• Journal of Korean Society for Atmospheric Environment
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• 제21권E3호
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• pp.75-85
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• 2005

A mathematical sensitivity analysis of the flow-through dynamic flux chamber technique, which has been utilized usually for various trace gas flux measurement from soil and water surface, was performed in an effort to provide physical and mathematical understandings of parameters essential for the NO flux calculation. The mass balance equation including chemical reactions was analytically solved for the soil NO flux under the steady state condition. The equilibrium concentration inside the chamber, $C_{eq}$, was found to be determined mainly by the balance between the soil flux and dilution of the gas concentration inside the chamber by introducing the ambient air. Surface deposition NO occurs inside the chamber when the $C_{eq}$ is greater than the ambient NO concentration ($C_{0}$) introducing to the chamber; NO emission from the soil occurs when the $C_{eq}$ is less than the ambient NO concentration. A sensitivity analysis of the significance of the chemical reactions of NO with the reactive species (i.e. $HO_{2},/CH_{3}O_{2},/O_{3}$) on the NO flux from soils was performed. The result of the analysis suggests that the NO flux calculated in the absence of chemical reactions and wall loss could be in error ranges from 40 to $85\%$ to the total flux.

• 한국농림기상학회지
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• 제9권3호
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• pp.170-178
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• 2007

지난 수 세기 동안 온실기체와 기타 화학적으로 중요한 미량기체들이 급격하게 증가하였다. 이러한 주요기체가 기후 변화에 미치는 영향을 이해하기 위해서는 각 기체들의 흡원과 발원을 규명하고, 생물권과 대기권 사이에서 발생하는 생물 기원 기체 플럭스들을 특성화하며, 주요 기체를 조절하는 프로세스들을 이해해야 한다. 본 논문에서는 야외 실험을 위한 실용적 방법인 enclosure 기반의 관측법을 소개한다. 특히, 토양표면에서 방출되는 일산화질소 플럭스에 대한 enclosure내에서의 질량수지 방정식과 flow-through dynamic 플럭스 챔버 기법의 민감도를 제시하고 flow-through dynamic 플럭스 챔버 방법의 물리적인 시스템과 이론을 소개한다. 또한 챔버 벽에서 발생하는 일산화질소의 손실을 고려하므로써 새로운 플럭스 계산식을 소개하였고 그 계산식의 불확실성을 논의하였다.

• 제어로봇시스템학회논문지
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• 제11권10호
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• pp.843-850
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• 2005

FBA(flux balance analysis) with Boolean rules for representing regulatory events has correctly predicted cellular behaviors, such as optimal flux distribution, maximal growth rate, metabolic by-product, and substrate concentration changes, with various environmental conditions. However, until now, since FBA has not taken into account a hierarchical regulatory network, it has limited the representation of the whole transcriptional regulation mechanism and interactions between specific regulatory proteins and genes. In this paper, in order to solve these problems, we describe the construction of hierarchical regulatory network with defined symbols and the introduction of a weight for representing interactions between symbols. Finally, the whole cellular behaviors with time were simulated through the linkage of a hierarchical regulatory network module and dynamic simulation module including FBA. The central metabolic network of E. coli was chosen as the basic model to identify our suggested modeling method.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.39-49
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• 2004

When there is a lack of detailed kinetic information, dFBA(dynamic flux balance analysis) has correctly predicted cellular behavior under given environmental conditions with FBA and different ial equations. However, until now, dFBA has centered on substrate concentration, cell growth, and gene on/off, but a detailed hierarchical structure of a regulatory network has not been taken into account. For this reason, the dFBA has limited the represen tation of interactions between specific regulatory proteins and genes and the whole transcriptional regulation mechanism with environmental change. Moreover, to calculate optimal metabolic flux distribution which maximizes the growth flux and predict the b ehavior of cell system, linear programming package(LINDO) and spreadsheet package(EXCEL) have been used simultaneously. thses two software package have limited in the visual representation of simulation results and it can be difficult for a user to look at the effects of changing inputs to the models. Here, we descirbes the construction of hierarchical regulatory network with defined symbolsand the development of an integrated system that can predict the total control mechanism of regulatory elements (opero ns, genes, effectors, etc.), substrate concentration, growth rate, and optimal flux distribution with time. All programming procedures were accoplished in a visual programming environment (LabVIEW).

• Journal of Microbiology and Biotechnology
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• 제15권3호
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• pp.551-559
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• 2005

The recent rapid increase in genomic data related to many microorganisms and the development of computational tools to accurately analyze large amounts of data have enabled us to design several kinds of simulation approaches for the complex behaviors of cells. Among these approaches, dFBA (dynamic flux balance analysis), which utilizes FBA, differential equations, and regulatory events, has correctly predicted cellular behaviors under given environmental conditions. However, until now, dFBA has centered on substrate concentration, cell growth, and gene on/off, but a detailed hierarchical structure of a regulatory network has not been taken into account. The use of Boolean rules for regulatory events in dFBA has limited the representation of interactions between specific regulatory proteins and genes and the whole transcriptional regulation mechanism with environmental change. In this paper, we adopted the operon as the basic structure, constructed a hierarchical structure for a regulatory network with defined fundamental symbols, and introduced a weight between symbols in order to solve the above problems. Finally, the total control mechanism of regulatory elements (operons, genes, effectors, etc.) with time was simulated through the linkage of dFBA with regulatory network modeling. The lac operon, trp operon, and tna operon in the central metabolic network of E. coli were chosen as the basic models for control patterns. The suggested modeling method in this study can be adopted as a basic framework to describe other transcriptional regulations, and provide biologists and engineers with useful information on transcriptional regulation mechanisms under extracellular environmental change.

• Journal of Microbiology and Biotechnology
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• 제16권6호
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• pp.993-998
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• 2006

We earlier suggested a hierarchical regulatory network using defined modeling symbols and weights in order to improve the flux balance analysis (FBA) with regulatory events that were represented by if-then rules and Boolean logic. In the present study, the simulation results of the models, which were developed and improved from the previou model by incorporating a hierarchical regulatory network into the FBA, were compared with the experimental outcome of an aerobic batch growth of E. coli on glucose and tryptophan. From the experimental result, a diauxic growth curve was observed, reflecting growth resumption, when tryptophan was used as an alternativee after the supply of glucose was exhausted. The model parameters, the initial concentration of substrates (0.92 mM glucose and 1 mM tryptophan), cell density (0.0086 g biomass/1), the maximal uptake rates of substrates (5.4 mmol glucose/g DCW h and 1.32 mmol tryptophan/g DCW h), and lag time (0.32 h) were derived from the experimental data for more accurate prediction. The simulation results agreed with the experimental outcome of the temporal profiles of cell density and glucose, and tryptophan concentrations.

• 한국수자원학회논문집
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• 제45권1호
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• pp.39-52
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• 2012

유역내에서 발생하는 유출은 지표 유출과 지표하 유출이 있으며, 서로 상호작용 상태를 유지하게 된다. 일반적으로 지표와 지표하 둘 중 한 가지 알고리즘으로 해석이 힘든 유역에 대해 지표와 지표하 사이의 동적인 관계를 상세하게 모의해야 하는 경우 상호작용에 관한 요소를 고려하여야 한다. 동적인 상호작용 시스템의 구동에서는 시 공간적인 매개변수가 중요하며, 적절한 모의를 위해시 공간적인 매개변수는 시스템 상에서 지표와 지표하 항에 대한 복합적인 메카니즘으로 구성되어야 한다. 본 연구에서는 이러한 지표 및 지표하 유출의상호작용에 관한 알고리즘을 위해 2차원 확산파 방정식을 이용하여 지표 유출을 해석하고, Darcy의 법칙과 Dupuit-Forchheimer의 가정을 이용한 Boussinesq 방정식을 적용하여 포화상태의 지표하 유출의 알고리즘을 구성하였다. 커플링 방정식으로 공간에 대해서는 유한체적법을 사용하고, 시간에 대해서는 Crank-Nicolson 방법을 이용하였으며, 지표와 지표하 흐름의 상호작용에 대해서는 질량보존의 법칙에 기반하여 구성하였다. 이상의 과정을 통하여 지표 유출해석, 지표하 유출해석, 상호작용, 수치해석 부분의 4가지 주요 모듈을 만들었으며, 4가지 주요 모듈을 통합하여 복합유역의 지표 및 지표하 유출해석 모듈을 개발하였다.