Separation of long DNA chains using a nonuniform electric field: A numerical study

Nagahiro, Shin-ichiro; Kotera, Hidetoshi

doi:10.1103/physreve.75.011902

Cited by 23 publications

(23 citation statements)

References 27 publications

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“…The results from the present computations are corrected by the energy shift. The computational accuracy of MM methods is higher than that of the present method, although more computational time is consumed, because all intermolecular and intramolecular interactions are counted and the long-range intermolecular interactions are considered up to the cutoff distances: 10Å for VDW interactions and 30Å for Coulomb interactions [44][45][46][47][48][49][50]. Therefore, the difference between the MM and our results was corrected by the energy shift.…”

Section: Resultsmentioning

confidence: 99%

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Characterization of polymer structures based on Burnside’s lemma

Doi

Kato

2011

Phys. Rev. E

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Polymer structure modeling is a trend of recent material sciences. Developments of computational science and nanotechnology make it possible to predict properties of complicated molecular structures. Many theoretical and computational methods have succeeded in elucidating the nature of polymer structures. It is not always best to model whole complicated structures depending on computer capabilities. Significant properties of materials may be manifested in simple structural aspects. In the present study, characteristics of a polymer structure are investigated by applying Burnside's lemma to the modeling procedure. This method is expected to be available to model polymers or molecular crystals in which functional groups play an important role in expressing their functions. Every structure under the symmetry and periodicity is counted completely and the energy distribution caused by the conformations of functional groups can be clarified. The detailed procedure is introduced and the present method is applied to a problem for investigating molecular structures of sulfonated poly(ether ether ketone) (SPEEK). SPEEK is focused on a candidate for proton exchange membranes in polymer electrolyte fuel cells. Sulfonic groups have a significant role in proton exchange membranes to make proton conduction channels. From our analysis, it is found that sulfonic groups tend to be dispersed in SPEEK membranes at their stable conditions. These are unfavorable characteristics for proton exchange membranes due to their difficulty to form desirable water channels inevitable for the high proton conductivity. This is one reason why SPEEK membranes are inferior to Nafion® membranes that express the highest performance as proton exchange membranes. Using the present method, experimental and theoretical results previously reported are confirmed and detailed characteristics are discussed in terms of structural simplicities.

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Section: Resultsmentioning

confidence: 99%

“…Two-dimensional matrices in SPEEK bundles are discussed focusing on the relationship between conformations of sulfonic groups and their energy stabilities. The total energy of a system is evaluated using potential energy functions as follows [44][45][46][47][48][49][50]:…”

Section: Theoretical Development and Computational Methodsmentioning

confidence: 99%

Characterization of polymer structures based on Burnside’s lemma

Doi

Kato

2011

Phys. Rev. E

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“…The micro-VFP could precisely control the flow rate in the range of 0.07 ± 0.02 to 0.38 ± 0.02 ll/min. Therefore, the micro-VFP is useful for accurate control of small amounts of fluid used in applications such as single-molecule studies (Perkins et al 1995;Nagahiro et al 2007;Hanasaki et al 2008;Doi et al 2010). The maximum pressure was 3.8 ± 0.4 Pa, which was sufficiently high to transport the liquid through the micro-scaled channels.…”

Section: Introductionmentioning

confidence: 88%

Development of micro-vibrating flow pumps using MEMS technologies

Osman

Shintaku

2012

Microfluid Nanofluid

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In the present paper, we propose a microvibrating flow pump (micro-VFP), which is a novel micropump. The micro-VFP is constructed using an actively vibrating valve that has a cantilever-like structure fixed on a wall of a microchannel and a slit orifice downstream. The slit orifice is designed to make the flow asymmetric around the vibrating valve and to effectively generate a net flow in one direction. At the same time, the valve works as an actuator to induce liquid flow in the microchannel. Since the valve is made of a flexible material including magnetic particles, it is manipulated by changing the magnetic field from outside the micro-VFP. This design allows external operation of the micro-VFP without any electrical or mechanical connections. In addition, the micro-VFP, which realizes pumping with a chamber free design, is advantageous for implementation in a small space. In order to demonstrate its basic pumping performance, a prototype micro-VFP was fabricated in a microchannel with a cross section of 240 lm 9 500 lm using microelectromechanical systems technologies. The vibration characteristics of the valve were investigated using a high-speed camera. The pump performance at various actuation frequencies in the range of 5 to 25 Hz was evaluated by measuring the hydrostatic head and the flow rate. The proposed micro-VFP design exhibited an increase in performance with the driving frequency and had a maximum shut-off pressure of 3.8 ± 0.4 Pa and a maximum flow rate of 0.38 ± 0.02 ll/min at 25 Hz. Furthermore, in order to clarify the detailed pumping process, the flow characteristics around the vibrating valve were investigated by analyzing the velocity field based on micron-resolution particle image velocimetry (micro-PIV). The validity of the hydrostatic measurement was confirmed by comparing the volume flow rate with that estimated from micro-PIV data. The present study revealed the basic performance of the developed micro-VFP.

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“…In the present model, strong effects of intramolecular interactions on the inertial force were coarse-grained and the kinetics of ssDNA were mainly affected by external electric fields. In such a case, the behavior of a particle can be expressed by an over-damped Langevin equation [16,45,46]: ζ i v i = − U i + F i + R i where ζ i is the friction coefficient of the i th particle, −∇ U i is the conservative force, including interactions between particles, and F i denotes the external electrostatic force, such that F i = − Q i ϕ, where Q i is the electric charge on the polymer molecule. For the purposes of a three-dimensional simulation, the electric potential, ϕ, in a rectangular nanofluidic channel was analyzed by solving for the Laplace equation 2 ϕ = 0 with Neumann boundary conditions n ·ϕ = 0 at the sidewall surfaces, where n was the surface normal vector, and with constant electric potentials at both ends of the channel.…”

Section: Langevin Dynamics Simulations Of Polymer Chain Motionmentioning

confidence: 99%

Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA

Qian

Doi

Uehara

et al. 2014

IJMS

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The electrokinetic transport dynamics of deoxyribonucleic acid (DNA) molecules have recently attracted significant attention in various fields of research. Our group is interested in the detailed examination of the behavior of DNA when confined in micro/nanofluidic channels. In the present study, the translocation mechanism of a DNA-like polymer chain in a nanofluidic channel was investigated using Langevin dynamics simulations. A coarse-grained bead-spring model was developed to simulate the dynamics of a long polymer chain passing through a rectangular cross-section nanopore embedded in a nanochannel, under the influence of a nonuniform electric field. Varying the cross-sectional area of the nanopore was found to allow optimization of the translocation process through modification of the electric field in the flow channel, since a drastic drop in the electric potential at the nanopore was induced by changing the cross-section. Furthermore, the configuration of the polymer chain in the nanopore was observed to determine its translocation velocity. The competition between the strength of the electric field and confinement in the small pore produces various transport mechanisms and the results of this study thus represent a means of optimizing the design of nanofluidic devices for single molecule detection.

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Separation of long DNA chains using a nonuniform electric field: A numerical study

Cited by 23 publications

References 27 publications

Characterization of polymer structures based on Burnside’s lemma

Characterization of polymer structures based on Burnside’s lemma

Development of micro-vibrating flow pumps using MEMS technologies

Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA

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