• 천문학회보
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• 제40권1호
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• pp.58.3-59
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• 2015

Dynamical expansion of H II regions plays a key role in dispersing surrounding gas and therefore in limiting the efficiency of star formation in molecular clouds. We use analytic methods and numerical simulations to explore expansions of spherical dusty H II regions, taking into account the effects of direct radiation pressure, gas pressure, and total gravity of the gas and stars. Simulations show that the structure of the ionized zone closely follows Draine (2011)'s static equilibrium model in which radiation pressure acting on gas and dust grains balances the gas pressure gradient. Strong radiation pressure creates a central cavity and a compressed shell at the ionized boundary. We analytically solve for the temporal evolution of a thin shell, finding a good agreement with the numerical experiments. We estimate the minimum star formation efficiency required for a cloud of given mass and size to be destroyed by an HII region expansion. We find that typical giant molecular clouds in the Milky Way can be destroyed by the gas-pressure driven expansion of an H II region, requiring an efficiency of less than a few percent. On the other hand, more dense cluster-forming clouds in starburst environments can be destroyed by the radiation pressure driven expansion, with an efficiency of more than ~30 percent that increases with the mean surface density, independent of the total (gas+stars) mass. The time scale of the expansion is always smaller than the dynamical time scale of the cloud, suggesting that H II regions are likely to be a dominant feedback process in protoclusters before supernova explosions occurs.

• Biomolecules & Therapeutics
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• 제2권1호
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• pp.34-38
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• 1994

In order to investigate the structure-activity relationships of the stereoisomers of angiotensin converting enzyme inhibitors, captopril and its derivatives were selected as model compounds. In vitro enzymatic activities of them depend on the symmetry at the asymmetric carbons. Especially, the alanyl carbon should have the S configuration to be biologically active. But the demethylated captopril having the achiral carbon also shows the activity although it is less active than captopril. Seven stereoisomers of captopril and its derivatives were chosen and their acidic and ionic forms were used for molecular dynamics simulations. Four computer simulations were practiced for each model compound in order to obtain the good condition for simulation to explain the experimental structure-activity relationships. From the computer simulation results, relativistic movements of three well-known pharmacophoric sites, carboxylate carbon, carbonyl oxygen, and sulfur atoms, were analyzed. Good results were obtained from the aqueous solution molecular dynamics simulation with ionic forms of model compounds. Active model compounds have the pharmacophoric areas of 6.08 to 6.38 $\AA$$^2$and the similarity in the geometrical data. But inactive ones have the largely deviated values of 4.51 to 4.87 $\AA$$^2$from those of active ones.

• 한국재료학회지
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• 제19권5호
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• pp.276-280
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• 2009

The effect of the initial packing structure on the plasticity of amorphous alloys was investigated by tracing the structural evolution of the amorphous solid inside a shear band. According to the molecular dynamics simulations, the structural evolution of the amorphous solids inside the shear band was more abrupt in the alloy with a higher initial packing density. Such a difference in the structural evolution within the shear band observed from the amorphous alloys with different initial packing density is believed to cause different degrees of shear localization, providing an answer to the fundamental question of why amorphous alloys show different plasticity. We clarify the structural origin of the plasticity of bulk amorphous alloys by exploring the microstructural aspects in view of the structural disordering, disorder-induced softening, and shear localization using molecular dynamics simulations based on the recently developed MEAM (modified embedded atom method) potential.

• Coupled systems mechanics
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• 제6권1호
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• pp.41-54
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• 2017

Shape-memory alloys (SMA) have interesting behaviors and important mechanical properties due to the solid-solid phase transformation. These phenomena are dominated by the evolution of microstructures. In recent years, the microstructures in SMAs have been studied extensively and modeled using molecular dynamics (MD) simulations. However, it remains difficult to identify the crystal variants in the simulation results, which consist of large numbers of atoms. In the present work, a method is developed to identify the austenite phase and the monoclinic martensite crystal variants in MD results. The transformation matrix of each lattice is calculated to determine the corresponding crystal variant. Evolution of the volume fraction of the crystal variants and the microstructure in Ni-Ti SMAs under thermal and mechanical boundary conditions are examined. The method is validated by comparing MD-simulated interface normals with theoretical solutions. In addition, the results show that, in certain cases, the interatomic potential used in the current study leads to inconsistent monoclinic lattices compared with crystallographic theory. Thus, a specific modification is applied and the applicability of the potential is discussed.

• 한국기계가공학회지
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• 제17권5호
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• pp.117-122
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• 2018

3D printing technology and its applications have grown rapidly in academia and industry. We consider a 3D printing system designed for the selective laser sintering (SLS) method, which is one of the powder bed fusion (PBF) techniques to build up the final product by layering sintered powder slices. Thermal distortion of printing products is a critical challenge in 3D printing. This study investigates temperature-dependent conformational behaviors of 3D printed samples of sintered poly-ether-ether-ketone (PEEK) powders using molecular dynamics simulations. The wear and chemical resistance properties of PEEK are understood, as it is a well-known biocompatible material used for implants. However, studies on physical phenomena at nanoscale in PEEK are rarely published in public. We simulate dissipative particle dynamics to elucidate how a cavity regime forms in PEEK at different system temperatures. We demonstrate how PEEK structures deform subject to the system temperature distribution.

• 한국기계가공학회지
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• 제18권5호
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• pp.60-65
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• 2019

Since nanofluids (NFs), which are a mixture of a small amount of nanoparticles and a bulk liquid solvent, were first proposed by Stephen Choi at the Argonne National Lab in 1995, they have been considered for use in many technical studies of power cooling systems and their practical application due to their high thermal conductivity and heat transfer coefficients compared to conventional coolants. Although nanofluids are a well-known form of engineering fluid that show great promise for use in future cooling systems, their underlying physics as demonstrated in experiments remain unclear. One proven method of determining the heat transfer performance of nanofluids is measuring the concentration of nanoparticles in a mixture. However, it is experimentally inefficient to build testbeds to systematically observe particle distributions on a nanoscale. In this paper, we demonstrate the distribution of nanoparticles under a temperature gradient in a solution using molecular dynamics simulations. First, temperature profiles based on substrate temperature are introduced. Following this, the radial pair distribution functions of pairs of nanoparticles, solvents, and substrates are calculated. Finally, the distribution of nanoparticles in different heating regions is determined.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2020년도 추계국제학술대회
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• pp.14-14
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• 2020

In December 2019, the COVID-19 epidemic was discovered in Wuhan, China, and since has disseminated around the world impacting human health for millions. Herein, in-silico drug discovery approaches were utilized to identify potential candidates as Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) main protease (M^pro) inhibitors. We investigated several databases including natural and natural-like products (>100,000 molecules), DrugBank database (10,036 drugs), major metabolites isolated from daily used spices (32 molecules), and current clinical drug candidates for the treatment of COVID-19 (18 drugs). All tested compounds were prepared and screened using molecular docking techniques. Based on the calculated docking scores, the top ones from each project under investigation were selected and subjected to molecular dynamics (MD) simulations followed by molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations. Combined long MD simulations and MM-GBSA calculations revealed the potent compounds with prospective binding affinities against M^pro. Structural and energetic analyses over the simulated time demonstrated the high stabilities of the selected compounds. Our results showed that 4-bis([1,3]dioxolo)pyran-5-carboxamide derivatives (natural and natural-like products database), DB02388 and Cobicistat (DB09065) (DrugBank database), salvianolic acid A (spices secondary metabolites) and TMC-310911 (clinical-trial drugs database) exhibited high binding affinities with SARS-CoV-2 M^pro. In conclusion, these compounds are up-and-coming anti-COVID-19 drug candidates that warrant further detailed in vitro and in vivo experimental estimations.

• Tribology and Lubricants
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• 제39권5호
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• pp.216-219
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• 2023

This study employs molecular dynamics simulations to investigate the material behavior of workpieces in waterjet machining processes. To gain fundamental insights into waterjet machining, simulations were conducted using pure water, excluding abrasive particles. The simulation model comprised thousands of water molecules interacting with a single crystal metal workpiece. Water molecule clusters were imparted with various velocities to initiate collisions with the metal workpiece. The material behavior of the metal surface was analyzed with respect to the applied velocity conditions, considering the intricate interplay between water molecules and the workpiece at the atomic scale. The results demonstrated that the machining of the metal workpiece occurred only when water molecules were endowed with velocities above a certain threshold. In cases where energy was insufficient, the metal workpiece exhibited a slight increase in surface roughness due to mild plastic deformation, without undergoing substantial material removal. When machining occurred, the ejection of material revealed a 3-fold symmetric pattern, confirming that material removal in waterjet machining of the metal workpiece is primarily driven by plastic deformation-induced material ejection. This research provides crucial insights into the mechanisms underlying waterjet machining and enhances our understanding of material behavior during the process. The findings can be valuable in optimizing waterjet machining techniques.

• Current Optics and Photonics
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• 제8권1호
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• pp.86-96
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• 2024

This research investigation employs a terahertz (THz) time-domain spectroscopy system to study the terahertz spectral characteristics of five different citrates in both solution and solid state. The citrates under examination are lithium citrate, monosodium citrate, disodium citrate, trisodium citrate, and potassium citrate. The results show that the THz absorption coefficients of the first four citrate solutions exhibit a decreasing trend with increasing concentration. However, the potassium citrate solution shows an opposite phenomenon. At the same time, the absorption coefficients of lithium citrate, trisodium citrate, and potassium citrate solutions are compared at the same concentration. The results indicate that the absorption coefficient of citrate solution increases in proportion to the increase of metal cation radius, which is explained from the perspective of the influence of metal cations on hydrogen bonds. In addition, we also study the absorption peaks of solid citrates, and characterize the formation mechanism of the absorption peaks by molecular dynamics simulations. This methodology can be further extended to the study of multitudinous salts, presenting theoretical foundations for the detection in food and medicine industries.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2003년도 생물공학의 동향(XIII)
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• pp.737-737
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• 2003