• Proceedings of the Computational Structural Engineering Institute Conference
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• 2006.04a
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• pp.389-394
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• 2006

Fully flexible cell preserves Hamiltonian in structure, so the symplectic time integrator is applied to the equations of motion. Primarily, generalized leapfrog time integration (GLF) is applicable, but the equations of motion by GLF have some of implicit formulas. The implicit formulas give rise to a complicate calculation for coding and need an iteration process. In this paper, the time integration formulas are obtained for the fully flexible cell molecular dynamics simulation by using the splitting time integration. It separates flexible cell Hamiltonian into terms corresponding to each of Hamiltonian term, so the simple and completely explicit recursion formula was obtained. The explicit formulas are easy to implementation for coding and may be reduced the integration time because they are not need iteration process. We are going to compare the resulting splitting time integration with the implicit generalized leapfrog time integration.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.31 no.8
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• pp.826-832
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• 2007

Fully flexible cell preserves Hamiltonian in structure so that the symplectic time integrator is applicable to the equations of motion. In the direct formulation of fully flexible cell N-Sigma-T ensemble, a generalized leapfrog time integration (GLF) is applicable for fully flexible cell simulation, but the equations of motion by GLF has structure of implicit algorithm. In this paper, the time integration formula is derived for the fully flexible cell molecular dynamics simulation by using the splitting time integration. It separates flexible cell Hamiltonian into terms corresponding to each of Hamiltonian term. Thus the simple and completely explicit recursion formula was obtained. We compare the performance and the result of present splitting time integration with those of the implicit generalized leapfrog time integration.

• Molecules and Cells
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• v.46 no.2
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• pp.106-119
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• 2023

With the increased number of single-cell RNA sequencing (scRNA-seq) datasets in public repositories, integrative analysis of multiple scRNA-seq datasets has become commonplace. Batch effects among different datasets are inevitable because of differences in cell isolation and handling protocols, library preparation technology, and sequencing platforms. To remove these batch effects for effective integration of multiple scRNA-seq datasets, a number of methodologies have been developed based on diverse concepts and approaches. These methods have proven useful for examining whether cellular features, such as cell subpopulations and marker genes, identified from a certain dataset, are consistently present, or whether their condition-dependent variations, such as increases in cell subpopulations in particular disease-related conditions, are consistently observed in different datasets generated under similar or distinct conditions. In this review, we summarize the concepts and approaches of the integration methods and their pros and cons as has been reported in previous literature.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.512-517
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• 2007

In the previous development of the recursive thermostat chained fully flexible cell molecular dynamics simulation, implicit time integration method such as generalized leapfrog integration is used. The implicit algorithm is very much complicated and not easy to show time reversibility because it is solved by the nonlinear iterative procedure. Thus we develop simple, explicit symplectic time integration formula for the recursive thermostat chained fully flexible unit cell simulation. Uniaxial tension test is performed to verify the present explicit algorithm. We check that the present simulation satisfies the ergodic hypothesis for various values of fictitious mass and coefficient of multiple thermostat system. The proposed method should be helpful to predict mechanical and thermal behavior of nano-scale structure.

• Journal of the Korean Society for Precision Engineering
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• v.12 no.5
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• pp.136-148
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• 1995

In this study, a model integration method is pressented as a new method for development of a parametric simulation model. This method enable us to integrate the special simulation models for each production subsystem into a large simulation model. Not only this large simulation model but also each special simulation model for each production subsytem can be used independently. Using this integration method man can reduce the development time and cost for simulation model development. To show the usefulness of this method, a simulation model for a production system with robots is developed by this model integration method. This simulation model is realized by the integration of two special simulation models, one model for a machining subsystem and the other model for a transport subsystem. The modeled production system consists of the robotic cells for machining and a transport subsystem which enable the material flow among the robotic cells. The flow of workpiece in each robotic cell is not fixed. All machines in a robotic cell are only served by robots.

• Transactions of the Korean Society of Automotive Engineers
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• v.12 no.3
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• pp.159-169
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• 2004

In this study, integration control of air-cell seat and semi-active suspension is proposed to minimize the road-tyre force which can cause uncomfortable feeling to rider. The proposed integration control with sliding perturbation observer is consisted of air-cell seat control which uses the force generated by air-cell and the sky-hook control. The air-cell seat itself has been modeled as a 1 degree of freedom spring-damper system. The actual characteristics of the air-cell have been analyzed through experiments. In this paper, we introduces a new robust motion control algorithm using partial state feedback for a nonlinear system with modelling uncertainties and external disturbances. The major contribution of this work is the development and design of robust observer for the state and the perturbation. The combination skyhook controller and air-cell controller using the observer improves control performance, because of the robust routine called Sliding Observer Design for Integration Control of Air-Cell Seat and Semi-active Suspension. The simulation results show a high accuracy and a good performance.

• Microbiology and Biotechnology Letters
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• v.39 no.4
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• pp.337-344
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• 2011

Integrase MJ1 from the bacteriophage ${\Phi}FC1$ carries out recombination between two DNA sequences (the phage attachment site, attP and the bacterial attachment site, attB) in NIH3T3 mouse cells. In this study, the integration vector containing attP, attB and the integrase gene MJ, was constructed. The integration mediated by integrase MJ1 in Escherichia coli led to excision of LacZ. Therefore, the frequency of integration was measured by the counting of the white colony, which is detectable on X-Gal plates. The extrachromosomal integration in NIH3T3 mouse cells was monitored by the expression of the green fluorescent protein (GFP) as a reporter. To demonstrate integration mediated integrase MJ1 in NIH3T3 cells, vectors containing attP and attB were co-transfected into NIH3T3 cells. The integration was confirmed by fluorescent microscopy. The expression of GFP was induced in NIH3T3 cells expressing MJ1 without accessory factors. By contrast, the excision mediated by the MJ1 between attR and attL had no effect on the expression of GFP. These results suggest that integrase MJ1 may enable a variety of genomic modifications for research and therapeutic purposes in higher living cells.

• Journal of Microbiology and Biotechnology
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• v.10 no.4
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• pp.470-475
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• 2000

Genetic chracterstics of the structural gene of guamerin (a novel elastase inhibitor from Korean leech), integrated into the HIS4 locus of chromosomal DNA of Pichia pastoris along with the $\alpha$-factor leader sequence, were investigated. In the selected clone from candidates, two copies of the integration cassette including the structural gene copies of the integration cassette including the structural gene of guamerin were found in the integration site of the chromosomal DNA of P.pastoris. It was demonstrated that the integrated structural gene of guamerin was stable up to about 70 generations in the relay flask culture. Then, a high-cell-density culture could be fulfilled easily by DO-stat fed-batch culture, in which the cell growth and the recombinant guamerin production reached about 250 of OD600nm and 260 mg/l, respectively. Finally, it was revealed that the DNA sequence of the integrated structural gene of guamerin in P. pastoris was maintained correctly in the end of production cells of relay flask culture and high-cell-density culture.

• BMB Reports
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• v.45 no.6
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• pp.365-370
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• 2012

Hepatitis B virus (HBV) DNA is often integrated into hepatocellular carcinoma (HCC). Although the relationship between HBV integration and HCC development has been widely studied, the role of HBV integration in HCC development is still not completely understood. In the present study, we constructed a pooled BAC library of 9 established cell lines derived from HCC patients with HBV infections. By amplifying viral genes and superpooling of BAC clones, we identified 2 clones harboring integrated HBV DNA. Screening of host-virus junctions by repeated sequencing revealed an HBV DNA integration site on chromosome 11q13 in the SNU-886 cell line. The structure and rearrangement of integrated HBV DNA were extensively analyzed. An inverted duplicated structure, with fusion of at least 2 HBV DNA molecules in opposite orientations, was identified in the region. The gene expression of cancer-related genes increased near the viral integration site in HCC cell line SNU-886.

• Mycobiology
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• v.43 no.1
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• pp.1-8
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• 2015

Mushroom transformation requires a series of experimental steps, including generation of host strains with a desirable selective marker, design of vector DNA, removal of host cell wall, introduction of foreign DNA across the cell membrane, and integration into host genomic DNA or maintenance of an autonomous vector DNA inside the host cell. This review introduces limitations and obstacles related to transformation technologies along with possible solutions. Current methods for cell wall removal and cell membrane permeabilization are summarized together with details of two popular technologies, Agrobacterium tumefaciens-mediated transformation and restriction enzyme-mediated integration.