A modular approach for modeling the cell cycle based on functional response curves

Modeling biochemical reactions by means of differential equations often results in systems with a large number of variables and parameters. As this might complicate the interpretation and generalization of the obtained results, it is often desirable to reduce the complexity of the model. One way to accomplish this is by replacing the detailed reaction mechanisms of certain modules in the model by a mathematical expression that qualitatively describes the dynamical behavior of these modules. Such an approach has been widely adopted for ultrasensitive responses, for which underlying reaction mechanisms are often replaced by a single Hill function. Also time delays are usually accounted for by using an explicit delay in delay differential equations. In contrast, however, S-shaped response curves, which by definition have multiple output values for certain input values and are often encountered in bistable systems, are not easily modeled in such an explicit way. Here, we extend the classical Hill function into a mathematical expression that can be used to describe both ultrasensitive and S-shaped responses. We show how three ubiquitous modules (ultrasensitive responses, S-shaped responses and time delays) can be combined in different configurations and explore the dynamics of these systems. As an example, we apply our strategy to set up a model of the cell cycle consisting of multiple bistable switches, which can incorporate events such as DNA damage and coupling to the circadian clock in a phenomenological way.

The nonequilibrium phase transition and the symmetry revival induced by time delay in a bistable system are investigated. The stationary probability distribution function (SPDF) of the bistable system with time delay and correlated noises are calculated by an analytical method and stochastic simulation respectively. The analytical and simulative results indicate that: (1) There is a certain value of λ(λ denotes the strength of correlations between the multiplicative and additive noises) to make the SPDF symmetric under some time delay; however, above or below the given value, the symmetry will be broken; (2) With the monotonic change of λ, the unimodal peak structure of SPDF becomes bimodal at the beginning, then it becomes unimodal again; this means that there is a reentrance phenomenon in the process; (3) There is a critical value of delay time, which makes the lower peak of SPDF equal to the higher one under the critical condition. This means that the symmetry revival phenomenon emerges.

The asymmetric bistable system with time delays in the feedback force and random force under multiplicative and additive Gaussian noise is studied. Using the small time delay approximation approach and time-delayed Fokker–Planck equations (FPE), the signal-to-noise ratio (SNR) of the proposed stochastic system is obtained. The stochastic resonance (SR) phenomena influenced by parameters — including system parameters [Formula: see text], [Formula: see text], asymmetry parameter [Formula: see text], time delay [Formula: see text], strength [Formula: see text] of the time-delayed feedback, noise intensities [Formula: see text] and [Formula: see text] of multiplicative and additive noise, and correlation strength [Formula: see text] between two noises, are also analyzed by numerical simulations. Results demonstrate that the SR performance of the asymmetric bistable system is superior to one symmetric bistable system. Besides, both time delay and strength of time-delayed feedback could enhance the SR to some extent. Then, the asymmetric time-delayed bistable SR (ATDBSR) method is used to the bearing fault diagnosis. The engineering applications of the ATDBSR method are realized and the value of the method is verified by effective experimental results.

Bistable switches have important roles in cellular decision-making processes. Bistability can be the consequence of positive or double-negative feedback loops. Although necessary, such feedback is not sufficient for bistability, which also requires nonlinearity. Nonlinearity can be provided by synergy of multiple feedback loops or by an ultrasensitive response within a single feedback loop. However, these two possibilities are not mutually exclusive; a combination of them is also possible. Here we analyze a biochemical regulatory network that controls a crucial cell cycle transition in all eukaryotic cells and contains multiple redundant feedback loops and nonlinearity. We show in this realistic biological example that two redundant feedback loops have different effects on the position of one of the saddle-node bifurcations of the system, which determines where the system switches. This illustrates that even though the roles of positive and double-negative feedbacks have been regarded as equivalent, the difference in their architectures can lead to differences in their effects on the system. We speculate that this conclusion could be general for other bistable systems with redundant feedback loops.

In 2013 the Editor of Journal of Vibration and Control and SAGE became aware of a peer review ring involving assumed and fabricated identities that appeared to centre around Peter Chen at National Pingtung University of Education, Taiwan (NPUE). SAGE and the Editor then began a complex investigation into the case during the rest of 2013 and 2014. Following an unsatisfactory response from Peter Chen, NPUE was notified. NPUE were serious in addressing the Journal and SAGE’s concerns. NPUE confirmed that the institution was investigating Peter Chen. SAGE subsequently uncovered a citation ring involving the above mentioned author and others. We regret that individual authors have compromised the academic record by perverting the peer review process and apologise to readers. On uncovering problems with peer review and citation SAGE immediately put steps in place to avoid similar vulnerability of the Journal to exploitation in the future. More information may be found at www.sagepub.co.uk/JVC_Statement_2014 . The Journal and SAGE understand from NPUE that Peter Chen has resigned his post at NPUE. The following articles are retracted because after thorough investigation evidence points towards them having at least one author or being reviewed by at least one reviewer who has been implicated in the peer review ring and/or citation ring. All authors have had an opportunity to respond to the allegations and proposed actions. OnlineFirst articles (these articles will not be published in an issue) Chen CY, Chen T-H, Chen Y-H, Yu S-E and Chung P-Y (2013) Information technology system modeling an integrated C-TAM-TPB model to the validation of ocean tidal analyses Journal of Vibration and Control Epub ahead of print 7 May 2013. doi: 10.1177/1077546312472924 Chang R-F, Chen CY, Su F-P and Lin H-C (2013) A two-step approach for broadband digital signal processing technique Journal of Vibration and Control Epub ahead of print 26 April 2013. doi: 10.1177/1077546312472925 Chen TH, Chang CJ, Yu SE, Chung PY and Liu C-K (2013) Nonlinear information analysis and system management technique: the influence of design experience and control complexity Journal of Vibration and Control Epub ahead of print 12 April 2013. doi: 10.1177/1077546312473321 Chen CY, Shih BY, Chen YH, Yu SE and Liu YC (2013) The exploration of a 3T flow model using vibrating NXT: II. Model validation Journal of Vibration and Control Epub ahead of print 10 April 2013. doi: 10.1177/1077546312470481 Chen CY, Shih BY, Chen YH, Yu SE and Liu YC (2013) The exploration of 3T flow model using vibrating NXT: I. model formulation Journal of Vibration and Control Epub ahead of print 6 February 2013. doi: 10.1177/1077546312467360 Lin M-L and Chen C-W (2013) Stability analysis of fuzzy-based NN modeling for ecosystems using fuzzy Lyapunov methods Journal of Vibration and Control Epub ahead of print 6 February 2013. doi: 10.1177/1077546312466687 Chen CY, Chen TH, Chen YH and Chiu J (2012) A multi-stage method for deterministic-statistical analysis: a mathematical case and measurement studies Journal of Vibration and Control Epub ahead of print 20 December 2012. doi: 10.1177/1077546312466579 Shih BY, Lin MC and Chen CY (2012) Autonomous navigation system for radiofrequency identification mobile robot e-book reader Journal of Vibration and Control Epub ahead of print 13 December 2012. doi: 10.1177/1077546312466578 Chang RF, Chen CY, Su FP, Lin HC and Lu C-K (2012) Multiphase SUMO robot based on an agile modeling-driven process for a small mobile robot Journal of Vibration and Control Epub ahead of print 13 December 2012. doi: 10.1177/1077546312464993 Shih B-Y, Lin Y-K, Cheng M-H, Chen C-Y and Chiu C-P (2012) The development of an application program interactive game-based information system Journal of Vibration and Control Epub ahead of print 12 December 2012. doi: 10.1177/1077546312464682 Chen C-Y, Chang C-J and Lin C-H (2012) On dynamic access control in web 2.0 and cloud interactive information hub: technologies Journal of Vibration and Control Epub ahead of print 12 December 2012. doi: 10.1177/1077546312464992 Shin BY, Chen CY and Hsu KH (2012) Robot cross platform system using innovative interactive theory and selection algorithms for Android application Journal of Vibration and Control Epub ahead of print 13 November 2012. doi: 10.1177/1077546312463757 Articles published in an issue Chen C-W (2014) Applications of neural-network-based fuzzy logic control to a nonlinear time-delay chaotic system Journal of Vibration and Control 20 (4): 589-605. Epub ahead of print 5 November 2012. doi: 10.1177/1077546312461370 Chen C-W (2014) A review of intelligent algorithm approaches and neural-fuzzy stability criteria for time-delay tension leg platform systems Journal of Vibration and Control 20 (4): 561-575. Epub ahead of print 5 November 2012. doi: 10.1177/1077546312463759 Chen C-Y, Chang C-J and Lin C-H (2014) On dynamic access control in web 2.0 and cloud interactive information hub: trends and theories Journal of Vibration and Control 20 (4): 548-560. Epub ahead of print 5 November 2012. doi: 10.1177/1077546312463762 Lin M-L and Chen C-W (2014) Stability conditions for ecosystem modeling using the fuzzy Lyapunov method Journal of Vibration and Control 20 (2): 290-302. Epub ahead of print 23 October 2012. doi: 10.1177/1077546312451301 Chen C-H, Kuo C-M, Hsieh S-H and Chen C-Y (2014) Highly efficient very-large-scale integration (VLSI) implementation of probabilistic neural network image interpolator Journal of Vibration and Control 20 (2): 218-224. Epub ahead of print 22 October 2012. doi: 10.1177/1077546312458822 Chen C-Y (2014) Wave vibration and simulation in dissipative media described by irregular boundary surfaces: a mathematical formulation Journal of Vibration and Control 20 (2): 191-203. Epub ahead of print 22 October 2012. doi: 10.1177/1077546312464258 Chen C-H, Yao T-K, Dai J-H and Chen C-Y (2014) A pipelined multiprocessor system- on-a-chip (SoC) design methodology for streaming signal processing Journal of Vibration and Control 20 (2): 163-178. Epub ahead of print 16 October 2012. doi: 10.1177/1077546312458821 Lin M-L and Chen C-W (2014) Fuzzy neural modeling for n-degree ecosystems using the linear matrix inequality approach Journal of Vibration and Control 20 (1): 82-93. Epub ahead of print 8 October 2012. doi: 10.1177/1077546312458533 Chen C-H, Wu W-X and Chen C-Y (2013) Ant-inspired collective problem-solving systems Journal of Vibration and Control 19 (16): 2481-2490. Epub ahead of print 18 September 2012. doi: 10.1177/1077546312456231 Chen C-H, Yao T-K, Kuo C-M and Chen C-Y (2013) Evolutionary design of constructive multilayer feedforward neural network Journal of Vibration and Control 19 (16): 2413-2420. Epub ahead of print 12 September 2012. doi: 10.1177/1077546312456726 Chen C-W (2013) Applications of the fuzzy-neural Lyapunov criterion to multiple time-delay systems Journal of Vibration and Control 19 (13): 2054-2067. Epub ahead of print 16 August 2012. doi: 10.1177/1077546312451034 Chung P-Y, Chen Y-H, Walter L and Chen C-Y (2013) Influence and dynamics of a mobile robot control on mechanical components Journal of Vibration and Control 19 (13): 1923-1935. Epub ahead of print 20 July 2012. doi: 10.1177/1077546312452184 Chen C-W (2013) Neural network-based fuzzy logic parallel distributed compensation controller for structural system Journal of Vibration and Control 19 (11): 1709-1727. Epub ahead of print 22 June 2012. doi: 10.1177/1077546312442233 Chen C-W, Yeh K, Yang H-C, Liu KFR and Liu C-C (2013) A critical review of structural system control by the large-scaled neural network linear-deferential-inclusion-based criterion Journal of Vibration and Control 19 (11): 1658-1673. Epub ahead of print 18 June 2012. doi: 10.1177/1077546312443377 Chen C-H, Kuo C-M, Chen C-Y and Dai J-H (2013) The design and synthesis using hierarchical robotic discrete-event modeling Journal of Vibration and Control 19 (11): 1603-1613. Epub ahead of print 27 June 2012. doi: 10.1177/1077546312449645 Chang CJ, Chen CY and Chou I-T (2013) The design of information and communication technologies: telecom MOD strength machines Journal of Vibration and Control 19 (10): 1499-1513. Epub ahead of print 27 June 2012. doi: 10.1177/1077546312449644 Shih B-Y, Chen C-Y, Li K-H, Wu T-Y, Chen G-Y (2013) A novel NXT control method for implementing force sensing and recycling in a training robot Journal of Vibration and Control 19 (10): 1443-1459. Epub ahead of print 1 June 2012. doi: 10.1177/1077546312446361 Chen C-W, Chen P-C and Chiang W-L (2013) Modified intelligent genetic algorithm-based adaptive neural network control for uncertain structural systems Journal of Vibration and Control 19 (9): 1333-1347. Epub ahead of print 31 May 2012. doi: 10.1177/1077546312442232 Chen C-Y, Shih B-Y, Shih C-H and Wang L-H (2013) Enhancing robust and stability control of a humanoid biped robot: system identification approach. Journal of Vibration and Control 19 (8): 1199-1207. Epub ahead of print 26 April 2012. doi: 10.1177/1077546312442947 Chang C-J, Chen C-Y and Huang C-W (2013) Applications for medical recovery using wireless control of a bluetooth ball with a hybrid G-sensor and human-computer interface technology Journal of Vi

In this study, a revisited improved approach of an initial frequency response based autotuner is proposed to enable PID controller design based on S-shaped step response data. In prior autotuner, the critical frequency value is found using relay test whereas process frequency response and its derivative at this frequency are calculated via the sine test. With the proposed approach, these values are estimated using the first order plus time delay models, which are employed to characterize S-shaped step response. Firstly, an identification method is used to find the model parameters, i.e. time constant <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$T$</tex> and delay time L. Secondly, the required values are estimated using the first order plus time delay model. The remaining tuner design steps are the same as in the prior autotuner. The simulations are performed on four different types of dynamical systems to show effectiveness of the proposed approach. The simulation results suggest that the performance of the control system using the proposed approach improves in terms of achievable performance indicators such as overshoot and settling time.

This paper addresses the problem of stochastic resonance (SR) in a time-delayed bistable system subjected to Gaussian white noise. Differing from the conventional studies, the statistical complexity measure and the normalized Shannon entropy have been defined and employed to quantify SR phenomenon of the time-delayed bistable system. According to the definitions of statistical complexity measure and normalized Shannon entropy, a minimum of entropy illustrates that the motion of system reaches some degree of order and a maximum of statistical complexity measure implies that the system’s intricate pattern tends to complexity. It has been found that for an optimal level of noise intensity, the statistical complexity measure displays a maximum and the normalized Shannon entropy exhibits a minimum, which demonstrates not only the occurrence of SR but also the severity of dynamical complexity. And the effects of different parameters on SR are also studied by means of the statistical complexity measure. To test the validity, the signal-to-noise ratio (SNR) is also calculated and a good agreement has been found between the statistical complexity measure and the SNR, which indicates that the statistical complexity measure is an effective method for quantify SR of the time-delayed bistable system.

The digital control system of modular multilevel converters (MMCs) normally synchronizes with the switching actions. The switching frequency of an MMC is generally selected as low as possible from an efficiency point of view, which leads to an unavoidable and relatively long time delay in the control system. Such a time delay might deteriorate the MMC performance and even reduce the stability margin by introducing infinite uncertain eigenvalues into the system state functions. Without a proper time-delay model and quantitative system stability analyses, MMCs might suffer from uncertainties and unstable risks during their operations, especially when the switching frequency is low. This paper derives an MMC model considering the time delay in the digital control system. A Pade-based stability analysis method is then proposed, which consists of three steps: information integration and critical eigenvalue extraction, and trajectory visualization and critical angle (CA) calculation, and quantitative assessment and extreme value determination. By the proposed model and method, the critical eigenvalue can be effectively extracted. With the Hopf bifurcation, the time delay in the digital control system induces a pair critical conjugate eigenvalues into MMC systems, which is detected as an instability cause. The CA and the critical impact are defined to quantitatively assess the stability, while selecting the controller parameters and minimum switching frequency. The proposed method for the MMC stability assessment is experimentally verified.

With the rapid development of vehicular sensor networks (VSNs) technology, the potential use of networked real-time control and automation is enormous and appealing. However, closed-loop control VSNs via the Internet are very difficult to implement practically because of their stochastic nature. One of the biggest challenges in VSNs is how to deal with sensor networks time delay and data loss. The authors investigate the potential of using the predictive control scheme for VSNs based on round-trip time (RTT) delay prediction to overcome the VSNs transmission delay and data loss. The predicted RTT delay is taken as the sampling interval reference for variable-period sampling approach. Modelling the time delay of networked control systems as a non-linear time series, the least mean square (LMS) filter algorithm is adopted to predict online the time delay induced in VSNs. The simulation results show that the LMS algorithm can achieve ideal efficacy if time delay has no variety abnormally. The predictive compensation strategy is proposed to reduce the detrimental effect of stochastic time delays induced by communication networks on control performance. The results of offline simulations via the Internet illustrate that the predictive control scheme based on RTT delay prediction has the potential to overcome the VSNs time delay and data loss.

Biochemical systems can be described by biochemical reactions. Biochemical reactions can be investigated through mathematical modeling and stochastic simulations. Deterministic and stochastic models are two basic categories of models for biochemical reactions. Due to transmembrane transportation of biochemical species and delayed degradation, time delays are ubiquitous in coupled biochemical systems. Therefore, models for biochemical reactions can be further classified into delayed and un-delayed ones. For biochemical systems without delays, researchers have established the connections between deterministic models and stochastic models directly from the deterministic ones. For delayed biochemical systems, researchers have proposed some stochastic simulation methods to cope with biochemical reactions with time delays. However, the existing delayed stochastic simulation algorithms (SSA) are all incapable of realizing the comparison between highly nonlinear deterministic delayed models and stochastic models directly from the the deterministic ones. In this paper, we proposed a delayed SSA, which can realize the comparison between deterministic models and its stochastic counterparts. Furthermore, one can also use the algorithm to investigate intrinsic noise-induced behaviors, and the effect of system volumes. Several numerical examples show the effectiveness and correctness of our algorithm.

Time delay exists inevitably in active control, which may not only degrade the system performance but also render instability to the dynamic system. In this paper, a novel active controller is developed to solve the time delay problem in flexible structures. By using the independent modal space control method, the differential equation of the controlled mode with time delay is obtained from the time-delay system dynamics. Then it is discretized and changed into a first-order difference equation without any explicit time delay by augmenting the state variables. The modal controller is derived based on the augmented system using the discrete variable structure control method. The switching surface is determined by minimizing a discrete quadratic performance index. The modal coordinate is extracted from sensor measurements and the actuator control force is converted from the modal one. Since the time delay is explicitly included throughout the entire controller design without any approximation, the system performance and stability are guaranteed. Numerical simulations show that the proposed controller is feasible and effective in active vibration control of dynamic systems with time delay. If the time delay is not explicitly included in the controller design, instability may occur.

Introduction: The problem of delay time estimation in ring self-oscillatory time-delay systems arises in various fields of science and is of great importance in the study of real systems generating chaotic time series. Purpose: To conduct a comparative analysis of the operation of methods for the reconstruction of time-delay systems from chaotic time series in the absence and presence of additive noise. Methods: Methods for estimating the delay time according to the statistics of extrema, using the autocorrelation function and the method of order time asymmetry are used. Based on the latter method, a method is proposed that is focused on estimating the delay times in systems with two delays. Results: We carry out a comparative analysis of the operation of four methods for reconstructing the delay times in self-oscillating time-delay systems from chaotic time series using the example of Ikeda systems with one and two delay times. We demonstrate that in the absence of additive noise, the delay time estimation method based on statistics of extrema is the most accurate one for the case of time series analysis of systems with both one and two delays. In the presence of additive noise, the modified method of order time asymmetry proposed in the work in the case of the analysis of systems with one delay time works no worse than the method of the autocorrelation function and order time asymmetry. In the case of two delay times, the modified order time asymmetry method works better than others. Practical relevance: The described methods can have a practical application in estimating the delay time of self-oscillating systems, yet the level of additive noise can affect the accuracy of the estimate.

Network Control.- Delay-Based Non-linear Observers for Congestion Control in Communication Networks.- On the Use of State Predictors in Networked Control Systems.- Networked Control Systems: Algorithms and Experiments.- Modeling and Closed Loop Control for Resource-Constrained Load Balancing with Time Delays in Parallel Computations.- Stability of Load Balancing Control.- Teleoperation.- Robust H ? Control of Bilateral Teleoperation Systems Under Communication Time-Delay.- Web Remote Control of Mechanical Systems: Delay Problems and Experimental Measurements of Round Trip Time.- PDE Approach for Time Delays in Robotized Teleoperation.- Emerging Methodologies.- From Time Delay to Distributed Parameter Systems in Communications.- Computing Maximum Delay Deviation Allowed to Retain Stability in Systems with Two Delays.- On Exact Controllability of Linear Time Delay Systems of Neutral Type.- New Computational Methods.- Applied Interval Computation: A New Approach for Time-Delays Systems Analysis.- Mathematical and Computational Tools for the Stability Analysis of Time-Varying Delay Systems and Applications in Mechanical Engineering.- Diffusive Representation for Operators Involving Delays.- OreModules: A Symbolic Package for the Study of Multidimensional Linear Systems.- Predictors, Inversion and Filtering.- Inversion and Tracking Problems for Time Delay Linear Systems.- Finite Impulse Response Systems for Almost Perfect Decoupling in Nonminimum-Phase Plants.- Linearization of the Power Amplifier in Mobile Telecommunications.- Merging Saturations and Input Delays.- Robust Sampled-Data Control: An Input Delay Approach.- Stabilization and Finite-Gain Stabilizability of Delay Linear Systems Subject to Input Saturation.- Global Asymptotic Stabilization of a PVTOL Aircraft Model with Delay in the Input.

Retraction notice

Many bridges in Taiwan have been in use from the period that Taiwan was governed by the Japanese, over 50 years ago, which is the average ultimate usable lifetime of such structures. Three-quarters of the bridges on major highways have been in use for more than 20 years and numerous bridges on country roads have also been in use for more than 20 years. In other words, most of the bridges in Taiwan are aging and may require repair or replacement. Ambient vibration tests are utilized to measure the response of old bridges, which are difficult to equip with accelerometers. The Fourier transform method is traditionally used to gain important information about ambient vibration records. However, the development of information technology over the last 20 years has meant that there are more kinds of signal management technologies, including the wavelet and Hilbert—Huang transform (HHT) methods. In this study we investigate the characteristics of aging bridges by comparison with their structural properties. We analyze their ambient vibration, and discuss the possible influence of the frequency function. Long-term environmental impacts create many structural problems, but with traditional methods examination of bridge health is difficult. Therefore, in our HHT management system, we examine destroyed bridges. The characteristics and behavior of bridges subjected to random loading can be understood by analysis with the random decrement technique and the frequency response function method.