Journal articles: 'Loop domain model'

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Aguirre, L. A. "Open-loop model matching in frequency domain." Electronics Letters 28, no. 5 (1992): 484. http://dx.doi.org/10.1049/el:19920305.

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Su, Y., and G. J. Weng. "A polycrystal hysteresis model for ferroelectric ceramics." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 462, no. 2069 (February 14, 2006): 1573–92. http://dx.doi.org/10.1098/rspa.2005.1616.

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Most key elements of ferroelectric properties are defined through the hysteresis loops. For a ferroelectric ceramic, its loop is contributed collectively by its constituent grains, each having its own hysteresis loop when the ceramic polycrystal is under a cyclic electric field. In this paper, we propose a polycrystal hysteresis model so that the hysteresis loop of a ceramic can be calculated from the loops of its constituent grains. In this model a micromechanics-based thermodynamic approach is developed to determine the hysteresis behaviour of the constituent grains, and a self-consistent scheme is introduced to translate these behaviours to the polycrystal level. This theory differs from the classical phenomenological ones in that it is a micromechanics-based thermodynamic approach and it can provide the evolution of new domain concentration among the constituent grains. It also differs from some recent micromechanics studies in its secant form of self-consistent formulation and in its application of irreversible thermodynamics to derive the kinetic equation of domain growth. To put this two-level micromechanics theory in perspective, it is applied to a ceramic PLZT 8/65/35, to calculate its hysteresis loop between the electric displacement and the electric field ( D versus E ), and the butterfly-shaped longitudinal strain versus the electric field relation ( ϵ versus E ). The calculated results are found to be in good quantitative agreement with the test data. The corresponding evolution of new domain concentration c 1 and the individual hysteresis loops of several selected grains—along with those of the overall polycrystal—are also illustrated.

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Chakrapani, Sudha, Timothy D. Bailey, and Anthony Auerbach. "Gating Dynamics of the Acetylcholine Receptor Extracellular Domain." Journal of General Physiology 123, no. 4 (March 29, 2004): 341–56. http://dx.doi.org/10.1085/jgp.200309004.

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We used single-channel recording and model-based kinetic analyses to quantify the effects of mutations in the extracellular domain (ECD) of the α-subunit of mouse muscle–type acetylcholine receptors (AChRs). The crystal structure of an acetylcholine binding protein (AChBP) suggests that the ECD is comprised of a β-sandwich core that is surrounded by loops. Here we focus on loops 2 and 7, which lie at the interface of the AChR extracellular and transmembrane domains. Side chain substitutions in these loops primarily affect channel gating by either decreasing or increasing the gating equilibrium constant. Many of the mutations to the β-core prevent the expression of functional AChRs, but of the mutants that did express almost all had wild-type behavior. Rate-equilibrium free energy relationship analyses reveal the presence of two contiguous, distinct synchronously-gating domains in the α-subunit ECD that move sequentially during the AChR gating reaction. The transmitter-binding site/loop 5 domain moves first (Φ = 0.93) and is followed by the loop 2/loop 7 domain (Φ = 0.80). These movements precede that of the extracellular linker (Φ = 0.69). We hypothesize that AChR gating occurs as the stepwise movements of such domains that link the low-to-high affinity conformational change in the TBS with the low-to-high conductance conformational change in the pore.

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Aguirre, L. A. "Erratum: Open-loop model matching in frequency domain." Electronics Letters 28, no. 8 (1992): 808. http://dx.doi.org/10.1049/el:19920509.

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Szewczyk, Roman. "Model of the Magnetostrictive Hysteresis Loop with Local Maximum." Materials 12, no. 1 (December 30, 2018): 105. http://dx.doi.org/10.3390/ma12010105.

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This paper presents a model of the magnetostrictive hysteresis loop with local maximum. The model is based on the differential equations describing magnetostriction due to the domain wall movement as well as domain magnetization rotation. The transition between these mechanisms of magnetization is quantified by the Maxwell–Boltzmann distribution. Moreover, the lift-off phenomenon in the magnetostrictive hysteresis loop is considered. The proposed model was validated on the results of measurements of magnetostrictive hysteresis loops of Mn0.70Zn0.24Fe2.06O4 ferrite for power application and 13CrMo4-5 construction steel. The results of modeling confirm that the proposed model corresponds well with experimental results. Good agreement was confirmed by determination coefficient R2, which exceeded 0.995 and 0.985 for Mn0.70Zn0.24Fe2.06O4 ferrite for power application and 13CrMo4-5 construction steel, respectively.

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Camia, Federico, Alberto Gandolfi, Giovanni Peccati, and Tulasi Ram Reddy. "Brownian Loops, Layering Fields and Imaginary Gaussian Multiplicative Chaos." Communications in Mathematical Physics 381, no. 3 (February 2021): 889–945. http://dx.doi.org/10.1007/s00220-020-03932-9.

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AbstractWe study fields reminiscent of vertex operators built from the Brownian loop soup in the limit as the loop soup intensity tends to infinity. More precisely, following Camia et al. (Nucl Phys B 902:483–507, 2016), we take a (massless or massive) Brownian loop soup in a planar domain and assign a random sign to each loop. We then consider random fields defined by taking, at every point of the domain, the exponential of a purely imaginary constant times the sum of the signs associated to the loops that wind around that point. For domains conformally equivalent to a disk, the sum diverges logarithmically due to the small loops, but we show that a suitable renormalization procedure allows to define the fields in an appropriate Sobolev space. Subsequently, we let the intensity of the loop soup tend to infinity and prove that these vertex-like fields tend to a conformally covariant random field which can be expressed as an explicit functional of the imaginary Gaussian multiplicative chaos with covariance kernel given by the Brownian loop measure. Besides using properties of the Brownian loop soup and the Brownian loop measure, a main tool in our analysis is an explicit Wiener–Itô chaos expansion of linear functionals of vertex-like fields. Our methods apply to other variants of the model in which, for example, Brownian loops are replaced by disks.

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Du, Wenhao, Haixia Zhu, Jiaqiang Qian, Dongmei Xue, Sen Zheng, and Qiang Huang. "Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State." International Journal of Molecular Sciences 24, no. 2 (January 7, 2023): 1204. http://dx.doi.org/10.3390/ijms24021204.

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Staphylococcus aureus Cas9 (SaCas9) is a widely used genome editing tool. Understanding its molecular mechanisms of DNA cleavage could effectively guide the engineering optimization of this system. Here, we determined the first cryo-electron microscopy structure of the SaCas9-sgRNA-DNA ternary complex. This structure reveals that the HNH nuclease domain is tightly bound to the cleavage site of the target DNA strand, and is in close contact with the WED and REC domains. Moreover, it captures the complete structure of the sgRNA, including the previously unresolved stem-loop 2. Based on this structure, we build a full-length model for the ternary complex in cleavage state. This model enables identification of the residues for the interactions between the HNH domain and the WED and REC domains. Moreover, we found that the stem-loop 2 of the sgRNA tightly binds to the PI and RuvC domains and may also regulate the position shift of the RuvC domain. Further mutagenesis and molecular dynamics simulations supported the idea that the interactions of the HNH domain with the WED and REC domains play an important role in the DNA cleavage. Thus, this study provides new mechanistic insights into the DNA cleavage of SaCas9 and is also useful for guiding the future engineering of SaCas9-mediated gene editing systems.

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Kumar, Sandip, David G. Priest, Yan Yan, Ian B. Dodd, Keith E. Shearwin, and David D. Dunlap. "Estimation of DNA Loop Interactions Supports the Loop Domain Model of Insulator Action." Biophysical Journal 108, no. 2 (January 2015): 164a. http://dx.doi.org/10.1016/j.bpj.2014.11.904.

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Sain, Chiranjit, Atanu Banerjee, and Pabitra Kumar Biswas. "Comparative Performance Study for Closed Loop Operation of an Adjustable Speed Permanent Magnet Synchronous Motor Drive with Different Controllers." International Journal of Power Electronics and Drive Systems (IJPEDS) 7, no. 4 (December 1, 2016): 1085. http://dx.doi.org/10.11591/ijpeds.v7.i4.pp1085-1099.

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In this paper an extensive comparative study is carried out between PI and PID controlled closed loop model of an adjustable speed Permanent Magnet Synchronous Motor (PMSM) drive. The incorporation of Sinusoidal Pulse Width Modulation (SPWM) strategy establishes near sinusoidal armature phase currents and comparatively less torque ripples without sacrificing torque/weight ratio. In this closed loop model of PMSM drive, the information about reference speed is provided to a speed controller, to ensure that actual drive speed tracks the reference speed with ideally zero steady state speed error. The entire model of PMSM closed loop drive is divided into two loops, inner loop current and outer loop speed. By taking the different combinations of two classical controllers (PI & PID) related with two loop control structure, different approximations are carried out. Hence a typical comparative study is introduced to familiar with the different performance indices of the system corresponding to time domain and frequency domain specifications. Therefore overall performance of closed loop PMSM drive is tested and effectiveness of controllers will be determined for different combinations.

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Jiang, Jian Hu, Chao Wu, and Ting Bu. "Open-Loop Frequency Domain Analysis Based on System Identification." Advanced Materials Research 452-453 (January 2012): 364–68. http://dx.doi.org/10.4028/www.scientific.net/amr.452-453.364.

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In this paper, an open-loop frequency domain analysis based on system identification is introduced. Using model identification tools in Matlab, the open-loop frequency domain characteristic could be derived accurately with the open-loop step response. Then, the closed-loop regulator could be designed with the open-loop frequency domain characteristic to fulfill the steady and dynamic requirements. This method is suitable for most of the systems. An example of Buck converter is proposed to represent the analysis process. Simulation model is built in Matlab software, and some factors which affect the precision of model identification and frequency domain analysis are taken into consideration. Finally, both open- and closed-loop experimental results verify the feasibility of the proposed scheme.

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Zheng, Jieji, Xin Xie, Ruoyu Tan, Lingyu Chen, Baoyu Li, and Dapeng Fan. "An Elaborate Dynamic Model of the Dual-Motor Precision Transmission Mechanism for Performance Optimization." Machines 10, no. 12 (December 7, 2022): 1181. http://dx.doi.org/10.3390/machines10121181.

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The dual-motor precision transmission mechanism (DMPTM) is an alternative way to eliminate backlash while ensuring the stiffness of the servo system. However, most of the established models of DMPTM are not accurate enough, and are not conducive to the optimization of system performance and the design of high-precision controllers. In this paper, based on the detailed linear model of the single components of the DMPTM, the dead-zone model, considering the time-varying stiffness, is proposed to describe the backlash of the two transmission chains, and the friction of the mechanism is depicted by the Stribeck model. Then, a high-precision dynamic model of the DMPTM is formed. Finally, the model validation experiments for the open-loop and closed-loop are carried out in the time domain and frequency domain. The experimental results show that the proposed model can accurately describe the nonlinear characteristics of the mechanism. The Pearson correlation coefficient between the proposed model and the actual system is ropen-loop > 99.41%, for the open-loop, and rclosed-loop > 83.7%, for the closed-loop, and these results are both better than those of the existing model. In the frequency domain, whether it is the open-loop or closed-loop model, the frequency response of the proposed model also reproduces the actual system well, which verifies the accuracy of the model.

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Sahu, Chinmay, V. Kirubakaran, TK Radhakrishnan, and N. Sivakumaran. "Explicit model predictive control of split-type air conditioning system." Transactions of the Institute of Measurement and Control 39, no. 5 (December 16, 2015): 754–62. http://dx.doi.org/10.1177/0142331215619976.

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Domestic air conditioners are a major source of energy consumption. In this study, utilizing real-time data from a public domain, a cascaded hardware in loop approach to the control of room temperature is considered. An inner loop to control the supply air temperature by adjusting the electronic expansion valve using a second-order plus delay time model is proposed. The room temperature control is considered the outer loop. A simplified lumped parameter representation of the thermal dynamics of the building is modelled in MATLAB using ordinary differential equations. A constrained multi parametric model predictive controller (mpMPC) is designed for both the control loops. The constraints include safety limits on the superheat and manipulation rates for the inner loop and a rate constraint on the reference signal in the outer loop. Model uncertainties like ambient temperature and thermal load variations (representing an office space) are considered for hardware in the loop testing of the proposed strategy. From performance analysis, using power spent and thermal comfort quantization, it is observed that the mpMPC scheme outperforms traditional control strategies.

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Kawata, M., Y. Asano, and A. Sano. "OPEN-LOOP AND CLOSED-LOOP IDENTIFICATION OF MODEL ERROR HARD BOUND IN FREQUENCY DOMAIN." Proceedings of the ISCIE International Symposium on Stochastic Systems Theory and its Applications 1994 (May 5, 1994): 229–36. http://dx.doi.org/10.5687/sss.1994.229.

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14

Hess, R. A. "Obtaining multi-loop pursuit-control pilot models from computer simulation." Proceedings of the Institution of Mechanical Engineers, Part G: Journal of Aerospace Engineering 222, no. 2 (February 1, 2008): 189–99. http://dx.doi.org/10.1243/09544100jaero260.

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A method for generating simplified pursuit-control pilot models for computer simulation of multi-axis flight control tasks has been developed. The method involves a sequential loop closure synthesis procedure for creating the pilot model and includes handling qualities estimation. The original model formulation previously reported in the literature used frequency-domain techniques, primarily Bode diagrams to select model gains. The present research demonstrates how similar results can be obtained in the time-domain. This latter approach is particularly useful when complex, non-linear aircraft models are being used. The time-domain approach is exercised in a six-degree of freedom rotorcraft control simulation and in a six-degree of freedom tailless fighter simulation, both involving linear models.

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Yu, Yang, Xiaoxue Gong, Lei Zhang, Hongguang Jia, and Ming Xuan. "Full-Closed-Loop Time-Domain Integrated Modeling Method of Optical Satellite Flywheel Micro-Vibration." Applied Sciences 11, no. 3 (February 2, 2021): 1328. http://dx.doi.org/10.3390/app11031328.

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Due to the micro-vibration of flywheels, the imaging quality of a high-resolution optical remote sensing satellite will be deteriorated, and the micro-vibration effect on the payload is complicated, so it is essential to establish a reasonable and accurate theoretical simulation model for it. This paper presents a method of full-closed-loop time-domain integrated modeling to estimate the impacts of micro-vibration generated by flywheels on optical satellites. The method consists of three parts. First, according to the satellites’ micro-vibration influence mechanism in orbit, this paper establishes a full-closed-loop model framework. The overall model input is the instructions received and the output is the image shift. Second, in order to meet the requirements of time-domain simulation, this paper proposes a time-domain vibration source subsystem model in the form of cosine harmonic superposition, and it integrates vibration source, structural, control, and optical subsystem models to create a full-closed-loop time-domain analysis model that can obtain the responses of micro-vibration in time and frequency domains. Lastly, the author designs a ground experiment and compares simulation results with experiment results. Compared with the ground experiment, frequency error is less than 0.4% at typical responses. Although the amplitude error is large at some typical responses, the mean root square error is less than 35%. Based on the data, the proposed integrated modeling method can be considered as an accurate methodology to predict the impacts of micro-vibration.

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John, Malte, and Axel Mertens. "HARMONIC DOMAIN MODEL OF AN OPEN-LOOP CONTROLLED PWM CONVERTER." Informatyka Automatyka Pomiary w Gospodarce i Ochronie Środowiska 8, no. 2 (May 30, 2018): 25–29. http://dx.doi.org/10.5604/01.3001.0012.0699.

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An harmonic domain model is developed for open-loop controlled voltage source inverters, which provides the steady-state solution for integer multiples of the fundamental frequency. The convolution of the switching function spectrum with the converter currents and voltages is used to describe the coupling of the AC side and the DC side. The modeling is based on a single phase leg and is extended to a single-phase and a three-phase voltage source inverter, which results in a non-linear algebraic equation system. For open-loop control the switching function is independent of the converter currents and voltages and the model is simplified to a linear equation system. This straightforward and fast model is verified by time domain simulations and experimental results. The modeling can be adapted to systems of coupled converters, which is presented for a back-to-back converter system showing the harmonic interaction of the connected subsystems.

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Kawada, T., M. Sugimachi, T. Sato, H. Miyano, T. Shishido, H. Miyashita, R. Yoshimura, H. Takaki, J. Alexander, and K. Sunagawa. "Closed-loop identification of carotid sinus baroreflex open-loop transfer characteristics in rabbits." American Journal of Physiology-Heart and Circulatory Physiology 273, no. 2 (August 1, 1997): H1024—H1031. http://dx.doi.org/10.1152/ajpheart.1997.273.2.h1024.

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In the circulatory system, a change in blood pressure operates through the baroreflex to alter sympathetic efferent nerve activity, which in turn affects blood pressure. Existence of this closed feedback loop makes it difficult to identify the baroreflex open-loop transfer characteristics by means of conventional frequency domain approaches. Although several investigators have demonstrated the advantages of the time domain approach using parametric models such as the autoregressive moving average model, specification of the model structure critically affects their results. Thus we investigated the applicability of a nonparametric closed-loop identification technique to the carotid sinus baroreflex system by using an exogenous perturbation according to a binary white-noise sequence. To validate the identification method, we compared the transfer functions estimated by the closed-loop identification with those estimated by open-loop identification. The transfer functions determined by the two identification methods did not differ statistically in their fitted parameters. We conclude that exogenous perturbation to the baroreflex system enables us to estimate the open-loop baroreflex transfer characteristics under closed-loop conditions.

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Lang, Zhe Yan, and Ai Guo Wu. "Study on Dual-Loop Controller of Helicopter Based on the Robust H-Infinite Loop Shaping Method." Applied Mechanics and Materials 130-134 (October 2011): 1182–85. http://dx.doi.org/10.4028/www.scientific.net/amm.130-134.1182.

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Helicopter is a typical MIMO system including the properties of non-stability, strong coupling, uncertainty. Firstly, a robust internal loop ACAH controller is designed and analyzed to ensure decoupling and robustness on each channel by the robust H-infinite loop shaping. Secondly, the external loop is designed using the classical PID method on the base of decoupling internal loop. Both loops contain the part of anti-windup. The simulation results of the prototype model demonstrate that in both time and frequency domain, the performance of the controller meets the design requirement with a comparative simple structure. The results can also prove that it has some effect against to the model perturbation and achieve LEVEL1 of ADS-33E-PRF.

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LAVANYA, K., B. UMAMAHESWARI, and RAMES C. PANDA. "DESIGN OF DIGITAL MULTI-RATE CONTROLLER USING FREQUENCY DOMAIN ANALYSIS." Journal of Circuits, Systems and Computers 17, no. 04 (August 2008): 675–84. http://dx.doi.org/10.1142/s0218126608004538.

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Multi-rate controllers are useful in providing fast control updates using slow measurements. The multi-rate control loop involves up-sampling, down-sampling, and systems considered at different timescales. The challenge is then, to present complete frequency domain model of the loop. This paper presents the frequency domain model of the loop which is suitable for analysis and design of controllers. The approach is illustrated through a numerical example.

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Cheng, Ming, Dikun Yang, and Qiang Luo. "Interpreting Surface Large-Loop Time-Domain Electromagnetic Data for Deep Mineral Exploration Using 3D Forward Modeling and Inversion." Minerals 13, no. 1 (December 26, 2022): 34. http://dx.doi.org/10.3390/min13010034.

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Surface transient electromagnetic (TEM) data with large transmitter loops for deep mineral exploration are often complicated by the non-trivial coupling between extended sources and arbitrarily oriented geological targets. This case study reports a TEM field data set acquired across terranes with strong lateral inhomogeneity, which is responsible for the high inconsistency in TEM data patterns along the survey line, as well as for the negative TEM transients (sign reversal) at some near-central loop stations. 3D forward modeling and inversion, as maturing tools in recent years, offer unique opportunities to extract as much geological information from such data as possible. 3D forward simulations of representative synthetic models found that the phenomenon of sign reversal at some TEM stations is associated with compact conductors enclosed by the transmitter loop and receivers that are in the loop, but off the conductor–a situation that is common in large-loop TEM and can only be explained by 3D models. However, 3D inversion of the field data with a uniform subspace as the initial and reference model fails to converge, another point of evidence that 3D inversions of large-loop TEM data are more likely to be subject to stability issues. Our solution is to warm-start the inversion with the representative model in the forward simulation experiments as the initial model, so the ill-posed 3D inversion can escape from local minima. Finally, the vertical contact structure in our 3D-inversion model is verified by a resistivity cross section of the CSAMT method. Our case study demonstrates the demand and capability of 3D electromagnetic modeling and inversion for high-resolution deep mineral exploration. It also provides an easy-to-follow template for carrying out 3D interpretation for complex geology in practice.

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Cormier, Emmanuel G., and Tatjana Dragic. "The Crown and Stem of the V3 Loop Play Distinct Roles in Human Immunodeficiency Virus Type 1 Envelope Glycoprotein Interactions with the CCR5 Coreceptor." Journal of Virology 76, no. 17 (September 1, 2002): 8953–57. http://dx.doi.org/10.1128/jvi.76.17.8953-8957.2002.

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ABSTRACT Human immunodeficiency virus type 1 envelope glycoprotein gp120 interacts with CD4 and the CCR5 coreceptor in order to mediate viral entry. A CD4-induced surface on gp120, primarily composed of residues in the V3 loop and the C4 domain, interacts with CCR5. In the present study, we generated envelope glycoproteins comprising chimeric V3 loops and/or V3 loops with deletions and studied their binding to CCR5 amino-terminal domain (Nt)-based sulfopeptides and cell surface CCR5, as well as their ability to mediate viral entry. We thus delineated two functionally distinct domains of the V3 loop, the V3 stem and the V3 crown. The V3 stem alone mediates soluble gp120 binding to the CCR5 Nt. In contrast, both the V3 stem and crown are required for soluble gp120 binding to cell surface CCR5. Within the context of a virion, however, the V3 crown alone determines coreceptor usage. Our data support a two-site gp120-CCR5 binding model wherein the V3 crown and stem interact with distinct regions of CCR5 in order to mediate viral entry.

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Davis, Aaron, and James Macnae. "Measuring AEM waveforms with a ground loop." GEOPHYSICS 73, no. 6 (November 2008): F213—F222. http://dx.doi.org/10.1190/1.2976791.

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Measuring a transmitter-current waveform provides critical data unavailable for some airborne electromagnetic (AEM) systems yet needed to model AEM data quantitatively. We developed a novel experimental method of measuring an airborne transmitter waveform by monitoring the current induced in a closed, multiturn, insulated ground loop of known inductance [Formula: see text] and resistance [Formula: see text]. The transmitter waveform of five different time-domain systems is deconvolved from the measured ground-loop response when excited by the primary electromagnetic field of the AEM system. In general, our measurements agree well with contractor-described transmitter current waveforms, although crucial differences exist between our deconvolved waveforms and those described in the literature. Using the pulse-per-second feature of a GPS antenna, the ground loop can monitor the frequency drift of a frequency-domain system. The ground loop behaves like a lossy electric-field antenna when the resistance closing the ground loop is too large. This leads to negatives in the response of coincident-loop systems without including induced polarization effects. After observing exponentially decaying, oscillating-current responses in high-resistance ground loops, we model the observed current with an LRC circuit whose resistance and capacitance represent generalized effective antenna and free-space values. Our model predicts responses that closely match the damped oscillations seen in the airborne response during flyover; however, it does not work well on conductive ground.

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Garabandić, D., and T. Petrović. "Robust Controllers for Pulse-Width-Modulated D.C./D.C. Converters Using Internal-Model-Control Design." Proceedings of the Institution of Mechanical Engineers, Part I: Journal of Systems and Control Engineering 207, no. 3 (August 1993): 127–34. http://dx.doi.org/10.1243/pime_proc_1993_207_331_02.

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A linear feedback controller for pulse-width-modulated d.c./d.c. regulator is designed using a frequency domain optimization method based on internal-model-control theory. This method aims to produce suboptimal low-order controllers which are ‘robust’, in the sense that the closed-loop system is guaranteed to meet stability objectives in the presence of model uncertainty. The small-signal model of a d.c./d.c. converter is used for the controller design. The model uncertainty description derived here is based on experiments and non-linear modelling. The result of the synthesis is a family of controllers, and each member of this family satisfies the robust control objectives. All controllers have a multi-loop structure including two feedback loops and one feedforward loop. A detailed design of the controller, including experimental results, is presented.

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BOEHM, Mark K., Adam L. CORPER, Tommy WAN, Maninder K. SOHI, Brian J. SUTTON, Jeremy D. THORNTON, Patricia A. KEEP, Kerry A. CHESTER, Richard H. J. BEGENT, and Stephen J. PERKINS. "Crystal structure of the anti-(carcinoembryonic antigen) single-chain Fv antibody MFE-23 and a model for antigen binding based on intermolecular contacts." Biochemical Journal 346, no. 2 (February 22, 2000): 519–28. http://dx.doi.org/10.1042/bj3460519.

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MFE-23 is the first single-chain Fv antibody molecule to be used in patients and is used to target colorectal cancer through its high affinity for carcinoembryonic antigen (CEA), a cell-surface member of the immunoglobulin superfamily. MFE-23 contains an N-terminal variable heavy-chain domain joined by a (Gly4Ser)3 linker to a variable light-chain (VL) domain (ĸ chain) with an 11-residue C-terminal Myc-tag. Its crystal structure was determined at 2.4 Å resolution by molecular replacement with an Rcryst of 19.0%. Five of the six antigen-binding loops, L1, L2, L3, H1 and H2, conformed to known canonical structures. The sixth loop, H3, displayed a unique structure, with a β-hairpin loop and a bifurcated apex characterized by a buried Thr residue. In the crystal lattice, two MFE-23 molecules were associated back-to-back in a manner not seen before. The antigen-binding site displayed a large acidic region located mainly within the H2 loop and a large hydrophobic region within the H3 loop. Even though this structure is unliganded within the crystal, there is an unusually large region of contact between the H1, H2 and H3 loops and the β-sheet of the VL domain of an adjacent molecule (strands DEBA) as a result of intermolecular packing. These interactions exhibited remarkably high surface and electrostatic complementarity. Of seven MFE-23 residues predicted to make contact with antigen, five participated in these lattice contacts, and this model for antigen binding is consistent with previously reported site-specific mutagenesis of MFE-23 and its effect on CEA binding.

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Opeiko, O. F. "CONTROL SYNTHESIS FOR TWO LOOPS DISCRET SYSTEM." «System analysis and applied information science», no. 1 (June 12, 2018): 22–26. http://dx.doi.org/10.21122/2309-4923-2018-1-22-26.

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The aim of this paper is the linear synthesis of two loops SISO systems with discreet time proportional integral (PI) controllers. This linear synthesis is dedicated for the systems with plant parameters uncertainty. The synthesis is based on the time scale method, providing the separate slow and fast components of the control low. The PI- controller parameters calculation is based on the modal control and plant model reduction. The conditions carried out for the each control loop dynamics still similar to the second order one. The discrete time microcontroller based numerical control restricts the stability domain of the system and each control loop in it. The stability domain of each loop is the round on the complex plane with radius, depending on the time period. Each inner loop must be more fast, then each outer one. Hence, in the outer loop the time period, required for the PI controller reaction computation, can be more then in the inner loop. This PI- controller parameter calculation method is approximate, and it is efficient for the systems, whose dynamics contains the slow and fast components. In particular, the electrical drives control systems contain the fast electromagnetic component and the slow mechanical part. The effectiveness of this method is illustrated by the example and simulation.

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Narod, B. B. "The origin of noise and magnetic hysteresis in crystalline permalloy ring-core fluxgate sensors." Geoscientific Instrumentation, Methods and Data Systems Discussions 4, no. 1 (June 19, 2014): 319–52. http://dx.doi.org/10.5194/gid-4-319-2014.

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Abstract. 6-81.3 Mo permalloy, developed in the 1960s for use in high performance ring-core fluxgate sensors, remains the state-of-the-art for permalloy-cored fluxgate magnetometers. The magnetic properties of 6-81.3, namely magnetocrystalline and magnetoelastic anisotropies and saturation induction are all optimum in the Fe–Ni–Mo system. In such polycrystalline permalloy fluxgate sensors a single phenomenon may cause both fluxgate noise and magnetic hysteresis, explain Barkhausen jumps, remanence and coercivity, and avoid domain denucleation. The phenomenon, domain wall reconnection, is presented as part of a theoretical model. In the unmagnetized state a coarse-grain high-quality permalloy foil ideally forms stripe domains, which present at the free surface as parallel, uniformly spaced domain walls that cross the entire thickness of the foil. Leakage flux "in" and "out" of alternating domains is a requirement of the random orientation, grain-by-grain, of magnetic easy axes' angles with respect to the foil free surface. Its magnetostatic energy together with domain wall energy determines an energy budget to be minimized. Throughout the magnetization cycle the free surface domain pattern remains essentially unchanged, due to the magnetostatic energy cost such a change would elicit. Thus domain walls are "pinned" to free surfaces. Driven to saturation, domain walls first bulge then reconnect via Barkhausen jumps to form a new domain configuration this author has called "channel domains", that are attached to free surfaces. The approach to saturation now continues as reversible channel domain compression. Driving the permalloy deeper into saturation compresses the channel domains to arbitrarily small thickness, but will not cause them to denucleate. Returning from saturation the channel domain structure will survive through zero H, thus explaining remanence. The Barkhausen jumps being irreversible exothermic events are sources of fluxgate noise, powered by the energy available from domain wall reconnection. A simplified domain energy model can then provide a predictive relation between ring core magnetic properties and fluxgate sensor noise power. Four properties are predicted to affect noise power, two of which, are well known: saturation total magnetic flux density and magnetic anisotropy. The two additional properties are easy axes alignment and foil thickness. Flux density and magnetic anisotropy are primary magnetic properties determined by an alloy's chemistry and crystalline lattice properties. Easy axes alignment and foil thickness are secondary, geometrical properties related to an alloy's polycrystalline fabric and manufacture. Improvements to fluxgate noise performance can in principle be achieved by optimizing any of these four properties in such a way as to minimize magnetostatic energy. Fluxgate signal power is proportional to B–H loop curvature (d2B/dH2). The degree to which Barkhausen jumps coincide with loop curvature is a measure of noise that accompanies fluxgate signal. B–H loops with significant curvature beyond the open hysteresis loop may be used to advantage to acquire fluxgate signal with reduced noise.

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Chen, Xin, Xiaoyu Liu, Yongxin Shan, Ying Zhang, Qiang Hu, Jun Li, Yuan Zhou, and Shiqi Lan. "Z-domain model procedure for heterodyne digital optical phase-locked loop." Optik 241 (September 2021): 167173. http://dx.doi.org/10.1016/j.ijleo.2021.167173.

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Hodges, Greg, and Tianyou Chen. "Geobandwidth: comparing time domain electromagnetic waveforms with a wire loop model." Exploration Geophysics 46, no. 1 (March 2015): 58–63. http://dx.doi.org/10.1071/eg14032.

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Stolz, Robert, Shaheen Sulthana, Stella R. Hartono, Maika Malig, Craig J. Benham, and Frederic Chedin. "Interplay between DNA sequence and negative superhelicity drives R-loop structures." Proceedings of the National Academy of Sciences 116, no. 13 (March 8, 2019): 6260–69. http://dx.doi.org/10.1073/pnas.1819476116.

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R-loops are abundant three-stranded nucleic-acid structures that formin cisduring transcription. Experimental evidence suggests that R-loop formation is affected by DNA sequence and topology. However, the exact manner by which these factors interact to determine R-loop susceptibility is unclear. To investigate this, we developed a statistical mechanical equilibrium model of R-loop formation in superhelical DNA. In this model, the energy involved in forming an R-loop includes four terms—junctional and base-pairing energies and energies associated with superhelicity and with the torsional winding of the displaced DNA single strand around the RNA:DNA hybrid. This model shows that the significant energy barrier imposed by the formation of junctions can be overcome in two ways. First, base-pairing energy can favor RNA:DNA over DNA:DNA duplexes in favorable sequences. Second, R-loops, by absorbing negative superhelicity, partially or fully relax the rest of the DNA domain, thereby returning it to a lower energy state. In vitro transcription assays confirmed that R-loops cause plasmid relaxation and that negative superhelicity is required for R-loops to form, even in a favorable region. Single-molecule R-loop footprinting following in vitro transcription showed a strong agreement between theoretical predictions and experimental mapping of stable R-loop positions and further revealed the impact of DNA topology on the R-loop distribution landscape. Our results clarify the interplay between base sequence and DNA superhelicity in controlling R-loop stability. They also reveal R-loops as powerful and reversible topology sinks that cells may use to nonenzymatically relieve superhelical stress during transcription.

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30

BUCHBINDER, I. L., and A. YU. PETROV. "ON QUANTUM MODEL OF SUPERGRAVITY COMPENSATOR." Modern Physics Letters A 11, no. 26 (August 30, 1996): 2159–69. http://dx.doi.org/10.1142/s0217732396002149.

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A new N=1 superfield model in D=4 flat superspace is suggested. This model describes dynamics of chiral compensator and can be treated as a low-energy limit of D=4, N=1 quantum superfield supergravity. Renormalization structure of this model is studied and one-loop counterterms are calculated. It is shown that the theory is infrared-free. An effective action for the model under consideration is investigated in the infrared domain. The lower contributions to the one-loop effective action are computed in explicit form.

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31

Narod, B. B. "The origin of noise and magnetic hysteresis in crystalline permalloy ring-core fluxgate sensors." Geoscientific Instrumentation, Methods and Data Systems 3, no. 2 (September 29, 2014): 201–10. http://dx.doi.org/10.5194/gi-3-201-2014.

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Abstract. Developed in the 1960s for use in high-performance ring-core fluxgate sensors, 6–81.3 Mo permalloy remains the state of the art for permalloy-cored fluxgate magnetometers. The magnetic properties of 6–81.3, namely magnetocrystalline and magnetoelastic anisotropies and saturation induction, are all optimum in the Fe–Ni–Mo system. In such polycrystalline permalloy fluxgate sensors, a single phenomenon may cause both fluxgate noise and magnetic hysteresis; explain Barkhausen jumps, remanence and coercivity; and avoid domain denucleation. This phenomenon, domain wall reconnection, is presented as part of a theoretical model. In the unmagnetized state a coarse-grain high-quality permalloy foil ideally forms stripe domains, which present at the free surface as parallel, uniformly spaced domain walls that cross the entire thickness of the foil. Leakage flux "in" and "out" of alternating domains is a requirement of the random orientation, grain by grain, of magnetic easy axes' angles with respect to the foil free surface. Its magnetostatic energy together with domain wall energy determines an energy budget to be minimized. Throughout the magnetization cycle the free-surface domain pattern remains essentially unchanged, due to the magnetostatic energy cost such a change would elicit. Thus domain walls are "pinned" to free surfaces. Driven to saturation, domain walls first bulge then reconnect via Barkhausen jumps to form a new domain configuration that I have called "channel domains", which are attached to free surfaces. The approach to saturation now continues as reversible channel domain compression. Driving the permalloy deeper into saturation compresses the channel domains to arbitrarily small thickness, but will not cause them to denucleate. Returning from saturation the channel domain structure will survive through zero H, thus explaining remanence. The Barkhausen jumps, being irreversible exothermic events, are sources of fluxgate noise powered by the energy available from domain wall reconnection. A simplified domain energy model can then provide a predictive relation between ring-core magnetic properties and fluxgate sensor noise power. Four properties are predicted to affect noise power, two of which are well known: saturation total magnetic flux density and magnetic anisotropy. The two additional properties are easy axes alignment and foil thickness. Flux density and magnetic anisotropy are primary magnetic properties determined by an alloy's chemistry and crystalline lattice properties. Easy axes alignment and foil thickness are secondary, geometrical properties related to an alloy's polycrystalline fabric and manufacture. Improvements to fluxgate noise performance can in principle be achieved by optimizing any of these four properties in such a way as to minimize magnetostatic energy. Fluxgate signal power is proportional to B − H loop curvature [d2B/dH2]. The degree to which Barkhausen jumps coincide with loop curvature is a measure of noise that accompanies the fluxgate signal. B − H loops with significant curvature beyond the open hysteresis loop may be used to advantage to acquire the fluxgate signal with reduced noise.

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32

Aguirre, L. A. "Robust Reference Models for Delayed Systems." Proceedings of the Institution of Mechanical Engineers, Part I: Journal of Systems and Control Engineering 208, no. 3 (August 1994): 197–99. http://dx.doi.org/10.1243/pime_proc_1994_208_328_02.

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This note is concerned with the design of open-loop reference models which lead to robust closed-loop control systems. A simple criterion is used to find the reference models in the frequency domain. The search is greatly facilitated by considering low-order reference models which are appropriate in approximate model matching problems. Numerical examples are provided.

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Baile, Matthew G., Evan L. Guiney, Ethan J. Sanford, Jason A. MacGurn, Marcus B. Smolka, and Scott D. Emr. "Activity of a ubiquitin ligase adaptor is regulated by disordered insertions in its arrestin domain." Molecular Biology of the Cell 30, no. 25 (December 1, 2019): 3057–72. http://dx.doi.org/10.1091/mbc.e19-08-0451.

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The protein composition of the plasma membrane is rapidly remodeled in response to changes in nutrient availability or cellular stress. This occurs, in part, through the selective ubiquitylation and endocytosis of plasma membrane proteins, which in the yeast Saccharomyces cerevisiae is mediated by the HECT E3 ubiquitin ligase Rsp5 and arrestin-related trafficking (ART) adaptors. Here, we provide evidence that the ART protein family members are composed of an arrestin fold with interspersed disordered loops. Using Art1 as a model, we show that these loop and tail regions, while not strictly required for function, regulate its activity through two separate mechanisms. Disruption of one loop mediates Art1 substrate specificity. Other loops are subjected to phosphorylation in a manner dependent on the Pho85 cyclins Clg1 and Pho80. Phosphorylation of the loops controls Art1’s localization to the plasma membrane, which promotes cargo ubiquitylation and endocytosis, demonstrating a mechanism through which Art1 activity is regulated.

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34

Das, Chinmaya Kumar, Umasankar Nayak, Preetinanda Pati, Mihir Ranjan Mohanty, Sujata Das, Parshuram Sial, Bhagban Kabat, and S. C. Swain. "Deciphering the Molecular Architecture of a Candidate R-gene (BjuWRR1) Product Mediating White Rust Resistance in Brassica juncea." International Journal of Bio-resource and Stress Management 12, no. 5 (August 31, 2021): 393–401. http://dx.doi.org/10.23910/1.2021.2205a.

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In this investigation, a three-dimensional model of a R-gene encoded product BjuWRR1 which is known to play a role in white rust resistance in Brassica juncea was developed to synthesize innovative ways for evolving white rust resistant cultivars. The model was built from the amino acid sequence of BjuWRR1 using structural template information of a disease resistance protein (RPP13-like protein 4 of Arabidopsis thaliana) with the help of homology-based modelling approach. Built models were validated for their stereochemical parameters and structural descriptors using Ramachandran plot analysis, protein structure analysis and ERRAT analysis. Structural analysis of BjuWRR1 model revealed that it is composed of three distinct domains namely a coiled-coil domain, a central NB-ARC nucleotide binding domain and a hypervariable leucine-rich repeat domain. Further, canonical conserved motifs such as P-loop, Kinase2-motif and HD-motif were found in the NB-ARC domain. The built model would help in understanding the molecular basis of plant-immunity against white rust pathogen by understanding the significance of inter-domain interactions in BuWRR1 in triggering the activation of downstream defense response against the white rust pathogen by promoting oligomerization of coiled-coil domains through stabilized hydrophobic interactions and interaction with NB-ARC domain. Presence of patches of charged residues in each domain of BjuWRR1 indicated their possible role in intra-molecular interaction with other domains. Therefore, this model can help in designing functional genomic studies to understand the role of intra-molecular interaction in BjuWRR1 to mediate resistance against white rust pathogen.

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35

Jo, Seri, Hwa Young Kim, Dong Hae Shin, and Mi-Sun Kim. "Dimerization Tendency of 3CLpros of Human Coronaviruses Based on the X-ray Crystal Structure of the Catalytic Domain of SARS-CoV-2 3CLpro." International Journal of Molecular Sciences 23, no. 9 (May 9, 2022): 5268. http://dx.doi.org/10.3390/ijms23095268.

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3CLpro of SARS-CoV-2 is a promising target for developing anti-COVID19 agents. In order to evaluate the catalytic activity of 3CLpros according to the presence or absence of the dimerization domain, two forms had been purified and tested. Enzyme kinetic studies with a FRET method revealed that the catalytic domain alone presents enzymatic activity, despite it being approximately 8.6 times less than that in the full domain. The catalytic domain was crystallized and its X-ray crystal structure has been determined to 2.3 Å resolution. There are four protomers in the asymmetric unit. Intriguingly, they were packed as a dimer though the dimerization domain was absent. The RMSD of superimposed two catalytic domains was 0.190 for 182 Cα atoms. A part of the long hinge loop (LH-loop) from Gln189 to Asp197 was not built in the model due to its flexibility. The crystal structure indicates that the decreased proteolytic activity of the catalytic domain was due to the incomplete construction of the substrate binding part built by the LH-loop. A structural survey with other 3CLpros showed that SARS-CoV families do not have interactions between DM-loop due to the conformational difference at the last turn of helix α7 compared with others. Therefore, we can conclude that the monomeric form contains nascent enzyme activity and that its efficiency increases by dimerization. This new insight may contribute to understanding the behavior of SARS-CoV-2 3CLpro and thus be useful in developing anti-COVID-19 agents.

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36

KAWAGUCHI, Sota, and Manabu KOSAKA. "Data-Driven Model Matching of Open Loop Transfer Function in Frequency Domain." Proceedings of Mechanical Engineering Congress, Japan 2020 (2020): J12107. http://dx.doi.org/10.1299/jsmemecj.2020.j12107.

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37

Alcalde, M. Aparicio, G. Flores Hidalgo, and N. F. Svaiter. "The two-loop massless (λ∕4!)φ4 model in nontranslational invariant domain." Journal of Mathematical Physics 47, no. 5 (May 2006): 052303. http://dx.doi.org/10.1063/1.2194632.

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38

Herbst, Gernot. "A Building-Block Approach to State-Space Modeling of DC-DC Converter Systems." J 2, no. 3 (July 8, 2019): 247–67. http://dx.doi.org/10.3390/j2030018.

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Small-signal models of DC-DC converters are often based on a state-space averaging approach, from which both control-oriented and other frequency-domain characteristics, such as input or output impedance, can be derived. Updating these models when extending the converter by filters or non-trivial loads, or adding control loops, can become a tedious task, however. To simplify this potentially error-prone process, a modular modeling approach is being proposed in this article. It consists of small state-space models for certain building blocks of a converter system on the one hand, and standardized operations for connecting these subsystem models to an overall converter system model on the other hand. The resulting state-space system model builds upon a two-port converter description and allows the extraction of control-oriented and impedance characteristics at any modeling stage, be it open loop or closed loop, single converter or series connections of converters. The ease of creating more complex models enabled by the proposed approach is also demonstrated with examples comprising multiple control loops or cascaded converters.

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39

Sanborn, Adrian L., Suhas S. P. Rao, Su-Chen Huang, Neva C. Durand, Miriam H. Huntley, Andrew I. Jewett, Ivan D. Bochkov, et al. "Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes." Proceedings of the National Academy of Sciences 112, no. 47 (October 23, 2015): E6456—E6465. http://dx.doi.org/10.1073/pnas.1518552112.

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We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic “tension globule.” In the other, CCCTC-binding factor (CTCF) and cohesin act together to extrude unknotted loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops. However, the extrusion model explains a far wider array of observations, such as why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loops in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.

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Valera Sifontes, Rimary, Hédison Kiuity Sato, and Zoukaneri Ibrahim Moumoni. "Relief geometric effects on frequency-domain electromagnetic data." GEOPHYSICS 81, no. 5 (September 2016): E287—E296. http://dx.doi.org/10.1190/geo2015-0344.1.

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A perpendicular transmitter-receiver coils arrangement used in the frequency-domain electromagnetic survey can have deviations in relation to its standard geometric definition due to the relief geometry of the surveyed area when combined with large transmitter-receiver distance and large transmitter loop size. This happens because the local relief characteristics along the transmitter loop wire laid on the ground can deviate the equivalent magnetic moment axis from the vertical, and the global characteristics locate the transmitter and receiver positions at different elevations. A study about that is carried on here substituting the rugged relief by an inclined plane. We have developed a new formulation for the [Formula: see text]-layered model that allowed us to investigate the relief geometry effects on FDEM data but restricting the analysis to the two-layer earth model, considering three cases of transmitter-receiver situations controlled by the relief conditions. The curves representing the Argand diagram and the apparent polarization parameter as a function of the apparent induction number were obtained for each relief model. Such procedures resulted to be very useful to demonstrate their behavior departing from those curves obtained for an inclined and a horizontal ground. These results show that small deviations in the verticality of the transmitter loop axis or in the horizontality of the surficial plane causes significant deviations, even for angles as small as 1°.

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Tiwari, A. K., S. P. Maurya, and N. P. Singh. "TEM Response of a Large Loop Source over the Multilayer Earth Models." International Journal of Geophysics 2018 (2018): 1–7. http://dx.doi.org/10.1155/2018/9891548.

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The general expression of TEM response of large loop source over the layered earth models is not available in the literature for arbitrary source-receiver positions, except for the case of central loop and coincident loop configurations over the homogeneous earth model. In the present study, an attempt is made to present the TEM response of a large loop source over the layered earth model for arbitrary receiver positions. The frequency domain responses of large loop source over the layer earth model for arbitrary receiver positions are converted into the impulse (time derivative of magnetic field) TEM response using Fourier cosine or sine transform. These impulse TEM responses in turn are converted into voltage responses for arbitrary receiver positions, namely, central loop, arbitrary in-loop, and offset-loop TEM responses over the layered earth models. For checking the accuracy of the method, results are compared with the results obtained using analytical expression over a homogeneous earth model. The complete matching of both of the results suggests that the present computational technique is capable of computing TEM response of large loop source over the homogeneous earth model with high accuracy. Thereafter, the technique is applied for computation of TEM response of a large loop source over the layered earth (2-layer, 3-layer, and 4-layer) models for the central loop, in-loop, and offset-loop configurations and the results are presented in voltage decay form. The results depict their characteristic variations. These results would be useful for modeling and inversion of large loop TEM data over the layer earth models for all the possible configurations resulting from a large loop source.

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Li, Rui Rui, Wei Dong Yang, and Zhi Hao Yu. "Frequency and Amplitude Dependent Dynamic Model of Rotor Elastomeric Damper with Refined Nonlinear Stiffness." Applied Mechanics and Materials 275-277 (January 2013): 888–93. http://dx.doi.org/10.4028/www.scientific.net/amm.275-277.888.

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Elastomeric damper is a very important component for helicopter rotor system; its dynamic property has strong nonlinear behavior characterized by complex hysteresis loops, and dependence on excitation frequency, amplitude and temperature. Based on internal variables theory, combined with the nonlinear spring model, a time domain nonlinear dynamic model of elastomeric damper used for helicopter rotor load prediction is presented. The model was characterized by using the genetic algorithm, the hysteresis loop of elastomeric dampers made of different elastomeric materials under several excitation frequencies and strain amplitudes was calculated with this model and compared with experimental data. It is shown that the presented model can predict the hysteresis loop of the elastomeric dampers with little relative errors, and the model is able to catch the variation of dynamic stiffness. Therefore, the presented method can be used for helicopter rotor load prediction and aeroelastic analysis.

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Weinstein, Ari, and Michael Littman. "Open-Loop Planning in Large-Scale Stochastic Domains." Proceedings of the AAAI Conference on Artificial Intelligence 27, no. 1 (June 29, 2013): 1436–42. http://dx.doi.org/10.1609/aaai.v27i1.8547.

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We focus on effective sample-based planning in the face of underactuation, high-dimensionality, drift, discrete system changes, and stochasticity. These are hallmark challenges for important problems, such as humanoid locomotion. In order to ensure broad applicability, we assume domain expertise is minimal and limited to a generative model. In order to make the method responsive, computational costs that scale linearly with the amount of samples taken from the generative model are required. We bring to bear a concrete method that satisfies all these requirements; it is a receding-horizon open-loop planner that employs cross-entropy optimization for policy construction. In simulation, we empirically demonstrate near-optimal decisions in a small domain and effective locomotion in several challenging humanoid control tasks.

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Koide, Hiroki, Noriyuki Kodera, Shveta Bisht, Shoji Takada, and Tsuyoshi Terakawa. "Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy." PLOS Computational Biology 17, no. 7 (July 30, 2021): e1009265. http://dx.doi.org/10.1371/journal.pcbi.1009265.

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The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain contacts dsDNA has remained unknown. Here, we conducted atomic force microscopy imaging of the budding yeast condensin holo-complex and used this data as basis for coarse-grained molecular dynamics simulations to model the hinge structure in a transient open conformation. We then simulated the dsDNA binding to open and closed hinge conformations, predicting that dsDNA binds to the outside surface when closed and to the outside and inside surfaces when open. Our simulations also suggested that the hinge can close around dsDNA bound to the inside surface. Based on these simulation results, we speculate that the conformational change of the hinge domain might be essential for the dsDNA binding regulation and play roles in condensin-mediated DNA-loop extrusion.

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Xu, Shuning, Lu Tang, and Junhao Yang. "Time-domain modelling and performance research of millimeter-wave all-digital phase-locked loop." Journal of Physics: Conference Series 2245, no. 1 (April 1, 2022): 012018. http://dx.doi.org/10.1088/1742-6596/2245/1/012018.

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Abstract In this paper, a modified time-domain model of millimeter-wave all-digital phase-locked loop (ADPLL) is implemented. In order to reflect the true behaviour of ADPLL, a quantified output digitally controlled-oscillator (DCO) with time domain jitter is proposed. In this ADPLL time-domain model, the DCO model can only output discrete frequency points to imitate the quantization effect of true DCO, and the overlap of different level tuning band is added into this model to imitate the true situation. In addition, the DCO time domain jitter and wander are also added into this model by using the Box-Muller method. Finally, a period estimation method is used to calculate the phase power spectrum density of the output signal, and then the phase noise is obtained through subsequent processing.

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Li, S. C., and A. Nassirharand. "Non-linear proportional–integral–derivative synthesis for unstable non-linear systems using describing function inversion with experimental verification." Proceedings of the Institution of Mechanical Engineers, Part I: Journal of Systems and Control Engineering 226, no. 2 (August 25, 2011): 145–53. http://dx.doi.org/10.1177/0959651811417767.

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This paper demonstrates a new non-linear proportional–integral–derivative (PID) controller synthesis approach using a describing function inversion technique for unstable systems where a mathematical model may not be available. The approach is applied to an inverted pendulum experimental set-up whose dynamic behaviour is very sensitive to the amplitude level of excitation. The procedure involves stabilization of the unstable system followed by generation of the describing function models of the stabilized closed-loop system. Then, the corresponding unstable open-loop frequency domain models at various operating regimes are extracted. A controller at nominal conditions is designed, followed by obtaining the corresponding desired open-loop frequency domain model. A set of controllers that force the open-loop behaviour of the system mimic, which is desired at various operating regimes, is designed by optimization. Finally, the controller gains are inverted using a describing function inversion technique followed by experimental verification. The non-linear PID design is compared with two other alternative designs. The experimental results indicate that the proposed approach is a viable and effective non-linear controller synthesis technique for use with unstable non-linear systems.

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47

Borot, G., J. Bouttier, and E. Guitter. "Loop models on random maps via nested loops: the case of domain symmetry breaking and application to the Potts model." Journal of Physics A: Mathematical and Theoretical 45, no. 49 (November 27, 2012): 494017. http://dx.doi.org/10.1088/1751-8113/45/49/494017.

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Walshe, James L., Rezwan Siddiquee, Karishma Patel, and Sandro F. Ataide. "Structural characterization of the ANTAR antiterminator domain bound to RNA." Nucleic Acids Research 50, no. 5 (February 12, 2022): 2889–904. http://dx.doi.org/10.1093/nar/gkac074.

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Abstract Regulated transcription termination provides an efficient and responsive means to control gene expression. In bacteria, rho-independent termination occurs through the formation of an intrinsic RNA terminator loop, which disrupts the RNA polymerase elongation complex, resulting in its dissociation from the DNA template. Bacteria have a number of pathways for overriding termination, one of which is the formation of mutually exclusive RNA motifs. ANTAR domains are a class of antiterminator that bind and stabilize dual hexaloop RNA motifs within the nascent RNA chain to prevent terminator loop formation. We have determined the structures of the dimeric ANTAR domain protein EutV, from Enterococcus faecialis, in the absence of and in complex with the dual hexaloop RNA target. The structures illustrate conformational changes that occur upon RNA binding and reveal that the molecular interactions between the ANTAR domains and RNA are restricted to a single hexaloop of the motif. An ANTAR domain dimer must contact each hexaloop of the dual hexaloop motif individually to prevent termination in eubacteria. Our findings thereby redefine the minimal ANTAR domain binding motif to a single hexaloop and revise the current model for ANTAR-mediated antitermination. These insights will inform and facilitate the discovery of novel ANTAR domain RNA targets.

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Lu, Luo, and Yu-Yueh Chang. "An integrative model of work/family interface for Chinese employees." Career Development International 19, no. 2 (May 6, 2014): 162–82. http://dx.doi.org/10.1108/cdi-09-2013-0110.

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Purpose – The purpose of this paper is to examine the mediating roles of four aspects of work and family interface (WFI: work-to-family conflict, WFC; family-to-work conflict, FWC; work-to-family enrichment, WFE; and family-to-work enrichment, FWE) in a Chinese context in Taiwan. Included in the integral model are demands and resources from the work and family domains as antecedents, and role satisfaction and burnout as consequences. Design/methodology/approach – Structured questionnaires were used to collect data from 499 full-time working Chinese parents in Taiwan. Findings – Structural equation modeling results showed that antecedents had cross-domain and within-domain effects on all aspects of the WFI; and conflict and enrichment also had cross-domain and within-domain effects on job satisfaction and family satisfaction, while influences from the work domain (WFC and WFE) had a significant impact on burnout. Overall, the partial mediation model was supported, showing that antecedent variables having both indirect (through the WFI variables) as well as direct relationships with the outcome variables. Originality/value – This is the first study testing a comprehensive model of the whole loop of antecedents-WFI-consequences with a non-Western sample. One unique contribution of the study is that the authors extended Western-based resources theories to Chinese employees, confirming that all four aspects of the WFI are important mediators linking up antecedents with consequences from both the work and family domains. Basing upon the findings, the authors suggests that both managers and employees should endeavor to break the destructive flow of conflict→dissatisfaction/burnout and to initiate the constructive flow of enrichment→satisfaction/free of burnout, by considering not only demands but also resources from both the work and family domains.

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Marcsa, Daniel, and Miklós Kuczmann. "Closed loop voltage control of a solenoid using parallel finite element method." COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering 35, no. 4 (July 4, 2016): 1439–49. http://dx.doi.org/10.1108/compel-09-2015-0339.

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Purpose – The purpose of this paper is to present the importance of model accuracy in closed loop control by the help of parallel finite element model of a voltage-fed solenoid with iron core. Design/methodology/approach – The axisymmetric formulation of the domain decomposition-based circuit-coupled finite element method (FEM) is embedded in a closed loop control system. The control parameters for the proportional-integral (PI) controller were estimated using the step response of the analytical, static and dynamic model of the solenoid. The controller measures the error of the output of the model after each time step and controls the applied voltage to reach the steady state as fast as possible. Findings – The results of the closed loop system simulation show why the model accuracy is important in the stage of the controller design. The FEM offers higher accuracy that the analytic model attained with magnetic circuit theory, because the inductance and resistance variation already take into account in the numerical calculation. Furthermore, parallel FEM incorporating domain decomposition to reduce the increased computation time. Originality/value – A closed loop control with PI controllers is applied for a voltage driven finite element model. The high computation time of the numerical model in the control loop is decreased by the finite element tearing and interconnecting method with direct and iterative solver.

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Journal articles on the topic 'Loop domain model'

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