generation-control-electrohydrodynamic-flows-aqueous-electrolyte

Generation and Control of Electrohydrodynamic Flows in Aqueous Electrolyte Solutions

To drive electrohydrodynamic (EHD) flows in aqueous solutions, the separation of cation and anion transport pathways is essential because a directed ...

Osaka University

Recently, analytical techniques have been developed for detecting single-nucleotide polymorphisms in DNA sequences. Improvements of the sequence identification techniques has attracted much attention in several fields. However, there are many things that have not been clarified about DNA. In the present study, we have developed a coarse-graining DNA model with single-nucleotide resolution, in which potential functions for hydrogen bonds and the pi-stack effect are taken into account. Using Langevin-dynamics simulations, several characteristics of the coarse-grained DNA have been clarified. The validity of the present model has been confirmed, compared with other experimental and computational results. In particular, the melting temperature and persistence length are in good agreement with the experimental results for a wide range of salt concentrations.

Development of coarse-graining DNA models for single-nucleotide resolution analysis.

DNA sequence analyzing and base pair separation techniques have attracted much attention, such as denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and capillary electrophoresis. However, details of sequence separation mechanisms in electrophoresis are not clarified enough. Understanding and controlling flow characteristics of DNA are important not only for fundamental research but also for further developments of bio-nano technologies. In the present study, we theoretically discuss the relationship between diffusivity and hydrated structures of DNA fragments in water solvent using molecular dynamics methods. In particular, influence of base pair substitutions on the diffusivity is investigated, focusing on an adenine-thymine (AT) rich B-DNA decamer 5'-dCGTATATATA-3'. Consequently, it is found that water molecules that concentrate on dissociated base pairs form hydrated structures and change the diffusivity of DNA decamers. The diffusion coefficients are affected by the substitution of GC for AT because of the different manner of interactions between the base molecules and water solvent. This result predicts a possibility of base pair separation according to differences in the diffusivity.

Molecular dynamics study of solvation effect on diffusivity changes of DNA fragments.

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.

Characterization of polymer structures based on Burnside's lemma.

Deoxyribonucleic acid (DNA) is a vital molecule for life since it contains genetic information. However, DNA has recently been reported to have unique properties that make it suitable for bionanoelectronic applications, such as the possibility of electrical conductivity and self-organisation. Self-assembled DNA network structures have been observed on several substrates, but the detailed self-assembly mechanism has yet to be determined. The present study investigates self-assembled structures of DNA both theoretically and experimentally. We developed a reaction-diffusion model and used it to investigate pattern formations observed by atomic force microscopy. The computational results qualitatively replicate the network patterns of DNA molecules based on a quantitative agreement with the surface size and timescale. The model can account for the effect of the DNA concentration on pattern formation. Furthermore, peculiar geometric patterns are simulated for mica and highly oriented pyrolytic graphite surfaces. 

Reaction-diffusion wave model for self-assembled network formation of poly(dA)·poly(dT) DNA on mica and HOPG surfaces.

Dermal papilla cells (DPCs) have the potential to induce differentiation of epithelial stem cells into hair, and Wnt signaling is deeply involved in the initiation process. The functional limitation of expanded adult DPCs has been a difficult challenge for cell-based hair regrowth therapy. We previously reported that 1α,25-dihydroxyvitamin D(3) (VD(3)) upregulates expression of transforming growth factor (TGF)-β2 and alkaline phosphatase (ALP) activity, both features of hair-inducing human DPCs (hDPCs). In this study, we further examined the effects and signaling pathways associated with VD(3) actions on DPCs. VD(3) suppressed hDPC proliferation in a dose-dependent, noncytotoxic manner. Among the Wnt-related genes investigated, Wnt10b expression was significantly upregulated by VD(3) in hDPCs. Wnt10b upregulation, as well as upregulation of ALPL (ALP, liver/bone/kidney) and TGF-β2, by VD(3) was specific in hDPCs and not detected in human dermal fibroblasts. Screening of paracrine or endocrine factors in the skin indicated that all-trans retinoic acid (atRA) upregulated Wnt10b gene expression, although synergistic upregulation (combined atRA and VD(3)) was not seen. RNA interference with vitamin D receptor (VDR) revealed that VD(3) upregulation of Wnt10b, ALPL, and TGF-β2 was mediated through the genomic VDR pathway. In a rat model of de novo hair regeneration by murine DPC transplantation, pretreatment with VD(3) significantly enhanced hair folliculogenesis. Specifically, a greater number of outgrowing hair shafts and higher maturation of regenerated follicles were observed. Together, these data suggest that VD(3) may promote functional differentiation of DPCs and be useful in preserving the hair follicle-inductive capacity of cultured DPCs for hair regeneration therapies.

1α,25-dihydroxyvitamin D3 modulates the hair-inductive capacity of dermal papilla cells: therapeutic potential for hair regeneration.

This study has investigated the formation patterns resulting from the self-assembly of deoxyribonucleic acid (DNA) on highly oriented pyrolytic graphite (HOPG), using both experimental and molecular dynamics approaches. Under optimized conditions based on pretreatment of HOPG surface and specific solution concentrations, DNA is found to self-assemble to form various patterned networks. The associated self-assembly mechanism is elucidated using coarse-grained molecular dynamics simulations and fractal dimension analysis. The results of this work demonstrate an effective technique allowing the formation of arrays of negatively charged biomacromolecules on negatively charged HOPG surfaces. 

Self-assembly of 50 bp poly(dA)·poly(dT) DNA on highly oriented pyrolytic graphite via atomic force microscopy observation and molecular dynamics simulation.

Novel experimental techniques allow for the manipulation and interrogation of biomolecules between metallic probes immersed in micro/nanofluidic channels. The behavior of ions in response to applied fields is a major issue in the use of these techniques in sensing applications. Here, we experimentally and theoretically elucidate the behavior of background currents in these systems. These large currents have a slowly decaying transient response, as well as noise that increases with ionic concentration. Using mechanically controllable break junctions (MCBJ), we study the ionic response in nanogaps with widths ranging from a few nanometers to millimeters. Moreover, we obtain an expression for the ionic current by solving time-dependent Nernst-Planck and Poisson equations. This expression shows that after turning on an applied voltage, ions rapidly respond to the strong fields near the electrode surface, screening the field in the process. Ions subsequently translocate in the weak electric field and slowly relax within the diffusion layer. Our theoretical results help to explain the short- and long-time behavior of the ionic response found in experiments, as well as the various length scales involved.

Nonequilibrium Ionic Response of Biased Mechanically Controllable Break Junction (MCBJ) Electrodes.

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. 

Theoretical study of the transpore velocity control of single-stranded DNA.

In recent years, the control of ionic currents has come to be recognized as one of the most important issues related to the efficient transport of single molecules and microparticles in aqueous solutions. However, the complicated liquid flows that are usually induced by applying electric potentials have made it difficult to address a number of unsolved problems in this area. In particular, the nonequilibrium phenomena that occur in electrically non-neutral fields must be more thoroughly understood. Herein, we report on the development of a theoretical model of liquid flows resulting from ion interactions while focusing on the so-called electrohydrodynamic (EHD) flow. We also discuss the development of an experimental system to optically and electrically observe EHD flows using a 1 mm(2) cross-section pore placed in an ion-exchange membrane where cation and anion flows can be separated without the use of a charged environment. Although micro/nanosized flow channels are usually applied to induce electric double layer overlaps to utilize strong electroosmotic effects, our system does not require such laborious fabrication processes. Instead, we visualize EHD flows by using a millimeter size pore immersed in an alkaline aqueous solution. In this setup, liquid flows passing through the pore along the direction of ion flow, whose velocity reaches on the order of 1 mm/s, can be clearly observed by applying a few volts of electric potential. Furthermore, the transient phenomena associated with ionic responses are theoretically elucidated. 

Electrohydrodynamic flow through a 1 mm(2) cross-section pore placed in an ion-exchange membrane.

Understanding and controlling electrophoretic motions of nanoscopic objects in fluidic channels are a central challenge in developing nanopore technology for molecular analyses. Although progress has been made in slowing the translocation velocity to meet the requirement for electrical detections of analytes via picoampere current measurements, there exists no method useful for regulating particle flows in the transverse directions. Here, we report the use of dielectrophoresis to manipulate the single-particle passage through a solid-state pore. We created a trap field by applying AC voltage between electrodes embedded in a low-aspect-ratio micropore. We demonstrated a traffic control of particles to go through center or near side surface via the voltage frequency. We also found enhanced capture efficiency along with faster escaping speed of particles by virtue of the AC-mediated electroosmosis. This method is compatible with nanopore sensing and would be widely applied for reducing off-axis effects to achieve single-molecule identification.

Tailoring particle translocation via dielectrophoresis in pore channels.

Electrokinetic phenomena in micro/nanofluidic channels have attracted considerable attention because precise control of molecular transport in liquids is required to optically and electrically capture the behavior of single molecules. However, the detailed mechanisms of polymer transport influenced by electroosmotic flows and electric fields in micro/nanofluidic channels have not yet been elucidated. In this study, a Langevin dynamics simulation was used to investigate the electrokinetic transport of single-stranded DNA (ssDNA) in a cylindrical nanochannel, employing a coarse-grained bead-spring model that quantitatively reproduced the radius of gyration, diffusion coefficient, and electrophoretic mobility of the polymer. Using this practical scale model, transport regimes of ssDNA with respect to the ζ-potential of the channel wall, the ion concentration, and the polymer length were successfully characterized. It was found that the relationship between the radius of gyration of ssDNA and the channel radius is critical to the formation of deformation regimes in a narrow channel. We conclude that a combination of electroosmotic flow velocity gradients and electric fields due to electrically polarized channel surfaces affects the alignment of molecular conformations, such that the ssDNA is stretched/compressed at negative/positive ζ-potentials in comparatively low-concentration solutions. Furthermore, this work suggests the possibility of controlling the center-of-mass position by tuning the salt concentration. These results should be applicable to the design of molecular manipulation techniques based on liquid flows in micro/nanofluidic devices.

Effects of Polymer Length and Salt Concentration on the Transport of ssDNA in Nanofluidic Channels.

Recently, single-molecule manipulation techniques in micro- and nanofluidic channels have attracted significant attention. To precisely control the transport velocity, the dynamics of the surrounding liquid must be understood in addition to the behavior of the target particles. Some unknowns about interactions between electrolyte ions and solvents remain to be clarified from a microscopic viewpoint. Herein, we propose a technique to generate a liquid flow driven by ion transport phenomena, the so-called electrohydrodynamic (EHD) flow, where electrolyte ions are dialyzed using a cation-exchange membrane. With this method, it is possible to apply an electric body force in liquids, which is different from electroosmotic flows that are limited to ion transport in electric double layers, and is expected to be a good candidate for detailed control of liquid flows in micro- and nanofluidic channels. To collect basic design data based on the knowledge of microscopic fluid dynamics of the present technique, a mathematical model of an EHD flow dragged by electrical carriers in an ionic current is developed and results are compared with experimental data. In our experiments, EHD flows are efficiently driven by applied electric fields in a cation dominant current. To induce such an EHD flow, the externally applied electric potential can be drastically reduced to 2.0 V in comparison with previous methods because we do not need an excessively high voltage to inject electrical charges into liquids. This method enables us to induce EHD flows in aqueous solutions and is expected to open the door to low-voltage driven liquid flow control.

Article	Year
Development of coarse-graining DNA models for single-nucleotide resolution analysis. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences\| PubMed ID: 20439265	2010
Molecular dynamics study of solvation effect on diffusivity changes of DNA fragments. Journal of molecular modeling\| PubMed ID: 20853125	2011
Characterization of polymer structures based on Burnside's lemma. Physical review. E, Statistical, nonlinear, and soft matter physics\| PubMed ID: 21867203	2011
Reaction-diffusion wave model for self-assembled network formation of poly(dA)·poly(dT) DNA on mica and HOPG surfaces. Computer methods in biomechanics and biomedical engineering\| PubMed ID: 23013145	2014
1α,25-dihydroxyvitamin D3 modulates the hair-inductive capacity of dermal papilla cells: therapeutic potential for hair regeneration. Stem cells translational medicine\| PubMed ID: 23197867	2012
Self-assembly of 50 bp poly(dA)·poly(dT) DNA on highly oriented pyrolytic graphite via atomic force microscopy observation and molecular dynamics simulation. The Journal of chemical physics\| PubMed ID: 24007039	2013
Nonequilibrium Ionic Response of Biased Mechanically Controllable Break Junction (MCBJ) Electrodes. The journal of physical chemistry. C, Nanomaterials and interfaces\| PubMed ID: 24803976	2014
Theoretical study of the transpore velocity control of single-stranded DNA. International journal of molecular sciences\| PubMed ID: 25116683	2014
Electrohydrodynamic flow through a 1 mm(2) cross-section pore placed in an ion-exchange membrane. The journal of physical chemistry. B\| PubMed ID: 25412032	2015
Tailoring particle translocation via dielectrophoresis in pore channels. Scientific reports\| PubMed ID: 27527126	2016
Effects of Polymer Length and Salt Concentration on the Transport of ssDNA in Nanofluidic Channels. Biophysical journal\| PubMed ID: 28297643	2017
Cation-induced electrohydrodynamic flow in aqueous solutions. The Journal of chemical physics\| PubMed ID: 29865816	2018

Kentaro Doi

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