• Journal of Korean Society for Atmospheric Environment
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• v.21 no.E3
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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.

• Korean Journal of Agricultural and Forest Meteorology
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• v.9 no.3
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• pp.170-178
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• 2007

Rapid increases in the concentrations of greenhouse gases and many other chemically important trace gases have occurred over the last several centuries. For understanding the roles of these important gases in global change, it is essential to identify their sources and sinks, to characterize biogenic gas fluxes between the biosphere and atmosphere, and to understand the processes that control them. In this paper, enclosure-based measurements are described in a practical manner for field experiments. Theoretical reviews of mass balance equation in the enclosure and sensitivity of the flow-through dynamic flux chamber technique are presented; specifically for the case of NO flux measurements from soil surface. The physical system and theory behind the flow-through dynamic flux chamber method are examined. New calculation flux formula was introduced by considering NO chemical loss on chamber wall and uncertainties of the NO flux calculation were discussed.

• Journal of Institute of Control, Robotics and Systems
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• v.11 no.10
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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.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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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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• v.15 no.3
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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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• v.16 no.6
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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.

• Journal of Korea Water Resources Association
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• v.45 no.1
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• pp.39-52
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• 2012

Surface-subsurface interactions are an intrinsic component of the hydrologic response within a watershed. In general, these interactions are considered to be one of the most difficult areas of the discipline, particularly for the modeler who intends simulate the dynamic relations between these two major domains of the hydrological cycle. In essence, one major complexity is the spatial and temporal variations in the dynamically interacting system behavior. The proper simulation of these variations requires the need for providing an appropriate coupling mechanism between the surface and subsurface components of the system. In this study, an approach for modelling surface-subsurface flow and transport in a fully intergrated way is presented. The model uses the 2-dimensional diffusion wave equation for sheet surface water flow, and the Boussinesq equation with the Darcy's law and Dupuit-Forchheimer's assumption for variably saturated subsurface water flow. The coupled system of equations governing surface and subsurface flows is discretized using the finite volume method with central differencing in space and the Crank-Nicolson method in time. The interactions between surface and subsurface flows are considered mass balance based on the continuity conditions of pressure head and exchange flux. The major module consists of four sub-module (SUBFA, SFA, IA and NS module) is developed.