A high speed, wide dynamic range digitizer circuit for photomultiplier tubes

International Nuclear Information System (INIS)

Yarema, R.J.; Foster, G.W.; Knickerbocker, K.; Sarraj, M.; Tschirhart, R.; Whitmore, J.; Zimmerman, T.; Lindgren, M.

1995-01-01

A circuit has been designed for digitizing PMT signals over a wide dynamic range (17-18 bits) with 8 bits of resolution at rates up to 53 MHz. Output from the circuit is in a floating point format with a 4 bit exponent and an 8 bit mantissa. The heart of the circuit is a full custom integrated circuit called the QIE (Charge Integrator and Encoder). The design of the QIE and associated circuitry reported here permits operation over a 17 bit dynamic range. Test results of a multirange device are presented for the first time. (orig.)

Nonlinear dynamics based digital logic and circuits.

Science.gov (United States)

Kia, Behnam; Lindner, John F; Ditto, William L

2015-01-01

We discuss the role and importance of dynamics in the brain and biological neural networks and argue that dynamics is one of the main missing elements in conventional Boolean logic and circuits. We summarize a simple dynamics based computing method, and categorize different techniques that we have introduced to realize logic, functionality, and programmability. We discuss the role and importance of coupled dynamics in networks of biological excitable cells, and then review our simple coupled dynamics based method for computing. In this paper, for the first time, we show how dynamics can be used and programmed to implement computation in any given base, including but not limited to base two.

A high speed, wide dynamic range digitizer circuit for photomultiplier tubes

Energy Technology Data Exchange (ETDEWEB)

Yarema, R.J.; Foster, G.W.; Knickerbocker, K.; Sarraj, M.; Tschirhart, R.; Whitmore, J.; Zimmerman, T. [Fermi National Accelerator Lab., Batavia, IL (United States); Lindgren, M. [Univ. of California, Los Angeles, CA (United States). Physics Dept.

1994-06-01

High energy physics experiments running at high interaction rates frequently require long record lengths for determining a level 1 trigger. The easiest way to provide a long event record is by digital means. In applications requiring wide dynamic range, however, digitization of an analog signal to obtain the digital record has been impossible due to lack of high speed, wide range FADCs. One such application is the readout of thousands of photomultiplier tubes in fixed target and colliding beam experiment calorimeters. A circuit has been designed for digitizing PMT signals over a wide dynamic range (17--18 bits) with 8 bits of resolution at rates up to 53 MHz. Output from the circuit is in a floating point format with a 4 bit exponent and an 8 bit mantissa. The heart of the circuit is a full custom integrated circuit called the QIE (Charge Integrator and Encoder). The design of the QIE and associated circuitry reported here permits operation over a 17 bit dynamic range. Tests of the circuit with a PMT input and a pulsed laser have provided respectable results with little off line correction. Performance of the circuit for demanding applications can be significantly enhanced with additional off line correction. Circuit design, packaging issues, and test results of a multirange device are presented for the first time.

A high speed, wide dynamic range digitizer circuit for photomultiplier tubes

International Nuclear Information System (INIS)

Yarema, R.J.; Foster, G.W.; Knickerbocker, K.; Sarraj, M.; Tschirhart, R.; Whitmore, J.; Zimmerman, T.; Lindgren, M.

1994-06-01

High energy physics experiments running at high interaction rates frequently require long record lengths for determining a level 1 trigger. The easiest way to provide a long event record is by digital means. In applications requiring wide dynamic range, however, digitization of an analog signal to obtain the digital record has been impossible due to lack of high speed, wide range FADCs. One such application is the readout of thousands of photomultiplier tubes in fixed target and colliding beam experiment calorimeters. A circuit has been designed for digitizing PMT signals over a wide dynamic range (17--18 bits) with 8 bits of resolution at rates up to 53 MHz. Output from the circuit is in a floating point format with a 4 bit exponent and an 8 bit mantissa. The heart of the circuit is a full custom integrated circuit called the QIE (Charge Integrator and Encoder). The design of the QIE and associated circuitry reported here permits operation over a 17 bit dynamic range. Tests of the circuit with a PMT input and a pulsed laser have provided respectable results with little off line correction. Performance of the circuit for demanding applications can be significantly enhanced with additional off line correction. Circuit design, packaging issues, and test results of a multirange device are presented for the first time

Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming

Science.gov (United States)

Huynh, Linh; Kececioglu, John; Köppe, Matthias; Tagkopoulos, Ilias

2012-01-01

Automatic design of synthetic gene circuits poses a significant challenge to synthetic biology, primarily due to the complexity of biological systems, and the lack of rigorous optimization methods that can cope with the combinatorial explosion as the number of biological parts increases. Current optimization methods for synthetic gene design rely on heuristic algorithms that are usually not deterministic, deliver sub-optimal solutions, and provide no guaranties on convergence or error bounds. Here, we introduce an optimization framework for the problem of part selection in synthetic gene circuits that is based on mixed integer non-linear programming (MINLP), which is a deterministic method that finds the globally optimal solution and guarantees convergence in finite time. Given a synthetic gene circuit, a library of characterized parts, and user-defined constraints, our method can find the optimal selection of parts that satisfy the constraints and best approximates the objective function given by the user. We evaluated the proposed method in the design of three synthetic circuits (a toggle switch, a transcriptional cascade, and a band detector), with both experimentally constructed and synthetic promoter libraries. Scalability and robustness analysis shows that the proposed framework scales well with the library size and the solution space. The work described here is a step towards a unifying, realistic framework for the automated design of biological circuits. PMID:22536398

Composite dynamical behaviors in a simple series–parallel LC circuit

International Nuclear Information System (INIS)

Manimehan, I.; Philominathan, P.

2012-01-01

Highlights: ► We have presented a simple circuit exhibiting rich dynamical behaviors. ► The detailed study of the circuit is given by two parameter bifurcation diagram. ► The numerical, analytical and experimental results are good in agreement. ► The Chosen system seems to have potential application in future. - Abstract: In this paper, we report a variety of dynamical behaviors exhibited in a compact series–parallel LC circuit system comprising of two active elements, one linear negative conductance and one ordinary junction diode with piecewise linear v − i characteristics. For convenience, we consider the amplitude (E f ) and frequency (f) of the driving force as control parameters amongst various other parameters. We observe the phenomenon of antimonotonicity, torus breakdown to chaos, bubbles to chaos, period doubling to chaos and emergence of multiple attractors which follow a progressive sequence, etc. As an overview to understand many more variety of bifurcations and attractors, the construction of two parameter phase diagram is also shown pictorially. The chaotic dynamics of this circuit is realized by laboratory experiment, numerical and analytical investigations and found that the results are in good agreement with each other.

Self-powered 'AND' logic circuit of dynamic type with positive safety and application of said 'AND' circuit

International Nuclear Information System (INIS)

Lefebvre, Claude; Therond, J.P.

1974-01-01

The present invention relates to a self-powered 'AND' logic circuit of dynamic type with positive safety, which delivers on duty operation an output signal equal to the logic product of the input logic signals. The invention relates also to the use of said 'AND' logic circuits in developing n/m logics also of dynamic types with positive safety, delivering on duty operation a zero valued signal when, at least n of the m input signals have the value zero. This type of logics can be inserted in nuclear reactor protection systems; when the value of the reactor operating physical characteristics go out of the safety margins, or true trouble affects 'AND' circuits the value of the output signal is zero, that triggers off the safety absorber drap, for instance [fr

Complex dynamics of memristive circuits: Analytical results and universal slow relaxation

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Caravelli, F.; Traversa, F. L.; Di Ventra, M.

2017-02-01

Networks with memristive elements (resistors with memory) are being explored for a variety of applications ranging from unconventional computing to models of the brain. However, analytical results that highlight the role of the graph connectivity on the memory dynamics are still few, thus limiting our understanding of these important dynamical systems. In this paper, we derive an exact matrix equation of motion that takes into account all the network constraints of a purely memristive circuit, and we employ it to derive analytical results regarding its relaxation properties. We are able to describe the memory evolution in terms of orthogonal projection operators onto the subspace of fundamental loop space of the underlying circuit. This orthogonal projection explicitly reveals the coupling between the spatial and temporal sectors of the memristive circuits and compactly describes the circuit topology. For the case of disordered graphs, we are able to explain the emergence of a power-law relaxation as a superposition of exponential relaxation times with a broad range of scales using random matrices. This power law is also universal, namely independent of the topology of the underlying graph but dependent only on the density of loops. In the case of circuits subject to alternating voltage instead, we are able to obtain an approximate solution of the dynamics, which is tested against a specific network topology. These results suggest a much richer dynamics of memristive networks than previously considered.

High-speed dynamic domino circuit implemented with gaas mesfets

Science.gov (United States)

Yang, Long (Inventor); Long, Stephen I. (Inventor)

1990-01-01

A dynamic logic circuit (AND or OR) utilizes one depletion-mode metal-semiconductor FET for precharging an internal node A, and a plurality of the same type of FETs in series, or a FET in parallel with one or more of the series connected FETs for implementing the logic function. A pair of FETs are connected to provide an output inverter with two series diodes for level shift. A coupling capacitor may be employed with a further FET to provide level shifting required between the inverter and the logic circuit output terminal. These circuits may be cascaded to form a domino chain.

Integrated genomic and gene expression profiling identifies two major genomic circuits in urothelial carcinoma.

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David Lindgren

Full Text Available Similar to other malignancies, urothelial carcinoma (UC is characterized by specific recurrent chromosomal aberrations and gene mutations. However, the interconnection between specific genomic alterations, and how patterns of chromosomal alterations adhere to different molecular subgroups of UC, is less clear. We applied tiling resolution array CGH to 146 cases of UC and identified a number of regions harboring recurrent focal genomic amplifications and deletions. Several potential oncogenes were included in the amplified regions, including known oncogenes like E2F3, CCND1, and CCNE1, as well as new candidate genes, such as SETDB1 (1q21, and BCL2L1 (20q11. We next combined genome profiling with global gene expression, gene mutation, and protein expression data and identified two major genomic circuits operating in urothelial carcinoma. The first circuit was characterized by FGFR3 alterations, overexpression of CCND1, and 9q and CDKN2A deletions. The second circuit was defined by E3F3 amplifications and RB1 deletions, as well as gains of 5p, deletions at PTEN and 2q36, 16q, 20q, and elevated CDKN2A levels. TP53/MDM2 alterations were common for advanced tumors within the two circuits. Our data also suggest a possible RAS/RAF circuit. The tumors with worst prognosis showed a gene expression profile that indicated a keratinized phenotype. Taken together, our integrative approach revealed at least two separate networks of genomic alterations linked to the molecular diversity seen in UC, and that these circuits may reflect distinct pathways of tumor development.

Modular design of synthetic gene circuits with biological parts and pools.

Science.gov (United States)

Marchisio, Mario Andrea

2015-01-01

Synthetic gene circuits can be designed in an electronic fashion by displaying their basic components-Standard Biological Parts and Pools of molecules-on the computer screen and connecting them with hypothetical wires. This procedure, achieved by our add-on for the software ProMoT, was successfully applied to bacterial circuits. Recently, we have extended this design-methodology to eukaryotic cells. Here, highly complex components such as promoters and Pools of mRNA contain hundreds of species and reactions whose calculation demands a rule-based modeling approach. We showed how to build such complex modules via the joint employment of the software BioNetGen (rule-based modeling) and ProMoT (modularization). In this chapter, we illustrate how to utilize our computational tool for synthetic biology with the in silico implementation of a simple eukaryotic gene circuit that performs the logic AND operation.

Optoisolation circuits nonlinearity applications in engineering : optoisolation nonlinear dynamics and chaos, application in engineering

CERN Document Server

Aluf, Ofer

2012-01-01

This book describes a new concept in analyzing circuits, which includes optoisolation elements. The analysis is based on nonlinear dynamics and chaos models and shows comprehensive benefits and results. All conceptual optoisolation circuits are innovative and can be broadly implemented in engineering applications. The dynamics of optoisolation circuits provides several ways to use them in a variety of applications covering wide areas. The presentation fills the gap of analytical methods for optoisolation circuits analysis, concrete examples, and geometric examples. The optoisolation circuits analysis is developed systematically, starting with basic optoisolation circuits differential equations and their bifurcations, followed by Fixed points analysis, limit cycles and their bifurcations. Optoisolation circuits can be characterized as Lorenz equations, chaos, iterated maps, period doubling and attractors. This book is aimed at electrical and electronic engineers, students and researchers in physics as well. A ...

pTRA - A reporter system for monitoring the intracellular dynamics of gene expression.

Science.gov (United States)

Wagner, Sabine G; Ziegler, Martin; Löwe, Hannes; Kremling, Andreas; Pflüger-Grau, Katharina

2018-01-01

The presence of standardised tools and methods to measure and represent accurately biological parts and functions is a prerequisite for successful metabolic engineering and crucial to understand and predict the behaviour of synthetic genetic circuits. Many synthetic gene networks are based on transcriptional circuits, thus information on transcriptional and translational activity is important for understanding and fine-tuning the synthetic function. To this end, we have developed a toolkit to analyse systematically the transcriptional and translational activity of a specific synthetic part in vivo. It is based on the plasmid pTRA and allows the assignment of specific transcriptional and translational outputs to the gene(s) of interest (GOI) and to compare different genetic setups. By this, the optimal combination of transcriptional strength and translational activity can be identified. The design is tested in a case study using the gene encoding the fluorescent mCherry protein as GOI. We show the intracellular dynamics of mRNA and protein formation and discuss the potential and shortcomings of the pTRA plasmid.

Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels.

Science.gov (United States)

Steinacher, Arno; Bates, Declan G; Akman, Ozgur E; Soyer, Orkun S

2016-01-01

the ubiquity of nonlinear dynamics in gene expression networks, and generate useful guidelines for the design of synthetic gene circuits.

Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels.

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Arno Steinacher

an explanation for the ubiquity of nonlinear dynamics in gene expression networks, and generate useful guidelines for the design of synthetic gene circuits.

Chaotic dynamics with high complexity in a simplified new nonautonomous nonlinear electronic circuit

International Nuclear Information System (INIS)

Arulgnanam, A.; Thamilmaran, K.; Daniel, M.

2009-01-01

A two dimensional nonautonomous dissipative forced series LCR circuit with a simple nonlinear element exhibiting an immense variety of dynamical features is proposed for the first time. Unlike the usual cases of nonlinear element, the nonlinear element used here possesses three segment piecewise linear character with one positive and one negative slope. This nonlinearity is verified to be sufficient to produce chaos with high complexity in many established nonautonomous nonlinear circuits, such as MLC, MLCV, driven Chua, etc., thus indicating an universal behavior similar to the familiar Chua's diode. The dynamics of the proposed circuit is studied experimentally, confirmed numerically, simulated through PSPICE and proved mathematically. An important feature of the circuit is its ability to show dual chaotic behavior.

Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae.

Science.gov (United States)

Wang, Meng; Li, Sijin; Zhao, Huimin

2016-01-01

The development of high-throughput phenotyping tools is lagging far behind the rapid advances of genotype generation methods. To bridge this gap, we report a new strategy for design, construction, and fine-tuning of intracellular-metabolite-sensing/regulation gene circuits by repurposing bacterial transcription factors and eukaryotic promoters. As proof of concept, we systematically investigated the design and engineering of bacterial repressor-based xylose-sensing/regulation gene circuits in Saccharomyces cerevisiae. We demonstrated that numerous properties, such as induction ratio and dose-response curve, can be fine-tuned at three different nodes, including repressor expression level, operator position, and operator sequence. By applying these gene circuits, we developed a cell sorting based, rapid and robust high-throughput screening method for xylose transporter engineering and obtained a sugar transporter HXT14 mutant with 6.5-fold improvement in xylose transportation capacity. This strategy should be generally applicable and highly useful for evolutionary engineering of proteins, pathways, and genomes in S. cerevisiae. © 2015 Wiley Periodicals, Inc.

Computation of magnetic suspension of maglev systems using dynamic circuit theory

Science.gov (United States)

He, J. L.; Rote, D. M.; Coffey, H. T.

1992-01-01

Dynamic circuit theory is applied to several magnetic suspensions associated with maglev systems. These suspension systems are the loop-shaped coil guideway, the figure-eight-shaped null-flux coil guideway, and the continuous sheet guideway. Mathematical models, which can be used for the development of computer codes, are provided for each of these suspension systems. The differences and similarities of the models in using dynamic circuit theory are discussed in the paper. The paper emphasizes the transient and dynamic analysis and computer simulation of maglev systems. In general, the method discussed here can be applied to many electrodynamic suspension system design concepts. It is also suited for the computation of the performance of maglev propulsion systems. Numerical examples are presented in the paper.

Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression

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Verd, Berta; Crombach, Anton

2017-01-01

Pattern formation during development is a highly dynamic process. In spite of this, few experimental and modelling approaches take into account the explicit time-dependence of the rules governing regulatory systems. We address this problem by studying dynamic morphogen interpretation by the gap gene network in Drosophila melanogaster. Gap genes are involved in segment determination during early embryogenesis. They are activated by maternal morphogen gradients encoded by bicoid (bcd) and caudal (cad). These gradients decay at the same time-scale as the establishment of the antero-posterior gap gene pattern. We use a reverse-engineering approach, based on data-driven regulatory models called gene circuits, to isolate and characterise the explicitly time-dependent effects of changing morphogen concentrations on gap gene regulation. To achieve this, we simulate the system in the presence and absence of dynamic gradient decay. Comparison between these simulations reveals that maternal morphogen decay controls the timing and limits the rate of gap gene expression. In the anterior of the embyro, it affects peak expression and leads to the establishment of smooth spatial boundaries between gap domains. In the posterior of the embryo, it causes a progressive slow-down in the rate of gap domain shifts, which is necessary to correctly position domain boundaries and to stabilise the spatial gap gene expression pattern. We use a newly developed method for the analysis of transient dynamics in non-autonomous (time-variable) systems to understand the regulatory causes of these effects. By providing a rigorous mechanistic explanation for the role of maternal gradient decay in gap gene regulation, our study demonstrates that such analyses are feasible and reveal important aspects of dynamic gene regulation which would have been missed by a traditional steady-state approach. More generally, it highlights the importance of transient dynamics for understanding complex regulatory

[Smart therapeutics based on synthetic gene circuits].

Science.gov (United States)

Peng, Shuguang; Xie, Zhen

2017-03-25

Synthetic biology has an important impact on biology research since its birth. Applying the thought and methods that reference from electrical engineering, synthetic biology uncovers many regulatory mechanisms of life systems, transforms and expands a series of biological components. Therefore, it brings a wide range of biomedical applications, including providing new ideas for disease diagnosis and treatment. This review describes the latest advances in the field of disease diagnosis and therapy based on mammalian cell or bacterial synthetic gene circuits, and provides new ideas for future smart therapy design.

Neuromorphic Implementation of Attractor Dynamics in a Two-Variable Winner-Take-All Circuit with NMDARs: A Simulation Study.

Science.gov (United States)

You, Hongzhi; Wang, Da-Hui

2017-01-01

Neural networks configured with winner-take-all (WTA) competition and N-methyl-D-aspartate receptor (NMDAR)-mediated synaptic dynamics are endowed with various dynamic characteristics of attractors underlying many cognitive functions. This paper presents a novel method for neuromorphic implementation of a two-variable WTA circuit with NMDARs aimed at implementing decision-making, working memory and hysteresis in visual perceptions. The method proposed is a dynamical system approach of circuit synthesis based on a biophysically plausible WTA model. Notably, slow and non-linear temporal dynamics of NMDAR-mediated synapses was generated. Circuit simulations in Cadence reproduced ramping neural activities observed in electrophysiological recordings in experiments of decision-making, the sustained activities observed in the prefrontal cortex during working memory, and classical hysteresis behavior during visual discrimination tasks. Furthermore, theoretical analysis of the dynamical system approach illuminated the underlying mechanisms of decision-making, memory capacity and hysteresis loops. The consistence between the circuit simulations and theoretical analysis demonstrated that the WTA circuit with NMDARs was able to capture the attractor dynamics underlying these cognitive functions. Their physical implementations as elementary modules are promising for assembly into integrated neuromorphic cognitive systems.

Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions

Science.gov (United States)

Yeo, Zhen Xuan; Wong, Sum Thai; Arjunan, Satya Nanda Vel; Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar; Giuliani, Alessandro; Tsuchiya, Masa

2007-01-01

Background Cellular signaling involves a sequence of events from ligand binding to membrane receptors through transcription factors activation and the induction of mRNA expression. The transcriptional-regulatory system plays a pivotal role in the control of gene expression. A novel computational approach to the study of gene regulation circuits is presented here. Methodology Based on the concept of finite state machine, which provides a discrete view of gene regulation, a novel sequential logic model (SLM) is developed to decipher control mechanisms of dynamic transcriptional regulation of gene expressions. The SLM technique is also used to systematically analyze the dynamic function of transcriptional inputs, the dependency and cooperativity, such as synergy effect, among the binding sites with respect to when, how much and how fast the gene of interest is expressed. Principal Findings SLM is verified by a set of well studied expression data on endo16 of Strongylocentrotus purpuratus (sea urchin) during the embryonic midgut development. A dynamic regulatory mechanism for endo16 expression controlled by three binding sites, UI, R and Otx is identified and demonstrated to be consistent with experimental findings. Furthermore, we show that during transition from specification to differentiation in wild type endo16 expression profile, SLM reveals three binary activities are not sufficient to explain the transcriptional regulation of endo16 expression and additional activities of binding sites are required. Further analyses suggest detailed mechanism of R switch activity where indirect dependency occurs in between UI activity and R switch during specification to differentiation stage. Conclusions/Significance The sequential logic formalism allows for a simplification of regulation network dynamics going from a continuous to a discrete representation of gene activation in time. In effect our SLM is non-parametric and model-independent, yet providing rich biological

Sequential logic model deciphers dynamic transcriptional control of gene expressions.

Directory of Open Access Journals (Sweden)

Zhen Xuan Yeo

Full Text Available BACKGROUND: Cellular signaling involves a sequence of events from ligand binding to membrane receptors through transcription factors activation and the induction of mRNA expression. The transcriptional-regulatory system plays a pivotal role in the control of gene expression. A novel computational approach to the study of gene regulation circuits is presented here. METHODOLOGY: Based on the concept of finite state machine, which provides a discrete view of gene regulation, a novel sequential logic model (SLM is developed to decipher control mechanisms of dynamic transcriptional regulation of gene expressions. The SLM technique is also used to systematically analyze the dynamic function of transcriptional inputs, the dependency and cooperativity, such as synergy effect, among the binding sites with respect to when, how much and how fast the gene of interest is expressed. PRINCIPAL FINDINGS: SLM is verified by a set of well studied expression data on endo16 of Strongylocentrotus purpuratus (sea urchin during the embryonic midgut development. A dynamic regulatory mechanism for endo16 expression controlled by three binding sites, UI, R and Otx is identified and demonstrated to be consistent with experimental findings. Furthermore, we show that during transition from specification to differentiation in wild type endo16 expression profile, SLM reveals three binary activities are not sufficient to explain the transcriptional regulation of endo16 expression and additional activities of binding sites are required. Further analyses suggest detailed mechanism of R switch activity where indirect dependency occurs in between UI activity and R switch during specification to differentiation stage. CONCLUSIONS/SIGNIFICANCE: The sequential logic formalism allows for a simplification of regulation network dynamics going from a continuous to a discrete representation of gene activation in time. In effect our SLM is non-parametric and model-independent, yet

Dynamical Analysis, Synchronization, Circuit Design, and Secure Communication of a Novel Hyperchaotic System

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Li Xiong

2017-01-01

Full Text Available This paper is devoted to introduce a novel fourth-order hyperchaotic system. The hyperchaotic system is constructed by adding a linear feedback control level based on a modified Lorenz-like chaotic circuit with reduced number of amplifiers. The local dynamical entities, such as the basic dynamical behavior, the divergence, the eigenvalue, and the Lyapunov exponents of the new hyperchaotic system, are all investigated analytically and numerically. Then, an active control method is derived to achieve global chaotic synchronization of the novel hyperchaotic system through making the synchronization error system asymptotically stable at the origin based on Lyapunov stability theory. Next, the proposed novel hyperchaotic system is applied to construct another new hyperchaotic system with circuit deformation and design a new hyperchaotic secure communication circuit. Furthermore, the implementation of two novel electronic circuits of the proposed hyperchaotic systems is presented, examined, and realized using physical components. A good qualitative agreement is shown between the simulations and the experimental results around 500 kHz and below 1 MHz.

Quantum Simulation of the Ultrastrong-Coupling Dynamics in Circuit Quantum Electrodynamics

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D. Ballester

2012-05-01

Full Text Available We propose a method to get experimental access to the physics of the ultrastrong- and deep-strong-coupling regimes of light-matter interaction through the quantum simulation of their dynamics in standard circuit QED. The method makes use of a two-tone driving scheme, using state-of-the-art circuit-QED technology, and can be easily extended to general cavity-QED setups. We provide examples of ultrastrong- and deep-strong-coupling quantum effects that would be otherwise inaccessible.

Pluripotency gene network dynamics: System views from parametric analysis.

Science.gov (United States)

Akberdin, Ilya R; Omelyanchuk, Nadezda A; Fadeev, Stanislav I; Leskova, Natalya E; Oschepkova, Evgeniya A; Kazantsev, Fedor V; Matushkin, Yury G; Afonnikov, Dmitry A; Kolchanov, Nikolay A

2018-01-01

Multiple experimental data demonstrated that the core gene network orchestrating self-renewal and differentiation of mouse embryonic stem cells involves activity of Oct4, Sox2 and Nanog genes by means of a number of positive feedback loops among them. However, recent studies indicated that the architecture of the core gene network should also incorporate negative Nanog autoregulation and might not include positive feedbacks from Nanog to Oct4 and Sox2. Thorough parametric analysis of the mathematical model based on this revisited core regulatory circuit identified that there are substantial changes in model dynamics occurred depending on the strength of Oct4 and Sox2 activation and molecular complexity of Nanog autorepression. The analysis showed the existence of four dynamical domains with different numbers of stable and unstable steady states. We hypothesize that these domains can constitute the checkpoints in a developmental progression from naïve to primed pluripotency and vice versa. During this transition, parametric conditions exist, which generate an oscillatory behavior of the system explaining heterogeneity in expression of pluripotent and differentiation factors in serum ESC cultures. Eventually, simulations showed that addition of positive feedbacks from Nanog to Oct4 and Sox2 leads mainly to increase of the parametric space for the naïve ESC state, in which pluripotency factors are strongly expressed while differentiation ones are repressed.

A new nonlinear magnetic circuit model for dynamic analysis of interior permanent magnet synchronous motor

International Nuclear Information System (INIS)

Nakamura, Kenji; Saito, Kenichi; Watanabe, Tadaaki; Ichinokura, Osamu

2005-01-01

Interior permanent magnet synchronous motors (IPMSMs) have high efficiency and torque, since the motors can utilize reluctance torque in addition to magnet torque. The IPMSMs are widely used for electric household appliances and electric bicycles and vehicles. A quantitative analysis method of dynamic characteristics of the IPMSMs, however, has not been clarified fully. For optimum design, investigation of dynamic characteristics considering magnetic nonlinearity is needed. This paper presents a new nonlinear magnetic circuit model of an IPMSM, and suggests a dynamic analysis method using the proposed magnetic circuit model

Behavioral modeling of the dominant dynamics in input-output transfer of linear(ized) circuits

NARCIS (Netherlands)

Beelen, T.G.J.; Maten, ter E.J.W.; Sihaloho, H.J.; Eijndhoven, van S.J.L.

2010-01-01

We present a powerful procedure for determining both the dominant dynamics of the inputoutput transfer and the corresponding most influential circuit parameters of a linear(ized) circuit. The procedure consists of several steps in which a specific (sub)problem is solved and its solution is used in

Atomic physics and quantum optics using superconducting circuits: from the Dynamical Casimir effect to Majorana fermions

Science.gov (United States)

Nori, Franco

2012-02-01

This talk will present an overview of some of our recent results on atomic physics and quantum optics using superconducting circuits. Particular emphasis will be given to photons interacting with qubits, interferometry, the Dynamical Casimir effect, and also studying Majorana fermions using superconducting circuits.[4pt] References available online at our web site:[0pt] J.Q. You, Z.D. Wang, W. Zhang, F. Nori, Manipulating and probing Majorana fermions using superconducting circuits, (2011). Arxiv. J.R. Johansson, G. Johansson, C.M. Wilson, F. Nori, Dynamical Casimir effect in a superconducting coplanar waveguide, Phys. Rev. Lett. 103, 147003 (2009). [0pt] J.R. Johansson, G. Johansson, C.M. Wilson, F. Nori, Dynamical Casimir effect in superconducting microwave circuits, Phys. Rev. A 82, 052509 (2010). [0pt] C.M. Wilson, G. Johansson, A. Pourkabirian, J.R. Johansson, T. Duty, F. Nori, P. Delsing, Observation of the Dynamical Casimir Effect in a superconducting circuit. Nature, in press (Nov. 2011). P.D. Nation, J.R. Johansson, M.P. Blencowe, F. Nori, Stimulating uncertainty: Amplifying the quantum vacuum with superconducting circuits, Rev. Mod. Phys., in press (2011). [0pt] J.Q. You, F. Nori, Atomic physics and quantum optics using superconducting circuits, Nature 474, 589 (2011). [0pt] S.N. Shevchenko, S. Ashhab, F. Nori, Landau-Zener-Stuckelberg interferometry, Phys. Reports 492, 1 (2010). [0pt] I. Buluta, S. Ashhab, F. Nori. Natural and artificial atoms for quantum computation, Reports on Progress in Physics 74, 104401 (2011). [0pt] I.Buluta, F. Nori, Quantum Simulators, Science 326, 108 (2009). [0pt] L.F. Wei, K. Maruyama, X.B. Wang, J.Q. You, F. Nori, Testing quantum contextuality with macroscopic superconducting circuits, Phys. Rev. B 81, 174513 (2010). [0pt] J.Q. You, X.-F. Shi, X. Hu, F. Nori, Quantum emulation of a spin system with topologically protected ground states using superconducting quantum circuit, Phys. Rev. A 81, 063823 (2010).

Methods and models for accelerating dynamic simulation of fluid power circuits

Energy Technology Data Exchange (ETDEWEB)

Aaman, R.

2011-07-01

The objective of this dissertation is to improve the dynamic simulation of fluid power circuits. A fluid power circuit is a typical way to implement power transmission in mobile working machines, e.g. cranes, excavators etc. Dynamic simulation is an essential tool in developing controllability and energy-efficient solutions for mobile machines. Efficient dynamic simulation is the basic requirement for the real-time simulation. In the real-time simulation of fluid power circuits there exist numerical problems due to the software and methods used for modelling and integration. A simulation model of a fluid power circuit is typically created using differential and algebraic equations. Efficient numerical methods are required since differential equations must be solved in real time. Unfortunately, simulation software packages offer only a limited selection of numerical solvers. Numerical problems cause noise to the results, which in many cases leads the simulation run to fail. Mathematically the fluid power circuit models are stiff systems of ordinary differential equations. Numerical solution of the stiff systems can be improved by two alternative approaches. The first is to develop numerical solvers suitable for solving stiff systems. The second is to decrease the model stiffness itself by introducing models and algorithms that either decrease the highest eigenvalues or neglect them by introducing steady-state solutions of the stiff parts of the models. The thesis proposes novel methods using the latter approach. The study aims to develop practical methods usable in dynamic simulation of fluid power circuits using explicit fixed-step integration algorithms. In this thesis, two mechanisms which make the system stiff are studied. These are the pressure drop approaching zero in the turbulent orifice model and the volume approaching zero in the equation of pressure build-up. These are the critical areas to which alternative methods for modelling and numerical simulation

Dynamic Coding of Signed Quantities in Cortical Feedback Circuits

Directory of Open Access Journals (Sweden)

Dana eBallard

2012-08-01

Full Text Available In the early sensory and motor areas of the cortex, individual neurons transmit information about specific sensory features via a peaked response. This concept has been crystallized as `labeled lines,' to denote that axons communicate the specific properties of their sensory or motor parent cell. Such cells also can be characterized as being polarized, that is, as representing a signed quantity that is either positive or negative. We show in a model simulation that there are two important consequences when learning receptive fields using such signed codings in circuits that subtract different inputs. The first is that, in feedback circuits using labeled lines, such arithmetic operations need to be distributed across multiple distinct pathways. The second consequence is that such pathways must be necessarily dynamic, i.e. that synapses can grow and retract when forming receptive fields. The model monitors the breaking and growing of new circuit connections when their synapses need to change polarities and predicts that the rate of such changes should be inversely correlated with the progress of receptive field formation.

A positive feedback-based gene circuit to increase the production of a membrane protein

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Gennis Robert B

2010-05-01

Full Text Available Abstract Background Membrane proteins are an important class of proteins, playing a key role in many biological processes, and are a promising target in pharmaceutical development. However, membrane proteins are often difficult to produce in large quantities for the purpose of crystallographic or biochemical analyses. Results In this paper, we demonstrate that synthetic gene circuits designed specifically to overexpress certain genes can be applied to manipulate the expression kinetics of a model membrane protein, cytochrome bd quinol oxidase in E. coli, resulting in increased expression rates. The synthetic circuit involved is an engineered, autoinducer-independent variant of the lux operon activator LuxR from V. fischeri in an autoregulatory, positive feedback configuration. Conclusions Our proof-of-concept experiments indicate a statistically significant increase in the rate of production of the bd oxidase membrane protein. Synthetic gene networks provide a feasible solution for the problem of membrane protein production.

Synthetic multicellular oscillatory systems: controlling protein dynamics with genetic circuits

International Nuclear Information System (INIS)

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.

Optogenetic interrogation of neural circuits: technology for probing mammalian brain structures

Science.gov (United States)

Zhang, Feng; Gradinaru, Viviana; Adamantidis, Antoine R; Durand, Remy; Airan, Raag D; de Lecea, Luis; Deisseroth, Karl

2015-01-01

Elucidation of the neural substrates underlying complex animal behaviors depends on precise activity control tools, as well as compatible readout methods. Recent developments in optogenetics have addressed this need, opening up new possibilities for systems neuroscience. Interrogation of even deep neural circuits can be conducted by directly probing the necessity and sufficiency of defined circuit elements with millisecond-scale, cell type-specific optical perturbations, coupled with suitable readouts such as electrophysiology, optical circuit dynamics measures and freely moving behavior in mammals. Here we collect in detail our strategies for delivering microbial opsin genes to deep mammalian brain structures in vivo, along with protocols for integrating the resulting optical control with compatible readouts (electrophysiological, optical and behavioral). The procedures described here, from initial virus preparation to systems-level functional readout, can be completed within 4–5 weeks. Together, these methods may help in providing circuit-level insight into the dynamics underlying complex mammalian behaviors in health and disease. PMID:20203662

A Small-Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage.

Science.gov (United States)

Kubiak, Jeffrey M; Culyba, Matthew J; Liu, Monica Yun; Mo, Charlie Y; Goulian, Mark; Kohli, Rahul M

2017-11-17

The bacterial SOS stress-response pathway is a pro-mutagenic DNA repair system that mediates bacterial survival and adaptation to genotoxic stressors, including antibiotics and UV light. The SOS pathway is composed of a network of genes under the control of the transcriptional repressor, LexA. Activation of the pathway involves linked but distinct events: an initial DNA damage event leads to activation of RecA, which promotes autoproteolysis of LexA, abrogating its repressor function and leading to induction of the SOS gene network. These linked events can each independently contribute to DNA repair and mutagenesis, making it difficult to separate the contributions of the different events to observed phenotypes. We therefore devised a novel synthetic circuit to unlink these events and permit induction of the SOS gene network in the absence of DNA damage or RecA activation via orthogonal cleavage of LexA. Strains engineered with the synthetic SOS circuit demonstrate small-molecule inducible expression of SOS genes as well as the associated resistance to UV light. Exploiting our ability to activate SOS genes independently of upstream events, we further demonstrate that the majority of SOS-mediated mutagenesis on the chromosome does not readily occur with orthogonal pathway induction alone, but instead requires DNA damage. More generally, our approach provides an exemplar for using synthetic circuit design to separate an environmental stressor from its associated stress-response pathway.

Ruggedizing Printed Circuit Boards Using a Wideband Dynamic Absorber

Directory of Open Access Journals (Sweden)

V.C. Ho

2003-01-01

Full Text Available The existing approaches to ruggedizing inherently fragile and sensitive critical components of electronic equipment such as printed circuit boards (PCB for use in hostile industrial and military environment are either insufficient or expensive. This paper addresses a novel approach towards ruggedizing commercial-off-the-shelf PCBs using a miniature wideband dynamic absorber. The optimisation technique used relies on the experimentally measured vibration spectra and complex receptance of the original PCB.

Dynamic Analysis and Circuit Design of a Novel Hyperchaotic System with Fractional-Order Terms

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Abir Lassoued

2017-01-01

Full Text Available A novel hyperchaotic system with fractional-order (FO terms is designed. Its highly complex dynamics are investigated in terms of equilibrium points, Lyapunov spectrum, and attractor forms. It will be shown that the proposed system exhibits larger Lyapunov exponents than related hyperchaotic systems. Finally, to enhance its potential application, a related circuit is designed by using the MultiSIM Software. Simulation results verify the effectiveness of the suggested circuit.

Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity--a large-scale system analysis of decoded bacterial genomes.

Science.gov (United States)

Shestov, Maksim; Ontañón, Santiago; Tozeren, Aydin

2015-10-13

Bacterial infections comprise a global health challenge as the incidences of antibiotic resistance increase. Pathogenic potential of bacteria has been shown to be context dependent, varying in response to environment and even within the strains of the same genus. We used the KEGG repository and extensive literature searches to identify among the 2527 bacterial genomes in the literature those implicated as pathogenic to the host, including those which show pathogenicity in a context dependent manner. Using data on the gene contents of these genomes, we identified sets of genes highly abundant in pathogenic but relatively absent in commensal strains and vice versa. In addition, we carried out genome comparison within a genus for the seventeen largest genera in our genome collection. We projected the resultant lists of ortholog genes onto KEGG bacterial pathways to identify clusters and circuits, which can be linked to either pathogenicity or synergy. Gene circuits relatively abundant in nonpathogenic bacteria often mediated biosynthesis of antibiotics. Other synergy-linked circuits reduced drug-induced toxicity. Pathogen-abundant gene circuits included modules in one-carbon folate, two-component system, type-3 secretion system, and peptidoglycan biosynthesis. Antibiotics-resistant bacterial strains possessed genes modulating phagocytosis, vesicle trafficking, cytoskeletal reorganization, and regulation of the inflammatory response. Our study also identified bacterial genera containing a circuit, elements of which were previously linked to Alzheimer's disease. Present study produces for the first time, a signature, in the form of a robust list of gene circuitry whose presence or absence could potentially define the pathogenicity of a microbiome. Extensive literature search substantiated a bulk majority of the commensal and pathogenic circuitry in our predicted list. Scanning microbiome libraries for these circuitry motifs will provide further insights into the complex

Comparison of stationary and oscillatory dynamics described by differential equations and Boolean maps in transcriptional regulatory circuits

Science.gov (United States)

Ye, Weiming; Li, Pengfei; Huang, Xuhui; Xia, Qinzhi; Mi, Yuanyuan; Chen, Runsheng; Hu, Gang

2010-10-01

Exploring the principle and relationship of gene transcriptional regulations (TR) has been becoming a generally researched issue. So far, two major mathematical methods, ordinary differential equation (ODE) method and Boolean map (BM) method have been widely used for these purposes. It is commonly believed that simplified BMs are reasonable approximations of more realistic ODEs, and both methods may reveal qualitatively the same essential features though the dynamical details of both systems may show some differences. In this Letter we exhaustively enumerated all the 3-gene networks and many autonomous randomly constructed TR networks with more genes by using both the ODE and BM methods. In comparison we found that both methods provide practically identical results in most of cases of steady solutions. However, to our great surprise, most of network structures showing periodic cycles with the BM method possess only stationary states in ODE descriptions. These observations strongly suggest that many periodic oscillations and other complicated oscillatory states revealed by the BM rule may be related to the computational errors of variable and time discretizations and rarely have correspondence in realistic biology transcriptional regulatory circuits.

Time- and Site-Resolved Dynamics in a Topological Circuit

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Jia Ningyuan

2015-06-01

Full Text Available From studies of exotic quantum many-body phenomena to applications in spintronics and quantum information processing, topological materials are poised to revolutionize the condensed-matter frontier and the landscape of modern materials science. Accordingly, there is a broad effort to realize topologically nontrivial electronic and photonic materials for fundamental science as well as practical applications. In this work, we demonstrate the first simultaneous site- and time-resolved measurements of a time-reversal-invariant topological band structure, which we realize in a radio-frequency photonic circuit. We control band-structure topology via local permutation of a traveling-wave capacitor-inductor network, increasing robustness by going beyond the tight-binding limit. We observe a gapped density of states consistent with a modified Hofstadter spectrum at a flux per plaquette of ϕ=π/2. In situ probes of the band gaps reveal spatially localized bulk states and delocalized edge states. Time-resolved measurements reveal dynamical separation of localized edge excitations into spin-polarized currents. The radio-frequency circuit paradigm is naturally compatible with nonlocal coupling schemes, allowing us to implement a Möbius strip topology inaccessible in conventional systems. This room-temperature experiment illuminates the origins of topology in band structure, and when combined with circuit quantum electrodynamics techniques, it provides a direct path to topologically ordered quantum matter.

A Novel Realization of Low-Power and Low-Distortion Multiplier Circuit with Improved Dynamic Range

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Ali Naderi Saatlo

2017-01-01

Full Text Available A novel topology of four-quadrant analog multiplier circuit is presented in this paper. The voltage mode technique is employed to design the circuit in CMOS technology. The dynamic input and output ranges of the circuit are improved owing to the fact that the circuit works in the saturation region not in weak inversion. Also the proposed multiplier is suitable for low voltage operation and its power consumption is relatively low. In order to verify the performance of the proposed circuit, performance of the circuit affected by second order effects including transistor mismatch and mobility reduction is analyzed in detail. It will be shown that any conceivable mismatch in the transistor parameters leads to second harmonic distortion. Additionally, the effect of mobility reduction in the third harmonic distortion will be computed. In order to simulate the circuit, Cadence and HSPICE software are used with TSMC level 49 (BSIM3v3 parameters for 0.18 μm CMOS technology, where under supply voltage of 1.5 V, total power consumption is 44 µW, the corresponding average nonlinearity remains as low as 1 %, and the input range of the circuit is ± 400 mV.

Growth-rate-dependent dynamics of a bacterial genetic oscillator

Science.gov (United States)

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.

Genome engineering using a synthetic gene circuit in Bacillus subtilis.

Science.gov (United States)

Jeong, Da-Eun; Park, Seung-Hwan; Pan, Jae-Gu; Kim, Eui-Joong; Choi, Soo-Keun

2015-03-31

Genome engineering without leaving foreign DNA behind requires an efficient counter-selectable marker system. Here, we developed a genome engineering method in Bacillus subtilis using a synthetic gene circuit as a counter-selectable marker system. The system contained two repressible promoters (B. subtilis xylA (Pxyl) and spac (Pspac)) and two repressor genes (lacI and xylR). Pxyl-lacI was integrated into the B. subtilis genome with a target gene containing a desired mutation. The xylR and Pspac-chloramphenicol resistant genes (cat) were located on a helper plasmid. In the presence of xylose, repression of XylR by xylose induced LacI expression, the LacIs repressed the Pspac promoter and the cells become chloramphenicol sensitive. Thus, to survive in the presence of chloramphenicol, the cell must delete Pxyl-lacI by recombination between the wild-type and mutated target genes. The recombination leads to mutation of the target gene. The remaining helper plasmid was removed easily under the chloramphenicol absent condition. In this study, we showed base insertion, deletion and point mutation of the B. subtilis genome without leaving any foreign DNA behind. Additionally, we successfully deleted a 2-kb gene (amyE) and a 38-kb operon (ppsABCDE). This method will be useful to construct designer Bacillus strains for various industrial applications. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study.

Science.gov (United States)

Fan, Ming; Kuwahara, Hiroyuki; Wang, Xiaolei; Wang, Suojin; Gao, Xin

2015-11-01

Parameter estimation is a challenging computational problem in the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter estimation of gene circuit models from such time-series mRNA data has become an important method for quantitatively dissecting the regulation of gene expression. By focusing on the modeling of gene circuits, we examine here the performance of three types of state-of-the-art parameter estimation methods: population-based methods, online methods and model-decomposition-based methods. Our results show that certain population-based methods are able to generate high-quality parameter solutions. The performance of these methods, however, is heavily dependent on the size of the parameter search space, and their computational requirements substantially increase as the size of the search space increases. In comparison, online methods and model decomposition-based methods are computationally faster alternatives and are less dependent on the size of the search space. Among other things, our results show that a hybrid approach that augments computationally fast methods with local search as a subsequent refinement procedure can substantially increase the quality of their parameter estimates to the level on par with the best solution obtained from the population-based methods while maintaining high computational speed. These suggest that such hybrid methods can be a promising alternative to the more commonly used population-based methods for parameter estimation of gene circuit models when limited prior knowledge about the underlying regulatory mechanisms makes the size of the parameter search space vastly large. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Dynamic Model of MR Dampers Based on a Hysteretic Magnetic Circuit

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Pengfei Guo

2018-01-01

Full Text Available As a key to understand dynamic performances of MR dampers, a comprehensive dynamic magnetic circuit model is proposed in this work on the basis of Ampere’s and Gauss’s laws. It takes into account not only the magnetic saturation, which many existing studies have focused on, but also the magnetic hysteresis and eddy currents in a MR damper. The hysteresis of steel parts of MR dampers is described by Jiles-Atherton (J-A models, and the eddy current is included based on the field separation. Compared with the FEM results, the proposed model is validated in low- and high-frequency studies for the predictions of the magnetic saturation, the hysteresis, and the effect of eddy currents. A simple multiphysics model is developed to demonstrate how to combine the proposed magnetic circuit model with the commonly used Bingham fluid model. The damping force in the high-frequency case obviously lags behind the coil current, which exhibits a hysteresis loop in the current-force plane. The lag of damping force even exists in a low-frequency varying magnetic field and becomes more severe in the presence of eddy currents.

Pulsewidth modulated DC-to-DC power conversion circuits, dynamics, and control designs

CERN Document Server

Choi, Byungcho

2013-01-01

This is the definitive reference for anyone involved in pulsewidth modulated DC-to-DC power conversion Pulsewidth Modulated DC-to-DC Power Conversion: Circuits, Dynamics, and Control Designs provides engineers, researchers, and students in the power electronics field with comprehensive and complete guidance to understanding pulsewidth modulated (PWM) DC-to-DC power converters. Presented in three parts, the book addresses the circuitry and operation of PWM DC-to-DC converters and their dynamic characteristics, along with in-depth discussions of control design of PWM DC-to

Tunable 13C/1H dual channel matching circuit for dynamic nuclear polarization system with cross-polarization

DEFF Research Database (Denmark)

Rybalko, Oleksandr; Bowen, Sean; Zhurbenko, Vitaliy

2016-01-01

In this paper we report initial results of design and practical implementation of tuning and matching circuit to estimate a performance of Dynamic Nuclear Polarization (DNP) at a magnetic field of 6.7 T. It is shown that developed circuit for signal observation is compact, easy to make and provides....... Measurement results with a tuning and matching circuit prototype are presented including obtained spectra (13C and 1H) and estimation of the signal-to-noise ratio....

Numerical simulation for arc-plasma dynamics during contact opening process in electrical circuit-breakers

International Nuclear Information System (INIS)

Gupta, D N; Srinivas, D; Patil, G N; Kale, S S; Potnis, S B

2010-01-01

The high-energy, high-current thermal plasma that develops between electric contacts in a gas circuit-breaker during circuit interruption is an important phenomenon in the power transmission industry. The high temperature and pressure arc dissipates the tremendous amount of energy generated by the fault current. Simultaneously, this energy has to be transferred away from the contacts to build the dielectric strength level of the circuit-breaker. In order to interrupt the current, the arc must be weakened and finally extinguished. We model these phenomena by using a computer software code based on the solution of the unsteady Euler equations of gas dynamics. We consider the equations of fluid flows. These equations are solved numerically in complex circuit breaker geometries using a finite-volume method. The domain is initially filled with SF 6 gas. We begin our simulations from cold mode, where the fault current is not present (hence no arc). An axis-symmetric geometry of a 145 kV gas circuit-breaker is considered to study the pressure, density, and temperature profile during contact opening process.

Dynamic Training Elements in a Circuit Theory Course to Implement a Self-Directed Learning Process

Science.gov (United States)

Krouk, B. I.; Zhuravleva, O. B.

2009-01-01

This paper reports on the implementation of a self-directed learning process in a circuit theory course, incorporating dynamic training elements which were designed on the basis of a cybernetic model of cognitive process management. These elements are centrally linked in a dynamic learning frame, created on the monitor screen, which displays the…

Equivalence between classical and quantum dynamics. Neutral kaons and electric circuits

International Nuclear Information System (INIS)

Caruso, M.; Fanchiotti, H.; Canal, C.A. Garcia

2011-01-01

An equivalence between the Schroedinger dynamics of a quantum system with a finite number of basis states and a classical dynamics is presented. The equivalence is an isomorphism that connects in univocal way both dynamical systems. We treat the particular case of neutral kaons and found a class of electric networks uniquely related to the kaon system finding the complete map between the matrix elements of the effective Hamiltonian of kaons and those elements of the classical dynamics of the networks. As a consequence, the relevant ε parameter that measures CP violation in the kaon system is completely determined in terms of network parameters. - Highlights: → We provide a formal equivalence between classical and quantum dynamics. → We make use of the decomplexification concept. → Neutral kaon systems can be represented by electric circuits. → CP symmetry violation can be taken into account by non-reciprocity. → Non-reciprocity is represented by gyrators.

Optogenetic dissection of neuronal circuits in zebrafish using viral gene transfer and the Tet system

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Peixin Zhu

2009-12-01

Full Text Available The conditional expression of transgenes at high levels in sparse and specific populations of neurons is important for high-resolution optogenetic analyses of neuronal circuits. We explored two complementary methods, viral gene delivery and the iTet-Off system, to express transgenes in the brain of zebrafish. High-level gene expression in neurons was achieved by Sindbis and Rabies viruses. The Tet system produced strong and specific gene expression that could be modulated conveniently by doxycycline. Moreover, transgenic lines showed expression in distinct, sparse and stable populations of neurons that appeared to be subsets of the neurons targeted by the promoter driving the Tet activator. The Tet system therefore provides the opportunity to generate libraries of diverse expression patterns similar to gene trap approaches or the thy-1 promoter in mice, but with the additional possibility to pre-select cell types of interest. In transgenic lines expressing channelrhodopsin-2, action potential firing could be precisely controlled by two-photon stimulation at low laser power, presumably because the expression levels of the Tet-controlled genes were high even in adults. In channelrhodopsin-2-expressing larvae, optical stimulation with a single blue LED evoked distinct swimming behaviors including backward swimming. These approaches provide new opportunities for the optogenetic dissection of neuronal circuit structure and function.

Predicting the topology of dynamic neural networks for the simulation of electronic circuits

NARCIS (Netherlands)

Schilders, W.H.A.

2009-01-01

In this paper we discuss the use of the state-space modelling MOESP algorithm to generate precise information about the number of neurons and hidden layers in dynamic neural networks developed for the behavioural modelling of electronic circuits. The Bartels–Stewart algorithm is used to transform

Simulation of the dynamic behaviour of the secondary circuit of a WWER-440 type nuclear power plant Pt. 2

International Nuclear Information System (INIS)

Doorenbos, J.; Gacs, A.; Kiss, Zs.

1987-12-01

This report describes the dynamic simulation models of the most important controllers of the secondary circuit of a WWER-440 type nuclear power plant, i.e., the hydraulic turbine controller and the level controls of the condenser hotwell and that of the feedwater tank. Simulation results are also presented. (For dynamic simulation models of the primary circuit of WWER-440 type reactors see Reports KFKI--1983-127 and KFKI--1985-08.) (author) 15 figs

The Complexity of Dynamics in Small Neural Circuits.

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Diego Fasoli

2016-08-01

Full Text Available Mean-field approximations are a powerful tool for studying large neural networks. However, they do not describe well the behavior of networks composed of a small number of neurons. In this case, major differences between the mean-field approximation and the real behavior of the network can arise. Yet, many interesting problems in neuroscience involve the study of mesoscopic networks composed of a few tens of neurons. Nonetheless, mathematical methods that correctly describe networks of small size are still rare, and this prevents us to make progress in understanding neural dynamics at these intermediate scales. Here we develop a novel systematic analysis of the dynamics of arbitrarily small networks composed of homogeneous populations of excitatory and inhibitory firing-rate neurons. We study the local bifurcations of their neural activity with an approach that is largely analytically tractable, and we numerically determine the global bifurcations. We find that for strong inhibition these networks give rise to very complex dynamics, caused by the formation of multiple branching solutions of the neural dynamics equations that emerge through spontaneous symmetry-breaking. This qualitative change of the neural dynamics is a finite-size effect of the network, that reveals qualitative and previously unexplored differences between mesoscopic cortical circuits and their mean-field approximation. The most important consequence of spontaneous symmetry-breaking is the ability of mesoscopic networks to regulate their degree of functional heterogeneity, which is thought to help reducing the detrimental effect of noise correlations on cortical information processing.

A constructive approach to gene expression dynamics

International Nuclear Information System (INIS)

Ochiai, T.; Nacher, J.C.; Akutsu, T.

2004-01-01

Recently, experiments on mRNA abundance (gene expression) have revealed that gene expression shows a stationary organization described by a scale-free distribution. Here we propose a constructive approach to gene expression dynamics which restores the scale-free exponent and describes the intermediate state dynamics. This approach requires only one assumption: Markov property

Wiring Together Synthetic Bacterial Consortia to Create a Biological Integrated Circuit.

Science.gov (United States)

Perry, Nicolas; Nelson, Edward M; Timp, Gregory

2016-12-16

The promise of adapting biology to information processing will not be realized until engineered gene circuits, operating in different cell populations, can be wired together to express a predictable function. Here, elementary biological integrated circuits (BICs), consisting of two sets of transmitter and receiver gene circuit modules with embedded memory placed in separate cell populations, were meticulously assembled using live cell lithography and wired together by the mass transport of quorum-sensing (QS) signal molecules to form two isolated communication links (comlinks). The comlink dynamics were tested by broadcasting "clock" pulses of inducers into the networks and measuring the responses of functionally linked fluorescent reporters, and then modeled through simulations that realistically captured the protein production and molecular transport. These results show that the comlinks were isolated and each mimicked aspects of the synchronous, sequential networks used in digital computing. The observations about the flow conditions, derived from numerical simulations, and the biofilm architectures that foster or silence cell-to-cell communications have implications for everything from decontamination of drinking water to bacterial virulence.

Simple mathematical models of gene regulatory dynamics

CERN Document Server

Mackey, Michael C; Tyran-Kamińska, Marta; Zeron, Eduardo S

2016-01-01

This is a short and self-contained introduction to the field of mathematical modeling of gene-networks in bacteria. As an entry point to the field, we focus on the analysis of simple gene-network dynamics. The notes commence with an introduction to the deterministic modeling of gene-networks, with extensive reference to applicable results coming from dynamical systems theory. The second part of the notes treats extensively several approaches to the study of gene-network dynamics in the presence of noise—either arising from low numbers of molecules involved, or due to noise external to the regulatory process. The third and final part of the notes gives a detailed treatment of three well studied and concrete examples of gene-network dynamics by considering the lactose operon, the tryptophan operon, and the lysis-lysogeny switch. The notes contain an index for easy location of particular topics as well as an extensive bibliography of the current literature. The target audience of these notes are mainly graduat...

A modular positive feedback-based gene amplifier

Directory of Open Access Journals (Sweden)

Bhalerao Kaustubh D

2010-02-01

Full Text Available Abstract Background Positive feedback is a common mechanism used in the regulation of many gene circuits as it can amplify the response to inducers and also generate binary outputs and hysteresis. In the context of electrical circuit design, positive feedback is often considered in the design of amplifiers. Similar approaches, therefore, may be used for the design of amplifiers in synthetic gene circuits with applications, for example, in cell-based sensors. Results We developed a modular positive feedback circuit that can function as a genetic signal amplifier, heightening the sensitivity to inducer signals as well as increasing maximum expression levels without the need for an external cofactor. The design utilizes a constitutively active, autoinducer-independent variant of the quorum-sensing regulator LuxR. We experimentally tested the ability of the positive feedback module to separately amplify the output of a one-component tetracycline sensor and a two-component aspartate sensor. In each case, the positive feedback module amplified the response to the respective inducers, both with regards to the dynamic range and sensitivity. Conclusions The advantage of our design is that the actual feedback mechanism depends only on a single gene and does not require any other modulation. Furthermore, this circuit can amplify any transcriptional signal, not just one encoded within the circuit or tuned by an external inducer. As our design is modular, it can potentially be used as a component in the design of more complex synthetic gene circuits.

A Cytomorphic Chip for Quantitative Modeling of Fundamental Bio-Molecular Circuits.

Science.gov (United States)

2015-08-01

We describe a 0.35 μm BiCMOS silicon chip that quantitatively models fundamental molecular circuits via efficient log-domain cytomorphic transistor equivalents. These circuits include those for biochemical binding with automatic representation of non-modular and loading behavior, e.g., in cascade and fan-out topologies; for representing variable Hill-coefficient operation and cooperative binding; for representing inducer, transcription-factor, and DNA binding; for probabilistic gene transcription with analogic representations of log-linear and saturating operation; for gain, degradation, and dynamics of mRNA and protein variables in transcription and translation; and, for faithfully representing biological noise via tunable stochastic transistor circuits. The use of on-chip DACs and ADCs enables multiple chips to interact via incoming and outgoing molecular digital data packets and thus create scalable biochemical reaction networks. The use of off-chip digital processors and on-chip digital memory enables programmable connectivity and parameter storage. We show that published static and dynamic MATLAB models of synthetic biological circuits including repressilators, feed-forward loops, and feedback oscillators are in excellent quantitative agreement with those from transistor circuits on the chip. Computationally intensive stochastic Gillespie simulations of molecular production are also rapidly reproduced by the chip and can be reliably tuned over the range of signal-to-noise ratios observed in biological cells.

Fault Diagnosis for Compensating Capacitors of Jointless Track Circuit Based on Dynamic Time Warping

Directory of Open Access Journals (Sweden)

Wei Dong

2014-01-01

Full Text Available Aiming at the problem of online fault diagnosis for compensating capacitors of jointless track circuit, a dynamic time warping (DTW based diagnosis method is proposed in this paper. Different from the existing related works, this method only uses the ground indoor monitoring signals of track circuit to locate the faulty compensating capacitor, not depending on the shunt current of inspection train, which is an indispensable condition for existing methods. So, it can be used for online diagnosis of compensating capacitor, which has not yet been realized by existing methods. To overcome the key problem that track circuit cannot obtain the precise position of the train, the DTW method is used for the first time in this situation to recover the function relationship between receiver’s peak voltage and shunt position. The necessity, thinking, and procedure of the method are described in detail. Besides the classical DTW based method, two improved methods for improving classification quality and reducing computation complexity are proposed. Finally, the diagnosis experiments based on the simulation model of track circuit show the effectiveness of the proposed methods.

Parameter estimation and determinability analysis applied to Drosophila gap gene circuits

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Jaeger Johannes

2008-09-01

Full Text Available Abstract Background Mathematical modeling of real-life processes often requires the estimation of unknown parameters. Once the parameters are found by means of optimization, it is important to assess the quality of the parameter estimates, especially if parameter values are used to draw biological conclusions from the model. Results In this paper we describe how the quality of parameter estimates can be analyzed. We apply our methodology to assess parameter determinability for gene circuit models of the gap gene network in early Drosophila embryos. Conclusion Our analysis shows that none of the parameters of the considered model can be determined individually with reasonable accuracy due to correlations between parameters. Therefore, the model cannot be used as a tool to infer quantitative regulatory weights. On the other hand, our results show that it is still possible to draw reliable qualitative conclusions on the regulatory topology of the gene network. Moreover, it improves previous analyses of the same model by allowing us to identify those interactions for which qualitative conclusions are reliable, and those for which they are ambiguous.

Beam dynamics requirements for HL–LHC electrical circuits

CERN Document Server

Gamba, Davide; Cerqueira Bastos, Miguel; Coello De Portugal - Martinez Vazquez, Jaime Maria; De Maria, Riccardo; Giovannozzi, Massimo; Martino, Michele; Tomas Garcia, Rogelio

2017-01-01

A certain number of LHC magnets and relative electrical circuits will be replaced for the HL-LHC upgrade. The performance of the new circuits will need to be compatible with the current installation, and to provide the necessary improvements to meet the tight requirements of the new operational scenario. This document summarises the present knowledge of the performance and use of the LHC circuits and, based on this and on the new optics requirements, provides the necessary specifications for the new HL-LHC electrical circuits.

Logarithmic circuit with wide dynamic range

Science.gov (United States)

Wiley, P. H.; Manus, E. A. (Inventor)

1978-01-01

A circuit deriving an output voltage that is proportional to the logarithm of a dc input voltage susceptible to wide variations in amplitude includes a constant current source which forward biases a diode so that the diode operates in the exponential portion of its voltage versus current characteristic, above its saturation current. The constant current source includes first and second, cascaded feedback, dc operational amplifiers connected in negative feedback circuit. An input terminal of the first amplifier is responsive to the input voltage. A circuit shunting the first amplifier output terminal includes a resistor in series with the diode. The voltage across the resistor is sensed at the input of the second dc operational feedback amplifier. The current flowing through the resistor is proportional to the input voltage over the wide range of variations in amplitude of the input voltage.

Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility.

Science.gov (United States)

Bagot, Rosemary C; Cates, Hannah M; Purushothaman, Immanuel; Lorsch, Zachary S; Walker, Deena M; Wang, Junshi; Huang, Xiaojie; Schlüter, Oliver M; Maze, Ian; Peña, Catherine J; Heller, Elizabeth A; Issler, Orna; Wang, Minghui; Song, Won-Min; Stein, Jason L; Liu, Xiaochuan; Doyle, Marie A; Scobie, Kimberly N; Sun, Hao Sheng; Neve, Rachael L; Geschwind, Daniel; Dong, Yan; Shen, Li; Zhang, Bin; Nestler, Eric J

2016-06-01

Depression is a complex, heterogeneous disorder and a leading contributor to the global burden of disease. Most previous research has focused on individual brain regions and genes contributing to depression. However, emerging evidence in humans and animal models suggests that dysregulated circuit function and gene expression across multiple brain regions drive depressive phenotypes. Here, we performed RNA sequencing on four brain regions from control animals and those susceptible or resilient to chronic social defeat stress at multiple time points. We employed an integrative network biology approach to identify transcriptional networks and key driver genes that regulate susceptibility to depressive-like symptoms. Further, we validated in vivo several key drivers and their associated transcriptional networks that regulate depression susceptibility and confirmed their functional significance at the levels of gene transcription, synaptic regulation, and behavior. Our study reveals novel transcriptional networks that control stress susceptibility and offers fundamentally new leads for antidepressant drug discovery. Copyright © 2016 Elsevier Inc. All rights reserved.

Simulation of the dynamic behaviour of the secondary circuit of a WWER-440 type nuclear power plant Pt. 1

International Nuclear Information System (INIS)

Gacs, A.; Janosy, J.S.; Kiss, Zs.

1987-07-01

This report describes the simulation model of the secondary circuit of a WWER-440 type nuclear power plant. The goal of this modelling is to simulate normal and small abnormal transients in a Basic Principles Simulator. The earlier reports describing the dynamic simulation of primary circuit of a WWER-440 nuclear power plant are KFKI--1983-127 and KFKI--1985-08. At present the controllers of the secondary circuit are not simulated. Finally, some simulation results are presented. (author)

Supply circuit for and dynamic characteristics of discharge in a nitrogen laser

Energy Technology Data Exchange (ETDEWEB)

Sidorov, Yu L; Sukhanov, A N

1978-03-01

The dynamic characteristics of discharge in a nitrogen laser with an output radiation power at the 1 MW level were measured in an experiment under pressures ranging from 30 to 350 mm Hg. At the same time, the design and the performance of a supply circuit on the basis of a Blumlein line as pumping source were evaluated. The results of this study indicate that the practically attainable efficiency, which depends on the characteristics impedance of the discharge circuit, can be increased from 0.07 to 0.1% with a two-stage laser, by shortening the pump discharge and supplying most energy to the second stage at higher E/p ratios. Multistage high-power lasers operating in the generator-amplifier mode with high gain in the active medium are thus feasible without the need for expensive optical decoupling of stages.

Heat and fluid dynamic in the primary circuit of a research reactor

International Nuclear Information System (INIS)

Gebrin, A.N.

1986-01-01

Aiming at the analysis of some thermohydraulic transients that may affect the safety of a reactor core, a FORTRAN program was developed which evaluates the heat and fluid dynamics in the primary circuit of a research reactor. The selection of the pump, the determination of the length and diameter of the pipes, as well as the appropriate arrangement of the pipes and heat exchanger, are determined from the stationary regime. (Author) [pt

MOS integrated circuit design

CERN Document Server

Wolfendale, E

2013-01-01

MOS Integral Circuit Design aims to help in the design of integrated circuits, especially large-scale ones, using MOS Technology through teaching of techniques, practical applications, and examples. The book covers topics such as design equation and process parameters; MOS static and dynamic circuits; logic design techniques, system partitioning, and layout techniques. Also featured are computer aids such as logic simulation and mask layout, as well as examples on simple MOS design. The text is recommended for electrical engineers who would like to know how to use MOS for integral circuit desi

Dichotomous noise models of gene switches

Energy Technology Data Exchange (ETDEWEB)

Potoyan, Davit A., E-mail: potoyan@rice.edu; Wolynes, Peter G., E-mail: pwolynes@rice.edu [Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005 (United States)

2015-11-21

Molecular noise in gene regulatory networks has two intrinsic components, one part being due to fluctuations caused by the birth and death of protein or mRNA molecules which are often present in small numbers and the other part arising from gene state switching, a single molecule event. Stochastic dynamics of gene regulatory circuits appears to be largely responsible for bifurcations into a set of multi-attractor states that encode different cell phenotypes. The interplay of dichotomous single molecule gene noise with the nonlinear architecture of genetic networks generates rich and complex phenomena. In this paper, we elaborate on an approximate framework that leads to simple hybrid multi-scale schemes well suited for the quantitative exploration of the steady state properties of large-scale cellular genetic circuits. Through a path sum based analysis of trajectory statistics, we elucidate the connection of these hybrid schemes to the underlying master equation and provide a rigorous justification for using dichotomous noise based models to study genetic networks. Numerical simulations of circuit models reveal that the contribution of the genetic noise of single molecule origin to the total noise is significant for a wide range of kinetic regimes.

Quantum circuit dynamics via path integrals: Is there a classical action for discrete-time paths?

Science.gov (United States)

Penney, Mark D.; Enshan Koh, Dax; Spekkens, Robert W.

2017-07-01

It is straightforward to compute the transition amplitudes of a quantum circuit using the sum-over-paths methodology when the gates in the circuit are balanced, where a balanced gate is one for which all non-zero transition amplitudes are of equal magnitude. Here we consider the question of whether, for such circuits, the relative phases of different discrete-time paths through the configuration space can be defined in terms of a classical action, as they are for continuous-time paths. We show how to do so for certain kinds of quantum circuits, namely, Clifford circuits where the elementary systems are continuous-variable systems or discrete systems of odd-prime dimension. These types of circuit are distinguished by having phase-space representations that serve to define their classical counterparts. For discrete systems, the phase-space coordinates are also discrete variables. We show that for each gate in the generating set, one can associate a symplectomorphism on the phase-space and to each of these one can associate a generating function, defined on two copies of the configuration space. For discrete systems, the latter association is achieved using tools from algebraic geometry. Finally, we show that if the action functional for a discrete-time path through a sequence of gates is defined using the sum of the corresponding generating functions, then it yields the correct relative phases for the path-sum expression. These results are likely to be relevant for quantizing physical theories where time is fundamentally discrete, characterizing the classical limit of discrete-time quantum dynamics, and proving complexity results for quantum circuits.

Phenotypic deconstruction of gene circuitry.

Science.gov (United States)

Lomnitz, Jason G; Savageau, Michael A

2013-06-01

It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.

Phenotypic deconstruction of gene circuitry

Science.gov (United States)

Lomnitz, Jason G.; Savageau, Michael A.

2013-06-01

It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.

Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study

KAUST Repository

Fan, M.

2015-03-29

Parameter estimation is a challenging computational problemin the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter esti- mation of gene circuitmodels fromsuch time-series mRNA data has become an importantmethod for quantitatively dissecting the regulation of gene expression. By focusing on themodeling of gene circuits, we examine here the perform- ance of three types of state-of-the-art parameter estimation methods: population-basedmethods, onlinemethods and model-decomposition-basedmethods. Our results show that certain population-basedmethods are able to generate high- quality parameter solutions. The performance of thesemethods, however, is heavily dependent on the size of the param- eter search space, and their computational requirements substantially increase as the size of the search space increases. In comparison, onlinemethods andmodel decomposition-basedmethods are computationally faster alternatives and are less dependent on the size of the search space. Among other things, our results show that a hybrid approach that augments computationally fastmethods with local search as a subsequent refinement procedure can substantially increase the qual- ity of their parameter estimates to the level on par with the best solution obtained fromthe population-basedmethods whilemaintaining high computational speed. These suggest that such hybridmethods can be a promising alternative to themore commonly used population-basedmethods for parameter estimation of gene circuit models when limited prior knowledge about the underlying regulatorymechanismsmakes the size of the parameter search space vastly large. © The Author 2015. Published by Oxford University Press.

Hidden attractors in dynamical models of phase-locked loop circuits: Limitations of simulation in MATLAB and SPICE

Science.gov (United States)

Kuznetsov, N. V.; Leonov, G. A.; Yuldashev, M. V.; Yuldashev, R. V.

2017-10-01

During recent years it has been shown that hidden oscillations, whose basin of attraction does not overlap with small neighborhoods of equilibria, may significantly complicate simulation of dynamical models, lead to unreliable results and wrong conclusions, and cause serious damage in drilling systems, aircrafts control systems, electromechanical systems, and other applications. This article provides a survey of various phase-locked loop based circuits (used in satellite navigation systems, optical, and digital communication), where such difficulties take place in MATLAB and SPICE. Considered examples can be used for testing other phase-locked loop based circuits and simulation tools, and motivate the development and application of rigorous analytical methods for the global analysis of phase-locked loop based circuits.

A Two-Layer Gene Circuit for Decoupling Cell Growth from Metabolite Production.

Science.gov (United States)

Lo, Tat-Ming; Chng, Si Hui; Teo, Wei Suong; Cho, Han-Saem; Chang, Matthew Wook

2016-08-01

We present a synthetic gene circuit for decoupling cell growth from metabolite production through autonomous regulation of enzymatic pathways by integrated modules that sense nutrient and substrate. The two-layer circuit allows Escherichia coli to selectively utilize target substrates in a mixed pool; channel metabolic resources to growth by delaying enzymatic conversion until nutrient depletion; and activate, terminate, and re-activate conversion upon substrate availability. We developed two versions of controller, both of which have glucose nutrient sensors but differ in their substrate-sensing modules. One controller is specific for hydroxycinnamic acid and the other for oleic acid. Our hydroxycinnamic acid controller lowered metabolic stress 2-fold and increased the growth rate 2-fold and productivity 5-fold, whereas our oleic acid controller lowered metabolic stress 2-fold and increased the growth rate 1.3-fold and productivity 2.4-fold. These results demonstrate the potential for engineering strategies that decouple growth and production to make bio-based production more economical and sustainable. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Circuit arrangement of an electronic component for the design of fail-safe protective circuits

International Nuclear Information System (INIS)

Centmaier, W.; Bernhard, U.; Friederich, B.; Heisecke, I.

1974-01-01

The critical parameters of reactors are controlled by safety circuits. These circuits are controlled designed as logic modules operating by the 'n-out-of-m' selection principle. In most cases, a combination of a '1-out-of-3' circuit with a '2-out-of-3' circuit and separate indication is sufficient for a dynamic fail-safe circuit. The basic logic elements are AND and OR gate circuits, respectively, which are triggered by pulse trains and in which the failure of a pulse train is indicated as an error at the output. The module allows the design of safety circuits offering various degrees of safety. If the indication of an error is made on the modules, faulty components can be exchanged by the maintenance crew right away. (DG) [de

Quantum circuit dynamics via path integrals: Is there a classical action for discrete-time paths?

International Nuclear Information System (INIS)

Penney, Mark D; Koh, Dax Enshan; Spekkens, Robert W

2017-01-01

It is straightforward to compute the transition amplitudes of a quantum circuit using the sum-over-paths methodology when the gates in the circuit are balanced, where a balanced gate is one for which all non-zero transition amplitudes are of equal magnitude. Here we consider the question of whether, for such circuits, the relative phases of different discrete-time paths through the configuration space can be defined in terms of a classical action, as they are for continuous-time paths. We show how to do so for certain kinds of quantum circuits, namely, Clifford circuits where the elementary systems are continuous-variable systems or discrete systems of odd-prime dimension. These types of circuit are distinguished by having phase-space representations that serve to define their classical counterparts. For discrete systems, the phase-space coordinates are also discrete variables. We show that for each gate in the generating set, one can associate a symplectomorphism on the phase-space and to each of these one can associate a generating function, defined on two copies of the configuration space. For discrete systems, the latter association is achieved using tools from algebraic geometry. Finally, we show that if the action functional for a discrete-time path through a sequence of gates is defined using the sum of the corresponding generating functions, then it yields the correct relative phases for the path-sum expression. These results are likely to be relevant for quantizing physical theories where time is fundamentally discrete, characterizing the classical limit of discrete-time quantum dynamics, and proving complexity results for quantum circuits. (paper)

Regulatory heterochronies and loose temporal scaling between sea star and sea urchin regulatory circuits.

Science.gov (United States)

Gildor, Tsvia; Hinman, Veronica; Ben-Tabou-De-Leon, Smadar

2017-01-01

It has long been argued that heterochrony, a change in relative timing of a developmental process, is a major source of evolutionary innovation. Heterochronic changes of regulatory gene activation could be the underlying molecular mechanism driving heterochronic changes through evolution. Here, we compare the temporal expression profiles of key regulatory circuits between sea urchin and sea star, representative of two classes of Echinoderms that shared a common ancestor about 500 million years ago. The morphologies of the sea urchin and sea star embryos are largely comparable, yet, differences in certain mesodermal cell types and ectodermal patterning result in distinct larval body plans. We generated high resolution temporal profiles of 17 mesodermally-, endodermally- and ectodermally-expressed regulatory genes in the sea star, Patiria miniata, and compared these to their orthologs in the Mediterranean sea urchin, Paracentrotus lividus. We found that the maternal to zygotic transition is delayed in the sea star compared to the sea urchin, in agreement with the longer cleavage stage in the sea star. Interestingly, the order of gene activation shows the highest variation in the relatively diverged mesodermal circuit, while the correlations of expression dynamics are the highest in the strongly conserved endodermal circuit. We detected loose scaling of the developmental rates of these species and observed interspecies heterochronies within all studied regulatory circuits. Thus, after 500 million years of parallel evolution, mild heterochronies between the species are frequently observed and the tight temporal scaling observed for closely related species no longer holds.

Sub-circuits of a gene regulatory network control a developmental epithelial-mesenchymal transition.

Science.gov (United States)

Saunders, Lindsay R; McClay, David R

2014-04-01

Epithelial-mesenchymal transition (EMT) is a fundamental cell state change that transforms epithelial to mesenchymal cells during embryonic development, adult tissue repair and cancer metastasis. EMT includes a complex series of intermediate cell state changes including remodeling of the basement membrane, apical constriction, epithelial de-adhesion, directed motility, loss of apical-basal polarity, and acquisition of mesenchymal adhesion and polarity. Transcriptional regulatory state changes must ultimately coordinate the timing and execution of these cell biological processes. A well-characterized gene regulatory network (GRN) in the sea urchin embryo was used to identify the transcription factors that control five distinct cell changes during EMT. Single transcription factors were perturbed and the consequences followed with in vivo time-lapse imaging or immunostaining assays. The data show that five different sub-circuits of the GRN control five distinct cell biological activities, each part of the complex EMT process. Thirteen transcription factors (TFs) expressed specifically in pre-EMT cells were required for EMT. Three TFs highest in the GRN specified and activated EMT (alx1, ets1, tbr) and the 10 TFs downstream of those (tel, erg, hex, tgif, snail, twist, foxn2/3, dri, foxb, foxo) were also required for EMT. No single TF functioned in all five sub-circuits, indicating that there is no EMT master regulator. Instead, the resulting sub-circuit topologies suggest EMT requires multiple simultaneous regulatory mechanisms: forward cascades, parallel inputs and positive-feedback lock downs. The interconnected and overlapping nature of the sub-circuits provides one explanation for the seamless orchestration by the embryo of cell state changes leading to successful EMT.

2.5 Gbit/s Optical Receiver Front-End Circuit with High Sensitivity and Wide Dynamic Range

Science.gov (United States)

Zhu, Tiezhu; Mo, Taishan; Ye, Tianchun

2017-12-01

An optical receiver front-end circuit is designed for passive optical network and fabricated in a 0.18 um CMOS technology. The whole circuit consists of a transimpedance amplifier (TIA), a single-ended to differential amplifier and an output driver. The TIA employs a cascode stage as the input stage and auxiliary amplifier to reduce the miller effect. Current injecting technique is employed to enlarge the input transistor's transconductance, optimize the noise performance and overcome the lack of voltage headroom. To achieve a wide dynamic range, an automatic gain control circuit with self-adaptive function is proposed. Experiment results show an optical sensitivity of -28 dBm for a bit error rate of 10-10 at 2.5 Gbit/s and a maxim input optical power of 2 dBm using an external photodiode. The chip occupies an area of 1×0.9 mm2 and consumes around 30 mW from single 1.8 V supply. The front-end circuit can be used in various optical receivers.

Modeling in fast dynamics of accidents in the primary circuit of PWR type reactors

International Nuclear Information System (INIS)

Robbe, M.F.

2003-12-01

Two kinds of accidents, liable to occur in the primary circuit of a Pressurized Water Reactor and involving fast dynamic phenomena, are analyzed. The Loss Of Coolant Accident (LOCA) is the accident used to define the current PWR. It consists in a large-size break located in a pipe of the primary circuit. A blowdown wave propagates through the circuit. The pressure differences between the different zones of the reactor induce high stresses in the structures of the lower head and may degrade the reactor core. The primary circuit starts emptying from the break opening. Pressure decreases very quickly, involving a large steaming. Two thermal-hydraulic simulations of the blowdown phase of a LOCA are computed with the Europlexus code. The primary circuit is represented by a pipe-model including the hydraulic peculiarities of the circuit. The main differences between both computations concern the kind of reactor, the break location and model, and the initialization of the accidental operation. Steam explosion is a hypothetical severe accident liable to happen after a core melting. The molten part of the core (called corium) falls in the lower part of the reactor. The interaction between the hot corium and the cold water remaining at the bottom of the vessel induces a massive and violent vaporization of water, similar to an explosive phenomenon. A shock wave propagates in the vessel. what can damage seriously the neighbouring structures or drill the vessel. This work presents a synthesis of in-vessel parametrical studies carried out with the Europlexus code, the linkage of the thermal-hydraulic code Mc3d dedicated to the pre-mixing phase with the Europlexus code dealing with the explosion, and finally a benchmark between the Cigalon and Europlexus codes relative to the Vulcano mock-up. (author)

Sensitive detection of proteasomal activation using the Deg-On mammalian synthetic gene circuit.

Science.gov (United States)

Zhao, Wenting; Bonem, Matthew; McWhite, Claire; Silberg, Jonathan J; Segatori, Laura

2014-04-08

The ubiquitin proteasome system (UPS) has emerged as a drug target for diverse diseases characterized by altered proteostasis, but pharmacological agents that enhance UPS activity have been challenging to establish. Here we report the Deg-On system, a genetic inverter that translates proteasomal degradation of the transcriptional regulator TetR into a fluorescent signal, thereby linking UPS activity to an easily detectable output, which can be tuned using tetracycline. We demonstrate that this circuit responds to modulation of UPS activity in cell culture arising from the inhibitor MG-132 and activator PA28γ. Guided by predictive modelling, we enhanced the circuit's signal sensitivity and dynamic range by introducing a feedback loop that enables self-amplification of TetR. By linking UPS activity to a simple and tunable fluorescence output, these genetic inverters will enable a variety of applications, including screening for UPS activating molecules and selecting for mammalian cells with different levels of proteasome activity.

Dynamic pulse difference circuit

International Nuclear Information System (INIS)

Erickson, G.L.

1978-01-01

A digital electronic circuit of especial use for subtracting background activity pulses in gamma spectrometry is disclosed which comprises an up-down counter connected to count up with signal-channel pulses and to count down with background-channel pulses. A detector responsive to the count position of the up-down counter provides a signal when the up-down counter has completed one scaling sequence cycle of counts in the up direction. In an alternate embodiment, a detector responsive to the count position of the up-down counter provides a signal upon overflow of the counter

Circuit- and Diagnosis-Specific DNA Methylation Changes at γ-Aminobutyric Acid-Related Genes in Postmortem Human Hippocampus in Schizophrenia and Bipolar Disorder.

Science.gov (United States)

Ruzicka, W Brad; Subburaju, Sivan; Benes, Francine M

2015-06-01

Dysfunction related to γ-aminobutyric acid (GABA)-ergic neurotransmission in the pathophysiology of major psychosis has been well established by the work of multiple groups across several decades, including the widely replicated downregulation of GAD1. Prior gene expression and network analyses within the human hippocampus implicate a broader network of genes, termed the GAD1 regulatory network, in regulation of GAD1 expression. Several genes within this GAD1 regulatory network show diagnosis- and sector-specific expression changes within the circuitry of the hippocampus, influencing abnormal GAD1 expression in schizophrenia and bipolar disorder. To investigate the hypothesis that aberrant DNA methylation contributes to circuit- and diagnosis-specific abnormal expression of GAD1 regulatory network genes in psychotic illness. This epigenetic association study targeting GAD1 regulatory network genes was conducted between July 1, 2012, and June 30, 2014. Postmortem human hippocampus tissue samples were obtained from 8 patients with schizophrenia, 8 patients with bipolar disorder, and 8 healthy control participants matched for age, sex, postmortem interval, and other potential confounds from the Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, Massachusetts. We extracted DNA from laser-microdissected stratum oriens tissue of cornu ammonis 2/3 (CA2/3) and CA1 postmortem human hippocampus, bisulfite modified it, and assessed it with the Infinium HumanMethylation450 BeadChip (Illumina, Inc). The subset of CpG loci associated with GAD1 regulatory network genes was analyzed in R version 3.1.0 software (R Foundation) using the minfi package. Findings were validated using bisulfite pyrosequencing. Methylation levels at 1308 GAD1 regulatory network-associated CpG loci were assessed both as individual sites to identify differentially methylated positions and by sharing information among colocalized probes to identify differentially methylated regions. A total of

Nonchaoticity of Ordinary Differential Equations Describing Autonomous Transcriptional Regulatory Circuits

International Nuclear Information System (INIS)

Li Pengfei; Hu Gang; Chen Runsheng

2008-01-01

Gene transcriptional regulation (TR) processes are often described by coupled nonlinear ordinary differential equations (ODEs). When the dimension of TR circuits is high (e.g. n ≥ 3) the motions of the corresponding ODEs may, very probably, show self-sustained oscillations and chaos. On the other hand, chaoticity may be harmful for the normal biological functions of TR processes. In this letter we numerically study the dynamics of 3-gene TR ODEs in great detail, and investigate many 4-, 5-, and 10-gene TR systems by randomly choosing figures and parameters in the conventionally accepted ranges. And we find that oscillations are very seldom and no chaotic motion is observed, even if the dimension of systems is sufficiently high (n ≥ 3). It is argued that the observation of nonchaoticity of these ODEs agrees with normal functions of actual TR processes

Dynamic effective connectivity of inter-areal brain circuits.

Directory of Open Access Journals (Sweden)

Demian Battaglia

Full Text Available Anatomic connections between brain areas affect information flow between neuronal circuits and the synchronization of neuronal activity. However, such structural connectivity does not coincide with effective connectivity (or, more precisely, causal connectivity, related to the elusive question "Which areas cause the present activity of which others?". Effective connectivity is directed and depends flexibly on contexts and tasks. Here we show that dynamic effective connectivity can emerge from transitions in the collective organization of coherent neural activity. Integrating simulation and semi-analytic approaches, we study mesoscale network motifs of interacting cortical areas, modeled as large random networks of spiking neurons or as simple rate units. Through a causal analysis of time-series of model neural activity, we show that different dynamical states generated by a same structural connectivity motif correspond to distinct effective connectivity motifs. Such effective motifs can display a dominant directionality, due to spontaneous symmetry breaking and effective entrainment between local brain rhythms, although all connections in the considered structural motifs are reciprocal. We show then that transitions between effective connectivity configurations (like, for instance, reversal in the direction of inter-areal interactions can be triggered reliably by brief perturbation inputs, properly timed with respect to an ongoing local oscillation, without the need for plastic synaptic changes. Finally, we analyze how the information encoded in spiking patterns of a local neuronal population is propagated across a fixed structural connectivity motif, demonstrating that changes in the active effective connectivity regulate both the efficiency and the directionality of information transfer. Previous studies stressed the role played by coherent oscillations in establishing efficient communication between distant areas. Going beyond these early

A high-precision synchronization circuit for clock distribution

International Nuclear Information System (INIS)

Lu Chong; Tan Hongzhou; Duan Zhikui; Ding Yi

2015-01-01

In this paper, a novel structure of a high-precision synchronization circuit, HPSC, using interleaved delay units and a dynamic compensation circuit is proposed. HPSCs are designed for synchronization of clock distribution networks in large-scale integrated circuits, where high-quality clocks are required. The application of a hybrid structure of a coarse delay line and dynamic compensation circuit performs roughly the alignment of the clock signal in two clock cycles, and finishes the fine tuning in the next three clock cycles with the phase error suppressed under 3.8 ps. The proposed circuit is implemented and fabricated using a SMIC 0.13 μm 1P6M process with a supply voltage at 1.2 V. The allowed operation frequency ranges from 200 to 800 MHz, and the duty cycle ranges between [20%, 80%]. The active area of the core circuits is 245 × 134 μm 2 , and the power consumption is 1.64 mW at 500 MHz. (paper)

Rational design of modular circuits for gene transcription: A test of the bottom-up approach

Directory of Open Access Journals (Sweden)

Giordano Emanuele

2010-11-01

Full Text Available Abstract Background Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to the design. Results We used interchangeable modular biological parts to create a set of novel synthetic devices for controlling gene transcription, and we developed a mathematical model of the modular circuits. Model parameters were identified by experimental measurements from a subset of modular combinations. The model revealed an unexpected feature of the lactose repressor system, i.e. a residual binding affinity for the operator site by induced lactose repressor molecules. Once this residual affinity was taken into account, the model properly reproduced the experimental data from the training set. The parameters identified in the training set allowed the prediction of the behavior of networks not included in the identification procedure. Conclusions This study provides new quantitative evidences that the use of independent and well-characterized biological parts and mathematical modeling, what is called a bottom-up approach to the construction of gene networks, can allow the design of new and different devices re-using the same modular parts.

Revealing networks from dynamics: an introduction

International Nuclear Information System (INIS)

Timme, Marc; Casadiego, Jose

2014-01-01

What can we learn from the collective dynamics of a complex network about its interaction topology? Taking the perspective from nonlinear dynamics, we briefly review recent progress on how to infer structural connectivity (direct interactions) from accessing the dynamics of the units. Potential applications range from interaction networks in physics, to chemical and metabolic reactions, protein and gene regulatory networks as well as neural circuits in biology and electric power grids or wireless sensor networks in engineering. Moreover, we briefly mention some standard ways of inferring effective or functional connectivity. (topical review)

Circuit topology of self-interacting chains: implications for folding and unfolding dynamics.

Science.gov (United States)

Mugler, Andrew; Tans, Sander J; Mashaghi, Alireza

2014-11-07

Understanding the relationship between molecular structure and folding is a central problem in disciplines ranging from biology to polymer physics and DNA origami. Topology can be a powerful tool to address this question. For a folded linear chain, the arrangement of intra-chain contacts is a topological property because rearranging the contacts requires discontinuous deformations. Conversely, the topology is preserved when continuously stretching the chain while maintaining the contact arrangement. Here we investigate how the folding and unfolding of linear chains with binary contacts is guided by the topology of contact arrangements. We formalize the topology by describing the relations between any two contacts in the structure, which for a linear chain can either be in parallel, in series, or crossing each other. We show that even when other determinants of folding rate such as contact order and size are kept constant, this 'circuit' topology determines folding kinetics. In particular, we find that the folding rate increases with the fractions of parallel and crossed relations. Moreover, we show how circuit topology constrains the conformational phase space explored during folding and unfolding: the number of forbidden unfolding transitions is found to increase with the fraction of parallel relations and to decrease with the fraction of series relations. Finally, we find that circuit topology influences whether distinct intermediate states are present, with crossed contacts being the key factor. The approach presented here can be more generally applied to questions on molecular dynamics, evolutionary biology, molecular engineering, and single-molecule biophysics.

Circuit- and Diagnosis-Specific DNA Methylation Changes at γ-Aminobutyric Acid–Related Genes in Postmortem Human Hippocampus in Schizophrenia and Bipolar Disorder

Science.gov (United States)

Ruzicka, W. Brad; Subburaju, Sivan; Benes, Francine M.

2017-01-01

IMPORTANCE Dysfunction related to γ-aminobutyric acid (GABA)–ergic neurotransmission in the pathophysiology of major psychosis has been well established by the work of multiple groups across several decades, including the widely replicated downregulation of GAD1. Prior gene expression and network analyses within the human hippocampus implicate a broader network of genes, termed the GAD1 regulatory network, in regulation of GAD1 expression. Several genes within this GAD1 regulatory network show diagnosis- and sector-specific expression changes within the circuitry of the hippocampus, influencing abnormal GAD1 expression in schizophrenia and bipolar disorder. OBJECTIVE To investigate the hypothesis that aberrant DNA methylation contributes to circuit- and diagnosis-specific abnormal expression of GAD1 regulatory network genes in psychotic illness. DESIGN, SETTING, AND PARTICIPANTS This epigenetic association study targeting GAD1 regulatory network genes was conducted between July 1, 2012, and June 30, 2014. Postmortem human hippocampus tissue samples were obtained from 8patients with schizophrenia, 8 patients with bipolar disorder, and 8 healthy control participants matched for age, sex, postmortem interval, and other potential confounds from the Harvard Brain Tissue Resource Center, McLean Hospital, Belmont,Massachusetts. We extracted DNA from laser-microdissected stratum oriens tissue of cornu ammonis 2/3 (CA2/3) and CA1 postmortem human hippocampus, bisulfite modified it, and assessed it with the Infinium HumanMethylation450 BeadChip (Illumina, Inc). The subset of CpG loci associated with GAD1 regulatory network genes was analyzed in R version 3.1.0 software (R Foundation) using the minfi package. Findings were validated using bisulfite pyrosequencing. MAIN OUTCOMES AND MEASURES Methylation levels at 1308 GAD1 regulatory network–associated CpG loci were assessed both as individual sites to identify differentially methylated positions and by sharing

Isocost Lines Describe the Cellular Economy of Genetic Circuits.

Science.gov (United States)

Gyorgy, Andras; Jiménez, José I; Yazbek, John; Huang, Hsin-Ho; Chung, Hattie; Weiss, Ron; Del Vecchio, Domitilla

2015-08-04

Genetic circuits in living cells share transcriptional and translational resources that are available in limited amounts. This leads to unexpected couplings among seemingly unconnected modules, which result in poorly predictable circuit behavior. In this study, we determine these interdependencies between products of different genes by characterizing the economy of how transcriptional and translational resources are allocated to the production of proteins in genetic circuits. We discover that, when expressed from the same plasmid, the combinations of attainable protein concentrations are constrained by a linear relationship, which can be interpreted as an isocost line, a concept used in microeconomics. We created a library of circuits with two reporter genes, one constitutive and the other inducible in the same plasmid, without a regulatory path between them. In agreement with the model predictions, experiments reveal that the isocost line rotates when changing the ribosome binding site strength of the inducible gene and shifts when modifying the plasmid copy number. These results demonstrate that isocost lines can be employed to predict how genetic circuits become coupled when sharing resources and provide design guidelines for minimizing the effects of such couplings. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Duffing–van der Pol oscillator type dynamics in Murali–Lakshmanan–Chua (MLC) circuit

International Nuclear Information System (INIS)

Srinivasan, K.; Chandrasekar, V.K.; Venkatesan, A.; Raja Mohamed, I.

2016-01-01

Highlights: • Proposed an electronic circuit with diode based nonlinear element equivalent to a well known Murali–Lakshmanan–Chua (MLC) circuit. • For chosen circuit parameters this circuit admits familiar MLC type attractor and also Duffing–van der Pol circuit type chaotic attractor. • The performance of the circuit is investigated by means of explicit laboratory experiments, numerical simulations and analytical studies. - Abstract: We have constructed a simple second-order dissipative nonautonomous circuit exhibiting ordered and chaotic behaviour. This circuit is the well known Murali–Lakshmanan–Chua(MLC) circuit but with diode based nonlinear element. For chosen circuit parameters this circuit admits familiar MLC type attractor and also Duffing–van der Pol circuit type chaotic attractors. It is interesting to note that depending upon the circuit parameters the circuit shows both period doubling route to chaos and quasiperiodic route to chaos. In our study we have constructed two-parameter bifurcation diagrams in the forcing amplitude–frequency plane, one parameter bifurcation diagrams, Lyapunov exponents, 0–1 test and phase portrait. The performance of the circuit is investigated by means of laboratory experiments, numerical integration of appropriate mathematical model and explicit analytic studies.

Inferring gene expression dynamics via functional regression analysis

Directory of Open Access Journals (Sweden)

Leng Xiaoyan

2008-01-01

Full Text Available Abstract Background Temporal gene expression profiles characterize the time-dynamics of expression of specific genes and are increasingly collected in current gene expression experiments. In the analysis of experiments where gene expression is obtained over the life cycle, it is of interest to relate temporal patterns of gene expression associated with different developmental stages to each other to study patterns of long-term developmental gene regulation. We use tools from functional data analysis to study dynamic changes by relating temporal gene expression profiles of different developmental stages to each other. Results We demonstrate that functional regression methodology can pinpoint relationships that exist between temporary gene expression profiles for different life cycle phases and incorporates dimension reduction as needed for these high-dimensional data. By applying these tools, gene expression profiles for pupa and adult phases are found to be strongly related to the profiles of the same genes obtained during the embryo phase. Moreover, one can distinguish between gene groups that exhibit relationships with positive and others with negative associations between later life and embryonal expression profiles. Specifically, we find a positive relationship in expression for muscle development related genes, and a negative relationship for strictly maternal genes for Drosophila, using temporal gene expression profiles. Conclusion Our findings point to specific reactivation patterns of gene expression during the Drosophila life cycle which differ in characteristic ways between various gene groups. Functional regression emerges as a useful tool for relating gene expression patterns from different developmental stages, and avoids the problems with large numbers of parameters and multiple testing that affect alternative approaches.

On the Possibility of the Jerk Derivative in Electrical Circuits

Directory of Open Access Journals (Sweden)

J. F. Gómez-Aguilar

2016-01-01

Full Text Available A subclass of dynamical systems with a time rate of change of acceleration are called Newtonian jerky dynamics. Some mechanical and acoustic systems can be interpreted as jerky dynamics. In this paper we show that the jerk dynamics are naturally obtained for electrical circuits using the fractional calculus approach with order γ. We consider fractional LC and RL electrical circuits with 1⩽γ<2 for different source terms. The LC circuit has a frequency ω dependent on the order of the fractional differential equation γ, since it is defined as ω(γ=ω0γγ1-γ, where ω0 is the fundamental frequency. For γ=3/2, the system is described by a third-order differential equation with frequency ω~ω03/2, and assuming γ=2 the dynamics are described by a fourth differential equation for jerk dynamics with frequency ω~ω02.

Reconstructing Dynamic Promoter Activity Profiles from Reporter Gene Data

DEFF Research Database (Denmark)

Kannan, Soumya; Sams, Thomas; Maury, Jérôme

2018-01-01

activity despite the fact that the observed output may be dynamic and is a number of steps away from the transcription process. In fact, some promoters that are often thought of as constitutive can show changes in activity when growth conditions change. For these reasons, we have developed a system......Accurate characterization of promoter activity is important when designing expression systems for systems biology and metabolic engineering applications. Promoters that respond to changes in the environment enable the dynamic control of gene expression without the necessity of inducer compounds......, for example. However, the dynamic nature of these processes poses challenges for estimating promoter activity. Most experimental approaches utilize reporter gene expression to estimate promoter activity. Typically the reporter gene encodes a fluorescent protein that is used to infer a constant promoter...

Synchronous long-term oscillations in a synthetic gene circuit.

Science.gov (United States)

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.

Plug-and-Play Multicellular Circuits with Time-Dependent Dynamic Responses.

Science.gov (United States)

Urrios, Arturo; Gonzalez-Flo, Eva; Canadell, David; de Nadal, Eulàlia; Macia, Javier; Posas, Francesc

2018-04-20

Synthetic biology studies aim to develop cellular devices for biomedical applications. These devices, based on living instead of electronic or electromechanic technology, might provide alternative treatments for a wide range of diseases. However, the feasibility of these devices depends, in many cases, on complex genetic circuits that must fulfill physiological requirements. In this work, we explored the potential of multicellular architectures to act as an alternative to complex circuits for implementation of new devices. As a proof of concept, we developed specific circuits for insulin or glucagon production in response to different glucose levels. Here, we show that fundamental features, such as circuit's affinity or sensitivity, are dependent on the specific configuration of the multicellular consortia, providing a method for tuning these properties without genetic engineering. As an example, we have designed and built circuits with an incoherent feed-forward loop architecture (FFL) that can be easily adjusted to generate single pulse responses. Our results might serve as a blueprint for future development of cellular devices for glycemia regulation in diabetic patients.

Propagating gene expression fronts in a one-dimensional coupled system of artificial cells

Science.gov (United States)

Tayar, Alexandra M.; Karzbrun, Eyal; Noireaux, Vincent; Bar-Ziv, Roy H.

2015-12-01

Living systems employ front propagation and spatiotemporal patterns encoded in biochemical reactions for communication, self-organization and computation. Emulating such dynamics in minimal systems is important for understanding physical principles in living cells and in vitro. Here, we report a one-dimensional array of DNA compartments in a silicon chip as a coupled system of artificial cells, offering the means to implement reaction-diffusion dynamics by integrated genetic circuits and chip geometry. Using a bistable circuit we programmed a front of protein synthesis propagating in the array as a cascade of signal amplification and short-range diffusion. The front velocity is maximal at a saddle-node bifurcation from a bistable regime with travelling fronts to a monostable regime that is spatially homogeneous. Near the bifurcation the system exhibits large variability between compartments, providing a possible mechanism for population diversity. This demonstrates that on-chip integrated gene circuits are dynamical systems driving spatiotemporal patterns, cellular variability and symmetry breaking.

Implementation of Chua's circuit using simulated inductance

Science.gov (United States)

Gopakumar, K.; Premlet, B.; Gopchandran, K. G.

2011-05-01

In this study we describe how to build an inductorless version of the classic Chua's circuit. A suitable inductor for Chua's circuit is often hard to procure. The required inductor for the circuit is designed using simple circuit elements such as resistors, capacitors and operational amplifiers. The complete circuit can be implemented by using off-the-shelf components, and it can readily be integrated on a single chip. This design of Chua's circuit allows the original dynamics to be slowed down to just a few hertz, enabling implementation of sophisticated control schemes without severe time restrictions. Another novel feature of the circuit is that losses associated with capacitors due to leakages can easily be compensated by providing negative resistance using the same setup. The chaotic behaviour of the circuit is verified by PSpice and Multisim simulation and also by experimental study on a circuit breadboard. The results give excellent agreement with each other and with the results of previous investigators.

Prediction of regulatory gene pairs using dynamic time warping and gene ontology.

Science.gov (United States)

Yang, Andy C; Hsu, Hui-Huang; Lu, Ming-Da; Tseng, Vincent S; Shih, Timothy K

2014-01-01

Selecting informative genes is the most important task for data analysis on microarray gene expression data. In this work, we aim at identifying regulatory gene pairs from microarray gene expression data. However, microarray data often contain multiple missing expression values. Missing value imputation is thus needed before further processing for regulatory gene pairs becomes possible. We develop a novel approach to first impute missing values in microarray time series data by combining k-Nearest Neighbour (KNN), Dynamic Time Warping (DTW) and Gene Ontology (GO). After missing values are imputed, we then perform gene regulation prediction based on our proposed DTW-GO distance measurement of gene pairs. Experimental results show that our approach is more accurate when compared with existing missing value imputation methods on real microarray data sets. Furthermore, our approach can also discover more regulatory gene pairs that are known in the literature than other methods.

Microwave RF antennas and circuits nonlinearity applications in engineering

CERN Document Server

Aluf, Ofer

2017-01-01

This book describes a new concept for analyzing RF/microwave circuits, which includes RF/microwave antennas. The book is unique in its emphasis on practical and innovative microwave RF engineering applications. The analysis is based on nonlinear dynamics and chaos models and shows comprehensive benefits and results. All conceptual RF microwave circuits and antennas are innovative and can be broadly implemented in engineering applications. Given the dynamics of RF microwave circuits and antennas, they are suitable for use in a broad range of applications. The book presents analytical methods for microwave RF antennas and circuit analysis, concrete examples, and geometric examples. The analysis is developed systematically, starting with basic differential equations and their bifurcations, and subsequently moving on to fixed point analysis, limit cycles and their bifurcations. Engineering applications include microwave RF circuits and antennas in a variety of topological structures, RFID ICs and antennas, micros...

Variational integrators for electric circuits

International Nuclear Information System (INIS)

Ober-Blöbaum, Sina; Tao, Molei; Cheng, Mulin; Owhadi, Houman; Marsden, Jerrold E.

2013-01-01

In this contribution, we develop a variational integrator for the simulation of (stochastic and multiscale) electric circuits. When considering the dynamics of an electric circuit, one is faced with three special situations: 1. The system involves external (control) forcing through external (controlled) voltage sources and resistors. 2. The system is constrained via the Kirchhoff current (KCL) and voltage laws (KVL). 3. The Lagrangian is degenerate. Based on a geometric setting, an appropriate variational formulation is presented to model the circuit from which the equations of motion are derived. A time-discrete variational formulation provides an iteration scheme for the simulation of the electric circuit. Dependent on the discretization, the intrinsic degeneracy of the system can be canceled for the discrete variational scheme. In this way, a variational integrator is constructed that gains several advantages compared to standard integration tools for circuits; in particular, a comparison to BDF methods (which are usually the method of choice for the simulation of electric circuits) shows that even for simple LCR circuits, a better energy behavior and frequency spectrum preservation can be observed using the developed variational integrator

Coupling a universal DNA circuit with graphene sheets/polyaniline/AuNPs nanocomposites for the detection of BCR/ABL fusion gene

Energy Technology Data Exchange (ETDEWEB)

Chen, Xueping [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Wang, Li [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Department of Medical Laboratory, Chongqing Emergency Medical Center (Chongqing The Fourth Hospital), Chongqing, 400016 (China); Sheng, Shangchun [The No.2 Peoples' Hospital of Yibin, Sichuan, 644000 (China); Wang, Teng; Yang, Juan [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Xie, Guoming, E-mail: guomingxie@cqmu.edu.cn [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Feng, Wenli, E-mail: fengwlcqmu@sina.com [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China)

2015-08-19

This article described a novel method by coupling a universal DNA circuit with graphene sheets/polyaniline/AuNPs nanocomposites (GS/PANI/AuNPs) for highly sensitive and specific detection of BCR/ABL fusion gene (bcr/abl) in chronic myeloid leukemia (CML). DNA circuit known as catalyzed hairpin assembly (CHA) is enzyme-free and can be simply operated to achieve exponential amplification, which has been widely employed in biosensing. However, application of CHA has been hindered by the need of specially redesigned sequences for each single-stranded DNA input. Herein, a transducer hairpin (HP) was designed to obtain a universal DNA circuit with favorable signal-to-background ratio. To further improve signal amplification, GS/PANI/AuNPs with excellent conductivity and enlarged effective area were introduced into this DNA circuit. Consequently, by combining the advantages of CHA and GS/PANI/AuNPs, bcr/abl could be detected in a linear range from 10 pM to 20 nM with a detection limit of 1.05 pM. Moreover, this protocol showed excellent specificity, good stability and was successfully applied for the detection of real sample, which demonstrated its great potential in clinical application. - Highlights: • A transducer hairpin was designed to improve the versatility of DNA circuit. • GS/PANI/AuNPs were introduced to the DNA circuit for further signal amplification. • The established biosensor displayed high sensitivity and good specificity.

Theory of circuit block switch-off

Directory of Open Access Journals (Sweden)

S. Henzler

2004-01-01

Full Text Available Switching-off unused circuit blocks is a promising approach to supress static leakage currents in ultra deep sub-micron CMOS digital systems. Basic performance parameters of Circuit Block Switch-Off (CBSO schemes are defined and their dependence on basic circuit parameters is estimated. Therefore the design trade-off between strong leakage suppression in idle mode and adequate dynamic performance in active mode can be supported by simple analytic investigations. Additionally, a guideline for the estimation of the minimum time for which a block deactivation is useful is derived.

Developing a Domain Model for Relay Circuits

DEFF Research Database (Denmark)

Haxthausen, Anne Elisabeth

2009-01-01

In this paper we stepwise develop a domain model for relay circuits as used in railway control systems. First we provide an abstract, property-oriented model of networks consisting of components that can be glued together with connectors. This model is strongly inspired by a network model...... for railways madeby Bjørner et.al., however our model is more general: the components can be of any kind and can later be refined to e.g. railway components or circuit components. Then we show how the abstract network model can be refined into an explicit model for relay circuits. The circuit model describes...... the statics as well as the dynamics of relay circuits, i.e. how a relay circuit can be composed legally from electrical components as well as how the components may change state over time. Finally the circuit model is transformed into an executable model, and we show how a concrete circuit can be defined...

Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data

Science.gov (United States)

Schrader, Alexandra; Meyer, Katharina; Walther, Neele; Stolz, Ailine; Feist, Maren; Hand, Elisabeth; von Bonin, Frederike; Evers, Maurits; Kohler, Christian; Shirneshan, Katayoon; Vockerodt, Martina; Klapper, Wolfram; Szczepanowski, Monika; Murray, Paul G.; Bastians, Holger; Trümper, Lorenz; Spang, Rainer; Kube, Dieter

2016-01-01

To discover new regulatory pathways in B lymphoma cells, we performed a combined analysis of experimental, clinical and global gene expression data. We identified a specific cluster of genes that was coherently expressed in primary lymphoma samples and suppressed by activation of the B cell receptor (BCR) through αIgM treatment of lymphoma cells in vitro. This gene cluster, which we called BCR.1, includes numerous cell cycle regulators. A reduced expression of BCR.1 genes after BCR activation was observed in different cell lines and also in CD10+ germinal center B cells. We found that BCR activation led to a delayed entry to and progression of mitosis and defects in metaphase. Cytogenetic changes were detected upon long-term αIgM treatment. Furthermore, an inverse correlation of BCR.1 genes with c-Myc co-regulated genes in distinct groups of lymphoma patients was observed. Finally, we showed that the BCR.1 index discriminates activated B cell-like and germinal centre B cell-like diffuse large B cell lymphoma supporting the functional relevance of this new regulatory circuit and the power of guided clustering for biomarker discovery. PMID:27166259

Reconstructing Dynamic Promoter Activity Profiles from Reporter Gene Data.

Science.gov (United States)

Kannan, Soumya; Sams, Thomas; Maury, Jérôme; Workman, Christopher T

2018-03-16

Accurate characterization of promoter activity is important when designing expression systems for systems biology and metabolic engineering applications. Promoters that respond to changes in the environment enable the dynamic control of gene expression without the necessity of inducer compounds, for example. However, the dynamic nature of these processes poses challenges for estimating promoter activity. Most experimental approaches utilize reporter gene expression to estimate promoter activity. Typically the reporter gene encodes a fluorescent protein that is used to infer a constant promoter activity despite the fact that the observed output may be dynamic and is a number of steps away from the transcription process. In fact, some promoters that are often thought of as constitutive can show changes in activity when growth conditions change. For these reasons, we have developed a system of ordinary differential equations for estimating dynamic promoter activity for promoters that change their activity in response to the environment that is robust to noise and changes in growth rate. Our approach, inference of dynamic promoter activity (PromAct), improves on existing methods by more accurately inferring known promoter activity profiles. This method is also capable of estimating the correct scale of promoter activity and can be applied to quantitative data sets to estimate quantitative rates.

A bio-inspired spatial patterning circuit.

Science.gov (United States)

Chen, Kai-Yuan; Joe, Danial J; Shealy, James B; Land, Bruce R; Shen, Xiling

2014-01-01

Lateral Inhibition (LI) is a widely conserved patterning mechanism in biological systems across species. Distinct from better-known Turing patterns, LI depend on cell-cell contact rather than diffusion. We built an in silico genetic circuit model to analyze the dynamic properties of LI. The model revealed that LI amplifies differences between neighboring cells to push them into opposite states, hence forming stable 2-D patterns. Inspired by this insight, we designed and implemented an electronic circuit that recapitulates LI patterning dynamics. This biomimetic system serve as a physical model to elucidate the design principle of generating robust patterning through spatial feedback, regardless of the underlying devices being biological or electrical.

Hopf bifurcation analysis of Chen circuit with direct time delay feedback

International Nuclear Information System (INIS)

Hai-Peng, Ren; Wen-Chao, Li; Ding, Liu

2010-01-01

Direct time delay feedback can make non-chaotic Chen circuit chaotic. The chaotic Chen circuit with direct time delay feedback possesses rich and complex dynamical behaviours. To reach a deep and clear understanding of the dynamics of such circuits described by delay differential equations, Hopf bifurcation in the circuit is analysed using the Hopf bifurcation theory and the central manifold theorem in this paper. Bifurcation points and bifurcation directions are derived in detail, which prove to be consistent with the previous bifurcation diagram. Numerical simulations and experimental results are given to verify the theoretical analysis. Hopf bifurcation analysis can explain and predict the periodical orbit (oscillation) in Chen circuit with direct time delay feedback. Bifurcation boundaries are derived using the Hopf bifurcation analysis, which will be helpful for determining the parameters in the stabilisation of the originally chaotic circuit

Dynamic performance of maximum power point tracking circuits using sinusoidal extremum seeking control for photovoltaic generation

Science.gov (United States)

Leyva, R.; Artillan, P.; Cabal, C.; Estibals, B.; Alonso, C.

2011-04-01

The article studies the dynamic performance of a family of maximum power point tracking circuits used for photovoltaic generation. It revisits the sinusoidal extremum seeking control (ESC) technique which can be considered as a particular subgroup of the Perturb and Observe algorithms. The sinusoidal ESC technique consists of adding a small sinusoidal disturbance to the input and processing the perturbed output to drive the operating point at its maximum. The output processing involves a synchronous multiplication and a filtering stage. The filter instance determines the dynamic performance of the MPPT based on sinusoidal ESC principle. The approach uses the well-known root-locus method to give insight about damping degree and settlement time of maximum-seeking waveforms. This article shows the transient waveforms in three different filter instances to illustrate the approach. Finally, an experimental prototype corroborates the dynamic analysis.

Precise linear gating circuit on integrated microcircuits

Energy Technology Data Exchange (ETDEWEB)

Butskii, V.V.; Vetokhin, S.S.; Reznikov, I.V.

Precise linear gating circuit on four microcircuits is described. A basic flowsheet of the gating circuit is given. The gating circuit consists of two input differential cascades total load of which is two current followers possessing low input and high output resistances. Follower outlets are connected to high ohmic dynamic load formed with a current source which permits to get high amplification (>1000) at one cascade. Nonlinearity amounts to <0.1% in the range of input signal amplitudes of -10-+10 V. Front duration for an output signal with 10 V amplitude amounts to 100 ns. Attenuation of input signal with a closed gating circuit is 60 db. The gating circuits described is used in the device intended for processing of scintillation sensor signals.

Designing Robustness to Temperature in a Feedforward Loop Circuit

OpenAIRE

Sen, Shaunak; Kim, Jongmin; Murray, Richard M.

2013-01-01

Incoherent feedforward loops represent important biomolecular circuit elements capable of a rich set of dynamic behavior including adaptation and pulsed responses. Temperature can modulate some of these properties through its effect on the underlying reaction rate parameters. It is generally unclear how to design such a circuit where the properties are robust to variations in temperature. Here, we address this issue using a combination of tools from control and dynamical systems theory as wel...

Multistability in Chua's circuit with two stable node-foci

International Nuclear Information System (INIS)

Bao, B. C.; Wang, N.; Xu, Q.; Li, Q. D.

2016-01-01

Only using one-stage op-amp based negative impedance converter realization, a simplified Chua's diode with positive outer segment slope is introduced, based on which an improved Chua's circuit realization with more simpler circuit structure is designed. The improved Chua's circuit has identical mathematical model but completely different nonlinearity to the classical Chua's circuit, from which multiple attractors including coexisting point attractors, limit cycle, double-scroll chaotic attractor, or coexisting chaotic spiral attractors are numerically simulated and experimentally captured. Furthermore, with dimensionless Chua's equations, the dynamical properties of the Chua's system are studied including equilibrium and stability, phase portrait, bifurcation diagram, Lyapunov exponent spectrum, and attraction basin. The results indicate that the system has two symmetric stable nonzero node-foci in global adjusting parameter regions and exhibits the unusual and striking dynamical behavior of multiple attractors with multistability.

Timing Analysis of Genetic Logic Circuits using D-VASim

DEFF Research Database (Denmark)

Baig, Hasan; Madsen, Jan

and propagation delay analysis of single as well as cascaded geneticlogic circuits can be performed. D-VASim allows user to change the circuit parameters during runtime simulation to observe its effectson circuit’s timing behavior. The results obtained from D-VASim can be used not only to characterize the timing...... delay analysis may play a very significant role in the designing of genetic logic circuits. In thisdemonstration, we present the capability of D-VASim (Dynamic Virtual Analyzer and Simulator) to perform the timing and propagationdelay analysis of genetic logic circuits. Using D-VASim, the timing...... behavior of geneticlogic circuits but also to analyze the timing constraints of cascaded genetic logic circuits....

Evolution dynamics of a model for gene duplication under adaptive conflict

Science.gov (United States)

Ancliff, Mark; Park, Jeong-Man

2014-06-01

We present and solve the dynamics of a model for gene duplication showing escape from adaptive conflict. We use a Crow-Kimura quasispecies model of evolution where the fitness landscape is a function of Hamming distances from two reference sequences, which are assumed to optimize two different gene functions, to describe the dynamics of a mixed population of individuals with single and double copies of a pleiotropic gene. The evolution equations are solved through a spin coherent state path integral, and we find two phases: one is an escape from an adaptive conflict phase, where each copy of a duplicated gene evolves toward subfunctionalization, and the other is a duplication loss of function phase, where one copy maintains its pleiotropic form and the other copy undergoes neutral mutation. The phase is determined by a competition between the fitness benefits of subfunctionalization and the greater mutational load associated with maintaining two gene copies. In the escape phase, we find a dynamics of an initial population of single gene sequences only which escape adaptive conflict through gene duplication and find that there are two time regimes: until a time t* single gene sequences dominate, and after t* double gene sequences outgrow single gene sequences. The time t* is identified as the time necessary for subfunctionalization to evolve and spread throughout the double gene sequences, and we show that there is an optimum mutation rate which minimizes this time scale.

Dynamic and modular gene regulatory networks drive the development of gametogenesis.

Science.gov (United States)

Che, Dongxue; Wang, Yang; Bai, Weiyang; Li, Leijie; Liu, Guiyou; Zhang, Liangcai; Zuo, Yongchun; Tao, Shiheng; Hua, Jinlian; Liao, Mingzhi

2017-07-01

Gametogenesis is a complex process, which includes mitosis and meiosis and results in the production of ovum and sperm. The development of gametogenesis is dynamic and needs many different genes to work synergistically, but it is lack of global perspective research about this process. In this study, we detected the dynamic process of gametogenesis from the perspective of systems biology based on protein-protein interaction networks (PPINs) and functional analysis. Results showed that gametogenesis genes have strong synergistic effects in PPINs within and between different phases during the development. Addition to the synergistic effects on molecular networks, gametogenesis genes showed functional consistency within and between different phases, which provides the further evidence about the dynamic process during the development of gametogenesis. At last, we detected and provided the core molecular modules of different phases about gametogenesis. The gametogenesis genes and related modules can be obtained from our Web site Gametogenesis Molecule Online (GMO, http://gametsonline.nwsuaflmz.com/index.php), which is freely accessible. GMO may be helpful for the reference and application of these genes and modules in the future identification of key genes about gametogenesis. Summary, this work provided a computational perspective and frame to the analysis of the gametogenesis dynamics and modularity in both human and mouse. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Npas4 regulates excitatory-inhibitory balance within neural circuits through cell-type-specific gene programs.

Science.gov (United States)

Spiegel, Ivo; Mardinly, Alan R; Gabel, Harrison W; Bazinet, Jeremy E; Couch, Cameron H; Tzeng, Christopher P; Harmin, David A; Greenberg, Michael E

2014-05-22

The nervous system adapts to experience by inducing a transcriptional program that controls important aspects of synaptic plasticity. Although the molecular mechanisms of experience-dependent plasticity are well characterized in excitatory neurons, the mechanisms that regulate this process in inhibitory neurons are only poorly understood. Here, we describe a transcriptional program that is induced by neuronal activity in inhibitory neurons. We find that, while neuronal activity induces expression of early-response transcription factors such as Npas4 in both excitatory and inhibitory neurons, Npas4 activates distinct programs of late-response genes in inhibitory and excitatory neurons. These late-response genes differentially regulate synaptic input to these two types of neurons, promoting inhibition onto excitatory neurons while inducing excitation onto inhibitory neurons. These findings suggest that the functional outcomes of activity-induced transcriptional responses are adapted in a cell-type-specific manner to achieve a circuit-wide homeostatic response. Copyright © 2014 Elsevier Inc. All rights reserved.

Modeling in fast dynamics of accidents in the primary circuit of PWR type reactors; Modelisation en dynamique rapide d'accidents dans le circuit primaire des reacteurs a eau pressurisee

Energy Technology Data Exchange (ETDEWEB)

Robbe, M.F

2003-12-01

Two kinds of accidents, liable to occur in the primary circuit of a Pressurized Water Reactor and involving fast dynamic phenomena, are analyzed. The Loss Of Coolant Accident (LOCA) is the accident used to define the current PWR. It consists in a large-size break located in a pipe of the primary circuit. A blowdown wave propagates through the circuit. The pressure differences between the different zones of the reactor induce high stresses in the structures of the lower head and may degrade the reactor core. The primary circuit starts emptying from the break opening. Pressure decreases very quickly, involving a large steaming. Two thermal-hydraulic simulations of the blowdown phase of a LOCA are computed with the Europlexus code. The primary circuit is represented by a pipe-model including the hydraulic peculiarities of the circuit. The main differences between both computations concern the kind of reactor, the break location and model, and the initialization of the accidental operation. Steam explosion is a hypothetical severe accident liable to happen after a core melting. The molten part of the core (called corium) falls in the lower part of the reactor. The interaction between the hot corium and the cold water remaining at the bottom of the vessel induces a massive and violent vaporization of water, similar to an explosive phenomenon. A shock wave propagates in the vessel. what can damage seriously the neighbouring structures or drill the vessel. This work presents a synthesis of in-vessel parametrical studies carried out with the Europlexus code, the linkage of the thermal-hydraulic code Mc3d dedicated to the pre-mixing phase with the Europlexus code dealing with the explosion, and finally a benchmark between the Cigalon and Europlexus codes relative to the Vulcano mock-up. (author)

SEMICONDUCTOR INTEGRATED CIRCUITS: A reconfigurable analog baseband circuit for WLAN, WCDMA, and Bluetooth

Science.gov (United States)

Tao, Tong; Baoyong, Chi; Ziqiang, Wang; Ying, Zhang; Hanjun, Jiang; Zhihua, Wang

2010-05-01

A reconfigurable analog baseband circuit for WLAN, WCDMA, and Bluetooth in 0.35 μm CMOS is presented. The circuit consists of two variable gain amplifiers (VGA) in cascade and a Gm-C elliptic low-pass filter (LPF). The filter-order and the cut-off frequency of the LPF can be reconfigured to satisfy the requirements of various applications. In order to achieve the optimum power consumption, the bandwidth of the VGAs can also be dynamically reconfigured and some Gm cells can be cut off in the given application. Simulation results show that the analog baseband circuit consumes 16.8 mW for WLAN, 8.9 mW for WCDMA and only 6.5 mW for Bluetooth, all with a 3 V power supply. The analog baseband circuit could provide -10 to +40 dB variable gain, third-order low pass filtering with 1 MHz cut-off frequency for Bluetooth, fourth-order low pass filtering with 2.2 MHz cut-off frequency for WCDMA, and fifth-order low pass filtering with 11 MHz cut-off frequency for WLAN, respectively.

116 dB dynamic range CMOS readout circuit for MEMS capacitive accelerometer

International Nuclear Information System (INIS)

Long Shanli; Liu Yan; He Kejun; Tang Xinggang; Chen Qian

2014-01-01

A high stability in-circuit reprogrammable technique control system for a capacitive MEMS accelerometer is presented. Modulation and demodulation are used to separate the signal from the low frequency noise. A low-noise low-offset charge integrator is employed in this circuit to implement a capacitance-to-voltage converter and minimize the noise and offset. The application-specific integrated circuit (ASIC) is fabricated in a 0.5 μm one-ploy three-metal CMOS process. The measured results of the proposed circuit show that the noise floor of the ASIC is −116 dBV, the sensitivity of the accelerometer is 66 mV/g with a nonlinearity of 0.5%. The chip occupies 3.5 × 2.5 mm 2 and the current is 3.5 mA. (semiconductor integrated circuits)

A big data pipeline: Identifying dynamic gene regulatory networks from time-course Gene Expression Omnibus data with applications to influenza infection.

Science.gov (United States)

Carey, Michelle; Ramírez, Juan Camilo; Wu, Shuang; Wu, Hulin

2018-07-01

A biological host response to an external stimulus or intervention such as a disease or infection is a dynamic process, which is regulated by an intricate network of many genes and their products. Understanding the dynamics of this gene regulatory network allows us to infer the mechanisms involved in a host response to an external stimulus, and hence aids the discovery of biomarkers of phenotype and biological function. In this article, we propose a modeling/analysis pipeline for dynamic gene expression data, called Pipeline4DGEData, which consists of a series of statistical modeling techniques to construct dynamic gene regulatory networks from the large volumes of high-dimensional time-course gene expression data that are freely available in the Gene Expression Omnibus repository. This pipeline has a consistent and scalable structure that allows it to simultaneously analyze a large number of time-course gene expression data sets, and then integrate the results across different studies. We apply the proposed pipeline to influenza infection data from nine studies and demonstrate that interesting biological findings can be discovered with its implementation.

Development of a computer code for dynamic analysis of the primary circuit of advanced reactors

Energy Technology Data Exchange (ETDEWEB)

Rocha, Jussie Soares da; Lira, Carlos A.B.O.; Magalhaes, Mardson A. de Sa, E-mail: cabol@ufpe.b [Universidade Federal de Pernambuco (DEN/UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear

2011-07-01

Currently, advanced reactors are being developed, seeking for enhanced safety, better performance and low environmental impacts. Reactor designs must follow several steps and numerous tests before a conceptual project could be certified. In this sense, computational tools become indispensable in the preparation of such projects. Thus, this study aimed at the development of a computational tool for thermal-hydraulic analysis by coupling two computer codes to evaluate the influence of transients caused by pressure variations and flow surges in the region of the primary circuit of IRIS reactor between the core and the pressurizer. For the simulation, it was used a situation of 'insurge', characterized by the entry of water in the pressurizer, due to the expansion of the refrigerant in the primary circuit. This expansion was represented by a pressure disturbance in step form, through the block 'step' of SIMULINK, thus enabling the transient startup. The results showed that the dynamic tool, obtained through the coupling of the codes, generated very satisfactory responses within model limitations, preserving the most important phenomena in the process. (author)

Development of a computer code for dynamic analysis of the primary circuit of advanced reactors

International Nuclear Information System (INIS)

Rocha, Jussie Soares da; Lira, Carlos A.B.O.; Magalhaes, Mardson A. de Sa

2011-01-01

Currently, advanced reactors are being developed, seeking for enhanced safety, better performance and low environmental impacts. Reactor designs must follow several steps and numerous tests before a conceptual project could be certified. In this sense, computational tools become indispensable in the preparation of such projects. Thus, this study aimed at the development of a computational tool for thermal-hydraulic analysis by coupling two computer codes to evaluate the influence of transients caused by pressure variations and flow surges in the region of the primary circuit of IRIS reactor between the core and the pressurizer. For the simulation, it was used a situation of 'insurge', characterized by the entry of water in the pressurizer, due to the expansion of the refrigerant in the primary circuit. This expansion was represented by a pressure disturbance in step form, through the block 'step' of SIMULINK, thus enabling the transient startup. The results showed that the dynamic tool, obtained through the coupling of the codes, generated very satisfactory responses within model limitations, preserving the most important phenomena in the process. (author)

Experimentally simulating the dynamics of quantum light and matter at ultrastrong coupling using circuit QED (1) - implementation and matter dynamics -

Science.gov (United States)

Kounalakis, M.; Langford, N. K.; Sagastizabal, R.; Dickel, C.; Bruno, A.; Luthi, F.; Thoen, D. J.; Endo, A.; Dicarlo, L.

The field dipole coupling of quantum light and matter, described by the quantum Rabi model, leads to exotic phenomena when the coupling strength g becomes comparable or larger than the atom and photon frequencies ωq , r. In this ultra-strong coupling regime, excitations are not conserved, leading to collapse-revival dynamics in atom and photon parity and Schrödinger-cat-like atom-photon entanglement. We realize a quantum simulation of the Rabi model using a transmon qubit coupled to a resonator. In this first part, we describe our analog-digital approach to implement up to 90 symmetric Trotter steps, combining single-qubit gates with the Jaynes-Cummings interaction naturally present in our circuit QED system. Controlling the phase of microwave pulses defines a rotating frame and enables simulation of arbitrary parameter regimes of the Rabi model. We demonstrate measurements of qubit parity dynamics showing revivals at g /ωr > 0 . 8 for ωq = 0 and characteristic dynamics for nondegenerate ωq from g / 4 to g. Funding from the EU FP7 Project ScaleQIT, an ERC Grant, the Dutch Research Organization NWO, and Microsoft Research.

Crisis induced intermittency in a fourth-order autonomous electric circuit

International Nuclear Information System (INIS)

Stouboulos, I.N.; Miliou, A.N.; Valaristos, A.P.; Kyprianidis, I.M.; Anagnostopoulos, A.N.

2007-01-01

The chaotic dynamics of a fourth-order autonomous nonlinear electric circuit has been studied. The circuit consists of two active elements, one linear negative conductance and one nonlinear resistor exhibiting a symmetrical piecewise-linear v-i characteristic and two capacitances C 1 and C 2 , which serve as the control parameters of the system. Experimental time series and the corresponding phase portraits were used to register the intermittent behaviour of the corresponding dynamical system between two interacting subattractors. The distribution of the times τ, between successive transitions from the one subattractor to the other indicates that a crisis induced intermittency occurs in the studied circuit

A simple electronic circuit realization of the tent map

Energy Technology Data Exchange (ETDEWEB)

Campos-Canton, I. [Fac. de Ciencias, Universidad Autonoma de San Luis Potosi, Alvaro Obregon 64, 78000 San Luis Potosi, SLP (Mexico)], E-mail: icampos@galia.fc.uaslp.mx; Campos-Canton, E. [Departamento de Fisico Matematicas, Universidad Autonoma de San Luis Potosi, Alvaro Obregon 64, 78000 San Luis Potosi, SLP (Mexico)], E-mail: ecamp@uaslp.mx; Murguia, J.S. [Departamento de Fisico Matematicas, Universidad Autonoma de San Luis Potosi, Alvaro Obregon 64, 78000 San Luis Potosi, SLP (Mexico)], E-mail: ondeleto@uaslp.mx; Rosu, H.C. [Division de Materiales Avanzados, Instituto Potosino de Investigacion Cientifica y Tecnologica, Camino a la presa San Jose 2055, 78216 San Luis Potosi, SLP (Mexico)], E-mail: hcr@ipicyt.edu.mx

2009-10-15

We present a very simple electronic implementation of the tent map, one of the best-known discrete dynamical systems. This is achieved by using integrated circuits and passive elements only. The experimental behavior of the tent map electronic circuit is compared with its numerical simulation counterpart. We find that the electronic circuit presents fixed points, periodicity, period doubling, chaos and intermittency that match with high accuracy the corresponding theoretical values.

Chaos and multi-scroll attractors in RCL-shunted junction coupled Jerk circuit connected by memristor

Science.gov (United States)

Zhou, Ping; Ahmad, Bashir; Ren, Guodong; Wang, Chunni

2018-01-01

In this paper, a new four-variable dynamical system is proposed to set chaotic circuit composed of memristor and Josephson junction, and the dependence of chaotic behaviors on nonlinearity is investigated. A magnetic flux-controlled memristor is used to couple with the RCL-shunted junction circuit, and the dynamical behaviors can be modulated by changing the coupling intensity between the memristor and the RCL-shunted junction. Bifurcation diagram and Lyapunov exponent are calculated to confirm the emergence of chaos in the improved dynamical system. The outputs and dynamical behaviors can be controlled by the initial setting and external stimulus as well. As a result, chaos can be suppressed and spiking occurs in the sampled outputs under negative feedback, while applying positive feedback type via memristor can be effective to trigger chaos. Furthermore, it is found that the number of multi-attractors in the Jerk circuit can be modulated when memristor coupling is applied on the circuit. These results indicate that memristor coupling can be effective to control chaotic circuits and it is also useful to reproduce dynamical behaviors for neuronal activities. PMID:29342178

Chaos and multi-scroll attractors in RCL-shunted junction coupled Jerk circuit connected by memristor.

Science.gov (United States)

Ma, Jun; Zhou, Ping; Ahmad, Bashir; Ren, Guodong; Wang, Chunni

2018-01-01

In this paper, a new four-variable dynamical system is proposed to set chaotic circuit composed of memristor and Josephson junction, and the dependence of chaotic behaviors on nonlinearity is investigated. A magnetic flux-controlled memristor is used to couple with the RCL-shunted junction circuit, and the dynamical behaviors can be modulated by changing the coupling intensity between the memristor and the RCL-shunted junction. Bifurcation diagram and Lyapunov exponent are calculated to confirm the emergence of chaos in the improved dynamical system. The outputs and dynamical behaviors can be controlled by the initial setting and external stimulus as well. As a result, chaos can be suppressed and spiking occurs in the sampled outputs under negative feedback, while applying positive feedback type via memristor can be effective to trigger chaos. Furthermore, it is found that the number of multi-attractors in the Jerk circuit can be modulated when memristor coupling is applied on the circuit. These results indicate that memristor coupling can be effective to control chaotic circuits and it is also useful to reproduce dynamical behaviors for neuronal activities.

Josephson junction in the quantum mesoscopic electric circuits with charge discreteness

Science.gov (United States)

Pahlavani, H.

2018-04-01

A quantum mesoscopic electrical LC-circuit with charge discreteness including a Josephson junction is considered and a nonlinear Hamiltonian that describing the dynamic of such circuit is introduced. The quantum dynamical behavior (persistent current probability) is studied in the charge and phase regimes by numerical solution approaches. The time evolution of charge and current, number-difference and the bosonic phase and also the energy spectrum of a quantum mesoscopic electric LC-circuit with charge discreteness that coupled with a Josephson junction device are investigated. We show the role of the coupling energy and the electrostatic Coulomb energy of the Josephson junction in description of the quantum behavior and the spectral properties of a quantum mesoscopic electrical LC-circuits with charge discreteness.

Computational aspects of feedback in neural circuits.

Directory of Open Access Journals (Sweden)

Wolfgang Maass

2007-01-01

Full Text Available It has previously been shown that generic cortical microcircuit models can perform complex real-time computations on continuous input streams, provided that these computations can be carried out with a rapidly fading memory. We investigate the computational capability of such circuits in the more realistic case where not only readout neurons, but in addition a few neurons within the circuit, have been trained for specific tasks. This is essentially equivalent to the case where the output of trained readout neurons is fed back into the circuit. We show that this new model overcomes the limitation of a rapidly fading memory. In fact, we prove that in the idealized case without noise it can carry out any conceivable digital or analog computation on time-varying inputs. But even with noise, the resulting computational model can perform a large class of biologically relevant real-time computations that require a nonfading memory. We demonstrate these computational implications of feedback both theoretically, and through computer simulations of detailed cortical microcircuit models that are subject to noise and have complex inherent dynamics. We show that the application of simple learning procedures (such as linear regression or perceptron learning to a few neurons enables such circuits to represent time over behaviorally relevant long time spans, to integrate evidence from incoming spike trains over longer periods of time, and to process new information contained in such spike trains in diverse ways according to the current internal state of the circuit. In particular we show that such generic cortical microcircuits with feedback provide a new model for working memory that is consistent with a large set of biological constraints. Although this article examines primarily the computational role of feedback in circuits of neurons, the mathematical principles on which its analysis is based apply to a variety of dynamical systems. Hence they may also

Tomonaga-Luttinger physics in electronic quantum circuits.

Science.gov (United States)

Jezouin, S; Albert, M; Parmentier, F D; Anthore, A; Gennser, U; Cavanna, A; Safi, I; Pierre, F

2013-01-01

In one-dimensional conductors, interactions result in correlated electronic systems. At low energy, a hallmark signature of the so-called Tomonaga-Luttinger liquids is the universal conductance curve predicted in presence of an impurity. A seemingly different topic is the quantum laws of electricity, when distinct quantum conductors are assembled in a circuit. In particular, the conductances are suppressed at low energy, a phenomenon called dynamical Coulomb blockade. Here we investigate the conductance of mesoscopic circuits constituted by a short single-channel quantum conductor in series with a resistance, and demonstrate a proposed link to Tomonaga-Luttinger physics. We reformulate and establish experimentally a recently derived phenomenological expression for the conductance using a wide range of circuits, including carbon nanotube data obtained elsewhere. By confronting both conductance data and phenomenological expression with the universal Tomonaga-Luttinger conductance curve, we demonstrate experimentally the predicted mapping between dynamical Coulomb blockade and the transport across a Tomonaga-Luttinger liquid with an impurity.

Functional roles for noise in genetic circuits.

Science.gov (United States)

Eldar, Avigdor; Elowitz, Michael B

2010-09-09

The genetic circuits that regulate cellular functions are subject to stochastic fluctuations, or 'noise', in the levels of their components. Noise, far from just a nuisance, has begun to be appreciated for its essential role in key cellular activities. Noise functions in both microbial and eukaryotic cells, in multicellular development, and in evolution. It enables coordination of gene expression across large regulons, as well as probabilistic differentiation strategies that function across cell populations. At the longest timescales, noise may facilitate evolutionary transitions. Here we review examples and emerging principles that connect noise, the architecture of the gene circuits in which it is present, and the biological functions it enables. We further indicate some of the important challenges and opportunities going forward.

Logic circuits based on molecular spider systems.

Science.gov (United States)

Mo, Dandan; Lakin, Matthew R; Stefanovic, Darko

2016-08-01

Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Maximum Temperature Detection System for Integrated Circuits

Science.gov (United States)

Frankiewicz, Maciej; Kos, Andrzej

2015-03-01

The paper describes structure and measurement results of the system detecting present maximum temperature on the surface of an integrated circuit. The system consists of the set of proportional to absolute temperature sensors, temperature processing path and a digital part designed in VHDL. Analogue parts of the circuit where designed with full-custom technique. The system is a part of temperature-controlled oscillator circuit - a power management system based on dynamic frequency scaling method. The oscillator cooperates with microprocessor dedicated for thermal experiments. The whole system is implemented in UMC CMOS 0.18 μm (1.8 V) technology.

Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.

Science.gov (United States)

Gat-Viks, Irit; Chevrier, Nicolas; Wilentzik, Roni; Eisenhaure, Thomas; Raychowdhury, Raktima; Steuerman, Yael; Shalek, Alex K; Hacohen, Nir; Amit, Ido; Regev, Aviv

2013-04-01

Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness quantitative trait loci or reQTLs) and to position these variants in molecular circuit diagrams. We apply this approach to study variation in transcriptional responsiveness to pathogen components in dendritic cells from recombinant inbred mouse strains. We identify reQTLs that correlate with particular stimuli and position them in known pathways. For example, in response to a virus-like stimulus, a trans-acting variant responds as an activator of the antiviral response; using RNA interference, we identify Rgs16 as the likely causal gene. Our approach charts an experimental and analytic path to decipher the mechanisms underlying genetic variation in circuits that control responses to stimuli.

INVESTIGATION OF MECHANICAL STRESSES IN THE DRIVE SHAFT OF MV VACUUM CIRCUIT BREAKER

Directory of Open Access Journals (Sweden)

E. I. Baida

2017-03-01

Full Text Available Introduction. In the last 10-15 years a dominant position in the market of medium voltage circuit breakers, vacuum circuit breakers have taken in which as an actuator mono- or bistable actuators with permanent magnets are used. Such circuit breakers are characterized by simplicity of design, high reliability, require preventive maintenance for many years. Development, research and improvement of vacuum circuit breakers are carried out at the Department for Electrical Apparatus, National Technical University «Kharkiv Polytechnic Institute». While working on the circuit breakers, developers have to deal with two related objectives – electrical and mechanical. This paper considers the solution of one of these problems – calculation of mechanical forces in the drive shaft of the vacuum circuit breaker in static and dynamic modes. This work was preceded by the failure of the results of measurements of the prototype circuit breakers’ contacts. Measurements have shown that these values do not match the expected values (there were less than the value of 0.8 to 1 mm. The assumption about the reasons for this discrepancy needed to be detailed checked. The results of the work done are presented in this paper. Purpose. Investigation of static and dynamic mechanical stresses and strains in the drive shaft of the vacuum circuit breaker mechanism to determine its characteristics and material selection. Methods. The investigation of mechanical processes is performed by the finite element method in the COMSOL software package. Results. We obtain the static and dynamic characteristics of the circuit breaker drive shaft: deformations, reaction forces, stresses. These characteristics made it possible to determine the actual course of the contacts, select shaft material and calculate the forces acting on the bearings. Conclusions. It is shown that the contact velocity and contact pressure are different from the theoretical value due to the deformation of the

Precise regulation of gene expression dynamics favors complex promoter architectures.

Directory of Open Access Journals (Sweden)

Dirk Müller

2009-01-01

Full Text Available Promoters process signals through recruitment of transcription factors and RNA polymerase, and dynamic changes in promoter activity constitute a major noise source in gene expression. However, it is barely understood how complex promoter architectures determine key features of promoter dynamics. Here, we employ prototypical promoters of yeast ribosomal protein genes as well as simplified versions thereof to analyze the relations among promoter design, complexity, and function. These promoters combine the action of a general regulatory factor with that of specific transcription factors, a common motif of many eukaryotic promoters. By comprehensively analyzing stationary and dynamic promoter properties, this model-based approach enables us to pinpoint the structural characteristics underlying the observed behavior. Functional tradeoffs impose constraints on the promoter architecture of ribosomal protein genes. We find that a stable scaffold in the natural design results in low transcriptional noise and strong co-regulation of target genes in the presence of gene silencing. This configuration also exhibits superior shut-off properties, and it can serve as a tunable switch in living cells. Model validation with independent experimental data suggests that the models are sufficiently realistic. When combined, our results offer a mechanistic explanation for why specific factors are associated with low protein noise in vivo. Many of these findings hold for a broad range of model parameters and likely apply to other eukaryotic promoters of similar structure.

Experimentally simulating the dynamics of quantum light and matter at ultrastrong coupling using circuit QED (2) - light dynamics and light-matter entanglement -

Science.gov (United States)

Sagastizabal, R.; Langford, N. K.; Kounalakis, M.; Dickel, C.; Bruno, A.; Luthi, F.; Thoen, D. J.; Endo, A.; Dicarlo, L.

Light-matter interaction can lead to large photon build-up and hybrid atom-photon entanglement in the ultrastrong coupling (USC) regime, where the coupling strength becomes comparable to the eigenenergies of the system. Accessing the cavity degree of freedom, however, is an outstanding challenge in natural USC systems. In this talk, we directly probe light field dynamics in the USC regime using a digital simulation of the quantum Rabi model in a planar circuit QED chip with a transmon moderately coupled to a resonator. We produce high-accuracy USC light-matter dynamics, using second-order Trotterisation and up to 90 Trotter steps. We probe the average photon number, photon parity and perform Wigner tomography of the simulated field. Finally, we combine tomography of the resonator with qubit measurements to evidence the Schrödinger-cat-like atom-photon entanglement which is a key signature of light-matter dynamics in the USC regime. Funding from the EU FP7 Project ScaleQIT, the ERC Synergy Grant QC-lab, the Netherlands Organization of Scientic Research (NWO), and Microsoft Research.

A New Simple Chaotic Circuit Based on Memristor

Science.gov (United States)

Wu, Renping; Wang, Chunhua

In this paper, a new memristor is proposed, and then an emulator built from off-the-shelf solid state components imitating the behavior of the proposed memristor is presented. Multisim simulation and breadboard experiment are done on the emulator, exhibiting a pinched hysteresis loop in the voltage-current plane when the emulator is driven by a periodic excitation voltage. In addition, a new simple chaotic circuit is designed by using the proposed memristor and other circuit elements. It is exciting that this circuit with only a linear negative resistor, a capacitor, an inductor and a memristor can generate a chaotic attractor. The dynamical behaviors of the proposed chaotic system are analyzed by Lyapunov exponents, phase portraits and bifurcation diagrams. Finally, an electronic circuit is designed to implement the chaotic system. For the sake of simple circuit topology, the proposed chaotic circuit can be easily manufactured at low cost.

Coherent quantum dynamics launched by incoherent relaxation in a quantum circuit simulator of a light-harvesting complex

Science.gov (United States)

Chin, A. W.; Mangaud, E.; Atabek, O.; Desouter-Lecomte, M.

2018-06-01

Engineering and harnessing coherent excitonic transport in organic nanostructures has recently been suggested as a promising way towards improving manmade light-harvesting materials. However, realizing and testing the dissipative system-environment models underlying these proposals is presently very challenging in supramolecular materials. A promising alternative is to use simpler and highly tunable "quantum simulators" built from programmable qubits, as recently achieved in a superconducting circuit by Potočnik et al. [A. Potočnik et al., Nat. Commun. 9, 904 (2018), 10.1038/s41467-018-03312-x]. We simulate the real-time dynamics of an exciton coupled to a quantum bath as it moves through a network based on the quantum circuit of Potočnik et al. Using the numerically exact hierarchical equations of motion to capture the open quantum system dynamics, we find that an ultrafast but completely incoherent relaxation from a high-lying "bright" exciton into a doublet of closely spaced "dark" excitons can spontaneously generate electronic coherences and oscillatory real-space motion across the network (quantum beats). Importantly, we show that this behavior also survives when the environmental noise is classically stochastic (effectively high temperature), as in present experiments. These predictions highlight the possibilities of designing matched electronic and spectral noise structures for robust coherence generation that do not require coherent excitation or cold environments.

A 35fJ/Step differential successive approximation capacitive sensor readout circuit with quasi-dynamic operation

KAUST Repository

Omran, Hesham

2016-10-06

We propose a successive-approximation capacitive sensor readout circuit that achieves 35fJ/Step energy efficiency FoM, which represents 4× improvement over the state-of-the-art. A fully differential architecture is employed to provide robustness against common mode noise and errors. An inverter-based amplifier with near-threshold biasing provides robust, fast, and energy-efficient operation. Quasi-dynamic operation is used to maintain the energy efficiency for a scalable sample rate. A hybrid coarse-fine capacitive DAC achieves 11.7bit effective resolution in a compact area. © 2016 IEEE.

Chaos and multi-scroll attractors in RCL-shunted junction coupled Jerk circuit connected by memristor.

Directory of Open Access Journals (Sweden)

Jun Ma

Full Text Available In this paper, a new four-variable dynamical system is proposed to set chaotic circuit composed of memristor and Josephson junction, and the dependence of chaotic behaviors on nonlinearity is investigated. A magnetic flux-controlled memristor is used to couple with the RCL-shunted junction circuit, and the dynamical behaviors can be modulated by changing the coupling intensity between the memristor and the RCL-shunted junction. Bifurcation diagram and Lyapunov exponent are calculated to confirm the emergence of chaos in the improved dynamical system. The outputs and dynamical behaviors can be controlled by the initial setting and external stimulus as well. As a result, chaos can be suppressed and spiking occurs in the sampled outputs under negative feedback, while applying positive feedback type via memristor can be effective to trigger chaos. Furthermore, it is found that the number of multi-attractors in the Jerk circuit can be modulated when memristor coupling is applied on the circuit. These results indicate that memristor coupling can be effective to control chaotic circuits and it is also useful to reproduce dynamical behaviors for neuronal activities.

Logic analysis and verification of n-input genetic logic circuits

DEFF Research Database (Denmark)

Baig, Hasan; Madsen, Jan

2017-01-01

. In this paper, we present an approach to analyze and verify the Boolean logic of a genetic circuit from the data obtained through stochastic analog circuit simulations. The usefulness of this analysis is demonstrated through different case studies illustrating how our approach can be used to verify the expected......Nature is using genetic logic circuits to regulate the fundamental processes of life. These genetic logic circuits are triggered by a combination of external signals, such as chemicals, proteins, light and temperature, to emit signals to control other gene expressions or metabolic pathways...... accordingly. As compared to electronic circuits, genetic circuits exhibit stochastic behavior and do not always behave as intended. Therefore, there is a growing interest in being able to analyze and verify the logical behavior of a genetic circuit model, prior to its physical implementation in a laboratory...

Modelling, simulating and optimizing boiler heating surfaces and evaporator circuits

DEFF Research Database (Denmark)

Sørensen, K.; Condra, T.; Houbak, Niels

2003-01-01

A model for optimizing the dynamic performance of boiler have been developed. Design variables related to the size of the boiler and its dynamic performance have been defined. The object function to be optimized takes the weight of the boiler and its dynamic capability into account. As constraints...... for the optimization a dynamic model for the boiler is applied. Furthermore a function for the value of the dynamic performance is included in the model. The dynamic models for simulating boiler performance consists of a model for the flue gas side, a model for the evaporator circuit and a model for the drum....... The dynamic model has been developed for the purpose of determining boiler material temperatures and heat transfer from the flue gas side to the water-/steam side in order to simulate the circulation in the evaporator circuit and hereby the water level fluctuations in the drum. The dynamic model has been...

Global Analysis of miRNA Gene Clusters and Gene Families Reveals Dynamic and Coordinated Expression

Directory of Open Access Journals (Sweden)

Li Guo

2014-01-01

Full Text Available To further understand the potential expression relationships of miRNAs in miRNA gene clusters and gene families, a global analysis was performed in 4 paired tumor (breast cancer and adjacent normal tissue samples using deep sequencing datasets. The compositions of miRNA gene clusters and families are not random, and clustered and homologous miRNAs may have close relationships with overlapped miRNA species. Members in the miRNA group always had various expression levels, and even some showed larger expression divergence. Despite the dynamic expression as well as individual difference, these miRNAs always indicated consistent or similar deregulation patterns. The consistent deregulation expression may contribute to dynamic and coordinated interaction between different miRNAs in regulatory network. Further, we found that those clustered or homologous miRNAs that were also identified as sense and antisense miRNAs showed larger expression divergence. miRNA gene clusters and families indicated important biological roles, and the specific distribution and expression further enrich and ensure the flexible and robust regulatory network.

Genes and Social Behavior

OpenAIRE

Robinson, Gene E.; Fernald, Russell D.; Clayton, David F.

2008-01-01

What specific genes and regulatory sequences contribute to the organization and functioning of brain circuits that support social behavior? How does social experience interact with information in the genome to modulate these brain circuits? Here we address these questions by highlighting progress that has been made in identifying and understanding two key “vectors of influence” that link genes, brain, and social behavior: 1) social information alters gene readout in the brain to influence beh...

Dynamic gene and protein expression patterns of the autism-associated met receptor tyrosine kinase in the developing mouse forebrain.

Science.gov (United States)

Judson, Matthew C; Bergman, Mica Y; Campbell, Daniel B; Eagleson, Kathie L; Levitt, Pat

2009-04-10

The establishment of appropriate neural circuitry depends on the coordination of multiple developmental events across space and time. These events include proliferation, migration, differentiation, and survival-all of which can be mediated by hepatocyte growth factor (HGF) signaling through the Met receptor tyrosine kinase. We previously found a functional promoter variant of the MET gene to be associated with autism spectrum disorder, suggesting that forebrain circuits governing social and emotional function may be especially vulnerable to developmental disruptions in HGF/Met signaling. However, little is known about the spatiotemporal distribution of Met expression in the forebrain during the development of such circuits. To advance our understanding of the neurodevelopmental influences of Met activation, we employed complementary Western blotting, in situ hybridization, and immunohistochemistry to comprehensively map Met transcript and protein expression throughout perinatal and postnatal development of the mouse forebrain. Our studies reveal complex and dynamic spatiotemporal patterns of expression during this period. Spatially, Met transcript is localized primarily to specific populations of projection neurons within the neocortex and in structures of the limbic system, including the amygdala, hippocampus, and septum. Met protein appears to be principally located in axon tracts. Temporally, peak expression of transcript and protein occurs during the second postnatal week. This period is characterized by extensive neurite outgrowth and synaptogenesis, supporting a role for the receptor in these processes. Collectively, these data suggest that Met signaling may be necessary for the appropriate wiring of forebrain circuits, with particular relevance to the social and emotional dimensions of behavior. (c) 2009 Wiley-Liss, Inc.

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes.

Science.gov (United States)

Wang, Jun; Tao, Feng; Marowsky, Nicholas C; Fan, Chuanzhu

2016-09-01

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. © 2016 American Society of Plant Biologists. All rights reserved.

On the calculation of the equivalent circuit for an electrostatic probe

International Nuclear Information System (INIS)

Alekseev, B.V.; Kotel'nikov, V.A.; Cherepanov, V.V.

1982-01-01

An electric circuit of the probe including a nonlinear element - the layer of a volumetric charge - is considered. Free-molecular and gas dynamical modes are investigated. Calculations of transition processes in the probe circuit are conducted. Characteristic times of formation of the excited zone and the transition process in the circuit are compared. The threshold value of time constant of the circuit at which the transition process in the excited zone can be neglected is determined

Non-Gaussianity in a quasiclassical electronic circuit

Science.gov (United States)

Suzuki, Takafumi J.; Hayakawa, Hisao

2017-05-01

We study the non-Gaussian dynamics of a quasiclassical electronic circuit coupled to a mesoscopic conductor. Non-Gaussian noise accompanying the nonequilibrium transport through the conductor significantly modifies the stationary probability density function (PDF) of the flux in the dissipative circuit. We incorporate weak quantum fluctuation of the dissipative LC circuit with a stochastic method and evaluate the quantum correction of the stationary PDF. Furthermore, an inverse formula to infer the statistical properties of the non-Gaussian noise from the stationary PDF is derived in the classical-quantum crossover regime. The quantum correction is indispensable to correctly estimate the microscopic transfer events in the QPC with the quasiclassical inverse formula.

A model of gene expression based on random dynamical systems reveals modularity properties of gene regulatory networks.

Science.gov (United States)

Antoneli, Fernando; Ferreira, Renata C; Briones, Marcelo R S

2016-06-01

Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node is modeled by a RDS. The main virtues of this approach are the following: (i) it provides a natural way to obtain arbitrarily large networks by coupling together simple basic pieces, thus revealing the modularity of regulatory networks; (ii) the assumptions about the stochastic processes used in the modeling are fairly general, in the sense that the only requirement is stationarity; (iii) there is a well developed mathematical theory, which is a blend of smooth dynamical systems theory, ergodic theory and stochastic analysis that allows one to extract relevant dynamical and statistical information without solving the system; (iv) one may obtain the classical rate equations form the corresponding stochastic version by averaging the dynamic random variables (small noise limit). It is important to emphasize that unlike the deterministic case, where coupling two equations is a trivial matter, coupling two RDS is non-trivial, specially in our case, where the coupling is performed between a state variable of one gene and the switching stochastic process of another gene and, hence, it is not a priori true that the resulting coupled system will satisfy the definition of a random dynamical system. We shall provide the necessary arguments that ensure that our coupling prescription does indeed furnish a coupled regulatory network of random dynamical systems. Finally, the fact that classical rate equations are the small noise limit of our stochastic model ensures that any validation or prediction made on the basis of the classical theory is also a validation or prediction of our model. We illustrate our framework with some simple examples of single-gene system and network motifs. Copyright © 2016 Elsevier Inc. All rights reserved.

Genetic Spot Optimization for Peak Power Estimation in Large VLSI Circuits

Directory of Open Access Journals (Sweden)

Michael S. Hsiao

2002-01-01

Full Text Available Estimating peak power involves optimization of the circuit's switching function. The switching of a given gate is not only dependent on the output capacitance of the node, but also heavily dependent on the gate delays in the circuit, since multiple switching events can result from uneven circuit delay paths in the circuit. Genetic spot expansion and optimization are proposed in this paper to estimate tight peak power bounds for large sequential circuits. The optimization spot shifts and expands dynamically based on the maximum power potential (MPP of the nodes under optimization. Four genetic spot optimization heuristics are studied for sequential circuits. Experimental results showed an average of 70.7% tighter peak power bounds for large sequential benchmark circuits was achieved in short execution times.

Interrogating the Spatiotemporal Landscape of Neuromodulatory GPCR Signaling by Real-Time Imaging of cAMP in Intact Neurons and Circuits

Directory of Open Access Journals (Sweden)

Brian S. Muntean

2018-01-01

Full Text Available Summary: Modulation of neuronal circuits is key to information processing in the brain. The majority of neuromodulators exert their effects by activating G-protein-coupled receptors (GPCRs that control the production of second messengers directly impacting cellular physiology. How numerous GPCRs integrate neuromodulatory inputs while accommodating diversity of incoming signals is poorly understood. In this study, we develop an in vivo tool and analytical suite for analyzing GPCR responses by monitoring the dynamics of a key second messenger, cyclic AMP (cAMP, with excellent quantitative and spatiotemporal resolution in various neurons. Using this imaging approach in combination with CRISPR/Cas9 editing and optogenetics, we interrogate neuromodulatory mechanisms of defined populations of neurons in an intact mesolimbic reward circuit and describe how individual inputs generate discrete second-messenger signatures in a cell- and receptor-specific fashion. This offers a resource for studying native neuronal GPCR signaling in real time. : Muntean et al. develop an in vivo reagent to study processing of neurotransmitter GPCR signals by monitoring real-time dynamics of cAMP responses. They demonstrate application of this approach, in combination with CRISPR/Cas9 gene editing and optogenetics, to interrogate the functional organization of a striatal circuit. Keywords: cAMP, GPCR, neuromodulation, dopamine, striatum, imaging, optogenetics

Estimating the short-circuit impedance

DEFF Research Database (Denmark)

Nielsen, Arne Hejde; Pedersen, Knud Ole Helgesen; Poulsen, Niels Kjølstad

1997-01-01

A method for establishing a complex value of the short-circuit impedance from naturally occurring variations in voltage and current is discussed. It is the symmetrical three phase impedance at the fundamental grid frequency there is looked for. The positive sequence components in voltage...... and current are derived each period, and the short-circuit impedance is estimated from variations in these components created by load changes in the grid. Due to the noisy and dynamic grid with high harmonic distortion it is necessary to threat the calculated values statistical. This is done recursively...... through a RLS-algorithm. The algorithms have been tested and implemented on a PC at a 132 kV substation supplying a rolling mill. Knowing the short-circuit impedance gives the rolling mill an opportunity to adjust the arc furnace operation to keep flicker below a certain level. Therefore, the PC performs...

Multistability in Chua's circuit with two stable node-foci

Energy Technology Data Exchange (ETDEWEB)

Bao, B. C.; Wang, N.; Xu, Q. [School of Information Science and Engineering, Changzhou University, Changzhou 213164 (China); Li, Q. D. [Research Center of Analysis and Control for Complex Systems, Chongqing University of Posts and Telecommunications, Chongqing 400065 (China)

2016-04-15

Only using one-stage op-amp based negative impedance converter realization, a simplified Chua's diode with positive outer segment slope is introduced, based on which an improved Chua's circuit realization with more simpler circuit structure is designed. The improved Chua's circuit has identical mathematical model but completely different nonlinearity to the classical Chua's circuit, from which multiple attractors including coexisting point attractors, limit cycle, double-scroll chaotic attractor, or coexisting chaotic spiral attractors are numerically simulated and experimentally captured. Furthermore, with dimensionless Chua's equations, the dynamical properties of the Chua's system are studied including equilibrium and stability, phase portrait, bifurcation diagram, Lyapunov exponent spectrum, and attraction basin. The results indicate that the system has two symmetric stable nonzero node-foci in global adjusting parameter regions and exhibits the unusual and striking dynamical behavior of multiple attractors with multistability.

The elusive memristor: properties of basic electrical circuits

Energy Technology Data Exchange (ETDEWEB)

Joglekar, Yogesh N; Wolf, Stephen J [Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202 (United States)], E-mail: yojoglek@iupui.edu

2009-07-15

We present an introduction to and a tutorial on the properties of the recently discovered ideal circuit element, a memristor. By definition, a memristor M relates the charge q and the magnetic flux {phi} in a circuit and complements a resistor R, a capacitor C and an inductor L as an ingredient of ideal electrical circuits. The properties of these three elements and their circuits are a part of the standard curricula. The existence of the memristor as the fourth ideal circuit element was predicted in 1971 based on symmetry arguments, but was clearly experimentally demonstrated just last year. We present the properties of a single memristor, memristors in series and parallel, as well as ideal memristor-capacitor (MC), memristor-inductor (ML) and memristor-capacitor-inductor (MCL) circuits. We find that the memristor has hysteretic current-voltage characteristics. We show that the ideal MC (ML) circuit undergoes non-exponential charge (current) decay with two time scales and that by switching the polarity of the capacitor, an ideal MCL circuit can be tuned from overdamped to underdamped. We present simple models which show that these unusual properties are closely related to the memristor's internal dynamics. This tutorial complements the pedagogy of ideal circuit elements (R, C and L) and the properties of their circuits, and is aimed at undergraduate physics and electrical engineering students.

The elusive memristor: properties of basic electrical circuits

International Nuclear Information System (INIS)

Joglekar, Yogesh N; Wolf, Stephen J

2009-01-01

We present an introduction to and a tutorial on the properties of the recently discovered ideal circuit element, a memristor. By definition, a memristor M relates the charge q and the magnetic flux φ in a circuit and complements a resistor R, a capacitor C and an inductor L as an ingredient of ideal electrical circuits. The properties of these three elements and their circuits are a part of the standard curricula. The existence of the memristor as the fourth ideal circuit element was predicted in 1971 based on symmetry arguments, but was clearly experimentally demonstrated just last year. We present the properties of a single memristor, memristors in series and parallel, as well as ideal memristor-capacitor (MC), memristor-inductor (ML) and memristor-capacitor-inductor (MCL) circuits. We find that the memristor has hysteretic current-voltage characteristics. We show that the ideal MC (ML) circuit undergoes non-exponential charge (current) decay with two time scales and that by switching the polarity of the capacitor, an ideal MCL circuit can be tuned from overdamped to underdamped. We present simple models which show that these unusual properties are closely related to the memristor's internal dynamics. This tutorial complements the pedagogy of ideal circuit elements (R, C and L) and the properties of their circuits, and is aimed at undergraduate physics and electrical engineering students

A new hyperchaotic system and its circuit implementation

Science.gov (United States)

Yujun, Niu; Xingyuan, Wang; Mingjun, Wang; Huaguang, Zhang

2010-11-01

In this paper, a new hyperchaotic system is presented by adding a nonlinear controller to the three-dimensional autonomous chaotic system. The generated hyperchaotic system undergoes hyperchaos, chaos, and some different periodic orbits with control parameters changed. The complex dynamic behaviors are verified by means of Lyapunov exponent spectrum, bifurcation analysis, phase portraits and circuit realization. The Multisim results of the hyperchaotic circuit were well agreed with the simulation results.

Novel communication scheme based on chaotic Roessler circuits

International Nuclear Information System (INIS)

GarcIa-Lopez, J H; Jaimes-Reategui, R; Pisarchik, A N; MurguIa-Hernandez, A; Medina-Gutierrez, C; Valdivia-Hernadez, R; Villafana-Rauda, E

2005-01-01

We present a novel synchronization scheme for secure communication with two chaotic unidirectionally coupled Roessler circuits. The circuits are synchronized via one of the variables, while a signal is transmitted through another variable. We show that this scheme allows more stable communications. The system dynamics is studied numerically and experimentally in a wide range of a control parameter. The possibility of secure communications with an audio signal is demonstrated

Short- circuit tests of circuit breakers

OpenAIRE

Chorovský, P.

2015-01-01

This paper deals with short-circuit tests of low voltage electrical devices. In the first part of this paper, there are described basic types of short- circuit tests and their principles. Direct and indirect (synthetic) tests with more details are described in the second part. Each test and principles are explained separately. Oscilogram is obtained from short-circuit tests of circuit breakers at laboratory. The aim of this research work is to propose a test circuit for performing indirect test.

Dynamic gene expression for metabolic engineering of mammalian cells in culture.

Science.gov (United States)

Le, Huong; Vishwanathan, Nandita; Kantardjieff, Anne; Doo, Inseok; Srienc, Michael; Zheng, Xiaolu; Somia, Nikunj; Hu, Wei-Shou

2013-11-01

Recombinant mammalian cells are the major hosts for the production of protein therapeutics. In addition to high expression of the product gene, a hyper-producer must also harbor superior phenotypic traits related to metabolism, protein secretion, and growth control. Introduction of genes endowing the relevant hyper-productivity traits is a strategy frequently used to enhance the productivity. Most of such cell engineering efforts have been performed using constitutive expression systems. However, cells respond to various environmental cues and cellular events dynamically according to cellular needs. The use of inducible systems allows for time dependent expression, but requires external manipulation. Ideally, a transgene's expression should be synchronous to the host cell's own rhythm, and at levels appropriate for the objective. To that end, we identified genes with different expression dynamics and intensity ranges using pooled transcriptome data. Their promoters may be used to drive the expression of the transgenes following the desired dynamics. We isolated the promoter of the Thioredoxin-interacting protein (Txnip) gene and demonstrated its capability to drive transgene expression in concert with cell growth. We further employed this Chinese hamster promoter to engineer dynamic expression of the mouse GLUT5 fructose transporter in Chinese hamster ovary (CHO) cells, enabling them to utilize sugar according to cellular needs rather than in excess as typically seen in culture. Thus, less lactate was produced, resulting in a better growth rate, prolonged culture duration, and higher product titer. This approach illustrates a novel concept in metabolic engineering which can potentially be used to achieve dynamic control of cellular behaviors for enhanced process characteristics. © 2013 Published by Elsevier Inc.

Programmed coherent coupling in a synthetic DNA-based excitonic circuit

Science.gov (United States)

Boulais, Étienne; Sawaya, Nicolas P. D.; Veneziano, Rémi; Andreoni, Alessio; Banal, James L.; Kondo, Toru; Mandal, Sarthak; Lin, Su; Schlau-Cohen, Gabriela S.; Woodbury, Neal W.; Yan, Hao; Aspuru-Guzik, Alán; Bathe, Mark

2018-02-01

Natural light-harvesting systems spatially organize densely packed chromophore aggregates using rigid protein scaffolds to achieve highly efficient, directed energy transfer. Here, we report a synthetic strategy using rigid DNA scaffolds to similarly program the spatial organization of densely packed, discrete clusters of cyanine dye aggregates with tunable absorption spectra and strongly coupled exciton dynamics present in natural light-harvesting systems. We first characterize the range of dye-aggregate sizes that can be templated spatially by A-tracts of B-form DNA while retaining coherent energy transfer. We then use structure-based modelling and quantum dynamics to guide the rational design of higher-order synthetic circuits consisting of multiple discrete dye aggregates within a DX-tile. These programmed circuits exhibit excitonic transport properties with prominent circular dichroism, superradiance, and fast delocalized exciton transfer, consistent with our quantum dynamics predictions. This bottom-up strategy offers a versatile approach to the rational design of strongly coupled excitonic circuits using spatially organized dye aggregates for use in coherent nanoscale energy transport, artificial light-harvesting, and nanophotonics.

Multi-qubit circuit quantum electrodynamics

International Nuclear Information System (INIS)

Viehmann, Oliver

2013-01-01

Circuit QED systems are macroscopic, man-made quantum systems in which superconducting artificial atoms, also called Josephson qubits, interact with a quantized electromagnetic field. These systems have been devised to mimic the physics of elementary quantum optical systems with real atoms in a scalable and more flexible framework. This opens up a variety of possible applications of circuit QED systems. For instance, they provide a promising platform for processing quantum information. Recent years have seen rapid experimental progress on these systems, and experiments with multi-component circuit QED architectures are currently starting to come within reach. In this thesis, circuit QED systems with multiple Josephson qubits are studied theoretically. We focus on simple and experimentally realistic extensions of the currently operated circuit QED setups and pursue investigations in two main directions. First, we consider the equilibrium behavior of circuit QED systems containing a large number of mutually noninteracting Josephson charge qubits. The currently accepted standard description of circuit QED predicts the possibility of superradiant phase transitions in such systems. However, a full microscopic treatment shows that a no-go theorem for superradiant phase transitions known from atomic physics applies to circuit QED systems as well. This reveals previously unknown limitations of the applicability of the standard theory of circuit QED to multi-qubit systems. Second, we explore the potential of circuit QED for quantum simulations of interacting quantum many-body systems. We propose and analyze a circuit QED architecture that implements the quantum Ising chain in a time-dependent transverse magnetic field. Our setup can be used to study quench dynamics, the propagation of localized excitations, and other non-equilibrium features in this paradigmatic model in the theory of non-equilibrium thermodynamics and quantumcritical phenomena. The setup is based on a

Multi-qubit circuit quantum electrodynamics

Energy Technology Data Exchange (ETDEWEB)

Viehmann, Oliver

2013-09-03

Circuit QED systems are macroscopic, man-made quantum systems in which superconducting artificial atoms, also called Josephson qubits, interact with a quantized electromagnetic field. These systems have been devised to mimic the physics of elementary quantum optical systems with real atoms in a scalable and more flexible framework. This opens up a variety of possible applications of circuit QED systems. For instance, they provide a promising platform for processing quantum information. Recent years have seen rapid experimental progress on these systems, and experiments with multi-component circuit QED architectures are currently starting to come within reach. In this thesis, circuit QED systems with multiple Josephson qubits are studied theoretically. We focus on simple and experimentally realistic extensions of the currently operated circuit QED setups and pursue investigations in two main directions. First, we consider the equilibrium behavior of circuit QED systems containing a large number of mutually noninteracting Josephson charge qubits. The currently accepted standard description of circuit QED predicts the possibility of superradiant phase transitions in such systems. However, a full microscopic treatment shows that a no-go theorem for superradiant phase transitions known from atomic physics applies to circuit QED systems as well. This reveals previously unknown limitations of the applicability of the standard theory of circuit QED to multi-qubit systems. Second, we explore the potential of circuit QED for quantum simulations of interacting quantum many-body systems. We propose and analyze a circuit QED architecture that implements the quantum Ising chain in a time-dependent transverse magnetic field. Our setup can be used to study quench dynamics, the propagation of localized excitations, and other non-equilibrium features in this paradigmatic model in the theory of non-equilibrium thermodynamics and quantumcritical phenomena. The setup is based on a

Multiple coupled landscapes and non-adiabatic dynamics with applications to self-activating genes.

Science.gov (United States)

Chen, Cong; Zhang, Kun; Feng, Haidong; Sasai, Masaki; Wang, Jin

2015-11-21

Many physical, chemical and biochemical systems (e.g. electronic dynamics and gene regulatory networks) are governed by continuous stochastic processes (e.g. electron dynamics on a particular electronic energy surface and protein (gene product) synthesis) coupled with discrete processes (e.g. hopping among different electronic energy surfaces and on and off switching of genes). One can also think of the underlying dynamics as the continuous motion on a particular landscape and discrete hoppings among different landscapes. The main difference of such systems from the intra-landscape dynamics alone is the emergence of the timescale involved in transitions among different landscapes in addition to the timescale involved in a particular landscape. The adiabatic limit when inter-landscape hoppings are fast compared to continuous intra-landscape dynamics has been studied both analytically and numerically, but the analytical treatment of the non-adiabatic regime where the inter-landscape hoppings are slow or comparable to continuous intra-landscape dynamics remains challenging. In this study, we show that there exists mathematical mapping of the dynamics on 2(N) discretely coupled N continuous dimensional landscapes onto one single landscape in 2N dimensional extended continuous space. On this 2N dimensional landscape, eddy current emerges as a sign of non-equilibrium non-adiabatic dynamics and plays an important role in system evolution. Many interesting physical effects such as the enhancement of fluctuations, irreversibility, dissipation and optimal kinetics emerge due to non-adiabaticity manifested by the eddy current illustrated for an N = 1 self-activator. We further generalize our theory to the N-gene network with multiple binding sites and multiple synthesis rates for discretely coupled non-equilibrium stochastic physical and biological systems.

Dynamical consequences of bandpass feedback loops in a bacterial phosphorelay.

Directory of Open Access Journals (Sweden)

Shaunak Sen

Full Text Available Under conditions of nutrient limitation, Bacillus subtilis cells terminally differentiate into a dormant spore state. Progression to sporulation is controlled by a genetic circuit consisting of a phosphorelay embedded in multiple transcriptional feedback loops, which is used to activate the master regulator Spo0A by phosphorylation. These transcriptional regulatory interactions are "bandpass"-like, in the sense that activation occurs within a limited band of Spo0A∼P concentrations. Additionally, recent results show that the phosphorelay activation occurs in pulses, in a cell-cycle dependent fashion. However, the impact of these pulsed bandpass interactions on the circuit dynamics preceding sporulation remains unclear. In order to address this question, we measured key features of the bandpass interactions at the single-cell level and analyzed them in the context of a simple mathematical model. The model predicted the emergence of a delayed phase shift between the pulsing activity of the different sporulation genes, as well as the existence of a stable state, with elevated Spo0A activity but no sporulation, embedded within the dynamical structure of the system. To test the model, we used time-lapse fluorescence microscopy to measure dynamics of single cells initiating sporulation. We observed the delayed phase shift emerging during the progression to sporulation, while a re-engineering of the sporulation circuit revealed behavior resembling the predicted additional state. These results show that periodically-driven bandpass feedback loops can give rise to complex dynamics in the progression towards sporulation.

cDREM: inferring dynamic combinatorial gene regulation.

Science.gov (United States)

Wise, Aaron; Bar-Joseph, Ziv

2015-04-01

Genes are often combinatorially regulated by multiple transcription factors (TFs). Such combinatorial regulation plays an important role in development and facilitates the ability of cells to respond to different stresses. While a number of approaches have utilized sequence and ChIP-based datasets to study combinational regulation, these have often ignored the combinational logic and the dynamics associated with such regulation. Here we present cDREM, a new method for reconstructing dynamic models of combinatorial regulation. cDREM integrates time series gene expression data with (static) protein interaction data. The method is based on a hidden Markov model and utilizes the sparse group Lasso to identify small subsets of combinatorially active TFs, their time of activation, and the logical function they implement. We tested cDREM on yeast and human data sets. Using yeast we show that the predicted combinatorial sets agree with other high throughput genomic datasets and improve upon prior methods developed to infer combinatorial regulation. Applying cDREM to study human response to flu, we were able to identify several combinatorial TF sets, some of which were known to regulate immune response while others represent novel combinations of important TFs.

Nucleic acids for the rational design of reaction circuits.

Science.gov (United States)

Padirac, Adrien; Fujii, Teruo; Rondelez, Yannick

2013-08-01

Nucleic acid-based circuits are rationally designed in vitro assemblies that can perform complex preencoded programs. They can be used to mimic in silico computations. Recent works emphasized the modularity and robustness of these circuits, which allow their scaling-up. Another new development has led to dynamic, time-responsive systems that can display emergent behaviors like oscillations. These are closely related to biological architectures and provide an in vitro model of in vivo information processing. Nucleic acid circuits have already been used to handle various processes for technological or biotechnological purposes. Future applications of these chemical smart systems will benefit from the rapidly growing ability to design, construct, and model nucleic acid circuits of increasing size. Copyright © 2012 Elsevier Ltd. All rights reserved.

Experimental realization of synchronization in complex networks with Chua's circuits like nodes

International Nuclear Information System (INIS)

Posadas-Castillo, C.; Cruz-Hernandez, C.; Lopez-Gutierrez, R.M.

2009-01-01

In this paper, an experimental study on practical realization of synchronization in globally coupled networks with Chua's circuits like nodes is presented. Synchronization of coupled multiple Chua's circuits is achieved by appealing to results from complex systems theory. In particular, we design and implement electronically complex dynamical networks composed by three coupled Chua's circuits, considering two scenarios: (i) without master node, and (ii) with (periodic and chaotic) master node. The interactions in the networks are defined by coupling the first state of each Chua's circuit.

Chaos controlling problems for circuit systems with Josephson junction

International Nuclear Information System (INIS)

Gou, X-F; Wang, X; Xie, J-L

2008-01-01

The complex dynamical characters of the Josephson junction circuit system are studied and the tunnel effect is considered. The dynamical equation of the system is established. The route from periodic motion to chaos is illustrated using bifurcation diagram. An adscititious coupling controller is constructed to control the chaos

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes1[OPEN

Science.gov (United States)

Wang, Jun; Tao, Feng; Marowsky, Nicholas C.; Fan, Chuanzhu

2016-01-01

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella. Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. PMID:27485883

Sequent Calculus Representations for Quantum Circuits

Directory of Open Access Journals (Sweden)

Cameron Beebe

2016-06-01

Full Text Available When considering a sequent-style proof system for quantum programs, there are certain elements of quantum mechanics that we may wish to capture, such as phase, dynamics of unitary transformations, and measurement probabilities. Traditional quantum logics which focus primarily on the abstract orthomodular lattice theory and structures of Hilbert spaces have not satisfactorily captured some of these elements. We can start from 'scratch' in an attempt to conceptually characterize the types of proof rules which should be in a system that represents elements necessary for quantum algorithms. This present work attempts to do this from the perspective of the quantum circuit model of quantum computation. A sequent calculus based on single quantum circuits is suggested, and its ability to incorporate important conceptual and dynamic aspects of quantum computing is discussed. In particular, preserving the representation of phase helps illustrate the role of interference as a resource in quantum computation. Interference also provides an intuitive basis for a non-monotonic calculus.

Commutation circuit for an HVDC circuit breaker

Science.gov (United States)

Premerlani, William J.

1981-01-01

A commutation circuit for a high voltage DC circuit breaker incorporates a resistor capacitor combination and a charging circuit connected to the main breaker, such that a commutating capacitor is discharged in opposition to the load current to force the current in an arc after breaker opening to zero to facilitate arc interruption. In a particular embodiment, a normally open commutating circuit is connected across the contacts of a main DC circuit breaker to absorb the inductive system energy trapped by breaker opening and to limit recovery voltages to a level tolerable by the commutating circuit components.

An optoelectronic integrated device including a laser and its driving circuit

Energy Technology Data Exchange (ETDEWEB)

Matsueda, H.; Nakano, H.; Tanaka, T.P.

1984-10-01

A monolithic optoelectronic integrated circuit (OEIC) including a laser diode, photomonitor and driving and detecting circuits has been fabricated on a semi-insulating GaAs substrate. The OEIC has a horizontal integrating structure which is suitable for realising high-density multifunctional devices. The fabricating process and the static and dynamic characteristics of the optical and electronic elements are described. The preliminary results of the co-operative operation of the laser and its driving circuit are also presented.

Synthetic Biology: A Unifying View and Review Using Analog Circuits.

Science.gov (United States)

Teo, Jonathan J Y; Woo, Sung Sik; Sarpeshkar, Rahul

2015-08-01

We review the field of synthetic biology from an analog circuits and analog computation perspective, focusing on circuits that have been built in living cells. This perspective is well suited to pictorially, symbolically, and quantitatively representing the nonlinear, dynamic, and stochastic (noisy) ordinary and partial differential equations that rigorously describe the molecular circuits of synthetic biology. This perspective enables us to construct a canonical analog circuit schematic that helps unify and review the operation of many fundamental circuits that have been built in synthetic biology at the DNA, RNA, protein, and small-molecule levels over nearly two decades. We review 17 circuits in the literature as particular examples of feedforward and feedback analog circuits that arise from special topological cases of the canonical analog circuit schematic. Digital circuit operation of these circuits represents a special case of saturated analog circuit behavior and is automatically incorporated as well. Many issues that have prevented synthetic biology from scaling are naturally represented in analog circuit schematics. Furthermore, the deep similarity between the Boltzmann thermodynamic equations that describe noisy electronic current flow in subthreshold transistors and noisy molecular flux in biochemical reactions has helped map analog circuit motifs in electronics to analog circuit motifs in cells and vice versa via a `cytomorphic' approach. Thus, a body of knowledge in analog electronic circuit design, analysis, simulation, and implementation may also be useful in the robust and efficient design of molecular circuits in synthetic biology, helping it to scale to more complex circuits in the future.

A CMOS integrated timing discriminator circuit for fast scintillation counters

International Nuclear Information System (INIS)

Jochmann, M.W.

1998-01-01

Based on a zero-crossing discriminator using a CR differentiation network for pulse shaping, a new CMOS integrated timing discriminator circuit is proposed for fast (t r ≥ 2 ns) scintillation counters at the cooler synchrotron COSY-Juelich. By eliminating the input signal's amplitude information by means of an analog continuous-time divider, a normalized pulse shape at the zero-crossing point is gained over a wide dynamic input amplitude range. In combination with an arming comparator and a monostable multivibrator this yields in a highly precise timing discriminator circuit, that is expected to be useful in different time measurement applications. First measurement results of a CMOS integrated logarithmic amplifier, which is part of the analog continuous-time divider, agree well with the corresponding simulations. Moreover, SPICE simulations of the integrated discriminator circuit promise a time walk well below 200 ps (FWHM) over a 40 dB input amplitude dynamic range

Oscillator circuits

CERN Document Server

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

Measuring circuits

CERN Document Server

Graf, Rudolf F

1996-01-01

This series of circuits provides designers with a quick source for measuring 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 listings

Integrated circuits with emitter coupling and their application in nanosecond nuclear electronics

International Nuclear Information System (INIS)

Basiladze, S.G.

1976-01-01

Principal static and dynamic characteristics are considered of integrated circuits with emitter coupling, as well as problems of signal transmission. Diagrams are given of amplifiers, discriminators, time interval drivers, generators, etc. Systems and units of nanosecond electronics employing integrated circuits with emitter coupling are briefly described

Dynamics of gene expression with positive feedback to histone modifications at bivalent domains

Science.gov (United States)

Huang, Rongsheng; Lei, Jinzhi

2018-03-01

Experiments have shown that in embryonic stem cells, the promoters of many lineage-control genes contain “bivalent domains”, within which the nucleosomes possess both active (H3K4me3) and repressive (H3K27me3) marks. Such bivalent modifications play important roles in maintaining pluripotency in embryonic stem cells. Here, to investigate gene expression dynamics when there are regulations in bivalent histone modifications and random partition in cell divisions, we study how positive feedback to histone methylation/demethylation controls the transition dynamics of the histone modification patterns along with cell cycles. We constructed a computational model that includes dynamics of histone marks, three-stage chromatin state transitions, transcription and translation, feedbacks from protein product to enzymes to regulate the addition and removal of histone marks, and the inheritance of nucleosome state between cell cycles. The model reveals how dynamics of both nucleosome state transition and gene expression are dependent on the enzyme activities and feedback regulations. Results show that the combination of stochastic histone modification at each cell division and the deterministic feedback regulation work together to adjust the dynamics of chromatin state transition in stem cell regenerations.

Ancestral regulatory circuits governing ectoderm patterning downstream of Nodal and BMP2/4 revealed by gene regulatory network analysis in an echinoderm.

Directory of Open Access Journals (Sweden)

Alexandra Saudemont

2010-12-01

Full Text Available Echinoderms, which are phylogenetically related to vertebrates and produce large numbers of transparent embryos that can be experimentally manipulated, offer many advantages for the analysis of the gene regulatory networks (GRN regulating germ layer formation. During development of the sea urchin embryo, the ectoderm is the source of signals that pattern all three germ layers along the dorsal-ventral axis. How this signaling center controls patterning and morphogenesis of the embryo is not understood. Here, we report a large-scale analysis of the GRN deployed in response to the activity of this signaling center in the embryos of the Mediterranean sea urchin Paracentrotus lividus, in which studies with high spatial resolution are possible. By using a combination of in situ hybridization screening, overexpression of mRNA, recombinant ligand treatments, and morpholino-based loss-of-function studies, we identified a cohort of transcription factors and signaling molecules expressed in the ventral ectoderm, dorsal ectoderm, and interposed neurogenic ("ciliary band" region in response to the known key signaling molecules Nodal and BMP2/4 and defined the epistatic relationships between the most important genes. The resultant GRN showed a number of striking features. First, Nodal was found to be essential for the expression of all ventral and dorsal marker genes, and BMP2/4 for all dorsal genes. Second, goosecoid was identified as a central player in a regulatory sub-circuit controlling mouth formation, while tbx2/3 emerged as a critical factor for differentiation of the dorsal ectoderm. Finally, and unexpectedly, a neurogenic ectoderm regulatory circuit characterized by expression of "ciliary band" genes was triggered in the absence of TGF beta signaling. We propose a novel model for ectoderm regionalization, in which neural ectoderm is the default fate in the absence of TGF beta signaling, and suggest that the stomodeal and neural subcircuits that we

Resonance circuits for adiabatic circuits

Directory of Open Access Journals (Sweden)

C. Schlachta

2003-01-01

Full Text Available One of the possible techniques to reduces the power consumption in digital CMOS circuits is to slow down the charge transport. This slowdown can be achieved by introducing an inductor in the charging path. Additionally, the inductor can act as an energy storage element, conserving the energy that is normally dissipated during discharging. Together with the parasitic capacitances from the circuit a LCresonant circuit is formed.

Dynamic simulation of natural convection bypass two-circuit cycle refrigerator-freezer and its application Part I: Component models

International Nuclear Information System (INIS)

Ding Guoliang; Zhang Chunlu; Lu Zhili

2004-01-01

In order to reduce the greenhouse gas emissions, efficient household refrigerator/freezers (RFs) are required. Bypass two-circuit cycle RFs with one compressor are proved to be more efficient than two-evaporator in series cycle RFs. In order to study the characteristics and improve the design of bypass two-circuit cycle RFs, a dynamic model is developed in this paper. In part I, the mathematic models of all components are presented, considering not only the accuracy of the models but also the computation stability and speed to solve the models. An efficiency model that requires a single calorimeter data point at the standard test condition is employed for compressor. A multi-zone model is employed for condenser and for evaporator, with its wall thermal capacity considered by effective metal method. The approximate integral analytic model is employed for adiabatic capillary tube, and the effective inlet enthalpy method is used to transfer the non-adiabatic capillary tube to adiabatic capillary tube. The z-transfer function model is employed for cabinet load calculation

A low-power, CMOS peak detect and hold circuit for nuclear pulse spectroscopy

International Nuclear Information System (INIS)

Ericson, M.N.; Simpson, M.L.; Britton, C.L.; Allen, M.D.; Kroeger, R.A.; Inderhees, S.E.

1994-01-01

A low-power CMOS peak detecting track and hold circuit optimized for nuclear pulse spectroscopy is presented. The circuit topology eliminates the need for a rectifying diode, reducing the effect of charge injection into the hold capacitor, incorporates a linear gate at the input to prevent pulse pileup, and uses dynamic bias control that minimizes both pedestal and droop. Both positive-going and negative-going pulses are accommodated using a complementary set of track and hold circuits. Full characterization of the design fabricated in 1.2μm CMOS including dynamic range, integral nonlinearity, droop rate, pedestal, and power measurements is presented. Additionally, analysis and design approaches for optimization of operational characteristics are discussed

Complexity and competition in appetitive and aversive neural circuits

Directory of Open Access Journals (Sweden)

Crista L. Barberini

2012-11-01

Full Text Available Decision-making often involves using sensory cues to predict possible rewarding or punishing reinforcement outcomes before selecting a course of action. Recent work has revealed complexity in how the brain learns to predict rewards and punishments. Analysis of neural signaling during and after learning in the amygdala and orbitofrontal cortex, two brain areas that process appetitive and aversive stimuli, reveals a dynamic relationship between appetitive and aversive circuits. Specifically, the relationship between signaling in appetitive and aversive circuits in these areas shifts as a function of learning. Furthermore, although appetitive and aversive circuits may often drive opposite behaviors – approaching or avoiding reinforcement depending upon its valence – these circuits can also drive similar behaviors, such as enhanced arousal or attention; these processes also may influence choice behavior. These data highlight the formidable challenges ahead in dissecting how appetitive and aversive neural circuits interact to produce a complex and nuanced range of behaviors.

Dynamic gene expression analysis in a H1N1 influenza virus mouse pneumonia model.

Science.gov (United States)

Bao, Yanyan; Gao, Yingjie; Shi, Yujing; Cui, Xiaolan

2017-06-01

H1N1, a major pathogenic subtype of influenza A virus, causes a respiratory infection in humans and livestock that can range from a mild infection to more severe pneumonia associated with acute respiratory distress syndrome. Understanding the dynamic changes in the genome and the related functional changes induced by H1N1 influenza virus infection is essential to elucidating the pathogenesis of this virus and thereby determining strategies to prevent future outbreaks. In this study, we filtered the significantly expressed genes in mouse pneumonia using mRNA microarray analysis. Using STC analysis, seven significant gene clusters were revealed, and using STC-GO analysis, we explored the significant functions of these seven gene clusters. The results revealed GOs related to H1N1 virus-induced inflammatory and immune functions, including innate immune response, inflammatory response, specific immune response, and cellular response to interferon-beta. Furthermore, the dynamic regulation relationships of the key genes in mouse pneumonia were revealed by dynamic gene network analysis, and the most important genes were filtered, including Dhx58, Cxcl10, Cxcl11, Zbp1, Ifit1, Ifih1, Trim25, Mx2, Oas2, Cd274, Irgm1, and Irf7. These results suggested that during mouse pneumonia, changes in the expression of gene clusters and the complex interactions among genes lead to significant changes in function. Dynamic gene expression analysis revealed key genes that performed important functions. These results are a prelude to advancements in mouse H1N1 influenza virus infection biology, as well as the use of mice as a model organism for human H1N1 influenza virus infection studies.

A Circuit for Gradient Climbing in C. elegans Chemotaxis

Directory of Open Access Journals (Sweden)

Johannes Larsch

2015-09-01

Full Text Available Animals have a remarkable ability to track dynamic sensory information. For example, the nematode Caenorhabditis elegans can locate a diacetyl odor source across a 100,000-fold concentration range. Here, we relate neuronal properties, circuit implementation, and behavioral strategies underlying this robust navigation. Diacetyl responses in AWA olfactory neurons are concentration and history dependent; AWA integrates over time at low odor concentrations, but as concentrations rise, it desensitizes rapidly through a process requiring cilia transport. After desensitization, AWA retains sensitivity to small odor increases. The downstream AIA interneuron amplifies weak odor inputs and desensitizes further, resulting in a stereotyped response to odor increases over three orders of magnitude. The AWA-AIA circuit drives asymmetric behavioral responses to odor increases that facilitate gradient climbing. The adaptation-based circuit motif embodied by AWA and AIA shares computational properties with bacterial chemotaxis and the vertebrate retina, each providing a solution for maintaining sensitivity across a dynamic range.

Methods and Tools for the Analysis, Verification and Synthesis of Genetic Logic Circuits,

DEFF Research Database (Denmark)

Baig, Hasan

2017-01-01

. This usually requires simulating the mathematical models of these genetic circuits and perceive whether or not the circuit behaves appropriately. Furthermore, synthetic biology utilizes the concepts from electronic design automation (EDA) of abstraction and automated construction to generate genetic circuits...... that the proposed approach is effective to determine the variation in the behavior of genetic circuits when the circuit’s parameters are changed. In addition, the thesis also attempts to propose a synthesis and technology mapping tool, called GeneTech, for genetic circuits. It allows users to construct a genetic...... important design characteristics. This thesis also introduces an automated approach to analyze the behavior of genetic logic circuits from the simulation data. With this capability, the boolean logic of complex genetic circuits can be analyzed and/or verified automatically. It is also shown in this thesis...

Development of wide range charge integration application specified integrated circuit for photo-sensor

Energy Technology Data Exchange (ETDEWEB)

Katayose, Yusaku, E-mail: katayose@ynu.ac.jp [Department of Physics, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501 (Japan); Ikeda, Hirokazu [Institute of Space and Astronautical Science (ISAS)/Japan Aerospace Exploration Agency (JAXA), 3-1-1 Yoshinodai, Chuo-ku, Sagamihara, Kanagawa 252-5210 (Japan); Tanaka, Manobu [National Laboratory for High Energy Physics, KEK, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Shibata, Makio [Department of Physics, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501 (Japan)

2013-01-21

A front-end application specified integrated circuit (ASIC) is developed with a wide dynamic range amplifier (WDAMP) to read-out signals from a photo-sensor like a photodiode. The WDAMP ASIC consists of a charge sensitive preamplifier, four wave-shaping circuits with different amplification factors and Wilkinson-type analog-to-digital converter (ADC). To realize a wider range, the integrating capacitor in the preamplifier can be changed from 4 pF to 16 pF by a two-bit switch. The output of a preamplifier is shared by the four wave-shaping circuits with four gains of 1, 4, 16 and 64 to adapt the input range of ADC. A 0.25-μm CMOS process (of UMC electronics CO., LTD) is used to fabricate the ASIC with four-channels. The dynamic range of four orders of magnitude is achieved with the maximum range over 20 pC and the noise performance of 0.46 fC + 6.4×10{sup −4} fC/pF. -- Highlights: ► A front-end ASIC is developed with a wide dynamic range amplifier. ► The ASIC consists of a CSA, four wave-shaping circuits and pulse-height-to-time converters. ► The dynamic range of four orders of magnitude is achieved with the maximum range over 20 pC.

On the dynamics of a gene regulatory network

International Nuclear Information System (INIS)

Grammaticos, B; Carstea, A S; Ramani, A

2006-01-01

We examine the dynamics of a network of genes focusing on a periodic chain of genes, of arbitrary length. We show that within a given class of sigmoids representing the equilibrium probability of the binding of the RNA polymerase to the core promoter, the system possesses a single stable fixed point. By slightly modifying the sigmoid, introducing 'stiffer' forms, we show that it is possible to find network configurations exhibiting bistable behaviour. Our results do not depend crucially on the length of the chain considered: calculations with finite chains lead to similar results. However, a realistic study of regulatory genetic networks would require the consideration of more complex topologies and interactions

A parity checker circuit based on microelectromechanical resonator logic elements

KAUST Repository

Hafiz, Md Abdullah Al

2017-01-11

Micro/nano-electromechanical resonator based logic computation has attracted significant attention in recent years due to its dynamic mode of operation, ultra-low power consumption, and potential for reprogrammable and reversible computing. Here we demonstrate a 4-bit parity checker circuit by utilizing recently developed logic gates based on MEMS resonators. Toward this, resonance frequencies of shallow arch shaped micro resonators are electrothermally tuned by the logic inputs to constitute the required logic gates for the proposed parity checker circuit. This study demonstrates that by utilizing MEMS resonator based logic elements, complex digital circuits can be realized.

A parity checker circuit based on microelectromechanical resonator logic elements

KAUST Repository

Hafiz, Md Abdullah Al; Li, Ren; Younis, Mohammad I.; Fariborzi, Hossein

2017-01-01

Micro/nano-electromechanical resonator based logic computation has attracted significant attention in recent years due to its dynamic mode of operation, ultra-low power consumption, and potential for reprogrammable and reversible computing. Here we demonstrate a 4-bit parity checker circuit by utilizing recently developed logic gates based on MEMS resonators. Toward this, resonance frequencies of shallow arch shaped micro resonators are electrothermally tuned by the logic inputs to constitute the required logic gates for the proposed parity checker circuit. This study demonstrates that by utilizing MEMS resonator based logic elements, complex digital circuits can be realized.

Realization of Electronically Controllable Current-mode Square-rooting Circuit Based on MO-CFTA

OpenAIRE

P. Silapan; C. Chanapromma; T. Worachak

2011-01-01

This article proposes a current-mode square-rooting circuit using current follower transconductance amplifier (CTFA). The amplitude of the output current can be electronically controlled via input bias current with wide input dynamic range. The proposed circuit consists of only single CFTA. Without any matching conditions and external passive elements, the circuit is then appropriate for an IC architecture. The magnitude of the output signal is temperature-insensitive. Th...

Stability of operation versus temperature of a three-phase clock-driven chaotic circuit

International Nuclear Information System (INIS)

Zhou Ji-Chao; Son Hyunsik; Song Han Jung; Kim Namtae

2013-01-01

We evaluate the influence of temperature on the behavior of a three-phase clock-driven metal—oxide—semiconductor (MOS) chaotic circuit. The chaotic circuit consists of two nonlinear functions, a level shifter, and three sample and hold blocks. It is necessary to analyze a CMOS-based chaotic circuit with respect to variation in temperature for stability because the circuit is sensitive to the behavior of the circuit design parameters. The temperature dependence of the proposed chaotic circuit is investigated via the simulation program with integrated circuit emphasis (SPICE) using 0.6-μm CMOS process technology with a 5-V power supply and a 20-kHz clock frequency. The simulation results demonstrate the effects of temperature on the chaotic dynamics of the proposed chaotic circuit. The time series, frequency spectra, bifurcation phenomena, and Lyapunov exponent results are provided. (general)

Functional optical probing of the hippocampal trisynaptic circuit in vitro: network dynamics, filter properties, and polysynaptic induction of CA1 LTP.

Science.gov (United States)

Stepan, Jens; Dine, Julien; Eder, Matthias

2015-01-01

Decades of brain research have identified various parallel loops linking the hippocampus with neocortical areas, enabling the acquisition of spatial and episodic memories. Especially the hippocampal trisynaptic circuit [entorhinal cortex layer II → dentate gyrus (DG) → cornu ammonis (CA)-3 → CA1] was studied in great detail because of its seemingly simple connectivity and characteristic structures that are experimentally well accessible. While numerous researchers focused on functional aspects, obtained from a limited number of cells in distinct hippocampal subregions, little is known about the neuronal network dynamics which drive information across multiple synapses for subsequent long-term storage. Fast voltage-sensitive dye imaging in vitro allows real-time recording of activity patterns in large/meso-scale neuronal networks with high spatial resolution. In this way, we recently found that entorhinal theta-frequency input to the DG most effectively passes filter mechanisms of the trisynaptic circuit network, generating activity waves which propagate across the entire DG-CA axis. These "trisynaptic circuit waves" involve high-frequency firing of CA3 pyramidal neurons, leading to a rapid induction of classical NMDA receptor-dependent long-term potentiation (LTP) at CA3-CA1 synapses (CA1 LTP). CA1 LTP has been substantially evidenced to be essential for some forms of explicit learning in mammals. Here, we review data with particular reference to whole network-level approaches, illustrating how activity propagation can take place within the trisynaptic circuit to drive formation of CA1 LTP.

A Dynamic Connectome Supports the Emergence of Stable Computational Function of Neural Circuits through Reward-Based Learning.

Science.gov (United States)

Kappel, David; Legenstein, Robert; Habenschuss, Stefan; Hsieh, Michael; Maass, Wolfgang

2018-01-01

Synaptic connections between neurons in the brain are dynamic because of continuously ongoing spine dynamics, axonal sprouting, and other processes. In fact, it was recently shown that the spontaneous synapse-autonomous component of spine dynamics is at least as large as the component that depends on the history of pre- and postsynaptic neural activity. These data are inconsistent with common models for network plasticity and raise the following questions: how can neural circuits maintain a stable computational function in spite of these continuously ongoing processes, and what could be functional uses of these ongoing processes? Here, we present a rigorous theoretical framework for these seemingly stochastic spine dynamics and rewiring processes in the context of reward-based learning tasks. We show that spontaneous synapse-autonomous processes, in combination with reward signals such as dopamine, can explain the capability of networks of neurons in the brain to configure themselves for specific computational tasks, and to compensate automatically for later changes in the network or task. Furthermore, we show theoretically and through computer simulations that stable computational performance is compatible with continuously ongoing synapse-autonomous changes. After reaching good computational performance it causes primarily a slow drift of network architecture and dynamics in task-irrelevant dimensions, as observed for neural activity in motor cortex and other areas. On the more abstract level of reinforcement learning the resulting model gives rise to an understanding of reward-driven network plasticity as continuous sampling of network configurations.

Convergent synaptic and circuit substrates underlying autism genetic risks.

Science.gov (United States)

McGee, Aaron; Li, Guohui; Lu, Zhongming; Qiu, Shenfeng

2014-02-01

There has been a surge of diagnosis of autism spectrum disorders (ASD) over the past decade. While large, high powered genome screening studies of children with ASD have identified numerous genetic risk factors, research efforts to understanding how each of these risk factors contributes to the development autism has met with limited success. Revealing the mechanisms by which these genetic risk factors affect brain development and predispose a child to autism requires mechanistic understanding of the neurobiological changes underlying this devastating group of developmental disorders at multifaceted molecular, cellular and system levels. It has been increasingly clear that the normal trajectory of neurodevelopment is compromised in autism, in multiple domains as much as aberrant neuronal production, growth, functional maturation, patterned connectivity, and balanced excitation and inhibition of brain networks. Many autism risk factors identified in humans have been now reconstituted in experimental mouse models to allow mechanistic interrogation of the biological role of the risk gene. Studies utilizing these mouse models have revealed that underlying the enormous heterogeneity of perturbed cellular events, mechanisms directing synaptic and circuit assembly may provide a unifying explanation for the pathophysiological changes and behavioral endophenotypes seen in autism, although synaptic perturbations are far from being the only alterations relevant for ASD. In this review, we discuss synaptic and circuit abnormalities obtained from several prevalent mouse models, particularly those reflecting syndromic forms of ASD that are caused by single gene perturbations. These compiled results reveal that ASD risk genes contribute to proper signaling of the developing gene networks that maintain synaptic and circuit homeostasis, which is fundamental to normal brain development.

Project Circuits in a Basic Electric Circuits Course

Science.gov (United States)

Becker, James P.; Plumb, Carolyn; Revia, Richard A.

2014-01-01

The use of project circuits (a photoplethysmograph circuit and a simple audio amplifier), introduced in a sophomore-level electric circuits course utilizing active learning and inquiry-based methods, is described. The development of the project circuits was initiated to promote enhanced engagement and deeper understanding of course content among…

Mixed-mode chaotic circuit with Wien-bridge configuration: The results of experimental verification

International Nuclear Information System (INIS)

Kilic, Recai

2007-01-01

In this paper, we deal with the experimentally implementation of inductorless Wien bridge-based mixed-mode chaotic circuit (MMCC) which is capable to exhibit both linear and nonlinear oscillations. The results of experimental implementation agree with the results of theoretical and computer simulation presented in literature. Since the proposed implementation of MMCC circuit uses different design blocks such as Wien bridge-based autonomous circuit part, CFOA (current feedback operational amplifier)-based floating inductance simulator, CFOA-based Chua's diode and switching mechanism, it offers very versatile chaotic circuit model for studying autonomous and nonautonomous chaotic dynamics

Noise Expands the Response Range of the Bacillus subtilis Competence Circuit.

Directory of Open Access Journals (Sweden)

Andrew Mugler

2016-03-01

Full Text Available Gene regulatory circuits must contend with intrinsic noise that arises due to finite numbers of proteins. While some circuits act to reduce this noise, others appear to exploit it. A striking example is the competence circuit in Bacillus subtilis, which exhibits much larger noise in the duration of its competence events than a synthetically constructed analog that performs the same function. Here, using stochastic modeling and fluorescence microscopy, we show that this larger noise allows cells to exit terminal phenotypic states, which expands the range of stress levels to which cells are responsive and leads to phenotypic heterogeneity at the population level. This is an important example of how noise confers a functional benefit in a genetic decision-making circuit.

Dynamic compression of chondrocyte-agarose constructs reveals new candidate mechanosensitive genes.

Directory of Open Access Journals (Sweden)

Carole Bougault

Full Text Available Articular cartilage is physiologically exposed to repeated loads. The mechanical properties of cartilage are due to its extracellular matrix, and homeostasis is maintained by the sole cell type found in cartilage, the chondrocyte. Although mechanical forces clearly control the functions of articular chondrocytes, the biochemical pathways that mediate cellular responses to mechanical stress have not been fully characterised. The aim of our study was to examine early molecular events triggered by dynamic compression in chondrocytes. We used an experimental system consisting of primary mouse chondrocytes embedded within an agarose hydrogel; embedded cells were pre-cultured for one week and subjected to short-term compression experiments. Using Western blots, we demonstrated that chondrocytes maintain a differentiated phenotype in this model system and reproduce typical chondrocyte-cartilage matrix interactions. We investigated the impact of dynamic compression on the phosphorylation state of signalling molecules and genome-wide gene expression. After 15 min of dynamic compression, we observed transient activation of ERK1/2 and p38 (members of the mitogen-activated protein kinase (MAPK pathways and Smad2/3 (members of the canonical transforming growth factor (TGF-β pathways. A microarray analysis performed on chondrocytes compressed for 30 min revealed that only 20 transcripts were modulated more than 2-fold. A less conservative list of 325 modulated genes included genes related to the MAPK and TGF-β pathways and/or known to be mechanosensitive in other biological contexts. Of these candidate mechanosensitive genes, 85% were down-regulated. Down-regulation may therefore represent a general control mechanism for a rapid response to dynamic compression. Furthermore, modulation of transcripts corresponding to different aspects of cellular physiology was observed, such as non-coding RNAs or primary cilium. This study provides new insight into how

DQ reference frame modeling and control of single-phase active power decoupling circuits

DEFF Research Database (Denmark)

Tang, Yi; Qin, Zian; Blaabjerg, Frede

2015-01-01

. This paper presents the dq synchronous reference frame modeling of single-phase power decoupling circuits and a complete model describing the dynamics of dc-link ripple voltage is presented. The proposed model is universal and valid for both inductive and capacitive decoupling circuits, and the input...... of decoupling circuits can be either dependent or independent of its front-end converters. Based on this model, a dq synchronous reference frame controller is designed which allows the decoupling circuit to operate in two different modes because of the circuit symmetry. Simulation and experimental results...... are presented to verify the effectiveness of the proposed modeling and control method....

Circuit Implementation of Coronary Artery Chaos Phenomenon and Optimal PID Synchronization Controller Design

Directory of Open Access Journals (Sweden)

Cheng-Yu Yeh

2012-01-01

Full Text Available This study aimed at the implementation and synchronization control of cardiac circuit. First, the MATLAB-Simulink was used to simulate the dynamic behavior of cardiac chaotic circuit, and simple electronic modules were used to implement the cardiac system. Then the Particle Swarm Optimization (PSO was used to seek for the proportional, integral, and derivative gains of optimal PID controller, and the PID controller which could synchronize the slave cardiac circuit and the master cardiac circuit was obtained, in order to synchronize the master/slave chaotic cardiac circuits. This method can be provided for cardiac doctors to diagnose and medicate cardiac abnormality.

Implementation of chaotic secure communication systems based on OPA circuits

International Nuclear Information System (INIS)

Huang, C.-K.; Tsay, S.-C.; Wu, Y.-R.

2005-01-01

In this paper, we proposed a novel three-order autonomous circuit to construct a chaotic circuit with double scroll characteristic. The design idea is to use RLC elements and a nonlinear resistor. The one of salient features of the chaotic circuit is that the circuit with two flexible breakpoints of nonlinear element, and the advantage of the flexible breakpoint is that it increased complexity of the dynamical performance. Here, if we take a large and suitable breakpoint value, then the chaotic state can masking a large input signal in the circuit. Furthermore, we proposed a secure communication hyperchaotic system based on the proposed chaotic circuits, where the chaotic communication system is constituted by a chaotic transmitter and a chaotic receiver. To achieve the synchronization between the transmitter and the receiver, we are using a suitable Lyapunov function and Lyapunov theorem to design the feedback control gain. Thus, the transmitting message masked by chaotic state in the transmitter can be guaranteed to perfectly recover in the receiver. To achieve the systems performance, some basic components containing OPA, resistor and capacitor elements are used to implement the proposed communication scheme. From the viewpoints of circuit implementation, this proposed chaotic circuit is superior to the Chua chaotic circuits. Finally, the test results containing simulation and the circuit measurement are shown to demonstrate that the proposed method is correct and feasible

A parity checker circuit based on microelectromechanical resonator logic elements

Energy Technology Data Exchange (ETDEWEB)

Hafiz, Md Abdullah Al, E-mail: abdullah.hafiz@kaust.edu.sa [CEMSE Division, King Abdullah University of Science and Technology, Thuwal (Saudi Arabia); Li, Ren [CEMSE Division, King Abdullah University of Science and Technology, Thuwal (Saudi Arabia); Younis, Mohammad I. [PSE Division, King Abdullah University of Science and Technology, Thuwal (Saudi Arabia); Fariborzi, Hossein [CEMSE Division, King Abdullah University of Science and Technology, Thuwal (Saudi Arabia)

2017-03-03

Micro/nano-electromechanical resonator based logic computation has attracted significant attention in recent years due to its dynamic mode of operation, ultra-low power consumption, and potential for reprogrammable and reversible computing. Here we demonstrate a 4-bit parity checker circuit by utilizing recently developed logic gates based on MEMS resonators. Toward this, resonance frequencies of shallow arch shaped micro-resonators are electrothermally tuned by the logic inputs to constitute the required logic gates for the proposed parity checker circuit. This study demonstrates that by utilizing MEMS resonator based logic elements, complex digital circuits can be realized. - Highlights: • A 4-bit parity checker circuit is proposed and demonstrated based on MEMS resonator based logic elements. • Multiple copies of MEMS resonator based XOR logic gates are used to construct a complex logic circuit. • Functionality and feasibility of micro-resonator based logic platform is demonstrated.

An extended Kalman filtering approach to modeling nonlinear dynamic gene regulatory networks via short gene expression time series.

Science.gov (United States)

Wang, Zidong; Liu, Xiaohui; Liu, Yurong; Liang, Jinling; Vinciotti, Veronica

2009-01-01

In this paper, the extended Kalman filter (EKF) algorithm is applied to model the gene regulatory network from gene time series data. The gene regulatory network is considered as a nonlinear dynamic stochastic model that consists of the gene measurement equation and the gene regulation equation. After specifying the model structure, we apply the EKF algorithm for identifying both the model parameters and the actual value of gene expression levels. It is shown that the EKF algorithm is an online estimation algorithm that can identify a large number of parameters (including parameters of nonlinear functions) through iterative procedure by using a small number of observations. Four real-world gene expression data sets are employed to demonstrate the effectiveness of the EKF algorithm, and the obtained models are evaluated from the viewpoint of bioinformatics.

Solution of multiple circuits of steam cycle HTR system

International Nuclear Information System (INIS)

Li, Fu; Wang, Dengying; Hao, Chen; Zheng, Yanhua

2014-01-01

In order to analyze the dynamic operation performance and safety characteristics of the steam cycle high temperature gas cooled reactor (HTR) systems, it is necessary to find the solution of the whole HTR systems with all coupled circuits, including the primary circuit, the secondary circuit, and the residual heat removal system (RHRS). Considering that those circuits have their own individual fluidity and characteristics, some existing code packages for independent circuits themselves have been developed, for example THEMRIX and TINTE code for the primary circuit of the pebble bed reactor, BLAST for once through steam generator. To solve the coupled steam cycle HTR systems, a feasible way is to develop coupling method to integrate these independent code packages. This paper presents several coupling methods, e.g. the equivalent component method between the primary circuit and steam generator which reflect the close coupling relationship, the overlapping domain decomposition method between the primary circuit and the passive RHRS which reflects the loose coupling relationship. Through this way, the whole steam cycle HTR system with multiple circuits can be easily and efficiently solved by integration of several existing code packages. Based on this methodology, a code package TINTE–BLAST–RHRS was developed. Using this code package, some operation performance of HTR–PM was analyzed, such as the start-up process of the plant, and the depressurized loss of forced cooling accident when different number of residual heat removal trains is operated

Inferring Drosophila gap gene regulatory network: Pattern analysis of simulated gene expression profiles and stability analysis

OpenAIRE

Fomekong-Nanfack, Y.; Postma, M.; Kaandorp, J.A.

2009-01-01

Abstract Background Inference of gene regulatory networks (GRNs) requires accurate data, a method to simulate the expression patterns and an efficient optimization algorithm to estimate the unknown parameters. Using this approach it is possible to obtain alternative circuits without making any a priori assumptions about the interactions, which all simulate the observed patterns. It is important to analyze the properties of the circuits. Findings We have analyzed the simulated gene expression ...

Metal/dielectric thermal interfacial transport considering cross-interface electron-phonon coupling: Theory, two-temperature molecular dynamics, and thermal circuit

Science.gov (United States)

Lu, Zexi; Wang, Yan; Ruan, Xiulin

2016-02-01

The standard two-temperature equations for electron-phonon coupled thermal transport across metal/nonmetal interfaces are modified to include the possible coupling between metal electrons with substrate phonons. The previous two-temperature molecular dynamics (TT-MD) approach is then extended to solve these equations numerically at the atomic scale, and the method is demonstrated using Cu/Si interface as an example. A key parameter in TT-MD is the nonlocal coupling distance of metal electrons and nonmetal phonons, and here we use two different approximations. The first is based on Overhauser's "joint-modes" concept, while we use an interfacial reconstruction region as the length scale of joint region rather than the phonon mean-free path as in Overhauser's original model. In this region, the metal electrons can couple to the joint phonon modes. The second approximation is the "phonon wavelength" concept where electrons couple to phonons nonlocally within the range of one phonon wavelength. Compared with the original TT-MD, including the cross-interface electron-phonon coupling can slightly reduce the total thermal boundary resistance. Whether the electron-phonon coupling within the metal block is nonlocal or not does not make an obvious difference in the heat transfer process. Based on the temperature profiles from TT-MD, we construct a new mixed series-parallel thermal circuit. We show that such a thermal circuit is essential for understanding metal/nonmetal interfacial transport, while calculating a single resistance without solving temperature profiles as done in most previous studies is generally incomplete. As a comparison, the simple series circuit that neglects the cross-interface electron-phonon coupling could overestimate the interfacial resistance, while the simple parallel circuit in the original Overhauser's model underestimates the total interfacial resistance.

Additional signature of the dynamical Casimir effect in a superconducting circuit

International Nuclear Information System (INIS)

Rego, Andreson L.C.; Farina, C.; Silva, Hector O.; Alves, Danilo T.

2013-01-01

Full text: The dynamical Casimir effect (DCE) is one of the most fascinating quantum vacuum effects that consists, essentially, on the particle creation as a result of the interaction between a quantized field and a moving mirror. In this sense, particle creation due to external time-dependent potentials or backgrounds, or even time dependent electromagnetic properties of a material medium can also be included in a general definition of DCE. For simplicity, this interaction is simulated, in general, by means of idealized boundary conditions (BC). As a consequence of the particle creation, the moving mirror experiences a dissipative radiation reaction force acting on it. In order to generate an appreciable number of photons to be observed, the DCE was investigated in other contexts, as for example, in the circuit quantum electrodynamics. This theory predicted high photon creation rate by the modulation of the length of an open transmission line coupled to a superconducting quantum interference device (SQUID), an extremely sensitive magnetometer (J.R. Johansson et al, 2009/2010). A time dependent magnetic flux can be applied to the SQUID changing its inductance, leading to a time-dependent BC which simulates a moving boundary It was in the last scenario that the first observation of the DCE was announced by Wilson and collaborators (Wilson et al, 2011). Taking as motivation the experiment that observed the DCE, we investigate the influence of the generalized time-dependent Robin BC, that presents an extra term involving the second order time derivative of the field, in the particle creation via DCE. This kind of BC may appear quite naturally in the context of circuit quantum electrodynamics and the extra term was neglected in the theoretical aspects of the first observation of the DCE. Appropriate adjustments of this new parameter can not only enhance the total number of created particles but also give rise to a non-parabolic shape of the particle creation spectral

Circadian pacemaking in cells and circuits of the suprachiasmatic nucleus.

Science.gov (United States)

Hastings, M H; Brancaccio, M; Maywood, E S

2014-01-01

The suprachiasmatic nucleus (SCN) of the hypothalamus is the principal circadian pacemaker of the brain. It co-ordinates the daily rhythms of sleep and wakefulness, as well as physiology and behaviour, that set the tempo to our lives. Disturbance of this daily pattern, most acutely with jet-lag but more insidiously with rotational shift-work, can have severely deleterious effects for mental function and long-term health. The present review considers recent developments in our understanding of the properties of the SCN that make it a robust circadian time-keeper. It first focuses on the intracellular transcriptional/ translational feedback loops (TTFL) that constitute the cellular clockwork of the SCN neurone. Daily timing by these loops pivots around the negative regulation of the Period (Per) and Cryptochrome (Cry) genes by their protein products. The period of the circadian cycle is set by the relative stability of Per and Cry proteins, and this can be controlled by both genetic and pharmacological interventions. It then considers the function of these feedback loops in the context of cytosolic signalling by cAMP and intracellular calcium ([Ca(2+) ]i ), which are both outputs from, and inputs to, the TTFL, as well as the critical role of vasoactive intestinal peptide (VIP) signalling in synchronising cellular clocks across the SCN. Synchronisation by VIP in the SCN is paracrine, operating over an unconventionally long time frame (i.e. 24 h) and wide spatial domain, mediated via the cytosolic pathways upstream of the TTFL. Finally, we show how intersectional pharmacogenetics can be used to control G-protein-coupled signalling in individual SCN neurones, and how manipulation of Gq/[Ca(2+) ]i -signalling in VIP neurones can re-programme the circuit-level encoding of circadian time. Circadian pacemaking in the SCN therefore provides an unrivalled context in which to understand how a complex, adaptive behaviour can be organised by the dynamic activity of a relatively

Dynamic changes in the interchromosomal interaction of early histone gene loci during development of sea urchin.

Science.gov (United States)

Matsushita, Masaya; Ochiai, Hiroshi; Suzuki, Ken-Ichi T; Hayashi, Sayaka; Yamamoto, Takashi; Awazu, Akinori; Sakamoto, Naoaki

2017-12-15

The nuclear positioning and chromatin dynamics of eukaryotic genes are closely related to the regulation of gene expression, but they have not been well examined during early development, which is accompanied by rapid cell cycle progression and dynamic changes in nuclear organization, such as nuclear size and chromatin constitution. In this study, we focused on the early development of the sea urchin Hemicentrotus pulcherrimus and performed three-dimensional fluorescence in situ hybridization of gene loci encoding early histones (one of the types of histone in sea urchin). There are two non-allelic early histone gene loci per sea urchin genome. We found that during the morula stage, when the early histone gene expression levels are at their maximum, interchromosomal interactions were often formed between the early histone gene loci on separate chromosomes and that the gene loci were directed to locate to more interior positions. Furthermore, these interactions were associated with the active transcription of the early histone genes. Thus, such dynamic interchromosomal interactions may contribute to the efficient synthesis of early histone mRNA during the morula stage of sea urchin development. © 2017. Published by The Company of Biologists Ltd.

Phylogenetics and Gene Structure Dynamics of Polygalacturonase Genes in Aspergillus and Neurospora crassa

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Jin-Sung Hong

2013-09-01

Full Text Available Polygalacturonase (PG gene is a typical gene family present in eukaryotes. Forty-nine PGs were mined from the genomes of Neurospora crassa and five Aspergillus species. The PGs were classified into 3 clades such as clade 1 for rhamno-PGs, clade 2 for exo-PGs and clade 3 for exo- and endo-PGs, which were further grouped into 13 sub-clades based on the polypeptide sequence similarity. In gene structure analysis, a total of 124 introns were present in 44 genes and five genes lacked introns to give an average of 2.5 introns per gene. Intron phase distribution was 64.5% for phase 0, 21.8% for phase 1, and 13.7% for phase 2, respectively. The introns varied in their sequences and their lengths ranged from 20 bp to 424 bp with an average of 65.9 bp, which is approximately half the size of introns in other fungal genes. There were 29 homologous intron blocks and 26 of those were sub-clade specific. Intron losses were counted in 18 introns in which no obvious phase preference for intron loss was observed. Eighteen introns were placed at novel positions, which is considerably higher than those of plant PGs. In an evolutionary sense both intron loss and gain must have taken place for shaping the current PGs in these fungi. Together with the small intron size, low conservation of homologous intron blocks and higher number of novel introns, PGs of fungal species seem to have recently undergone highly dynamic evolution.

Protein dynamics in individual human cells: experiment and theory.

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Ariel Aharon Cohen

Full Text Available A current challenge in biology is to understand the dynamics of protein circuits in living human cells. Can one define and test equations for the dynamics and variability of a protein over time? Here, we address this experimentally and theoretically, by means of accurate time-resolved measurements of endogenously tagged proteins in individual human cells. As a model system, we choose three stable proteins displaying cell-cycle-dependant dynamics. We find that protein accumulation with time per cell is quadratic for proteins with long mRNA life times and approximately linear for a protein with short mRNA lifetime. Both behaviors correspond to a classical model of transcription and translation. A stochastic model, in which genes slowly switch between ON and OFF states, captures measured cell-cell variability. The data suggests, in accordance with the model, that switching to the gene ON state is exponentially distributed and that the cell-cell distribution of protein levels can be approximated by a Gamma distribution throughout the cell cycle. These results suggest that relatively simple models may describe protein dynamics in individual human cells.

Spontaneous Synchronization in Two Mutually Coupled Memristor-Based Chua’s Circuits: Numerical Investigations

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Eleonora Bilotta

2014-01-01

Full Text Available Chaotic dynamics of numerous memristor-based circuits is widely reported in literature. Recently, some works have appeared which study the problem of synchronization control of these systems in a master-slave configuration. In the present paper, the spontaneous dynamic behavior of two chaotic memristor-based Chua’s circuits, mutually interacting through a coupling resistance, was studied via computer simulations in order to study possible self-organized synchronization phenomena. The used memristor is a flux controlled memristor with a cubic nonlinearity, and it can be regarded as a time-varying memductance. The memristor, in effect, retains memory of its past dynamic and any difference in the initial conditions of the two circuits results in different values of the corresponding memductances. In this sense, due to the memory effect of the memristor, even if coupled circuits have the same parameters they do not constitute two completely identical chaotic oscillators. As is known, for nonidentical chaotic systems, in addition to complete synchronizations (CS other weaker forms of synchronization which provide correlations between the signals of the two systems can also occur. Depending on initial conditions and coupling strength, both chaotic and nonchaotic synchronization are observed for the system considered in this work.

On the dynamic rounding-off in analogue and RF optimal circuit sizing

Science.gov (United States)

Kotti, Mouna; Fakhfakh, Mourad; Fino, Maria Helena

2014-04-01

Frequently used approaches to solve discrete multivariable optimisation problems consist of computing solutions using a continuous optimisation technique. Then, using heuristics, the variables are rounded-off to their nearest available discrete values to obtain a discrete solution. Indeed, in many engineering problems, and particularly in analogue circuit design, component values, such as the geometric dimensions of the transistors, the number of fingers in an integrated capacitor or the number of turns in an integrated inductor, cannot be chosen arbitrarily since they have to obey to some technology sizing constraints. However, rounding-off the variables values a posteriori and can lead to infeasible solutions (solutions that are located too close to the feasible solution frontier) or degradation of the obtained results (expulsion from the neighbourhood of a 'sharp' optimum) depending on how the added perturbation affects the solution. Discrete optimisation techniques, such as the dynamic rounding-off technique (DRO) are, therefore, needed to overcome the previously mentioned situation. In this paper, we deal with an improvement of the DRO technique. We propose a particle swarm optimisation (PSO)-based DRO technique, and we show, via some analog and RF-examples, the necessity to implement such a routine into continuous optimisation algorithms.

Experimental verification of a thermal equivalent circuit dynamic model on an extended range electric vehicle battery pack

Science.gov (United States)

Ramotar, Lokendra; Rohrauer, Greg L.; Filion, Ryan; MacDonald, Kathryn

2017-03-01

The development of a dynamic thermal battery model for hybrid and electric vehicles is realized. A thermal equivalent circuit model is created which aims to capture and understand the heat propagation from the cells through the entire pack and to the environment using a production vehicle battery pack for model validation. The inclusion of production hardware and the liquid battery thermal management system components into the model considers physical and geometric properties to calculate thermal resistances of components (conduction, convection and radiation) along with their associated heat capacity. Various heat sources/sinks comprise the remaining model elements. Analog equivalent circuit simulations using PSpice are compared to experimental results to validate internal temperature nodes and heat rates measured through various elements, which are then employed to refine the model further. Agreement with experimental results indicates the proposed method allows for a comprehensive real-time battery pack analysis at little computational expense when compared to other types of computer based simulations. Elevated road and ambient conditions in Mesa, Arizona are simulated on a parked vehicle with varying quiescent cooling rates to examine the effect on the diurnal battery temperature for longer term static exposure. A typical daily driving schedule is also simulated and examined.

Mixed-mode chaotic circuit with Wien-bridge configuration: The results of experimental verification

Energy Technology Data Exchange (ETDEWEB)

Kilic, Recai [Erciyes University, Department of Electronic Engineering, 38039 Kayseri (Turkey)]. E-mail: kilic@erciyes.edu.tr

2007-05-15

In this paper, we deal with the experimentally implementation of inductorless Wien bridge-based mixed-mode chaotic circuit (MMCC) which is capable to exhibit both linear and nonlinear oscillations. The results of experimental implementation agree with the results of theoretical and computer simulation presented in literature. Since the proposed implementation of MMCC circuit uses different design blocks such as Wien bridge-based autonomous circuit part, CFOA (current feedback operational amplifier)-based floating inductance simulator, CFOA-based Chua's diode and switching mechanism, it offers very versatile chaotic circuit model for studying autonomous and nonautonomous chaotic dynamics.

Sociability Deficits and Altered Amygdala Circuits in Mice Lacking Pcdh10, an Autism Associated Gene.

Science.gov (United States)

Schoch, Hannah; Kreibich, Arati S; Ferri, Sarah L; White, Rachel S; Bohorquez, Dominique; Banerjee, Anamika; Port, Russell G; Dow, Holly C; Cordero, Lucero; Pallathra, Ashley A; Kim, Hyong; Li, Hongzhe; Bilker, Warren B; Hirano, Shinji; Schultz, Robert T; Borgmann-Winter, Karin; Hahn, Chang-Gyu; Feldmeyer, Dirk; Carlson, Gregory C; Abel, Ted; Brodkin, Edward S

2017-02-01

Behavioral symptoms in individuals with autism spectrum disorder (ASD) have been attributed to abnormal neuronal connectivity, but the molecular bases of these behavioral and brain phenotypes are largely unknown. Human genetic studies have implicated PCDH10, a member of the δ2 subfamily of nonclustered protocadherin genes, in ASD. PCDH10 expression is enriched in the basolateral amygdala, a brain region implicated in the social deficits of ASD. Previous reports indicate that Pcdh10 plays a role in axon outgrowth and glutamatergic synapse elimination, but its roles in social behaviors and amygdala neuronal connectivity are unknown. We hypothesized that haploinsufficiency of Pcdh10 would reduce social approach behavior and alter the structure and function of amygdala circuits. Mice lacking one copy of Pcdh10 (Pcdh10 +/- ) and wild-type littermates were assessed for social approach and other behaviors. The lateral/basolateral amygdala was assessed for dendritic spine number and morphology, and amygdala circuit function was studied using voltage-sensitive dye imaging. Expression of Pcdh10 and N-methyl-D-aspartate receptor (NMDAR) subunits was assessed in postsynaptic density fractions of the amygdala. Male Pcdh10 +/- mice have reduced social approach behavior, as well as impaired gamma synchronization, abnormal spine morphology, and reduced levels of NMDAR subunits in the amygdala. Social approach deficits in Pcdh10 +/- male mice were rescued with acute treatment with the NMDAR partial agonist d-cycloserine. Our studies reveal that male Pcdh10 +/- mice have synaptic and behavioral deficits, and establish Pcdh10 +/- mice as a novel genetic model for investigating neural circuitry and behavioral changes relevant to ASD. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Visualization of the Dynamics of Gene Expression in the Living Mouse

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Amy Ryan

2004-01-01

Full Text Available Reporter genes can monitor the status and activity of recombinant genomes in a diverse array of organisms, from bacteria and yeast to plants and animals. We have combined luciferase reporter genes with a conditional gene expression system based on regulatory elements from the lac Operon of Escherichia coli to visualize the dynamics of gene expression in realtime in the living mouse. Using this technology, we have determined the rate of gene induction and repression, the level of target gene activity in response to different doses of inducer, and the schedule of induction during early embryogenesis of both the endogenous and the experimentally manipulated programs of mammalian gene expression associated with the HD/Hdh locus. The combination of in vivo imaging and lac regulation is a powerful tool for generating conditional transgenic mice that can be screened rapidly for optimal regulation and expression patterns, and for monitoring the induction and repression of regulated genes noninvasively in the living animal.

Experimental realization of synchronization in complex networks with Chua's circuits like nodes

Energy Technology Data Exchange (ETDEWEB)

Posadas-Castillo, C. [Engineering Faculty, Baja California Autonomous University (UABC), Km. 103, Carretera Tijuana-Ensenada, 22860 Ensenada, BC (Mexico); Engineering Mechanic and Electric Faculty of Nuevo Leon Autonomous University (UANL), Pedro de Alba, S.N., Cd. Universitaria, San Nicolas de los Garza, NL (Mexico); Cruz-Hernandez, C. [Electronics and Telecommunications Department, Scientific Research and Advanced Studies of Ensenada (CICESE), Km. 107, Carretera Tijuana-Ensenada, 22860 Ensenada, BC (Mexico)], E-mail: ccruz@cicese.mx; Lopez-Gutierrez, R.M. [Engineering Faculty, Baja California Autonomous University (UABC), Km. 103, Carretera Tijuana-Ensenada, 22860 Ensenada, BC (Mexico)

2009-05-30

In this paper, an experimental study on practical realization of synchronization in globally coupled networks with Chua's circuits like nodes is presented. Synchronization of coupled multiple Chua's circuits is achieved by appealing to results from complex systems theory. In particular, we design and implement electronically complex dynamical networks composed by three coupled Chua's circuits, considering two scenarios: (i) without master node, and (ii) with (periodic and chaotic) master node. The interactions in the networks are defined by coupling the first state of each Chua's circuit.

Improving dynamic performances of PWM-driven servo-pneumatic systems via a novel pneumatic circuit.

Science.gov (United States)

Taghizadeh, Mostafa; Ghaffari, Ali; Najafi, Farid

2009-10-01

In this paper, the effect of pneumatic circuit design on the input-output behavior of PWM-driven servo-pneumatic systems is investigated and their control performances are improved using linear controllers instead of complex and costly nonlinear ones. Generally, servo-pneumatic systems are well known for their nonlinear behavior. However, PWM-driven servo-pneumatic systems have the advantage of flexibility in the design of pneumatic circuits which affects the input-output linearity of the whole system. A simple pneumatic circuit with only one fast switching valve is designed which leads to a quasi-linear input-output relation. The quasi-linear behavior of the proposed circuit is verified both experimentally and by simulations. Closed loop position control experiments are then carried out using linear P- and PD-controllers. Since the output position is noisy and cannot be directly differentiated, a Kalman filter is designed to estimate the velocity of the cylinder. Highly improved tracking performances are obtained using these linear controllers, compared to previous works with nonlinear controllers.

Online Open Circuit Fault Diagnosis for Rail Transit Traction Converter Based on Object-Oriented Colored Petri Net Topology Reasoning

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Lei Wang

2016-01-01

Full Text Available For online open circuit fault diagnosis of the traction converter in rail transit vehicles, conventional approaches depend heavily on component parameters and circuit layouts. For better universality and less parameter sensitivity during the diagnosis, this paper proposes a novel topology analysis approach to diagnose switching device open circuit failures. During the diagnosis, the topology is analyzed with fault reasoning mechanism, which is based on object-oriented Petri net (OOCPN. The OOCPN model takes in digitalized current inputs as fault signatures, and dynamical transitions between discrete switching states of a circuit with broken device are symbolized with the dynamical transitions of colored tokens in OOCPN. Such transitions simulate natural reasoning process of an expert’s brain during diagnosis. The dependence on component parameters and on circuit layouts is finally eliminated by such circuit topology reasoning process. In the last part, the proposed online reasoning and diagnosis process is exemplified with the case of a certain switching device failure in the power circuit of traction converter.

Early signatures of regime shifts in gene expression dynamics

Science.gov (United States)

Pal, Mainak; Pal, Amit Kumar; Ghosh, Sayantari; Bose, Indrani

2013-06-01

Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. The signatures of regime shifts in gene expression dynamics are less systematically investigated. In this paper, we consider sudden regime shifts in the gene expression dynamics described by a fold-bifurcation model involving bistability and hysteresis. We consider two alternative models, models 1 and 2, of competence development in the bacterial population B. subtilis and determine some early signatures of the regime shifts between competence and noncompetence. We use both deterministic and stochastic formalisms for the purpose of our study. The early signatures studied include the critical slowing down as a transition point is approached, rising variance and the lag-1 autocorrelation function, skewness and a ratio of two mean first passage times. Some of the signatures could provide the experimental basis for distinguishing between bistability and excitability as the correct mechanism for the development of competence.

Early signatures of regime shifts in gene expression dynamics

International Nuclear Information System (INIS)

Pal, Mainak; Pal, Amit Kumar; Ghosh, Sayantari; Bose, Indrani

2013-01-01

Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. The signatures of regime shifts in gene expression dynamics are less systematically investigated. In this paper, we consider sudden regime shifts in the gene expression dynamics described by a fold-bifurcation model involving bistability and hysteresis. We consider two alternative models, models 1 and 2, of competence development in the bacterial population B. subtilis and determine some early signatures of the regime shifts between competence and noncompetence. We use both deterministic and stochastic formalisms for the purpose of our study. The early signatures studied include the critical slowing down as a transition point is approached, rising variance and the lag-1 autocorrelation function, skewness and a ratio of two mean first passage times. Some of the signatures could provide the experimental basis for distinguishing between bistability and excitability as the correct mechanism for the development of competence. (paper)

Ultra-low power integrated circuit design circuits, systems, and applications

CERN Document Server

Li, Dongmei; Wang, Zhihua

2014-01-01

This book describes the design of CMOS circuits for ultra-low power consumption including analog, radio frequency (RF), and digital signal processing circuits (DSP). The book addresses issues from circuit and system design to production design, and applies the ultra-low power circuits described to systems for digital hearing aids and capsule endoscope devices. Provides a valuable introduction to ultra-low power circuit design, aimed at practicing design engineers; Describes all key building blocks of ultra-low power circuits, from a systems perspective; Applies circuits and systems described to real product examples such as hearing aids and capsule endoscopes.

Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.

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Pierre Lefeuvre

Full Text Available Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.

Near-Threshold Computing and Minimum Supply Voltage of Single-Rail MCML Circuits

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Ruiping Cao

2014-01-01

Full Text Available In high-speed applications, MOS current mode logic (MCML is a good alternative. Scaling down supply voltage of the MCML circuits can achieve low power-delay product (PDP. However, the current almost all MCML circuits are realized with dual-rail scheme, where the NMOS configuration in series limits the minimum supply voltage. In this paper, single-rail MCML (SRMCML circuits are described, which can avoid the devices configuration in series, since their logic evaluation block can be realized by only using MOS devices in parallel. The relationship between the minimum supply voltage of the SRMCML circuits and the model parameters of MOS transistors is derived, so that the minimum supply voltage can be estimated before circuit designs. An MCML dynamic flop-flop based on SRMCML is also proposed. The optimization algorithm for near-threshold sequential circuits is presented. A near-threshold SRMCML mode-10 counter based on the optimization algorithm is verified. Scaling down the supply voltage of the SRMCML circuits is also investigated. The power dissipation, delay, and power-delay products of these circuits are carried out. The results show that the near-threshold SRMCML circuits can obtain low delay and small power-delay product.

Design of organic complementary circuits and systems on foil

CERN Document Server

Abdinia, Sahel; Cantatore, Eugenio

2015-01-01

This book describes new approaches to fabricate complementary organic electronics, and focuses on the design of circuits and practical systems created using these manufacturing approaches. The authors describe two state-of-the-art, complementary organic technologies, characteristics and modeling of their transistors and their capability to implement circuits and systems on foil. Readers will benefit from the valuable overview of the challenges and opportunities that these extremely innovative technologies provide. ·         Demonstrates first circuits implemented using specific complementary organic technologies, including first printed analog to digital converter, first dynamic logic on foil and largest complementary organic circuit ·         Includes step-by-step design from single transistor level to complete systems on foil ·         Provides a platform for comparing state-of-the-art complementary organic technologies and for comparing these with other similar technologies, spec...

Paper-based synthetic gene networks.

Science.gov (United States)

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.

Paper-based Synthetic Gene Networks

Science.gov (United States)

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

Electronic circuit encyclopedia 2

Energy Technology Data Exchange (ETDEWEB)

Park, Sun Ho

1992-10-15

This book is composed of 15 chapters, which are amplification of weak signal and measurement circuit audio control and power amplification circuit, data transmission and wireless system, forwarding and isolation, signal converting circuit, counter and comparator, discriminator circuit, oscillation circuit and synthesizer, digital and circuit on computer image processing circuit, sensor drive circuit temperature sensor circuit, magnetic control and application circuit, motor driver circuit, measuring instrument and check tool and power control and stability circuit.

Electronic circuit encyclopedia 2

International Nuclear Information System (INIS)

Park, Sun Ho

1992-10-01

This book is composed of 15 chapters, which are amplification of weak signal and measurement circuit audio control and power amplification circuit, data transmission and wireless system, forwarding and isolation, signal converting circuit, counter and comparator, discriminator circuit, oscillation circuit and synthesizer, digital and circuit on computer image processing circuit, sensor drive circuit temperature sensor circuit, magnetic control and application circuit, motor driver circuit, measuring instrument and check tool and power control and stability circuit.

Dynamic analysis and electronic circuit implementation of a novel 3D autonomous system without linear terms

Science.gov (United States)

Kengne, J.; Jafari, S.; Njitacke, Z. T.; Yousefi Azar Khanian, M.; Cheukem, A.

2017-11-01

Mathematical models (ODEs) describing the dynamics of almost all continuous time chaotic nonlinear systems (e.g. Lorenz, Rossler, Chua, or Chen system) involve at least a nonlinear term in addition to linear terms. In this contribution, a novel (and singular) 3D autonomous chaotic system without linear terms is introduced. This system has an especial feature of having two twin strange attractors: one ordinary and one symmetric strange attractor when the time is reversed. The complex behavior of the model is investigated in terms of equilibria and stability, bifurcation diagrams, Lyapunov exponent plots, time series and Poincaré sections. Some interesting phenomena are found including for instance, period-doubling bifurcation, antimonotonicity (i.e. the concurrent creation and annihilation of periodic orbits) and chaos while monitoring the system parameters. Compared to the (unique) case previously reported by Xu and Wang (2014) [31], the system considered in this work displays a more 'elegant' mathematical expression and experiences richer dynamical behaviors. A suitable electronic circuit (i.e. the analog simulator) is designed and used for the investigations. Pspice based simulation results show a very good agreement with the theoretical analysis.

Evaluation of artificial time series microarray data for dynamic gene regulatory network inference.

Science.gov (United States)

Xenitidis, P; Seimenis, I; Kakolyris, S; Adamopoulos, A

2017-08-07

High-throughput technology like microarrays is widely used in the inference of gene regulatory networks (GRNs). We focused on time series data since we are interested in the dynamics of GRNs and the identification of dynamic networks. We evaluated the amount of information that exists in artificial time series microarray data and the ability of an inference process to produce accurate models based on them. We used dynamic artificial gene regulatory networks in order to create artificial microarray data. Key features that characterize microarray data such as the time separation of directly triggered genes, the percentage of directly triggered genes and the triggering function type were altered in order to reveal the limits that are imposed by the nature of microarray data on the inference process. We examined the effect of various factors on the inference performance such as the network size, the presence of noise in microarray data, and the network sparseness. We used a system theory approach and examined the relationship between the pole placement of the inferred system and the inference performance. We examined the relationship between the inference performance in the time domain and the true system parameter identification. Simulation results indicated that time separation and the percentage of directly triggered genes are crucial factors. Also, network sparseness, the triggering function type and noise in input data affect the inference performance. When two factors were simultaneously varied, it was found that variation of one parameter significantly affects the dynamic response of the other. Crucial factors were also examined using a real GRN and acquired results confirmed simulation findings with artificial data. Different initial conditions were also used as an alternative triggering approach. Relevant results confirmed that the number of datasets constitutes the most significant parameter with regard to the inference performance. Copyright © 2017 Elsevier

Solid-state circuits

CERN Document Server

Pridham, G J

2013-01-01

Solid-State Circuits provides an introduction to the theory and practice underlying solid-state circuits, laying particular emphasis on field effect transistors and integrated circuits. Topics range from construction and characteristics of semiconductor devices to rectification and power supplies, low-frequency amplifiers, sine- and square-wave oscillators, and high-frequency effects and circuits. Black-box equivalent circuits of bipolar transistors, physical equivalent circuits of bipolar transistors, and equivalent circuits of field effect transistors are also covered. This volume is divided

A high resolution large dynamic range TDC circuit implementation

International Nuclear Information System (INIS)

Lei Wuhu; Liu Songqiu; Ye Weiguo; Han Hui; Li Pengyu

2003-01-01

Time measurement technology is usually used in nuclear experimentation. There are many methods of time measurement. The implementation method of Time to Digital Conversion (TDC) by means of electronic is a classical technology. The range and resolution of TDC is different according with different usage. A wide range and high resolution TDC circuit, including its theory and implementation way, is introduced in this paper. The test result is also given. (authors)

A high resolution large dynamic range TDC circuit implementation

International Nuclear Information System (INIS)

Lei Wuhu; Liu Songqiu; Li Pengyu; Han Hui; Ye Yanlin

2005-01-01

Time measurement technology is usually used in nuclear experimentation. There are many methods of time measurement. The implementation method of Time to Digital Conversion (TDC) by means of electronics is a classical technology. The range and resolution of TDC is different according with different usage. A wide range and high resolution TDC circuit, including its theory and implementation way, is introduced in this paper. The test result is also given. (authors)

Numerical Simulation Bidirectional Chaotic Synchronization of Spiegel-Moore Circuit and Its Application for Secure Communication

Science.gov (United States)

Sanjaya, W. S. M.; Anggraeni, D.; Denya, R.; Ismail, N.

2017-03-01

Spiegel-Moore is a dynamical chaotic system which shows irregular variability in the luminosity of stars. In this paper present the performed the design and numerical simulation of the synchronization Spiegel-Moore circuit and applied to security system for communication. The initial study in this paper is to analyze the eigenvalue structures, various attractors, Bifurcation diagram, and Lyapunov exponent analysis. We have studied the dynamic behavior of the system in the case of the bidirectional coupling via a linear resistor. Both experimental and simulation results have shown that chaotic synchronization is possible. Finally, the effectiveness of the bidirectional coupling scheme between two identical Spiegel-Moore circuits in a secure communication system is presented in details. Integration of theoretical electronic circuit, the numerical simulation by using MATLAB®, as well as the implementation of circuit simulations by using Multisim® has been performed in this study.

Log-ratio circuit for beam position monitoring

International Nuclear Information System (INIS)

Wells, F.D.; Shafer, R.E.; Gilpatrick, J.D.; Shurter, R.B.

1990-01-01

A synopsis is given of work in progress on a new signal processing technique for obtaining real-time normalized beam position information from sensing electrodes in accelerator beam pipes. The circuit employs wideband logarithmic amplifiers in a configuration that converts pickup electrode signals to position signals that are substantially independent of beam current. The circuit functions as a ratio detector that computes the logarithm of (A/B) as (Log A-Log B), and presents the result in a video (real-time analog) format representing beam position. It has potential benefits of greater dynamic range and better linearity than other techniques currently used and it may be able to operate at substantially higher frequencies. 4 refs., 8 figs

Coherent defects in superconducting circuits

International Nuclear Information System (INIS)

Mueller, Clemens

2011-01-01

The interaction of superconducting circuits with additional quantum systems is a topic that has found extensive study in the recent past. In the limit where the added system are incoherent, this is the standard field of decoherence and the system dynamics can be described by a simple master equation. In the other limit however, when the additional parts are coherent, the resulting time-evolution can become more complicated. In this thesis we have investigated the interaction of superconducting circuits with coherent and incoherent two-level defects. We have shown theoretical calculations characterizing this interaction for all relevant parameter regimes. In the weak coupling limit, the interaction can be described in an effective bath picture, where the TLS act as parts of a large, decohering environment. For strong coupling, however, the coherent dynamics of the full coupled system has to be considered. We show the calculations of the coupled time-evolution and again characterize the interaction by an effective decoherence rate. We also used experimental data to characterize the microscopic origin of the defects and the details of their interaction with the circuits. The results obtained by analyzing spectroscopic data allow us to place strong constraint on several microscopic models for the observed TLS. However, these calculations are not yet fully conclusive as to the physical nature of the TLS. We propose additional experiments to fully characterize the interaction part of the Hamiltonian, thus providing the answer to the question of the physical origin of the coupling. Additionally we have developed a method to directly drive individual defect states via virtual excitation of the qubit. This method allows one to directly probe the properties of single TLS and possibly make use of their superior coherence times for quantum information purposes. The last part of this thesis provided a way for a possible implementation of geometric quantum computation in

Collective of mechatronics circuit

International Nuclear Information System (INIS)

1987-02-01

This book is composed of three parts, which deals with mechatronics system about sensor, circuit and motor. The contents of the first part are photo sensor of collector for output, locating detection circuit with photo interrupts, photo sensor circuit with CdS cell and lamp, interface circuit with logic and LED and temperature sensor circuit. The second part deals with oscillation circuit with crystal, C-R oscillation circuit, F-V converter, timer circuit, stability power circuit, DC amp and DC-DC converter. The last part is comprised of bridge server circuit, deformation bridge server, controlling circuit of DC motor, controlling circuit with IC for PLL and driver circuit of stepping motor and driver circuit of Brushless.

Collective of mechatronics circuit

Energy Technology Data Exchange (ETDEWEB)

NONE

1987-02-15

This book is composed of three parts, which deals with mechatronics system about sensor, circuit and motor. The contents of the first part are photo sensor of collector for output, locating detection circuit with photo interrupts, photo sensor circuit with CdS cell and lamp, interface circuit with logic and LED and temperature sensor circuit. The second part deals with oscillation circuit with crystal, C-R oscillation circuit, F-V converter, timer circuit, stability power circuit, DC amp and DC-DC converter. The last part is comprised of bridge server circuit, deformation bridge server, controlling circuit of DC motor, controlling circuit with IC for PLL and driver circuit of stepping motor and driver circuit of Brushless.

Experimental Device for Learning of Logical Circuit Design using Integrated Circuits

OpenAIRE

石橋, 孝昭

2012-01-01

This paper presents an experimental device for learning of logical circuit design using integrated circuits and breadboards. The experimental device can be made at a low cost and can be used for many subjects such as logical circuits, computer engineering, basic electricity, electrical circuits and electronic circuits. The proposed device is effective to learn the logical circuits than the usual lecture.

Measuring RF circuits exhibiting nonlinear responses combined with short and long term memory effects

NARCIS (Netherlands)

Janssen, E.J.G.; Milosevic, D.; Baltus, P.G.M.

2010-01-01

All RF circuits that incorporate active devices exhibit nonlinear behavior. Nonlinearities result in signal distortion, and therefore state the upper limit of the dynamic range of the circuits. A measure for linearity used quite commonly in RF is the P1dB and/or IP3 point. These quantities are

A simple electric circuit model for proton exchange membrane fuel cells

Science.gov (United States)

Lazarou, Stavros; Pyrgioti, Eleftheria; Alexandridis, Antonio T.

A simple and novel dynamic circuit model for a proton exchange membrane (PEM) fuel cell suitable for the analysis and design of power systems is presented. The model takes into account phenomena like activation polarization, ohmic polarization, and mass transport effect present in a PEM fuel cell. The proposed circuit model includes three resistors to approach adequately these phenomena; however, since for the PEM dynamic performance connection or disconnection of an additional load is of crucial importance, the proposed model uses two saturable inductors accompanied by an ideal transformer to simulate the double layer charging effect during load step changes. To evaluate the effectiveness of the proposed model its dynamic performance under load step changes is simulated. Experimental results coming from a commercial PEM fuel cell module that uses hydrogen from a pressurized cylinder at the anode and atmospheric oxygen at the cathode, clearly verify the simulation results.

Dynamic association rules for gene expression data analysis.

Science.gov (United States)

Chen, Shu-Chuan; Tsai, Tsung-Hsien; Chung, Cheng-Han; Li, Wen-Hsiung

2015-10-14

The purpose of gene expression analysis is to look for the association between regulation of gene expression levels and phenotypic variations. This association based on gene expression profile has been used to determine whether the induction/repression of genes correspond to phenotypic variations including cell regulations, clinical diagnoses and drug development. Statistical analyses on microarray data have been developed to resolve gene selection issue. However, these methods do not inform us of causality between genes and phenotypes. In this paper, we propose the dynamic association rule algorithm (DAR algorithm) which helps ones to efficiently select a subset of significant genes for subsequent analysis. The DAR algorithm is based on association rules from market basket analysis in marketing. We first propose a statistical way, based on constructing a one-sided confidence interval and hypothesis testing, to determine if an association rule is meaningful. Based on the proposed statistical method, we then developed the DAR algorithm for gene expression data analysis. The method was applied to analyze four microarray datasets and one Next Generation Sequencing (NGS) dataset: the Mice Apo A1 dataset, the whole genome expression dataset of mouse embryonic stem cells, expression profiling of the bone marrow of Leukemia patients, Microarray Quality Control (MAQC) data set and the RNA-seq dataset of a mouse genomic imprinting study. A comparison of the proposed method with the t-test on the expression profiling of the bone marrow of Leukemia patients was conducted. We developed a statistical way, based on the concept of confidence interval, to determine the minimum support and minimum confidence for mining association relationships among items. With the minimum support and minimum confidence, one can find significant rules in one single step. The DAR algorithm was then developed for gene expression data analysis. Four gene expression datasets showed that the proposed

A New Chaotic System with Multiple Attractors: Dynamic Analysis, Circuit Realization and S-Box Design

Directory of Open Access Journals (Sweden)

Qiang Lai

2017-12-01

Full Text Available This paper reports about a novel three-dimensional chaotic system with three nonlinearities. The system has one stable equilibrium, two stable equilibria and one saddle node, two saddle foci and one saddle node for different parameters. One salient feature of this novel system is its multiple attractors caused by different initial values. With the change of parameters, the system experiences mono-stability, bi-stability, mono-periodicity, bi-periodicity, one strange attractor, and two coexisting strange attractors. The complex dynamic behaviors of the system are revealed by analyzing the corresponding equilibria and using the numerical simulation method. In addition, an electronic circuit is given for implementing the chaotic attractors of the system. Using the new chaotic system, an S-Box is developed for cryptographic operations. Moreover, we test the performance of this produced S-Box and compare it to the existing S-Box studies.

Electron commutator on integrated circuits

International Nuclear Information System (INIS)

Demidenko, V.V.

1975-01-01

The scheme and the parameters of an electron 16-channel contactless commutator based entirely on integrated circuits are described. The device consists of a unit of analog keys based on field-controlled metal-insulator-semiconductor (m.i.s.) transistors, operation amplifier comparators controlling these keys, and a level distributor. The distributor is based on a ''matrix'' scheme and comprises two ring-shaped shift registers plugged in series and a decoder base on two-input logical elements I-NE. The principal dynamical parameters of the circuit are as follows: the control signal delay in the distributor. 50 nsec; the total channel switch-over time, 500-600 nsec. The commutator transmits both constant signals and pulses whose duration reaches tens of nsec. The commutator can be used in data acquisition and processing systems, for shaping complicated signals (for example), (otherwise signals), for simultaneous oscillographing of several signals, and so forth [ru

Local changes in neocortical circuit dynamics coincide with the spread of seizures to thalamus in a model of epilepsy.

Science.gov (United States)

Neubauer, Florian B; Sederberg, Audrey; MacLean, Jason N

2014-01-01

During the generalization of epileptic seizures, pathological activity in one brain area recruits distant brain structures into joint synchronous discharges. However, it remains unknown whether specific changes in local circuit activity are related to the aberrant recruitment of anatomically distant structures into epileptiform discharges. Further, it is not known whether aberrant areas recruit or entrain healthy ones into pathological activity. Here we study the dynamics of local circuit activity during the spread of epileptiform discharges in the zero-magnesium in vitro model of epilepsy. We employ high-speed multi-photon imaging in combination with dual whole-cell recordings in acute thalamocortical (TC) slices of the juvenile mouse to characterize the generalization of epileptic activity between neocortex and thalamus. We find that, although both structures are exposed to zero-magnesium, the initial onset of focal epileptiform discharge occurs in cortex. This suggests that local recurrent connectivity that is particularly prevalent in cortex is important for the initiation of seizure activity. Subsequent recruitment of thalamus into joint, generalized discharges is coincident with an increase in the coherence of local cortical circuit activity that itself does not depend on thalamus. Finally, the intensity of population discharges is positively correlated between both brain areas. This suggests that during and after seizure generalization not only the timing but also the amplitude of epileptiform discharges in thalamus is entrained by cortex. Together these results suggest a central role of neocortical activity for the onset and the structure of pathological recruitment of thalamus into joint synchronous epileptiform discharges.

Synthesis of energy-efficient FSMs implemented in PLD circuits

Science.gov (United States)

Nawrot, Radosław; Kulisz, Józef; Kania, Dariusz

2017-11-01

The paper presents an outline of a simple synthesis method of energy-efficient FSMs. The idea consists in using local clock gating to selectively block the clock signal, if no transition of a state of a memory element is required. The research was dedicated to logic circuits using Programmable Logic Devices as the implementation platform, but the conclusions can be applied to any synchronous circuit. The experimental section reports a comparison of three methods of implementing sequential circuits in PLDs with respect to clock distribution: the classical fully synchronous structure, the structure exploiting the Enable Clock inputs of memory elements, and the structure using clock gating. The results show that the approach based on clock gating is the most efficient one, and it leads to significant reduction of dynamic power consumed by the FSM.

The collective biology of the gene: Towards genetic dynamics engineering

International Nuclear Information System (INIS)

Chela-Flores, J.

1985-11-01

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

Color Coding of Circuit Quantities in Introductory Circuit Analysis Instruction

Science.gov (United States)

Reisslein, Jana; Johnson, Amy M.; Reisslein, Martin

2015-01-01

Learning the analysis of electrical circuits represented by circuit diagrams is often challenging for novice students. An open research question in electrical circuit analysis instruction is whether color coding of the mathematical symbols (variables) that denote electrical quantities can improve circuit analysis learning. The present study…

ECCS control circuit

International Nuclear Information System (INIS)

Sato, Takashi.

1986-01-01

Purpose: To afford a sufficient margin to pressure vibrations upon starting of an automatic depressurization system by dispersing pressure vibration in suppression water due to the opening action of an automatic releaf valve in the automatic depressurization system thereby reducing the dynamic load exerted to the surface of the suppression walls. Constitution: Upon occurrence of loss of coolant accidents, an automatic releaf valve for automatic depressurization is opened to deliver the steams in the pressure vessel into the suppression pool. Since a plurality of automatic releaf valves have usually been disposed, if they are opened simultaneously, excess dynamic loads are exerted due to the pressure vibrations to the wall surface of the suppression pool. In this invention, a control circuit is disposed such that the opening timing for each of the automatic releaf valves is deviated upon occurrence of a driving signal for the automatic depressurization system to thereby disperse the pressure vibrations in the suppression water. (Kamimura, M.)

Design of an improved RCD buffer circuit for full bridge circuit

Science.gov (United States)

Yang, Wenyan; Wei, Xueye; Du, Yongbo; Hu, Liang; Zhang, Liwei; Zhang, Ou

2017-05-01

In the full bridge inverter circuit, when the switch tube suddenly opened or closed, the inductor current changes rapidly. Due to the existence of parasitic inductance of the main circuit. Therefore, the surge voltage between drain and source of the switch tube can be generated, which will have an impact on the switch and the output voltage. In order to ab sorb the surge voltage. An improve RCD buffer circuit is proposed in the paper. The peak energy will be absorbed through the buffer capacitor of the circuit. The part energy feedback to the power supply, another part release through the resistor in the form of heat, and the circuit can absorb the voltage spikes. This paper analyzes the process of the improved RCD snubber circuit, According to the specific parameters of the main circuit, a reasonable formula for calculating the resistance capacitance is given. A simulation model will be modulated in Multisim, which compared the waveform of tube voltage and the output waveform of the circuit without snubber circuit with the improved RCD snubber circuit. By comparing and analyzing, it is proved that the improved buffer circuit can absorb surge voltage. Finally, experiments are demonstrated to validate that the correctness of the RC formula and the improved RCD snubber circuit.

Photonic integrated circuits unveil crisis-induced intermittency.

Science.gov (United States)

Karsaklian Dal Bosco, Andreas; Akizawa, Yasuhiro; Kanno, Kazutaka; Uchida, Atsushi; Harayama, Takahisa; Yoshimura, Kazuyuki

2016-09-19

We experimentally investigate an intermittent route to chaos in a photonic integrated circuit consisting of a semiconductor laser with time-delayed optical feedback from a short external cavity. The transition from a period-doubling dynamics to a fully-developed chaos reveals a stage intermittently exhibiting these two dynamics. We unveil the bifurcation mechanism underlying this route to chaos by using the Lang-Kobayashi model and demonstrate that the process is based on a phenomenon of attractor expansion initiated by a particular distribution of the local Lyapunov exponents. We emphasize on the crucial importance of the distribution of the steady-state solutions introduced by the time-delayed feedback on the existence of this intermittent dynamics.

On the origin of reproducible sequential activity in neural circuits

Science.gov (United States)

Afraimovich, V. S.; Zhigulin, V. P.; Rabinovich, M. I.

2004-12-01

Robustness and reproducibility of sequential spatio-temporal responses is an essential feature of many neural circuits in sensory and motor systems of animals. The most common mathematical images of dynamical regimes in neural systems are fixed points, limit cycles, chaotic attractors, and continuous attractors (attractive manifolds of neutrally stable fixed points). These are not suitable for the description of reproducible transient sequential neural dynamics. In this paper we present the concept of a stable heteroclinic sequence (SHS), which is not an attractor. SHS opens the way for understanding and modeling of transient sequential activity in neural circuits. We show that this new mathematical object can be used to describe robust and reproducible sequential neural dynamics. Using the framework of a generalized high-dimensional Lotka-Volterra model, that describes the dynamics of firing rates in an inhibitory network, we present analytical results on the existence of the SHS in the phase space of the network. With the help of numerical simulations we confirm its robustness in presence of noise in spite of the transient nature of the corresponding trajectories. Finally, by referring to several recent neurobiological experiments, we discuss possible applications of this new concept to several problems in neuroscience.

A 14-bit 50 MS/s sample-and-hold circuit for pipelined ADC

International Nuclear Information System (INIS)

Yue Sen; Zhao Yiqiang; Pang Ruilong; Sheng Yun

2014-01-01

A high performance sample-and-hold (S/H) circuit used in a pipelined analog-to-digital converter (ADC) is presented. Capacitor flip-around architecture is used in this S/H circuit with a novel gain-boosted differential folded cascode operational transconductance amplifier. A double-bootstrapped switch is designed to improve the performance of the circuit. The circuit is implemented using a 0.18 μm 1P6M CMOS process. Measurement results show that the effective number of bits is 14.03 bits, the spurious free dynamic range is 94.62 dB, the signal to noise and distortion ratio is 86.28 dB, and the total harmonic distortion is −91:84 dB for a 5 MHz input signal with 50 MS/s sampling rate. A pipeline ADC with the designed S/H circuit has been implemented. (semiconductor integrated circuits)

Effect of Sensors on the Reliability and Control Performance of Power Circuits in the Web of Things (WoT

Directory of Open Access Journals (Sweden)

Sungwoo Bae

2016-09-01

Full Text Available In order to realize a true WoT environment, a reliable power circuit is required to ensure interconnections among a range of WoT devices. This paper presents research on sensors and their effects on the reliability and response characteristics of power circuits in WoT devices. The presented research can be used in various power circuit applications, such as energy harvesting interfaces, photovoltaic systems, and battery management systems for the WoT devices. As power circuits rely on the feedback from voltage/current sensors, the system performance is likely to be affected by the sensor failure rates, sensor dynamic characteristics, and their interface circuits. This study investigated how the operational availability of the power circuits is affected by the sensor failure rates by performing a quantitative reliability analysis. In the analysis process, this paper also includes the effects of various reconstruction and estimation techniques used in power processing circuits (e.g., energy harvesting circuits and photovoltaic systems. This paper also reports how the transient control performance of power circuits is affected by sensor interface circuits. With the frequency domain stability analysis and circuit simulation, it was verified that the interface circuit dynamics may affect the transient response characteristics of power circuits. The verification results in this paper showed that the reliability and control performance of the power circuits can be affected by the sensor types, fault tolerant approaches against sensor failures, and the response characteristics of the sensor interfaces. The analysis results were also verified by experiments using a power circuit prototype.

Signal processing: opportunities for superconductive circuits

International Nuclear Information System (INIS)

Ralston, R.W.

1985-01-01

Prime motivators in the evolution of increasingly sophisticated communication and detection systems are the needs for handling ever wider signal bandwidths and higher data processing speeds. These same needs drive the development of electronic device technology. Until recently the superconductive community has been tightly focused on digital devices for high speed computers. The purpose of this paper is to describe opportunities and challenges which exist for both analog and digital devices in a less familiar area, that of wideband signal processing. The function and purpose of analog signal-processing components, including matched filters, correlators and Fourier transformers, will be described and examples of superconductive implementations given. A canonic signal-processing system is then configured using these components in combination with analog/digital converters and digital output circuits to highlight the important issues of dynamic range, accuracy and equivalent computation rate. Superconductive circuits hold promise for processing signals of 10-GHz bandwidth. Signal processing systems, however, can be properly designed and implemented only through a synergistic combination of the talents of device physicists, circuit designers, algorithm architects and system engineers. An immediate challenge to the applied superconductivity community is to begin sharing ideas with these other researchers

Chaotic behaviour of a fourth-order autonomous electric circuit

International Nuclear Information System (INIS)

Koliopanos, Ch.L.; Kyprianidis, I.M.; Stouboulos, I.N.; Anagnostopoulos, A.N.; Magafas, L.

2003-01-01

The chaotic dynamics of a fourth-order autonomous nonlinear electric circuit was studied by measuring its response in the form of chaotic time series. The circuit consists of two active elements, one linear negative conductance and one nonlinear resistor exhibiting a symmetrical piecewise-linear v-i characteristic and two capacitances C 1 and C 2 , which serve as the control parameters of the system. From the experimental time series the minimum embedding dimensions m min =4, correlation dimensions ν, with positive noninteger values, and Kolmogorov entropies, tending to constant positive values, were determined by numerical evaluation for the examined states of the system

Corticostriatal circuit mechanisms of value-based action selection: Implementation of reinforcement learning algorithms and beyond.

Science.gov (United States)

Morita, Kenji; Jitsev, Jenia; Morrison, Abigail

2016-09-15

Value-based action selection has been suggested to be realized in the corticostriatal local circuits through competition among neural populations. In this article, we review theoretical and experimental studies that have constructed and verified this notion, and provide new perspectives on how the local-circuit selection mechanisms implement reinforcement learning (RL) algorithms and computations beyond them. The striatal neurons are mostly inhibitory, and lateral inhibition among them has been classically proposed to realize "Winner-Take-All (WTA)" selection of the maximum-valued action (i.e., 'max' operation). Although this view has been challenged by the revealed weakness, sparseness, and asymmetry of lateral inhibition, which suggest more complex dynamics, WTA-like competition could still occur on short time scales. Unlike the striatal circuit, the cortical circuit contains recurrent excitation, which may enable retention or temporal integration of information and probabilistic "soft-max" selection. The striatal "max" circuit and the cortical "soft-max" circuit might co-implement an RL algorithm called Q-learning; the cortical circuit might also similarly serve for other algorithms such as SARSA. In these implementations, the cortical circuit presumably sustains activity representing the executed action, which negatively impacts dopamine neurons so that they can calculate reward-prediction-error. Regarding the suggested more complex dynamics of striatal, as well as cortical, circuits on long time scales, which could be viewed as a sequence of short WTA fragments, computational roles remain open: such a sequence might represent (1) sequential state-action-state transitions, constituting replay or simulation of the internal model, (2) a single state/action by the whole trajectory, or (3) probabilistic sampling of state/action. Copyright © 2016. Published by Elsevier B.V.

A spiking neuron circuit based on a carbon nanotube transistor

International Nuclear Information System (INIS)

Chen, C-L; Kim, K; Truong, Q; Shen, A; Li, Z; Chen, Y

2012-01-01

A spiking neuron circuit based on a carbon nanotube (CNT) transistor is presented in this paper. The spiking neuron circuit has a crossbar architecture in which the transistor gates are connected to its row electrodes and the transistor sources are connected to its column electrodes. An electrochemical cell is incorporated in the gate of the transistor by sandwiching a hydrogen-doped poly(ethylene glycol)methyl ether (PEG) electrolyte between the CNT channel and the top gate electrode. An input spike applied to the gate triggers a dynamic drift of the hydrogen ions in the PEG electrolyte, resulting in a post-synaptic current (PSC) through the CNT channel. Spikes input into the rows trigger PSCs through multiple CNT transistors, and PSCs cumulate in the columns and integrate into a ‘soma’ circuit to trigger output spikes based on an integrate-and-fire mechanism. The spiking neuron circuit can potentially emulate biological neuron networks and their intelligent functions. (paper)

Advance elements of optoisolation circuits nonlinearity applications in engineering

CERN Document Server

Aluf, Ofer

2017-01-01

This book on advanced optoisolation circuits for nonlinearity applications in engineering addresses two separate engineering and scientific areas, and presents advanced analysis methods for optoisolation circuits that cover a broad range of engineering applications. The book analyzes optoisolation circuits as linear and nonlinear dynamical systems and their limit cycles, bifurcation, and limit cycle stability by using Floquet theory. Further, it discusses a broad range of bifurcations related to optoisolation systems: cusp-catastrophe, Bautin bifurcation, Andronov-Hopf bifurcation, Bogdanov-Takens (BT) bifurcation, fold Hopf bifurcation, Hopf-Hopf bifurcation, Torus bifurcation (Neimark-Sacker bifurcation), and Saddle-loop or Homoclinic bifurcation. Floquet theory helps as to analyze advance optoisolation systems. Floquet theory is the study of the stability of linear periodic systems in continuous time. Another way to describe Floquet theory, it is the study of linear systems of differential equations with p...

Resilience of the quantum Rabi model in circuit QED

International Nuclear Information System (INIS)

Manucharyan, Vladimir E; Baksic, Alexandre; Ciuti, Cristiano

2017-01-01

In circuit quantum electrodynamics (circuit QED), an artificial ‘circuit atom’ can couple to a quantized microwave radiation much stronger than its real atomic counterpart. The celebrated quantum Rabi model describes the simplest interaction of a two-level system with a single-mode boson field. When the coupling is large enough, the bare multilevel structure of a realistic circuit atom cannot be ignored even if the circuit is strongly anharmonic. We explored this situation theoretically for flux (fluxonium) and charge (Cooper pair box) type multi-level circuits tuned to their respective flux/charge degeneracy points. We identified which spectral features of the quantum Rabi model survive and which are renormalized for large coupling. Despite significant renormalization of the low-energy spectrum in the fluxonium case, the key quantum Rabi feature—nearly-degenerate vacuum consisting of an atomic state entangled with a multi-photon field—appears in both types of circuits when the coupling is sufficiently large. Like in the quantum Rabi model, for very large couplings the entanglement spectrum is dominated by only two, nearly equal eigenvalues, in spite of the fact that a large number of bare atomic states are actually involved in the atom-resonator ground state. We interpret the emergence of the two-fold degeneracy of the vacuum of both circuits as an environmental suppression of flux/charge tunneling due to their dressing by virtual low-/high-impedance photons in the resonator. For flux tunneling, the dressing is nothing else than the shunting of a Josephson atom with a large capacitance of the resonator. Suppression of charge tunneling is a manifestation of the dynamical Coulomb blockade of transport in tunnel junctions connected to resistive leads. (paper)

Stopping single photons in one-dimensional circuit quantum electrodynamics systems

International Nuclear Information System (INIS)

Shen, J.-T.; Povinelli, M. L.; Sandhu, Sunil; Fan Shanhui

2007-01-01

We propose a mechanism to stop and time reverse single photons in one-dimensional circuit quantum electrodynamics systems. As a concrete example, we exploit the large tunability of the superconducting charge quantum bit (charge qubit) to predict one-photon transport properties in multiple-qubit systems with dynamically controlled transition frequencies. In particular, two qubits coupled to a waveguide give rise to a single-photon transmission line shape that is analogous to electromagnetically induced transparency in atomic systems. Furthermore, by cascading double-qubit structures to form an array and dynamically controlling the qubit transition frequencies, a single photon can be stopped, stored, and time reversed. With a properly designed array, two photons can be stopped and stored in the system at the same time. Moreover, the unit cell of the array can be designed to be of deep subwavelength scale, miniaturizing the circuit

Quorum sensing circuit and reactive oxygen species resistance in Deinococcus sp.

Science.gov (United States)

Fernandez-Bunster, G; Gonzalez, C; Barros, J; Martinez, M

2012-12-01

Genus Deinococcus is characterized by an increased resistance toward reactive oxygen species (ROS). The chromosome of five strains belonging to this genus has been sequenced and the presence of a luxS-like gene was deduced from their genome sequences. The aim of this study was to assess if a complete QS circuit is present in Deinococcus sp. and if this QS is associated with ROS. Primers for searching luxS-like gene and the putative receptor gene, namely ai2R, were designed. AI-2 signal production was evaluated by luminescence analysis using Vibrio harveyi BB170 as reporter strain. AI-2 signal was also evaluated by competitive assays using cinnamaldehyde, ascorbic acid, and 3-mercaptopropionic acid as interfering molecules. Potassium tellurite and metronidazole were used as oxidative stressors. A luxS-like gene as well as an ai2R gene was detected in strain UDEC-P1 by PCR. Cell-free supernatant of strain UDEC-P1 culture induced luminescence in V. harveyi BB170, and this property was inhibited with the three interfering molecules. The oxidative stressors metronidazole and potassium tellurite decreased Deinococcus sp. viability, but increased luminescence of the reporter strain. The results demonstrate that both a functional luxS-like gene and a putative receptor for AI-2 signal are present in Deinococcus sp. strain UDEC-P1. This finding also suggests that a complete QS circuit is present in this genus, which could be related to oxidative stress.

Feeding the developing brain: Juvenile rats fed diet rich in prebiotics and bioactive milk fractions exhibit reduced anxiety-related behavior and modified gene expression in emotion circuits.

Science.gov (United States)

Mika, Agnieszka; Gaffney, Michelle; Roller, Rachel; Hills, Abigail; Bouchet, Courtney A; Hulen, Kristina A; Thompson, Robert S; Chichlowski, Maciej; Berg, Brian M; Fleshner, Monika

2018-01-30

Early life nutrition is critical for brain development. Dietary prebiotics and bioactive milk fractions support brain development by increasing plasticity and altering activity in brain regions important for cognition and emotion regulation, perhaps through the gut-microbiome-brain axis. Here we examined the impact of a diet containing prebiotics, lactoferrin, and milk fat globule membrane (test diet) on beneficial gut bacteria, basal gene expression for activity and plasticity markers within brain circuits important for cognition and anxiety, and anxiety-related behavior in the open field. Juvenile male F344 rats were fed the test diet or a calorically matched control diet beginning postnatal day 24. After 4 weeks on diets, rats were sacrificed and brains were removed. Test diet significantly increased mRNA expression for cfos, brain derived neurotropic factor, and the GluN1 subunit of the NMDA receptor in the prefrontal cortex and reduced cfos mRNA within the amygdala. Diet-induced increases in fecal Lactobacillus spp., measured using selective bacterial culture, positively correlated with altered gene expression for cfos and serotonin receptors within multiple brain regions. In a separate cohort of juvenile rats, 4 weeks of the test diet increased time spent in the center of the open field, a behavior indicative of reduced anxiety. These data demonstrate that early life diets containing prebiotics and bioactive milk fractions can adaptively alter genes in neural circuits underlying emotion regulation and decrease anxiety-related behavior. Copyright © 2018. Published by Elsevier B.V.

Ultra-low power circuits based on tunnel FETs for energy harvesting applications

OpenAIRE

Cavalheiro, David

2017-01-01

There has been a tremendous evolution in integrated circuit technology in the past decades. With the scaling of complementary metal-oxide-semiconductor (CMOS) transistors, faster, less power consuming and more complex chips per unit area have made possible electronic gadgets to evolve to what we see today. The increasing demand in electronic portability imposes low power consumption as a key metric to analog and digital circuit design. While dynamic power consumption decreases quadraticall...

Carbon Nanotube Driver Circuit for 6 × 6 Organic Light Emitting Diode Display

KAUST Repository

Zou, Jianping; Zhang, Kang; Li, Jingqi; Zhao, Yongbiao; Wang, Yilei; Pillai, Suresh Kumar Raman; Volkan Demir, Hilmi; Sun, Xiaowei; Chan-Park, Mary B.; Zhang, Qing

2015-01-01

Single-walled carbon nanotube (SWNT) is expected to be a very promising material for flexible and transparent driver circuits for active matrix organic light emitting diode (AM OLED) displays due to its high field-effect mobility, excellent current carrying capacity, optical transparency and mechanical flexibility. Although there have been several publications about SWNT driver circuits, none of them have shown static and dynamic images with the AM OLED displays. Here we report on the first successful chemical vapor deposition (CVD)-grown SWNT network thin film transistor (TFT) driver circuits for static and dynamic AM OLED displays with 6 × 6 pixels. The high device mobility of ~45 cm2V−1s−1 and the high channel current on/off ratio of ~105 of the SWNT-TFTs fully guarantee the control capability to the OLED pixels. Our results suggest that SWNT-TFTs are promising backplane building blocks for future OLED displays.

Carbon Nanotube Driver Circuit for 6 × 6 Organic Light Emitting Diode Display

KAUST Repository

Zou, Jianping

2015-06-29

Single-walled carbon nanotube (SWNT) is expected to be a very promising material for flexible and transparent driver circuits for active matrix organic light emitting diode (AM OLED) displays due to its high field-effect mobility, excellent current carrying capacity, optical transparency and mechanical flexibility. Although there have been several publications about SWNT driver circuits, none of them have shown static and dynamic images with the AM OLED displays. Here we report on the first successful chemical vapor deposition (CVD)-grown SWNT network thin film transistor (TFT) driver circuits for static and dynamic AM OLED displays with 6 × 6 pixels. The high device mobility of ~45 cm2V−1s−1 and the high channel current on/off ratio of ~105 of the SWNT-TFTs fully guarantee the control capability to the OLED pixels. Our results suggest that SWNT-TFTs are promising backplane building blocks for future OLED displays.

Signals and Circuits in the Purkinje Neuron

Directory of Open Access Journals (Sweden)

Ze'ev R Abrams

2011-09-01

Full Text Available Purkinje neurons in the cerebellum have over 100,000 inputs organized in an orthogonal geometry, and a single output channel. As the sole output of the cerebellar cortex layer, their complex firing pattern has been associated with motor control and learning. As such they have been extensively modeled and measured using tools ranging from electrophysiology and neuroanatomy, to dynamic systems and artificial intelligence methods. However, there is an alternative approach to analyze and describe the neuronal output of these cells using concepts from Electrical Engineering, particularly signal processing and digital/analog circuits. By viewing the Purkinje neuron as an unknown circuit to be reverse-engineered, we can use the tools that provide the foundations of today’s integrated circuits and communication systems to analyze the Purkinje system at the circuit level. We use Fourier transforms to analyze and isolate the inherent frequency modes in the Purkinje neuron and define 3 unique frequency ranges associated with the cells’ output. Comparing the Purkinje neuron to a signal generator that can be externally modulated adds an entire level of complexity to the functional role of these neurons both in terms of data analysis and information processing, relying on Fourier analysis methods in place of statistical ones. We also re-describe some of the recent literature in the field, using the nomenclature of signal processing. Furthermore, by comparing the experimental data of the past decade with basic electronic circuitry, we can resolve the outstanding controversy in the field, by recognizing that the Purkinje neuron can act as a multivibrator circuit.

A reconfigurable analog baseband circuit for WLAN, WCDMA, and Bluetooth

International Nuclear Information System (INIS)

Tong Tao; Chi Baoyong; Wang Ziqiang; Zhang Ying; Jiang Hanjun; Wang Zhihua

2010-01-01

A reconfigurable analog baseband circuit for WLAN, WCDMA, and Bluetooth in 0.35 μm CMOS is presented. The circuit consists of two variable gain amplifiers (VGA) in cascade and a G m -C elliptic low-pass filter (LPF). The filter-order and the cut-off frequency of the LPF can be reconfigured to satisfy the requirements of various applications. In order to achieve the optimum power consumption, the bandwidth of the VGAs can also be dynamically reconfigured and some G m cells can be cut off in the given application. Simulation results show that the analog baseband circuit consumes 16.8 mW for WLAN, 8.9 mW for WCDMA and only 6.5 mW for Bluetooth, all with a 3 V power supply. The analog baseband circuit could provide -10 to +40 dB variable gain, third-order low pass filtering with 1 MHz cut-off frequency for Bluetooth, fourth-order low pass filtering with 2.2 MHz cut-off frequency for WCDMA, and fifth-order low pass filtering with 11 MHz cut-off frequency for WLAN, respectively. (semiconductor integrated circuits)

A reconfigurable analog baseband circuit for WLAN, WCDMA, and Bluetooth

Energy Technology Data Exchange (ETDEWEB)

Tong Tao; Chi Baoyong; Wang Ziqiang; Zhang Ying; Jiang Hanjun; Wang Zhihua, E-mail: tongt05@gmail.co [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China)

2010-05-15

A reconfigurable analog baseband circuit for WLAN, WCDMA, and Bluetooth in 0.35 {mu}m CMOS is presented. The circuit consists of two variable gain amplifiers (VGA) in cascade and a G{sub m}-C elliptic low-pass filter (LPF). The filter-order and the cut-off frequency of the LPF can be reconfigured to satisfy the requirements of various applications. In order to achieve the optimum power consumption, the bandwidth of the VGAs can also be dynamically reconfigured and some G{sub m} cells can be cut off in the given application. Simulation results show that the analog baseband circuit consumes 16.8 mW for WLAN, 8.9 mW for WCDMA and only 6.5 mW for Bluetooth, all with a 3 V power supply. The analog baseband circuit could provide -10 to +40 dB variable gain, third-order low pass filtering with 1 MHz cut-off frequency for Bluetooth, fourth-order low pass filtering with 2.2 MHz cut-off frequency for WCDMA, and fifth-order low pass filtering with 11 MHz cut-off frequency for WLAN, respectively. (semiconductor integrated circuits)

Differential regulation of polarized synaptic vesicle trafficking and synapse stability in neural circuit rewiring in Caenorhabditis elegans.

Directory of Open Access Journals (Sweden)

Naina Kurup

2017-06-01

Full Text Available Neural circuits are dynamic, with activity-dependent changes in synapse density and connectivity peaking during different phases of animal development. In C. elegans, young larvae form mature motor circuits through a dramatic switch in GABAergic neuron connectivity, by concomitant elimination of existing synapses and formation of new synapses that are maintained throughout adulthood. We have previously shown that an increase in microtubule dynamics during motor circuit rewiring facilitates new synapse formation. Here, we further investigate cellular control of circuit rewiring through the analysis of mutants obtained in a forward genetic screen. Using live imaging, we characterize novel mutations that alter cargo binding in the dynein motor complex and enhance anterograde synaptic vesicle movement during remodeling, providing in vivo evidence for the tug-of-war between kinesin and dynein in fast axonal transport. We also find that a casein kinase homolog, TTBK-3, inhibits stabilization of nascent synapses in their new locations, a previously unexplored facet of structural plasticity of synapses. Our study delineates temporally distinct signaling pathways that are required for effective neural circuit refinement.

Correction: The role of coupled positive feedback in the expression of the SPI1 type three secretion system in Salmonella.

Directory of Open Access Journals (Sweden)

Supreet Saini

2010-08-01

Full Text Available Salmonella enterica serovar Typhimurium is a common food-borne pathogen that induces inflammatory diarrhea and invades intestinal epithelial cells using a type three secretion system (T3SS encoded within Salmonella pathogenicity island 1 (SPI1. The genes encoding the SPI1 T3SS are tightly regulated by a network of interacting transcriptional regulators involving three coupled positive feedback loops. While the core architecture of the SPI1 gene circuit has been determined, the relative roles of these interacting regulators and associated feedback loops are still unknown. To determine the function of this circuit, we measured gene expression dynamics at both population and single-cell resolution in a number of SPI1 regulatory mutants. Using these data, we constructed a mathematical model of the SPI1 gene circuit. Analysis of the model predicted that the circuit serves two functions. The first is to place a threshold on SPI1 activation, ensuring that the genes encoding the T3SS are expressed only in response to the appropriate combination of environmental and cellular cues. The second is to amplify SPI1 gene expression. To experimentally test these predictions, we rewired the SPI1 genetic circuit by changing its regulatory architecture. This enabled us to directly test our predictions regarding the function of the circuit by varying the strength and dynamics of the activating signal. Collectively, our experimental and computational results enable us to deconstruct this complex circuit and determine the role of its individual components in regulating SPI1 gene expression dynamics.

Biological 2-Input Decoder Circuit in Human Cells

Science.gov (United States)

2015-01-01

Decoders are combinational circuits that convert information from n inputs to a maximum of 2n outputs. This operation is of major importance in computing systems yet it is vastly underexplored in synthetic biology. Here, we present a synthetic gene network architecture that operates as a biological decoder in human cells, converting 2 inputs to 4 outputs. As a proof-of-principle, we use small molecules to emulate the two inputs and fluorescent reporters as the corresponding four outputs. The experiments are performed using transient transfections in human kidney embryonic cells and the characterization by fluorescence microscopy and flow cytometry. We show a clear separation between the ON and OFF mean fluorescent intensity states. Additionally, we adopt the integrated mean fluorescence intensity for the characterization of the circuit and show that this metric is more robust to transfection conditions when compared to the mean fluorescent intensity. To conclude, we present the first implementation of a genetic decoder. This combinational system can be valuable toward engineering higher-order circuits as well as accommodate a multiplexed interface with endogenous cellular functions. PMID:24694115

Biological 2-input decoder circuit in human cells.

Science.gov (United States)

Guinn, Michael; Bleris, Leonidas

2014-08-15

Decoders are combinational circuits that convert information from n inputs to a maximum of 2(n) outputs. This operation is of major importance in computing systems yet it is vastly underexplored in synthetic biology. Here, we present a synthetic gene network architecture that operates as a biological decoder in human cells, converting 2 inputs to 4 outputs. As a proof-of-principle, we use small molecules to emulate the two inputs and fluorescent reporters as the corresponding four outputs. The experiments are performed using transient transfections in human kidney embryonic cells and the characterization by fluorescence microscopy and flow cytometry. We show a clear separation between the ON and OFF mean fluorescent intensity states. Additionally, we adopt the integrated mean fluorescence intensity for the characterization of the circuit and show that this metric is more robust to transfection conditions when compared to the mean fluorescent intensity. To conclude, we present the first implementation of a genetic decoder. This combinational system can be valuable toward engineering higher-order circuits as well as accommodate a multiplexed interface with endogenous cellular functions.

Gene expression from polynomial dynamics in the 2-adic information space

International Nuclear Information System (INIS)

Khrennikov, Andrei Yu.

2009-01-01

We perform geometrization of genetics by representing genetic information by points of the 4-adic information space. By well known theorem of number theory this space can also be represented as the 2-adic space. The process of DNA-reproduction is described by the action of a 4-adic (or equivalently 2-adic) dynamical system. As we know, the genes contain information for production of proteins. The genetic code is a degenerate map of codons to proteins. We model this map as functioning of a polynomial dynamical system. The purely mathematical problem under consideration is to find a dynamical system reproducing the degenerate structure of the genetic code. We present one of possible solutions of this problem.

A Novel Notch-YAP Circuit Drives Stemness and Tumorigenesis in Embryonal Rhabdomyosarcoma.

Science.gov (United States)

Slemmons, Katherine K; Crose, Lisa E S; Riedel, Stefan; Sushnitha, Manuela; Belyea, Brian; Linardic, Corinne M

2017-12-01

Rhabdomyosarcoma (RMS), a cancer characterized by skeletal muscle features, is the most common soft-tissue sarcoma of childhood. While low- and intermediate-risk groups have seen improved outcomes, high-risk patients still face a 5-year survival rate of statistic that has not changed in over 40 years. Understanding the biologic underpinnings of RMS is critical. The developmental pathways of Notch and YAP have been identified as potent but independent oncogenic signals that support the embryonal variant of RMS (eRMS). Here, the cross-talk between these pathways and the impact on eRMS tumorigenesis is reported. Using human eRMS cells grown as three-dimensional (3D) rhabdospheres, which enriches in stem cells, it was found that Notch signaling transcriptionally upregulates YAP1 gene expression and YAP activity. Reciprocally, YAP transcriptionally upregulates the Notch ligand genes JAG1 and DLL1 and the core Notch transcription factor RBPJ This bidirectional circuit boosts expression of key stem cell genes, including SOX2 , which is functionally required for eRMS spheres. Silencing this circuit for therapeutic purposes may be challenging, because the inhibition of one node (e.g., pharmacologic Notch blockade) can be rescued by upregulation of another (constitutive YAP expression). Instead, dual inhibition of Notch and YAP is necessary. Finally, supporting the existence of this circuit beyond a model system, nuclear Notch and YAP protein expression are correlated in human eRMS tumors, and YAP suppression in vivo decreases Notch signaling and SOX2 expression. Implications: This study identifies a novel oncogenic signaling circuit driving eRMS stemness and tumorigenesis, and provides evidence and rationale for combination therapies co-targeting Notch and YAP. Mol Cancer Res; 15(12); 1777-91. ©2017 AACR . ©2017 American Association for Cancer Research.

Boolean network model of the Pseudomonas aeruginosa quorum sensing circuits.

Science.gov (United States)

Dallidis, Stylianos E; Karafyllidis, Ioannis G

2014-09-01

To coordinate their behavior and virulence and to synchronize attacks against their hosts, bacteria communicate by continuously producing signaling molecules (called autoinducers) and continuously monitoring the concentration of these molecules. This communication is controlled by biological circuits called quorum sensing (QS) circuits. Recently QS circuits and have been recognized as an alternative target for controlling bacterial virulence and infections without the use of antibiotics. Pseudomonas aeruginosa is a Gram-negative bacterium that infects insects, plants, animals and humans and can cause acute infections. This bacterium has three interconnected QS circuits that form a very complex and versatile QS system, the operation of which is still under investigation. Here we use Boolean networks to model the complete QS system of Pseudomonas aeruginosa and we simulate and analyze its operation in both synchronous and asynchronous modes. The state space of the QS system is constructed and it turned out to be very large, hierarchical, modular and scale-free. Furthermore, we developed a simulation tool that can simulate gene knock-outs and study their effect on the regulons controlled by the three QS circuits. The model and tools we developed will give to life scientists a deeper insight to this complex QS system.

The dynamic landscape of gene regulation during Bombyx mori oogenesis.

Science.gov (United States)

Zhang, Qiang; Sun, Wei; Sun, Bang-Yong; Xiao, Yang; Zhang, Ze

2017-09-11

Oogenesis in the domestic silkworm (Bombyx mori) is a complex process involving previtellogenesis, vitellogenesis and choriogenesis. During this process, follicles show drastic morphological and physiological changes. However, the genome-wide regulatory profiles of gene expression during oogenesis remain to be determined. In this study, we obtained time-series transcriptome data and used these data to reveal the dynamic landscape of gene regulation during oogenesis. A total of 1932 genes were identified to be differentially expressed among different stages, most of which occurred during the transition from late vitellogenesis to early choriogenesis. Using weighted gene co-expression network analysis, we identified six stage-specific gene modules that correspond to multiple regulatory pathways. Strikingly, the biosynthesis pathway of the molting hormone 20-hydroxyecdysone (20E) was enriched in one of the modules. Further analysis showed that the ecdysteroid 20-hydroxylase gene (CYP314A1) of steroidgenesis genes was mainly expressed in previtellogenesis and early vitellogenesis. However, the 20E-inactivated genes, particularly the ecdysteroid 26-hydroxylase encoding gene (Cyp18a1), were highly expressed in late vitellogenesis. These distinct expression patterns between 20E synthesis and catabolism-related genes might ensure the rapid decline of the hormone titer at the transition point from vitellogenesis to choriogenesis. In addition, we compared landscapes of gene regulation between silkworm (Lepidoptera) and fruit fly (Diptera) oogeneses. Our results show that there is some consensus in the modules of gene co-expression during oogenesis in these insects. The data presented in this study provide new insights into the regulatory mechanisms underlying oogenesis in insects with polytrophic meroistic ovaries. The results also provide clues for further investigating the roles of epigenetic reconfiguration and circadian rhythm in insect oogenesis.

Using circuit theory to model connectivity in ecology, evolution, and conservation.

Science.gov (United States)

McRae, Brad H; Dickson, Brett G; Keitt, Timothy H; Shah, Viral B

2008-10-01

Connectivity among populations and habitats is important for a wide range of ecological processes. Understanding, preserving, and restoring connectivity in complex landscapes requires connectivity models and metrics that are reliable, efficient, and process based. We introduce a new class of ecological connectivity models based in electrical circuit theory. Although they have been applied in other disciplines, circuit-theoretic connectivity models are new to ecology. They offer distinct advantages over common analytic connectivity models, including a theoretical basis in random walk theory and an ability to evaluate contributions of multiple dispersal pathways. Resistance, current, and voltage calculated across graphs or raster grids can be related to ecological processes (such as individual movement and gene flow) that occur across large population networks or landscapes. Efficient algorithms can quickly solve networks with millions of nodes, or landscapes with millions of raster cells. Here we review basic circuit theory, discuss relationships between circuit and random walk theories, and describe applications in ecology, evolution, and conservation. We provide examples of how circuit models can be used to predict movement patterns and fates of random walkers in complex landscapes and to identify important habitat patches and movement corridors for conservation planning.

Circuit analysis for dummies

CERN Document Server

Santiago, John

2013-01-01

Circuits overloaded from electric circuit analysis? Many universities require that students pursuing a degree in electrical or computer engineering take an Electric Circuit Analysis course to determine who will ""make the cut"" and continue in the degree program. Circuit Analysis For Dummies will help these students to better understand electric circuit analysis by presenting the information in an effective and straightforward manner. Circuit Analysis For Dummies gives you clear-cut information about the topics covered in an electric circuit analysis courses to help

A novel variational method for deriving Lagrangian and Hamiltonian models of inductor-capacitor circuits

NARCIS (Netherlands)

Moreau, L.; Aeyels, D.

2004-01-01

We study the dynamical equations of nonlinear inductor-capacitor circuits. We present a novel Lagrangian description of the dynamics and provide a variational interpretation, which is based on the maximum principle of optimal control theory. This gives rise to an alternative method for deriving the

Experiment and CFD simulation of exhaust tube in highvoltage circuit breaker

Directory of Open Access Journals (Sweden)

Ye Xiangyang

2018-01-01

Full Text Available In a high-voltage circuit breaker, the exhaust tube connects the arc zone with the exhaust volume. During the arc interruption process, the exhaust tube transports the hot gas from the arc interruption zone to the exhaust volume through its distributed holes. The design of a high performance exhaust tube in the circuit breaker development aims for well controlled hot gas evacuation mass flow and pressure waves. In this paper, the exhaust tube behaviour is investigated using Computational Fluid Dynamics (CFD. To verify the CFD simulation, a basic experimental study with pressure measurements at different positions of the exhaust tube is performed. Further, the design parameters influencing the exhaust tube behaviour and circuit breaker performance are investigated and discussed.

High theory/mass markets: Newsweek magazine and the circuits of medical culture.

Science.gov (United States)

Lewis, Bradley

2007-01-01

Medicine is driven by much more than science and reason (ethics); it is also driven by the circuits of culture within which it operates. This article examines how postmodern theory deconstructs standard ideals of science and reason and allows medical humanities scholars to better contextualize the world of medicine. As such, postmodern theory provides an invaluable tool for understanding the circuits of popular culture and medicine's place within these circuits. Using a recent issue of Newsweek magazine devoted to health and technology to illustrate the main points, this essay argues that contemporary popular influences on medicine are deeply problematic, and that through an appreciation of the dynamics of culture, medical humanities scholars can join the struggle over medical culture. This perspective allows medical humanities to make important contributions toward alternative circuits of medical representation, consumption, and identification.

FEA identification of high order generalized equivalent circuits for MF high voltage transformers

CERN Document Server

Candolfi, Sylvain; Cros, Jérôme; Aguglia, Davide

2015-01-01

This paper presents a specific methodology to derive high order generalized equivalent circuits from electromagnetic finite element analysis for high voltage medium frequency and pulse transformers by splitting the main windings in an arbitrary number of elementary windings. With this modeling approach, the dynamic model of the transformer over a large bandwidth is improved and the order of the generalized equivalent circuit can be adapted to a specified bandwidth. This efficient tool can be used by the designer to quantify the influence of the local structure of transformers on their dynamic behavior. The influence of different topologies and winding configurations is investigated. Several application examples and an experimental validation are also presented.

Current limiter circuit system

Science.gov (United States)

Witcher, Joseph Brandon; Bredemann, Michael V.

2017-09-05

An apparatus comprising a steady state sensing circuit, a switching circuit, and a detection circuit. The steady state sensing circuit is connected to a first, a second and a third node. The first node is connected to a first device, the second node is connected to a second device, and the steady state sensing circuit causes a scaled current to flow at the third node. The scaled current is proportional to a voltage difference between the first and second node. The switching circuit limits an amount of current that flows between the first and second device. The detection circuit is connected to the third node and the switching circuit. The detection circuit monitors the scaled current at the third node and controls the switching circuit to limit the amount of the current that flows between the first and second device when the scaled current is greater than a desired level.

Noise processing by microRNA-mediated circuits: The Incoherent Feed-Forward Loop, revisited

Directory of Open Access Journals (Sweden)

Silvia Grigolon

2016-04-01

Full Text Available The intrinsic stochasticity of gene expression is usually mitigated in higher eukaryotes by post-transcriptional regulation channels that stabilise the output layer, most notably protein levels. The discovery of small non-coding RNAs (miRNAs in specific motifs of the genetic regulatory network has led to identifying noise buffering as the possible key function they exert in regulation. Recent in vitro and in silico studies have corroborated this hypothesis. It is however also known that miRNA-mediated noise reduction is hampered by transcriptional bursting in simple topologies. Here, using stochastic simulations validated by analytical calculations based on van Kampen's expansion, we revisit the noise-buffering capacity of the miRNA-mediated Incoherent Feed Forward Loop (IFFL, a small module that is widespread in the gene regulatory networks of higher eukaryotes, in order to account for the effects of intermittency in the transcriptional activity of the modulator gene. We show that bursting considerably alters the circuit's ability to control static protein noise. By comparing with other regulatory architectures, we find that direct transcriptional regulation significantly outperforms the IFFL in a broad range of kinetic parameters. This suggests that, under pulsatile inputs, static noise reduction may be less important than dynamical aspects of noise and information processing in characterising the performance of regulatory elements.

The voltage—current relationship and equivalent circuit implementation of parallel flux-controlled memristive circuits

International Nuclear Information System (INIS)

Bao Bo-Cheng; Feng Fei; Dong Wei; Pan Sai-Hu

2013-01-01

A flux-controlled memristor characterized by smooth cubic nonlinearity is taken as an example, upon which the voltage—current relationships (VCRs) between two parallel memristive circuits — a parallel memristor and capacitor circuit (the parallel MC circuit), and a parallel memristor and inductor circuit (the parallel ML circuit) — are investigated. The results indicate that the VCR between these two parallel memristive circuits is closely related to the circuit parameters, and the frequency and amplitude of the sinusoidal voltage stimulus. An equivalent circuit model of the memristor is built, upon which the circuit simulations and experimental measurements of both the parallel MC circuit and the parallel ML circuit are performed, and the results verify the theoretical analysis results

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data.

Science.gov (United States)

Gong, Wuming; Koyano-Nakagawa, Naoko; Li, Tongbin; Garry, Daniel J

2015-03-07

Decoding the temporal control of gene expression patterns is key to the understanding of the complex mechanisms that govern developmental decisions during heart development. High-throughput methods have been employed to systematically study the dynamic and coordinated nature of cardiac differentiation at the global level with multiple dimensions. Therefore, there is a pressing need to develop a systems approach to integrate these data from individual studies and infer the dynamic regulatory networks in an unbiased fashion. We developed a two-step strategy to integrate data from (1) temporal RNA-seq, (2) temporal histone modification ChIP-seq, (3) transcription factor (TF) ChIP-seq and (4) gene perturbation experiments to reconstruct the dynamic network during heart development. First, we trained a logistic regression model to predict the probability (LR score) of any base being bound by 543 TFs with known positional weight matrices. Second, four dimensions of data were combined using a time-varying dynamic Bayesian network model to infer the dynamic networks at four developmental stages in the mouse [mouse embryonic stem cells (ESCs), mesoderm (MES), cardiac progenitors (CP) and cardiomyocytes (CM)]. Our method not only infers the time-varying networks between different stages of heart development, but it also identifies the TF binding sites associated with promoter or enhancers of downstream genes. The LR scores of experimentally verified ESCs and heart enhancers were significantly higher than random regions (p network inference model identified a region with an elevated LR score approximately -9400 bp upstream of the transcriptional start site of Nkx2-5, which overlapped with a previously reported enhancer region (-9435 to -8922 bp). TFs such as Tead1, Gata4, Msx2, and Tgif1 were predicted to bind to this region and participate in the regulation of Nkx2-5 gene expression. Our model also predicted the key regulatory networks for the ESC-MES, MES-CP and CP

Optimization of a primary circuit of the nuclear power plant from the vibration point of view

International Nuclear Information System (INIS)

Dupal, J.; Zeman, V.

2003-01-01

The primary circuit of the nuclear power plant (NPP) as a dynamical vibrating system can be disturbed by various excitation including earthquake or pressure pulsation generated by main circulation pumps (MCP). Especially, unpleasant pulsation vibration growth can be caused by the small differences of revolutions between main circulation pumps of the individual coolant loops. This growth corresponds to the well known beats. The paper deals with an approach to the improving and optimization of dynamical properties of the whole primary circuit system including the reactor and coolant loops under pressure pulsation. (author)

Explicit logic circuits discriminate neural states.

Directory of Open Access Journals (Sweden)

Lane Yoder

Full Text Available The magnitude and apparent complexity of the brain's connectivity have left explicit networks largely unexplored. As a result, the relationship between the organization of synaptic connections and how the brain processes information is poorly understood. A recently proposed retinal network that produces neural correlates of color vision is refined and extended here to a family of general logic circuits. For any combination of high and low activity in any set of neurons, one of the logic circuits can receive input from the neurons and activate a single output neuron whenever the input neurons have the given activity state. The strength of the output neuron's response is a measure of the difference between the smallest of the high inputs and the largest of the low inputs. The networks generate correlates of known psychophysical phenomena. These results follow directly from the most cost-effective architectures for specific logic circuits and the minimal cellular capabilities of excitation and inhibition. The networks function dynamically, making their operation consistent with the speed of most brain functions. The networks show that well-known psychophysical phenomena do not require extraordinarily complex brain structures, and that a single network architecture can produce apparently disparate phenomena in different sensory systems.

The persistent current and energy spectrum on a driven mesoscopic LC-circuit with Josephson junction

Science.gov (United States)

Pahlavanias, Hassan

2018-03-01

The quantum theory for a mesoscopic electric circuit including a Josephson junction with charge discreteness is studied. By considering coupling energy of the mesoscopic capacitor in Josephson junction device, a Hamiltonian describing the dynamics of a quantum mesoscopic electric LC-circuit with charge discreteness is introduced. We first calculate the persistent current on a quantum driven ring including Josephson junction. Then we obtain the persistent current and energy spectrum of a quantum mesoscopic electrical circuit which includes capacitor, inductor, time-dependent external source and Josephson junction.

Robust variable selection method for nonparametric differential equation models with application to nonlinear dynamic gene regulatory network analysis.

Science.gov (United States)

Lu, Tao

2016-01-01

The gene regulation network (GRN) evaluates the interactions between genes and look for models to describe the gene expression behavior. These models have many applications; for instance, by characterizing the gene expression mechanisms that cause certain disorders, it would be possible to target those genes to block the progress of the disease. Many biological processes are driven by nonlinear dynamic GRN. In this article, we propose a nonparametric differential equation (ODE) to model the nonlinear dynamic GRN. Specially, we address following questions simultaneously: (i) extract information from noisy time course gene expression data; (ii) model the nonlinear ODE through a nonparametric smoothing function; (iii) identify the important regulatory gene(s) through a group smoothly clipped absolute deviation (SCAD) approach; (iv) test the robustness of the model against possible shortening of experimental duration. We illustrate the usefulness of the model and associated statistical methods through a simulation and a real application examples.

An Improved Memristive Diode Bridge-Based Band Pass Filter Chaotic Circuit

Directory of Open Access Journals (Sweden)

Quan Xu

2017-01-01

Full Text Available By replacing a series resistor in active band pass filter (BPF with an improved memristive diode bridge emulator, a third-order memristive BPF chaotic circuit is presented. The improved memristive diode bridge emulator without grounded limitation is equivalently achieved by a diode bridge cascaded with only one inductor, whose fingerprints of pinched hysteresis loop are examined by numerical simulations and hardware experiments. The memristive BPF chaotic circuit has only one zero unstable saddle point but causes complex dynamical behaviors including period, chaos, period doubling bifurcation, and coexisting bifurcation modes. Specially, it should be highly significant that two kinds of bifurcation routes are displayed under different initial conditions and the coexistence of three different topological attractors is found in a narrow parameter range. Moreover, hardware circuit using discrete components is fabricated and experimental measurements are performed, upon which the numerical simulations are validated. Notably, the proposed memristive BPF chaotic circuit is only third-order and has simple topological structure.

Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction.

Science.gov (United States)

Kuwahara, Hiroyuki; Myers, Chris J; Samoilov, Michael S

2010-03-26

Uropathogenic Escherichia coli (UPEC) represent the predominant cause of urinary tract infections (UTIs). A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element-the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role in shutting down fimbriae expression, the primary function of FimB recombinase may be to effect a controlled down-regulation (rather than increase) of the ON-to-OFF fim switching rate via temperature-dependent suppression of competing dynamics mediated by recombinase FimE. Our computational analysis further implies that this down

Gene Expression Dynamics Accompanying the Sponge Thermal Stress Response.

Science.gov (United States)

Guzman, Christine; Conaco, Cecilia

2016-01-01

Marine sponges are important members of coral reef ecosystems. Thus, their responses to changes in ocean chemistry and environmental conditions, particularly to higher seawater temperatures, will have potential impacts on the future of these reefs. To better understand the sponge thermal stress response, we investigated gene expression dynamics in the shallow water sponge, Haliclona tubifera (order Haplosclerida, class Demospongiae), subjected to elevated temperature. Using high-throughput transcriptome sequencing, we show that these conditions result in the activation of various processes that interact to maintain cellular homeostasis. Short-term thermal stress resulted in the induction of heat shock proteins, antioxidants, and genes involved in signal transduction and innate immunity pathways. Prolonged exposure to thermal stress affected the expression of genes involved in cellular damage repair, apoptosis, signaling and transcription. Interestingly, exposure to sublethal temperatures may improve the ability of the sponge to mitigate cellular damage under more extreme stress conditions. These insights into the potential mechanisms of adaptation and resilience of sponges contribute to a better understanding of sponge conservation status and the prediction of ecosystem trajectories under future climate conditions.

A voltage biased superconducting quantum interference device bootstrap circuit

International Nuclear Information System (INIS)

Xie Xiaoming; Wang Huiwu; Wang Yongliang; Dong Hui; Jiang Mianheng; Zhang Yi; Krause, Hans-Joachim; Braginski, Alex I; Offenhaeusser, Andreas; Mueck, Michael

2010-01-01

We present a dc superconducting quantum interference device (SQUID) readout circuit operating in the voltage bias mode and called a SQUID bootstrap circuit (SBC). The SBC is an alternative implementation of two existing methods for suppression of room-temperature amplifier noise: additional voltage feedback and current feedback. Two circuit branches are connected in parallel. In the dc SQUID branch, an inductively coupled coil connected in series provides the bias current feedback for enhancing the flux-to-current coefficient. The circuit branch parallel to the dc SQUID branch contains an inductively coupled voltage feedback coil with a shunt resistor in series for suppressing the preamplifier noise current by increasing the dynamic resistance. We show that the SBC effectively reduces the preamplifier noise to below the SQUID intrinsic noise. For a helium-cooled planar SQUID magnetometer with a SQUID inductance of 350 pH, a flux noise of about 3 μΦ 0 Hz -1/2 and a magnetic field resolution of less than 3 fT Hz -1/2 were obtained. The SBC leads to a convenient direct readout electronics for a dc SQUID with a wider adjustment tolerance than other feedback schemes.

Generalized reconfigurable memristive dynamical system (MDS) for neuromorphic applications.

Science.gov (United States)

Bavandpour, Mohammad; Soleimani, Hamid; Linares-Barranco, Bernabé; Abbott, Derek; Chua, Leon O

2015-01-01

This study firstly presents (i) a novel general cellular mapping scheme for two dimensional neuromorphic dynamical systems such as bio-inspired neuron models, and (ii) an efficient mixed analog-digital circuit, which can be conveniently implemented on a hybrid memristor-crossbar/CMOS platform, for hardware implementation of the scheme. This approach employs 4n memristors and no switch for implementing an n-cell system in comparison with 2n (2) memristors and 2n switches of a Cellular Memristive Dynamical System (CMDS). Moreover, this approach allows for dynamical variables with both analog and one-hot digital values opening a wide range of choices for interconnections and networking schemes. Dynamical response analyses show that this circuit exhibits various responses based on the underlying bifurcation scenarios which determine the main characteristics of the neuromorphic dynamical systems. Due to high programmability of the circuit, it can be applied to a variety of learning systems, real-time applications, and analytically indescribable dynamical systems. We simulate the FitzHugh-Nagumo (FHN), Adaptive Exponential (AdEx) integrate and fire, and Izhikevich neuron models on our platform, and investigate the dynamical behaviors of these circuits as case studies. Moreover, error analysis shows that our approach is suitably accurate. We also develop a simple hardware prototype for experimental demonstration of our approach.

Mathematical model of flagella gene expression dynamics in Salmonella enterica serovar typhimurium

OpenAIRE

Jain, Kirti; Pradhan, Amit; Mokashi, Chaitanya; Saini, Supreet

2015-01-01

Flagellar assembly in Salmonella is controlled by an intricate genetic and biochemical network. This network comprises of a number of inter-connected feedback loops, which control the assembly process dynamically. Critical among these are the FliA–FlgM feedback, FliZ-mediated positive feedback, and FliT-mediated negative feedback. In this work, we develop a mathematical model to track the dynamics of flagellar gene expression in Salmonella. Analysis of our model demonstrates that the network ...

30 CFR 75.518 - Electric equipment and circuits; overload and short circuit protection.

Science.gov (United States)

2010-07-01

... short circuit protection. 75.518 Section 75.518 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... Equipment-General § 75.518 Electric equipment and circuits; overload and short circuit protection... installed so as to protect all electric equipment and circuits against short circuit and overloads. Three...

GATA Factor-Dependent Positive-Feedback Circuit in Acute Myeloid Leukemia Cells

Directory of Open Access Journals (Sweden)

Koichi R. Katsumura

2016-08-01

Full Text Available The master regulatory transcription factor GATA-2 triggers hematopoietic stem and progenitor cell generation. GATA2 haploinsufficiency is implicated in myelodysplastic syndrome (MDS and acute myeloid leukemia (AML, and GATA2 overexpression portends a poor prognosis for AML. However, the constituents of the GATA-2-dependent genetic network mediating pathogenesis are unknown. We described a p38-dependent mechanism that phosphorylates GATA-2 and increases GATA-2 target gene activation. We demonstrate that this mechanism establishes a growth-promoting chemokine/cytokine circuit in AML cells. p38/ERK-dependent GATA-2 phosphorylation facilitated positive autoregulation of GATA2 transcription and expression of target genes, including IL1B and CXCL2. IL-1β and CXCL2 enhanced GATA-2 phosphorylation, which increased GATA-2-mediated transcriptional activation. p38/ERK-GATA-2 stimulated AML cell proliferation via CXCL2 induction. As GATA2 mRNA correlated with IL1B and CXCL2 mRNAs in AML-M5 and high expression of these genes predicted poor prognosis of cytogenetically normal AML, we propose that the circuit is functionally important in specific AML contexts.

Dynamic gene expression response to altered gravity in human T cells.

Science.gov (United States)

Thiel, Cora S; Hauschild, Swantje; Huge, Andreas; Tauber, Svantje; Lauber, Beatrice A; Polzer, Jennifer; Paulsen, Katrin; Lier, Hartwin; Engelmann, Frank; Schmitz, Burkhard; Schütte, Andreas; Layer, Liliana E; Ullrich, Oliver

2017-07-12

We investigated the dynamics of immediate and initial gene expression response to different gravitational environments in human Jurkat T lymphocytic cells and compared expression profiles to identify potential gravity-regulated genes and adaptation processes. We used the Affymetrix GeneChip® Human Transcriptome Array 2.0 containing 44,699 protein coding genes and 22,829 non-protein coding genes and performed the experiments during a parabolic flight and a suborbital ballistic rocket mission to cross-validate gravity-regulated gene expression through independent research platforms and different sets of control experiments to exclude other factors than alteration of gravity. We found that gene expression in human T cells rapidly responded to altered gravity in the time frame of 20 s and 5 min. The initial response to microgravity involved mostly regulatory RNAs. We identified three gravity-regulated genes which could be cross-validated in both completely independent experiment missions: ATP6V1A/D, a vacuolar H + -ATPase (V-ATPase) responsible for acidification during bone resorption, IGHD3-3/IGHD3-10, diversity genes of the immunoglobulin heavy-chain locus participating in V(D)J recombination, and LINC00837, a long intergenic non-protein coding RNA. Due to the extensive and rapid alteration of gene expression associated with regulatory RNAs, we conclude that human cells are equipped with a robust and efficient adaptation potential when challenged with altered gravitational environments.

30 CFR 77.506 - Electric equipment and circuits; overload and short-circuit protection.

Science.gov (United States)

2010-07-01

... short-circuit protection. 77.506 Section 77.506 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION... circuits; overload and short-circuit protection. Automatic circuit-breaking devices or fuses of the correct type and capacity shall be installed so as to protect all electric equipment and circuits against short...

Dynamics of antibiotic resistance genes and presence of putative pathogens during ambient temperature anaerobic digestion.

Science.gov (United States)

Resende, J A; Diniz, C G; Silva, V L; Otenio, M H; Bonnafous, A; Arcuri, P B; Godon, J-J

2014-12-01

This study was focused on evaluating the persistency of antimicrobial resistance (AR) genes and putative pathogenic bacteria in an anaerobic digesters operating at mesophilic ambient temperature, in two different year seasons: summer and winter. Abundance and dynamic of AR genes encoding resistance to macrolides (ermB), aminoglycosides (aphA2) and beta-lactams (blaTEM -1 ) and persistency of potentially pathogenic bacteria in pilot-scale anaerobic digesters were investigated. AR genes were determined in the influent and effluent in both conditions. Overall, after 60 days, reduction was observed for all evaluated genes. However, during the summer, anaerobic digestion was more related to the gene reduction as compared to winter. Persistency of potentially pathogenic bacteria was also evaluated by metagenomic analyses compared to an in-house created database. Clostridium, Acinetobacter and Stenotrophomonas were the most identified. Overall, considering the mesophilic ambient temperature during anaerobic digestion (summer and winter), a decrease in pathogenic bacteria detection through metagenomic analysis and AR genes is reported. Although the mesophilic anaerobic digestion has been efficient, the results may suggest medically important bacteria and AR genes persistency during the process. This is the first report to show AR gene dynamics and persistency of potentially pathogenic bacteria through metagenomic approach in cattle manure ambient temperature anaerobic digestion. © 2014 The Society for Applied Microbiology.

An HIV feedback resistor: auto-regulatory circuit deactivator and noise buffer.

Science.gov (United States)

Weinberger, Leor S; Shenk, Thomas

2007-01-01

Animal viruses (e.g., lentiviruses and herpesviruses) use transcriptional positive feedback (i.e., transactivation) to regulate their gene expression. But positive-feedback circuits are inherently unstable when turned off, which presents a particular dilemma for latent viruses that lack transcriptional repressor motifs. Here we show that a dissipative feedback resistor, composed of enzymatic interconversion of the transactivator, converts transactivation circuits into excitable systems that generate transient pulses of expression, which decay to zero. We use HIV-1 as a model system and analyze single-cell expression kinetics to explore whether the HIV-1 transactivator of transcription (Tat) uses a resistor to shut off transactivation. The Tat feedback circuit was found to lack bi-stability and Tat self-cooperativity but exhibited a pulse of activity upon transactivation, all in agreement with the feedback resistor model. Guided by a mathematical model, biochemical and genetic perturbation of the suspected Tat feedback resistor altered the circuit's stability and reduced susceptibility to molecular noise, in agreement with model predictions. We propose that the feedback resistor is a necessary, but possibly not sufficient, condition for turning off noisy transactivation circuits lacking a repressor motif (e.g., HIV-1 Tat). Feedback resistors may be a paradigm for examining other auto-regulatory circuits and may inform upon how viral latency is established, maintained, and broken.

Volumetric and chemical control auxiliary circuit for a PWR primary circuit

International Nuclear Information System (INIS)

Costes, D.

1990-01-01

The volumetric and chemical control circuit has an expansion tank with at least one water-steam chamber connected to the primary circuit by a sampling pipe and a reinjection pipe. The sampling pipe feeds jet pumps controlled by valves. An action on these valves and pumps regulates the volume of the water in the primary circuit. A safety pipe controlled by a flap automatically injects water from the chamber into the primary circuit in case of ruptures. The auxiliary circuit has also systems for purifying the water and controlling the boric acid and hydrogen content [fr

Inferring network topology from complex dynamics

International Nuclear Information System (INIS)

Shandilya, Srinivas Gorur; Timme, Marc

2011-01-01

Inferring the network topology from dynamical observations is a fundamental problem pervading research on complex systems. Here, we present a simple, direct method for inferring the structural connection topology of a network, given an observation of one collective dynamical trajectory. The general theoretical framework is applicable to arbitrary network dynamical systems described by ordinary differential equations. No interference (external driving) is required and the type of dynamics is hardly restricted in any way. In particular, the observed dynamics may be arbitrarily complex; stationary, invariant or transient; synchronous or asynchronous and chaotic or periodic. Presupposing a knowledge of the functional form of the dynamical units and of the coupling functions between them, we present an analytical solution to the inverse problem of finding the network topology from observing a time series of state variables only. Robust reconstruction is achieved in any sufficiently long generic observation of the system. We extend our method to simultaneously reconstructing both the entire network topology and all parameters appearing linear in the system's equations of motion. Reconstruction of network topology and system parameters is viable even in the presence of external noise that distorts the original dynamics substantially. The method provides a conceptually new step towards reconstructing a variety of real-world networks, including gene and protein interaction networks and neuronal circuits.

Global sensitivity analysis of a dynamic model for gene expression in Drosophila embryos

Science.gov (United States)

McCarthy, Gregory D.; Drewell, Robert A.

2015-01-01

It is well known that gene regulation is a tightly controlled process in early organismal development. However, the roles of key processes involved in this regulation, such as transcription and translation, are less well understood, and mathematical modeling approaches in this field are still in their infancy. In recent studies, biologists have taken precise measurements of protein and mRNA abundance to determine the relative contributions of key factors involved in regulating protein levels in mammalian cells. We now approach this question from a mathematical modeling perspective. In this study, we use a simple dynamic mathematical model that incorporates terms representing transcription, translation, mRNA and protein decay, and diffusion in an early Drosophila embryo. We perform global sensitivity analyses on this model using various different initial conditions and spatial and temporal outputs. Our results indicate that transcription and translation are often the key parameters to determine protein abundance. This observation is in close agreement with the experimental results from mammalian cells for various initial conditions at particular time points, suggesting that a simple dynamic model can capture the qualitative behavior of a gene. Additionally, we find that parameter sensitivites are temporally dynamic, illustrating the importance of conducting a thorough global sensitivity analysis across multiple time points when analyzing mathematical models of gene regulation. PMID:26157608

Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations

DEFF Research Database (Denmark)

Lucotte, Elise A; Skov, Laurits; Jensen, Jacob Malte

2018-01-01

we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read-depth on modified X and Y chromosome targets containing...... related Y haplogroups, that diversified less than 50,000 years ago. Moreover, X and Y-linked ampliconic genes seem to have a faster amplification dynamic than autosomal multicopy genes. Looking at expression data from another study, we also find that XY-linked ampliconic genes with extensive copy number...

A platform for rapid prototyping of synthetic gene networks in mammalian cells

Science.gov (United States)

Duportet, Xavier; Wroblewska, Liliana; Guye, Patrick; Li, Yinqing; Eyquem, Justin; Rieders, Julianne; Rimchala, Tharathorn; Batt, Gregory; Weiss, Ron

2014-01-01

Mammalian synthetic biology may provide novel therapeutic strategies, help decipher new paths for drug discovery and facilitate synthesis of valuable molecules. Yet, our capacity to genetically program cells is currently hampered by the lack of efficient approaches to streamline the design, construction and screening of synthetic gene networks. To address this problem, here we present a framework for modular and combinatorial assembly of functional (multi)gene expression vectors and their efficient and specific targeted integration into a well-defined chromosomal context in mammalian cells. We demonstrate the potential of this framework by assembling and integrating different functional mammalian regulatory networks including the largest gene circuit built and chromosomally integrated to date (6 transcription units, 27kb) encoding an inducible memory device. Using a library of 18 different circuits as a proof of concept, we also demonstrate that our method enables one-pot/single-flask chromosomal integration and screening of circuit libraries. This rapid and powerful prototyping platform is well suited for comparative studies of genetic regulatory elements, genes and multi-gene circuits as well as facile development of libraries of isogenic engineered cell lines. PMID:25378321

Calculation of the soft error rate of submicron CMOS logic circuits

International Nuclear Information System (INIS)

Juhnke, T.; Klar, H.

1995-01-01

A method to calculate the soft error rate (SER) of CMOS logic circuits with dynamic pipeline registers is described. This method takes into account charge collection by drift and diffusion. The method is verified by comparison of calculated SER's to measurement results. Using this method, the SER of a highly pipelined multiplier is calculated as a function of supply voltage for a 0.6 microm, 0.3 microm, and 0.12 microm technology, respectively. It has been found that the SER of such highly pipelined submicron CMOS circuits may become too high so that countermeasures have to be taken. Since the SER greatly increases with decreasing supply voltage, low-power/low-voltage circuits may show more than eight times the SER for half the normal supply voltage as compared to conventional designs

Enhanced charging kinetics of porous electrodes: surface conduction as a short-circuit mechanism.

Science.gov (United States)

Mirzadeh, Mohammad; Gibou, Frederic; Squires, Todd M

2014-08-29

We use direct numerical simulations of the Poisson-Nernst-Planck equations to study the charging kinetics of porous electrodes and to evaluate the predictive capabilities of effective circuit models, both linear and nonlinear. The classic transmission line theory of de Levie holds for general electrode morphologies, but only at low applied potentials. Charging dynamics are slowed appreciably at high potentials, yet not as significantly as predicted by the nonlinear transmission line model of Biesheuvel and Bazant. We identify surface conduction as a mechanism which can effectively "short circuit" the high-resistance electrolyte in the bulk of the pores, thus accelerating the charging dynamics and boosting power densities. Notably, the boost in power density holds only for electrode morphologies with continuous conducting surfaces in the charging direction.

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

Directory of Open Access Journals (Sweden)

Bradon R. McDonald

2017-06-01

Full Text Available Lateral gene transfer (LGT profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces. Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.

Intuitive analog circuit design

CERN Document Server

Thompson, Marc

2013-01-01

Intuitive Analog Circuit Design outlines ways of thinking about analog circuits and systems that let you develop a feel for what a good, working analog circuit design should be. This book reflects author Marc Thompson's 30 years of experience designing analog and power electronics circuits and teaching graduate-level analog circuit design, and is the ideal reference for anyone who needs a straightforward introduction to the subject. In this book, Dr. Thompson describes intuitive and ""back-of-the-envelope"" techniques for designing and analyzing analog circuits, including transistor amplifi

The circuit designer's companion

CERN Document Server

Williams, Tim

1991-01-01

The Circuit Designer's Companion covers the theoretical aspects and practices in analogue and digital circuit design. Electronic circuit design involves designing a circuit that will fulfill its specified function and designing the same circuit so that every production model of it will fulfill its specified function, and no other undesired and unspecified function.This book is composed of nine chapters and starts with a review of the concept of grounding, wiring, and printed circuits. The subsequent chapters deal with the passive and active components of circuitry design. These topics are foll

Electronic devices and circuits

CERN Document Server

Pridham, Gordon John

1972-01-01

Electronic Devices and Circuits, Volume 3 provides a comprehensive account on electronic devices and circuits and includes introductory network theory and physics. The physics of semiconductor devices is described, along with field effect transistors, small-signal equivalent circuits of bipolar transistors, and integrated circuits. Linear and non-linear circuits as well as logic circuits are also considered. This volume is comprised of 12 chapters and begins with an analysis of the use of Laplace transforms for analysis of filter networks, followed by a discussion on the physical properties of

Mixed signal learning by spike correlation propagation in feedback inhibitory circuits.

Directory of Open Access Journals (Sweden)

Naoki Hiratani

2015-04-01

Full Text Available The brain can learn and detect mixed input signals masked by various types of noise, and spike-timing-dependent plasticity (STDP is the candidate synaptic level mechanism. Because sensory inputs typically have spike correlation, and local circuits have dense feedback connections, input spikes cause the propagation of spike correlation in lateral circuits; however, it is largely unknown how this secondary correlation generated by lateral circuits influences learning processes through STDP, or whether it is beneficial to achieve efficient spike-based learning from uncertain stimuli. To explore the answers to these questions, we construct models of feedforward networks with lateral inhibitory circuits and study how propagated correlation influences STDP learning, and what kind of learning algorithm such circuits achieve. We derive analytical conditions at which neurons detect minor signals with STDP, and show that depending on the origin of the noise, different correlation timescales are useful for learning. In particular, we show that non-precise spike correlation is beneficial for learning in the presence of cross-talk noise. We also show that by considering excitatory and inhibitory STDP at lateral connections, the circuit can acquire a lateral structure optimal for signal detection. In addition, we demonstrate that the model performs blind source separation in a manner similar to the sequential sampling approximation of the Bayesian independent component analysis algorithm. Our results provide a basic understanding of STDP learning in feedback circuits by integrating analyses from both dynamical systems and information theory.

Signal sampling circuit

NARCIS (Netherlands)

Louwsma, S.M.; Vertregt, Maarten

2011-01-01

A sampling circuit for sampling a signal is disclosed. The sampling circuit comprises a plurality of sampling channels adapted to sample the signal in time-multiplexed fashion, each sampling channel comprising a respective track-and-hold circuit connected to a respective analogue to digital

Signal sampling circuit

NARCIS (Netherlands)

Louwsma, S.M.; Vertregt, Maarten

2010-01-01

A sampling circuit for sampling a signal is disclosed. The sampling circuit comprises a plurality of sampling channels adapted to sample the signal in time-multiplexed fashion, each sampling channel comprising a respective track-and-hold circuit connected to a respective analogue to digital

We present an experimental circuit realization of a simple jerk ...

Indian Academy of Sciences (India)

IAS Admin

dimensional dynamical systems that exhibit chaos. Some of the jerk equations found have simple nonlinear functions that should permit easy electronic implementations. A chaotic jerk equation has been chosen from the list given by. Sprott [8] so that a hardware circuit may be built to observe the chaotic attractor.

Dynamic thermoelectricity in uniform bipolar semiconductor

Energy Technology Data Exchange (ETDEWEB)

Volovichev, I.N., E-mail: vin@ire.kharkov.ua

2016-07-01

The theory of the dynamic thermoelectric effect has been developed. The effect lies in an electric current flowing in a closed circuit that consists of a uniform bipolar semiconductor, in which a non-uniform temperature distribution in the form of the traveling wave is created. The calculations are performed for the one-dimensional model in the quasi-neutrality approximation. It was shown that the direct thermoelectric current prevails, despite the periodicity of the thermal excitation, the circuit homogeneity and the lack of rectifier properties of the semiconductor system. Several physical reasons underlining the dynamic thermoelectric effect are found. One of them is similar to the Dember photoelectric effect, its contribution to the current flowing is determined by the difference in the electron and hole mobilities, and is completely independent of the carrier Seebeck coefficients. The dependence of the thermoelectric short circuit current magnitude on the semiconductor parameters, as well as on the temperature wave amplitude, length and velocity is studied. It is shown that the magnitude of the thermoelectric current is proportional to the square of the temperature wave amplitude. The dependence of the thermoelectric short circuit current on the temperature wave length and velocity is the nonmonotonic function. The optimum values for the temperature wave length and velocity, at which the dynamic thermoelectric effect is the greatest, have been deduced. It is found that the thermoelectric short circuit current changes its direction with decreasing the temperature wave length under certain conditions. The prospects for the possible applications of the dynamic thermoelectric effect are also discussed.

A two-layered diffusion model traces the dynamics of information processing in the valuation-and-choice circuit of decision making.

Science.gov (United States)

Piu, Pietro; Fargnoli, Francesco; Innocenti, Alessandro; Rufa, Alessandra

2014-01-01

A circuit of evaluation and selection of the alternatives is considered a reliable model in neurobiology. The prominent contributions of the literature to this topic are reported. In this study, valuation and choice of a decisional process during Two-Alternative Forced-Choice (TAFC) task are represented as a two-layered network of computational cells, where information accrual and processing progress in nonlinear diffusion dynamics. The evolution of the response-to-stimulus map is thus modeled by two linked diffusive modules (2LDM) representing the neuronal populations involved in the valuation-and-decision circuit of decision making. Diffusion models are naturally appropriate for describing accumulation of evidence over the time. This allows the computation of the response times (RTs) in valuation and choice, under the hypothesis of ex-Wald distribution. A nonlinear transfer function integrates the activities of the two layers. The input-output map based on the infomax principle makes the 2LDM consistent with the reinforcement learning approach. Results from simulated likelihood time series indicate that 2LDM may account for the activity-dependent modulatory component of effective connectivity between the neuronal populations. Rhythmic fluctuations of the estimate gain functions in the delta-beta bands also support the compatibility of 2LDM with the neurobiology of DM.

Electric circuits essentials

CERN Document Server

REA, Editors of

2012-01-01

REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Electric Circuits I includes units, notation, resistive circuits, experimental laws, transient circuits, network theorems, techniques of circuit analysis, sinusoidal analysis, polyph

Approximate circuits for increased reliability

Science.gov (United States)

Hamlet, Jason R.; Mayo, Jackson R.

2015-08-18

Embodiments of the invention describe a Boolean circuit having a voter circuit and a plurality of approximate circuits each based, at least in part, on a reference circuit. The approximate circuits are each to generate one or more output signals based on values of received input signals. The voter circuit is to receive the one or more output signals generated by each of the approximate circuits, and is to output one or more signals corresponding to a majority value of the received signals. At least some of the approximate circuits are to generate an output value different than the reference circuit for one or more input signal values; however, for each possible input signal value, the majority values of the one or more output signals generated by the approximate circuits and received by the voter circuit correspond to output signal result values of the reference circuit.

Toward a generalized and high-throughput enzyme screening system based on artificial genetic circuits.

Science.gov (United States)

Choi, Su-Lim; Rha, Eugene; Lee, Sang Jun; Kim, Haseong; Kwon, Kilkoang; Jeong, Young-Su; Rhee, Young Ha; Song, Jae Jun; Kim, Hak-Sung; Lee, Seung-Goo

2014-03-21

Large-scale screening of enzyme libraries is essential for the development of cost-effective biological processes, which will be indispensable for the production of sustainable biobased chemicals. Here, we introduce a genetic circuit termed the Genetic Enzyme Screening System that is highly useful for high-throughput enzyme screening from diverse microbial metagenomes. The circuit consists of two AND logics. The first AND logic, the two inputs of which are the target enzyme and its substrate, is responsible for the accumulation of a phenol compound in cell. Then, the phenol compound and its inducible transcription factor, whose activation turns on the expression of a reporter gene, interact in the other logic gate. We confirmed that an individual cell harboring this genetic circuit can present approximately a 100-fold higher cellular fluorescence than the negative control and can be easily quantified by flow cytometry depending on the amounts of phenolic derivatives. The high sensitivity of the genetic circuit enables the rapid discovery of novel enzymes from metagenomic libraries, even for genes that show marginal activities in a host system. The crucial feature of this approach is that this single system can be used to screen a variety of enzymes that produce a phenol compound from respective synthetic phenyl-substrates, including cellulase, lipase, alkaline phosphatase, tyrosine phenol-lyase, and methyl parathion hydrolase. Consequently, the highly sensitive and quantitative nature of this genetic circuit along with flow cytometry techniques could provide a widely applicable toolkit for discovering and engineering novel enzymes at a single cell level.

Equivalent circuit models of two-layer flexure beams with excitation by temperature, humidity, pressure, piezoelectric or piezomagnetic interactions

Directory of Open Access Journals (Sweden)

U. Marschner

2014-09-01

Full Text Available Two-layer flexure beams often serve as basic transducers in actuators and sensors. In this paper a generalized description of their stimuli-influenced mechanical behavior is derived. For small deflection angles this description includes a multi-port circuit or network representation with lumped elements for a beam part of finite length. A number of coupled finite beam parts model the dynamic behavior including the first natural frequencies of the beam. For piezoelectric and piezomagnetic interactions, reversible transducer models are developed. The piezomagnetic two-layer beam model is extended to include solenoid and planar coils. Linear network theory is applied in order to determine network parameters and to simplify the circuit representation. The resulting circuit model is the basis for a fast simulation of the dynamic system behavior with advanced circuit simulators and, thus, the optimization of the system. It is also a useful tool for understanding and explaining this multi-domain system through basic principles of general system theory.

Short-circuit logic

NARCIS (Netherlands)

Bergstra, J.A.; Ponse, A.

2010-01-01

Short-circuit evaluation denotes the semantics of propositional connectives in which the second argument is only evaluated if the first argument does not suffice to determine the value of the expression. In programming, short-circuit evaluation is widely used. A short-circuit logic is a variant of

Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling.

Science.gov (United States)

Wu, Hulin; Lu, Tao; Xue, Hongqi; Liang, Hua

2014-04-02

The gene regulation network (GRN) is a high-dimensional complex system, which can be represented by various mathematical or statistical models. The ordinary differential equation (ODE) model is one of the popular dynamic GRN models. High-dimensional linear ODE models have been proposed to identify GRNs, but with a limitation of the linear regulation effect assumption. In this article, we propose a sparse additive ODE (SA-ODE) model, coupled with ODE estimation methods and adaptive group LASSO techniques, to model dynamic GRNs that could flexibly deal with nonlinear regulation effects. The asymptotic properties of the proposed method are established and simulation studies are performed to validate the proposed approach. An application example for identifying the nonlinear dynamic GRN of T-cell activation is used to illustrate the usefulness of the proposed method.

The effect of a negative capacitance circuit on the out-of-plane dissipation and stiffness of a piezoelectric membrane

International Nuclear Information System (INIS)

Korde, Umesh A; Wickersham, Miles A; Carr, Stephen G

2008-01-01

This paper investigates the out-of-plane dynamics of a piezoelectric membrane with a negative capacitance circuit connected in parallel. The theoretically possible large changes in stiffness and dissipation could, at full implementation, enable the design of selectively electroded piezoelectric skins that are spatially and temporally highly adaptive. A tunable negative capacitance circuit is here connected in parallel with a polyvinylidene fluoride (PVDF) membrane (Date et al 2000 J. Appl. Phys. 87 863–8). The goal of this paper is to investigate the extent to which such a circuit may influence the out-of-plane stiffness and dissipation characteristics and the associated vibration response of a PVDF membrane strip. We consider strips with a non-vanishing thickness and under a constant boundary-applied tension. As our analytical and experimental results for harmonic loading show, successful application of the method on out-of-plane dynamics is possible with a correct choice of the circuit parameters, and the out-of-plane stiffness and dissipation and the associated vibration response near the first resonance can be altered noticeably by adjusting the circuit settings

Monolithically Integrated Flexible Black Phosphorus Complementary Inverter Circuits.

Science.gov (United States)

Liu, Yuanda; Ang, Kah-Wee

2017-07-25

Two-dimensional (2D) inverters are a fundamental building block for flexible logic circuits which have previously been realized by heterogeneously wiring transistors with two discrete channel materials. Here, we demonstrate a monolithically integrated complementary inverter made using a homogeneous black phosphorus (BP) nanosheet on flexible substrates. The digital logic inverter circuit is demonstrated via effective threshold voltage tuning within a single BP material, which offers both electron and hole dominated conducting channels with nearly symmetric pinch-off and current saturation. Controllable electron concentration is achieved by accurately modulating the aluminum (Al) donor doping, which realizes BP n-FET with a room-temperature on/off ratio >10 3 . Simultaneously, work function engineering is employed to obtain a low Schottky barrier contact electrode that facilities hole injection, thus enhancing the current density of the BP p-FET by 9.4 times. The flexible inverter circuit shows a clear digital logic voltage inversion operation along with a larger-than-unity direct current voltage gain, while exhibits alternating current dynamic signal switching at a record high frequency up to 100 kHz and remarkable electrical stability upon mechanical bending with a radii as small as 4 mm. Our study demonstrates a practical monolithic integration strategy for achieving functional logic circuits on one material platform, paving the way for future high-density flexible electronic applications.

Load testing circuit

DEFF Research Database (Denmark)

2009-01-01

A load testing circuit a circuit tests the load impedance of a load connected to an amplifier. The load impedance includes a first terminal and a second terminal, the load testing circuit comprising a signal generator providing a test signal of a defined bandwidth to the first terminal of the load...

Timergenerator circuits manual

CERN Document Server

Marston, R M

2013-01-01

Timer/Generator Circuits Manual is an 11-chapter text that deals mainly with waveform generator techniques and circuits. Each chapter starts with an explanation of the basic principles of its subject followed by a wide range of practical circuit designs. This work presents a total of over 300 practical circuits, diagrams, and tables.Chapter 1 outlines the basic principles and the different types of generator. Chapters 2 to 9 deal with a specific type of waveform generator, including sine, square, triangular, sawtooth, and special waveform generators pulse. These chapters also include pulse gen

CMOS circuits manual

CERN Document Server

Marston, R M

1995-01-01

CMOS Circuits Manual is a user's guide for CMOS. The book emphasizes the practical aspects of CMOS and provides circuits, tables, and graphs to further relate the fundamentals with the applications. The text first discusses the basic principles and characteristics of the CMOS devices. The succeeding chapters detail the types of CMOS IC, including simple inverter, gate and logic ICs and circuits, and complex counters and decoders. The last chapter presents a miscellaneous collection of two dozen useful CMOS circuits. The book will be useful to researchers and professionals who employ CMOS circu

Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts.

Science.gov (United States)

Viñuelas, José; Kaneko, Gaël; Coulon, Antoine; Vallin, Elodie; Morin, Valérie; Mejia-Pous, Camila; Kupiec, Jean-Jacques; Beslon, Guillaume; Gandrillon, Olivier

2013-02-25

A number of studies have established that stochasticity in gene expression may play an important role in many biological phenomena. This therefore calls for further investigations to identify the molecular mechanisms at stake, in order to understand and manipulate cell-to-cell variability. In this work, we explored the role played by chromatin dynamics in the regulation of stochastic gene expression in higher eukaryotic cells. For this purpose, we generated isogenic chicken-cell populations expressing a fluorescent reporter integrated in one copy per clone. Although the clones differed only in the genetic locus at which the reporter was inserted, they showed markedly different fluorescence distributions, revealing different levels of stochastic gene expression. Use of chromatin-modifying agents showed that direct manipulation of chromatin dynamics had a marked effect on the extent of stochastic gene expression. To better understand the molecular mechanism involved in these phenomena, we fitted these data to a two-state model describing the opening/closing process of the chromatin. We found that the differences between clones seemed to be due mainly to the duration of the closed state, and that the agents we used mainly seem to act on the opening probability. In this study, we report biological experiments combined with computational modeling, highlighting the importance of chromatin dynamics in stochastic gene expression. This work sheds a new light on the mechanisms of gene expression in higher eukaryotic cells, and argues in favor of relatively slow dynamics with long (hours to days) periods of quiet state.

Cell-to-Cell Communication Circuits: Quantitative Analysis of Synthetic Logic Gates

Science.gov (United States)

Hoffman-Sommer, Marta; Supady, Adriana; Klipp, Edda

2012-01-01

One of the goals in the field of synthetic biology is the construction of cellular computation devices that could function in a manner similar to electronic circuits. To this end, attempts are made to create biological systems that function as logic gates. In this work we present a theoretical quantitative analysis of a synthetic cellular logic-gates system, which has been implemented in cells of the yeast Saccharomyces cerevisiae (Regot et al., 2011). It exploits endogenous MAP kinase signaling pathways. The novelty of the system lies in the compartmentalization of the circuit where all basic logic gates are implemented in independent single cells that can then be cultured together to perform complex logic functions. We have constructed kinetic models of the multicellular IDENTITY, NOT, OR, and IMPLIES logic gates, using both deterministic and stochastic frameworks. All necessary model parameters are taken from literature or estimated based on published kinetic data, in such a way that the resulting models correctly capture important dynamic features of the included mitogen-activated protein kinase pathways. We analyze the models in terms of parameter sensitivity and we discuss possible ways of optimizing the system, e.g., by tuning the culture density. We apply a stochastic modeling approach, which simulates the behavior of whole populations of cells and allows us to investigate the noise generated in the system; we find that the gene expression units are the major sources of noise. Finally, the model is used for the design of system modifications: we show how the current system could be transformed to operate on three discrete values. PMID:22934039

30 CFR 75.601-1 - Short circuit protection; ratings and settings of circuit breakers.

Science.gov (United States)

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Short circuit protection; ratings and settings... Trailing Cables § 75.601-1 Short circuit protection; ratings and settings of circuit breakers. Circuit breakers providing short circuit protection for trailing cables shall be set so as not to exceed the...

SELANSI: a toolbox for simulation of stochastic gene regulatory networks.

Science.gov (United States)

Pájaro, Manuel; Otero-Muras, Irene; Vázquez, Carlos; Alonso, Antonio A

2018-03-01

Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort. This work presents SELANSI (SEmi-LAgrangian SImulation of GRNs), a software toolbox for the simulation of stochastic multidimensional gene regulatory networks. SELANSI exploits intrinsic structural properties of gene regulatory networks to accurately approximate the corresponding Chemical Master Equation with a partial integral differential equation that is solved by a semi-lagrangian method with high efficiency. Networks under consideration might involve multiple genes with self and cross regulations, in which genes can be regulated by different transcription factors. Moreover, the validity of the method is not restricted to a particular type of kinetics. The tool offers total flexibility regarding network topology, kinetics and parameterization, as well as simulation options. SELANSI runs under the MATLAB environment, and is available under GPLv3 license at https://sites.google.com/view/selansi. antonio@iim.csic.es. © The Author(s) 2017. Published by Oxford University Press.

Quantum networks in divergence-free circuit QED

Science.gov (United States)

Parra-Rodriguez, A.; Rico, E.; Solano, E.; Egusquiza, I. L.

2018-04-01

Superconducting circuits are one of the leading quantum platforms for quantum technologies. With growing system complexity, it is of crucial importance to develop scalable circuit models that contain the minimum information required to predict the behaviour of the physical system. Based on microwave engineering methods, divergent and non-divergent Hamiltonian models in circuit quantum electrodynamics have been proposed to explain the dynamics of superconducting quantum networks coupled to infinite-dimensional systems, such as transmission lines and general impedance environments. Here, we study systematically common linear coupling configurations between networks and infinite-dimensional systems. The main result is that the simple Lagrangian models for these configurations present an intrinsic natural length that provides a natural ultraviolet cutoff. This length is due to the unavoidable dressing of the environment modes by the network. In this manner, the coupling parameters between their components correctly manifest their natural decoupling at high frequencies. Furthermore, we show the requirements to correctly separate infinite-dimensional coupled systems in local bases. We also compare our analytical results with other analytical and approximate methods available in the literature. Finally, we propose several applications of these general methods to analogue quantum simulation of multi-spin-boson models in non-perturbative coupling regimes.

Sequential circuit design for radiation hardened multiple voltage integrated circuits

Science.gov (United States)

Clark, Lawrence T [Phoenix, AZ; McIver, III, John K.

2009-11-24

The present invention includes a radiation hardened sequential circuit, such as a bistable circuit, flip-flop or other suitable design that presents substantial immunity to ionizing radiation while simultaneously maintaining a low operating voltage. In one embodiment, the circuit includes a plurality of logic elements that operate on relatively low voltage, and a master and slave latches each having storage elements that operate on a relatively high voltage.

Application of source biasing technique for energy efficient DECODER circuit design: memory array application

Science.gov (United States)

Gupta, Neha; Parihar, Priyanka; Neema, Vaibhav

2018-04-01

Researchers have proposed many circuit techniques to reduce leakage power dissipation in memory cells. If we want to reduce the overall power in the memory system, we have to work on the input circuitry of memory architecture i.e. row and column decoder. In this research work, low leakage power with a high speed row and column decoder for memory array application is designed and four new techniques are proposed. In this work, the comparison of cluster DECODER, body bias DECODER, source bias DECODER, and source coupling DECODER are designed and analyzed for memory array application. Simulation is performed for the comparative analysis of different DECODER design parameters at 180 nm GPDK technology file using the CADENCE tool. Simulation results show that the proposed source bias DECODER circuit technique decreases the leakage current by 99.92% and static energy by 99.92% at a supply voltage of 1.2 V. The proposed circuit also improves dynamic power dissipation by 5.69%, dynamic PDP/EDP 65.03% and delay 57.25% at 1.2 V supply voltage.

LTS and FS inhibitory interneurons, short-term synaptic plasticity, and cortical circuit dynamics.

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Itai Hayut

2011-10-01

Full Text Available Somatostatin-expressing, low threshold-spiking (LTS cells and fast-spiking (FS cells are two common subtypes of inhibitory neocortical interneuron. Excitatory synapses from regular-spiking (RS pyramidal neurons to LTS cells strongly facilitate when activated repetitively, whereas RS-to-FS synapses depress. This suggests that LTS neurons may be especially relevant at high rate regimes and protect cortical circuits against over-excitation and seizures. However, the inhibitory synapses from LTS cells usually depress, which may reduce their effectiveness at high rates. We ask: by which mechanisms and at what firing rates do LTS neurons control the activity of cortical circuits responding to thalamic input, and how is control by LTS neurons different from that of FS neurons? We study rate models of circuits that include RS cells and LTS and FS inhibitory cells with short-term synaptic plasticity. LTS neurons shift the RS firing-rate vs. current curve to the right at high rates and reduce its slope at low rates; the LTS effect is delayed and prolonged. FS neurons always shift the curve to the right and affect RS firing transiently. In an RS-LTS-FS network, FS neurons reach a quiescent state if they receive weak input, LTS neurons are quiescent if RS neurons receive weak input, and both FS and RS populations are active if they both receive large inputs. In general, FS neurons tend to follow the spiking of RS neurons much more closely than LTS neurons. A novel type of facilitation-induced slow oscillations is observed above the LTS firing threshold with a frequency determined by the time scale of recovery from facilitation. To conclude, contrary to earlier proposals, LTS neurons affect the transient and steady state responses of cortical circuits over a range of firing rates, not only during the high rate regime; LTS neurons protect against over-activation about as well as FS neurons.

Low latency asynchronous interface circuits

Science.gov (United States)

Sadowski, Greg

2017-06-20

In one form, a logic circuit includes an asynchronous logic circuit, a synchronous logic circuit, and an interface circuit coupled between the asynchronous logic circuit and the synchronous logic circuit. The asynchronous logic circuit has a plurality of asynchronous outputs for providing a corresponding plurality of asynchronous signals. The synchronous logic circuit has a plurality of synchronous inputs corresponding to the plurality of asynchronous outputs, a stretch input for receiving a stretch signal, and a clock output for providing a clock signal. The synchronous logic circuit provides the clock signal as a periodic signal but prolongs a predetermined state of the clock signal while the stretch signal is active. The asynchronous interface detects whether metastability could occur when latching any of the plurality of the asynchronous outputs of the asynchronous logic circuit using said clock signal, and activates the stretch signal while the metastability could occur.

Photovoltaic Pixels for Neural Stimulation: Circuit Models and Performance.

Science.gov (United States)

Boinagrov, David; Lei, Xin; Goetz, Georges; Kamins, Theodore I; Mathieson, Keith; Galambos, Ludwig; Harris, James S; Palanker, Daniel

2016-02-01

Photovoltaic conversion of pulsed light into pulsed electric current enables optically-activated neural stimulation with miniature wireless implants. In photovoltaic retinal prostheses, patterns of near-infrared light projected from video goggles onto subretinal arrays of photovoltaic pixels are converted into patterns of current to stimulate the inner retinal neurons. We describe a model of these devices and evaluate the performance of photovoltaic circuits, including the electrode-electrolyte interface. Characteristics of the electrodes measured in saline with various voltages, pulse durations, and polarities were modeled as voltage-dependent capacitances and Faradaic resistances. The resulting mathematical model of the circuit yielded dynamics of the electric current generated by the photovoltaic pixels illuminated by pulsed light. Voltages measured in saline with a pipette electrode above the pixel closely matched results of the model. Using the circuit model, our pixel design was optimized for maximum charge injection under various lighting conditions and for different stimulation thresholds. To speed discharge of the electrodes between the pulses of light, a shunt resistor was introduced and optimized for high frequency stimulation.

Trends in integrated circuit design for particle physics experiments

International Nuclear Information System (INIS)

Atkin, E V

2017-01-01

Integrated circuits are one of the key complex units available to designers of multichannel detector setups. A whole number of factors makes Application Specific Integrated Circuits (ASICs) valuable for Particle Physics and Astrophysics experiments. Among them the most important ones are: integration scale, low power dissipation, radiation tolerance. In order to make possible future experiments in the intensity, cosmic, and energy frontiers today ASICs should provide new level of functionality at a new set of constraints and trade-offs, like low-noise high-dynamic range amplification and pulse shaping, high-speed waveform sampling, low power digitization, fast digital data processing, serialization and data transmission. All integrated circuits, necessary for physical instrumentation, should be radiation tolerant at an earlier not reached level (hundreds of Mrad) of total ionizing dose and allow minute almost 3D assemblies. The paper is based on literary source analysis and presents an overview of the state of the art and trends in nowadays chip design, using partially own ASIC lab experience. That shows a next stage of ising micro- and nanoelectronics in physical instrumentation. (paper)

The transcriptomes of two heritable cell types illuminate the circuit governing their differentiation.

Directory of Open Access Journals (Sweden)

Brian B Tuch

2010-08-01

Full Text Available The differentiation of cells into distinct cell types, each of which is heritable for many generations, underlies many biological phenomena. White and opaque cells of the fungal pathogen Candida albicans are two such heritable cell types, each thought to be adapted to unique niches within their human host. To systematically investigate their differences, we performed strand-specific, massively-parallel sequencing of RNA from C. albicans white and opaque cells. With these data we first annotated the C. albicans transcriptome, finding hundreds of novel differentially-expressed transcripts. Using the new annotation, we compared differences in transcript abundance between the two cell types with the genomic regions bound by a master regulator of the white-opaque switch (Wor1. We found that the revised transcriptional landscape considerably alters our understanding of the circuit governing differentiation. In particular, we can now resolve the poor concordance between binding of a master regulator and the differential expression of adjacent genes, a discrepancy observed in several other studies of cell differentiation. More than one third of the Wor1-bound differentially-expressed transcripts were previously unannotated, which explains the formerly puzzling presence of Wor1 at these positions along the genome. Many of these newly identified Wor1-regulated genes are non-coding and transcribed antisense to coding transcripts. We also find that 5' and 3' UTRs of mRNAs in the circuit are unusually long and that 5' UTRs often differ in length between cell-types, suggesting UTRs encode important regulatory information and that use of alternative promoters is widespread. Further analysis revealed that the revised Wor1 circuit bears several striking similarities to the Oct4 circuit that specifies the pluripotency of mammalian embryonic stem cells. Additional characteristics shared with the Oct4 circuit suggest a set of general hallmarks characteristic of

Calculation methods and algorithms development of dynamic loadings on NPP secondary circuit equipment at shock and pulse actions

International Nuclear Information System (INIS)

Kuznetsov, D.V.; Kormilitsyn, V.M.; Proskuryakov, K.N.

2010-01-01

Calculation results of acoustic parameters fluctuations in low-pressure regenerative heating system of NPP with WWER-1000 type reactor were presented. The spectral structure of acoustic fluctuations was shown to depend on configuration of secondary circuit equipment, its geometrical sizes and operation mode. Estimations of natural oscillations frequencies of working medium pressure in the secondary circuit equipment were resulted. The developed calculation methods and algorithms are intended for revealing and prevention of initiation conditions of vibrations resonances in elements of the secondary circuit equipment with acoustic oscillations in working medium, both under operating conditions and in the design stage of the second circuit of NPP with WWER-1000 type reactor. Analysis of pass-band dependence on operation mode was carried out to solve the given problem [ru

The Pleiotropic MET Receptor Network: Circuit Development and the Neural-Medical Interface of Autism.

Science.gov (United States)

Eagleson, Kathie L; Xie, Zhihui; Levitt, Pat

2017-03-01

People with autism spectrum disorder and other neurodevelopmental disorders (NDDs) are behaviorally and medically heterogeneous. The combination of polygenicity and gene pleiotropy-the influence of one gene on distinct phenotypes-raises questions of how specific genes and their protein products interact to contribute to NDDs. A preponderance of evidence supports developmental and pathophysiological roles for the MET receptor tyrosine kinase, a multifunctional receptor that mediates distinct biological responses depending upon cell context. MET influences neuron architecture and synapse maturation in the forebrain and regulates homeostasis in gastrointestinal and immune systems, both commonly disrupted in NDDs. Peak expression of synapse-enriched MET is conserved across rodent and primate forebrain, yet regional differences in primate neocortex are pronounced, with enrichment in circuits that participate in social information processing. A functional risk allele in the MET promoter, enriched in subgroups of children with autism spectrum disorder, reduces transcription and disrupts socially relevant neural circuits structurally and functionally. In mice, circuit-specific deletion of Met causes distinct atypical behaviors. MET activation increases dendritic complexity and nascent synapse number, but synapse maturation requires reductions in MET. MET mediates its specific biological effects through different intracellular signaling pathways and has a complex protein interactome that is enriched in autism spectrum disorder and other NDD candidates. The interactome is coregulated in developing human neocortex. We suggest that a gene as pleiotropic and highly regulated as MET, together with its interactome, is biologically relevant in normal and pathophysiological contexts, affecting central and peripheral phenotypes that contribute to NDD risk and clinical symptoms. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Piezoelectric drive circuit

Science.gov (United States)

Treu, C.A. Jr.

1999-08-31

A piezoelectric motor drive circuit is provided which utilizes the piezoelectric elements as oscillators and a Meacham half-bridge approach to develop feedback from the motor ground circuit to produce a signal to drive amplifiers to power the motor. The circuit automatically compensates for shifts in harmonic frequency of the piezoelectric elements due to pressure and temperature changes. 7 figs.

Coexistence of multiple attractors and crisis route to chaos in a novel memristive diode bidge-based Jerk circuit

International Nuclear Information System (INIS)

Njitacke, Z.T.; Kengne, J.; Fotsin, H.B.; Negou, A. Nguomkam; Tchiotsop, D.

2016-01-01

In the present paper, a new memristor based oscillator is obtained from the autonomous Jerk circuit [Kengne et al., Nonlinear Dynamics (2016) 83: 751̶765] by substituting the nonlinear element of the original circuit with a first order memristive diode bridge. The model is described by a continuous time four-dimensional autonomous system with smooth nonlinearities. Various nonlinear analysis tools such as phase portraits, time series, bifurcation diagrams, Poincaré section and the spectrum of Lyapunov exponents are exploited to characterize different scenarios to chaos in the novel circuit. It is found that the system experiences period doubling and crisis routes to chaos. One of the major results of this work is the finding of a window in the parameters’ space in which the circuit develops hysteretic behaviors characterized by the coexistence of four different (periodic and chaotic) attractors for the same values of the system parameters. Basins of attractions of various coexisting attractors are plotted showing complex basin boundaries. As far as the authors’ knowledge goes, the novel memristive jerk circuit represents one of the simplest electrical circuits (no analog multiplier chip is involved) capable of four disconnected coexisting attractors reported to date. Both PSpice simulations of the nonlinear dynamics of the oscillator and laboratory experimental measurements are carried out to validate the theoretical analysis.

[Lower urinary tract dysfunction and neuropathological findings of the neural circuits controlling micturition in familial amyotrophic lateral sclerosis with L106V mutation in the SOD1 gene].

Science.gov (United States)

Hineno, Akiyo; Oyanagi, Kiyomitsu; Nakamura, Akinori; Shimojima, Yoshio; Yoshida, Kunihiro; Ikeda, Shu-Ichi

2016-01-01

We report lower urinary tract dysfunction and neuropathological findings of the neural circuits controlling micturition in the patients with familial amyotrophic lateral sclerosis having L106V mutation in the SOD1 gene. Ten of 20 patients showed lower urinary tract dysfunction and 5 patients developed within 1 year after the onset of weakness. In 8 patients with an artificial respirator, 6 patients showed lower urinary tract dysfunction. Lower urinary tract dysfunction and respiratory failure requiring an artificial respirator occurred simultaneously in 3 patients. Neuronal loss and gliosis were observed in the neural circuits controlling micturition, such as frontal lobe, thalamus, hypothalamus, striatum, periaqueductal gray, ascending spinal tract, lateral corticospinal tract, intermediolateral nucleus and Onufrowicz' nucleus. Lower urinary tract dysfunction, especially storage symptoms, developed about 1 year after the onset of weakness, and the dysfunction occurred simultaneously with artificial respirator use in the patients.

Feedback in analog circuits

CERN Document Server

Ochoa, Agustin

2016-01-01

This book describes a consistent and direct methodology to the analysis and design of analog circuits with particular application to circuits containing feedback. The analysis and design of circuits containing feedback is generally presented by either following a series of examples where each circuit is simplified through the use of insight or experience (someone else’s), or a complete nodal-matrix analysis generating lots of algebra. Neither of these approaches leads to gaining insight into the design process easily. The author develops a systematic approach to circuit analysis, the Driving Point Impedance and Signal Flow Graphs (DPI/SFG) method that does not require a-priori insight to the circuit being considered and results in factored analysis supporting the design function. This approach enables designers to account fully for loading and the bi-directional nature of elements both in the feedback path and in the amplifier itself, properties many times assumed negligible and ignored. Feedback circuits a...

Frank Beach Award Winner: Steroids as Neuromodulators of Brain Circuits and Behavior

Science.gov (United States)

Remage-Healey, Luke

2014-01-01

Neurons communicate primarily via action potentials that transmit information on the timescale of milliseconds. Neurons also integrate information via alterations in gene transcription and protein translation that are sustained for hours to days after initiation. Positioned between these two signaling timescales are the minute-by-minute actions of neuromodulators. Over the course of minutes, the classical neuromodulators (such as serotonin, dopamine, octopamine, and norepinephrine) can alter and/or stabilize neural circuit patterning as well as behavioral states. Neuromodulators allow many flexible outputs from neural circuits and can encode information content into the firing state of neural networks. The idea that steroid molecules can operate as genuine behavioral neuromodulators - synthesized by and acting within brain circuits on a minute-by-minute timescale - has gained traction in recent years. Evidence for brain steroid synthesis at synaptic terminals has converged with evidence for the rapid actions of brain-derived steroids on neural circuits and behavior. The general principle emerging from this work is that the production of steroid hormones within brain circuits can alter their functional connectivity and shift sensory representations by enhancing their information coding. Steroids produced in the brain can therefore change the information content of neuronal networks to rapidly modulate sensory experience and sensorimotor functions. PMID:25110187

Quantum circuit behaviour

International Nuclear Information System (INIS)

Poulton, D.

1989-09-01

Single electron tunnelling in multiply connected weak link systems is considered. Using a second quantised approach the tunnel current, in both normal and superconducting systems, using perturbation theory, is derived. The tunnel currents are determined as a function of an Aharanov-Bohm phase (acquired by the electrons). Using these results, the multiply connected system is then discussed when coupled to a resonant LC circuit. The resulting dynamics of this composite system are then determined. In the superconducting case the results are compared and contrasted with flux mode behaviour seen in large superconducting weak link rings. Systems in which the predicted dynamics may be seen are also discussed. In analogy to the electron tunnelling analysis, the tunnelling of magnetic flux quanta through the weak link is also considered. Here, the voltage across the weak link, due to flux tunnelling, is determined as a function of an externally applied current. This is done for both singly and multiply connected flux systems. The results are compared and contrasted with charge mode behaviour seen in superconducting weak link systems. Finally, the behaviour of simple quantum fluids is considered when subject to an external rotation. Using a microscopic analysis it is found that the microscopic quantum behaviour of the particles is manifest on a macroscopic level. Results are derived for bosonic, fermionic and BCS pair-type systems. The connection between flux quantisation in electromagnetic systems is also made. Using these results, the dynamics of such a quantum fluid is considered when coupled to a rotating torsional oscillator. The results are compared with those found in SQUID devices. A model is also presented which discusses the possible excited state dynamics of such a fluid. (author)

Reconstructing a Network of Stress-Response Regulators via Dynamic System Modeling of Gene Regulation

Directory of Open Access Journals (Sweden)

Wei-Sheng Wu

2008-01-01

Full Text Available Unicellular organisms such as yeasts have evolved mechanisms to respond to environmental stresses by rapidly reorganizing the gene expression program. Although many stress-response genes in yeast have been discovered by DNA microarrays, the stress-response transcription factors (TFs that regulate these stress-response genes remain to be investigated. In this study, we use a dynamic system model of gene regulation to describe the mechanism of how TFs may control a gene’s expression. Then, based on the dynamic system model, we develop the Stress Regulator Identification Algorithm (SRIA to identify stress-response TFs for six kinds of stresses. We identified some general stress-response TFs that respond to various stresses and some specific stress-response TFs that respond to one specifi c stress. The biological significance of our findings is validated by the literature. We found that a small number of TFs is probably suffi cient to control a wide variety of expression patterns in yeast under different stresses. Two implications can be inferred from this observation. First, the response mechanisms to different stresses may have a bow-tie structure. Second, there may be regulatory cross-talks among different stress responses. In conclusion, this study proposes a network of stress-response regulators and the details of their actions.

Developmental programming of hypothalamic neuronal circuits: impact on energy balance control

Directory of Open Access Journals (Sweden)

Thanuja eGali Ramamoorthy

2015-04-01

Full Text Available The prevalence of obesity in adults and children has increased globally at an alarming rate. Mounting evidence from both epidemiological studies and animal models indicates that adult obesity and associated metabolic disorders can be programmed by intrauterine and early postnatal environment- a phenomenon known as fetal programming of adult disease. Data from nutritional intervention studies in animals including maternal under- and over-nutrition support the developmental origins of obesity and metabolic syndrome. The hypothalamic neuronal circuits located in the arcuate nucleus controlling appetite and energy expenditure are set early in life and are perturbed by maternal nutritional insults. In this review, we focus on the effects of maternal nutrition in programming permanent changes in these hypothalamic circuits, with experimental evidence from animal models of maternal under- and over-nutrition. We discuss the epigenetic modifications which regulate hypothalamic gene expression as potential molecular mechanisms linking maternal diet during pregnancy to the offspring’s risk of obesity at a later age. Understanding these mechanisms in key metabolic genes may provide insights into the development of preventative intervention strategies.

Developmental programming of hypothalamic neuronal circuits: impact on energy balance control

Science.gov (United States)

Gali Ramamoorthy, Thanuja; Begum, Ghazala; Harno, Erika; White, Anne

2015-01-01

The prevalence of obesity in adults and children has increased globally at an alarming rate. Mounting evidence from both epidemiological studies and animal models indicates that adult obesity and associated metabolic disorders can be programmed by intrauterine and early postnatal environment- a phenomenon known as “fetal programming of adult disease.” Data from nutritional intervention studies in animals including maternal under- and over-nutrition support the developmental origins of obesity and metabolic syndrome. The hypothalamic neuronal circuits located in the arcuate nucleus controlling appetite and energy expenditure are set early in life and are perturbed by maternal nutritional insults. In this review, we focus on the effects of maternal nutrition in programming permanent changes in these hypothalamic circuits, with experimental evidence from animal models of maternal under- and over-nutrition. We discuss the epigenetic modifications which regulate hypothalamic gene expression as potential molecular mechanisms linking maternal diet during pregnancy to the offspring's risk of obesity at a later age. Understanding these mechanisms in key metabolic genes may provide insights into the development of preventative intervention strategies. PMID:25954145

Timing control by redundant inhibitory neuronal circuits

International Nuclear Information System (INIS)

Tristan, I.; Rulkov, N. F.; Huerta, R.; Rabinovich, M.

2014-01-01

Rhythms and timing control of sequential activity in the brain is fundamental to cognition and behavior. Although experimental and theoretical studies support the understanding that neuronal circuits are intrinsically capable of generating different time intervals, the dynamical origin of the phenomenon of functionally dependent timing control is still unclear. Here, we consider a new mechanism that is related to the multi-neuronal cooperative dynamics in inhibitory brain motifs consisting of a few clusters. It is shown that redundancy and diversity of neurons within each cluster enhances the sensitivity of the timing control with the level of neuronal excitation of the whole network. The generality of the mechanism is shown to work on two different neuronal models: a conductance-based model and a map-based model

Timing control by redundant inhibitory neuronal circuits

Energy Technology Data Exchange (ETDEWEB)

Tristan, I., E-mail: itristan@ucsd.edu; Rulkov, N. F.; Huerta, R.; Rabinovich, M. [BioCircuits Institute, University of California, San Diego, La Jolla, California 92093-0402 (United States)

2014-03-15

Rhythms and timing control of sequential activity in the brain is fundamental to cognition and behavior. Although experimental and theoretical studies support the understanding that neuronal circuits are intrinsically capable of generating different time intervals, the dynamical origin of the phenomenon of functionally dependent timing control is still unclear. Here, we consider a new mechanism that is related to the multi-neuronal cooperative dynamics in inhibitory brain motifs consisting of a few clusters. It is shown that redundancy and diversity of neurons within each cluster enhances the sensitivity of the timing control with the level of neuronal excitation of the whole network. The generality of the mechanism is shown to work on two different neuronal models: a conductance-based model and a map-based model.

Dynamic changes in prefrontal cortex gene expression following lysergic acid diethylamide administration.

Science.gov (United States)

Nichols, Charles D; Garcia, Efrain E; Sanders-Bush, Elaine

2003-03-17

Lysergic acid diethylamide (LSD) is a psychoactive drug that transiently alters human perception, behavior, and mood at extremely low doses. Certain aspects of the behavior elicited by acute doses of LSD closely resemble symptoms of mental disorders such as schizophrenia. Characterizing gene expression profiles after LSD will be important for understanding how it alters behavior, and will lead to novel insights into disorders, such as schizophrenia, whose behavioral symptoms resemble the temporary effects of hallucinogenic drugs. We previously identified a small collection of genes within the rat prefrontal cortex that respond to LSD. Many of the products of these genes are involved in the process of synaptic plasticity. In the current report, we present a detailed analysis of the expression of these genes within the brain using RNase protection analysis. We find that the gene response to LSD is quite dynamic. The expression of some genes increases rapidly and decreases rapidly, while other genes change more gradually. Dose-response studies show two classes of expression; gene expression maximally stimulated at lower doses, versus gene expression that continues to rise at the higher doses. The role of the 5-HT(1A) and 5-HT(2A) receptor in mediating the increases in gene expression was examined in a series of experiments using receptor specific antagonists. Most expression increases were due to activation of the 5-HT(2A) receptor, however expression of two genes had neither a 5-HT(1A) nor a 5-HT(2A) receptor component.

Analog circuits cookbook

CERN Document Server

Hickman, Ian

2013-01-01

Analog Circuits Cookbook presents articles about advanced circuit techniques, components and concepts, useful IC for analog signal processing in the audio range, direct digital synthesis, and ingenious video op-amp. The book also includes articles about amplitude measurements on RF signals, linear optical imager, power supplies and devices, and RF circuits and techniques. Professionals and students of electrical engineering will find the book informative and useful.

Phase transition in traffic jam experiment on a circuit

International Nuclear Information System (INIS)

Tadaki, Shin-ichi; Kikuchi, Macoto; Fukui, Minoru; Yosida, Taturu; Nakayama, Akihiro; Nishinari, Katsuhiro; Shibata, Akihiro; Sugiyama, Yuki; Yukawa, Satoshi

2013-01-01

The emergence of a traffic jam is considered to be a dynamical phase transition in a physics point of view; traffic flow becomes unstable and changes phase into a traffic jam when the car density exceeds a critical value. In order to verify this view, we have been performing a series of circuit experiments. In our previous work (2008 New J. Phys. 10 033001), we demonstrated that a traffic jam emerges even in the absence of bottlenecks at a certain high density. In this study, we performed a larger indoor circuit experiment in the Nagoya Dome in which the positions of cars were observed using a high-resolution laser scanner. Over a series of sessions at various values of density, we found that jammed flow occurred at high densities, whereas free flow was conserved at low densities. We also found indications of metastability at an intermediate density. The critical density is estimated by analyzing the fluctuations in speed and the density–flow relation. The value of this critical density is consistent with that observed on real expressways. This experiment provides strong support for physical interpretations of the emergence of traffic jams as a dynamical phase transition. (paper)

Phase transition in traffic jam experiment on a circuit

Science.gov (United States)

Tadaki, Shin-ichi; Kikuchi, Macoto; Fukui, Minoru; Nakayama, Akihiro; Nishinari, Katsuhiro; Shibata, Akihiro; Sugiyama, Yuki; Yosida, Taturu; Yukawa, Satoshi

2013-10-01

The emergence of a traffic jam is considered to be a dynamical phase transition in a physics point of view; traffic flow becomes unstable and changes phase into a traffic jam when the car density exceeds a critical value. In order to verify this view, we have been performing a series of circuit experiments. In our previous work (2008 New J. Phys. 10 033001), we demonstrated that a traffic jam emerges even in the absence of bottlenecks at a certain high density. In this study, we performed a larger indoor circuit experiment in the Nagoya Dome in which the positions of cars were observed using a high-resolution laser scanner. Over a series of sessions at various values of density, we found that jammed flow occurred at high densities, whereas free flow was conserved at low densities. We also found indications of metastability at an intermediate density. The critical density is estimated by analyzing the fluctuations in speed and the density-flow relation. The value of this critical density is consistent with that observed on real expressways. This experiment provides strong support for physical interpretations of the emergence of traffic jams as a dynamical phase transition.

A memristor-based nonvolatile latch circuit

International Nuclear Information System (INIS)

Robinett, Warren; Pickett, Matthew; Borghetti, Julien; Xia Qiangfei; Snider, Gregory S; Medeiros-Ribeiro, Gilberto; Williams, R Stanley

2010-01-01

Memristive devices, which exhibit a dynamical conductance state that depends on the excitation history, can be used as nonvolatile memory elements by storing information as different conductance states. We describe the implementation of a nonvolatile synchronous flip-flop circuit that uses a nanoscale memristive device as the nonvolatile memory element. Controlled testing of the circuit demonstrated successful state storage and restoration, with an error rate of 0.1%, during 1000 power loss events. These results indicate that integration of digital logic devices and memristors could open the way for nonvolatile computation with applications in small platforms that rely on intermittent power sources. This demonstrated feasibility of tight integration of memristors with CMOS (complementary metal-oxide-semiconductor) circuitry challenges the traditional memory hierarchy, in which nonvolatile memory is only available as a large, slow, monolithic block at the bottom of the hierarchy. In contrast, the nonvolatile, memristor-based memory cell can be fast, fine-grained and small, and is compatible with conventional CMOS electronics. This threatens to upset the traditional memory hierarchy, and may open up new architectural possibilities beyond it.

Note: A 102 dB dynamic-range charge-sampling readout for ionizing particle/radiation detectors based on an application-specific integrated circuit (ASIC)

Science.gov (United States)

Pullia, A.; Zocca, F.; Capra, S.

2018-02-01

An original technique for the measurement of charge signals from ionizing particle/radiation detectors has been implemented in an application-specific integrated circuit form. The device performs linear measurements of the charge both within and beyond its output voltage swing. The device features an unprecedented spectroscopic dynamic range of 102 dB and is suitable for high-resolution ion and X-γ ray spectroscopy. We believe that this approach may change a widespread paradigm according to which no high-resolution spectroscopy is possible when working close to or beyond the limit of the preamplifier's output voltage swing.

Electric circuits and signals

CERN Document Server

Sabah, Nassir H

2007-01-01

Circuit Variables and Elements Overview Learning Objectives Electric Current Voltage Electric Power and Energy Assigned Positive Directions Active and Passive Circuit Elements Voltage and Current Sources The Resistor The Capacitor The Inductor Concluding Remarks Summary of Main Concepts and Results Learning Outcomes Supplementary Topics on CD Problems and Exercises Basic Circuit Connections and Laws Overview Learning Objectives Circuit Terminology Kirchhoff's Laws Voltage Division and Series Connection of Resistors Current Division and Parallel Connection of Resistors D-Y Transformation Source Equivalence and Transformation Reduced-Voltage Supply Summary of Main Concepts and Results Learning Outcomes Supplementary Topics and Examples on CD Problems and Exercises Basic Analysis of Resistive Circuits Overview Learning Objectives Number of Independent Circuit Equations Node-Voltage Analysis Special Considerations in Node-Voltage Analysis Mesh-Current Analysis Special Conside...

[Shunt and short circuit].

Science.gov (United States)

Rangel-Abundis, Alberto

2006-01-01

Shunt and short circuit are antonyms. In French, the term shunt has been adopted to denote the alternative pathway of blood flow. However, in French, as well as in Spanish, the word short circuit (court-circuit and cortocircuito) is synonymous with shunt, giving rise to a linguistic and scientific inconsistency. Scientific because shunt and short circuit made reference to a phenomenon that occurs in the field of the physics. Because shunt and short circuit are antonyms, it is necessary to clarify that shunt is an alternative pathway of flow from a net of high resistance to a net of low resistance, maintaining the stream. Short circuit is the interruption of the flow, because a high resistance impeaches the flood. This concept is applied to electrical and cardiovascular physiology, as well as to the metabolic pathways.

Equivalent circuit modeling of a superconducting synchronous generator with double electromagnetic shields. Part II. Equivalent circuit model and estimation of its constants for design examples

International Nuclear Information System (INIS)

Muta, I.; Magarikaji, N.

1980-01-01

Operational impedances of synchronous machine are very important in the study of dynamic and transient stability. In recent years, it has become possible to analyze the transient behavior of operational impedance by the direct Fourier transformation of frequency response characteristics of operational impedance. It is desired very much to derive the equivalent circuit based on exact operational impedances. In this paper, we calculate the frequency characteristics of operational impedances which are derived in a companion paper. Also, we analyze the effects of various parameters on the equivalent circuit constants. Approximate expressions for sub-subtransient, subtransient and transient reactances are derived from the theoretical expressions for operational impedances. The validity of theoretical calculations is confirmed by comparison with experimental results

A multi-Poisson dynamic mixture model to cluster developmental patterns of gene expression by RNA-seq.

Science.gov (United States)

Ye, Meixia; Wang, Zhong; Wang, Yaqun; Wu, Rongling

2015-03-01

Dynamic changes of gene expression reflect an intrinsic mechanism of how an organism responds to developmental and environmental signals. With the increasing availability of expression data across a time-space scale by RNA-seq, the classification of genes as per their biological function using RNA-seq data has become one of the most significant challenges in contemporary biology. Here we develop a clustering mixture model to discover distinct groups of genes expressed during a period of organ development. By integrating the density function of multivariate Poisson distribution, the model accommodates the discrete property of read counts characteristic of RNA-seq data. The temporal dependence of gene expression is modeled by the first-order autoregressive process. The model is implemented with the Expectation-Maximization algorithm and model selection to determine the optimal number of gene clusters and obtain the estimates of Poisson parameters that describe the pattern of time-dependent expression of genes from each cluster. The model has been demonstrated by analyzing a real data from an experiment aimed to link the pattern of gene expression to catkin development in white poplar. The usefulness of the model has been validated through computer simulation. The model provides a valuable tool for clustering RNA-seq data, facilitating our global view of expression dynamics and understanding of gene regulation mechanisms. © The Author 2014. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Macromodels of digital integrated circuits for program packages of circuit engineering design

Science.gov (United States)

Petrenko, A. I.; Sliusar, P. B.; Timchenko, A. P.

1984-04-01

Various aspects of the generation of macromodels of digital integrated circuits are examined, and their effective application in program packages of circuit engineering design is considered. Three levels of macromodels are identified, and the application of such models to the simulation of circuit outputs is discussed.

Microscale solid-state thermal diodes enabling ambient temperature thermal circuits for energy applications

KAUST Repository

Wang, Song; Cottrill, Anton L.; Kunai, Yuichiro; Toland, Aubrey R.; Liu, Pingwei; Wang, Wen-Jun; Strano, Michael S.

2017-01-01

rectifications range from 1.18 to 1.34. We show that such devices perform reliably enough to operate in thermal diode bridges, dynamic thermal circuits capable of transforming oscillating temperature inputs into single polarity temperature differences – analogous

Transistor analogs of emergent iono-neuronal dynamics.

Science.gov (United States)

Rachmuth, Guy; Poon, Chi-Sang

2008-06-01

Neuromorphic analog metal-oxide-silicon (MOS) transistor circuits promise compact, low-power, and high-speed emulations of iono-neuronal dynamics orders-of-magnitude faster than digital simulation. However, their inherently limited input voltage dynamic range vs power consumption and silicon die area tradeoffs makes them highly sensitive to transistor mismatch due to fabrication inaccuracy, device noise, and other nonidealities. This limitation precludes robust analog very-large-scale-integration (aVLSI) circuits implementation of emergent iono-neuronal dynamics computations beyond simple spiking with limited ion channel dynamics. Here we present versatile neuromorphic analog building-block circuits that afford near-maximum voltage dynamic range operating within the low-power MOS transistor weak-inversion regime which is ideal for aVLSI implementation or implantable biomimetic device applications. The fabricated microchip allowed robust realization of dynamic iono-neuronal computations such as coincidence detection of presynaptic spikes or pre- and postsynaptic activities. As a critical performance benchmark, the high-speed and highly interactive iono-neuronal simulation capability on-chip enabled our prompt discovery of a minimal model of chaotic pacemaker bursting, an emergent iono-neuronal behavior of fundamental biological significance which has hitherto defied experimental testing or computational exploration via conventional digital or analog simulations. These compact and power-efficient transistor analogs of emergent iono-neuronal dynamics open new avenues for next-generation neuromorphic, neuroprosthetic, and brain-machine interface applications.

Comparison of modified driver circuit and capacitor-transfer circuit in longitudinally excited N2 laser.

Science.gov (United States)

Uno, Kazuyuki; Akitsu, Tetsuya; Nakamura, Kenshi; Jitsuno, Takahisa

2013-04-01

We developed a modified driver circuit composed of a capacitance and a spark gap, called a direct-drive circuit, for a longitudinally excited gas laser. The direct-drive circuit uses a large discharge impedance caused by a long discharge length of the longitudinal excitation scheme and eliminates the buffer capacitance used in the traditional capacitor-transfer circuit. We compared the direct-drive circuit and the capacitor-transfer circuit in a longitudinally excited N2 laser (wavelength: 337 nm). Producing high output energy with the capacitor-transfer circuit requires a large storage capacitance and a discharge tube with optimum dimensions (an inner diameter of 4 mm and a length of 10 cm in this work); in contrast, the direct-drive circuit requires a high breakdown voltage, achieved with a small storage capacitance and a large discharge tube. Additionally, for the same input energy of 792 mJ, the maximum output energy of the capacitor-transfer circuit was 174.2 μJ, and that of the direct-drive circuit was 344.7 μJ.

Evolution-development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures.

Science.gov (United States)

Kohsokabe, Takahiro; Kaneko, Kunihiko

2016-01-01

Search for possible relationships between phylogeny and ontogeny is important in evolutionary-developmental biology. Here we uncover such relationships by numerical evolution and unveil their origin in terms of dynamical systems theory. By representing developmental dynamics of spatially located cells with gene expression dynamics with cell-to-cell interaction under external morphogen gradient, gene regulation networks are evolved under mutation and selection with the fitness to approach a prescribed spatial pattern of expressed genes. For most numerical evolution experiments, evolution of pattern over generations and development of pattern by an evolved network exhibit remarkable congruence. Both in the evolution and development pattern changes consist of several epochs where stripes are formed in a short time, while for other temporal regimes, pattern hardly changes. In evolution, these quasi-stationary regimes are generations needed to hit relevant mutations, while in development, they are due to some gene expression that varies slowly and controls the pattern change. The morphogenesis is regulated by combinations of feedback or feedforward regulations, where the upstream feedforward network reads the external morphogen gradient, and generates a pattern used as a boundary condition for the later patterns. The ordering from up to downstream is common in evolution and development, while the successive epochal changes in development and evolution are represented as common bifurcations in dynamical-systems theory, which lead to the evolution-development congruence. Mechanism of exceptional violation of the congruence is also unveiled. Our results provide a new look on developmental stages, punctuated equilibrium, developmental bottlenecks, and evolutionary acquisition of novelty in morphogenesis. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc.

Comparing SiGe HBT Amplifier Circuits for Fast Single-shot Spin Readout

Science.gov (United States)

England, Troy; Curry, Matthew; Carr, Stephen; Mounce, Andrew; Jock, Ryan; Sharma, Peter; Bureau-Oxton, Chloe; Rudolph, Martin; Hardin, Terry; Carroll, Malcolm

Fast, low-power quantum state readout is one of many challenges facing quantum information processing. Single electron transistors (SETs) are potentially fast, sensitive detectors for performing spin readout. From a circuit perspective, however, their output impedance and nonlinear conductance are ill suited to drive the parasitic capacitance of coaxial conductors used in cryogenic environments, necessitating a cryogenic amplification stage. We will compare two amplifiers based on single-transistor circuits implemented with silicon germanium heterojunction bipolar transistors. Both amplifiers provide gain at low power levels, but the dynamics of each circuit vary significantly. We will explore the gain mechanisms, linearity, and noise of each circuit and explain the situations in which each amplifier is best used. This work was performed, in part, at the Center for Integrated Nanotechnologies, a U.S. DOE Office of Basic Energy Sciences user facility. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a Lockheed-Martin Company, for the U. S. Department of Energy under Contract No. DE-AC04-94AL85000.

ASDTIC control and standardized interface circuits applied to buck, parallel and buck-boost dc to dc power converters

Science.gov (United States)

Schoenfeld, A. D.; Yu, Y.

1973-01-01

Versatile standardized pulse modulation nondissipatively regulated control signal processing circuits were applied to three most commonly used dc to dc power converter configurations: (1) the series switching buck-regulator, (2) the pulse modulated parallel inverter, and (3) the buck-boost converter. The unique control concept and the commonality of control functions for all switching regulators have resulted in improved static and dynamic performance and control circuit standardization. New power-circuit technology was also applied to enhance reliability and to achieve optimum weight and efficiency.

Exogenous reference gene normalization for real-time reverse transcription-polymerase chain reaction analysis under dynamic endogenous transcription.

Science.gov (United States)

Johnston, Stephen; Gallaher, Zachary; Czaja, Krzysztof

2012-05-15

Quantitative real-time reverse transcription-polymerase chain reaction (qPCR) is widely used to investigate transcriptional changes following experimental manipulations to the nervous system. Despite the widespread utilization of qPCR, the interpretation of results is marred by the lack of a suitable reference gene due to the dynamic nature of endogenous transcription. To address this inherent deficiency, we investigated the use of an exogenous spike-in mRNA, luciferase, as an internal reference gene for the 2(-∆∆Ct) normalization method. To induce dynamic transcription, we systemically administered capsaicin, a neurotoxin selective for C-type sensory neurons expressing the TRPV-1 receptor, to adult male Sprague-Dawley rats. We later isolated nodose ganglia for qPCR analysis with the reference being either exogenous luciferase mRNA or the commonly used endogenous reference β-III tubulin. The exogenous luciferase mRNA reference clearly demonstrated the dynamic expression of the endogenous reference. Furthermore, variability of the endogenous reference would lead to misinterpretation of other genes of interest. In conclusion, traditional reference genes are often unstable under physiologically normal situations, and certainly unstable following the damage to the nervous system. The use of exogenous spike-in reference provides a consistent and easily implemented alternative for the analysis of qPCR data.

Aging evaluation of electrical circuits using the ECCAD [Electrical Circuit Characterization and Diagnostic] system

International Nuclear Information System (INIS)

Edson, J.L.

1988-01-01

As a part of the Nuclear Regulatory Commission Nuclear Plant Aging Research Program, an aging assessment of electrical circuits was conducted at the Shippingport Atomic Power Station Decommissioning Project. The objective of this work was to evaluate the effectiveness of the Electrical Circuit Characterization and Diagnostic (ECCAD) system in identifying circuit conditions, to determine the present condition of selected electrical circuits, and correlate the results with aging effects. To accomplish this task, a series of electrical tests was performed on each circuit using the ECCAD system, which is composed of commercially available electronic test equipment under computer control. Test results indicate that the ECCAD system is effective in detecting and identifying aging and service wear in selected electrical circuits. The major area of degradation in the circuits tested was at the termination/connection points, whereas the cables were in generally good condition

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

Science.gov (United States)

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.

Dynamic changes in protein functional linkage networks revealed by integration with gene expression data.

Directory of Open Access Journals (Sweden)

Shubhada R Hegde

2008-11-01

Full Text Available Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein:protein interactions might yield useful insights into the cellular responses. The large-scale protein interaction data sets are, however, unable to capture the changes in the profile of protein:protein interactions. In order to understand how these interactions change dynamically, we have constructed conditional protein linkages for Escherichia coli by integrating functional linkages and gene expression information. As a case study, we have chosen to analyze UV exposure in wild-type and SOS deficient E. coli at 20 minutes post irradiation. The conditional networks exhibit similar topological properties. Although the global topological properties of the networks are similar, many subtle local changes are observed, which are suggestive of the cellular response to the perturbations. Some such changes correspond to differences in the path lengths among the nodes of carbohydrate metabolism correlating with its loss in efficiency in the UV treated cells. Similarly, expression of hubs under unique conditions reflects the importance of these genes. Various centrality measures applied to the networks indicate increased importance for replication, repair, and other stress proteins for the cells under UV treatment, as anticipated. We thus propose a novel approach for studying an organism at the systems level by integrating genome-wide functional linkages and the gene expression data.

Enhancement of galloping-based wind energy harvesting by synchronized switching interface circuits

Science.gov (United States)

Zhao, Liya; Liang, Junrui; Tang, Lihua; Yang, Yaowen; Liu, Haili

2015-04-01

Galloping phenomenon has attracted extensive research attention for small-scale wind energy harvesting. In the reported literature, the dynamics and harvested power of a galloping-based energy harvesting system are usually evaluated with a resistive AC load; these characteristics might shift when a practical harvesting interface circuit is connected for extracting useful DC power. In the family of piezoelectric energy harvesting interface circuits, synchronized switching harvesting on inductor (SSHI) has demonstrated its advantage for enhancing the harvested power from existing base vibrations. This paper investigates the harvesting capability of a galloping-based wind energy harvester using SSHI interfaces, with a focus on comparing the performances of Series SSHI (S-SSHI) and Parallel SSHI (P-SSHI) with that of a standard DC interface, in terms of power at various wind speeds. The prototyped galloping-based piezoelectric energy harvester (GPEH) comprises a piezoelectric cantilever attached with a square-sectioned bluff body made of foam. Equivalent circuit model (ECM) of the GPEH is established and system-level circuit simulations with SSHI and standard interfaces are performed and validated with wind tunnel tests. The benefits of SSHI compared to standard circuit become more significant when the wind speed gets higher; while SSHI circuits lose the benefits at small wind speeds. In both experiment and simulation, the superiority of P-SSHI is confirmed while S-SSHI demands further investigation. The power output is increased by 43.75% with P-SSHI compared to the standard circuit at a wind speed of 6m/s.

Multi-Layer E-Textile Circuits

Science.gov (United States)

Dunne, Lucy E.; Bibeau, Kaila; Mulligan, Lucie; Frith, Ashton; Simon, Cory

2012-01-01

Stitched e-textile circuits facilitate wearable, flexible, comfortable wearable technology. However, while stitched methods of e-textile circuits are common, multi-layer circuit creation remains a challenge. Here, we present methods of stitched multi-layer circuit creation using accessible tools and techniques.

Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction.

Directory of Open Access Journals (Sweden)

Hiroyuki Kuwahara

2010-03-01

Full Text Available Uropathogenic Escherichia coli (UPEC represent the predominant cause of urinary tract infections (UTIs. A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element-the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role in shutting down fimbriae expression, the primary function of FimB recombinase may be to effect a controlled down-regulation (rather than increase of the ON-to-OFF fim switching rate via temperature-dependent suppression of competing dynamics mediated by recombinase FimE. Our computational analysis further implies

Analog circuit design

CERN Document Server

Dobkin, Bob

2012-01-01

Analog circuit and system design today is more essential than ever before. With the growth of digital systems, wireless communications, complex industrial and automotive systems, designers are being challenged to develop sophisticated analog solutions. This comprehensive source book of circuit design solutions aids engineers with elegant and practical design techniques that focus on common analog challenges. The book's in-depth application examples provide insight into circuit design and application solutions that you can apply in today's demanding designs. <

Integrating Neural Circuits Controlling Female Sexual Behavior.

Science.gov (United States)

Micevych, Paul E; Meisel, Robert L

2017-01-01

The hypothalamus is most often associated with innate behaviors such as is hunger, thirst and sex. While the expression of these behaviors important for survival of the individual or the species is nested within the hypothalamus, the desire (i.e., motivation) for them is centered within the mesolimbic reward circuitry. In this review, we will use female sexual behavior as a model to examine the interaction of these circuits. We will examine the evidence for a hypothalamic circuit that regulates consummatory aspects of reproductive behavior, i.e., lordosis behavior, a measure of sexual receptivity that involves estradiol membrane-initiated signaling in the arcuate nucleus (ARH), activating β-endorphin projections to the medial preoptic nucleus (MPN), which in turn modulate ventromedial hypothalamic nucleus (VMH) activity-the common output from the hypothalamus. Estradiol modulates not only a series of neuropeptides, transmitters and receptors but induces dendritic spines that are for estrogenic induction of lordosis behavior. Simultaneously, in the nucleus accumbens of the mesolimbic system, the mating experience produces long term changes in dopamine signaling and structure. Sexual experience sensitizes the response of nucleus accumbens neurons to dopamine signaling through the induction of a long lasting early immediate gene. While estrogen alone increases spines in the ARH, sexual experience increases dendritic spine density in the nucleus accumbens. These two circuits appear to converge onto the medial preoptic area where there is a reciprocal influence of motivational circuits on consummatory behavior and vice versa . While it has not been formally demonstrated in the human, such circuitry is generally highly conserved and thus, understanding the anatomy, neurochemistry and physiology can provide useful insight into the motivation for sexual behavior and other innate behaviors in humans.

Integrating Neural Circuits Controlling Female Sexual Behavior

Directory of Open Access Journals (Sweden)

Paul E. Micevych

2017-06-01

Full Text Available The hypothalamus is most often associated with innate behaviors such as is hunger, thirst and sex. While the expression of these behaviors important for survival of the individual or the species is nested within the hypothalamus, the desire (i.e., motivation for them is centered within the mesolimbic reward circuitry. In this review, we will use female sexual behavior as a model to examine the interaction of these circuits. We will examine the evidence for a hypothalamic circuit that regulates consummatory aspects of reproductive behavior, i.e., lordosis behavior, a measure of sexual receptivity that involves estradiol membrane-initiated signaling in the arcuate nucleus (ARH, activating β-endorphin projections to the medial preoptic nucleus (MPN, which in turn modulate ventromedial hypothalamic nucleus (VMH activity—the common output from the hypothalamus. Estradiol modulates not only a series of neuropeptides, transmitters and receptors but induces dendritic spines that are for estrogenic induction of lordosis behavior. Simultaneously, in the nucleus accumbens of the mesolimbic system, the mating experience produces long term changes in dopamine signaling and structure. Sexual experience sensitizes the response of nucleus accumbens neurons to dopamine signaling through the induction of a long lasting early immediate gene. While estrogen alone increases spines in the ARH, sexual experience increases dendritic spine density in the nucleus accumbens. These two circuits appear to converge onto the medial preoptic area where there is a reciprocal influence of motivational circuits on consummatory behavior and vice versa. While it has not been formally demonstrated in the human, such circuitry is generally highly conserved and thus, understanding the anatomy, neurochemistry and physiology can provide useful insight into the motivation for sexual behavior and other innate behaviors in humans.

ESD analog circuits and design

CERN Document Server

Voldman, Steven H

2014-01-01

A comprehensive and in-depth review of analog circuit layout, schematic architecture, device, power network and ESD design This book will provide a balanced overview of analog circuit design layout, analog circuit schematic development, architecture of chips, and ESD design.  It will start at an introductory level and will bring the reader right up to the state-of-the-art. Two critical design aspects for analog and power integrated circuits are combined. The first design aspect covers analog circuit design techniques to achieve the desired circuit performance. The second and main aspect pres

Composite behaviors of dual meminductor circuits

International Nuclear Information System (INIS)

Zheng Ci-Yan; Yu Dong-Sheng; Liang Yan; Chen Meng-Ke

2015-01-01

This paper focuses on analyzing the composite dynamic behaviors of two meminductors in serial and parallel connections with different polarities. Based on the constitutive relations, two time-integral-of-flux (TIF) controlled meminductors are adopted to theoretically demonstrate the variation of memductance in terms of TIF, charge, flux, and current. By utilizing a floating memristor-less meminductor emulator, the theoretical analysis reported in this paper is confirmed via a PSPICE simulation study and hardware experiment. Good agreement among theoretical analysis, simulation, and hardware validation confirms that dual meminductor circuits in composite connections behave as a new meminductor with higher complexity. (paper)

Cell fate determination dynamics in bacteria

Science.gov (United States)

Kuchina, Anna; Espinar, Lorena; Cagatay, Tolga; Garcia-Ojalvo, Jordi; Suel, Gurol

2010-03-01

The fitness of an organism depends on many processes that serve the purpose to adapt to changing environment in a robust and coordinated fashion. One example of such process is cellular fate determination. In the presence of a variety of alternative responses each cell adopting a particular fate represents a ``choice'' that must be tightly regulated to ensure the best survival strategy for the population taking into account the broad range of possible environmental challenges. We investigated this problem in the model organism B.Subtilis which under stress conditions differentiates terminally into highly resistant spores or initiates an alternative transient state of competence. The dynamics underlying cell fate choice remains largely unknown. We utilize quantitative fluorescent microscopy to track the activities of genes involved in these responses on a single-cell level. We explored the importance of temporal interactions between competing cell fates by re- engineering the differentiation programs. I will discuss how the precise dynamics of cellular ``decision-making'' governed by the corresponding biological circuits may enable cells to adjust to diverse environments and determine survival.

'Speedy' superconducting circuits

International Nuclear Information System (INIS)

Holst, T.

1994-01-01

The most promising concept for realizing ultra-fast superconducting digital circuits is the Rapid Single Flux Quantum (RSFQ) logic. The basic physical principle behind RSFQ logic, which include the storage and transfer of individual magnetic flux quanta in Superconducting Quantum Interference Devices (SQUIDs), is explained. A Set-Reset flip-flop is used as an example of the implementation of an RSFQ based circuit. Finally, the outlook for high-temperature superconducting materials in connection with RSFQ circuits is discussed in some details. (au)

Electronic devices and circuits

CERN Document Server

Pridham, Gordon John

1968-01-01

Electronic Devices and Circuits, Volume 1 deals with the design and applications of electronic devices and circuits such as passive components, diodes, triodes and transistors, rectification and power supplies, amplifying circuits, electronic instruments, and oscillators. These topics are supported with introductory network theory and physics. This volume is comprised of nine chapters and begins by explaining the operation of resistive, inductive, and capacitive elements in direct and alternating current circuits. The theory for some of the expressions quoted in later chapters is presented. Th

System dynamics and control with bond graph modeling

CERN Document Server

Kypuros, Javier

2013-01-01

Part I Dynamic System ModelingIntroduction to System DynamicsIntroductionSystem Decomposition and Model ComplexityMathematical Modeling of Dynamic SystemsAnalysis and Design of Dynamic SystemsControl of Dynamic SystemsDiagrams of Dynamic SystemsA Graph-Centered Approach to ModelingSummaryPracticeExercisesBasic Bond Graph ElementsIntroductionPower and Energy VariablesBasic 1-Port ElementsBasic 2-Ports ElementsJunction ElementsSimple Bond Graph ExamplesSummaryPracticeExercisesBond Graph Synthesis and Equation DerivationIntroductionGeneral GuidelinesMechanical TranslationMechanical RotationElectrical CircuitsHydraulic CircuitsMixed SystemsState Equation DerivationState-Space RepresentationsAlgebraic Loops and Derivative CausalitySummaryPracticeExercisesImpedance Bond GraphsIntroductionLaplace Transform of the State-Space EquationBasic 1-Port ImpedancesImpedance Bond Graph SynthesisJunctions, Transformers, and GyratorsEffort and Flow DividersSign ChangesTransfer Function DerivationAlternative Derivation of Transf...

Circuit motifs for contrast-adaptive differentiation in early sensory systems: the role of presynaptic inhibition and short-term plasticity.

Science.gov (United States)

Zhang, Danke; Wu, Si; Rasch, Malte J

2015-01-01

In natural signals, such as the luminance value across of a visual scene, abrupt changes in intensity value are often more relevant to an organism than intensity values at other positions and times. Thus to reduce redundancy, sensory systems are specialized to detect the times and amplitudes of informative abrupt changes in the input stream rather than coding the intensity values at all times. In theory, a system that responds transiently to fast changes is called a differentiator. In principle, several different neural circuit mechanisms exist that are capable of responding transiently to abrupt input changes. However, it is unclear which circuit would be best suited for early sensory systems, where the dynamic range of the natural input signals can be very wide. We here compare the properties of different simple neural circuit motifs for implementing signal differentiation. We found that a circuit motif based on presynaptic inhibition (PI) is unique in a sense that the vesicle resources in the presynaptic site can be stably maintained over a wide range of stimulus intensities, making PI a biophysically plausible mechanism to implement a differentiator with a very wide dynamical range. Moreover, by additionally considering short-term plasticity (STP), differentiation becomes contrast adaptive in the PI-circuit but not in other potential neural circuit motifs. Numerical simulations show that the behavior of the adaptive PI-circuit is consistent with experimental observations suggesting that adaptive presynaptic inhibition might be a good candidate neural mechanism to achieve differentiation in early sensory systems.

Unstable oscillators based hyperchaotic circuit

DEFF Research Database (Denmark)

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...

The test of VLSI circuits

Science.gov (United States)

Baviere, Ph.

Tests which have proven effective for evaluating VLSI circuits for space applications are described. It is recommended that circuits be examined after each manfacturing step to gain fast feedback on inadequacies in the production system. Data from failure modes which occur during operational lifetimes of circuits also permit redefinition of the manufacturing and quality control process to eliminate the defects identified. Other tests include determination of the operational envelope of the circuits, examination of the circuit response to controlled inputs, and the performance and functional speeds of ROM and RAM memories. Finally, it is desirable that all new circuits be designed with testing in mind.

Custom integrated front-end circuit for the CMS electromagnetic calorimeter

CERN Document Server

Walder, J P; Denes, P; Mathez, H; Pangaud, P

2001-01-01

A wide dynamic range multi-gain transimpedance amplifier custom integrated circuit has been developed for the readout of avalanche photodiode and vacuum photodiode in the CMS electromagnetic calorimeter for LHC experiment. The 92 db input dynamic range is divided into four ranges of 12 bits each in order to provide 40 MHz analog sampled data to a 12 bits ADC. This concept, which has been integrated in rad-hard full complementary bipolar technology, will be described. Experimental results obtained in lab and under irradiation will be presented along with test strategy being used for mass production. 6 Refs.

Renewable hydrogen generation from a dual-circuit redox flow battery

OpenAIRE

Amstutz, Veronique; Toghill, Kathryn Ellen; Powlesland, Francis; Vrubel, Heron; Comninellis, Christos; Hu, Xile; Girault, Hubert H.

2014-01-01

Redox flow batteries (RFBs) are particularly well suited for storing the intermittent excess supply of renewable electricity; so-called “junk” electricity. Conventional RFBs are charged and discharged electrochemically, with electricity stored as chemical energy in the electrolytes. In the RFB system reported here, the electrolytes are conventionally charged but are then chemically discharged over catalytic beds in separate external circuits. The catalytic reaction of particular interest gene...

Dendritic nonlinearities are tuned for efficient spike-based computations in cortical circuits.

Science.gov (United States)

Ujfalussy, Balázs B; Makara, Judit K; Branco, Tiago; Lengyel, Máté

2015-12-24

Cortical neurons integrate thousands of synaptic inputs in their dendrites in highly nonlinear ways. It is unknown how these dendritic nonlinearities in individual cells contribute to computations at the level of neural circuits. Here, we show that dendritic nonlinearities are critical for the efficient integration of synaptic inputs in circuits performing analog computations with spiking neurons. We developed a theory that formalizes how a neuron's dendritic nonlinearity that is optimal for integrating synaptic inputs depends on the statistics of its presynaptic activity patterns. Based on their in vivo preynaptic population statistics (firing rates, membrane potential fluctuations, and correlations due to ensemble dynamics), our theory accurately predicted the responses of two different types of cortical pyramidal cells to patterned stimulation by two-photon glutamate uncaging. These results reveal a new computational principle underlying dendritic integration in cortical neurons by suggesting a functional link between cellular and systems--level properties of cortical circuits.

Circuits and filters handbook

CERN Document Server

Chen, Wai-Kai

2003-01-01

A bestseller in its first edition, The Circuits and Filters Handbook has been thoroughly updated to provide the most current, most comprehensive information available in both the classical and emerging fields of circuits and filters, both analog and digital. This edition contains 29 new chapters, with significant additions in the areas of computer-aided design, circuit simulation, VLSI circuits, design automation, and active and digital filters. It will undoubtedly take its place as the engineer's first choice in looking for solutions to problems encountered in the design, analysis, and behavi

Security electronics circuits manual

CERN Document Server

MARSTON, R M

1998-01-01

Security Electronics Circuits Manual is an invaluable guide for engineers and technicians in the security industry. It will also prove to be a useful guide for students and experimenters, as well as providing experienced amateurs and DIY enthusiasts with numerous ideas to protect their homes, businesses and properties.As with all Ray Marston's Circuits Manuals, the style is easy-to-read and non-mathematical, with the emphasis firmly on practical applications, circuits and design ideas. The ICs and other devices used in the practical circuits are modestly priced and readily available ty

Changes to the shuttle circuits

CERN Multimedia

GS Department

2011-01-01

To fit with passengers expectation, there will be some changes to the shuttle circuits as from Monday 10 October. See details on http://cern.ch/ShuttleService (on line on 7 October). Circuit No. 5 is cancelled as circuit No. 1 also stops at Bldg. 33. In order to guarantee shorter travel times, circuit No. 1 will circulate on Meyrin site only and circuit No. 2, with departures from Bldg. 33 and 500, on Prévessin site only. Site Services Section

Troubleshooting analog circuits

CERN Document Server

Pease, Robert A

1991-01-01

Troubleshooting Analog Circuits is a guidebook for solving product or process related problems in analog circuits. The book also provides advice in selecting equipment, preventing problems, and general tips. The coverage of the book includes the philosophy of troubleshooting; the modes of failure of various components; and preventive measures. The text also deals with the active components of analog circuits, including diodes and rectifiers, optically coupled devices, solar cells, and batteries. The book will be of great use to both students and practitioners of electronics engineering. Other

Optoelectronics circuits manual

CERN Document Server

Marston, R M

2013-01-01

Optoelectronics Circuits Manual covers the basic principles and characteristics of the best known types of optoelectronic devices, as well as the practical applications of many of these optoelectronic devices. The book describes LED display circuits and LED dot- and bar-graph circuits and discusses the applications of seven-segment displays, light-sensitive devices, optocouplers, and a variety of brightness control techniques. The text also tackles infrared light-beam alarms and multichannel remote control systems. The book provides practical user information and circuitry and illustrations.