• Journal of Biosystems Engineering
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• v.37 no.4
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• pp.258-264
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• 2012

Purpose: This review aims at introducing 3 modeling approaches classified into 3 categories based on the purpose (estimation or prediction), structure (linear or non-linear) and phase (steady-state or dynamic-state); 1) statistical approaches, 2) kinetic modeling and 3) mechanistic modeling. We hope that this review can be a useful guide in the model-based approach of calcium metabolism as well as illustrates an application of engineering tools in studying biosystems. Background: The meaning of biosystems has been expanded, including agricultural/food system as well as biological systems like genes, cells and metabolisms. This expansion has required a useful tool for assessing the biosystems and modeling has arisen as a method that satisfies the current inquiry. To suit for the flow of the era, examining the system which is a little bit far from the traditional biosystems may be interesting issue, which can enlarge our insights and provide new ideas for prospective biosystem-researches. Herein, calcium metabolic models reviewed as an example of application of modeling approaches into the biosystems. Review: Calcium is an essential nutrient widely involved in animal and human metabolism including bone mineralization and signaling pathways. For this reason, the calcium metabolic system has been studied in various research fields of academia and industries. To study calcium metabolism, model-based system analyses have been utilized according to the purpose, subject characteristics, metabolic sites of interest, and experimental design. Either individual metabolic pathways or a whole homeostasis has been modeled in a number of studies.

• Journal of Biosystems Engineering
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• v.43 no.1
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• pp.45-58
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• 2018

Background: Metabolic modeling has been an essential tool in metabolic reconstruction, which has dramatically advanced in the last decades as a part of systems biology. At present, the protocol for metabolic reconstruction has been systematically established, and it provides the basis for the analysis of complex systems, which has been limited in the past. Therefore, metabolic reconstruction can be adapted to analyze agricultural systems whose metabolic data has been accumulated recently. Purpose: The aim of this review is to suggest the suitability of metabolic modeling for understanding agricultural metabolic data and to encourage the potential use of this modeling in the field of agriculture. Review: We reviewed the procedure of metabolic reconstruction using computational modeling with applicable strategies and software tools. Additionally, we presented the initial attempts of metabolic reconstruction in the field of agriculture and proposed further applications.

• Journal of Biosystems Engineering
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• v.38 no.2
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• pp.129-137
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• 2013

Purpose: Modeling has been used for elucidating the mechanism of complex biosystems. In spite of importance and uniqueness of adolescent calcium (Ca) metabolism characterized by a threshold Ca intake, its regulatory mechanism has not been covered and even not proposed. Hence, this study aims at model-based proposing potential mechanisms regulating adolescent Ca metabolism. Methods: Two different hypothetic mechanisms were proposed. The main mechanism is conceived based on Ca-protein binding which induces renal Ca filtration, while additional mechanism assumed that active renal Ca re-absorption regulated Ca metabolism in adolescents. Mathematical models were developed to represent the proposed mechanism and simulated them whether they could produce adolescent Ca profiles in serum and urine. Results: Simulation showed that both mechanisms resulted in the unique behavior of Ca metabolism in adolescents. Based on the simulation insulin-like growth factor-1 (IGF-1) is suggested as a potential regulator because it is related to both growth, a remarkable characteristic of adolescence, and Ca metabolism including absorption and bone accretion. Then, descriptive modeling is employed to conceptualize the hypothesized mechanisms governing adolescent Ca metabolism. Conclusions: This study demonstrated that modeling is a powerful tool for elucidating an unknown mechanism by simulating potential regulatory mechanisms in adolescent Ca metabolism. It is expected that various analytic applications would be plausible in the study of biosystems, particularly with combination of experimental and modeling approaches.

• Korean Journal of Agricultural Science
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• v.43 no.2
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• pp.163-175
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• 2016

For the past decades, advances in computational devices have propelled mathematical modeling to become an effective tool for solving the black box of complex biological systems because of its prominent analytical power and comprehensive insight. Nevertheless, modeling is still limitedly used in the fields of agriculture and food which generally concentrate on producing experimental data rather than processing them. This study, hence, intends to introduce modeling in terms of its procedure types of structure, formulation, analyses, and software, with reviews of current notable studies from micro to macro scales so as to propose the modeling technique as a novel approach in discerning conundrums in agriculture and food systems. We expect this review to provide an eligible source for researchers who are willing to apply modeling techniques into the unexplored fields related to bio-systems that comprehensively include biology, nutrition, agriculture, food, animal science, and ecology.

• Journal of Biosystems Engineering
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• v.43 no.4
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• pp.410-419
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• 2018

Purpose: CLIMEX, a species distribution modeling tool, includes various types of parameters representing climatic conditions; the estimation of these parameters directly determines the model accuracy. In this study, we investigated the sensitivity of parameters for the climatic suitability calculated by CLIMEX for Metcalfa pruinosa in South Korea. Methods: We first changed 12 parameters and identified the three significant parameters that considerably affected the CLIMEX simulation response. Results: The result indicated that the simulation was highly sensitive to changes in lower optimal temperatures, lower soil moisture thresholds, and cold stress accumulation rate based on the sensitivity index, suggesting that these were the fundamental parameters to be used for fitting the simulation into the actual distribution. Conclusion: Sensitivity analysis is effective for estimating parameter values, and selecting the most important parameters for improving model accuracy.

• Food Engineering Progress
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• v.21 no.3
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• pp.233-241
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• 2017

Scaffolds of cell substrates are biophysical platforms for cell attachment, proliferation, and differentiation. They ultimately play a leading-edge role in the regeneration of tissues. Recent studies have shown the potential of bioactive scaffolds (i.e., osteo-inductive) through 3D printing. In this study, rice bran-derived biocomposite was fabricated for fused deposition modeling (FDM)-based 3D printing as a potential bone-graft analogue. Rice bran by-product was blended with poly caprolactone (PCL), a synthetic commercial biodegradable polymer. An extruder with extrusion process molding was adopted to manufacture the newly blended "green material." Processing conditions affected the performance of these blends. Bio-filament composite was characterized using field emission scanning electron microscopy (FE-SEM) and energy dispersive X-ray spectroscopy (EDX). Mechanical characterization of bio-filament composite was carried out to determine stress-strain and compressive strength. Biological behaviors of bio-filament composites were also investigated by assessing cell cytotoxicity and water contact angle. EDX results of bio-filament composites indicated the presence of organic compounds. These bio-filament composites were found to have higher tensile strength than conventional PCL filament. They exhibited positive response in cytotoxicity. Biological analysis revealed better compatibility of r-PCL with rice bran. Such rice bran blended bio-filament composite was found to have higher elongation and strength compared to control PCL.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.197-201
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• 2005

When we want to find out the regulatory relationships between genes from gene expression data, dimensionality is one of the big problem. In general, the size of search space in modeling the regulatory relationships grows in O(n$^2$) while the number of genes is increasing. However, hopefully it can be reduced to O(kn) with selected k by applying divide and conquer heuristics which depend on some assumptions about genetic network. In this paper, we approach the modeling problem in divide-and-conquer manner. We applied clustering to make the problem into small sub-problems, then hierarchical model process is applied to those small sub-problems.

• Journal of Biosystems Engineering
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• v.40 no.1
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• pp.78-88
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• 2015

Purpose: The objective of this study is to review researches regarding factors that potentially affect adolescent calcium (Ca) metabolism, and to suggest a potential modeling approach for optimizing gastrointestinal Ca absorption and peak bone mass. Background: Optimal gastrointestinal Ca absorption is a key to maximizing peak bone mass in adolescents. Urine Ca excretion in adolescents rises only after bone accretion is saturated, indicating that higher intestinal Ca absorption and bone retention is necessary to ensure maximum bone accretion. Hence, maximizing peak bone mass is possible by controlling the factors influencing gastrointestinal Ca absorption and bone accretion. However, a mechanism that explains the unique adolescent Ca metabolism has not yet been elucidated. Review: Dietary factors that enhance gastrointestinal Ca absorption may increase the available Ca pool usable for bone accretion, and a specific hormone may direct optimal Ca utilization to maximize peak bone mass. IGF-1 is an endocrine hormone whose levels peak during adolescence and increase fractional Ca absorption and bone Ca accretion. Prebiotics, generally obtained from dietary sources, have been reported to exert a beneficial effect on Ca absorption via microbiota activity. We selected and reviewed three candidates that could be used to propose a comprehensive Ca metabolic model for optimal Ca absorption and peak bone mass in adolescents. Modeling: Modeling has been used to investigate Ca metabolism and its regulators. Herein, we reviewed previous Ca modeling studies. Based on this review, we proposed a method for developing a comprehensive model that includes regulatory effectors of IGF-1 and prebiotics.

• Journal of Biosystems Engineering
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• v.37 no.1
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• pp.11-18
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• 2012

Purpose: Short-circuit current of a solar module that is widely used as a power source for wireless environmental sensors is proportional to solar radiation although there are a lot of factors affecting the short-circuit current. The objective of this study is to develop a model for estimating solar radiation for using the solar module as a power source and an irradiance sensor. Methods: An experiment system collected data on the short-circuit current and environmental factors (ambient temperature, cloud cover and solar radiation) during 65 days. Based on these data, two linear regression models and a non-linear regression model were developed and evaluated. Results: The best model was a linear regression model with short-circuit current, angle of incidence and cloud cover and its overall RMSE(Root Means Square Error) was 66.671 $W/m^2$. The other linear model (RMSE 69.038 $W/m^2$) was also acceptable when the cloud cover data is not available.

• Journal of Biosystems Engineering
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• v.37 no.6
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• pp.385-397
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• 2012

Purpose: Drying characteristics of sawdust was studied under batch mode using lab scale microwave dryer. The objective of this study was to investigate the effect of material load and microwave output power on drying characteristics of sawdust. Methods: Material load and microwave output power were varied from 23 to 186 g and 530 to 370 W respectively. Different kinetic models were tested to fit the drying rates of sawdust. Similarly, the activation energy was calculated by employing the Arrhenius equation. Results: The drying efficiency increased considerably, whereas the specific energy consumption significantly decreased with increase in material load and microwave output power. The cumulative energy efficiency increased by 9%, and the specific energy consumption decreased by 8% when the material load was increased from 23 to 186 g. The effective diffusivity increased with decrease in material load and increase in microwave output power. The previously published model gave the best fit for data points with $R^2$ and RMSE values of 0.999 and 0.01, respectively. Conclusions: The data obtained from this study could be used as a basis for modeling of large scale industrial microwave dryers for the pellet production.