• Interaction and multiscale mechanics
• /
• 제6권4호
• /
• pp.395-409
• /
• 2013

Molecular dynamics (MD) systems are highly nonlinear and nonlocal, and the conventional model order reduction methods are ineffective for MD systems. The RBF-POD method (Lee and Chen, 2013) employed a radial basis function (RBF) approximated potential energies and inter-atomic forces of MD systems under the framework of the proper orthogonal decomposition (POD) method for the reduced-order modeling of MD systems. In this work, we focus on the numerical procedures of the RBF-POD method and demonstrate how to apply this approach to the modeling of ds-DNA molecules under stretching and bending conditions.

• BMB Reports
• /
• 제55권5호
• /
• pp.213-219
• /
• 2022

The blood-brain barrier (BBB) is an interface between cerebral blood and the brain parenchyma. As a gate keeper, BBB regulates passage of nutrients and exogeneous compounds. Owing to this highly selective barrier, many drugs targeting brain diseases are not likely to pass through the BBB. Thus, a large amount of time and cost have been paid for the development of BBB targeted therapeutics. However, many drugs validated in in vitro models and animal models have failed in clinical trials primarily due to the lack of an appropriate BBB model. Human BBB has a unique cellular architecture. Different physiologies between human and animal BBB hinder the prediction of drug responses. Therefore, a more physiologically relevant alternative BBB model needs to be developed. In this review, we summarize major features of human BBB and current BBB models and describe organ-on-chip models for BBB modeling and their applications in neurological complications.

• Journal of Microbiology and Biotechnology
• /
• 제17권10호
• /
• pp.1598-1606
• /
• 2007

A new series comprising 7 analogs of N-(sulfanyl ethanoyl)-L-HSL derivatives, 2 analogs of N-(fluoroalkanoyl)-$_L$-HSL derivatives, N-(fluorosulfonyl)-L-HSL, and 2,2-dimethyl butanoyl HSL were synthesized using a solid-phase organic synthesis method. Each of the 11 synthesized compounds was analyzed using NMR and mass spectroscopies, and molecular modeling studies of the 11 ligands were performed using SYBYL packages. Thereafter, a bacterial test was designed to identify their quorum-sensing inhibition activity and antifouling efficacy. Most of the synthesized compounds were found to be effective as quorum-sensing antagonists, where antagonist screening revealed that 10 among the 11 synthesized ligands were able to antagonize the quorum sensing of A. tumefaciens.

• Journal of Microbiology and Biotechnology
• /
• 제20권2호
• /
• pp.294-300
• /
• 2010

The Iro protein is a member of the HiPIP family with the [$Fe_4S_4$] cluster for electron transfer. Many reports proposed that the conserved aromatic residues might be responsible for the stability of the iron-sulfur cluster in HiPIP. In this study, Tyr10 was found to be a critical residue for the stability of the [$Fe_4S_4$] cluster, according to site-directed mutagenesis results. Tyr10, Phe26, and Phe48 were essential for the stability of the [$Fe_4S_4$] cluster under acidic condition. Trp44 was not involved in the stability of the [$Fe_4S_4$] cluster. Molecular structure modeling for the mutant Tyr10 proteins revealed that the aromatic group of Tyr10 may form a hydrophobic barrier to protect the [$Fe_4S_4$] cluster from solvent.

• 한국재료학회지
• /
• 제20권9호
• /
• pp.478-482
• /
• 2010

A series of molecular dynamic (MD), finite element (FE) and ab initio simulations are carried out to establish suitable modeling schemes for the continuum-based analysis of aluminum matrix nanocomposites reinforced with carbon nanotubes (CNTs). From a comparison of the MD with FE models and inferences based on bond structures and electron distributions, we propose that the effective thickness of a CNT wall for its continuum representation should be related to the graphitic inter-planar spacing of 3.4${\AA}$. We also show that shell element representation of a CNT structure in the FE models properly simulated the carbon-carbon covalent bonding and long-range interactions in terms of the load-displacement behaviors. Estimation of the effective interfacial elastic properties by ab initio simulations showed that the in-plane interfacial bond strength is negligibly weaker than the normal counterpart due to the nature of the weak secondary bonding at the CNT-Al interface. Therefore, we suggest that a third-phase solid element representation of the CNT-Al interface in nanocomposites is not physically meaningful and that spring or bar element representation of the weak interfacial bonding would be more appropriate as in the cases of polymer matrix counterparts. The possibility of treating the interface as a simply contacted phase boundary is also discussed.

• Interaction and multiscale mechanics
• /
• 제4권3호
• /
• pp.173-185
• /
• 2011

A multiscale modeling scheme that addresses the influence of the nanoparticle size in nanocomposites consisting of nano-sized spherical particles embedded in a polymer matrix is presented. A micromechanics-based constitutive model for nanoparticle-reinforced polymer composites is derived by incorporating the Eshelby tensor considering the interface effects (Duan et al. 2005a) into the ensemble-volume average method (Ju and Chen 1994). A numerical investigation is carried out to validate the proposed micromechanics-based constitutive model, and a parametric study on the interface moduli is conducted to investigate the effect of interface moduli on the overall behavior of the composites. In addition, molecular dynamics (MD) simulations are performed to determine the mechanical properties of the nanoparticles and polymer. Finally, the overall elastic moduli of the nanoparticle-reinforced polymer composites are estimated using the proposed multiscale approach combining the ensemble-volume average method and the MD simulation. The predictive capability of the proposed multiscale approach has been demonstrated through the multiscale numerical simulations.

• 한국컴퓨터그래픽스학회논문지
• /
• 제10권2호
• /
• pp.1-9
• /
• 2004

본 논문에서는 바이러스와 같은 생화학 물질의 분자구조를 3 차원 모델로 시각화하여 관찰하고, 그 분자모델을 직관적인 방법으로 조작하기 위한 가상 현실 분자 모델링 시스템을 제안한다. 이 시스템을 사용하면, 입체영상 디스플레이 장치와 데이터 글러브 및 동작 추적 장치를 사용하여 3 차원 분자 모델을 실감나게 조작할 수 있어서 효율적으로 분자들을 관찰하고 결합, 분리하는 등의 분자 모델링 작업이 가능하다. 사용자들은 마우스나 키보드 등의 장비 대신에 자연스러운 몸 동작이나 손 동작을 이용하여 분자 모델링 작업을 위한 동작을 하게 된다. 분자들의 결합을 화학적으로 정확하게, 그리고 실시간으로 시뮬레이션 하기 위해서 에너지 계산 알고리즘을 구현하였으며 이러한 작업이 가능하도록 분자 구조를 표현하는 새로운 자료구조를 제안하였다. 본 연구에서 제안하는 동작 기반의 VR 분자 모델링 시스템의 타당성을 검증하기 위하여 HIV 바이러스 분자를 가지고 분자 모델링 작업을 수행하였고, 사용자 테스트를 실시하여 기존의 방식과 작업 성능 및 사용자 만족도를 비교하였다.

• 한국축산식품학회지
• /
• 제32권3호
• /
• pp.274-284
• /
• 2012

In this study, the effects of physical parameters (30-270 MPa of pressure, 3-57 min of time, and 1-$49^{\circ}C$ of temperature) on pork quality were investigated. Response surface methodology was used in order to monitor and model the changes in pork quality under varied pressure conditions. As quality characteristics, shear force, water holding capacity (WHC) and the CIE color of pork were measured, and optimum pressure conditions were evaluated by statistical modeling. Pressure improved the WHC of pork at relatively low temperature ($<25^{\circ}C$); however, the opposite occurred with increasing temperature. Although pressure and temperature affected the tenderness of the meat, interaction effects among variations were not observed. At pressure levels higher than 200 MPa, the color of pork differed markedly from that of the untreated controls. In particular, differential scanning calorimetry (DSC) revealed marked evidence of myosin denaturation. The present study demonstrates that pork quality varies depending on pressure conditions.

• Genomics & Informatics
• /
• 제8권2호
• /
• pp.70-75
• /
• 2010

Asp66his, Asp54Lys, and Asp50Asn are mutations in connexin 26 that are observed in the clinic and give rise to autosomal dominant syndromes. They are the result of point mutations in the human gap junction ${\beta}-2$ gene. In order to investigate the structural mechanism of Bart-Pumphrey Syndrome, Keratitis-Ichthyosis-Deafness Syndrome, and Vohwinkel Syndrome, homology modeling was carried out. Asp66 has direct contact with Asn62 by two hydrogen bonds in the wild-type protein, and in Asp66His, the biggest change observed is a tremendous energy increase caused by hydrogen bond breakage to Asn62. Shifts in the side chain and new hydrogen bond formation are observed for Lys54 compared to the wild-type protein (Asn54) and result in closer contact to Val84. Asp50Asn causes a significant decrease in bond energy, and residual charge reversal repels the ion and metabolites and, hence, inhibits their transportation. Such perturbations are likely to be a factor contributing to abnormal functioning of ion channels, resulting cell death and disease.

• Applied Biological Chemistry
• /
• 제38권6호
• /
• pp.516-521
• /
• 1995

항 MRSA 물질을 찾기 위하여 찬국 해양 토양을 검색하였고, 거기서 분리된 방선균의 이차 대사물질 중 항 MRSA 효능을 보이는 물질을 AM3이라고 명명하고 이에 대한 연구를 하였다.