Modeling electrochemical systems with weakly imposed Dirichlet boundary conditions

Finite element modeling of charged species transport has enabled analysis, design, and optimization of a diverse array of electrochemical and electrokinetic devices. These systems are represented by the Poisson-Nernst-Planck equations coupled with the Navier-Stokes equation, with a key quantity of interest being the current at the system boundaries. Accurately computing the current flux is challenging due to the small critical dimension of the boundary layers (small Debye layer) that require fine mesh resolution at the boundaries. We resolve this challenge by using the Dirichlet-to-Neumanntransformation to weakly impose the Dirichlet conditions for the Poisson-Nernst-Planck equations. The results obtained with weakly imposed Dirichlet boundary conditions showed excellent agreement with those obtained when conventional boundary conditions with highly resolved mesh we reemployed. Furthermore, the calculated current flux showed faster mesh convergence using weakly imposed conditions compared to the conventionally imposed Dirichlet boundary conditions. We illustrate the approach on canonical 3D problems that otherwise would have been computationally intractable to solve accurately. This approach substantially reduces the computational cost of model-ing electrochemical systems.Comment: 24 pages, 14 figure

Principal factors that determine the extension of detection range in molecular beacon aptamer/conjugated polyelectrolyte bioassays.

A strategy to extend the detection range of weakly-binding targets is reported that takes advantage of fluorescence resonance energy transfer (FRET)-based bioassays based on molecular beacon aptamers (MBAs) and cationic conjugated polyelectrolytes (CPEs). In comparison to other aptamer-target pairs, the aptamer-based adenosine triphosphate (ATP) detection assays are limited by the relatively weak binding between the two partners. In response, a series of MBAs were designed that have different stem stabilities while keeping the constant ATP-specific aptamer sequence in the loop part. The MBAs are labeled with a fluorophore and a quencher at both termini. In the absence of ATP, the hairpin MBAs can be opened by CPEs via a combination of electrostatic and hydrophobic interactions, showing a FRET-sensitized fluorophore signal. In the presence of ATP, the aptamer forms a G-quadruplex and the FRET signal decreases due to tighter contact between the fluorophore and quencher in the ATP/MBA/CPE triplex structure. The FRET-sensitized signal is inversely proportional to [ATP]. The extension of the detection range is determined by the competition between opening of the ATP/MBA G-quadruplex by CPEs and the composite influence by ATP/aptamer binding and the stem interactions. With increasing stem stability, the weak binding of ATP and its aptamer is successfully compensated to show the resistance to disruption by CPEs, resulting in a substantially broadened detection range (from millimolar up to nanomolar concentrations) and a remarkably improved limit of detection. From a general perspective, this strategy has the potential to be extended to other chemical- and biological-assays with low target binding affinity

Hydroxyapatite Humidifier Vibrator Housing Fabrication and Characteristics

The humidifier vibrator housing is difficult to clean and prone to contamination due to its metallic material. To overcome these shortcomings, the humidifier vibrator housing was manufactured using Hydroxyapatite as a raw material. Although hydroxyapatite has excellent antibacterial properties and biocompatibility, it is difficult to manufacture a sintered body due to its weak fracture toughness. Therefore, hydroxyapatite sintered compacts were prepared according to the amount of plasticizer added and their physical properties were compared. The average compressive strength was 395.1 N·mm-2 at 8 % of the amount of added plasticizer, and the average bending strength was 61.8 N·mm-2 at 6 % of the amount of added plasticizer. The hydroxyapatite sintered compact showed the effect of inhibiting the production of bacteria regardless of the amount of plasticizer added. As a result of this physical property study, it was possible to develop a humidifier vibrator housing with excellent antibacterial properties and maintaining mechanical strength

Direct numerical simulation of electrokinetic transport phenomena: variational multi-scale stabilization and octree-based mesh refinement

Finite element modeling of charged species transport has enabled the analysis, design, and optimization of a diverse array of electrochemical and electrokinetic devices. These systems are represented by the Poisson-Nernst-Planck (PNP) equations coupled with the Navier-Stokes (NS) equation. Direct numerical simulation (DNS) to accurately capture the spatio-temporal variation of ion concentration and current flux remains challenging due to the (a) small critical dimension of the electric double layer (EDL), (b) stiff coupling, large advective effects, and steep gradients close to boundaries, and (c) complex geometries exhibited by electrochemical devices. In the current study, we address these challenges by presenting a direct numerical simulation framework that incorporates: (a) a variational multiscale (VMS) treatment, (b) a block-iterative strategy in conjunction with semi-implicit (for NS) and implicit (for PNP) time integrators, and (c) octree based adaptive mesh refinement. The VMS formulation provides numerical stabilization critical for capturing the electro-convective instabilities often observed in engineered devices. The block-iterative strategy decouples the difficulty of non-linear coupling between the NS and PNP equations and allows using tailored numerical schemes separately for NS and PNP equations. The carefully designed second-order, hybrid implicit methods circumvent the harsh timestep requirements of explicit time steppers, thus enabling simulations over longer time horizons. Finally, the octree-based meshing allows efficient and targeted spatial resolution of the EDL. These features are incorporated into a massively parallel computational framework, enabling the simulation of realistic engineering electrochemical devices. The numerical framework is illustrated using several challenging canonical examples

Density Functional Theory Studies of the [2]Rotaxane Component of the Stoddart−Heath Molecular Switch

The central component of the programmable molecular switch recently demonstrated by Stoddart and Heath is [2]rotaxane, which consists of a cyclobis(paraquat-p-phenylene) shuttle (CBPQT^(4+))(PF_6-)_4 (the ring) encircling a finger and moving between two stations, tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP). As a step toward understanding the mechanism of this switch, we report here its electronic structure using two flavors of density functional theory (DFT):  B3LYP/6-31G^(**) and PBE/6-31G^(**). We find that the electronic structure of composite [2]rotaxane can be constructed reasonably well from its parts by combining the states of separate stations (TTF and DNP) with or without the (CBPQT)(PF_6)_4 shuttle around them. That is, the “CBPQT@TTF” state, (TTF)(CBPQT)(PF_6)_4−(DNP), is described well as a combination of the (TTF)(CBPQT)(PF_6)_4 complex and free DNP, and the “CBPQT@DNP” state, (TTF)−(DNP)(CBPQT)(PF_6)_4, is described well as a combination of free TTF and the (DNP)(CBPQT)(PF_6)_4 complex. This allows an aufbau or a “bottom-up” approach to predict the complicated [n]rotaxanes in terms of their components. This should be useful in designing new components to lead to improved properties of the switches. A critical function of the (CBPQT^(4+))(PF_6-)_4 shuttle in switching is that it induces a downshift of the frontier orbital energy levels of the station it is on (TTF or DNP). This occurs because of the net positive electrostatic potential exerted by the CBPQT^(4+) ring, which is located closer to the active station than the four PF_6-'s. This downshift alters the relative position of energy levels between TTF and DNP, which in turn alters the electron tunneling rate between them, even when the shuttle is not involved directly in the actual tunneling process. Based on this switching mechanism, the “CBPQT@TTF” state is expected to be a better conductor since it has better aligned levels between the two stations. A second potential role of the (CBPQT^(4+))(PF_6-)_4 shuttle in switching is to provide low-lying LUMO levels. If the shuttle is involved in the actual tunneling process, the reduced HOMO−LUMO gap (from 3.6 eV for the isolated finger to 1.1 eV for “CBPQT@TTF” or to 0.6 eV for “CBPQT@DNP” using B3LYP) would significantly facilitate the electron tunneling through the system. This might occur in a folded conformation where a direct contact between free station and the shuttle on the other station is possible. When this becomes the main switching mechanism, we expect the “CBPQT@DNP” state to become a better conductor because its HOMO−LUMO gap is smaller and because its HOMO and LUMO are localized at different stations (HOMO exclusively at TTF and LUMO at CBPQT encircling DNP) so that the HOMO-to-LUMO tunneling would be through the entire molecule of [2]rotaxane. Thus an essential element in designing these switches is to determine the configuration of the molecules (e.g., through self-assembled monolayers or incorporation of conformation stabilizing units)

Experimental and computational methods for electrokinetic charged species enrichment

Science and engineering of enrichment, separation, detection, and extraction of chemical species in a liquid sample have had a significant impact on our society. It has a wide ranges of applications in environment, biotechnology, oil industry, and public health. Some of the examples include, but not limited to, heavy metal detection, DNA analysis, sea water desalination, and hemodialysis. For last decades, there have been a growing interest in a electrokinetic methods for enrichment or separation using a perm-selective membrane or a reactive electrode. The method applies an electric current across the perm-selective membrane or the electrode, then, leverages the unique electric field formation nearby to manipulate target analytes in the electrolytes. The methods prevents direct contacts between the target analytes and the membrane. Therefore, the membrane is more robust on fouling. In addition, the fabrication is easy allowing convenient testing of new ideas for various applications. The electrokientics is a complex multi-physic dealing with fluid flow, electro-dynamics, and mass transport, which controls diffusion, convection, and electro-migration of the species in the electrolytes. This system can be modelled by Navier-Stokes and Poisson-Nernst-Planck equations, which has no analytic solutions except for extremely simplified case. On the other hand, most experimental methods are limited to the current measurement or visualizing concentrations. Therefore, only limited amount of information is accessible making understanding the enrichment/separation system challenging. The research directions in this work are divided into two: First, extend the current capabilities of enrichment/separation by introducing unconventional ways of using the perm-selective membrane or the reactive electrode. Second, develop a numerical framework to solve Navier-Stokes and Poisson-Nernst-Planck equations to simulate charged species transport in electrokinetic separation/enrichment system. To achieve the first goal, the enrichment efficiency was improved by introducing packed bed silver particles on the conventional planar gold electrode. Separately, the perm-selective membrane based electrokinetic system was incorporated into the droplet microfluidics. It was shown that the proposed method can concentrate, separate, and inject ions into the droplets. Then, the method was tested for a cell lysis and enzymatic assay in the microdroplets. For the second goal, highly paralleled finite element method based numerical method was developed. To minimize numerical instabilities and improve the accuracy, variational multiscale method along with Dirichlet to Neumann boundary condition transition were applied. The numerical results showed high efficiency and accuracy in boundary flux calculation. In addition, the numerical results provided detailed information on spatio-temporal electrokinetic instabilities. The results in this work is significant, as it proposed a new method of handling analytes in microdroplets, which has many potential applications. The numerical plate form successfully simulates the charged transport in electrolytes, and provides design suggestions and insights to the experimental part of the study.</p

Experimental and computational methods for electrokinetic charged species enrichment

Science and engineering of enrichment, separation, detection, and extraction of chemical species in a liquid sample have had a significant impact on our society. It has a wide ranges of applications in environment, biotechnology, oil industry, and public health. Some of the examples include, but not limited to, heavy metal detection, DNA analysis, sea water desalination, and hemodialysis. For last decades, there have been a growing interest in a electrokinetic methods for enrichment or separation using a perm-selective membrane or a reactive electrode. The method applies an electric current across the perm-selective membrane or the electrode, then, leverages the unique electric field formation nearby to manipulate target analytes in the electrolytes. The methods prevents direct contacts between the target analytes and the membrane. Therefore, the membrane is more robust on fouling. In addition, the fabrication is easy allowing convenient testing of new ideas for various applications. The electrokientics is a complex multi-physic dealing with fluid flow, electro-dynamics, and mass transport, which controls diffusion, convection, and electro-migration of the species in the electrolytes. This system can be modelled by Navier-Stokes and Poisson-Nernst-Planck equations, which has no analytic solutions except for extremely simplified case. On the other hand, most experimental methods are limited to the current measurement or visualizing concentrations. Therefore, only limited amount of information is accessible making understanding the enrichment/separation system challenging. The research directions in this work are divided into two: First, extend the current capabilities of enrichment/separation by introducing unconventional ways of using the perm-selective membrane or the reactive electrode. Second, develop a numerical framework to solve Navier-Stokes and Poisson-Nernst-Planck equations to simulate charged species transport in electrokinetic separation/enrichment system. To achieve the first goal, the enrichment efficiency was improved by introducing packed bed silver particles on the conventional planar gold electrode. Separately, the perm-selective membrane based electrokinetic system was incorporated into the droplet microfluidics. It was shown that the proposed method can concentrate, separate, and inject ions into the droplets. Then, the method was tested for a cell lysis and enzymatic assay in the microdroplets. For the second goal, highly paralleled finite element method based numerical method was developed. To minimize numerical instabilities and improve the accuracy, variational multiscale method along with Dirichlet to Neumann boundary condition transition were applied. The numerical results showed high efficiency and accuracy in boundary flux calculation. In addition, the numerical results provided detailed information on spatio-temporal electrokinetic instabilities. The results in this work is significant, as it proposed a new method of handling analytes in microdroplets, which has many potential applications. The numerical plate form successfully simulates the charged transport in electrolytes, and provides design suggestions and insights to the experimental part of the study

Designing Asymmetrically Modified Nanochannel Sensors Using Virtual EIS

We devised an approach to capture the physics of localized charge modulation and its effect on ionic transport across asymmetrically charged nanopores by combining computational and experimental strategies. A virtual EIS tool has been developed to compute the impedance across nanopores. Nanoporous anodic alumina membrane (NAA) is employed for thrombin detection with thrombin binding aptamer to experimentally validate the computed impedance results. Using the approach proposed in this work, a novel biosensor is designed and a way to enhance the sensitivity of the sensor is established