Analysis of Field-Effect Biosensors using Self-Consistent 3D Drift-Diffusion and Monte-Carlo Simulations

AbstractField-effect biosensors based on nanowires enjoy considerable popularity due to their high sensitivity and direct electrical readout [1]. However, crucial issues such as the influence of the biomolecules on the charge-carrier transport or the binding of molecules to the surface have not been described satisfactorily yet in a quantitative manner. In order to analyze these effects, we present simulation results based on a 3D macroscopic transport model coupled with Monte-Carlo simulations for the bio-functionalized surface layer. Excellent agreement with measurement data has been found, while detailed study of the influence of the most prominent biomolecules, namely double-stranded DNA and single-stranded DNA, on the current through the semiconductor transducer has been carried out

Protein Transport through Nanopores Illuminated by Long-Time-Scale Simulations

The transport of molecules through nanoscale confined space is relevant in biology, biosensing, and industrial filtration. Microscopically modeling transport through nanopores is required for a fundamental understanding and guiding engineering, but the short duration and low replica number of existing simulation approaches limit statistically relevant insight. Here we explore protein transport in nanopores with a high-throughput computational method that realistically simulates hundreds of up to seconds-long protein trajectories by combining Brownian dynamics and continuum simulation and integrating both driving forces of electroosmosis and electrophoresis. Ionic current traces are computed to enable experimental comparison. By examining three biological and synthetic nanopores, our study answers questions about the kinetics and mechanism of protein transport and additionally reveals insight that is inaccessible from experiments yet relevant for pore design. The discovery of extremely frequent unhindered passage can guide the improvement of biosensor pores to enhance desired biomolecular recognition by pore-tethered receptors. Similarly, experimentally invisible nontarget adsorption to pore walls highlights how to improve recently developed DNA nanopores. Our work can be expanded to pressure-driven flow to model industrial nanofiltration processes

Analysis of a diffusive effective mass model for nanowires

We propose in this paper to derive and analyze a self-consistent model describing the diffusive transport in a nanowire. From a physical point of view, it describes the electron transport in an ultra-scaled confined structure, taking in account the interactions of charged particles with phonons. The transport direction is assumed to be large compared to the wire section and is described by a drift-diffusion equation including effective quantities computed from a Bloch problem in the crystal lattice. The electrostatic potential solves a Poisson equation where the particle density couples on each energy band a two dimensional confinement density with the monodimensional transport density given by the Boltzmann statistics. On the one hand, we study the derivation of this Nanowire Drift-Diffusion Poisson model from a kinetic level description. On the other hand, we present an existence result for this model in a bounded domain

Strain and electronic structure interactions in realistically scaled quantum dot stacks

NRC publication: Ye

Protein Transport through Nanopores Illuminated by Long-Time-Scale Simulations

The transport of molecules through nanoscale confined space is relevant in biology, biosensing, and industrial filtration. Microscopically modeling transport through nanopores is required for a fundamental understanding and guiding engineering, but the short duration and low replica number of existing simulation approaches limit statistically relevant insight. Here we explore protein transport in nanopores with a high-throughput computational method that realistically simulates hundreds of up to seconds-long protein trajectories by combining Brownian dynamics and continuum simulation and integrating both driving forces of electroosmosis and electrophoresis. Ionic current traces are computed to enable experimental comparison. By examining three biological and synthetic nanopores, our study answers questions about the kinetics and mechanism of protein transport and additionally reveals insight that is inaccessible from experiments yet relevant for pore design. The discovery of extremely frequent unhindered passage can guide the improvement of biosensor pores to enhance desired biomolecular recognition by pore-tethered receptors. Similarly, experimentally invisible nontarget adsorption to pore walls highlights how to improve recently developed DNA nanopores. Our work can be expanded to pressure-driven flow to model industrial nanofiltration processes

Assessment of the feasibility and acceptability of using water pasteurization indicators to increase access to safe drinking water in the Peruvian Amazon

Approximately 2 billion people lack access to microbiologically safe drinking water globally. Boiling is the most popular household water treatment method and significantly reduces diarrheal disease, but is often practiced inconsistently or ineffectively. The use of low-cost technologies to improve boiling is one approach with potential for increasing access to safe drinking water. We conducted household trials to evaluate the feasibility and acceptability of water pasteurization indicators (WAPIs) in the Peruvian Amazon in 2015. A total of 28 randomly selected households were enrolled from a rural and a peri-urban community. All households trialed 2 WAPI designs, each for a 2-week period. Ninety-six percent of participants demonstrated the correct use of the WAPIs at the end of each trial, and 88% expressed satisfaction with both WAPI models. Ease of use, short treatment time, knowledge of the association between WAPI use and improved health, and the taste of treated water were among the key factors that influenced acceptability. Ease of use was the key factor that influenced design preference. Participants in both communities preferred a WAPI with a plastic box that floated on the water’s surface compared to a WAPI with a wire that was dipped into the pot of drinking water while it was heating (77% vs. 15%, p < 0.001); we selected the box design for a subsequent randomized trial of this intervention. The high feasibility and acceptability of the WAPIs in this study suggest that these interventions have potential to increase access to safe water in resource-limited settings

ANISOTROPIC MESH ADAPTION GOVERNED BY A HESSIAN MATRIX METRIC

ABSTRACT An essential task for any finite element method is to provide appropriate resolution of the mesh to resolve the initial solution. We present a computational method for anisotropic tetrahedral mesh refinement according to an adjustable discretization error. The initial attribute profile is given by an analytical function which is twice continously differentiable. Anisotropy is taken into account to reduce the amount of elements compared to pure isotropic meshes. By the proposed method the spatial resolution in three-dimensional unstructured tetrahedral meshes used for diffusion simulation is locally increased and the accuracy of the discretization improved