Solid State Nanopores: From Fabrication to Biosensing (Nanostructure Science and Technology)

✍ Scribed by Jean-Pierre Leburton (editor)

• Publisher: Springer
• Year: 2023
• Tongue: English
• Leaves: 234
• Category: Library

✦ Synopsis

This contributed volume provides an overview of the recent advances in solid-state nanopore technology, featuring contributions by leading experts in the field. It discusses several aspects of solid-state nanopores, covering their fabrication as well as multiple biosensing applications. It successfully bridges the gap between various scientific and engineering disciplines and highlights the progress made in this area. This title is a useful tool for acquiring basic knowledge of this field and following recent progress. It is a valuable contribution to the area of nanopore biosensing and is of interest to graduate students, postdocs, or senior researchers working in the fields of physical chemistry, biochemistry, bio- and electrical engineering, and biophysics.

✦ Table of Contents

Preface
Contents
1 Fabricating Solid-State Nanopores for Single-Molecule Sensing
1.1 Introduction
1.2 Energetic Particle Beam Drilling
1.2.1 Fabrication
1.2.2 Size Control
1.2.3 Outlook
1.3 Nanopipettes
1.3.1 Fabrication
1.3.2 Size Control
1.3.3 Outlook
1.4 Controlled Breakdown
1.4.1 Fabrication
1.4.2 Controlling Membrane Breakdown
1.4.3 Size Control
1.4.4 Kinetics
1.4.5 Localization
1.4.6 Outlook
1.5 Conclusions
References
2 Emerging Abnormal Phenomena in Confined Nanofluidics
2.1 Basic Concepts
2.1.1 Electrical Double Layer (EDL) and Debye Length
2.1.2 Noise
2.1.3 Resistance
2.2 Research Technique
2.2.1 Confinement Dimension
2.2.2 Fabrication
2.2.3 Regulation, Observation, and Quantification
2.3 Ion Transport
2.3.1 Ionic Coulomb Blockade
2.3.2 Gating
2.3.3 Mechanically Activated Ion Transport
2.3.4 Ion Current Rectification
2.3.5 Liquid–Solid Interaction
2.4 Water Transport
2.4.1 Ultra-Low Dielectric Constant
2.4.2 Structural Phase Transition
2.4.3 Layering
2.4.4 Ultrafast Water Flow
2.5 Molecule Transport
2.6 Conclusions and Perspective
2.6.1 Molecular Sieving
2.6.2 Energy Harvesting
2.6.3 Biomimic Channel for Information Storage and Transfer
References
3 Detecting DNA-Binding Sites of Regulation Proteins with Ion Beam Sculpted Silicon Nitride Nanopores
3.1 Introduction
3.1.1 Background of Low Energy Noble Gas Ion Beam Sculpted Silicon Nitride Nanopores and Their Applications
3.1.2 The Importance of DNA–Protein Binding
3.1.3 Methods Used to Measure DNA–Protein Binding Sites Today
3.1.4 Detecting the Binding Sites of Proteins on DNA Molecules with Nanopore Technology
3.2 Principle of Nanopore Detecting DNA-Binding Sites of Regulation Proteins
3.3 Experimental Setup and Sample Preparation
3.3.1 Silicon Nitride Nanopore Fabrication by Ion Beam Sculpting
3.3.2 DNA and Protein Sample Preparation
3.3.3 Nanopore Experimental Setup
3.3.4 Initial Current Blockage Event Sorting and Analysis
3.4 Results and Discussion: Classification and Selecting of λDNA * RNAPcomp Events
3.5 Subevent Analysis: Estimate the RNAP Binding Positions on a λ DNA
3.5.1 Subevent Analysis for Estimating Protein Binding Position on DNA
3.5.2 Relative Binding Position of RNAP on λ DNA
3.6 Conclusions
References
4 Solid-State Nanopore Sensing Enhanced by Designed DNA Nanostructures
4.1 Conformation of DNA During Its Translocation Through Solid-State Nanopores
4.2 DNA Carrier for Protein Sensing
4.3 DNA Sequence Detection
4.4 Digital Data Storage on Polymers
References
5 Protein Profiling by a Confined Nanopore
5.1 Introduction
5.2 Confined Nanopipette Sensing
5.2.1 Nanopipette for Biological Sample Delivery
5.2.2 Application of Wireless Nanopore Electrode
5.2.3 Sensing of Single Nanoparticles and Single Molecules by Nanopipette
5.3 Snapshotting the Transient Conformation and Dynamics of Single Peptides
5.3.1 Confining a Single Protein into a Nanopore with High Throughput
5.3.2 Investigation of the Dynamic Conformation Changes
5.3.3 Folding Pathway Model for a Single β-Hairpin Peptide
5.3.4 Hidden Transition Pathways and Confined Effects of Individual Peptides Within a Confined Nanopore
5.4 Nanopore Combined Measurement Platform for Single Protein Molecules
5.4.1 System Composition
5.4.2 Performance Test for Single Protein Analysis
5.5 Conclusion
References
6 Self-consistent Brownian Dynamics Simulations of the Ionic Current Blockade in Solid State Nanopores
6.1 Introduction
6.2 Continuum Model for the Ionic Current Calculations in Nanopores
6.2.1 Simulated System
6.2.2 Poisson-Nernst-Planck-Navier-Stokes Model
6.3 Brownian Dynamics Simulations of the Ionic Current
6.3.1 Brownian Dynamics Model
6.3.2 Drag Coefficient in Nanopores
6.3.3 Force and Current Mapping
6.3.4 Ionic Current Traces
6.4 Concentration Polarization and the Ionic Current Blockade in Nanopores
6.4.1 Ionic Current Blockade Calculations
6.4.2 Analysis of Experimental Data
6.5 Conclusion
References
7 Modeling of Ionic and Electronic Bio-Sensing with Semiconductor Nanopores
7.1 Introduction
7.2 Semiconductor Nanopore Electronic Device Structure
7.3 Comprehensive Modeling
7.3.1 Molecular Dynamics and Ionic Current Modeling
7.3.2 Electronic Current Modeling
7.4 Multilayer Membrane Structures
7.4.1 DNA quenching in solid-state nanopore sensor
7.4.2 2D solid-state nanopore multi-probe sensor
7.5 Scalability and Parallel Detection
7.6 Conclusion
References
Index