• Bulletin of the Korean Chemical Society
• /
• 제24권6호
• /
• pp.809-811
• /
• 2003

This brief review contains surveys of both four-component and two-component relativistic molecular theories. First the four-component relativistic approach is reviewed. Emphasis is placed on efficient computational schemes for the four-component Dirac-Hartree-Fock and Dirac-Kohn-Sham methods. Next, in the twocomponent relativistic framework, two relativistic Hamiltonians, RESC and higher-order Douglas-Kroll (DK), are introduced. An illustrative application is shown for the relativistic study on valence photoelectron spectrum of OsO₄. The developing four-component relativistic and approximate quasi-relativistic methods have been packed in a program suite named REL4D.

• 대한기계학회논문집A
• /
• 제24권4호
• /
• pp.830-838
• /
• 2000

The paper addresses an application of molecular dynamics technique for fracture mechanics. Molecular dynamics simulation is an atomistic approach, while typical numerical methods such as finite element methods are macroscopic. Using the potential functions, which express the energy of a molecular system, a virtual specimen with molecules is set up and the trajectory of every molecule can be calculated by Newton's equation of motion. Several three-dimensional models with various types of cracks are considered. The stress intensity factors, the sizes of plastic zone as well as the dislocation emission are sought to be compared with the analytical solutions, which result in good agreement.

• BMB Reports
• /
• 제50권4호
• /
• pp.201-207
• /
• 2017

Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene. Recent findings of transcriptome-wide alternative polyadenylation (APA) as a molecular response to changes in biology position APA not only as a molecular event of early transcriptional termination but also as a cellular regulatory step affecting various biological pathways. With the development of high-throughput profiling technologies at a single nucleotide level and their applications targeted to the 3'-end of mRNAs, dynamics in the landscape of mRNA 3'-end is measureable at a global scale. In this review, methods and technologies that have been adopted to study APA events are discussed. In addition, various bioinformatics algorithms for APA isoform analysis using publicly available RNA-seq datasets are introduced.

• BMB Reports
• /
• 제37권3호
• /
• pp.356-361
• /
• 2004

To develop a simplified method that can rapidly prepare DNA microarray probes in a massive scale, a lambda phage genomic DNA-fragments library was constructed for the microarray-probes collection. Four methods of DNA band recovery from the first PCR products were tested and compared. The DNA microarray probes were collected by a novel method of nested PCR that was mediated by gel isolation of the first PCR products. This method was named GIN-PCR. The probes that were prepared by this GIN-PCR technique were used as subjects to fabricate a DNA microarray. The results showed that a wooden toothpick was superior to the other 3 methods, since this technique can steadily transfer the DNA bands as the template of the second PCR after the first PCR. A group of probes were successfully collected and DNA microarrays were constructed using these probes. Hybridization results demonstrated that this technique of DNA recovery and probe preparation was rapid, efficient, and effective. We developed a cost-effective and less labor-intensive method for DNA microarray probe preparation by nested PCR that is mediated by wooden toothpick transfer of the DNA bands in the gel after electrophoresis.

• 한국멀티미디어학회논문지
• /
• 제9권12호
• /
• pp.1580-1587
• /
• 2006

The term molecular imaging can be broadly defined as the in vivo characterization and measurement of biologic processes at the cellular and molecular level. Optical imaging that has highly reproducibility and repetition used in molecular imaging research. In the bioluminescence imaging, animals carrying the luciferase gene are imaged with a cooled CCD(Charge-Coupled Device) camera to pick up the small number of photons transmitted through tissues. Molecular imaging analysis will allow us to observe the incipience and progression of the disease. But hardware device for molecular imaging and software for molecular image analysis were dependent on imports. In this paper, we suggest image processing methods and designed software for bioluminescence signal analysis. And we demonstrated high correlation(r=0.99) between our software's photon counts and commercial software's photon counts. ROI function and processing functions were accomplished without error. This study have the importance of the development software for bioluminescence image processing and analysis. And this study built the foundations for creative development of analysis methods. We expected this study lead the development of image technology.

• Asian Pacific Journal of Cancer Prevention
• /
• 제15권6호
• /
• pp.2733-2737
• /
• 2014

Objective: Molecular pathology tests are often carried for clinicopathological diagnosis and pathologists have established large collections of formalin-fixed, paraffin-embedded tissue (FFPE) banks. However, extraction of DNA from FFPE is a laborious and challenging for researchers in clinical laboratories. The aim of this study was to compare two widely used DNA extraction methods: using a QIAamp DNA FFPE kit from Qiagen and a Cobas Sample Preparation Kit from Roche, and evaluated the effect of the DNA quality on molecular diagnostics. Methods: DNA from FFPE non-small cell lung carcinoma tissues including biopsy and surgical specimens was extracted with both QIAamp DNA FFPE and Cobas Sample Preparation Kits and EGFR mutations of non-small cell lung carcinomas were detected by real-time quantitative PCR using the extracted DNA. Results and Conclusion: Our results showed that DNA extracted by QIAamp and Cobas methods were both suitable to detect downstream EGFR mutation in surgical specimens. Howover, Cobas method could yield more DNA from biopsy specimens, and gain much better EGFR mutation results.

• 한국고분자학회:학술대회논문집
• /
• 한국고분자학회 2006년도 IUPAC International Symposium on Advanced Polymers for Emerging Technologies
• /
• pp.113-113
• /
• 2006

Polymer separations are used to obtain information on molecular distributions (molecular-weight distribution, chemical-composition distribution, functionality-type distribution, etc.). The existing methods, such as size-exclusion chromatography are reliable, but imperfect. New methods and improvements to existing methods are being studied and some of the results will be discussed. In addition, comprehensive two-dimensional liquid chromatography allows the complete characterization of two mutually dependent distributions. LCxSEC chromatograms provide a very good qualitative impression of the distributions, but calibration is not straightforward. Finally, progress in mass spectrometry allows much better information to be obtained.

• 한국군사과학기술학회지
• /
• 제11권3호
• /
• pp.154-160
• /
• 2008

We investigated molecular polarity by using theoretical means and comparing empirical solvent polarity. Our approach employed electrostatic potentials at the molecular surface calculated by density functional methods. A number of molecular descriptors related to molecular polarities were computed from molecular surface electrostatic potentials. Among computed molecular descriptors, the most positive electrostatic potential provided the best correlation with the empirical solvent polarities. A regression equation was developed in order to predict molecular polarities of molecules whose experimental solvent polarities were unknown. The new regression equations were utilized in estimating solvent polarities of cubane derivatives which are considered important precusors of high-energy density meterials.

• 한국환경보건학회지
• /
• 제50권2호
• /
• pp.113-124
• /
• 2024

Background: The increasing need to minimize animal testing has sparked interest in alternative methods with more humane, cost-effective, and time-saving attributes. In particular, in silico-based computational toxicology is gaining prominence. Adverse outcome pathway (AOP) is a biological map depicting toxicological mechanisms, composed of molecular initiating events (MIEs), key events (KEs), and adverse outcomes (AOs). To understand toxicological mechanisms, predictive models are essential for AOP components in computational toxicology, including molecular structures. Objectives: This study reviewed the literature and investigated previous research cases related to AOP and in silico methodologies. We describe the results obtained from the analysis, including predictive techniques and approaches that can be used for future in silico-based alternative methods to animal testing using AOP. Methods: We analyzed in silico methods and databases used in the literature to identify trends in research on in silico prediction models. Results: We reviewed 26 studies related to AOP and in silico methodologies. The ToxCast/Tox21 database was commonly used for toxicity studies, and MIE was the most frequently used predictive factor among the AOP components. Machine learning was most widely used among prediction techniques, and various in silico methods, such as deep learning, molecular docking, and molecular dynamics, were also utilized. Conclusions: We analyzed the current research trends regarding in silico-based alternative methods for animal testing using AOPs. Developing predictive techniques that reflect toxicological mechanisms will be essential to replace animal testing with in silico methods. In the future, since the applicability of various predictive techniques is increasing, it will be necessary to continue monitoring the trend of predictive techniques and in silico-based approaches.

• The Korean Journal of Physiology and Pharmacology
• /
• 제17권1호
• /
• pp.23-30
• /
• 2013

Neural stem cells (NSCs) have the ability to proliferate and differentiate into various types of cells that compose the nervous system. To study functions of genes in stem cell biology, genes or siRNAs need to be transfected. However, it is difficult to transfect ectopic genes into NSCs. Thus to identify the suitable method to achieve high transfection efficiency, we compared lipid transfection, electroporation, nucleofection and retroviral transduction. Among the methods that we tested, we found that nucleofection and retroviral transduction showed significantly increased transfection efficiency. In addition, with retroviral transduction of Ngn2 that is known to induce neurogenesis in various types of cells, we observed facilitated final cell division in rat NSCs. These data suggest that nucleofection and retroviral transduction provide high efficiency of gene delivery system to study functions of genes in rat NSCs.