• Applied Chemistry for Engineering
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• v.25 no.2
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• pp.147-151
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• 2014

In many polymer processing operations, the diffusion of small molecules in polymeric materials plays an important role. The fundamental physical property required to design and optimize processing operations is the mutual diffusion coefficient. To investigate the transport properties of polymer/solvent systems at infinite dilution, capillary column inverse gas chromatography (CCIGC) is often employed. In this study, diffusion and partition coefficients of cyclic solvents in styrene/butadiene/styrene (SBS) block copolymer were measured over a wide temperature range using the CCIGC technique.

• KSBB Journal
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• v.32 no.1
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• pp.29-34
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• 2017

The completion of the Human Genome Project that identified all 3 billion base pairs in the human genome can be seen as a step towards understanding the relay of information and intention within an organism, or in other words, the language of life. The faculty of human language, key to differentiating humans from other animate species, works for conveying information to others by mapping meaning to sound based on syntactic structures. This resemblance between life and language has not gone unnoticed; the literature on RNA transcription and translation research regularly uses linguistic metaphors and the biolinguistic perspective of language has also been studied. By examining the biological characteristics of language and the linguistic characteristics of life, this study aims to identify key mechanisms shared between the two systems in order to promote a stronger connection between them. It furthers this goal by pointing out two general messages to which these mechanisms aim, productivity and accuracy, and discovers what lesson these messages give to a human society geared for sustainability.

• International Journal of Control, Automation, and Systems
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• v.4 no.3
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• pp.382-393
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• 2006

Mechanical system dynamics plays an important role in the area of computational structural biology. Elastic network models (ENMs) for macromolecules (e.g., polymers, proteins, and nucleic acids such as DNA and RNA) have been developed to understand the relationship between their structure and biological function. For example. a protein, which is basically a folded polypeptide chain, can be simply modeled as a mass-spring system from the mechanical viewpoint. Since the conformational flexibility of a protein is dominantly subject to its chemical bond interactions (e.g., covalent bonds, salt bridges, and hydrogen bonds), these constraints can be modeled as linear spring connections between spatially proximal representatives in a variety of coarse-grained ENMs. Coarse-graining approaches enable one to simulate harmonic and anharmonic motions of large macromolecules in a PC, while all-atom based molecular dynamics (MD) simulation has been conventionally performed with an aid of supercomputer. A harmonic analysis of a macroscopic mechanical system, called normal mode analysis, has been adopted to analyze thermal fluctuations of a microscopic biological system around its equilibrium state. Furthermore, a structure-based system optimization, called elastic network interpolation, has been developed to predict nonlinear transition (or folding) pathways between two different functional states of a same macromolecule. The good agreement of simulation and experiment allows the employment of coarse-grained ENMs as a versatile tool for the study of macromolecular dynamics.

• Journal of the Korean Institute of Intelligent Systems
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• v.16 no.2
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• pp.222-227
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• 2006

Recently the research for Traveling Salesman Problem (TSP) using DNA computing with massive parallelism has been. However, there were difficulties in real biological experiments because the conventional method didn't reflect the precise characteristics of DNA when it express graph. Therefore, we need DNA sequence generation algorithm which can reflect DNA features and reduce biological experiment error. In this paper we proposed a DNA sequence generation algorithm that applied DNA coding method of evolution model to DNA computing. The algorithm was applied to TSP, and compared with a simple genetic algorithm. As a result, the algorithm could generate good sequences which minimize error and reduce the biologic experiment error rate.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.11 no.3
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• pp.971-977
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• 2010

A flood of biological data has caused many challenges in computing. Bioinformatics, the application of computational techniques to analyze the information associated with biomolecules on a large-scale, has now firmly established itself as an interdisciplinary subject in molecular biology, and encompasses a wide range of subject areas from structural biology, genomics, proteomics, systems biology, biostatistics to computer science. In this review, I provide an introduction and overview of the current state of bioinformatics. Looking at the types of biological information and databases that are commonly used, I also deals with some of bioinformatics application domains which are closely related to areas of computer science.

• Toxicological Research
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• v.30 no.3
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• pp.179-184
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• 2014

Xenobiotics causing a variety of toxicity in biological systems could be classified as two types, inorganic and organic chemicals. It is estimated that the organic xenobiotics are responsible for approximately 80~90% of chemical-induced toxicity in human population. In the class for toxicology, we have encountered some difficulties in explaining the mechanisms of toxicity caused especially by organic chemicals. Here, a simple flowchart was introduced for explaining the mechanism of toxicity caused by organic xenobiotics, as the central dogma of molecular biology. This flowchart, referred to as a central dogma, was described based on a view of various aspects as follows: direct-acting chemicals vs. indirect-acting chemicals, cytochrome P450-dependent vs. cytochrome P450-independent biotransformation, reactive intermediates, reactivation, toxicokinetics vs. toxicodynamics, and reversibility vs. irreversibility. Thus, the primary objective of this flowchart is to help better understanding of the organic xenobiotics-induced toxic mechanisms, providing a major pathway for toxicity occurring in biological systems.

• Molecules and Cells
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• v.42 no.2
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• pp.166-174
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• 2019

Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.

• Genomics & Informatics
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• v.6 no.4
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• pp.210-222
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• 2008

Due to the polygenic nature of cancer, it is believed that breast cancer is caused by the perturbation of multiple genes and their complex interactions, which contribute to the wide aspects of disease phenotypes. A systems biology approach for the identification of subnetworks of interconnected genes as functional modules is required to understand the complex nature of diseases such as breast cancer. In this study, we apply a 3-step strategy for the interpretation of microarray data, focusing on identifying significantly perturbed metabolic pathways rather than analyzing a large amount of overexpressed and underexpressed individual genes. The selected pathways are considered to be dysregulated functional modules that putatively contribute to the progression of disease. The subnetwork of protein-protein interactions for these dysregulated pathways are constructed for further detailed analysis. We evaluated the method by analyzing microarray datasets of breast cancer tissues; i.e., normal and invasive breast cancer tissues. Using the strategy of microarray analysis, we selected several significantly perturbed pathways that are implicated in the regulation of progression of breast cancers, including the extracellular matrix-receptor interaction pathway and the focal adhesion pathway. Moreover, these selected pathways include several known breast cancer-related genes. It is concluded from this study that the present strategy is capable of selecting interesting perturbed pathways that putatively play a role in the progression of breast cancer and provides an improved interpretability of networks of protein-protein interactions.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2000.11a
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• pp.452-455
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• 2000

There are increasingly important financial incentives and environmental consideration to improve the effluent quality of wastewater from domestic and industrial users. The activated sludge process is a widely used biological wastewater treatment process. The activated sludge process is complicated due to the many factors such as the variation of influent flowrate and concentration, the complexity of biological reactions and the various operation conditions. Nowadays, not only suspended solids and residual carbon, but also nitrogen and phosphorous concentration of the effluent water must be taken into account for the design and operation of wastewater treatment plants. Also, the effluent quality to be met are more stringent. Therefore, an intelligent control approach is required in order to successful biological nitrogen removal. In this paper, the strategies for dosage of extra carbon in the anoxic zone and DO concentration in the aerobic zone are presented and evaluated through the simulation using the denitrification layout of the IWA simulation benchmark implemented by Matlab$\^$/5.3/Simulink$\^$/3.0. The control strategy to achieve sufficient denitrification rates in an anoxic zone. Methanol is used as an external extra carbon source. The external extra carbon source is required for the nitrogen removal process because nitrogen and organic concentration are fluctuated in the influent flowrate. The dissolved oxygen is calculated by So concentration in the activated sludge model NO.1. The air flowrate of each aerobic reactor is intelligently controlled to achieve the predefined setpoints. Air flowrate is adjusted by the fuzzy logic controller that includes two inputs and one output. The objective function for the optimization procedure is designed to improve effluent quality and reduce the operating cost.

• Journal of The Korean Society of Agricultural Engineers
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• v.60 no.3
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• pp.135-148
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• 2018

Reservoir sedimentation is a major environmental issue, and various sediment load controls and plans have been proposed to secure clean and safe water resources. The objectives of this study were to estimate soil loss in the upper basins and predict sediment deposition in Ipjang reservoir using hydrologic and hydraulic model. To do so, SWAT (Soil and Water Assessment Tool) and EFDC (Environmental Fluid Dynamics Code) was used to estimate soil loss in two upper basins and to predict spatial distribution and amount of sediment deposition in the Ipjang reservoir, respectively. The hydrologic modeling results showed that annual average soil loss from the upper basins was 500 ton. The hydraulic modeling results demonstrated that sediment particles transported to the reservoir were mostly trapped in the vicinity of the reservoir inlet and then moved toward the bank over time. If long-term water quality monitoring and sediment survey are performed, this study can be used as a tool for predicting the dredging amount, dredging location and proper dredging cycle in the reservoir. The study findings are expected to be used as a basis to establish management solutions for sediment reduction.