusing on piecewise linear (PWL) oscillator models. Not only do these allow for the explicit construction of periodic orbits, their variational analysis can also be explicitly performed. The price for adopting such nonsmooth systems is that many of the notions from smooth dynamical systems, and in particular linear stability, need to be modified to take into account possible jumps in the components of Jacobians. This is naturally accommodated with the use of saltation matrices. By augmenting the variational approach for studying smooth dynamical systems with such matrices we show that, for a wide variety of networks that have been used as models of biological systems, cluster states can be explicitly investigated. By way of illustration, we analyze an integrate-and-fire network model with event-driven synaptic coupling as well as a diffusively coupled network built from planar PWL nodes, including a reduction of the popular Morris-Lecar neuron model. We use these examples to emphasize that the stability of network cluster states can depend as much on the choice of single node dynamics as it does on the form of network structural connectivity. Importantly, the procedure that we present here, for understanding cluster synchronization in networks, is valid for a wide variety of systems in

  10. Power oscillations in BWR reactors

    Espinosa P, G.

    2002-01-01

    One of the main problems in the operation of BWR type reactors is the instability in power that these could present. One type of oscillations and that is the objective of this work is the named density wave, which is attributed to the thermohydraulic processes that take place in the reactor core. From the beginnings of the development of BWR reactors, the stability of these has been an important aspect in their design, due to its possible consequences on the fuel integrity. The reactor core operates in two phase flow conditions and it is observed that under certain power and flow conditions, power instabilities appear. Studying this type of phenomena is complex, due to that a reactor core is constituted approximately by 27,000 fuel bars with different distributions of power and flow. The phenomena that cause the instability in BWR reactors continue being matter of scientific study. In the literature mainly in nuclear subject, it can be observed that exist different methods and approximations for studying this type of phenomena, nevertheless, their results are focused to establish safety limits in the reactor operation, instead of studying in depth of the knowledge about. Also in this line sense of the reactor data analysis, the oscillations characteristic frequencies are obtained for trying to establish if the power is growing or decreasing. In addition to that before mentioned in this paper it is presented a rigorous study applying the volumetric average method, for obtaining the vacuum waves propagation velocities and its possible connection with the power oscillations. (Author)

  11. Modeling of Coupled Chaotic Oscillators

    Lai, Y.; Grebogi, C.

    1999-01-01

    Chaotic dynamics may impose severe limits to deterministic modeling by dynamical equations of natural systems. We give theoretical argument that severe modeling difficulties may occur for high-dimensional chaotic systems in the sense that no model is able to produce reasonably long solutions that are realized by nature. We make these ideas concrete by investigating systems of coupled chaotic oscillators. They arise in many situations of physical and biological interests, and they also arise from discretization of nonlinear partial differential equations. copyright 1999 The American Physical Society

  12. Magnus approximation in neutrino oscillations

    Acero, Mario A; Aguilar-Arevalo, Alexis A; D'Olivo, J C

    2011-01-01

    Oscillations between active and sterile neutrinos remain as an open possibility to explain some anomalous experimental observations. In a four-neutrino (three active plus one sterile) mixing scheme, we use the Magnus expansion of the evolution operator to study the evolution of neutrino flavor amplitudes within the Earth. We apply this formalism to calculate the transition probabilities from active to sterile neutrinos with energies of the order of a few GeV, taking into account the matter effect for a varying terrestrial density.

  13. Waves and Oscillations in Plasmas

    Pecseli, Hans L

    2012-01-01

    The result of more than 15 years of lectures in plasma sciences presented at universities in Denmark, Norway, and the United States, Waves and Oscillations in Plasmas addresses central issues in modern plasma sciences. The book covers fluid models as well as kinetic plasma models, including a detailed discussion of, for instance, collisionless Landau damping. Offering a clear separation of linear and nonlinear models, the book can be tailored for readers of varying levels of expertise.Designed to provide basic training in linear as well as nonlinear plasma dynamics, and practical in areas as d

  14. Pair creation and plasma oscillations

    Prozorkevich, A. V.; Vinnik, D. V.; Schmidt, S. M.; Hecht, M. B.; Roberts, C. D.

    2000-01-01

    We describe aspects of particle creation in strong fields using a quantum kinetic equation with a relaxation-time approximation to the collision term. The strong electric background field is determined by solving Maxwell's equation in tandem with the Vlasov equation. Plasma oscillations appear as a result of feedback between the background field and the field generated by the particles produced. The plasma frequency depends on the strength of the initial background fields and the collision frequency, and is sensitive to the necessary momentum-dependence of dressed-parton masses

  15. Wave Physics Oscillations - Solitons - Chaos

    Nettel, Stephen

    2009-01-01

    This textbook is intended for those second year undergraduates in science and engineering who will later need an understanding of electromagnetic theory and quantum mechanics. The classical physics of oscillations and waves is developed at a more advanced level than has been customary for the second year, providing a basis for the quantum mechanics that follows. In this new edition the Green's function is explained, reinforcing the integration of quantum mechanics with classical physics. The text may also form the basis of an "introduction to theoretical physics" for physics majors. The concluding chapters give special attention to topics in current wave physics: nonlinear waves, solitons, and chaotic behavior.

  16. Cortical oscillations modulated by congruent and incongruent audiovisual stimuli.

    Herdman, A T; Fujioka, T; Chau, W; Ross, B; Pantev, C; Picton, T W

    2004-11-30

    Congruent or incongruent grapheme-phoneme stimuli are easily perceived as one or two linguistic objects. The main objective of this study was to investigate the changes in cortical oscillations that reflect the processing of congruent and incongruent audiovisual stimuli. Graphemes were Japanese Hiragana characters for four different vowels (/a/, /o/, /u/, and /i/). They were presented simultaneously with their corresponding phonemes (congruent) or non-corresponding phonemes (incongruent) to native-speaking Japanese participants. Participants' reaction times to the congruent audiovisual stimuli were significantly faster by 57 ms as compared to reaction times to incongruent stimuli. We recorded the brain responses for each condition using a whole-head magnetoencephalograph (MEG). A novel approach to analysing MEG data, called synthetic aperture magnetometry (SAM), was used to identify event-related changes in cortical oscillations involved in audiovisual processing. The SAM contrast between congruent and incongruent responses revealed greater event-related desynchonization (8-16 Hz) bilaterally in the occipital lobes and greater event-related synchronization (4-8 Hz) in the left transverse temporal gyrus. Results from this study further support the concept of interactions between the auditory and visual sensory cortices in multi-sensory processing of audiovisual objects.

  17. The Role of Synthetic Fuels for a Carbon Neutral Economy

    Rui Namorado Rosa

    2017-04-01

    Full Text Available Fossil fuels depletion and increasing environmental impacts arising from their use call for seeking growing supplies from renewable and nuclear primary energy sources. However, it is necessary to simultaneously attend to both the electrical power needs and the specificities of the transport and industrial sector requirements. A major question posed by the shift away from traditional fossil fuels towards renewable energy sources lies in matching the power demand with the daily and seasonal oscillation and the intermittency of these natural energy fluxes. Huge energy storage requirements become necessary or otherwise the decline of the power factor of both the renewable and conventional generation would mean loss of resources. On the other hand, liquid and gaseous fuels, for which there is vast storage and distribution capacity available, appear essential to supply the transport sector for a very long time ahead, besides their domestic and industrial roles. Within this context, the present assessment suggests that proven technologies and sound tested principles are available to develop an integrated energy system, relying on synthetic fuels. These would incorporate carbon capture and utilization in a closed carbon cycle, progressively relying mostly on solar and/or nuclear primary sources, providing both electric power and gaseous/liquid hydrocarbon fuels, having ample storage capacity, and able to timely satisfy all forms of energy demand. The principles and means are already available to develop a carbon-neutral synthetic fuel economy.

  18. Coupled oscillators with parity-time symmetry

    Tsoy, Eduard N., E-mail: etsoy@uzsci.net

    2017-02-05

    Different models of coupled oscillators with parity-time (PT) symmetry are studied. Hamiltonian functions for two and three linear oscillators coupled via coordinates and accelerations are derived. Regions of stable dynamics for two coupled oscillators are obtained. It is found that in some cases, an increase of the gain-loss parameter can stabilize the system. A family of Hamiltonians for two coupled nonlinear oscillators with PT-symmetry is obtained. An extension to high-dimensional PT-symmetric systems is discussed. - Highlights: • A generalization of a Hamiltonian system of linear coupled oscillators with the parity-time (PT) symmetry is suggested. • It is found that an increase of the gain-loss parameter can stabilize the system. • A family of Hamiltonian functions for two coupled nonlinear oscillators with PT-symmetry is obtained.

  19. Phase noise and frequency stability in oscillators

    Rubiola, Enrico

    2009-01-01

    Presenting a comprehensive account of oscillator phase noise and frequency stability, this practical text is both mathematically rigorous and accessible. An in-depth treatment of the noise mechanism is given, describing the oscillator as a physical system, and showing that simple general laws govern the stability of a large variety of oscillators differing in technology and frequency range. Inevitably, special attention is given to amplifiers, resonators, delay lines, feedback, and flicker (1/f) noise. The reverse engineering of oscillators based on phase-noise spectra is also covered, and end-of-chapter exercises are given. Uniquely, numerous practical examples are presented, including case studies taken from laboratory prototypes and commercial oscillators, which allow the oscillator internal design to be understood by analyzing its phase-noise spectrum. Based on tutorials given by the author at the Jet Propulsion Laboratory, international IEEE meetings, and in industry, this is a useful reference for acade...

  20. Driven, autoresonant three-oscillator interactions

    Yaakobi, O.; Friedland, L.; Henis, Z.

    2007-01-01

    An efficient control scheme of resonant three-oscillator interactions using an external chirped frequency drive is suggested. The approach is based on formation of a double phase-locked (autoresonant) state in the system, as the driving oscillation passes linear resonance with one of the interacting oscillators. When doubly phase locked, the amplitudes of the oscillators increase with time in proportion to the driving frequency deviation from the linear resonance. The stability of this phase-locked state and the effects of dissipation and of the initial three-oscillator frequency mismatch on the autoresonance are analyzed. The associated autoresonance threshold phenomenon in the driving amplitude is also discussed. In contrast to other nonlinear systems, driven, autoresonant three-oscillator excitations are independent of the sign of the driving frequency chirp rate

  1. Lepton asymmetry and neutrino oscillations interplay

    Kirilova, Daniela, E-mail: dani@astro.bas.bg [Bulgarian Academy of Sciences, Institute of Astronomy and NAO (Bulgaria)

    2013-03-15

    We discuss the interplay between lepton asymmetry L and {nu} oscillations in the early Universe. Neutrino oscillations may suppress or enhance previously existing L. On the other hand L is capable to suppress or enhance neutrino oscillations. The mechanism of L enhancement in MSW resonant {nu} oscillations in the early Universe is numerically analyzed. L cosmological effects through {nu} oscillations are discussed. We discuss how L may change the cosmological BBN constraints on neutrino and show that BBN model with {nu}{sub e}{r_reversible}{nu}{sub s} oscillations is extremely sensitive to L - it allows to obtain the most stringent constraints on L value. We discuss also the cosmological role of active-sterile {nu} mixing and L in connection with the indications about additional relativistic density in the early Universe, pointed out by BBN, CMB and LSS data and the analysis of global {nu} data.

  2. Synthetic Aperture Vector Flow Imaging

    Villagómez Hoyos, Carlos Armando

    The main objective of this project was to continue the development of a synthetic aperture vector flow estimator. This type of estimator is capable of overcoming two of the major limitations in conventional ultrasound systems: 1) the inability to scan large region of interest with high temporal......, this thesis showed that novel information can be obtained with vector velocity methods providing quantitative estimates of blood flow and insight into the complexity of the hemodynamics dynamics. This could give the clinician a new tool in assessment and treatment of a broad range of diseases....

  3. Synthetic Biology Guides Biofuel Production

    Michael R. Connor

    2010-01-01

    Full Text Available The advancement of microbial processes for the production of renewable liquid fuels has increased with concerns about the current fuel economy. The development of advanced biofuels in particular has risen to address some of the shortcomings of ethanol. These advanced fuels have chemical properties similar to petroleum-based liquid fuels, thus removing the need for engine modification or infrastructure redesign. While the productivity and titers of each of these processes remains to be improved, progress in synthetic biology has provided tools to guide the engineering of these processes through present and future challenges.

  4. A Survey on Forced Oscillations in Power System

    Ghorbaniparvar, Mohammadreza

    2016-01-01

    Oscillations in a power system can be categorized into free oscillations and forced oscillations. Many algorithms have been developed to estimate the modes of free oscillations in a power system. Recently, forced oscillations caught many attentions. Techniques are proposed to detect forced oscillations and locate their sources. In addition, forced oscillations may have negative impact on the estimation of mode and mode-shape if they are not properly accounted for. To improve the power system ...

  5. Phase-locked Josephson soliton oscillators

    Holst, T.; Hansen, Jørn Bindslev; Grønbech-Jensen, N.

    1991-01-01

    Detailed experimental characterization of the phase-locking at both DC and at microwave frequencies is presented for two closely spaced Josephson soliton (fluxon) oscillators. In the phase-locked state, the radiated microwave power exhibited an effective gain. With one common bias source......, a frequency tunability of the phase-locked oscillators up to 7% at 10 GHz was observed. The interacting soliton oscillators were modeled by two inductively coupled nonlinear transmission lines...

  6. Chimera States in Mechanical Oscillator Networks

    Martens, Erik Andreas; Thutupalli, Shashi; Fourrière, Antoine; Hallatschek, Oskar

    2013-01-01

    The synchronization of coupled oscillators is a fascinating manifestation of self-organization that nature uses to orchestrate essential processes of life, such as the beating of the heart. Although it was long thought that synchrony and disorder were mutually exclusive steady states for a network of identical oscillators, numerous theoretical studies in recent years have revealed the intriguing possibility of “chimera states,” in which the symmetry of the oscillator population is broken into...

  7. Oscillations of neutral B mesons systems

    Boucrot, J.

    1999-01-01

    The oscillation phenomenon in the neutral B mesons systems is now well established. The motivations and principles of the measurements are given; then the most recent results from the LEP experiments, the CDF collaboration at Fermilab and the SLD collaboration at SLAC are reviewed. The present world average of the $\\bd$ meson oscillation frequency is $\\dmd = 0.471 \\pm 0.016 \\ps$ and the lower limit on the $\\bs$ oscillation frequency is

  8. Recent Progress in Silicon Mems Oscillators

    2008-12-01

    MEMS oscillator. As shown, a MEMS resonator is connected to an IC. The reference oscillator, which is basically a transimpedance amplifier ...small size), and (3) DC bias voltage required to operate the resonators. As a result, instead of Colpitts or Pierce architecture, a transimpedence ... amplifier is typically used for sustain the oscillation. The frequency of the resonators is determined by both material properties and geometry of

  9. Cyanohydrin reactions enhance glycolytic oscillations in yeast

    Hald, Bjørn Olav; Nielsen, Astrid Gram; Tortzen, Christian

    2015-01-01

    Synchronous metabolic oscillations can be induced in yeast by addition of glucose and removal of extracellular acetaldehyde (ACAx). Compared to other means of ACAx removal, cyanide robustly induces oscillations, indicating additional cyanide reactions besides ACA to lactonitrile conversion. Here......: a) by reducing [ACAx] relative to oscillation amplitude, b) by targeting multiple intracellular carbonyl compounds during fermentation, and c) by acting as a phase resetting stimulus....

  10. Electrochemical Oscillation of Vanadium Ions in Anolyte

    Hao Peng

    2017-08-01

    Full Text Available Periodic electrochemical oscillation of the anolyte was reported for the first time in a simulated charging process of the vanadium redox flow batteries. The electrochemical oscillation could be explained in terms of the competition between the growth and the chemical dissolution of V2O5 film. Also, the oscillation phenomenon was possible to regular extra power consumption. The results of this paper might enable new methods to improve the charge efficiency and energy saving for vanadium redox flow batteries.

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

    Lihong Jiang

    2018-06-01

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

  12. The interaction of synthetic jets with turbulent boundary layers

    Cui, Jing

    In recent years, a promising approach to the control of wall bounded as well as free shear flows, using synthetic jet (oscillatory jet with zero-net-mass-flux) actuators, has received a great deal of attention. A variety of impressive flow control results have been achieved experimentally by many researchers including the vectoring of conventional propulsive jets, modification of aerodynamic characteristics of bluff bodies, control of lift and drag of airfoils, reduction of skin-friction of a flat plate boundary layer, enhanced mixing in circular jets, and control of external as well as internal flow separation and of cavity oscillations. More recently, attempts have been made to numerically simulate some of these flowfields. Numerically several of the above mentioned flow fields have been simulated primarily by employing the Unsteady Reynolds-Averaged Navier Stokes (URANS) equations with a turbulence model and a limited few by Direct Numerical Simulation (DNS). In simulations, both the simplified boundary conditions at the exit of the jet as well as the details of the cavity and lip have been included. In this dissertation, I describe the results of simulations for several two- and three-dimensional flowfields dealing with the interaction of a synthetic jet with a turbulent boundary layer and control of separation. These simulations have been performed using the URANS equations in conjunction with either one- or a two-equation turbulence model. 2D simulations correspond to the experiments performed by Honohan at Georgia Tech. and 3D simulations correspond to the CFD validation test cases proposed in the NASA Langley Research Center Workshop---"CFD Validation of Synthetic Jets and Turbulent Separation Control" held at Williamsburg VA in March 2004. The sources of uncertainty due to grid resolution, time step, boundary conditions, turbulence modeling etc. have been examined during the computations. Extensive comparisons for various flow variables are made with the

  13. Journal of Genetics | Indian Academy of Sciences

    Home; Journals; Journal of Genetics; Volume 87; Issue 5. Issue front cover thumbnail. Volume 87, Issue 5. December 2008, pages 435-519. Special issue - Circadian rhythms: from genes to behaviour. pp 435-436. Preface · Vijay K. Sharma Robert J. Lucas · More Details Fulltext PDF. pp 437-446 Review Article. Oscillating ...

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

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

    2011-01-01

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

  15. Cardiogenic oscillation induced ventilator autotriggering

    Narender Kaloria

    2015-01-01

    Full Text Available Cardiogenic oscillation during mechanical ventilation can auto-trigger the ventilator resembling patient initiated breadth. This gives a false sense of intact respiratory drive and determination brain death, even if other tests are positive, is not appropriate in such a situation. It will prolong the ICU stay and confound the brain-death determination. In this case report, we describe a 35 year old man who was brought to the hospital after many hours of critical delay following multiple gun shot injuries. The patient suffered a cardiac arrest while on the way from another hospital. After an emergency laparotomy, patient was shifted to Intensive Care Unit (ICU with Glasgow Coma Scale (GCS score of E1VTM1 and was mechanically ventilated. Despite absence of brainstem reflexes, the ventilator continued to be triggered on continuous positive airway pressure (CPAP mode and the patient maintained normal oxygen saturation and acceptable levels of carbon dioxide. An apnoea test confirmed absent respiratory drive. Ventilatory waveform graph analysis, revealed cardiogenic oscillation as the cause for autotrigerring.

  16. Energy measurements from betatron oscillations

    Himel, T.; Thompson, K.

    1989-03-01

    In the Stanford Linear Collider the electron beam is accelerated from 1--50 GeV in a distance of 3 km. The energy is measured and corrected at the end with an energy feedback loop. There are no bends within the linear accelerator itself, so no intermediate energy measurements are made. Errors in the energy profile due to mis-phasing of the rf, or due to calibration errors in the klystrons' rf outputs are difficult to detect. As the total betatron phase advance down the accelerator is about 30 /times/ 2π, an energy error of a few percent can cause a large error in the total phase advance. This in turn degrades the performance of auto-steering programs. We have developed a diagnostic program which generates and measures several betatron oscillations in the accelerator. It then analyzes this oscillation, looking for frequency changes which indicate energy errors. One can then compensate for or correct these energy errors. 6 refs., 1 fig

  17. Stochastic Kuramoto oscillators with discrete phase states

    Jörg, David J.

    2017-09-01

    We present a generalization of the Kuramoto phase oscillator model in which phases advance in discrete phase increments through Poisson processes, rendering both intrinsic oscillations and coupling inherently stochastic. We study the effects of phase discretization on the synchronization and precision properties of the coupled system both analytically and numerically. Remarkably, many key observables such as the steady-state synchrony and the quality of oscillations show distinct extrema while converging to the classical Kuramoto model in the limit of a continuous phase. The phase-discretized model provides a general framework for coupled oscillations in a Markov chain setting.

  18. Stochastic Kuramoto oscillators with discrete phase states.

    Jörg, David J

    2017-09-01

    We present a generalization of the Kuramoto phase oscillator model in which phases advance in discrete phase increments through Poisson processes, rendering both intrinsic oscillations and coupling inherently stochastic. We study the effects of phase discretization on the synchronization and precision properties of the coupled system both analytically and numerically. Remarkably, many key observables such as the steady-state synchrony and the quality of oscillations show distinct extrema while converging to the classical Kuramoto model in the limit of a continuous phase. The phase-discretized model provides a general framework for coupled oscillations in a Markov chain setting.

  19. Optimal parameters uncoupling vibration modes of oscillators

    Le, K. C.; Pieper, A.

    2017-07-01

    This paper proposes a novel optimization concept for an oscillator with two degrees of freedom. By using specially defined motion ratios, we control the action of springs to each degree of freedom of the oscillator. We aim at showing that, if the potential action of the springs in one period of vibration, used as the payoff function for the conservative oscillator, is maximized among all admissible parameters and motions satisfying Lagrange's equations, then the optimal motion ratios uncouple vibration modes. A similar result holds true for the dissipative oscillator having dampers. The application to optimal design of vehicle suspension is discussed.

  20. Neuromorphic computing with nanoscale spintronic oscillators.

    Torrejon, Jacob; Riou, Mathieu; Araujo, Flavio Abreu; Tsunegi, Sumito; Khalsa, Guru; Querlioz, Damien; Bortolotti, Paolo; Cros, Vincent; Yakushiji, Kay; Fukushima, Akio; Kubota, Hitoshi; Yuasa, Shinji; Stiles, Mark D; Grollier, Julie

    2017-07-26

    Neurons in the brain behave as nonlinear oscillators, which develop rhythmic activity and interact to process information. Taking inspiration from this behaviour to realize high-density, low-power neuromorphic computing will require very large numbers of nanoscale nonlinear oscillators. A simple estimation indicates that to fit 10 8 oscillators organized in a two-dimensional array inside a chip the size of a thumb, the lateral dimension of each oscillator must be smaller than one micrometre. However, nanoscale devices tend to be noisy and to lack the stability that is required to process data in a reliable way. For this reason, despite multiple theoretical proposals and several candidates, including memristive and superconducting oscillators, a proof of concept of neuromorphic computing using nanoscale oscillators has yet to be demonstrated. Here we show experimentally that a nanoscale spintronic oscillator (a magnetic tunnel junction) can be used to achieve spoken-digit recognition with an accuracy similar to that of state-of-the-art neural networks. We also determine the regime of magnetization dynamics that leads to the greatest performance. These results, combined with the ability of the spintronic oscillators to interact with each other, and their long lifetime and low energy consumption, open up a path to fast, parallel, on-chip computation based on networks of oscillators.

  1. Introduction to classical and quantum harmonic oscillators

    Bloch, Sylvan C

    2013-01-01

    From conch shells to lasers . harmonic oscillators, the timeless scientific phenomenon As intriguing to Galileo as they are to scientists today, harmonic oscillators have provided a simple and compelling paradigm for understanding the complexities that underlie some of nature's and mankind's most fascinating creations. From early string and wind instruments fashioned from bows and seashells to the intense precision of lasers, harmonic oscillators have existed in various forms, as objects of beauty and scientific use. And harmonic oscillation has endured as one of science's most fascinating con

  2. Theory of a quantum anharmonic oscillator

    Carusotto, S.

    1988-01-01

    The time evolution of a quantum single-quartic anharmonic oscillator is considered. The study is carried on in operational form by use of the raising and lowering operators of the oscillator. The equation of motion is solved by application of a new integration method based on iteration techniques, and the rigorous solutions that describe the time development of the displacement and momentum operators of the oscillator are obtained. These operators are presented as a Laplace transform and a subsequent inverse Laplace transform of suitable functionals. Finally, the results are employed to describe the time evolution of a quasiclassical anharmonic oscillator

  3. Waves and oscillations in nature an introduction

    Narayanan, A Satya

    2015-01-01

    Waves and oscillations are found in large scales (galactic) and microscopic scales (neutrino) in nature. Their dynamics and behavior heavily depend on the type of medium through which they propagate.Waves and Oscillations in Nature: An Introduction clearly elucidates the dynamics and behavior of waves and oscillations in various mediums. It presents different types of waves and oscillations that can be observed and studied from macroscopic to microscopic scales. The book provides a thorough introduction for researchers and graduate students in assorted areas of physics, such as fluid dynamics,

  4. Tracking the emergence of synthetic biology.

    Shapira, Philip; Kwon, Seokbeom; Youtie, Jan

    2017-01-01

    Synthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research, innovation, and policy interest in recent years. This paper contributes to efforts to delineate this emerging domain by presenting a newly constructed bibliometric definition of synthetic biology. Our approach is dimensioned from a core set of papers in synthetic biology, using procedures to obtain benchmark synthetic biology publication records, extract keywords from these benchmark records, and refine the keywords, supplemented with articles published in dedicated synthetic biology journals. We compare our search strategy with other recent bibliometric approaches to define synthetic biology, using a common source of publication data for the period from 2000 to 2015. The paper details the rapid growth and international spread of research in synthetic biology in recent years, demonstrates that diverse research disciplines are contributing to the multidisciplinary development of synthetic biology research, and visualizes this by profiling synthetic biology research on the map of science. We further show the roles of a relatively concentrated set of research sponsors in funding the growth and trajectories of synthetic biology. In addition to discussing these analyses, the paper notes limitations and suggests lines for further work.

  5. DNA recognition by synthetic constructs.

    Pazos, Elena; Mosquera, Jesús; Vázquez, M Eugenio; Mascareñas, José L

    2011-09-05

    The interaction of transcription factors with specific DNA sites is key for the regulation of gene expression. Despite the availability of a large body of structural data on protein-DNA complexes, we are still far from fully understanding the molecular and biophysical bases underlying such interactions. Therefore, the development of non-natural agents that can reproduce the DNA-recognition properties of natural transcription factors remains a major and challenging goal in chemical biology. In this review we summarize the basics of double-stranded DNA recognition by transcription factors, and describe recent developments in the design and preparation of synthetic DNA binders. We mainly focus on synthetic peptides that have been designed by following the DNA interaction of natural proteins, and we discuss how the tools of organic synthesis can be used to make artificial constructs equipped with functionalities that introduce additional properties to the recognition process, such as sensing and controllability. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Synthetic Biology of Polyhydroxyalkanoates (PHA).

    Meng, De-Chuan; Chen, Guo-Qiang

    Microbial polyhydroxyalkanoates (PHA) are a family of biodegradable and biocompatible polyesters which have been extensively studied using synthetic biology and metabolic engineering methods for improving production and for widening its diversity. Synthetic biology has allowed PHA to become composition controllable random copolymers, homopolymers, and block copolymers. Recent developments showed that it is possible to establish a microbial platform for producing not only random copolymers with controllable monomers and their ratios but also structurally defined homopolymers and block copolymers. This was achieved by engineering the genome of Pseudomonas putida or Pseudomonas entomophiles to weaken the β-oxidation and in situ fatty acid synthesis pathways, so that a fatty acid fed to the bacteria maintains its original chain length and structures when incorporated into the PHA chains. The engineered bacterium allows functional groups in a fatty acid to be introduced into PHA, forming functional PHA, which, upon grafting, generates endless PHA variety. Recombinant Escherichia coli also succeeded in producing efficiently poly(3-hydroxypropionate) or P3HP, the strongest member of PHA. Synthesis pathways of P3HP and its copolymer P3HB3HP of 3-hydroxybutyrate and 3-hydroxypropionate were assembled respectively to allow their synthesis from glucose. CRISPRi was also successfully used to manipulate simultaneously multiple genes and control metabolic flux in E. coli to obtain a series of copolymer P3HB4HB of 3-hydroxybutyrate (3HB) and 4-hydroxybutyrate (4HB). The bacterial shapes were successfully engineered for enhanced PHA accumulation.

  7. Vectoring of parallel synthetic jets

    Berk, Tim; Ganapathisubramani, Bharathram; Gomit, Guillaume

    2015-11-01

    A pair of parallel synthetic jets can be vectored by applying a phase difference between the two driving signals. The resulting jet can be merged or bifurcated and either vectored towards the actuator leading in phase or the actuator lagging in phase. In the present study, the influence of phase difference and Strouhal number on the vectoring behaviour is examined experimentally. Phase-locked vorticity fields, measured using Particle Image Velocimetry (PIV), are used to track vortex pairs. The physical mechanisms that explain the diversity in vectoring behaviour are observed based on the vortex trajectories. For a fixed phase difference, the vectoring behaviour is shown to be primarily influenced by pinch-off time of vortex rings generated by the synthetic jets. Beyond a certain formation number, the pinch-off timescale becomes invariant. In this region, the vectoring behaviour is determined by the distance between subsequent vortex rings. We acknowledge the financial support from the European Research Council (ERC grant agreement no. 277472).

  8. Synthetic membrane-targeted antibiotics.

    Vooturi, S K; Firestine, S M

    2010-01-01

    Antimicrobial resistance continues to evolve and presents serious challenges in the therapy of both nosocomial and community-acquired infections. The rise of resistant strains like methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Staphylococcus aureus (VRSA) and vancomycin-resistant enterococci (VRE) suggests that antimicrobial resistance is an inevitable evolutionary response to antimicrobial use. This highlights the tremendous need for antibiotics against new bacterial targets. Agents that target the integrity of bacterial membrane are relatively novel in the clinical armamentarium. Daptomycin, a lipopeptide is a classical example of membrane-bound antibiotic. Nature has also utilized this tactic. Antimicrobial peptides (AMPs), which are found in all kingdoms, function primarily by permeabilizing the bacterial membrane. AMPs have several advantages over existing antibiotics including a broad spectrum of activity, rapid bactericidal activity, no cross-resistance with the existing antibiotics and a low probability for developing resistance. Currently, a small number of peptides have been developed for clinical use but therapeutic applications are limited because of poor bioavailability and high manufacturing cost. However, their broad specificity, potent activity and lower probability for resistance have spurred the search for synthetic mimetics of antimicrobial peptides as membrane-active antibiotics. In this review, we will discuss the different classes of synthetic membrane-bound antibiotics published since 2004.

  9. Synthetic vision display evaluation studies

    Regal, David M.; Whittington, David H.

    1994-01-01

    The goal of this research was to help us understand the display requirements for a synthetic vision system for the High Speed Civil Transport (HSCT). Four experiments were conducted to examine the effects of different levels of perceptual cue complexity in displays used by pilots in a flare and landing task. Increased levels of texture mapping of terrain and runway produced mixed results, including harder but shorter landings and a lower flare initiation altitude. Under higher workload conditions, increased texture resulted in an improvement in performance. An increase in familiar size cues did not result in improved performance. Only a small difference was found between displays using two patterns of high resolution texture mapping. The effects of increased perceptual cue complexity on performance was not as strong as would be predicted from the pilot's subjective reports or from related literature. A description of the role of a synthetic vision system in the High Speed Civil Transport is provide along with a literature review covering applied research related to perceptual cue usage in aircraft displays.

  10. Oscillations of Difference Equations with Several Oscillating Coefficients

    L. Berezansky

    2014-01-01

    Full Text Available We study the oscillatory behavior of the solutions of the difference equation Δx(n+∑i=1mpi(nx(τi(n=0,n∈N0[∇xn-∑i=1mpinxσin=0, n∈N] where (pi(n, 1≤i≤m are real sequences with oscillating terms, τi(n[σi(n], 1≤i≤m are general retarded (advanced arguments, and Δ[∇] denotes the forward (backward difference operator Δx(n=x(n+1-x(n[∇x(n=x(n-x(n-1]. Examples illustrating the results are also given.

  11. Experimental dynamical characterization of five autonomous chaotic oscillators with tunable series resistance

    Minati, Ludovico, E-mail: lminati@ieee.org, E-mail: ludovico.minati@unitn.it [MR-Lab, Center for Mind/Brain Science, University of Trento, Trento, Italy and Scientific Department, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan (Italy)

    2014-09-01

    In this paper, an experimental characterization of the dynamical properties of five autonomous chaotic oscillators, based on bipolar-junction transistors and obtained de-novo through a genetic algorithm in a previous study, is presented. In these circuits, a variable resistor connected in series to the DC voltage source acts as control parameter, for a range of which the largest Lyapunov exponent, correlation dimension, approximate entropy, and amplitude variance asymmetry are calculated, alongside bifurcation diagrams and spectrograms. Numerical simulations are compared to experimental measurements. The oscillators can generate a considerable variety of regular and chaotic sine-like and spike-like signals.

  12. Circuit oscillations in odor perception and memory.

    Kay, Leslie M

    2014-01-01

    Olfactory system neural oscillations as seen in the local field potential have been studied for many decades. Recent research has shown that there is a functional role for the most studied gamma oscillations (40-100Hz in rats and mice, and 20Hz in insects), without which fine odor discrimination is poor. When these oscillations are increased artificially, fine discrimination is increased, and when rats learn difficult and highly overlapping odor discriminations, gamma is increased in power. Because of the depth of study on this oscillation, it is possible to point to specific changes in neural firing patterns as represented by the increase in gamma oscillation amplitude. However, we know far less about the mechanisms governing beta oscillations (15-30Hz in rats and mice), which are best associated with associative learning of responses to odor stimuli. These oscillations engage every part of the olfactory system that has so far been tested, plus the hippocampus, and the beta oscillation frequency band is the one that is most reliably coherent with other regions during odor processing. Respiratory oscillations overlapping with the theta frequency band (2-12Hz) are associated with odor sniffing and normal breathing in rats. They also show coupling in some circumstances between olfactory areas and rare coupling between the hippocampus and olfactory bulb. The latter occur in specific learning conditions in which coherence strength is negatively or positively correlated with performance, depending on the task. There is still much to learn about the role of neural oscillations in learning and memory, but techniques that have been brought to bear on gamma oscillations (current source density, computational modeling, slice physiology, behavioral studies) should deliver much needed knowledge of these events. © 2014 Elsevier B.V. All rights reserved.

  13. Word selection affects perceptions of synthetic biology

    Tonidandel Scott

    2011-07-01

    Full Text Available Abstract Members of the synthetic biology community have discussed the significance of word selection when describing synthetic biology to the general public. In particular, many leaders proposed the word "create" was laden with negative connotations. We found that word choice and framing does affect public perception of synthetic biology. In a controlled experiment, participants perceived synthetic biology more negatively when "create" was used to describe the field compared to "construct" (p = 0.008. Contrary to popular opinion among synthetic biologists, however, low religiosity individuals were more influenced negatively by the framing manipulation than high religiosity people. Our results suggest that synthetic biologists directly influence public perception of their field through avoidance of the word "create".

  14. Creating biological nanomaterials using synthetic biology

    Rice, MaryJoe K; Ruder, Warren C

    2014-01-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems. (review)

  15. Creating biological nanomaterials using synthetic biology.

    Rice, MaryJoe K; Ruder, Warren C

    2014-02-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

  16. Coherent Performance Analysis of the HJ-1-C Synthetic Aperture Radar

    Li Hai-ying

    2014-06-01

    Full Text Available Synthetic Aperture Radar (SAR is a coherent imaging radar. Hence, coherence is critical in SAR imaging. In a coherent system, several sources can degrade performance. Based on the HJ-1-C SAR system implementation and sensor characteristics, this study evaluates the effect of frequency stability and pulse-to-pulse timing jitter on the SAR coherent performance. A stable crystal oscillator with short-term stability of 10×1.0−10 / 5 ms is used to generate the reference frequency by using a direct multiplier and divider. Azimuth ISLR degradation owing to the crystal oscillator phase noise is negligible. The standard deviation of the pulse-to-pulse timing jitter of HJ-1-C SAR is lower than 2ns (rms and the azimuth random phase error in the synthetic aperture time slightly degrades the side lobe of the azimuth impulse response. The mathematical expressions and simulation results are presented and suggest that the coherent performance of the HJ-1-C SAR system meets the requirements of synthetic aperture radar imaging.

  17. Phage Therapy in the Era of Synthetic Biology.

    Barbu, E Magda; Cady, Kyle C; Hubby, Bolyn

    2016-10-03

    For more than a century, bacteriophage (or phage) research has enabled some of the most important discoveries in biological sciences and has equipped scientists with many of the molecular biology tools that have advanced our understanding of replication, maintenance, and expression of genetic material. Phages have also been recognized and exploited as natural antimicrobial agents and nanovectors for gene therapy, but their potential as therapeutics has not been fully exploited in Western medicine because of challenges such as narrow host range, bacterial resistance, and unique pharmacokinetics. However, increasing concern related to the emergence of bacteria resistant to multiple antibiotics has heightened interest in phage therapy and the development of strategies to overcome hurdles associated with bacteriophage therapeutics. Recent progress in sequencing technologies, DNA manipulation, and synthetic biology allowed scientists to refactor the entire bacterial genome of Mycoplasma mycoides, thereby creating the first synthetic cell. These new strategies for engineering genomes may have the potential to accelerate the construction of designer phage genomes with superior therapeutic potential. Here, we discuss the use of phage as therapeutics, as well as how synthetic biology can create bacteriophage with desirable attributes. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

  18. Genetically Engineering Entomopathogenic Fungi.

    Zhao, H; Lovett, B; Fang, W

    2016-01-01

    Entomopathogenic fungi have been developed as environmentally friendly alternatives to chemical insecticides in biocontrol programs for agricultural pests and vectors of disease. However, mycoinsecticides currently have a small market share due to low virulence and inconsistencies in their performance. Genetic engineering has made it possible to significantly improve the virulence of fungi and their tolerance to adverse conditions. Virulence enhancement has been achieved by engineering fungi to express insect proteins and insecticidal proteins/peptides from insect predators and other insect pathogens, or by overexpressing the pathogen's own genes. Importantly, protein engineering can be used to mix and match functional domains from diverse genes sourced from entomopathogenic fungi and other organisms, producing insecticidal proteins with novel characteristics. Fungal tolerance to abiotic stresses, especially UV radiation, has been greatly improved by introducing into entomopathogens a photoreactivation system from an archaean and pigment synthesis pathways from nonentomopathogenic fungi. Conversely, gene knockout strategies have produced strains with reduced ecological fitness as recipients for genetic engineering to improve virulence; the resulting strains are hypervirulent, but will not persist in the environment. Coupled with their natural insect specificity, safety concerns can also be mitigated by using safe effector proteins with selection marker genes removed after transformation. With the increasing public concern over the continued use of synthetic chemical insecticides and growing public acceptance of genetically modified organisms, new types of biological insecticides produced by genetic engineering offer a range of environmentally friendly options for cost-effective control of insect pests. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Synthetic approaches to uniform polymers.

    Ali, Monzur; Brocchini, Steve

    2006-12-30

    Uniform polymers are characterised by a narrow molecular weight distribution (MWD). Uniformity is also defined by chemical structure in respect of (1) monomer orientation, sequence and stereo-regularity, (2) polymer shape and morphology and (3) chemical functionality. The function of natural polymers such as polypeptides and polynucleotides is related to their conformational structure (e.g. folded tertiary structure). This is only possible because of their high degree of uniformity. While completely uniform synthetic polymers are rare, polymers with broad structure and MWD are widely used in medicine and the biomedical sciences. They are integral components in final dosage forms, drug delivery systems (DDS) and in implantable devices. Increasingly uniform polymers are being used to develop more complex medicines (e.g. delivery of biopharmaceuticals, enhanced formulations or DDS's for existing actives). In addition to the function imparted by any new polymer it will be required to meet stringent specifications in terms of cost containment, scalability, biocompatibility and performance. Synthetic polymers with therapeutic activity are also being developed to exploit their polyvalent properties, which is not possible with low molecular weight molecules. There is need to utilise uniform polymers for applications where the polymer may interact with the systemic circulation, tissues or cellular environment. There are also potential applications (e.g. stimuli responsive coatings) where uniform polymers may be used for their more defined property profile. While it is not yet practical to prepare synthetic polymers to the same high degree of uniformity as proteins, nature also effectively utilises many polymers with lower degrees of uniformity (e.g. polysaccharides, poly(amino acids), polyhydroxyalkanoates). In recent years it has become possible to prepare with practical experimental protocols sufficient quantities of polymers that display many aspects of uniformity. This

  20. Synthetic Lipoproteins as Carriers for Drug Delivery.

    Huang, Gangliang; Liu, Yang; Huang, Hualiang

    2016-01-01

    Synthetic lipoprotein is an effective carrier of targeted delivery for drugs. It has the very small size, good biocompatibility, suitable half-life, and specific lipoprotein receptorbinding capacity. Compared with the traditional natural lipoprotein, synthetic lipoprotein not only retains the original biological characteristics and functions, but also exhibits the excellent characteristics in drug delivery. Herein, the advantages, development, applications, and prospect of synthetic lipoproteins as drug carriers were summarized.