Effects of porosity and contaminant on evaporation from nanopores

Evaporation from nanopores, owing to its high mass/heat fluxes and high heat transfer coefficients, have found widespread applications in various industrial process, including electronics cooling, solar steam generation, membrane distillation and power generation. To further improve the performance of these nanopore-evaporation-associated processes, it is necessary to experimentally quantify the ultimate transport limit of evaporation from nanopores and understand its dependence on nanoscale confinement and operating conditions. This ultimate transport limit has now been widely accepted to be dictated by evaporation kinetics at the liquid-vapor interface, which is very difficult to quantify experimentally due to the ultra-small evaporation rates from single nanopores. To overcome this challenge, a new measurement approach based on a hybrid nanochannel-nanopore device design has been developed recently. This measurement approach can accurately measure evaporation rates/fluxes from single nanopore and has been used to investigate the effect of nanopore diameter on kinetic-limited evaporation flux. Although this study provides us new fundamental understanding about how nanoscale confinements change evaporation from nanopore, the effects of contaminant and pore porosity, which to some extent determines the practical performance of evaporation from nanopores, have remained elusive. Such lacking understanding has prevented us from developing optimized evaporative nanoporous structures for practical applications. This works aims to investigate the effects of porosity and contaminant on kinetic-limited evaporation flux by experimentally measuring kinetic-limited evaporation rates from nanopore arrays. A modified hybrid nanochannel-nanopore device design is used to achieve this goal. In this modified device design, a nanopore array is directly connected to a 2-D nanochannel and the total evaporation rate from the nanopore array is measured by tracking meniscus receding in the nanochannel during a drying/evaporation process. Using this modified device design, we measured the kinetic-limited evaporation rates from 3x3 nanopore arrays with different interval distances ranging from 200 nm to 1 μm. To facilitate comparison between different devices, the total evaporation rates were converted to evaporation fluxes based on the nanopore projected area. Our results showed that that porosity or nanopore interval distance has negligible effect on the kinetic-limited evaporation flux. We also performed evaporation experiment using water with impurity and studied the effect of contaminant on kinetic-limit evaporation flux. It was observed that the contaminants in water can significantly reduce the kinetic-limited evaporation flux in nanopores and the contaminant effect becomes much more obvious in smaller nanopore due to contaminant-accumulation-induced pore blockage

Forensic SNP genotyping using nanopore MinION sequencing

One of the latest developments in next generation sequencing is the Oxford Nanopore Technologies' (ONT) MinION nanopore sequencer. We studied the applicability of this system to perform forensic genotyping of the forensic female DNA standard 9947 A using the 52 SNP-plex assay developed by the SNPforID consortium. All but one of the loci were correctly genotyped. Several SNP loci were identified as problematic for correct and robust genotyping using nanopore sequencing. All these loci contained homopolymers in the sequence flanking the forensic SNP and most of them were already reported as problematic in studies using other sequencing technologies. When these problematic loci are avoided, correct forensic genotyping using nanopore sequencing is technically feasible

Models and information-theoretic bounds for nanopore sequencing

Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore sequencers can acquire long reads, the high error rates (20%-30%) pose a technical challenge. In a nanopore sequencer, a DNA is migrated through a nanopore and current variations are measured. The DNA sequence is inferred from this observed current pattern using an algorithm called a base-caller. In this paper, we propose a mathematical model for the "channel" from the input DNA sequence to the observed current, and calculate bounds on the information extraction capacity of the nanopore sequencer. This model incorporates impairments like (non-linear) inter-symbol interference, deletions, as well as random response. These information bounds have two-fold application: (1) The decoding rate with a uniform input distribution can be used to calculate the average size of the plausible list of DNA sequences given an observed current trace. This bound can be used to benchmark existing base-calling algorithms, as well as serving a performance objective to design better nanopores. (2) When the nanopore sequencer is used as a reader in a DNA storage system, the storage capacity is quantified by our bounds

Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages, and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we 1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and 2) provide guidelines for determining the appropriate tools for each step. We analyze various combinations of different tools and expose the tradeoffs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious and effective choices for each step of the genome assembly pipeline using nanopore sequence data. Also, with the help of bottlenecks we have found, developers can improve the current tools or build new ones that are both accurate and fast, in order to overcome the high error rates of the nanopore sequencing technology.Comment: To appear in Briefings in Bioinformatics (BIB), 201

Ionic Capillary Evaporation in Weakly Charged Nanopores

Using a variational field theory, we show that an electrolyte confined to a neutral cylindrical nanopore traversing a low dielectric membrane exhibits a first-order ionic liquid-vapor pseudo-phase-transition from an ionic-penetration "liquid" phase to an ionic-exclusion "vapor" phase, controlled by nanopore-modified ionic correlations and dielectric repulsion. For weakly charged nanopores, this pseudotransition survives and may shed light on the mechanism behind the rapid switching of nanopore conductivity observed in experiments.Comment: This version is accepted for publication in PR