• Journal of Electrochemical Science and Technology
• /
• 제10권3호
• /
• pp.257-270
• /
• 2019

The inhibition performance of sodium gluconate (SG), cetyltrimethylammonium bromide (CTAB) and their mixture (SG/CTAB) on the corrosion behavior of ${\alpha}$-brass in 0.5 M $H_2SO_4$ solution has been investigated by potentiodynamic polarization, electrochemical impedance spectroscopy (EIS), Scanning Electron Microscope with Energy-Dispersive Spectrometer (SEM-EDS), Inductively Coupled Plasma Spectrometry (ICPS) and molecular dynamics (MD) simulation techniques. The results reveal that SG with 5ppm CTAB, noted SG/CTAB, acts as a good corrosion inhibitor and its inhibition efficiency reached 89% after 24 h immersion in sulfuric acid solution, but slightly decreased at higher temperatures. The polarization curves displayed that SG/CTAB acts as a cathodic-kind inhibitor. Electrochemical impedance spectroscopy (EIS) studies revealed that the addition of 5ppm CTAB to different concentrations of SG considerably increases the corrosion resistance of ${\alpha}$-brass. The SEM-EDS and ICPS analyses support the experimental results. Further, molecular dynamics (MD) simulations were used to understand the adsorption profiles of SG/CTAB on Cu(111) and Zn(111) surfaces.

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

• 한국진공학회지
• /
• 제14권1호
• /
• pp.40-48
• /
• 2005

분자 위치제어 메모리 시스템에 대하여 고전적인 분자동역학을 이용하여 결합에너지 및 다양한 외부전기장의 형태에 따른 셔틀 풀러렌 동작에 관하여 연구하였다. 단일 나노피포드 형(single-nanopeapod type)은 질화붕소 나노튜브(boron-nitride nanotube)속에 세 개의 엔도풀러렌(endo-fullerene)과 양쪽 끝에 구리 전극이 채워져 있는 구조를 갖고 있는 구조를 갖고 있다. 결론적으로, 분자동역학 시뮬레이션 결과로부터 이 나노메모리 시스템은 비휘발성임을 알 수 있었다. 안정적인 bit 변화를 위해서는 단일 나노피포드 형은 0.1 eV/Å 외부전기장이 필요로 함을 알 수 있었다.

• Bulletin of the Korean Chemical Society
• /
• 제23권3호
• /
• pp.447-453
• /
• 2002

In this paper we have presented the results of thermodynamic, structural, and dynamic properties of model systems for liquid benzene, toluene and p-xylene in an isobaric-isothermal (NpT) ensemble at 283.15, 303.15, 323.15, and 343.15 K using molecular dynamics (MD) simulation. This work is initiated to compensate for our previous canonical (NVT) ensemble MD simulations [Bull. Kor. Chem. Soc. 2001, 23, 441] for the same systems in which the calculated pressures were too low. The calculated pressures in the NpT ensemble MD simulations are close to 1 atm and the volume of each system increases with increasing temperature. The first and second peaks in the center of mass g(r) diminish gradually and the minima increase as usual for the three liquids as the temperature increases. The three peaks of the site-site gC-C(r) at 283.15 K support the perpendicular structure of nearest neighbors in liquid benzene. Two self-diffusion coefficients of liquid benzene via the Einstein equation and via the Green-Kubo relation are in excellent agreement with the experimental measures. The self-diffusion coefficients of liquid toluene and p-xylene are in accord with the trend that the self-diffusion coefficient decreases with increasing number of methyl group. The friction constants calculated from the force auto-correlation (FAC) function with the assumption that the fast random force correlation ends at time which the FAC has the first negative value give a correct qualitative trends: decrease with increase of temperature and increase with the number of methyl group. The friction constants calculated from the FAC's are always less than those obtained from the friction-diffusion relation which reflects that the random FAC decays slower than the total FAC as described by Kubo [Rep. Prog. Phys. 1966, 29, 255].

• Bulletin of the Korean Chemical Society
• /
• 제25권6호
• /
• pp.838-842
• /
• 2004

Amyloid peptide (A${\beta}$) is the major component of senile plaques found in the brain of patient of Alzheimer's disease. ${\beta}$-amyloid peptide (25-35) (A${\beta}$25-35) is biologically active fragment of A${\beta}$. The three-dimensional structure of A${\beta}$25-35 in aqueous solution with 50% (vol/vol) TFE determined by NMR spectroscopy previously adopts an ${\alpha}$-helical conformation from $Ala^{30}$ to $Met^{35}$. It has been proposed that A${\beta}$(25-35) exhibits pH- and concentration-dependent ${\alpha}-helix{\leftrightarrow}{\beta}$sheet transition. This conformational transition with concomitant peptide aggregation is a possible mechanism of plaque formation. Here, in order to gain more insight into the mechanism of ${\alpha}$-helix formation of A${\beta}$25-35 peptide by TFE, which particularly stabilizes ${\alpha}$-helical conformation, we studied the secondary-structural elements of A${\beta}$25-35 peptide by molecular dynamics simulations. Secondary structural elements determined from NMR spectroscopy in aqueous TFE solution are preserved during the MD simulation. TFE/water mixed solvent has reduced capacity for forming hydrogen bond to the peptide compared to pure water solvent. TFE allows A${\beta}$25-35 to form bifurcated hydrogen bonds to TFE as well as to residues in peptide itself. MD simulation in this study supports the notion that TFE can act as an ${\alpha}$-helical structure forming solvent.

• 한국윤활학회:학술대회논문집
• /
• 한국윤활학회 2002년도 proceedings of the second asia international conference on tribology
• /
• pp.59-60
• /
• 2002

In this digest, we briefly review our current molecular dynamics (MD) simulations that utilize both the reactive empirical bond order potential (REBO) and the adaptive intermolecular REBO (AIREBO) potential energy functions. The AIREBO potential includes intermolecular interactions, so that self·assembled monolayers, and liquids, can be modeled. We have examined the mechanical and tribological properties of model self assembled monolayers and amorphous carbon films. Self-assembled monolayers are modeled by covalently bonding hydrocarbon chains to diamond substrates. Because the REBO potentials can model chemical reactions, specific compression and sliding induced chemical reactions were identified.

• 한국정보과학회논문지:정보통신
• /
• 제29권5호
• /
• pp.501-509
• /
• 2002

기존 TCP가 이동 환경에 그대로 적용될 경우, 빈번하게 발생하는 핸드오프에 의한 패킷 손실에 대해 불필요한 폭주 제어 알고리즘을 수행함으로 인해 TCP의 성능 저하를 초래한다. 본 논문에서는 이동호스트의 핸드오프 발생 사실을 최대한 빨리 감지하기 위한 TCP-MD 방식과 핸드오프 시 등록 과정동안 송신측에서 전송을 중지하여 패킷 손실을 최소화하는 TCP-R 방식을 제안한다. 제안된 방식은 종단간 TCP 연결을 유지하며 이로 인해 기존망과 호환이 가능하도록 한다. 또한, 유선 구간에서는 기존 TCP의 수정없이 사용하고, 핸드오프 발생 사실을 알리기 위해 별도의 메시지 정의 없이, 단지 이동 호스트 내 TCP에서 Mobile IP 핸드오프 시 등록 관련 메시지를 이용함으로써 TCP 성능을 향상시킬 수 있고 구현이 단순하다는 장점이 있다. 다양한 환경에 대한 시뮬레이션을 수행하여 각 제안된 방식들을 적용할 경우 TCP의 성능을 크게 향상시킬 수 있음을 보였다.

• Genomics & Informatics
• /
• 제21권1호
• /
• pp.9.1-9.13
• /
• 2023

Matrix metalloproteinase-9 (MMP-9) is a zinc and calcium-dependent proteolytic enzyme involved in extracellular matrix degradation. Overexpression of MMP-9 has been confirmed in several disorders, including cancers, Alzheimer's disease, autoimmune diseases, cardiovascular diseases, and dental caries. Therefore, MMP-9 inhibition is recommended as a therapeutic strategy for combating various diseases. Cinnamic acid derivatives have shown therapeutic effects in different cancers, Alzheimer's disease, cardiovascular diseases, and dental caries. A computational drug discovery approach was performed to evaluate the binding affinity of selected cinnamic acid derivatives to the MMP-9 active site. The stability of docked poses for top-ranked compounds was also examined. Twelve herbal cinnamic acid derivatives were tested for possible MMP-9 inhibition using the AutoDock 4.0 tool. The stability of the docked poses for the most potent MMP-9 inhibitors was assessed by molecular dynamics (MD) in 10 nanosecond simulations. Interactions between the best MMP-9 inhibitors in this study and residues incorporated in the MMP-9 active site were studied before and after MD simulations. Cynarin, chlorogenic acid, and rosmarinic acid revealed a considerable binding affinity to the MMP-9 catalytic domain (ΔG_binding < -10 kcal/ mol). The inhibition constant value for cynarin and chlorogenic acid were calculated at the picomolar scale and assigned as the most potent MMP-9 inhibitor from the cinnamic acid derivatives. The root-mean-square deviations for cynarin and chlorogenic acid were below 2 Å in the 10 ns simulation. Cynarin, chlorogenic acid, and rosmarinic acid might be considered drug candidates for MMP-9 inhibition.

• International Journal of Aeronautical and Space Sciences
• /
• 제18권1호
• /
• pp.129-137
• /
• 2017

When the micro-Doppler (MD) image of a ballistic missile is derived, the translational motion compensation (TMC) method is usually applied to the inverse synthetic aperture radar (ISAR) image, but yields poor results because of the micro-motion of the ballistic missile. This paper proposes an efficient TMC method to obtain a focused MD image of a ballistic missile engaged in complicated micro-motion. During range alignment, range profiles (RPs) are coarsely aligned by using the 1D entropy cost function of RPs as a mark, then the coarsely-aligned RPs are fine-aligned by using the minimum 2D entropy of the MD image. During phase adjustment, the gradient of the phase error is appropriately weighted and added to the previous phase error to further fine-tune the aligned RPs. In simulations using the point scatterer model and the measured data from the real missile model, the proposed method provided better image focus than the existing method.

• Bulletin of the Korean Chemical Society
• /
• 제12권5호
• /
• pp.490-494
• /
• 1991

The ${\beta} to {\alpha}$ phase transition in silver iodide is studied with the (N, V, E) and (N, P, T) molecular dynamics (MD) method. In experiments, the phase transition temperature is 420 K. Upon heating of ${\beta}$ form, the iodine ions undergo hcp to bcc transformation and silver ions become mobile. MD simulations for the ${\beta}$ and ${\alpha}$ phases are carried out at several temperatures and the radial distribution functions (rdf) are obtained at those temperatures in the (N, V, E) ensemble. But the phase transition is not found in our calculation. Next the phase transition is studied with the (N, P, T) MD and we find some evidences of phase transition. At 3 Kbars and 2 Kbars the phase transition temperatu re is about 300 K. For 3.55 Kbars, the phase transition is higher (420 K) than the low pressure case. The phase transition temperature is somewhat dependent on the pressure in our calculations.