• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.770-774
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• 2012

Protein loops are often involved in diverse biological functions, and some functional loops show conformational changes upon ligand binding. Since this conformational change is directly related to ligand binding pose and protein function, there have been numerous attempts to predict this change accurately. In this study, we show that it is plausible to obtain meaningful ensembles of loop conformations for flexible, ligand-binding protein loops efficiently by applying a loop modeling method. The loop modeling method employs triaxial loop closure algorithm for trial conformation generation and conformational space annealing for global energy optimization. When loop modeling was performed on the framework of ligand-free structure, loop structures within $3\AA$ RMSD from the crystal loop structure for the ligand-bound state were sampled in 4 out of 6 cases. This result is encouraging considering that no information on the ligand-bound state was used during the loop modeling process. We therefore expect that the present loop modeling method will be useful for future developments of flexible protein-ligand docking methods.

• Industrial Engineering and Management Systems
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• v.7 no.1
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• pp.78-89
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• 2008

The need for holistic modeling efforts for returns that capture the extended closed loop supply chain (CLSC) system at strategic as well as operational level has been clearly recognized by the industry and academia. Strategic decision-makers need comprehensive models that can guide them in efficient decision-making to increase the profitability of the entire forward and return chain. Therefore, determination of a near optimal design configuration, which includes the environmental, economical and technological capability factors, is important in strategic decision-making effort that affect the profitability of the closed loop supply chain. In this paper, we adopted an improved system dynamics methodology to tackle strategic issues that affect various performance measures, like market, time/cost, environment etc., for closed loop supply chains. After studying real life implementation issues in CLSC design, we presented guidelines for the PBM (Participative Business Modeling) methodology and presented its extension for the strategic dynamic system modeling of return chains. Finally, we demonstrated the measurement of operational performance by extending SD (system dynamic) application to closed loop supply chain management.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 1995.10a
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• pp.509-512
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• 1995

A new modeling incorporating the role of control arm is proposed for the Macpherson type suspension system. Vertical displacement of the sprung mass and angular displacement of the control arm are selected as main control variables in the new modeling. With the same values of suspension vehicle parameters the conventional modeling and the new modeling are compared in terms of open loop characteristics.

• 제어로봇시스템학회:학술대회논문집
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• 1992.10a
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• pp.747-753
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• 1992

The modeling and control design schemes are developed for maglev systems with a combined lift and guidance. First, bond graph techniques are applied for modeling these multi-energy domain systems more logically and systematically. And the stability loop via pole placement and the performance loop via loop-shaping LQ control are designed. The suggested controller satisfies the required characteristics of stability and performance simultaneously. Finally, the robustness of the synthesized maglev control system is evaluated for the variations of air gap and vehicle mass through computer simulation.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.63-74
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• 2014

Predicting protein loop structures is an important modeling problem since protein loops are often involved in diverse biological functions by participating in enzyme active sites, ligand binding sites, etc. However, loop structure prediction is difficult even when structures of homologous proteins are known due to large sequence and structure variability among loops of homologous proteins. Therefore, an ab initio approach is necessary to solve loop modeling problems. One of the difficulties in the development of ab initio loop modeling method is to derive an accurate scoring function that closely approximates the true free energy function. In particular, entropy as well as energy contribution have to be considered adequately for loops because loops tend to be flexible compared to other parts of protein. In this study, the contribution of conformational entropy is considered in scoring loop conformations by employing "colony energy" which was previously proposed to estimate the free energy for an ensemble of conformations. Loop conformations were generated by using two EDISON_Chem programs GalaxyFill and GalaxySC, and colony energy was designed for this sampling by tuning relevant parameters. On a test set of 40 loops, the accuracy of predicted loop structure improved on average by scoring with the colony energy compared to scoring by energy alone. In addition, high correlation between colony energy and deviation from the native structure suggested that more extensive sampling can further improve the prediction accuracy. In another test on 6 ligand-binding loops that show conformational changes by ligand binding, both ligand-free and ligand-bound states could be identified by using colony energy when no information on the ligand-bound conformation is used.

• BMB Reports
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• v.35 no.5
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• pp.498-507
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• 2002

A gene that encodes a thermostable protease, coined thermicin, has been isolated from Thermoanaerobacter yonseiensis that is expressed and characterized in E. coli.. In order to elucidate the molecular characteristics on thermostability of the enzyme, molecular modeling and mutagenesis technology were applied. In the modeling structure, the structural core, including the active site, was well conserved; whereas, the two loop regions were unique when compared to thermitase. The mutant enzyme with the small loop deleted (D190-I196), based on modeling structural information, showed identical enzyme activity. However, when the large loop was deleted (P233-P244), a little lower $K_m$ and even a lower kcat was found. This indicates that the large loop could influence catalytic activity. However, the unfolding temperature ($T_m$), which was determined by a differential-scanning calorimetry for the mutant enzyme deleted the small loop, was $96^{\circ}C$. This is $14^{\circ}C$ lower than that for the parent thermicin. These results suggest that the small loop may play a role in maintaining the proper folding of the enzyme at high temperatures, whereas the large loop might be related to catalysis.

• Journal of Power Electronics
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• v.17 no.2
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• pp.442-452
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• 2017

This paper deals with the input-output modeling of a vector controlled PMSM drive system and design of a simple multiple model adaptive control (MMAC) scheme with desired transient responses. We present a discrete-time modeling technique using closed-loop identification that can experimentally identify the equivalent models in the d-q coordinates. A bank of linear models for the equivalent plant of the current loop is first obtained by identifying them at several operating points of the current to account for nonlinearity. Based on these models, we suggest a simple q-axis MMAC combined with a fixed d-axis controller. After the current controller is designed, another equivalent model including the current controller in the speed control loop shall be similarly obtained, and then a fixed speed controller is synthesized. The proposed approach is demonstrated by experiments. The experimental set up consists of a surface mounted PMSM (5 KW, 220V, 8 poles) equipped with a flywheel load of 220kg and a digital controller using DSP (TMS320F28335).

• 제어로봇시스템학회:학술대회논문집
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• 1996.10b
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• pp.779-782
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• 1996

Repetitive control is a proposed control strategy in view of the internal model principle and achieves a high accuracy asymptotic tracking property by implementing a model that generates the periodic signals of period into the closed-loop system. Since the repetitive control system contains a periodic signal generator with positive feedback loop, which reduces the stability margin, in the overall closed-loop system, the stability of the closed-loop system should be considered as an important problem. In case that a real system has plant uncertainties which are not represented through modeling, the robust stability problem of the repetitive control system has not been considered sufficiently. In this paper, we propose the robust stability condition for the system with modeling uncertainty. The proposed robust stability condition will be obtained using the robust performance condition in the H$_{\infty}$ control. Moreover, by use of the proposed robust stability condition, we propose a procedure that designs a repetitive controller and a feedback controller simultaneously which can stabilize the overall closed-loop system robustly and which can also do the closedloop system without repetitive controller..

• Geophysics and Geophysical Exploration
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• v.10 no.4
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• pp.308-313
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• 2007

The small-loop electromagnetic technique has been used successfully for many geophysical qualitative investigations, particularly for shallow engineering and environmental surveys. Recently, various geophysical imaging methods based on numerical modeling and inversion have been tried in order to get more quantitative subsurface structure. However, conventional 2.5D small loop EM modeling takes a lot of time because responses should be calculated for several wave numbers and transformed into space domain. In this study, we developed a 2.5D HCP small loop EM modeling algorithm using extended Born approximation, which does not require transformation. Also, we checked its validity by comparison with other numerical results.

• The Transactions of the Korean Institute of Power Electronics
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• v.25 no.6
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• pp.442-450
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• 2020

A small-signal modeling approach for a three-level boost (TLB) converter and a design methodology for a double-loop controller are proposed in this study. Conventional modeling of TLB converters involves three state variables. Moreover, TLB converters have two operation modes depending on the duty ratio. Consequently, complex mathematical calculations are required for controller design. This study proposes a simple system modeling method that uses two state variables, unlike previous methods that require three state variables. Analysis shows that the transfer functions of the two operation modes can be expressed as identical equations. This condition means that the linear feedback controller can be applied to all operational ranges, that is, for full duty ratios. The design method for a double-loop controller using a PI controller is presented in step-by-step sequences. Simulation and experimental verifications are conducted to verify the effectiveness of the small-signal analysis and control system design.