A finite element method for elasticity systems with discontinuities in the coefficients and the flux across an arbitrary interface is proposed in this paper. The method is based on a Cartesian mesh with local modifications to the mesh. The total degrees of the freedom of the finite element method remains the same as that of the Cartesian mesh. The local modifications lead to a quasi-uniform body-fitted mesh from the original Cartesian mesh. The standard finite element theory and implementation are applicable. Numerical examples that involve discontinuous material coefficients and non-homogeneous jump in the flux across the interface demonstrate the efficiency of the proposed method.
{"title":"A FINITE ELEMENT METHOD FOR ELASTICITY INTERFACE PROBLEMS WITH LOCALLY MODIFIED TRIANGULATIONS.","authors":"Hui Xie, Zhilin Li, Zhonghua Qiao","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A finite element method for elasticity systems with discontinuities in the coefficients and the flux across an arbitrary interface is proposed in this paper. The method is based on a Cartesian mesh with local modifications to the mesh. The total degrees of the freedom of the finite element method remains the same as that of the Cartesian mesh. The local modifications lead to a quasi-uniform body-fitted mesh from the original Cartesian mesh. The standard finite element theory and implementation are applicable. Numerical examples that involve discontinuous material coefficients and non-homogeneous jump in the flux across the interface demonstrate the efficiency of the proposed method.</p>","PeriodicalId":50301,"journal":{"name":"International Journal of Numerical Analysis and Modeling","volume":"8 2","pages":"189-200"},"PeriodicalIF":1.1,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777444/pdf/nihms495048.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31751403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Khawla Qamhieh, Ka-Yiu Wong, Gillian C Lynch, B Montgomery Pettitt
The details of melting of DNA immobilized on a chip or nanoparticle determines the sensitivity and operating characteristics of many analytical and synthetic biotechnological devices. Yet, little is known about the differences in how the DNA melting occurs between a homogeneous solution and that on a chip. We used molecular dynamics simulations to explore possible pathways for DNA melting on a chip. Simulation conditions were chosen to ensure that melting occurred in a submicrosecond timescale. The temperature was set to 400 K and the NaCl concentration was set to 0.1 M. We found less symmetry than in the solution case where for oligomeric double-stranded nucleic acids both ends melted with roughly equal probability. On a prepared silica surface we found melting is dominated by fraying from the end away from the surface. Strand separation was hindered by nonspecific surface adsorption at this temperature. At elevated temperatures the melted DNA was attracted to even uncharged organically coated surfaces demonstrating surface fouling. While hybridization is not the simple reverse of melting, this simulation has implications for the kinetics of hybridization.
{"title":"THE MELTING MECHANISM OF DNA TETHERED TO A SURFACE.","authors":"Khawla Qamhieh, Ka-Yiu Wong, Gillian C Lynch, B Montgomery Pettitt","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The details of melting of DNA immobilized on a chip or nanoparticle determines the sensitivity and operating characteristics of many analytical and synthetic biotechnological devices. Yet, little is known about the differences in how the DNA melting occurs between a homogeneous solution and that on a chip. We used molecular dynamics simulations to explore possible pathways for DNA melting on a chip. Simulation conditions were chosen to ensure that melting occurred in a submicrosecond timescale. The temperature was set to 400 K and the NaCl concentration was set to 0.1 M. We found less symmetry than in the solution case where for oligomeric double-stranded nucleic acids both ends melted with roughly equal probability. On a prepared silica surface we found melting is dominated by fraying from the end away from the surface. Strand separation was hindered by nonspecific surface adsorption at this temperature. At elevated temperatures the melted DNA was attracted to even uncharged organically coated surfaces demonstrating surface fouling. While hybridization is not the simple reverse of melting, this simulation has implications for the kinetics of hybridization.</p>","PeriodicalId":50301,"journal":{"name":"International Journal of Numerical Analysis and Modeling","volume":"6 3","pages":"474-488"},"PeriodicalIF":1.1,"publicationDate":"2009-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755589/pdf/nihms106763.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40055846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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