• The Bulletin of The Korean Astronomical Society
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• v.45 no.1
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• pp.29.3-29.3
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• 2020

Cosmology is a study to understand the origin, fundamental property, and evolution of the universe. Nowadays, many observational data of galaxies have become available, and one needs large-volume numerical simulations with good quality of the spatial distribution for a fair comparison with observation data. On the other hand, since galaxies' evolution is affected by both gravitational and baryonic effects, it is nontrivial to populate galaxies only by N-body simulations. However, full hydrodynamic simulations with large volume are computationally costly. Therefore, alternative galaxy assignment methods to N-body simulations are necessary for successful cosmological studies. In this talk, I would like to introduce the MBP-galaxy abundance matching. This novel galaxy assignment method agrees with the spatial distribution of observed galaxies between 0.1Mpc ~ 100Mpc scales. I also would like to introduce mock galaxy catalogs of the Horizon Run 4 and Multiverse simulations, large-volume cosmological N-body simulations done by the Korean community. Finally, I would like to introduce some recent works with those mock galaxies used to understand our universe better.

• Journal of Environmental Science International
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• v.18 no.8
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• pp.833-839
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• 2009

The calculation of the wind field for resource assessment is done by using CFD Reynolds-Averaged Navier-Stokes simulations performed with the commercial software WindSim. A new interface has been created to use mesoscale simulation data from a meteorological model as driving data for the simulations. This method makes it necessary to take into account thermal effects on the wind field to exploit the full potential of this method. The procedure for considering thermal effects in CFD wind field simulations as well as the impact of thermal effects on the wind field simulations is presented. Simulations for non-neutral atmospheric conditions with the developed method are consistent with expected behavior and show an improvement of simulation results compared with observations.

• The Bulletin of The Korean Astronomical Society
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• v.38 no.2
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• pp.57.2-57.2
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• 2013

Cosmology is entering an era of percent precision with large surveys, demanding accurate simulations. In this paper, we aim to study the effects of initial conditions on the results of cosmological simulations, which will help us to make percent-level accuracy simulations. For this purpose, we use a series of cosmological N-body simulations with varying initial conditions. We test the influence of the initial conditions, namely the pre-initial configuration (preIC), the order of the perturbation theory, and the initial redshift, on the statistics associated with the large scale structures of the universe such as the halo mass function, the density power spectrum, and the maximal extent of the large scale structures. We find that glass or grid pre-initial conditions give similar results. However, the order of the Lagrangian perturbation theory used to generate the initial conditions and the starting epoch of the simulations play a crucial role, especially at high redshift (z ~ 2-4). The initial conditions have to be chosen with care, taking into account the specificity of the simulation.

• Bulletin of the Korean Chemical Society
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• v.24 no.1
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• pp.95-98
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• 2003

Enantioselectivity of the propranolol on β-cyclodextrin was simulated by molecular modeling. Monte Carlo (MC) docking and molecular dynamics (MD) simulations were applied to investigate the molecular mechanism of enantioselective difference of both enantiomeric complexes. An energetic analysis of MC docking simulations coupled to the MD simulations successfully explains the experimental elution order of propranolol enantiomers. Molecular dynamics simulations indicate that average energy difference between the enantiomeric complexes, frequently used as a measure of chiral recognition, depends on the length of the simulation time. We found that, only in case of much longer MD simulations, noticeable chiral separation was observed.

• The Bulletin of The Korean Astronomical Society
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• v.45 no.1
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• pp.50.2-50.2
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• 2020

The dark matter (DM) only simulations have been exploited to study e.g. the large scale structures and properties of a halo. In a baryon side, the high-resolution hydrodynamic simulation such as IllustrisTNG has helped extend the physics of gas along with stars and DM. However, the expansive computational cost of hydrodynamic simulations limits the size of a simulated universe whereas DM-only simulations can generate the universe of the cosmological horizon size approximately. I will introduce a pipeline to estimate baryonic properties of a galaxy inside a dark matter (DM) halo in DM-only simulations using a machine trained on high-resolution hydrodynamic simulations. An extremely randomized tree (ERT) algorithm is used together with multiple novel improvements such as a refined error function in machine training and two-stage learning. By applying our machine to the DM-only simulation of a large volume, I then validate the pipeline that rapidly generates a galaxy catalog from a DM halo catalog using the correlations the machine found in hydrodynamic simulations. I will discuss the benefits that machine-based approaches like this entail, as well as suggestions to raise the scientific potential of such approaches.

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1505-1509
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• 2008

Comparative molecular simulations were performed to establish molecular interaction and inhibitory effect of flavonoid myricetin on formation of amyloid fibris. For computational comparison, the conformational stability of myricetin with amyloid $\beta$ -peptide (A$\beta$ ) and $\beta$ -amyloid fibrils (fA$\beta$) were traced with multiple molecular dynamics simulations (MD) using the CHARMM program from Monte Carlo docked structures. Simulations showed that the inhibition by myricetin involves binding of the flavonoid to fA$\beta$ rather than A$\beta$ . Even in MD simulations over 5 ns at 300 K, myricetin/fA$\beta$ complex remained stable in compact conformation for multiple trajectories. In contrast, myricetin/A$\beta$ complex mostly turned into the dissociated conformation during the MD simulations at 300 K. These multiple MD simulations provide a theoretical basis for the higher inhibitory effect of myricetin on fibrillogenesis of fA$\beta$ relative to A$\beta$ . Significant binding between myricetin and fA$\beta$ observed from the computational simulations clearly reflects the previous experimental results in which only fA$\beta$ had bound to the myricetin molecules.

• Journal of The Korean Association of Information Education
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• v.21 no.2
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• pp.231-245
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• 2017

This study is to review current state of web-based simulations for science learning about magnets and magnetic field, and evaluate the appropriateness of simulations in terms of contents, strategies and design. We designed a set of criteria for evaluating science simulations and applied it to 14 simulations about magnets and magnetic field. For the evaluation, eight elementary teachers participated and they described specific characteristics of each simulation according to the criteria. Based on the evaluation, we divided the simulations into two groups, excellent vs. normal groups. We analyzed strengths from the simulations in excellent group and weaknesses from the simulations in normal group according to the contents, learning strategies, screen format, and technical features. Implications for ways of improvement in developing web-based science simulations effective to science teaching and learning about magnets and magnetic field were discussed.

• Bulletin of the Korean Chemical Society
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• v.26 no.5
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• pp.769-775
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• 2005

An efficiency of Monte Carlo (MC) docking simulations was examined for the prediction of chiral discrimination by cyclodextrins. Docking simulations were performed with various computational parameters for the chiral discrimination of a series of 17 enantiomers by $\beta$-cyclodextrin ($\beta$-CD) or by 6-amino-6-deoxy-$\beta$-cyclodextrin (am-$\beta$-CD). A total of 30 sets of enantiomeric complexes were tested to find the optimal simulation parameters for accurate predictions. Rigid-body MC docking simulations gave more accurate predictions than flexible docking simulations. The accuracy was also affected by both the simulation temperature and the kind of force field. The prediction rate of chiral preference was improved by as much as 76.7% when rigid-body MC docking simulations were performed at low-temperatures (100 K) with a sugar22 parameter set in the CHARMM force field. Our approach for MC docking simulations suggested that the conformational rigidity of both the host and guest molecule, due to either the low-temperature or rigid-body docking condition, contributed greatly to the prediction of chiral discrimination.

• Publications of The Korean Astronomical Society
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• v.25 no.3
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• pp.71-76
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• 2010

The current status of numerical simulations of galaxy formation is reviewed. After a description of the main numerical simulation techniques, I will present several applications in order to illustrate how numerical simulations have improved our understanding of the galaxy formation process.

• Journal of computational fluids engineering
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• v.11 no.2 s.33
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• pp.25-31
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• 2006

A two-dimensional backward facing step flow is simulated by using URANS and Detached Eddy Simulations(DES) approaches. Turbulence models adopted for URANS and DES simulations are Spalart-Allmaras(S-A) model and Shear Stress Transport(SST) model. The target flow with ER=1.125, $Re_H=37,500$ is experimentally studied by Driver & Seegmiller. Various versions of DES have been tested in this paper. Results of the simulations are compared with the experimental data available to evaluate the merits and demerits of URANS and several versions of DES. URANS simulation converges to a steady state and hence unsteady characteristics are not featured. DES simulations in general successfully mimic large scale structures and oscillation characteristics of the flow.