scholarly journals Clog and Release, and Reverse Motions of DNA in a Nanopore

Polymers ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 84 ◽  
Author(s):  
Tomoya Kubota ◽  
Kento Lloyd ◽  
Naoto Sakashita ◽  
Seiya Minato ◽  
Kentaro Ishida ◽  
...  
Keyword(s):  
Finite Element Method ◽  
Finite Element ◽  
Fluorescence Microscopy ◽  
Numerical Simulations ◽  
Electric Fields ◽  
Reverse Direction ◽  
Dna Molecules ◽  
Circular Dna ◽  
Linear Dna ◽  
Streaming Flow

Motions of circular and linear DNA molecules of various lengths near a nanopore of 100 or 200 nm diameter were experimentally observed and investigated by fluorescence microscopy. The movement of DNA molecules through nanopores, known as translocation, is mainly driven by electric fields near and inside the pores. We found significant clogging of nanopores by DNA molecules, particularly by circular DNA and linear T4 DNA (165.65 kbp). Here, the probabilities of DNA clogging events, depending on the DNA length and shape—linear or circular—were determined. Furthermore, two distinct DNA motions were observed: clog and release by linear T4 DNA, and a reverse direction motion at the pore entrance by circular DNA, after which both molecules moved away from the pore. Finite element method-based numerical simulations were performed. The results indicated that DNA molecules with pores 100–200 nm in diameter were strongly influenced by opposing hydrodynamic streaming flow, which was further enhanced by bulky DNA configurations.

scholarly journals Imaging Mueller matrix ellipsometry setup for optical nanoform metrology

2020 ◽  
Vol 238 ◽  
pp. 06006
Author(s):  
Tim Käseberg ◽  
Jana Grundmann ◽  
Johannes Dickmann ◽  
Stefanie Kroker ◽  
Bernd Bodermann
Keyword(s):  
Finite Element Method ◽  
Finite Element ◽  
Numerical Simulations ◽  
Mueller Matrix ◽  
The Finite Element Method ◽  
Mueller Matrices ◽  
Microscope Images ◽  
Element Method

We designed, realized, and characterised an imaging Mueller matrix ellipsometry setup for the pixelwise measurement of the Mueller matrices in microscope images. Our setup is capable of performing measurements in reflection as well as in transmission in a broad range of angles of incidence for wavelengths between 400 nm and 700 nm. We compared measurements of specially designed nanostructured samples with AFM and SEM measurements as well as with numerical simulations using the finite element method.

A hybrid solver based on the integral equation method and vector finite-element method for 3D controlled-source electromagnetic method modeling

Geophysics ◽  
2018 ◽  
Vol 83 (5) ◽  
pp. E319-E333 ◽  
Author(s):  
Rong Liu ◽  
Rongwen Guo ◽  
Jianxin Liu ◽  
Changying Ma ◽  
Zhenwei Guo
Keyword(s):  
Differential Equation ◽  
Finite Element Method ◽  
Integral Equation ◽  
Finite Element ◽  
Differential Equations ◽  
Electric Fields ◽  
Hybrid Method ◽  
Linear Equations ◽  
Integral Equation Method ◽  
Controlled Source

The integral equation method (IEM) and differential equation methods have been widely applied to provide numerical solutions of the electromagnetic (EM) fields caused by inhomogeneity for the controlled-source EM method. IEM has a bounded computational domain and has been well-known for its efficiency, whereas differential equation methods are commonly used for complex geologic models. To use the advantages of the two types of approaches, a hybrid method is developed based on the combination of IEM and the edge-based finite-element method (vector FEM). In the hybrid scheme, Maxwell’s differential equations of the secondary electric fields in the frequency domain are derived for a volume with boundary placed slightly away from the inhomogeneity. The vector FEM is applied to solve Maxwell’s differential equations, and a system of linear equations for the secondary electric fields can be derived by the minimum theorem. The secondary electric fields on the boundary are represented by IEM in terms of the secondary electric fields inside the inhomogeneity. The linear equations from substituting the boundary values into the vector FEM linear equations then can be solved to obtain the secondary electric fields inside the inhomogeneity. The secondary electric fields at receivers are calculated by IEM based on the secondary electric field solutions inside the inhomogeneity. The hybrid algorithm is verified by comparison of simulated results with earlier works on canonical 3D disc models with a high accuracy. Numerical comparisons with two conventional IEMs demonstrate that the hybrid method is more accurate and efficient for high-conductivity contrast media.

scholarly journals Numerical Estimation of the Pile Toe and Shaft Unit Resistances During the Installation Process in Sands

2015 ◽  
Vol 37 (1) ◽  
pp. 37-44 ◽  
Author(s):  
Jakub Konkol
Keyword(s):  
Finite Element Method ◽  
Finite Element ◽  
Constitutive Model ◽  
Numerical Simulations ◽  
Numerical Estimation ◽  
Computing Environment ◽  
Coulomb Model ◽  
Model Of Friction ◽  
Shaft Unit ◽  
Large Deformation Problems

Abstract Numerical simulations of a pile jacking were carried out. A Coupled Eulerian-Lagrangian (CEL) formulation was used to treat with large deformation problems. An Abaqus, a commercial Finite Element Method software suit, was used as a computing environment. The Mohr-Coulomb constitutive model was applied and the Coulomb model of friction was used to describe pile-soil interaction. Calculations were made for three different pile diameters. Toe and shaft unit resistances versus depth for each pile were investigated and plotted. CPT-based solutions were compared with the results of numerical simulations.

scholarly journals Analysis of Vertical Displacements of the Esperanto Footbridge in Bydgoszcz

2018 ◽  
Vol 28 (2) ◽  
pp. 5-17 ◽  
Author(s):  
Adam Bujarkiewicz ◽  
Jarosław Gajewski ◽  
Tomasz Janiak ◽  
Justyna Sobczak-Piąstka ◽  
Jacek Sztubecki ◽  
...  
Keyword(s):  
Finite Element Method ◽  
Finite Element ◽  
Numerical Simulations ◽  
The Finite Element Method ◽  
Test Load ◽  
Vertical Displacements ◽  
The Subject ◽  
Theoretical Results ◽  
Element Method

Abstract The subject of the research is a footbridge across the river Brda in Bydgoszcz. The measurements of the footbridge displacements with the test load were undertaken. The paper presents the results of the measurements and compares them with the theoretical results obtained using the finite element method (FEM). On this basis, discrepancy between actual work of the structure and numerical simulations was found. Attempt to explain the reasons for the observed differences and direction of further research were included in the conclusions.

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