• Journal of the Korean Society of Manufacturing Process Engineers
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• v.8 no.1
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• pp.43-47
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• 2009

Recently, an approach for nano-scale material deformation has been developed that couples the atomistic and continuum approaches using Finite Element Method (FEM) and Molecular Dynamics (MD). However, this approach still has problems to connect two approaches because of the difference of basic assumptions, continuum and atomistic modeling. To solve this problem, an alternative way is developed that connects the QuasiMolecular Dynamics (QMD) and molecular dynamics. In this paper, we suggest the way to make and validate the MD-QMD coupled model.

• Smart Structures and Systems
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• v.13 no.4
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• pp.685-709
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• 2014

Carbon nanotubes are due to their outstanding mechanical properties destined for a wide range of possible applications. Since the knowledge of the material behavior is vital regarding the possible applications, experimental and theoretical studies have been conducted to investigate the properties of this promising material. The aim of the present research is the calculation of mechanical properties and of the mechanical behavior of single wall carbon nanotubes (SWCNTs). The numerical simulation was performed on basis of a molecular mechanics approach. Within this approach two different issues were taken into account: (i) the nanotube geometry and (ii) the modeling of the covalent bond. The nanotube geometry is captured by two different approaches, the roll-up and the exact polyhedral model. The covalent bond is modeled by a structural molecular mechanics approach according to Li and Chou. After a short introduction in the applied modeling techniques, the results for the Young's modulus for several SWCNTs are presented and are discussed extensively. The obtained numerical results are compared to results available in literature and show an excellent agreement. Furthermore, deviations in the geometry stemming from the different models are given and the resulting differences in the numerical findings are shown. Within the investigation of the deformation mechanisms occurring in SWCNTs, the basic contributions of each individual covalent bond are considered. The presented results of this decomposition provide a deeper understanding of the governing deformation mechanisms in SWCNTs.

• Molecules and Cells
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• v.43 no.9
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• pp.804-812
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• 2020

In cells, proteins form macromolecular complexes to execute their own unique roles in biological processes. Conventional structural biology methods adopt a bottom-up approach starting from defined sets of proteins to investigate the structures and interactions of protein complexes. However, this approach does not reflect the diverse and complex landscape of endogenous molecular architectures. Here, we introduce a top-down approach called Electron Microscopy screening for endogenous Protein ArchitectureS (EMPAS) to investigate the diverse and complex landscape of endogenous macromolecular architectures in an unbiased manner. By applying EMPAS, we discovered a spiral architecture and identified it as AdhE. Furthermore, we performed screening to examine endogenous molecular architectures of human embryonic stem cells (hESCs), mouse brains, cyanobacteria and plant leaves, revealing their diverse repertoires of molecular architectures. This study suggests that EMPAS may serve as a tool to investigate the molecular architectures of endogenous macromolecular proteins.

• ALGAE
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• v.21 no.4
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• pp.349-375
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• 2006

The application of modern ecological, ultrastructural and molecular methods, aided by the cultivation of numerous cyanobacterial morphotypes, has substantially changed our knowledge of these organisms. It has led to major advances in cyanobacterial taxonomy and criteria for their phylogenetic classification. Molecular data provide basic criteria for cyanobacterial taxonomy; however, a correct phylogenetic system cannot be constructed without combining genetic data with knowledge from the previous 150 years research of cyanobacterial diversity. Thus, studies of morphological variation in nature, and modern morphological, ultrastructural, ecophysiological and biochemical characters need to be combined in a “polyphasic” approach. Taxonomic concepts for generic and infrageneric ranks are re-evaluated in light of combined phenotypic and molecular criteria. Despite their usefulness in experimental studies, the limitations of using strains from culture collections for systematic and nomenclatural purposes is highlighted. The need for a continual revision of strain identification and proper nomenclatural practice associated with either the bacteriological or botanical codes is emphasized. Recent advances in taxonomy are highlighted in the context of prospects for understanding cyanobacterial diversity from natural habitats, and the evolutionary and adaptational processes that cyanobacteria undergo.

• Proceedings of the Korean Society for Technology of Plasticity Conference
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• 2004.05a
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• pp.62-65
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• 2004

Recently, an approach for nanoscale deformation has been developed that couples the atomistic and continuum approaches using Finite Element Method (FEM) and Molecular Dynamics (MD). However, this approach still has problems to connect two approaches because of the difference of basic assumptions, continuum and atomistic. To solve this problem, an alternative way is developed that connects the quasimolecular dynamics (QMD) and molecular dynamics (MD). In this paper, we suggest the way to make and validate the MD-QMD coupled model.

• Bulletin of the Korean Chemical Society
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• v.25 no.11
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• pp.1611-1612
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• 2004

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.265-265
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• 2005

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.13
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• pp.5499-5500
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• 2014

• Bulletin of the Korean Chemical Society
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• v.25 no.1
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• pp.29-30
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• 2004

• Genomics & Informatics
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• v.7 no.2
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• pp.122-130
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• 2009

A systems biology approach for the identification of perturbed molecular functions is required to understand the complex progressive disease such as breast cancer. In this study, we analyze the microarray data with Gene Ontology terms of molecular functions to select perturbed molecular functional modules in breast cancer tissues based on the definition of Gene ontology Functional Code. The Gene Ontology is three structured vocabularies describing genes and its products in terms of their associated biological processes, cellular components and molecular functions. The Gene Ontology is hierarchically classified as a directed acyclic graph. However, it is difficult to visualize Gene Ontology as a directed tree since a Gene Ontology term may have more than one parent by providing multiple paths from the root. Therefore, we applied the definition of Gene Ontology codes by defining one or more GO code(s) to each GO term to visualize the hierarchical classification of GO terms as a network. The selected molecular functions could be considered as perturbed molecular functional modules that putatively contributes to the progression of disease. We evaluated the method by analyzing microarray dataset of breast cancer tissues; i.e., normal and invasive breast cancer tissues. Based on the integration approach, we selected several interesting perturbed molecular functions that are implicated in the progression of breast cancers. Moreover, these selected molecular functions include several known breast cancer-related genes. It is concluded from this study that the present strategy is capable of selecting perturbed molecular functions that putatively play roles in the progression of diseases and provides an improved interpretability of GO terms based on the definition of Gene Ontology codes.