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

• Proceedings of the Optical Society of Korea Conference
• /
• 2000.08a
• /
• pp.64-66
• /
• 2000

Theoretical foundations of atom dynamics in laser fields are reviewed in relation with applications to laser spectroscopy, control of atomic motion, atom traps and frequency standards. Quasiclassical kinetic equations are applied to multilevel atomic schemes interacting with counter-propagating laser waves to describe the properties of atomic populations and coherence and the time evolution of atomic distribution function. Basic types of the dipole radiation forces on atoms are discussed for the realistic cases of multilevel dipole interaction schemes such as 3(g)＋5(e), 3(g)＋3(e), 5(g)＋3(e), 5(g)＋7(e), 3(g)＋3(e)＋5(e) and 1(g)＋3(g)＋3(e)＋5(e).

• Journal of Ecology and Environment
• /
• v.35 no.2
• /
• pp.99-109
• /
• 2012

Litterfall dynamics in forests are assessed by estimating biomass production and decomposition. However, there have been few studies on how litter dynamics impact the health and management of ecosystems. Here, a new approach to measure and assess ecosystem function is presented based on conventional methods using littertraps, litterbags, and the mass on the forest floor. To assess the status of litter dynamics, the decay rate (k) was estimated from a litterbag experiment, and removal rates ($k_i$) were determined from mass balance on the forest floor at 21 sites on three mountains in South Korea. The $k_3$ (organic mass ratio of $O_i$ and $O_e+O_a$ + A horizons in November) values in an equilibrium state in South Korea were within the range of $k{\pm}0.174$ when considering the annual variation of litterfall production. This study also suggests that sampling sites for these types of studies should be in the middle, not at the ends, of steady slopes on the forest floor.

• Korean System Dynamics Review
• /
• v.10 no.3
• /
• pp.105-124
• /
• 2009

The situation of the global food markets has been being rapidly restructured and entering on a new phase by new dynamic and driving forces. The factors such as economic growth and income increase, high energy price, globalization, urbanization, and global climate change are transforming patterns of food consumption, production, and markets. The prices and markets of world food and energy are getting increasingly linked each other. Food and fuel are the global dilemma issues associated with the risk of diverting farmland or of consuming cereals for biofuel production in detriment of the cereals supply to the global food markets. An estimated 100 million tons of grain per year are being redirected from food to fuel. Therefore, the objectives of this study are as follows: Firstly, the study examines situations of the world food and energy resources, analyzes the trends of prices of the crude oil and biofuel, and formulates the food-energy links mechanism. Secondly, the study builds a simulation model, based on system dynamics approach, for not only analyzing the global cereals market and energy market but also forecasting the global production, consumption, and stock of those markets by 2030 in the future. The model of this study consists of four sectors, i.e., world population dynamics sector, global food market dynamics sector, global energy market dynamics sector, scenario sector of world economic growth and oil price.

• Journal of the Korean Vacuum Society
• /
• v.14 no.2
• /
• pp.97-102
• /
• 2005

NO adsorption can be used in synthesizing oxynitride thin films which have potential application in nanodevices. However, it is very difficult to understand the oxynitridation Process since too many factors are involved in it. In this paper, we present our first-principles molecular dynamics calculation of the NO molecule adsorption on the Si(001) surface as the initial stage of the oxynitridation process. The previous first-principles calculation has argued the NO molecule is dissociated with a very small activation barrier, 0.07eV, which acutally corresponds to 1.60eV considering thermodynamics. This is in clear contrast to the observation that NO is dissociated at temperatures as low as 20K From extensive searches of NO on the Si(001) surface, we have found the new dissociation processes that have the much lower activation energies, less than 0.01 eV. We also present the dissociation and penetration processes with the corresponding activation energies and discuss their experimental implications.

• International Journal of Fluid Machinery and Systems
• /
• v.3 no.1
• /
• pp.39-49
• /
• 2010

In this paper, a numerical study has been carried out to investigate the influence of jet fan design variables on the performance of a jet fan. In order to achieve an optimum jet fan design and to explain the interactions between the different geometric configurations in the jet fan, three-dimensional computational fluid dynamics and the DOE method have been applied. Several geometric variables, i.e., hub-tip ratio, meridional shape, rotor stagger angle, number of rotor-stator blades and stator geometry, were employed to improve the performance of the jet fan. The objective functions are defined as the exit velocity and total efficiency at the operating condition. Based on the results of computational analyses, the performance of the jet fan was significantly improved. The performance degradations when the jet fan is operated in the reverse direction are also discussed.

• IMMUNE NETWORK
• /
• v.22 no.1
• /
• pp.1.1-1.3
• /
• 2022

• Journal of The Korean Society of Agricultural Engineers
• /
• v.56 no.6
• /
• pp.45-53
• /
• 2014

This study presents a system dynamics modeling approach to simulate daily streamflow in a watershed including wastewater treatment plant which contributes to irrigation water supply. The conceptual system dynamics model considering the complex and dynamic hydrological processes in the watershed was developed. The model was calibrated and validated each for two years based on observed flow data. Model performances in terms of $E_{NS}$, RSR, PBIAS, and $R^2$ were 0.64, 0.60, -3.6 %, and 0.64 for calibration period, and 0.66, 0.58, -2.6 %, and 0.66 for validation period, respectively, showing an applicability on generating the daily streamflow. System dynamics modeling approach could help better understand the hydrological behavior of the watershed being reused wastewater for agriculture, by providing graphical dynamics of the hydrological processes as well as conventional rainfall-runoff model results.

• Journal of the Korean Electrochemical Society
• /
• v.14 no.3
• /
• pp.145-151
• /
• 2011

ZnSe, as a II-VI compound semiconductor which has a wide band gap in the visible region is applicable to the various fields such as laser diode, display and solar cell. By using the electrochemical deposition method, ZnSe thin film was synthesized on the ITO glass substrate. The synthesis of ZnSe grains and their structure having zinc blende shape were verified through the analysis of XRD and SEM. UV spectrophotometric method determined the band gap as the value of 2.76 eV. Applying the DFT (Density Functional Theory) in the molecular dynamics, the band structure of ZnSe grains was analyzed. For ZnSe grains with zinc blende structure, the band structure and its density of state were simulated using LDA (Local Density Approximation), PBE (Perdew Burke Ernzerhof), and B3LYP (Becke, 3-parameter, Lee-Yang-Parr) functionals. Among the calculations of energy band gap upon each functional, the simulated one of 2.65 eV based on the B3LYP functional was mostly near by the experimental measurement.

• The Korean Journal of Malacology
• /
• v.13 no.2
• /
• pp.185-192
• /
• 1997

1990젼 3월부터 1991년 2월까지 전라북도 군산시 내초도 연안에 서식하는 동죽의 성장을 조사하였다. 1.조사해역의 연간 수온분포는 2.0-26.3$^{\circ}C$이고, 간석지 온도는 0.7-36.2$^{\circ}C$이었다. 2. 동죽의 패각에 나타나는 윤문은 연 1회 형성되며 윤문 형성시기는 3-4월로 조사되었다. 3. 초륜 형성기간은 9개월(0.75년)로 나타났다. 4. 각장(SL: mm)과 체중(TW: G)간의 관계는 TW=1.090 x $10^{-4}$ S $L^{3.2798}$( $r^{2}$=0.99)이었으며, 각장과 각고(SH:mm)간의 관계는 SH=0.865 SL + 0.250( $r^{2}$=0.99)이고, 각장과 각폭(SW: mm) 간의 관계는 SW=0.599 SL - 0.203 ( $r^{2}$=0.98; 각장 22 mm미만), SW=0.724 SL - 2.796( $r^{2}$=0.91; 각장 22 mm이상)이었다.5. 연령(t)에 대한 각장(S $L_{t}$ )의 Bertalanffy성장식은 $L_{t}$ =51.399(1- $e^{0.585}$8(t+0.064)이고, 연령(t)에 대한 체중 (T $W_{t}$ )의 Bertalanffy성장식은 $W_{t}$ =44.467(1- $e^{0.585}$8(t+0.064)$^{3}$로 나타났다.타났다.