• Journal of the Korean Magnetic Resonance Society
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• v.26 no.1
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• pp.1-9
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• 2022

There are two distinct approaches to improving the quality of protein NMR structures during refinement: all-atom force fields and accumulated knowledge-assisted methods that include Rosetta. Mao et al. reported that, for 40 proteins, Rosetta increased the accuracies of their NMR-determined structures with respect to the X-ray crystal structures (Mao et al., J. Am. Chem. Soc. 136, 1893 (2014)). In this study, we calculated 32 structures of those studied by Mao et al. using all-atom force field and implicit solvent model, and we compared the results with those obtained from Rosetta. For a single protein, using only the experimental NOE-derived distances and backbone torsion angle restraints, 20 of the lowest energy structures were extracted as an ensemble from 100 generated structures. Restrained simulated annealing by molecular dynamics simulation searched conformational spaces with a total time step of 1-ns. The use of GPU-accelerated AMBER code allowed the calculations to be completed in hours using a single GPU computer-even for proteins larger than 20 kDa. Remarkably, statistical analyses indicated that the structures determined in this way showed overall higher accuracies to their X-ray structures compared to those refined by Rosetta (p-value < 0.01). Our data demonstrate the capability of sophisticated atomistic force fields in refining NMR structures, particularly when they are coupled with the latest GPU-based calculations. The straightforwardness of the protocol allows its use to be extended to all NMR structures.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.10 no.5
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• pp.2081-2101
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• 2016

Successive interference cancellation (SIC) is considered to be a promising technique to mitigate multi-user interference and achieve concurrent uplink transmissions, but the optimal power allocation (PA) issue for SIC users is not well addressed. In this article, we focus on the optimization of the PA ratio of users on an SIC channel and analytically obtain the optimal PA ratio with regard to the signal-to-interference-plus-noise ratio (SINR) threshold for successful demodulation and the sustainable demodulation error rate. Then, we design an efficient resource allocation (RA) scheme using the obtained optimal PA ratio. Finally, we compare the proposal with the near-optimum RA obtained by a simulated annealing search and the RA scheme with random PA. Simulation results show that our proposal achieves a performance close to the near-optimum and much higher performance than the random scheme in terms of total utility and Jain's fairness index. To demonstrate the applicability of our proposal, we also simulate the proposal in various network paradigms, including wireless local area network, body area network, and vehicular ad hoc network.

• International Journal of Computer Science & Network Security
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• v.21 no.3
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• pp.304-310
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• 2021

The paper presents problems of optimization of the synthesis of embedded systems, in particular Pareto optimization. The model of such a system for its design for high-level of abstract is based on the classic approach known from the theory of task scheduling, but it is significantly extended, among others, by the characteristics of tasks and resources as well as additional criteria of optimal system in scope structure and operation. The metaheuristic algorithm operating according to this model introduces a new approach to system synthesis, in which parallelism of task scheduling and resources partition is applied. An algorithm based on a genetic approach with simulated annealing and Boltzmann tournaments, avoids local minima and generates optimized solutions. Such a synthesis is based on the implementation of task scheduling, resources identification and partition, allocation of tasks and resources and ultimately on the optimization of the designed system in accordance with the optimization criteria regarding cost of implementation, execution speed of processes and energy consumption by the system during operation. This paper presents examples and results for multi-criteria optimization, based on calculations for specifying non-dominated solutions and indicating a subset of Pareto solutions in the space of all solutions.

• Journal of the Korea Institute of Military Science and Technology
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• v.26 no.5
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• pp.400-408
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• 2023

The tracking accuracy of buoy-based LBL(Long Base Line) systems can be significantly influenced by sea environmental conditions. Particularly, the position of buoys that may have drifted due to sea currents. Therefore it is necessary to predict and optimize the drifted-buoy positions in the deploying step. This research introduces a free-drift simulation model using ocean data from the European CMEMS. The simulation model's predictions are validated by comparing them to actual sea buoy drift tracks, showing a substantial match in averaged drift speed and direction. Using this drift model, we optimize the initial buoy layout and compare the tracking performance between the center hexagonal layout and close track layout. Our results verify that the optimized layout achieves lower tracking errors compared to the other two layout.

• Proceedings of the Computational Structural Engineering Institute Conference
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• 2008.04a
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• pp.416-421
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• 2008

A Metropolis genetic algorithm (MGA) is a newly-developed hybrid algorithm combining simple genetic algorithm (SGA) and simulated annealing (SA). In the algorithm, favorable features of Metropolis criterion of SA are incorporated in the reproduction operations of SGA. This way, MGA alleviates the disadvantages of finding imprecise solution in SGA and time-consuming computation in SA. It has been successfully applied and the efficiency has been verified for the practical structural design optimization. However, applicability of MGA for the wider range of problems should be rigorously proved through the solution of mathematical optimization problems. Thus, performances of MGA for the typical mathematical problems are investigated and compared with those of conventional algorithms such as SGA, micro genetic algorithm (${\mu}GA$), and SA. And, for better application of MGA, the effects of acceptance level are also presented. From numerical Study, it is again verified that MGA is more efficient and robust than SA, SGA and ${\mu}GA$ in the solution of mathematical optimization problems having various features.

• Journal of Korean Institute of Industrial Engineers
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• v.34 no.1
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• pp.49-56
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• 2008

Reliability has been considered as an important design measure in various industrial systems. We discuss a reliability optimization problem with component choices (ROP-CC) subject to a budget constraint. This problem has been known as a NP-hard problem in the reliability design fields. Several researchers have been working to find the optimal solution through different heuristic methods. In this paper, we describe our development of simulated annealing (SA) and tabu search (TS) algorithms and a reoptimization procedure of the two algorithms for solving the problem. Experimental results for some examples are shown to evaluate the performance of these methods. We compare the results with the solutions of a previous study which used ant system (AS) and the global optimal solution of each example obtained through an optimization package, CPLEX 9.1. The computational results indicate that the developed algorithms outperform the previous results.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.349-353
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• 2007

The main functions of excavator are mainly carried out by excavator attachments such as arm and boom. These components should be designed to be light as well as durable enough because their effects on the whole structure are significant. In this paper, an optimization procedure for lightweight design considering fatigue strength for excavator attachments is presented. The weight of attachments and allowable fatigue stresses at critical areas are used as objective function and constraints, respectively, in which design variables are the thickness of the plates of attachments. The simulated annealing search method is adopted for a global optimization solution. Besides, the response surface method using the artificial neural network is used to simulate constraint function for the sake of practical fast calculation. Some example case of optimization is presented here for a sample excavator. This weight optimization is expected to contribute to a considerable improvement of fuel efficiency of excavator.

• Journal of the Korean Institute of Telematics and Electronics C
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• v.35C no.12
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• pp.23-30
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• 1998

We present a partial bus-invert coding scheme for system-level power optimization. In the proposed scheme, we select a sub-group of bus lines involved in bus encoding to avoid unnecessary inversion of bus lines not in the sub-group thereby reducing the total number of bus transitions. We propose a heuristic algorithm that selects the sub-group of bus lines for bus encoding. Experiments on benchmark examples indicate that the partial bus-invert coding reduces the total bus transitions by 62.6% on the average, compared to that of the unencoded patterns. We also compare the performance of the proposed heuristic algorithm with that of simulated annealing, which shows that it is highly efficient.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.11 no.9
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• pp.4438-4460
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• 2017

The Kernelized Correlation Filters (KCF) tracker has caused the extensive concern in recent years because of the high efficiency. Numerous improvements have been made successively. However, due to the abrupt motion between the consecutive image frames, these methods cannot track object well. To cope with the problem, we propose an extended KCF tracker based on swarm intelligence method. Unlike existing KCF-based trackers, we firstly introduce a swarm-based sampling method to KCF tracker and design a unified framework to track smooth or abrupt motion simultaneously. Secondly, we propose a global motion estimation method, where the exploration factor is constructed to search the whole state space so as to adapt abrupt motion. Finally, we give an adaptive threshold in light of confidence map, which ensures the accuracy of the motion estimation strategy. Extensive experimental results in both quantitative and qualitative measures demonstrate the effectiveness of our proposed method in tracking abrupt motion.

• Journal of the Korean Society of Marine Environment & Safety
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• v.1 no.2
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• pp.69-82
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• 1995

This study is concerned with developing a heuristic algorithm for solving a class of ninlinear integer programs(NLIP). Exact algrithm for solving a NLIP either may not exist, or may take an unrealistically large amount of computing time. This study develops a new heuristic, the Excursion Algorithm(EA), for solving a class of NLIP's. It turns out that excursions over a bounded feasible and/or infeasible region is effective in alleviation the risks of being trapped at a lical optimum. The developed EA is applied to the redundancy optimization problems for improving the system safety, and is compared with other existing heuristic methods. We also include simulated annealing(SA) method in the comparision experiment due to ist populatrity for solving complex combinatorial problems. Computational results indicate that the proposed EA performs consistently better than the other in terms of solution quality, with moderate increase in computing time. Therefore, the proposed EA is believed to be an attractive alternative to other heuristic methods.