Nanopore sensing of individual transcription factors bound to DNA

PubMed Central

Squires, Allison; Atas, Evrim; Meller, Amit

2015-01-01

Transcription factor (TF)-DNA interactions are the primary control point in regulation of gene expression. Characterization of these interactions is essential for understanding genetic regulation of biological systems and developing novel therapies to treat cellular malfunctions. Solid-state nanopores are a highly versatile class of single-molecule sensors that can provide rich information about local properties of long charged biopolymers using the current blockage patterns generated during analyte translocation, and provide a novel platform for characterization of TF-DNA interactions. The DNA-binding domain of the TF Early Growth Response Protein 1 (EGR1), a prototypical zinc finger protein known as zif268, is used as a model system for this study. zif268 adopts two distinct bound conformations corresponding to specific and nonspecific binding, according to the local DNA sequence. Here we implement a solid-state nanopore platform for direct, label- and tether-free single-molecule detection of zif268 bound to DNA. We demonstrate detection of single zif268 TFs bound to DNA according to current blockage sublevels and duration of translocation through the nanopore. We further show that the nanopore can detect and discriminate both specific and nonspecific binding conformations of zif268 on DNA via the distinct current blockage patterns corresponding to each of these two known binding modes. PMID:26109509

Nanopore sensing of individual transcription factors bound to DNA

NASA Astrophysics Data System (ADS)

Squires, Allison; Atas, Evrim; Meller, Amit

2015-06-01

Transcription factor (TF)-DNA interactions are the primary control point in regulation of gene expression. Characterization of these interactions is essential for understanding genetic regulation of biological systems and developing novel therapies to treat cellular malfunctions. Solid-state nanopores are a highly versatile class of single-molecule sensors that can provide rich information about local properties of long charged biopolymers using the current blockage patterns generated during analyte translocation, and provide a novel platform for characterization of TF-DNA interactions. The DNA-binding domain of the TF Early Growth Response Protein 1 (EGR1), a prototypical zinc finger protein known as zif268, is used as a model system for this study. zif268 adopts two distinct bound conformations corresponding to specific and nonspecific binding, according to the local DNA sequence. Here we implement a solid-state nanopore platform for direct, label- and tether-free single-molecule detection of zif268 bound to DNA. We demonstrate detection of single zif268 TFs bound to DNA according to current blockage sublevels and duration of translocation through the nanopore. We further show that the nanopore can detect and discriminate both specific and nonspecific binding conformations of zif268 on DNA via the distinct current blockage patterns corresponding to each of these two known binding modes.

Structural Integrity of Proteins under Applied Bias during Solid-State Nanopore Translocation

NASA Astrophysics Data System (ADS)

Hasan, Mohammad R.; Khanzada, Raja Raheel; Mahmood, Mohammed A. I.; Ashfaq, Adnan; Iqbal, Samir M.

2015-03-01

The translocation behavior of proteins through solid-state nanopores can be used as a new way to detect and identify proteins. The ionic current through a nanopore that flows under applied bias gets perturbed when a biomolecule traverses the Nanopore. It is important for a protein detection scheme to know of any changes in the three-dimensional structure of the molecule during the process. Here we report the data on structural integrity of protein during translocation through nanopore under different applied biases. Nanoscale Molecular Dynamic was used to establish a framework to study the changes in protein structures as these travelled across the nanopore. The analysis revealed the contributions of structural changes of protein to its ionic current signature. As a model, thrombin protein crystalline structure was imported and positioned inside a 6 nm diameter pore in a 6 nm thick silicon nitride membrane. The protein was solvated in 1 M KCl at 295 K and the system was equilibrated for 20 ns to attain its minimum energy state. The simulation was performed at different electric fields from 0 to 1 kCal/(mol.Å.e). RMSD, radial distribution function, movement of the center of mass and velocity of the protein were calculated. The results showed linear increments in the velocity and perturbations in ionic current profile with increasing electric potential. Support Acknowledged from NSF through ECCS-1201878.

Integration of solid-state nanopores in a 0.5 μm cmos foundry process

PubMed Central

Uddin, A; Yemenicioglu, S; Chen, C-H; Corigliano, E; Milaninia, K; Theogarajan, L

2013-01-01

High-bandwidth and low-noise nanopore sensor and detection electronics are crucial in achieving single-DNA base resolution. A potential way to accomplish this goal is to integrate solid-state nanopores within a CMOS platform, in close proximity to the biasing electrodes and custom-designed amplifier electronics. Here we report the integration of solid-state nanopore devices in a commercial complementary metal-oxide semiconductor (CMOS) potentiostat chip implemented in On-Semiconductor’s 0.5 μm technology. Nanopore membranes incorporating electrodes are fabricated by post-CMOS micromachining utilizing the N+ polysilicon/SiO2/N+ polysilicon capacitor structure available in the aforementioned process. Nanopores are created in the CMOS process by drilling in a transmission electron microscope and shrinking by atomic layer deposition. We also describe a batch fabrication method to process a large of number of electrode-embedded nanopores with sub-10 nm diameter across CMOS-compatible wafers by electron beam lithography and atomic layer deposition. The CMOS-compatibility of our fabrication process is verified by testing the electrical functionality of on-chip circuitry. We observe high current leakage with the CMOS nanopore devices due to the ionic diffusion through the SiO2 membrane. To prevent this leakage, we coat the membrane with Al2O3 which acts as an efficient diffusion barrier against alkali ions. The resulting nanopore devices also exhibit higher robustness and lower 1/f noise as compared to SiO2 and SiNx. Furthermore, we propose a theoretical model for our low-capacitance CMOS nanopore devices, showing good agreement with the experimental value. In addition, experiments and theoretical models of translocation studies are presented using 48.5 kbp λ-DNA in order to prove the functionality of on-chip pores coated with Al2O3. PMID:23519330

Highly sensitive detection using microring resonator and nanopores

NASA Astrophysics Data System (ADS)

Bougot-Robin, K.; Hoste, J. W.; Le Thomas, N.; Bienstman, P.; Edel, J. B.

2016-04-01

One of the most significant challenges facing physical and biological scientists is the accurate detection and identification of single molecules in free-solution environments. The ability to perform such sensitive and selective measurements opens new avenues for a large number of applications in biological, medical and chemical analysis, where small sample volumes and low analyte concentrations are the norm. Access to information at the single or few molecules scale is rendered possible by a fine combination of recent advances in technologies. We propose a novel detection method that combines highly sensitive label-free resonant sensing obtained with high-Q microcavities and position control in nanoscale pores (nanopores). In addition to be label-free and highly sensitive, our technique is immobilization free and does not rely on surface biochemistry to bind probes on a chip. This is a significant advantage, both in term of biology uncertainties and fewer biological preparation steps. Through combination of high-Q photonic structures with translocation through nanopore at the end of a pipette, or through a solid-state membrane, we believe significant advances can be achieved in the field of biosensing. Silicon microrings are highly advantageous in term of sensitivity, multiplexing, and microfabrication and are chosen for this study. In term of nanopores, we both consider nanopore at the end of a nanopipette, with the pore being approach from the pipette with nanoprecise mechanical control. Alternatively, solid state nanopores can be fabricated through a membrane, supporting the ring. Both configuration are discussed in this paper, in term of implementation and sensitivity.

Solid-State and Biological Nanopore for Real-Time Sensing of Single Chemical and Sequencing of DNA.

PubMed

Haque, Farzin; Li, Jinghong; Wu, Hai-Chen; Liang, Xing-Jie; Guo, Peixuan

2013-02-01

Sensitivity and specificity are two most important factors to take into account for molecule sensing, chemical detection and disease diagnosis. A perfect sensitivity is to reach the level where a single molecule can be detected. An ideal specificity is to reach the level where the substance can be detected in the presence of many contaminants. The rapidly progressing nanopore technology is approaching this threshold. A wide assortment of biomotors and cellular pores in living organisms perform diverse biological functions. The elegant design of these transportation machineries has inspired the development of single molecule detection based on modulations of the individual current blockage events. The dynamic growth of nanotechnology and nanobiotechnology has stimulated rapid advances in the study of nanopore based instrumentation over the last decade, and inspired great interest in sensing of single molecules including ions, nucleotides, enantiomers, drugs, and polymers such as PEG, RNA, DNA, and polypeptides. This sensing technology has been extended to medical diagnostics and third generation high throughput DNA sequencing. This review covers current nanopore detection platforms including both biological pores and solid state counterparts. Several biological nanopores have been studied over the years, but this review will focus on the three best characterized systems including α-hemolysin and MspA, both containing a smaller channel for the detection of single-strand DNA, as well as bacteriophage phi29 DNA packaging motor connector that contains a larger channel for the passing of double stranded DNA. The advantage and disadvantage of each system are compared; their current and potential applications in nanomedicine, biotechnology, and nanotechnology are discussed.

Solid-State and Biological Nanopore for Real-Time Sensing of Single Chemical and Sequencing of DNA

PubMed Central

Haque, Farzin; Li, Jinghong; Wu, Hai-Chen; Liang, Xing-Jie; Guo, Peixuan

2013-01-01

Sensitivity and specificity are two most important factors to take into account for molecule sensing, chemical detection and disease diagnosis. A perfect sensitivity is to reach the level where a single molecule can be detected. An ideal specificity is to reach the level where the substance can be detected in the presence of many contaminants. The rapidly progressing nanopore technology is approaching this threshold. A wide assortment of biomotors and cellular pores in living organisms perform diverse biological functions. The elegant design of these transportation machineries has inspired the development of single molecule detection based on modulations of the individual current blockage events. The dynamic growth of nanotechnology and nanobiotechnology has stimulated rapid advances in the study of nanopore based instrumentation over the last decade, and inspired great interest in sensing of single molecules including ions, nucleotides, enantiomers, drugs, and polymers such as PEG, RNA, DNA, and polypeptides. This sensing technology has been extended to medical diagnostics and third generation high throughput DNA sequencing. This review covers current nanopore detection platforms including both biological pores and solid state counterparts. Several biological nanopores have been studied over the years, but this review will focus on the three best characterized systems including α-hemolysin and MspA, both containing a smaller channel for the detection of single-strand DNA, as well as bacteriophage phi29 DNA packaging motor connector that contains a larger channel for the passing of double stranded DNA. The advantage and disadvantage of each system are compared; their current and potential applications in nanomedicine, biotechnology, and nanotechnology are discussed. PMID:23504223

Precise fabrication of a 5 nm graphene nanopore with a helium ion microscope for biomolecule detection

NASA Astrophysics Data System (ADS)

Deng, Yunsheng; Huang, Qimeng; Zhao, Yue; Zhou, Daming; Ying, Cuifeng; Wang, Deqiang

2017-01-01

We report a scalable method to fabricate high-quality graphene nanopores for biomolecule detection using a helium ion microscope (HIM). HIM milling shows promising capabilities for precisely controlling the size and shape, and may allow for the potential production of nanopores at wafer scale. Nanopores could be fabricated at different sizes ranging from 5 to 30 nm in diameter in few minutes. Compared with the current solid-state nanopore fabrication techniques, e.g. transmission electron microscopy, HIM is fast. Furthermore, we investigated the exposure-time dependence of graphene nanopore formation: the rate of pore expansion did not follow a simple linear relationship with exposure time, but a fast expansion rate at short exposure time and a slow rate at long exposure time. In addition, we performed biomolecule detection with our patterned graphene nanopore. The ionic current signals induced by 20-base single-stranded DNA homopolymers could be used as a basis for homopolymer differentiation. However, the charge interaction of homopolymer chains with graphene nanopores, and the conformations of homopolymer chains need to be further considered to improve the accuracy of discrimination.

Integration of solid-state nanopores in a 0.5 μm CMOS foundry process.

PubMed

Uddin, A; Yemenicioglu, S; Chen, C-H; Corigliano, E; Milaninia, K; Theogarajan, L

2013-04-19

High-bandwidth and low-noise nanopore sensor and detection electronics are crucial in achieving single-DNA-base resolution. A potential way to accomplish this goal is to integrate solid-state nanopores within a CMOS platform, in close proximity to the biasing electrodes and custom-designed amplifier electronics. Here we report the integration of solid-state nanopore devices in a commercial complementary metal-oxide-semiconductor (CMOS) potentiostat chip implemented in On-Semiconductor's 0.5 μm technology. Nanopore membranes incorporating electrodes are fabricated by post-CMOS micromachining utilizing the n+ polysilicon/SiO2/n+ polysilicon capacitor structure available in the aforementioned process. Nanopores are created in the CMOS process by drilling in a transmission electron microscope and shrinking by atomic layer deposition. We also describe a batch fabrication method to process a large of number of electrode-embedded nanopores with sub-10 nm diameter across CMOS-compatible wafers by electron beam lithography and atomic layer deposition. The CMOS-compatibility of our fabrication process is verified by testing the electrical functionality of on-chip circuitry. We observe high current leakage with the CMOS nanopore devices due to the ionic diffusion through the SiO2 membrane. To prevent this leakage, we coat the membrane with Al2O3, which acts as an efficient diffusion barrier against alkali ions. The resulting nanopore devices also exhibit higher robustness and lower 1/f noise as compared to SiO2 and SiNx. Furthermore, we propose a theoretical model for our low-capacitance CMOS nanopore devices, showing good agreement with the experimental value. In addition, experiments and theoretical models of translocation studies are presented using 48.5 kbp λ-DNA in order to prove the functionality of on-chip pores coated with Al2O3.

Probe DNA-Cisplatin Interaction with Solid-State Nanopores

NASA Astrophysics Data System (ADS)

Zhou, Zhi; Hu, Ying; Li, Wei; Xu, Zhi; Wang, Pengye; Bai, Xuedong; Shan, Xinyan; Lu, Xinghua; Nanopore Collaboration

2014-03-01

Understanding the mechanism of DNA-cisplatin interaction is essential for clinical application and novel drug design. As an emerging single-molecule technology, solid-state nanopore has been employed in biomolecule detection and probing DNA-molecule interactions. Herein, we reported a real-time monitoring of DNA-cisplatin interaction by employing solid-state SiN nanopores. The DNA-cisplatin interacting process is clearly classified into three stages by measuring the capture rate of DNA-cisplatin adducts. In the first stage, the negative charged DNA molecules were partially discharged due to the bonding of positive charged cisplatin and forming of mono-adducts. In the second stage, forming of DNA-cisplatin di-adducts with the adjacent bases results in DNA bending and softening. The capture rate increases since the softened bi-adducts experience a lower barrier to thread into the nanopores. In the third stage, complex structures, such as micro-loop, are formed and the DNA-cisplatin adducts are aggregated. The capture rate decreases to zero as the aggregated adduct grows to the size of the pore. The characteristic time of this stage was found to be linear with the diameter of the nanopore and this dynamic process can be described with a second-order reaction model. We are grateful to Laboratory of Microfabrication, Dr. Y. Yao, and Prof. R.C. Yu (Institute of Physics, Chinese Academy of Sciences) for technical assistance.

Rapid ultrasensitive single particle surface-enhanced Raman spectroscopy using metallic nanopores.

PubMed

Cecchini, Michael P; Wiener, Aeneas; Turek, Vladimir A; Chon, Hyangh; Lee, Sangyeop; Ivanov, Aleksandar P; McComb, David W; Choo, Jaebum; Albrecht, Tim; Maier, Stefan A; Edel, Joshua B

2013-10-09

Nanopore sensors embedded within thin dielectric membranes have been gaining significant interest due to their single molecule sensitivity and compatibility of detecting a large range of analytes, from DNA and proteins, to small molecules and particles. Building on this concept we utilize a metallic Au solid-state membrane to translocate and rapidly detect single Au nanoparticles (NPs) functionalized with 589 dye molecules using surface-enhanced resonance Raman spectroscopy (SERRS). We show that, due to the plasmonic coupling between the Au metallic nanopore surface and the NP, signal intensities are enhanced when probing analyte molecules bound to the NP surface. Although not single molecule, this nanopore sensing scheme benefits from the ability of SERRS to provide rich vibrational information on the analyte, improving on current nanopore-based electrical and optical detection techniques. We show that the full vibrational spectrum of the analyte can be detected with ultrahigh spectral sensitivity and a rapid temporal resolution of 880 μs.

Nanopore arrays in a silicon membrane for parallel single-molecule detection: fabrication

NASA Astrophysics Data System (ADS)

Schmidt, Torsten; Zhang, Miao; Sychugov, Ilya; Roxhed, Niclas; Linnros, Jan

2015-08-01

Solid state nanopores enable translocation and detection of single bio-molecules such as DNA in buffer solutions. Here, sub-10 nm nanopore arrays in silicon membranes were fabricated by using electron-beam lithography to define etch pits and by using a subsequent electrochemical etching step. This approach effectively decouples positioning of the pores and the control of their size, where the pore size essentially results from the anodizing current and time in the etching cell. Nanopores with diameters as small as 7 nm, fully penetrating 300 nm thick membranes, were obtained. The presented fabrication scheme to form large arrays of nanopores is attractive for parallel bio-molecule sensing and DNA sequencing using optical techniques. In particular the signal-to-noise ratio is improved compared to other alternatives such as nitride membranes suffering from a high-luminescence background.

Nanopore arrays in a silicon membrane for parallel single-molecule detection: fabrication.

PubMed

Schmidt, Torsten; Zhang, Miao; Sychugov, Ilya; Roxhed, Niclas; Linnros, Jan

2015-08-07

Solid state nanopores enable translocation and detection of single bio-molecules such as DNA in buffer solutions. Here, sub-10 nm nanopore arrays in silicon membranes were fabricated by using electron-beam lithography to define etch pits and by using a subsequent electrochemical etching step. This approach effectively decouples positioning of the pores and the control of their size, where the pore size essentially results from the anodizing current and time in the etching cell. Nanopores with diameters as small as 7 nm, fully penetrating 300 nm thick membranes, were obtained. The presented fabrication scheme to form large arrays of nanopores is attractive for parallel bio-molecule sensing and DNA sequencing using optical techniques. In particular the signal-to-noise ratio is improved compared to other alternatives such as nitride membranes suffering from a high-luminescence background.

Noise in solid-state nanopores

PubMed Central

Smeets, R. M. M.; Keyser, U. F.; Dekker, N. H.; Dekker, C.

2008-01-01

We study ionic current fluctuations in solid-state nanopores over a wide frequency range and present a complete description of the noise characteristics. At low frequencies (f ≲ 100 Hz) we observe 1/f-type of noise. We analyze this low-frequency noise at different salt concentrations and find that the noise power remarkably scales linearly with the inverse number of charge carriers, in agreement with Hooge's relation. We find a Hooge parameter α = (1.1 ± 0.1) × 10−4. In the high-frequency regime (f ≳ 1 kHz), we can model the increase in current power spectral density with frequency through a calculation of the Johnson noise. Finally, we use these results to compute the signal-to-noise ratio for DNA translocation for different salt concentrations and nanopore diameters, yielding the parameters for optimal detection efficiency. PMID:18184817

Noise in solid-state nanopores.

PubMed

Smeets, R M M; Keyser, U F; Dekker, N H; Dekker, C

2008-01-15

We study ionic current fluctuations in solid-state nanopores over a wide frequency range and present a complete description of the noise characteristics. At low frequencies (f approximately < 100 Hz) we observe 1/f-type of noise. We analyze this low-frequency noise at different salt concentrations and find that the noise power remarkably scales linearly with the inverse number of charge carriers, in agreement with Hooge's relation. We find a Hooge parameter alpha = (1.1 +/- 0.1) x 10(-4). In the high-frequency regime (f approximately > 1 kHz), we can model the increase in current power spectral density with frequency through a calculation of the Johnson noise. Finally, we use these results to compute the signal-to-noise ratio for DNA translocation for different salt concentrations and nanopore diameters, yielding the parameters for optimal detection efficiency.

DNA Origami-Graphene Hybrid Nanopore for DNA Detection.

PubMed

Barati Farimani, Amir; Dibaeinia, Payam; Aluru, Narayana R

2017-01-11

DNA origami nanostructures can be used to functionalize solid-state nanopores for single molecule studies. In this study, we characterized a nanopore in a DNA origami-graphene heterostructure for DNA detection. The DNA origami nanopore is functionalized with a specific nucleotide type at the edge of the pore. Using extensive molecular dynamics (MD) simulations, we computed and analyzed the ionic conductivity of nanopores in heterostructures carpeted with one or two layers of DNA origami on graphene. We demonstrate that a nanopore in DNA origami-graphene gives rise to distinguishable dwell times for the four DNA base types, whereas for a nanopore in bare graphene, the dwell time is almost the same for all types of bases. The specific interactions (hydrogen bonds) between DNA origami and the translocating DNA strand yield different residence times and ionic currents. We also conclude that the speed of DNA translocation decreases due to the friction between the dangling bases at the pore mouth and the sequencing DNA strands.

DNA translocation measurements in solid-state nanopores fabricated using helium-ion microscope

NASA Astrophysics Data System (ADS)

Liu, Liping; Miao, Wang; Huynh, Chuong; Liu, Quanjun; Ling, Xinsheng

2012-02-01

We report high-quality DNA translocation measurements in solid-state nanopores drilled in free-standing SiN membranes by using a helium-ion beam in a Zeiss helium-ion microscope (HIM). We show that the HIM nanopores have similar performance as the TEM-drilled pores.

Nanoscale Bio-engineering Solutions for Space Exploration: The Nanopore Sequencer

NASA Technical Reports Server (NTRS)

Stolc, Viktor; Cozmuta, Ioana

2004-01-01

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation, with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes.

Nanoscale Bioengineering Solutions for Space Exploration the Nanopore Sequencer

NASA Technical Reports Server (NTRS)

Ioana, Cozmuta; Viktor, Stoic

2005-01-01

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation. with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes. http://phenomrph.arc.nasa.gov/index.php

Highly Sensitive Biosensing with Solid-State Nanopores Displaying Enzymatically Reconfigurable Rectification Properties.

PubMed

Pérez-Mitta, Gonzalo; Peinetti, Ana S; Cortez, M Lorena; Toimil-Molares, María Eugenia; Trautmann, Christina; Azzaroni, Omar

2018-05-09

Molecular design of biosensors based on enzymatic processes taking place in nanofluidic elements is receiving increasing attention by the scientific community. In this work, we describe the construction of novel ultrasensitive enzymatic nanopore biosensors employing "reactive signal amplifiers" as key elements coupled to the transduction mechanism. The proposed framework offers innovative design concepts not only to amplify the detected ionic signal and develop ultrasensitive nanopore-based sensors but also to construct nanofluidic diodes displaying specific chemo-reversible rectification properties. The integrated approach is demonstrated by electrostatically assembling poly(allylamine) on the anionic pore walls followed by the assembly of urease. We show that the cationic weak polyelectrolyte acts as a "reactive signal amplifier" in the presence of local pH changes induced by the enzymatic reaction. These bioinduced variations in proton concentration ultimately alter the protonation degree of the polyamine resulting in amplifiable, controlled, and reproducible changes in the surface charge of the pore walls, and consequently on the generated ionic signals. The "iontronic" response of the as-obtained devices is fully reversible, and nanopores are reused and assayed with different urea concentrations, thus ensuring reliable design. The limit of detection (LOD) was 1 nM. To the best of our knowledge, this value is the lowest LOD reported to date for enzymatic urea detection. In this context, we envision that this approach based on the use of "reactive signal amplifiers" into solid-state nanochannels will provide new alternatives for the molecular design of highly sensitive nanopore biosensors as well as (bio)chemically addressable nanofluidic elements.

Reaching the Ionic Current Detection Limit in Silicon-Based Nanopores

NASA Astrophysics Data System (ADS)

Puster, Matthew; Rodriguez-Manzo, Julio Alejandro; Nicolai, Adrien; Meunier, Vincent; Drndic, Marija

2015-03-01

Solid-state nanopores act as single-molecule sensors whereby passage of an individual molecule in aqueous electrolyte through a nanopore is registered as a change in ionic conductance (ΔG). Future nanopore applications such as DNA sequencing at high bandwidth require high ΔG for optimal signal-to-noise ratio. Reducing the nanopore diameter and thickness increase ΔG. Molecule size limits the diameter, thus efforts concentrate on minimizing the thickness by thinning oxide/nitride films or using 2D materials. Weighted by electrolyte conductivity the highest ΔG reported to date for DNA translocations were obtained with nanopores made in oxide/nitride films. We present a controlled electron irradiation technique to thin such films to the limit of their stability, producing nanopores tailored to molecule size in amorphous Si with thicknesses less than 2 nm. We compare ΔG values with results found in the literature for DNA translocation through these nanopores, where access resistance becomes comparable to the resistance through the nanopore itself.

Multichannel detection of ionic currents through two nanopores fabricated on integrated Si3N4 membranes.

PubMed

Yanagi, Itaru; Akahori, Rena; Aoki, Mayu; Harada, Kunio; Takeda, Ken-Ichi

2016-08-16

Integration of solid-state nanopores and multichannel detection of signals from each nanopore are effective measures for realizing high-throughput nanopore sensors. In the present study, we demonstrated fabrication of Si3N4 membrane arrays and the simultaneous measurement of ionic currents through two nanopores formed in two adjacent membranes. Membranes with thicknesses as low as 6.4 nm and small nanopores with diameters of less than 2 nm could be fabricated using the poly-Si sacrificial-layer process and multilevel pulse-voltage injection. Using the fabricated nanopore membranes, we successfully achieved simultaneous detection of clear ionic-current blockades when single-stranded short homopolymers (poly(dA)60) passed through two nanopores. In addition, we investigated the signal crosstalk and leakage current among separated chambers. When two nanopores were isolated on the front surface of the membrane, there was no signal crosstalk or leakage current between the chambers. However, when two nanopores were isolated on the backside of the Si substrate, signal crosstalk and leakage current were observed owing to high-capacitance coupling between the chambers and electrolysis of water on the surface of the Si substrate. The signal crosstalk and leakage current could be suppressed by oxidizing the exposed Si surface in the membrane chip. Finally, the observed ionic-current blockade when poly(dA)60 passed through the nanopore in the oxidized chip was approximately half of that observed in the non-oxidized chip.

Characterization of Noble Gas Ion Beam Fabricated Single Molecule Nanopore Detectors

NASA Astrophysics Data System (ADS)

Rollings, Ryan; Ledden, Bradley; Shultz, John; Fologea, Daniel; Li, Jiali; Chervinsky, John; Golovchenko, Jene

2006-03-01

Nanopores fabricated with low energy noble gas ion beams in a silicon nitride membrane can be employed as the fundamental element of single biomolecule detection and characterization devices [1,2]. With the help of X-ray Photoelectron Spectroscopy (XPS) and Rutherford Backscattering (RBS), we demonstrate that the electrical noise properties, and hence ultimate sensitivity of nanopore single molecule detectors depends on ion beam species and nanopore annealing conditions. .1. Li, J., D. Stein, C. McMullan, D. Branton, M.J. Aziz, and J.A. Golovchenko, Ion-beam sculpting at nanometre length scales. Nature, 2001. 412(12 July): p. 166-169. 2. Li, J., M. Gershow, D. Stein, E. Brandin, and J.A. Golovchenko, DNA Molecules and Configurations in a Solid-state Nanopore Microscope. Nature Materials, 2003. 2: p. 611-615.

Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases.

PubMed

Ahmed, Towfiq; Haraldsen, Jason T; Rehr, John J; Di Ventra, Massimiliano; Schuller, Ivan; Balatsky, Alexander V

2014-03-28

Nanopore-based sequencing has demonstrated a significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multilayered graphene-based nanopore device architecture for the recognition of single biomolecules. Molecular detection and analysis can be accomplished through the detection of transverse currents as the molecule or DNA base translocates through the nanopore. To increase the overall signal-to-noise ratio and the accuracy, we implement a new 'multi-point cross-correlation' technique for identification of DNA bases or other molecules on the single molecular level. We demonstrate that the cross-correlations between each nanopore will greatly enhance the transverse current signal for each molecule. We implement first-principles transport calculations for DNA bases surveyed across a multilayered graphene nanopore system to illustrate the advantages of the proposed geometry. A time-series analysis of the cross-correlation functions illustrates the potential of this method for enhancing the signal-to-noise ratio. This work constitutes a significant step forward in facilitating fingerprinting of single biomolecules using solid state technology.

Single Nanoparticle Translocation Through Chemically Modified Solid Nanopore

NASA Astrophysics Data System (ADS)

Tan, Shengwei; Wang, Lei; Liu, Hang; Wu, Hongwen; Liu, Quanjun

2016-02-01

The nanopore sensor as a high-throughput and low-cost technology can detect single nanoparticle in solution. In the present study, the silicon nitride nanopores were fabricated by focused Ga ion beam (FIB), and the surface was functionalized with 3-aminopropyltriethoxysilane to change its surface charge density. The positively charged nanopore surface attracted negatively charged nanoparticles when they were in the vicinity of the nanopore. And, nanoparticle translocation speed was slowed down to obtain a clear and deterministic signal. Compared with previous studied small nanoparticles, the electrophoretic translocation of negatively charged polystyrene (PS) nanoparticles (diameter ~100 nm) was investigated in solution using the Coulter counter principle in which the time-dependent nanopore current was recorded as the nanoparticles were driven across the nanopore. A linear dependence was found between current drop and biased voltage. An exponentially decaying function ( t d ~ e -v/v0 ) was found between the duration time and biased voltage. The interaction between the amine-functionalized nanopore wall and PS microspheres was discussed while translating PS microspheres. We explored also translocations of PS microspheres through amine-functionalized solid-state nanopores by varying the solution pH (5.4, 7.0, and 10.0) with 0.02 M potassium chloride (KCl). Surface functionalization showed to provide a useful step to fine-tune the surface property, which can selectively transport molecules or particles. This approach is likely to be applied to gene sequencing.

High capacity and stable all-solid-state Li ion battery using SnO2-embedded nanoporous carbon.

PubMed

Notohara, Hiroo; Urita, Koki; Yamamura, Hideyuki; Moriguchi, Isamu

2018-06-08

Extensive research efforts are devoted to development of high performance all-solid-state lithium ion batteries owing to their potential in not only improving safety but also achieving high stability and high capacity. However, conventional approaches based on a fabrication of highly dense electrode and solid electrolyte layers and their close contact interface is not always applicable to high capacity alloy- and/or conversion-based active materials such as SnO 2 accompanied with large volume change in charging-discharging. The present work demonstrates that SnO 2 -embedded nanoporous carbons without solid electrolyte inside the nanopores are a promising candidate for high capacity and stable anode material of all-solid-state battery, in which the volume change reactions are restricted in the nanopores to keep the constant electrode volume. A prototype all-solid-state full cell consisting of the SnO 2 -based anode and a LiNi 1/3 Co 1 / 3 Mn 1/3 O 2 -based cathode shows a good performance of 2040 Wh/kg at 268.6 W/kg based on the anode material weight.

DNA translocation through graphene nanopores.

PubMed

Merchant, Christopher A; Healy, Ken; Wanunu, Meni; Ray, Vishva; Peterman, Neil; Bartel, John; Fischbein, Michael D; Venta, Kimberly; Luo, Zhengtang; Johnson, A T Charlie; Drndić, Marija

2010-08-11

We report on DNA translocations through nanopores created in graphene membranes. Devices consist of 1-5 nm thick graphene membranes with electron-beam sculpted nanopores from 5 to 10 nm in diameter. Due to the thin nature of the graphene membranes, we observe larger blocked currents than for traditional solid-state nanopores. However, ionic current noise levels are several orders of magnitude larger than those for silicon nitride nanopores. These fluctuations are reduced with the atomic-layer deposition of 5 nm of titanium dioxide over the device. Unlike traditional solid-state nanopore materials that are insulating, graphene is an excellent electrical conductor. Use of graphene as a membrane material opens the door to a new class of nanopore devices in which electronic sensing and control are performed directly at the pore.

15N and 31P solid-state NMR study of transmembrane domain alignment of M2 protein of influenza A virus in hydrated cylindrical lipid bilayers confined to anodic aluminum oxide nanopores.

PubMed

Chekmenev, Eduard Y; Hu, Jun; Gor'kov, Peter L; Brey, William W; Cross, Timothy A; Ruuge, Andres; Smirnov, Alex I

2005-04-01

This communication reports the first example of a high resolution solid-state 15N 2D PISEMA NMR spectrum of a transmembrane peptide aligned using hydrated cylindrical lipid bilayers formed inside nanoporous anodic aluminum oxide (AAO) substrates. The transmembrane domain SSDPLVVA(A-15N)SIIGILHLILWILDRL of M2 protein from influenza A virus was reconstituted in hydrated 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine bilayers that were macroscopically aligned by a conventional micro slide glass support or by the AAO nanoporous substrate. 15N and 31P NMR spectra demonstrate that both the phospholipids and the protein transmembrane domain are uniformly aligned in the nanopores. Importantly, nanoporous AAO substrates may offer several advantages for membrane protein alignment in solid-state NMR studies compared to conventional methods. Specifically, higher thermal conductivity of aluminum oxide is expected to suppress thermal gradients associated with inhomogeneous radio frequency heating. Another important advantage of the nanoporous AAO substrate is its excellent accessibility to the bilayer surface for exposure to solute molecules. Such high accessibility achieved through the substrate nanochannel network could facilitate a wide range of structure-function studies of membrane proteins by solid-state NMR.

PREFACE New developments in nanopore research—from fundamentals to applications New developments in nanopore research—from fundamentals to applications

NASA Astrophysics Data System (ADS)

Albrecht, Tim; Edel, Joshua B.; Winterhalter, Mathias

2010-11-01

Biological and solid-state nanopores are an exciting field of research, which has seen a rapid development over the last 10 to 20 years. Activities in this area range from theoretical and experimental work on the underlying fundamental (bio)physics to applications in single-molecule biosensing. And while the prospect of DNA sequencing continues to be a major driving force, other applications with potentially similar impact begin to emerge, for example the detection of small molecules, proteins, protein/protein and protein/DNA complexes, and RNA to name just a few. It has also become apparent that both classes of nanopore devices have intrinsic advantages and disadvantages; hybrid structures combining the better of the two worlds would be a logical consequence and are beginning to appear in the literature. Many other highly innovative ideas and concepts continue to emerge and the number of nanopore-related publications has increased drastically over recent years. We found that more than 100 research groups worldwide are active in this area; several commercial settings are in the process of translating fundamental research into real-life applications. We therefore felt that now is the right time to showcase these new developments in a special issue: to inspire researchers active in the field, to liberate inherent synergies, and not least, to demonstrate to the outside world the current state-of-the-art and future opportunities. The title 'New developments in nanopore research—from fundamentals to applications' in some way reflects these ambitions and, even though not everyone invited was able to contribute, we were able to assemble 34 high-quality research papers from all over the world. We would like to acknowledge and thank all the contributors for their submissions, which made this special issue possible in the first place. Moreover, we would like to thank the staff at IOP Publishing for helping us with the administrative aspects and for coordinating the refereeing process, and Ms Natalia Goehring for the beautiful cover artwork. Finally, to the readers, we hope you find this special issue a valuable source of information and insight into the field of nanopores. New developments in nanopore research—from fundamentals to applications contents Mathematical modeling and simulation of nanopore blocking by precipitation M-T Wolfram, M Burger and Z S Siwy Protein conducting nanopores Anke Harsman, Vivien Krüger, Philipp Bartsch, Alf Honigmann, Oliver Schmidt, Sanjana Rao, Christof Meisinger and Richard Wagner Electrically sensing protease activity with nanopores Mikiembo Kukwikila and Stefan Howorka Electrical characterization of DNA-functionalized solid state nanopores for bio-sensing V Mussi, P Fanzio, L Repetto, G Firpo, P Scaruffi, S Stigliani, M Menotta, M Magnani, G P Tonini and U Valbusa Automatable lipid bilayer formation and ion channel measurement using sessile droplets J L Poulos, S A Portonovo, H Bang and J J Schmidt Critical assessment of OmpF channel selectivity: merging information from different experimental protocols M L López, E García-Giménez, V M Aguilella and A Alcaraz Chemically modified solid state nanopores for high throughput nanoparticle separation Anmiv S Prabhu, Talukder Zaki N Jubery, Kevin J Freedman, Rafael Mulero, Prashanta Dutta and Min Jun Kim Changes in ion channel geometry resolved to sub-ångström precision via single molecule mass spectrometry Joseph W F Robertson, John J Kasianowicz and Joseph E Reiner Entropic transport of finite size particles W Riefler, G Schmid, P S Burada and P Hänggi Osmotic stress regulates the strength and kinetics of sugar binding to the maltoporin channel Philip A Gurnev, Daniel Harries, V Adrian Parsegian and Sergey M Bezrukov Detection of urea-induced internal denaturation of dsDNA using solid-state nanoporesn Alon Singer, Heiko Kuhn, Maxim Frank-Kamenetskii and Amit Meller Translocation events in a single-walled carbon nanotube Jin He, Hao Liu, Pei Pang, Di Cao and Stuart Lindsay Probing DNA with micro- and nanocapillaries and optical tweezers L J Steinbock, O Otto, D R Skarstam, S Jahn, C Chimerel, J L Gornall and U F Keyser Fabrication of nanopores with embedded annular electrodes and transverse carbon nanotube electrodes Zhijun Jiang, Mirna Mihovilovic, Jason Chan and Derek Stein Fabrication and electrical characterization of a pore-cavity-pore device D Pedone, M Langecker, A M Münzer, R Wei, R D Nagel and U Rant Use of tunable nanopore blockade rates to investigate colloidal dispersions G R Willmott, R Vogel, S S C Yu, L G Groenewegen, G S Roberts, D Kozak, W Anderson and M Trau Facilitated translocation of polypeptides through a single nanopore Robert Bikwemu, Aaron J Wolfe, Xiangjun Xing and Liviu Movileanu Mechanistic insight into gramicidin-based detection of protein-ligand interactions via sensitized photoinactivation Tatyana I Rokitskaya, Michael X Macrae, Steven Blake, Natalya S Egorova, Elena A Kotova, Jerry Yang and Yuri N Antonenko Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy Stephan Renner, Andrey Bessonov, Ulrich Gerland and Friedrich C Simmel Hydration properties of mechanosensitive channel pores define the energetics of gating A Anishkin, B Akitake, K Kamaraju, C-S Chiang and S Sukharev Dynamic translocation of ligand-complexed DNA through solid-state nanopores with optical tweezers Andy Sischka, Andre Spiering, Maryam Khaksar, Miriam Laxa, Janine König, Karl-Josef Dietz and Dario Anselmetti Force fluctuations assist nanopore unzipping of DNA V Viasnoff, N Chiaruttini, J Muzard and U Bockelmann Control and reversal of the electrophoretic force on DNA in a charged nanopore Binquan Luan and Aleksei Aksimentiev The properties of the outer membrane localized Lipid A transporter LptD Raimund Haarmann, Mohamed Ibrahim, Mara Stevanovic, Rolf Bredemeier and Enrico Schleiff Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations Amit Kumar, Eric Hajjar, Paolo Ruggerone and Matteo Ceccarelli Dehydration and ionic conductance quantization in nanopores Michael Zwolak, James Wilson and Massimiliano Di Ventra Current oscillations generated by precipitate formation in the mixing zone between two solutions inside a nanopore Erik C Yusko, Yazan N Billeh and Michael Mayer Precise electrochemical fabrication of sub-20 nm solid-state nanopores for single-molecule biosensing Mariam Ayub, Aleksandar Ivanov, Jongin Hong, Phillip Kuhn, Emanuele Instuli, Joshua B Edel and Tim Albrecht The distribution of DNA translocation times in solid-state nanopores Jiali Li and David S Talaga Crowding effects in non-equilibrium transport through nano-channels A Zilman and G Bel Permeation through nanochannels: revealing fast kinetics Kozhinjampara R Mahendran, Pratik Raj Singh, Jürgen Arning, Stefan Stolte, Ulrich Kleinekathöfer and Mathias Winterhalter LILBID-mass spectrometry of the mitochondrial preprotein translocase TOM Frauke Mager, Lucie Sokolova, Julia Lintzel, Bernhard Brutschy and Stephan Nussberger Evidence that small proteins translocate through silicon nitride pores in a folded conformation Radu I Stefureac, Dhruti Trivedi, Andre Marziali and Jeremy S Lee Methods for controlling the pore properties of ultra-thin nanocrystalline silicon membranes D Z Fang, C C Striemer, T R Gaborski, J L McGrath and P M Fauchet

Ultra-Thin Solid-State Nanopores: Fabrication and Applications

NASA Astrophysics Data System (ADS)

Kuan, Aaron Tzeyang

Solid-state nanopores are a nanofluidic platform with unique advantages for single-molecule analysis and filtration applications. However, significant improvements in device performance and scalable fabrication methods are needed to make nanopore devices competitive with existing technologies. This dissertation investigates the potential advantages of ultra-thin nanopores in which the thickness of the membrane is significantly smaller than the nanopore diameter. Novel, scalable fabrication methods were first developed and then utilized to examine device performance for water filtration and single molecule sensing applications. Fabrication of nanometer-thin pores in silicon nitride membranes was achieved using a feedback-controlled ion beam method in which ion sputtering is arrested upon detection of the first few ions that drill through the membrane. Performing fabrication at liquid nitrogen temperatures prevents surface atom rearrangements that have previously complicated similar processes. A novel cross-sectional imaging method was also developed to allow careful examination of the full nanopore geometry. Atomically-thin graphene nanopores were fabricated via an electrical pulse method in which sub-microsecond electrical pulses applied across a graphene membrane in electrolyte solution are used to create a defect in the membrane and controllably enlarge it into a nanopore. This method dramatically increases the accuracy and reliability of graphene nanopore production, allowing consistent production of single nanopores down to subnanometer sizes. In filtration applications in which nanopores are used to selectively restrict the passage of dissolved contaminants, ultra-thin nanopores minimize the flow resistance, increasing throughput and energy-efficiency. The ability of graphene nanopores to separate different ions was characterized via ionic conductance and reversal potential measurements. Graphene nanopores were observed to conduct cations preferentially over anions with selectivity ratios of 100 or higher for pores as large as 20 nm in diameter, suggesting that porous graphene membranes can be used to create highly effective cation exchange membranes for electrodialysis filtration. These surprisingly high selectivities cannot be explained by current models of ionic conduction in graphene nanopores, motivating the development of a new model in which elevated concentrations of mobile cations near the graphene surface generate additional ion selectivity.

Multilevel description of the DNA molecule translocation in solid-state synthetic nanopores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nosik, V. L., E-mail: v-nosik@yandex.ru; Rudakova, E. B.

2016-07-15

Interest of researchers in micro- and nanofluidics of polymer solutions and, in particular, DNA ionic solutions is constantly increasing. The use of DNA translocation with a controlled velocity through solid-state nanopores and pulsed X-ray beams in new sequencing schemes opens up new possibilities for studying the structure of DNA and other biopolymers. The problems related to the description of DNA molecular motion in a limited volume of nanopore are considered.

Discrimination of three types of homopolymers in single-stranded DNA with solid-state nanopores through external control of the DNA motion.

PubMed

Akahori, Rena; Yanagi, Itaru; Goto, Yusuke; Harada, Kunio; Yokoi, Takahide; Takeda, Ken-Ichi

2017-08-22

To achieve DNA sequencing with solid-state nanopores, the speed of the DNA in the nanopore must be controlled to obtain sequence-specific signals. In this study, we fabricated a nanopore-sensing system equipped with a DNA motion controller. DNA strands were immobilized on a Si probe, and approach of this probe to the nanopore vicinity could be controlled using a piezo actuator and stepper motor. The area of the Si probe was larger than the area of the membrane, which meant that the immobilized DNA could enter the nanopore without the need for the probe to scan to determine the location of the nanopore in the membrane. We demonstrated that a single-stranded DNA could be inserted into and removed from a nanopore in our experimental system. The number of different ionic-current levels observed while DNA remained in the nanopore corresponded to the number of different types of homopolymers in the DNA.

Measurement of DNA translocation dynamics in a solid-state nanopore at 100-ns temporal resolution

PubMed Central

Shekar, Siddharth; Niedzwiecki, David J.; Chien, Chen-Chi; Ong, Peijie; Fleischer, Daniel A.; Lin, Jianxun; Rosenstein, Jacob K.; Drndic, Marija; Shepard, Kenneth L.

2017-01-01

Despite the potential for nanopores to be a platform for high-bandwidth study of single-molecule systems, ionic current measurements through nanopores have been limited in their temporal resolution by noise arising from poorly optimized measurement electronics and large parasitic capacitances in the nanopore membranes. Here, we present a complementary metal-oxide-semiconductor (CMOS) nanopore (CNP) amplifier capable of low noise recordings at an unprecedented 10 MHz bandwidth. When integrated with state-of-the-art solid-state nanopores in silicon nitride membranes, we achieve an SNR of greater than 10 for ssDNA translocations at a measurement bandwidth of 5 MHz, which represents the fastest ion current recordings through nanopores reported to date. We observe transient features in ssDNA translocation events that are as short as 200 ns, which are hidden even at bandwidths as high as 1 MHz. These features offer further insights into the translocation kinetics of molecules entering and exiting the pore. This platform highlights the advantages of high-bandwidth translocation measurements made possible by integrating nanopores and custom-designed electronics. PMID:27332998

Single Molecule Sensing by Nanopores and Nanopore Devices

PubMed Central

Gu, Li-Qun; Shim, Ji Wook

2010-01-01

Molecular-scale pore structures, called nanopores, can be assembled by protein ion channels through genetic engineering or be artificially fabricated on solid substrates using fashion nanotechnology. When target molecules interact with the functionalized lumen of a nanopore, they characteristically block the ion pathway. The resulting conductance changes allow for identification of single molecules and quantification of target species in the mixture. In this review, we first overview nanopore-based sensory techniques that have been created for the detection of myriad biomedical targets, from metal ions, drug compounds, and cellular second messengers to proteins and DNA. Then we introduce our recent discoveries in nanopore single molecule detection: (1) using the protein nanopore to study folding/unfolding of the G-quadruplex aptamer; (2) creating a portable and durable biochip that is integrated with a single-protein pore sensor (this chip is compared with recently developed protein pore sensors based on stabilized bilayers on glass nanopore membranes and droplet interface bilayer); and (3) creating a glass nanopore-terminated probe for single-molecule DNA detection, chiral enantiomer discrimination, and identification of the bioterrorist agent ricin with an aptamer-encoded nanopore. PMID:20174694

Negative differential electrolyte resistance in a solid-state nanopore resulting from electroosmotic flow bistability.

PubMed

Luo, Long; Holden, Deric A; White, Henry S

2014-03-25

A solid-state nanopore separating two aqueous solutions containing different concentrations of KCl is demonstrated to exhibit negative differential resistance (NDR) when a constant pressure is applied across the nanopore. NDR refers to a decrease in electrical current when the voltage applied across the nanopore is increased. NDR results from the interdependence of solution flow (electroosmotic and pressure-engendered) with the distributions of K+ and Cl- within the nanopore. A switch from a high-conductivity state to a low-conductivity state occurs over a very narrow voltage window (<2 mV) that depends on the nanopore geometry, electrolyte concentration, and nanopore surface charge density. Finite element simulations based on a simultaneous solution of the Navier-Stokes, Poisson, and Nernst-Planck equations demonstrate that NDR results from a positive feedback mechanism between the ion distributions and electroosmotic flow, yielding a true bistability in fluid flow and electrical current at a critical applied voltage, i.e., the NDR "switching potential". Solution pH and Ca2+ were separately employed as chemical stimuli to investigate the dependence of the NDR on the surface charge density. The NDR switching potential is remarkably sensitive to the surface charge density, and thus to pH and the presence of Ca2+, suggesting possible applications in chemical sensing.

Solid-state nanopore localization by controlled breakdown of selectively thinned membranes

NASA Astrophysics Data System (ADS)

Carlsen, Autumn T.; Briggs, Kyle; Hall, Adam R.; Tabard-Cossa, Vincent

2017-02-01

We demonstrate precise positioning of nanopores fabricated by controlled breakdown (CBD) on solid-state membranes by spatially varying the electric field strength with localized membrane thinning. We show 100 × 100 nm2 precision in standard SiN x membranes (30-100 nm thick) after selective thinning by as little as 25% with a helium ion beam. Control over nanopore position is achieved through the strong dependence of the electric field-driven CBD mechanism on membrane thickness. Confinement of pore formation to the thinned region of the membrane is confirmed by TEM imaging and by analysis of DNA translocations. These results enhance the functionality of CBD as a fabrication approach and enable the production of advanced nanopore devices for single-molecule sensing applications.

Enhanced translocation of single DNA molecules through α-hemolysin nanopores by manipulation of internal charge

PubMed Central

Maglia, Giovanni; Restrepo, Marcela Rincon; Mikhailova, Ellina; Bayley, Hagan

2008-01-01

Both protein and solid-state nanopores are under intense investigation for the analysis of nucleic acids. A crucial advantage of protein nanopores is that site-directed mutagenesis permits precise tuning of their properties. Here, by augmenting the internal positive charge within the α-hemolysin pore and varying its distribution, we increase the frequency of translocation of a 92-nt single-stranded DNA through the pore at +120 mV by ≈10-fold over the wild-type protein and dramatically lower the voltage threshold at which translocation occurs, e.g., by 50 mV for 1 event·s−1·μM−1. Further, events in which DNA enters the pore, but is not immediately translocated, are almost eliminated. These experiments provide a basis for improved nucleic acid analysis with protein nanopores, which might be translated to solid-state nanopores by using chemical surface modification. PMID:19060213

Development of Active DNA Control Technique for DNA Sequencer With a Solid-state Nanopore

NASA Astrophysics Data System (ADS)

Akahori, Rena; Harada, Kunio; Goto, Yusuke; Yanagi, Itaru; Yokoi, Takahide; Oura, Takeshi; Shibahara, Masashi; Takeda, Ken-Ichi

We have developed a technique that can control the arbitrary speeds of DNA passing through a solid-state nanopore of a DNA sequencer. For this active DNA control technique, we used a DNA-immobilized Si probe, larger than the membrane with a nanopore, and used a piezoelectric actuator and stepper motor to drive the probe. This probe enables a user to adjust the relative position between the nanopore and DNA immobilized on the probe without the need for precise lateral control. In this presentation, we demonstrate how DNA (block copolymer ([(dT)25-(dC)25-(dA)50]m)), immobilized on the probe, slid through a nanopore and was pulled out using the active DNA control technique. As the DNA-immobilized probe was being pulled out, we obtained various ion-current signal levels corresponding to the number of different nucleotides in a single strand of DNA.

Solid-State Ionic Diodes Demonstrated in Conical Nanopores

DOE PAGES

Plett, Timothy S.; Cai, Wenjia; Le Thai, Mya; ...

2017-02-27

Ionic transport at the nanoscale features phenomena that are not observed in larger systems. Nonlinear current–voltage curves characteristic of ionic diodes as well as ion selectivity are examples of effects observed at the nanoscale. Many man-made nanopore systems are inspired by biological channels in a cell membrane, thus measurements are often performed in aqueous solutions. Consequently, much less is known about ionic transport in nonaqueous systems, especially in solid-state electrolytes. Here we show ionic transport through single pores filled with gel electrolyte of poly(methyl methacrylate) (PMMA) doped with LiClO 4 in propylene carbonate. The system has no liquid interface andmore » the ionic transport occurs through the porous gel structure. We demonstrate that a conically shaped nanopore filled with the gel rectifies the current and works as a solid-state ionic diode.« less

Functional Nanopores: A Solid-state Concept for Artificial Reaction Compartments and Molecular Factories.

PubMed

Puebla-Hellmann, Gabriel; Mayor, Marcel; Lörtscher, Emanuel

2016-01-01

On the road towards the long-term goal of the NCCR Molecular Systems Engineering to create artificial molecular factories, we aim at introducing a compartmentalization strategy based on solid-state silicon technology targeting zeptoliter reaction volumes and simultaneous electrical contact to ensembles of well-oriented molecules. This approach allows the probing of molecular building blocks under a controlled environment prior to their use in a complex molecular factory. Furthermore, these ultra-sensitive electrical conductance measurements allow molecular responses to a variety of external triggers to be used as sensing and feedback mechanisms. So far, we demonstrate the proof-of-concept by electrically contacting self-assembled mono-layers of alkane-dithiols as an established test system. Here, the molecular films are laterally constrained by a circular dielectric confinement, forming a so-called 'nanopore'. Device yields above 85% are consistently achieved down to sub-50 nm nanopore diameters. This generic platform will be extended to create distributed, cascaded reactors with individually addressable reaction sites, including interconnecting micro-fluidic channels for electrochemical communication among nanopores and sensing sites for reaction control and feedback. In this scientific outlook, we will sketch how such a solid-state nanopore concept can be used to study various aspects of molecular compounds tailored for operation in a molecular factory.

Ion Current Rectification, Limiting and Overlimiting Conductances in Nanopores

PubMed Central

van Oeffelen, Liesbeth; Van Roy, Willem; Idrissi, Hosni; Charlier, Daniel; Lagae, Liesbet; Borghs, Gustaaf

2015-01-01

Previous reports on Poisson-Nernst-Planck (PNP) simulations of solid-state nanopores have focused on steady state behaviour under simplified boundary conditions. These are Neumann boundary conditions for the voltage at the pore walls, and in some cases also Donnan equilibrium boundary conditions for concentrations and voltages at both entrances of the nanopore. In this paper, we report time-dependent and steady state PNP simulations under less restrictive boundary conditions, including Neumann boundary conditions applied throughout the membrane relatively far away from the nanopore. We simulated ion currents through cylindrical and conical nanopores with several surface charge configurations, studying the spatial and temporal dependence of the currents contributed by each ion species. This revealed that, due to slow co-diffusion of oppositely charged ions, steady state is generally not reached in simulations or in practice. Furthermore, it is shown that ion concentration polarization is responsible for the observed limiting conductances and ion current rectification in nanopores with asymmetric surface charges or shapes. Hence, after more than a decade of collective research attempting to understand the nature of ion current rectification in solid-state nanopores, a relatively intuitive model is retrieved. Moreover, we measured and simulated current-voltage characteristics of rectifying silicon nitride nanopores presenting overlimiting conductances. The similarity between measurement and simulation shows that overlimiting conductances can result from the increased conductance of the electric double-layer at the membrane surface at the depletion side due to voltage-induced polarization charges. The MATLAB source code of the simulation software is available via the website http://micr.vub.ac.be. PMID:25978328

Aptamer-Encoded Nanopore for Ultrasensitive Detection of Bioterrorist Agent Ricin at Single-Molecule Resolution

PubMed Central

Gu, Li-Qun; Ding, Shu; Gao, Changlu

2011-01-01

The molecular-scale pore structure, called nanopore, can be formed from protein ion channels by genetic engineering or fabricated on solid substrates using fashion nanotechnology. Target molecules in interaction with the functionalized lumen of nanopore, can produce characteristic changes in the pore conductance, which act as fingerprints, allowing us to identify single molecules and simultaneously quantify each target species in the mixture. Nanopore sensors have been created for tremendous biomedical detections, with targets ranging from metal ions, drug compounds and cellular second messengers, to proteins and DNAs. Here we will review our recent discoveries with a lab-in-hand glass nanopore: single-molecule discrimination of chiral enantiomers with a trapped cyclodextrin, and sensing of bioterrorist agent ricin. PMID:19964179

Buckling Causes Nonlinear Dynamics of Filamentous Viruses Driven through Nanopores.

PubMed

McMullen, Angus; de Haan, Hendrick W; Tang, Jay X; Stein, Derek

2018-02-16

Measurements and Langevin dynamics simulations of filamentous viruses driven through solid-state nanopores reveal a superlinear rise in the translocation velocity with driving force. The mobility also scales with the length of the virus in a nontrivial way that depends on the force. These dynamics are consequences of the buckling of the leading portion of a virus as it emerges from the nanopore and is put under compressive stress by the viscous forces it encounters. The leading tip of a buckled virus stalls and this reduces the total viscous drag force. We present a scaling theory that connects the solid mechanics to the nonlinear dynamics of polyelectrolytes translocating nanopores.

Buckling Causes Nonlinear Dynamics of Filamentous Viruses Driven through Nanopores

NASA Astrophysics Data System (ADS)

McMullen, Angus; de Haan, Hendrick W.; Tang, Jay X.; Stein, Derek

2018-02-01

Measurements and Langevin dynamics simulations of filamentous viruses driven through solid-state nanopores reveal a superlinear rise in the translocation velocity with driving force. The mobility also scales with the length of the virus in a nontrivial way that depends on the force. These dynamics are consequences of the buckling of the leading portion of a virus as it emerges from the nanopore and is put under compressive stress by the viscous forces it encounters. The leading tip of a buckled virus stalls and this reduces the total viscous drag force. We present a scaling theory that connects the solid mechanics to the nonlinear dynamics of polyelectrolytes translocating nanopores.

SEM-induced shrinkage and site-selective modification of single-crystal silicon nanopores

NASA Astrophysics Data System (ADS)

Chen, Qi; Wang, Yifan; Deng, Tao; Liu, Zewen

2017-07-01

Solid-state nanopores with feature sizes around 5 nm play a critical role in bio-sensing fields, especially in single molecule detection and sequencing of DNA, RNA and proteins. In this paper we present a systematic study on shrinkage and site-selective modification of single-crystal silicon nanopores with a conventional scanning electron microscope (SEM). Square nanopores with measurable sizes as small as 8 nm × 8 nm and rectangle nanopores with feature sizes (the smaller one between length and width) down to 5 nm have been obtained, using the SEM-induced shrinkage technique. The analysis of energy dispersive x-ray spectroscopy and the recovery of the pore size and morphology reveal that the grown material along with the edge of the nanopore is the result of deposition of hydrocarbon compounds, without structural damage during the shrinking process. A simplified model for pore shrinkage has been developed based on observation of the cross-sectional morphology of the shrunk nanopore. The main factors impacting on the task of controllably shrinking the nanopores, such as the accelerating voltage, spot size, scanned area of e-beam, and the initial pore size have been discussed. It is found that single-crystal silicon nanopores shrink linearly with time under localized irradiation by SEM e-beam in all cases, and the pore shrinkage rate is inversely proportional to the initial equivalent diameter of the pore under the same e-beam conditions.

Microfluidic systems with ion-selective membranes.

PubMed

Slouka, Zdenek; Senapati, Satyajyoti; Chang, Hsueh-Chia

2014-01-01

When integrated into microfluidic chips, ion-selective nanoporous polymer and solid-state membranes can be used for on-chip pumping, pH actuation, analyte concentration, molecular separation, reactive mixing, and molecular sensing. They offer numerous functionalities and are hence superior to paper-based devices for point-of-care biochips, with only slightly more investment in fabrication and material costs required. In this review, we first discuss the fundamentals of several nonequilibrium ion current phenomena associated with ion-selective membranes, many of them revealed by studies with fabricated single nanochannels/nanopores. We then focus on how the plethora of phenomena has been applied for transport, separation, concentration, and detection of biomolecules on biochips.

Microfluidic Systems with Ion-Selective Membranes

NASA Astrophysics Data System (ADS)

Slouka, Zdenek; Senapati, Satyajyoti; Chang, Hsueh-Chia

2014-06-01

When integrated into microfluidic chips, ion-selective nanoporous polymer and solid-state membranes can be used for on-chip pumping, pH actuation, analyte concentration, molecular separation, reactive mixing, and molecular sensing. They offer numerous functionalities and are hence superior to paper-based devices for point-of-care biochips, with only slightly more investment in fabrication and material costs required. In this review, we first discuss the fundamentals of several nonequilibrium ion current phenomena associated with ion-selective membranes, many of them revealed by studies with fabricated single nanochannels/nanopores. We then focus on how the plethora of phenomena has been applied for transport, separation, concentration, and detection of biomolecules on biochips.

Nanopore detection of DNA molecules in crowded neutral polymer solutions

NASA Astrophysics Data System (ADS)

Sharma, Rajesh Kumar; Dai, Liang; Doyle, Patrick; Garaj, Slaven

Nanopore sensing is a precise technique for analysis of the structure and dynamics of individual biomolecules in different environments, and has even become a prominent technique for next-gen DNA sequencing. In the nanopore sensor, an individual DNA molecule is electrophoretically translocated through a single, nanometer-scaled pore in a solid-state membrane separating two chambers filled with electrolyte. The conformation of the molecule is deduced from modulations in the ionic current through the pore during the translocation event. Using nanopores, we investigated the dynamics of the DNA molecules in a crowded solution of neutral polymers of different sizes and concentrations. The translocation dynamics depends significantly on the size and concentration of the polymers, as different contributions to the electrophoretic and entropic forces on the DNA molecules come into play. This setup offers an excellent, tuneable model-system for probing biologically relevant questions regarding the behaviour of DNA molecules in highly confined and crowded environments. Singapore-MIT Alliance for Research and Technology.

Modulation of Molecular Flux Using a Graphene Nanopore Capacitor.

PubMed

Shankla, Manish; Aksimentiev, Aleksei

2017-04-20

Modulation of ionic current flowing through nanoscale pores is one of the fundamental biological processes. Inspired by nature, nanopores in synthetic solid-state membranes are being developed to enable rapid analysis of biological macromolecules and to serve as elements of nanofludic circuits. Here, we theoretically investigate ion and water transport through a graphene-insulator-graphene membrane containing a single, electrolyte-filled nanopore. By means of all-atom molecular dynamics simulations, we show that the charge state of such a graphene nanopore capacitor can regulate both the selectivity and the magnitude of the nanopore ionic current. At a fixed transmembrane bias, the ionic current can be switched from being carried by an equal mixture of cations and anions to being carried almost exclusively by either cationic or anionic species, depending on the sign of the charge assigned to both plates of the capacitor. Assigning the plates of the capacitor opposite sign charges can either increase the nanopore current or reduce it substantially, depending on the polarity of the bias driving the transmembrane current. Facilitated by the changes of the nanopore surface charge, such ionic current modulations are found to occur despite the physical dimensions of the nanopore being an order of magnitude larger than the screening length of the electrolyte. The ionic current rectification is accompanied by a pronounced electro-osmotic effect that can transport neutral molecules such as proteins and drugs across the solid-state membrane and thereby serve as an interface between electronic and chemical signals.

Single molecule transistor based nanopore for the detection of nicotine

NASA Astrophysics Data System (ADS)

Ray, S. J.

2014-12-01

A nanopore based detection methodology was proposed and investigated for the detection of Nicotine. This technique uses a Single Molecular Transistor working as a nanopore operational in the Coulomb Blockade regime. When the Nicotine molecule is pulled through the nanopore area surrounded by the Source(S), Drain (D), and Gate electrodes, the charge stability diagram can detect the presence of the molecule and is unique for a specific molecular structure. Due to the weak coupling between the different electrodes which is set by the nanopore size, the molecular energy states stay almost unaffected by the electrostatic environment that can be realised from the charge stability diagram. Identification of different orientation and position of the Nicotine molecule within the nanopore area can be made from specific regions of overlap between different charge states on the stability diagram that could be used as an electronic fingerprint for detection. This method could be advantageous and useful to detect the presence of Nicotine in smoke which is usually performed using chemical chromatography techniques.

Preparation of resveratrol-loaded nanoporous silica materials with different structures

NASA Astrophysics Data System (ADS)

Popova, Margarita; Szegedi, Agnes; Mavrodinova, Vesselina; Novak Tušar, Natasa; Mihály, Judith; Klébert, Szilvia; Benbassat, Niko; Yoncheva, Krassimira

2014-11-01

Solid, nanoporous silica-based spherical mesoporous MCM-41 and KIL-2 with interparticle mesoporosity as well as nanosized zeolite BEA materials differing in morphology and pore size distribution, were used as carriers for the preparation of resveratrol-loaded delivery systems. Two preparation methods have been applied: (i) loading by mixing of resveratrol and mesoporous carrier in solid state and (ii) deposition in ethanol solution. The parent and the resveratrol loaded carriers were characterized by XRD, TEM, N2 physisorption, thermal analysis, and FT-IR spectroscopy. The influence of the support structure on the adsorption capacity and the release kinetics of this poorly soluble compound were investigated. Our results indicated that the chosen nanoporous silica supports are suitable for stabilization of trans-resveratrol and reveal controlled release and ability to protect the supported compound against degradation regardless of loading method. The solid-state dry mixing appears very effective for preparation of drug formulations composed of poorly soluble compound.

WS2 nanopores for molecule analysis

NASA Astrophysics Data System (ADS)

Danda, Gopinath; Masih Das, Paul; Chou, Yung-Chien; Mlack, Jerome; Naylor, Carl; Perea-Lopez, Nestor; Lin, Zhong; Fulton, Laura Beth; Terrones, Mauricio; Johnson, A. T. Charlie; Drndic, Marija

Atomically thin 2D materials like graphene and transition metal dichalcogenides (TMDs) are interesting as membranes in solid state nanopore sensors for DNA analysis as they may facilitate single base resolution sequencing. These materials also exhibit unique optical and electronic properties which may be exploited to enhance the functionality of nanopore sensors. Here, we report WS2 nanopores, fabricated using a focused TEM beam. We also report their controlled laser-induced expansion in ionic solution. This study demonstrates the possibility of dynamic control of nanopore characteristics optically. NIH Grant R21HG007856, NSF EFRI-1542707.

Theoretical models for electrochemical impedance spectroscopy and local ζ-potential of unfolded proteins in nanopores

NASA Astrophysics Data System (ADS)

Vitarelli, Michael J.; Talaga, David S.

2013-09-01

Single solid-state nanopores find increasing use for electrical detection and/or manipulation of macromolecules. These applications exploit the changes in signals due to the geometry and electrical properties of the molecular species found within the nanopore. The sensitivity and resolution of such measurements are also influenced by the geometric and electrical properties of the nanopore. This paper continues the development of an analytical theory to predict the electrochemical impedance spectra of nanopores by including the influence of the presence of an unfolded protein using the variable topology finite Warburg impedance model previously published by the authors. The local excluded volume of, and charges present on, the segment of protein sampled by the nanopore are shown to influence the shape and peak frequency of the electrochemical impedance spectrum. An analytical theory is used to relate the capacitive response of the electrical double layer at the surface of the protein to both the charge density at the protein surface and the more commonly measured zeta potential. Illustrative examples show how the theory predicts that the varying sequential regions of surface charge density and excluded volume dictated by the protein primary structure may allow for an impedance-based approach to identifying unfolded proteins.

Single molecule transistor based nanopore for the detection of nicotine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ray, S. J., E-mail: ray.sjr@gmail.com

A nanopore based detection methodology was proposed and investigated for the detection of Nicotine. This technique uses a Single Molecular Transistor working as a nanopore operational in the Coulomb Blockade regime. When the Nicotine molecule is pulled through the nanopore area surrounded by the Source(S), Drain (D), and Gate electrodes, the charge stability diagram can detect the presence of the molecule and is unique for a specific molecular structure. Due to the weak coupling between the different electrodes which is set by the nanopore size, the molecular energy states stay almost unaffected by the electrostatic environment that can be realisedmore » from the charge stability diagram. Identification of different orientation and position of the Nicotine molecule within the nanopore area can be made from specific regions of overlap between different charge states on the stability diagram that could be used as an electronic fingerprint for detection. This method could be advantageous and useful to detect the presence of Nicotine in smoke which is usually performed using chemical chromatography techniques.« less

Label-free in-flow detection of single DNA molecules using glass nanopipettes.

PubMed

Gong, Xiuqing; Patil, Amol V; Ivanov, Aleksandar P; Kong, Qingyuan; Gibb, Thomas; Dogan, Fatma; deMello, Andrew J; Edel, Joshua B

2014-01-07

With the view of enhancing the functionality of label-free single molecule nanopore-based detection, we have designed and developed a highly robust, mechanically stable, integrated nanopipette-microfluidic device which combines the recognized advantages of microfluidic systems and the unique properties/advantages of nanopipettes. Unlike more typical planar solid-state nanopores, which have inherent geometrical constraints, nanopipettes can be easily positioned at any point within a microfluidic channel. This is highly advantageous, especially when taking into account fluid flow properties. We show that we are able to detect and discriminate between DNA molecules of varying lengths when motivated through a microfluidic channel, upon the application of appropriate voltage bias across the nanopipette. The effects of applied voltage and volumetric flow rates have been studied to ascertain translocation event frequency and capture rate. Additionally, by exploiting the advantages associated with microfluidic systems (such as flow control and concomitant control over analyte concentration/presence), we show that the technology offers a new opportunity for single molecule detection and recognition in microfluidic devices.

Polymer translocation in solid-state nanopores: Dependence on hydrodynamic interactions and polymer configuration

NASA Astrophysics Data System (ADS)

Edmonds, Christopher M.; Hesketh, Peter J.; Nair, Sankar

2013-11-01

We present a Brownian dynamics investigation of 3-D Rouse and Zimm polymer translocation through solid-state nanopores. We obtain different scaling exponents α for both polymers using two initial configurations: minimum energy, and 'steady-state'. For forced translocation, Rouse polymers (no hydrodynamic interactions), shows a large dependence of α on initial configuration and voltage. Higher voltages result in crowding at the nanopore exit and reduced α. When the radius of gyration is in equilibrium at the beginning and end of translocation, α = 1 + υ where υ is the Flory exponent. For Zimm polymers (including hydrodynamic interactions), crowding is reduced and α = 2υ. Increased pore diameter does not affect α at moderate voltages that reduce diffusion effects. For unforced translocation using narrow pores, both polymers give α = 1 + 2υ. Due to increased polymer-pore interactions in the narrow pore, hydrodynamic drag effects are reduced, resulting in identical scaling.

Development of Solid-State Nanopore Technology for Life Detection

NASA Technical Reports Server (NTRS)

Bywaters, K. B.; Schmidt, H.; Vercoutere, W.; Deamer, D.; Hawkins, A. R.; Quinn, R. C.; Burton, A. S.; Mckay, C. P.

2017-01-01

Biomarkers for life on Earth are an important starting point to guide the search for life elsewhere. However, the search for life beyond Earth should incorporate technologies capable of recognizing an array of potential biomarkers beyond what we see on Earth, in order to minimize the risk of false negatives from life detection missions. With this in mind, charged linear polymers may be a universal signature for life, due to their ability to store information while also inherently reducing the tendency of complex tertiary structure formation that significantly inhibit replication. Thus, these molecules are attractive targets for biosignature detection as potential "self-sustaining chemical signatures." Examples of charged linear polymers, or polyelectrolytes, include deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) as well as synthetic polyelectrolytes that could potentially support life, including threose nucleic acid (TNA) and other xenonucleic acids (XNAs). Nanopore analysis is a novel technology that has been developed for singlemolecule sequencing with exquisite single nucleotide resolution which is also well-suited for analysis of polyelectrolyte molecules. Nanopore analysis has the ability to detect repeating sequences of electrical charges in organic linear polymers, and it is not molecule- specific (i.e. it is not restricted to only DNA or RNA). In this sense, it is a better life detection technique than approaches that are based on specific molecules, such as the polymerase chain reaction (PCR), which requires that the molecule being detected be composed of DNA.

Preparation of resveratrol-loaded nanoporous silica materials with different structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Popova, Margarita, E-mail: mpopova@orgchem.bas.bg; Szegedi, Agnes; Mavrodinova, Vesselina

2014-11-15

Solid, nanoporous silica-based spherical mesoporous MCM-41 and KIL-2 with interparticle mesoporosity as well as nanosized zeolite BEA materials differing in morphology and pore size distribution, were used as carriers for the preparation of resveratrol-loaded delivery systems. Two preparation methods have been applied: (i) loading by mixing of resveratrol and mesoporous carrier in solid state and (ii) deposition in ethanol solution. The parent and the resveratrol loaded carriers were characterized by XRD, TEM, N2 physisorption, thermal analysis, and FT-IR spectroscopy. The influence of the support structure on the adsorption capacity and the release kinetics of this poorly soluble compound were investigated.more » Our results indicated that the chosen nanoporous silica supports are suitable for stabilization of trans-resveratrol and reveal controlled release and ability to protect the supported compound against degradation regardless of loading method. The solid-state dry mixing appears very effective for preparation of drug formulations composed of poorly soluble compound. - Graphical abstract: trans-Resveratrol was stabilized in the pores of BEA zeolite, MCM-41and KIL2 mesoporous silicas. - Highlights: • BEA, KIL-2 and MCM-41 materials were used as carriers for resveratrol loading. • Resveratrol encapsulation in ethanol solution and solid state procedure were applied. • The solid-state preparation appears very effective for stabilization of trans-resveratrol.« less

Solid-state nanopores of controlled geometry fabricated in a transmission electron microscope

NASA Astrophysics Data System (ADS)

Qian, Hui; Egerton, Ray F.

2017-11-01

Energy-filtered transmission electron microscopy and electron tomography were applied to in situ studies of the formation, shape, and diameter of nanopores formed in a silicon nitride membrane in a transmission electron microscope. The nanopore geometry was observed in three dimensions by electron tomography. Drilling conditions, such as probe current, beam convergence angle, and probe position, affect the formation rate and the geometry of the pores. With a beam convergence semi-angle of α = 22 mrad, a conical shaped nanopore is formed but at α = 45 mrad, double-cone (hourglass-shaped) nanopores were produced. Nanopores with an effective diameter between 10 nm and 1.8 nm were fabricated by controlling the drilling time.

Nanopores formed by DNA origami: a review.

PubMed

Bell, Nicholas A W; Keyser, Ulrich F

2014-10-01

Nanopores have emerged over the past two decades to become an important technique in single molecule experimental physics and biomolecule sensing. Recently DNA nanotechnology, in particular DNA origami, has been used for the formation of nanopores in insulating materials. DNA origami is a very attractive technique for the formation of nanopores since it enables the construction of 3D shapes with precise control over geometry and surface functionality. DNA origami has been applied to nanopore research by forming hybrid architectures with solid state nanopores and by direct insertion into lipid bilayers. This review discusses recent experimental work in this area and provides an outlook for future avenues and challenges. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Automated and inexpensive method to manufacture solid- state nanopores and micropores in robust silicon wafers

NASA Astrophysics Data System (ADS)

Vega, M.; Granell, P.; Lasorsa, C.; Lerner, B.; Perez, M.

2016-02-01

In this work an easy, reproducible and inexpensive technique for the production of solid state nanopores and micropores using silicon wafer substrate is proposed. The technique is based on control of pore formation, by neutralization etchant (KOH) with a strong acid (HCl). Thus, a local neutralization is produced around the nanopore, which stops the silicon etching. The etching process was performed with 7M KOH at 80°C, where 1.23µm/min etching speed was obtained, similar to those published in literature. The control of the pore formation with the braking acid method was done using 12M HCl and different extreme conditions: i) at 25°C, ii) at 80°C and iii) at 80°C applying an electric potential. In these studies, it was found that nanopores and micropores can be obtained automatically and at a low cost. Additionally, the process was optimized to obtain clean silicon wafers after the pore fabrication process. This method opens the possibility for an efficient scale-up from laboratory production.

Static charge outside chamber induces dielectric breakdown of solid-state nanopore membranes

NASA Astrophysics Data System (ADS)

Matsui, Kazuma; Goto, Yusuke; Yanagi, Itaru; Yanagawa, Yoshimitsu; Ishige, Yu; Takeda, Ken-ichi

2018-04-01

Reducing device capacitance is effective for decreasing current noise observed in a solid-state nanopore-based DNA sequencer. On the other hand, we have recently found that voltage stress causes pinhole-like defects in such low-capacitance devices. The origin of voltage stress, however, has not been determined. In this research, we identified that a dominant origin is static charge on the outer surface of a flow cell. Even though the outer surface was not in direct contact with electrolytes in the flow cell, the charge induces high voltage stress on a membrane according to the capacitance coupling ratio of the flow cell to the membrane.

Nanoporous frameworks exhibiting multiple stimuli responsiveness

NASA Astrophysics Data System (ADS)

Kundu, Pintu K.; Olsen, Gregory L.; Kiss, Vladimir; Klajn, Rafal

2014-04-01

Nanoporous frameworks are polymeric materials built from rigid molecules, which give rise to their nanoporous structures with applications in gas sorption and storage, catalysis and others. Conceptually new applications could emerge, should these beneficial properties be manipulated by external stimuli in a reversible manner. One approach to render nanoporous frameworks responsive to external signals would be to immobilize molecular switches within their nanopores. Although the majority of molecular switches require conformational freedom to isomerize, and switching in the solid state is prohibited, the nanopores may provide enough room for the switches to efficiently isomerize. Here we describe two families of nanoporous materials incorporating the spiropyran molecular switch. These materials exhibit a variety of interesting properties, including reversible photochromism and acidochromism under solvent-free conditions, light-controlled capture and release of metal ions, as well reversible chromism induced by solvation/desolvation.

Pulsed plasma polymerization for controlling shrinkage and surface composition of nanopores

NASA Astrophysics Data System (ADS)

Asghar, Waseem; Ilyas, Azhar; Deshmukh, Rajendra R.; Sumitsawan, Sulak; Timmons, Richard B.; Iqbal, Samir M.

2011-07-01

Solid-state nanopores have emerged as sensors for single molecules and these have been employed to examine the biophysical properties of an increasingly large variety of biomolecules. Herein we describe a novel and facile approach to precisely adjust the pore size, while simultaneously controlling the surface chemical composition of the solid-state nanopores. Specifically, nanopores fabricated using standard ion beam technology are shrunk to the requisite molecular dimensions via the deposition of highly conformal pulsed plasma generated thin polymeric films. The plasma treatment process provides accurate control of the pore size as the conformal film deposition depends linearly on the deposition time. Simultaneously, the pore and channel chemical compositions are controlled by appropriate selection of the gaseous monomer and plasma conditions employed in the deposition of the polymer films. The controlled pore shrinkage is characterized with high resolution AFM, and the film chemistry of the plasma generated polymers is analyzed with FTIR and XPS. The stability and practical utility of this new approach is demonstrated by successful single molecule sensing of double-stranded DNA. The process offers a viable new advance in the fabrication of tailored nanopores, in terms of both the pore size and surface composition, for usage in a wide range of emerging applications.

Electrochemical Protection of Thin Film Electrodes in Solid State Nanopores

PubMed Central

Harrer, Stefan; Waggoner, Philip S.; Luan, Binquan; Afzali-Ardakani, Ali; Goldfarb, Dario L.; Peng, Hongbo; Martyna, Glenn; Rossnagel, Stephen M.; Stolovitzky, Gustavo A.

2011-01-01

We have eliminated electrochemical surface oxidation and reduction as well as water decomposition inside sub-5-nm wide nanopores in conducting TiN membranes using a surface passivation technique. Nanopore ionic conductances, and therefore pore diameters, were unchanged in passivated pores after applying potentials of ±4.5 V for as long as 24 h. Water decomposition was eliminated by using aqueous 90% glycerol solvent. The use of a protective self-assembled monolayer of hexadecylphosphonic acid was also investigated. PMID:21597142

Solid-State Explosive Reaction for Nanoporous Bulk Thermoelectric Materials.

PubMed

Zhao, Kunpeng; Duan, Haozhi; Raghavendra, Nunna; Qiu, Pengfei; Zeng, Yi; Zhang, Wenqing; Yang, Jihui; Shi, Xun; Chen, Lidong

2017-11-01

High-performance thermoelectric materials require ultralow lattice thermal conductivity typically through either shortening the phonon mean free path or reducing the specific heat. Beyond these two approaches, a new unique, simple, yet ultrafast solid-state explosive reaction is proposed to fabricate nanoporous bulk thermoelectric materials with well-controlled pore sizes and distributions to suppress thermal conductivity. By investigating a wide variety of functional materials, general criteria for solid-state explosive reactions are built upon both thermodynamics and kinetics, and then successfully used to tailor material's microstructures and porosity. A drastic decrease in lattice thermal conductivity down below the minimum value of the fully densified materials and enhancement in thermoelectric figure of merit are achieved in porous bulk materials. This work demonstrates that controlling materials' porosity is a very effective strategy and is easy to be combined with other approaches for optimizing thermoelectric performance. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hierarchical nanoporous metals as a path toward the ultimate three-dimensional functionality.

PubMed

Fujita, Takeshi

2017-01-01

Nanoporous metals prepared via dealloying or selective leaching of solid solution alloys and compounds represent an emerging class of materials. They possess a three-dimensional (3D) structure of randomly interpenetrating ligaments/nanopores with sizes between 5 nm and several tens of micrometers, which can be tuned by varying their preparation conditions (such as dealloying time and temperature) or additional thermal coarsening. As compared to other nanostructured materials, nanoporous metals have many advantages, including their bicontinuous structure, tunable pore sizes, bulk form, good electrical conductivity, and high structural stability. Therefore, nanoporous metals represent ideal 3D materials with versatile functionality, which can be utilized in various fields. In this review, we describe the recent applications of nanoporous metals in molecular detection, catalysis, 3D graphene synthesis, hierarchical pore formation, and additive manufacturing (3D printing) together with our own achievements in these areas. Finally, we discuss possible ways of realizing the ultimate 3D functionality beyond the scope of nanoporous metals.

Hierarchical nanoporous metals as a path toward the ultimate three-dimensional functionality

PubMed Central

Fujita, Takeshi

2017-01-01

Abstract Nanoporous metals prepared via dealloying or selective leaching of solid solution alloys and compounds represent an emerging class of materials. They possess a three-dimensional (3D) structure of randomly interpenetrating ligaments/nanopores with sizes between 5 nm and several tens of micrometers, which can be tuned by varying their preparation conditions (such as dealloying time and temperature) or additional thermal coarsening. As compared to other nanostructured materials, nanoporous metals have many advantages, including their bicontinuous structure, tunable pore sizes, bulk form, good electrical conductivity, and high structural stability. Therefore, nanoporous metals represent ideal 3D materials with versatile functionality, which can be utilized in various fields. In this review, we describe the recent applications of nanoporous metals in molecular detection, catalysis, 3D graphene synthesis, hierarchical pore formation, and additive manufacturing (3D printing) together with our own achievements in these areas. Finally, we discuss possible ways of realizing the ultimate 3D functionality beyond the scope of nanoporous metals. PMID:29057026

Hierarchical nanoporous metals as a path toward the ultimate three-dimensional functionality

NASA Astrophysics Data System (ADS)

Fujita, Takeshi

2017-12-01

Nanoporous metals prepared via dealloying or selective leaching of solid solution alloys and compounds represent an emerging class of materials. They possess a three-dimensional (3D) structure of randomly interpenetrating ligaments/nanopores with sizes between 5 nm and several tens of micrometers, which can be tuned by varying their preparation conditions (such as dealloying time and temperature) or additional thermal coarsening. As compared to other nanostructured materials, nanoporous metals have many advantages, including their bicontinuous structure, tunable pore sizes, bulk form, good electrical conductivity, and high structural stability. Therefore, nanoporous metals represent ideal 3D materials with versatile functionality, which can be utilized in various fields. In this review, we describe the recent applications of nanoporous metals in molecular detection, catalysis, 3D graphene synthesis, hierarchical pore formation, and additive manufacturing (3D printing) together with our own achievements in these areas. Finally, we discuss possible ways of realizing the ultimate 3D functionality beyond the scope of nanoporous metals.

Nanopore-based fourth-generation DNA sequencing technology.

PubMed

Feng, Yanxiao; Zhang, Yuechuan; Ying, Cuifeng; Wang, Deqiang; Du, Chunlei

2015-02-01

Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than $100. The single-molecule techniques used by this technology allow us to further study the interaction between DNA and protein, as well as between protein and protein. Nanopore analysis opens a new door to molecular biology investigation at the single-molecule scale. In this article, we have reviewed academic achievements in nanopore technology from the past as well as the latest advances, including both biological and solid-state nanopores, and discussed their recent and potential applications. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Differential Enzyme Flexibility Probed Using Solid-State Nanopores.

PubMed

Hu, Rui; Rodrigues, João V; Waduge, Pradeep; Yamazaki, Hirohito; Cressiot, Benjamin; Chishti, Yasmin; Makowski, Lee; Yu, Dapeng; Shakhnovich, Eugene; Zhao, Qing; Wanunu, Meni

2018-05-22

Enzymes and motor proteins are dynamic macromolecules that coexist in a number of conformations of similar energies. Protein function is usually accompanied by a change in structure and flexibility, often induced upon binding to ligands. However, while measuring protein flexibility changes between active and resting states is of therapeutic significance, it remains a challenge. Recently, our group has demonstrated that breadth of signal amplitudes in measured electrical signatures as an ensemble of individual protein molecules is driven through solid-state nanopores and correlates with protein conformational dynamics. Here, we extend our study to resolve subtle flexibility variation in dihydrofolate reductase mutants from unlabeled single molecules in solution. We first demonstrate using a canonical protein system, adenylate kinase, that both size and flexibility changes can be observed upon binding to a substrate that locks the protein in a closed conformation. Next, we investigate the influence of voltage bias and pore geometry on the measured electrical pulse statistics during protein transport. Finally, using the optimal experimental conditions, we systematically study a series of wild-type and mutant dihydrofolate reductase proteins, finding a good correlation between nanopore-measured protein conformational dynamics and equilibrium bulk fluorescence probe measurements. Our results unequivocally demonstrate that nanopore-based measurements reliably probe conformational diversity in native protein ensembles.

Nanoscale dynamics of Joule heating and bubble nucleation in a solid-state nanopore.

PubMed

Levine, Edlyn V; Burns, Michael M; Golovchenko, Jene A

2016-01-01

We present a mathematical model for Joule heating of an electrolytic solution in a nanopore. The model couples the electrical and thermal dynamics responsible for rapid and extreme superheating of the electrolyte within the nanopore. The model is implemented numerically with a finite element calculation, yielding a time and spatially resolved temperature distribution in the nanopore region. Temperatures near the thermodynamic limit of superheat are predicted to be attained just before the explosive nucleation of a vapor bubble is observed experimentally. Knowledge of this temperature distribution enables the evaluation of related phenomena including bubble nucleation kinetics, relaxation oscillation, and bubble dynamics.

Bioinspired integrated nanosystems based on solid-state nanopores: “iontronic” transduction of biological, chemical and physical stimuli

PubMed Central

Pérez-Mitta, Gonzalo; Albesa, Alberto G.; Trautmann, Christina; Toimil-Molares, María Eugenia

2017-01-01

The ability of living systems to respond to stimuli and process information has encouraged scientists to develop integrated nanosystems displaying similar functions and capabilities. In this regard, biological pores have been a source of inspiration due to their exquisite control over the transport of ions within cells, a feature that ultimately plays a major role in multiple physiological processes, e.g. transduction of physical stimuli into nervous signals. Developing abiotic nanopores, which respond to certain chemical, biological or physical inputs producing “iontronic” signals, is now a reality thanks to the combination of “soft” surface science with nanofabrication techniques. The interplay between the functional richness of predesigned molecular components and the remarkable physical characteristics of nanopores plays a critical role in the rational integration of molecular functions into nanopore environments, permitting us to envisage nanopore-based biomimetic integrated nanosystems that respond to a variety of external stimuli such as pH, redox potential, molecule concentration, temperature, or light. Transduction of these stimuli into a predefined “iontronic” response can be amplified by exploiting nanoconfinement and physico-chemical effects such as charge distribution, steric constraints, equilibria displacement, or local changes in ionic concentration, to name but a few examples. While in past decades the focus has been mostly on their fundamental aspects and the in-depth study of their interesting transport properties, for several years now nanopore research has started to shift towards specific practical applications. This work is dedicated to bringing together the latest developments in the use of nanopores as “iontronic” transducing elements. Our aim is to show the wide potential of abiotic nanopores in sensing and signal transduction and also to promote the potential of this technology among doctoral students, postdocs, and researchers. We believe that even a casual reader of this perspective will not fail to be impressed by the wealth of opportunities that solid-state nanopores can offer to the transduction of biological, physical and chemical stimuli. PMID:28572900

Nanoporous adsorption effect on altering Li+ diffusion pathway by a highly ordered porous electrolyte additive for high rate all-solid-state lithium metal batteries.

PubMed

Li, Wenwen; Zhang, Sanpei; Wang, Bangrun; Gu, Sui; Xu, Dong; Wang, Jianing; Chen, Chunhua; Wen, Zhaoyin

2018-06-19

Solid polymer electrolytes (SPEs) have shown extraordinary promise for all-solid-state lithium metal batteries with high energy density and flexibility but are mainly limited by the low ionic conductivity and their poor stability with lithium metal anode. In this work, we propose a highly ordered porous electrolyte additive derived from SSZ-13 for high-rate all-solid-state lithium metal batteries. The nanoporous adsorption effect provided by the highly ordered porous nanoparticles in the poly (ethylene oxide) (PEO) electrolyte are found to significantly improve the Li + conductivity (1.91×10 -3 S cm -1 at 60°C, 4.43×10 -5 S cm -1 at 20°C) and widen the electrochemical stability window to 4.7 V vs Li + /Li. Meanwhile, the designed PEO-based electrolyte demonstrates enhanced stability with the lithium metal anode. Through systematically increasing Li + diffusion, widening the electrochemical stability window and enhancing the stability of the SSZ-CPE electrolyte, the LiFePO4/SSZ-CPE/Li cell is optimized to deliver high-rate capability and stable cycling performance, which demonstrates great potential for all-solid-state energy storage application.

Streaming current magnetic fields in a charged nanopore.

PubMed

Mansouri, Abraham; Taheri, Peyman; Kostiuk, Larry W

2016-11-11

Magnetic fields induced by currents created in pressure driven flows inside a solid-state charged nanopore were modeled by numerically solving a system of steady state continuum partial differential equations, i.e., Poisson, Nernst-Planck, Ampere and Navier-Stokes equations (PNPANS). This analysis was based on non-dimensional transport governing equations that were scaled using Debye length as the characteristic length scale, and applied to a finite length cylindrical nano-channel. The comparison of numerical and analytical studies shows an excellent agreement and verified the magnetic fields density both inside and outside the nanopore. The radially non-uniform currents resulted in highly non-uniform magnetic fields within the nanopore that decay as 1/r outside the nanopore. It is worth noting that for either streaming currents or streaming potential cases, the maximum magnetic field occurred inside the pore in the vicinity of nanopore wall, as opposed to a cylindrical conductor that carries a steady electric current where the maximum magnetic fields occur at the perimeter of conductor. Based on these results, it is suggested and envisaged that non-invasive external magnetic fields readouts generated by streaming/ionic currents may be viewed as secondary electronic signatures of biomolecules to complement and enhance current DNA nanopore sequencing techniques.

Streaming current magnetic fields in a charged nanopore

NASA Astrophysics Data System (ADS)

Mansouri, Abraham; Taheri, Peyman; Kostiuk, Larry W.

2016-11-01

Magnetic fields induced by currents created in pressure driven flows inside a solid-state charged nanopore were modeled by numerically solving a system of steady state continuum partial differential equations, i.e., Poisson, Nernst-Planck, Ampere and Navier-Stokes equations (PNPANS). This analysis was based on non-dimensional transport governing equations that were scaled using Debye length as the characteristic length scale, and applied to a finite length cylindrical nano-channel. The comparison of numerical and analytical studies shows an excellent agreement and verified the magnetic fields density both inside and outside the nanopore. The radially non-uniform currents resulted in highly non-uniform magnetic fields within the nanopore that decay as 1/r outside the nanopore. It is worth noting that for either streaming currents or streaming potential cases, the maximum magnetic field occurred inside the pore in the vicinity of nanopore wall, as opposed to a cylindrical conductor that carries a steady electric current where the maximum magnetic fields occur at the perimeter of conductor. Based on these results, it is suggested and envisaged that non-invasive external magnetic fields readouts generated by streaming/ionic currents may be viewed as secondary electronic signatures of biomolecules to complement and enhance current DNA nanopore sequencing techniques.

Single-Molecule Sensing with Nanopore Confinement: From Chemical Reactions to Biological Interactions.

PubMed

Lin, Yao; Ying, Yi-Lun; Gao, Rui; Long, Yi-Tao

2018-03-25

The nanopore can generate an electrochemical confinement for single-molecule sensing that help understand the fundamental chemical principle in nanoscale dimensions. By observing the generated ionic current, individual bond-making and bond-breaking steps, single biomolecule dynamic conformational changes and electron transfer processes that occur within pore can be monitored with high temporal and current resolution. These single-molecule studies in nanopore confinement are revealing information about the fundamental chemical and biological processes that cannot be extracted from ensemble measurements. In this Concept article, we introduce and discuss the electrochemical confinement effects on single-molecule covalent reactions, conformational dynamics of individual molecules and host-guest interactions in protein nanopores. Then, we extend the concept of nanopore confinement effects to confine electrochemical redox reactions in solid-state nanopores for developing new sensing mechanisms. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transport of Proteins through Nanopores

NASA Astrophysics Data System (ADS)

Luan, Binquan

In biological cells, a malfunctioned protein (such as misfolded or damaged) is degraded by a protease in which an unfoldase actively drags the protein into a nanopore-like structure and then a peptidase cuts the linearized protein into small fragments (i.e. a recycling process). Mimicking this biological process, many experimental studies have focused on the transport of proteins through a biological protein pore or a synthetic solid-state nanopore. Potentially, the nanopore-based sensors can provide a platform for interrogating proteins that might be disease-related or be targeted by a new drug molecule. The single-profile of a protein chain inside an extremely small nanopore might even permit the sequencing of the protein. Here, through all-atom molecular dynamics simulations, I will show various types of protein transport through a nanopore and reveal the nanoscale mechanics/energetics that plays an important role governing the protein transport.

Development and characterization of nanopore system for nano-vesicle analysis

NASA Astrophysics Data System (ADS)

Goyal, Gaurav

Nano-vesicles have recently attracted a lot of attention in research and medical communities and are very promising next-generation drug delivery vehicles. This is due to their biocompatibility, biodegradability and their ability to protect drug cargo and deliver it to site-specific locations, while maintaining the desired pharmacokinetic profile. The interaction of these drug loaded vesicles with the recipient cells via adsorption, endocytosis or receptor mediated internalization involve significant bending and deformation and is governed by mechanical properties of the nano-vesicles. Currently, the mechanical characteristics of nano-vesicles are left unexplored because of the difficulties associated with vesicle analysis at sub-100 nm length scale. The need for a complete understanding of nano-vesicle interaction with each other and the recipient cells warrants development of an analytical tool capable of mechanical investigation of individual vesicles at sub-100 nm scale. This dissertation presents investigation of nano-vesicle deformability using resistive pulse sensing and solid-state nanopore devices. The dissertation is divided into four chapters. Chapter 1 discusses the motivation, specific aims and presents an overview of nanoparticle characterization techniques, resistive pulse sensing background and principles, techniques for fabricating solid-state nanopores, as well the deformation behavior of giant vesicles when placed in electric field. Chapter 2 is dedicated to understanding of the scientific principles governing transport of sub-100 nm particles in dilute solutions. We investigated the translocation of rigid nanoparticles through nanopores at salt concentrations < 50 mM. When using low electrolyte strength, surface effects become predominant and resulted in unconventional current signatures in our experiments. It prompted us to explore the effects of different experimental parameters using Multiphysics simulations, in order to optimize our system for nano-vesicle detection and analysis. Chapter 3, discusses translocation of ~85 nm DOPC liposomes through the nanopore and their co-translocational deformation due to high field strength and confinement/ flow induced strain inside the nanopore. The behavior of liposomes was compared to the rigid polystyrene particles which maintained their shape and did not exhibit any deformation. Chapter 4 extends the vesicle deformation analysis to exosomes derived from human breast cancer cell line. Exosomes also exhibit co-translocational deformation behavior; however, they appear to be less affected by the deforming force inside the nanopore compared to the DOPC liposomes. We believe, the results of this research will bring about a novel nano-bioanalytical platform that can be used to capture comprehensive size and deformability data on nano-vesicles with high temporal resolution.

Single-molecule Protein Unfolding in Solid State Nanopores

PubMed Central

Talaga, David S.; Li, Jiali

2009-01-01

We use single silicon nitride nanopores to study folded, partially folded and unfolded single proteins by measuring their excluded volumes. The DNA-calibrated translocation signals of β-lactoglobulin and histidine-containing phosphocarrier protein match quantitatively with that predicted by a simple sum of the partial volumes of the amino acids in the polypeptide segment inside the pore when translocation stalls due to the primary charge sequence. Our analysis suggests that the majority of the protein molecules were linear or looped during translocation and that the electrical forces present under physiologically relevant potentials can unfold proteins. Our results show that the nanopore translocation signals are sensitive enough to distinguish the folding state of a protein and distinguish between proteins based on the excluded volume of a local segment of the polypeptide chain that transiently stalls in the nanopore due to the primary sequence of charges. PMID:19530678

Fundamental characteristics of degradation-recoverable solid-state DFB polymer laser.

PubMed

Yoshioka, Hiroaki; Yang, Yu; Watanabe, Hirofumi; Oki, Yuji

2012-02-13

A novel solid-state dye laser with degradation recovery was proposed and demonstrated. Polydimethylsiloxane was used as a nanoporous solid matrix to enable the internal circulation of dye molecules in the solid state. An internal circulation model for the dye molecules was also proposed and verified numerically by assuming molecular mobility and using a proposed diffusion equation. The durability of the laser was increased 20.5-fold compared with that of a conventional polymethylmethacrylate laser. This novel laser solves the low-durability problem of dye-doped polymer lasers.

Rh6G released from solid and nanoporous SiO2 spheres prepared by sol-gel route

NASA Astrophysics Data System (ADS)

García-Macedo, J. A.; Francisco S., P.; Franco, A.

2015-10-01

Porous silica nanoparticles are considering good systems for drug cargo and liquid separation. In this work we studied the release of rhodamine 6G (Rh6G) from solid and porous silica nanoparticles. Solid and porous SiO2 spheres were prepared by sol-gel method. Nanoporous channels were produced by using a surfactant that was removed by chemical procedure. Rh6G was incorporated into the channels by impregnation. The hexagonal structure of the pores was detected by XRD and confirmed by HRTEM micrographs. Rh6G released from the particles by stirring them in water at controlled speed was studied as function of time by photoluminescence. Released ratio was faster in the solid nanoparticles than in the porous ones. In the last case, a second release mechanism was observed. It was related with rhodamine coming out from the porous.

Tailoring particle translocation via dielectrophoresis in pore channels

PubMed Central

Tanaka, Shoji; Tsutsui, Makusu; Theodore, Hu; Yuhui, He; Arima, Akihide; Tsuji, Tetsuro; Doi, Kentaro; Kawano, Satoyuki; Taniguchi, Masateru; Kawai, Tomoji

2016-01-01

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. PMID:27527126

Streaming current magnetic fields in a charged nanopore

PubMed Central

Mansouri, Abraham; Taheri, Peyman; Kostiuk, Larry W.

2016-01-01

Magnetic fields induced by currents created in pressure driven flows inside a solid-state charged nanopore were modeled by numerically solving a system of steady state continuum partial differential equations, i.e., Poisson, Nernst-Planck, Ampere and Navier-Stokes equations (PNPANS). This analysis was based on non-dimensional transport governing equations that were scaled using Debye length as the characteristic length scale, and applied to a finite length cylindrical nano-channel. The comparison of numerical and analytical studies shows an excellent agreement and verified the magnetic fields density both inside and outside the nanopore. The radially non-uniform currents resulted in highly non-uniform magnetic fields within the nanopore that decay as 1/r outside the nanopore. It is worth noting that for either streaming currents or streaming potential cases, the maximum magnetic field occurred inside the pore in the vicinity of nanopore wall, as opposed to a cylindrical conductor that carries a steady electric current where the maximum magnetic fields occur at the perimeter of conductor. Based on these results, it is suggested and envisaged that non-invasive external magnetic fields readouts generated by streaming/ionic currents may be viewed as secondary electronic signatures of biomolecules to complement and enhance current DNA nanopore sequencing techniques. PMID:27833119

Nanoscale Dynamics of Joule heating and Bubble Nucleation in a Solid-State Nanopore

PubMed Central

Levine, Edlyn V.; Burns, Michael M.; Golovchenko, Jene A.

2016-01-01

We present a mathematical model for Joule heating of an electrolytic solution in a nanopore. The model couples the electrical and thermal dynamics responsible for rapid and extreme superheating of the electrolyte within the nanopore. The model is implemented numerically with a finite element calculation, yielding a time and spatially resolved temperature distribution in the nanopore region. Temperatures near the thermodynamic limit of superheat are predicted to be attained just before the explosive nucleation of a vapor bubble is observed experimentally. Knowledge of this temperature distribution enables the evaluation of related phenomena including bubble nucleation kinetics, relaxation oscillation, and bubble dynamics. PACS numbers 47.55.dp, 47.55.db, 85.35.-p, 05.70Fh PMID:26871171

Nanopore fabricated in pyramidal HfO2 film by dielectric breakdown method

NASA Astrophysics Data System (ADS)

Wang, Yifan; Chen, Qi; Deng, Tao; Liu, Zewen

2017-10-01

The dielectric breakdown method provides an innovative solution to fabricate solid-state nanopores on insulating films. A nanopore generation event via this method is considered to be caused by random charged traps (i.e., structural defects) and high electric fields in the membrane. Thus, the position and number of nanopores on planar films prepared by the dielectric breakdown method is hard to control. In this paper, we propose to fabricate nanopores on pyramidal HfO2 films (10-nm and 15-nm-thick) to improve the ability to control the location and number during the fabrication process. Since the electric field intensity gets enhanced at the corners of the pyramid-shaped film, the probability of nanopore occurrence at vertex and edge areas increases. This priority of appearance provides us chance to control the location and number of nanopores by monitoring a sudden irreversible discrete increase in current. The experimental results showed that the probability of nanopore occurrence decreases in an order from the vertex area, the edge area to the side face area. The sizes of nanopores ranging from 30 nm to 10 nm were obtained. Nanopores fabricated on the pyramid-shaped HfO2 film also showed an obvious ion current rectification characteristic, which might improve the nanopore performance as a biomolecule sequencing platform.

Voltage-Rectified Current and Fluid Flow in Conical Nanopores.

PubMed

Lan, Wen-Jie; Edwards, Martin A; Luo, Long; Perera, Rukshan T; Wu, Xiaojian; Martin, Charles R; White, Henry S

2016-11-15

Ion current rectification (ICR) refers to the asymmetric potential-dependent rate of the passage of solution ions through a nanopore, giving rise to electrical current-voltage characteristics that mimic those of a solid-state electrical diode. Since the discovery of ICR in quartz nanopipettes two decades ago, synthetic nanopores and nanochannels of various geometries, fabricated in membranes and on wafers, have been extensively investigated to understand fundamental aspects of ion transport in highly confined geometries. It is now generally accepted that ICR requires an asymmetric electrical double layer within the nanopore, producing an accumulation or depletion of charge-carrying ions at opposite voltage polarities. Our research groups have recently explored how the voltage-dependent ion distributions and ICR within nanopores can induce novel nanoscale flow phenomena that have applications in understanding ionics in porous materials used in energy storage devices, chemical sensing, and low-cost electrical pumping of fluids. In this Account, we review our most recent investigations on this topic, based on experiments using conical nanopores (10-300 nm tip opening) fabricated in thin glass, mica, and polymer membranes. Measurable fluid flow in nanopores can be induced either using external pressure forces, electrically via electroosmotic forces, or by a combination of these two forces. We demonstrate that pressure-driven flow can greatly alter the electrical properties of nanopores and, vice versa, that the nonlinear electrical properties of conical nanopores can impart novel and useful flow phenomena. Electroosmotic flow (EOF), which depends on the magnitude of the ion fluxes within the double layer of the nanopore, is strongly coupled to the accumulation/depletion of ions. Thus, the same underlying cause of ICR also leads to EOF rectification, i.e., unequal flows occurring for the same voltage but opposite polarities. EOF rectification can be used to electrically pump fluids with very precise control across membranes containing conical pores via the application of a symmetric sinusoidal voltage. The combination of pressure and asymmetric EOF can also provide a means to generate new nanopore electrical behaviors, including negative differential resistance (NDR), in which the current through a conical pore decreases with increasing driving force (applied voltage), similar to solid-state tunnel diodes. NDR results from a positive feedback mechanism between the ion distributions and EOF, yielding a true bistability in both fluid flow and electrical current at a critical applied voltage. Nanopore-based NDR is extremely sensitive to the surface charge near the nanopore opening, suggesting possible applications in chemical sensing.

Integrated nanopore sensing platform with sub-microsecond temporal resolution

PubMed Central

Rosenstein, Jacob K; Wanunu, Meni; Merchant, Christopher A; Drndic, Marija; Shepard, Kenneth L

2012-01-01

Nanopore sensors have attracted considerable interest for high-throughput sensing of individual nucleic acids and proteins without the need for chemical labels or complex optics. A prevailing problem in nanopore applications is that the transport kinetics of single biomolecules are often faster than the measurement time resolution. Methods to slow down biomolecular transport can be troublesome and are at odds with the natural goal of high-throughput sensing. Here we introduce a low-noise measurement platform that integrates a complementary metal-oxide semiconductor (CMOS) preamplifier with solid-state nanopores in thin silicon nitride membranes. With this platform we achieved a signal-to-noise ratio exceeding five at a bandwidth of 1 MHz, which to our knowledge is the highest bandwidth nanopore recording to date. We demonstrate transient signals as brief as 1 μs from short DNA molecules as well as current signatures during molecular passage events that shed light on submolecular DNA configurations in small nanopores. PMID:22426489

Magnetic solid-phase extraction using nanoporous three dimensional graphene hybrid materials for high-capacity enrichment and simultaneous detection of nine bisphenol analogs from water sample.

PubMed

Wang, Lingling; Zhang, Zhenzhen; Zhang, Jing; Zhang, Lei

2016-09-09

The synthesis of a magnetic nanoporous three dimensional graphene (3DG)/ZnFe2O4 composite has been achieved. Through formation of graphene hydrogel, ZnFe2O4 magnetic particles was successfully introduced into the nanoporous 3DG, resulting in a magnetic porous carbon material. The morphology, structure, and magnetic behavior of the as-prepared 3DG/ZnFe2O4 were characterized by using the techniques of SEM, XRD, BET, VSM, FTIR, Raman and TGA. The 3DG/ZnFe2O4 has a high specific surface area and super paramagnetism. Its performance was evaluated by the magnetic solid-phase extraction of nine bisphenol analogs (BPs) from water samples followed by HPLC analysis, and showed excellent adsorption capability for the nine target compounds. Under optimized condition, the lower method detection limits (0.05-0.18ngmL(-1)), the higher enrichment factors (800 fold) and good recoveries (95.1-103.8%) with relative standard deviation (RSD) values less than 6.2% were achieved. The results indicated that the developed method based on the use of 3DG/ZnFe2O4 as the magnetic adsorbent has the advantages of convenience and high efficiency, and can be successfully applied to detect the nine BPs in real water samples. Copyright © 2016 Elsevier B.V. All rights reserved.

A Quasi-Solid-State Sodium-Ion Capacitor with High Energy Density.

PubMed

Wang, Faxing; Wang, Xiaowei; Chang, Zheng; Wu, Xiongwei; Liu, Xiang; Fu, Lijun; Zhu, Yusong; Wu, Yuping; Huang, Wei

2015-11-18

A quasi-solid-state sodium-ion capacitor is demonstrated with nanoporous disordered carbon and macroporous graphene as the negative and positive electrodes, respectively, using a sodium-ion-conducting gel polymer electrolyte. It can operate at a cell voltage as high as 4.2 V with an energy density of record high 168 W h kg(-1). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nanopore Kinetic Proofreading of DNA Sequences

NASA Astrophysics Data System (ADS)

Ling, Xinsheng Sean

The concept of DNA sequencing using the time dependence of the nanopore ionic current was proposed in 1996 by Kasianowicz, Brandin, Branton, and Deamer (KBBD). The KBBD concept has generated tremendous amount interests in recent decade. In this talk, I will review the current understanding of the DNA ``translocation'' dynamics and how it can be described by Schrodinger's 1915 paper on first-passage-time distribution function. Schrodinger's distribution function can be used to give a rigorous criterion for achieving nanopore DNA sequencing which turns out to be identical to that of gel electrophoresis used by Sanger in the first-generation Sanger method. A nanopore DNA sequencing technology also requires discrimination of bases with high accuracies. I will describe a solid-state nanopore sandwich structure that can function as a proofreading device capable of discriminating between correct and incorrect hybridization probes with an accuracy rivaling that of high-fidelity DNA polymerases. The latest results from Nanjing will be presented. This work is supported by China 1000-Talent Program at Southeast University, Nanjing, China.

Roles of Chemical Functionality and Pore Curvature in the Design of Nanoporous Proton Conductors

DOE PAGES

Jackson, Grayson L.; Perroni, Dominic V.; Mahanthappa, Mahesh K.

2017-10-03

Nanoporous proton-transporting media are critical components in fuel cells and other electrochemical devices, yet general molecular design criteria for new materials with enhanced performance remain obscure. Aqueous lyotropic liquid crystals (LLCs) comprise a platform for detailed studies of the molecular-level features governing proton transport in monodisperse, water-filled nanopores lined with well-defined chemical functionalities. Here, we report new alkylsulfonic acid LLCs that exhibit H+ conductivities as high as σ = 380 mS/cm at 80°C, which rival those of more acidic, perfluorinated polymers, thus demonstrating that the acidity of the pore functionality is not the sole determinant of proton transport. Direct experimentalmore » comparisons of LLCs with convex and concave nanopores of similar dimensions indicate that H+ conductivities therein sensitively depend on the hydration state of the acid functionalities and the pore curvature. These experiments suggest that judicious manipulation of pore curvature provides a new means for optimizing the activities of proton-exchange membranes and nanoporous solid acid catalysts.« less

Expanding the functionality and applications of nanopore sensors

NASA Astrophysics Data System (ADS)

Venta, Kimberly E.

Nanopore sensors have developed into powerful tools for single-molecule studies since their inception two decades ago. Nanopore sensors function as nanoscale Coulter counters, by monitoring ionic current modulations as particles pass through a nanopore. While nanopore sensors can be used to study any nanoscale particle, their most notable application is as a low cost, fast alternative to current DNA sequencing technologies. In recent years, signifcant progress has been made toward the goal of nanopore-based DNA sequencing, which requires an ambitious combination of a low-noise and high-bandwidth nanopore measurement system and spatial resolution. In this dissertation, nanopore sensors in thin membranes are developed to improve dimensional resolution, and these membranes are used in parallel with a high-bandwidth amplfier. Using this nanopore sensor system, the signals of three DNA homopolymers are differentiated for the first time in solid-state nanopores. The nanopore noise is also reduced through the addition of a layer of SU8, a spin-on polymer, to the supporting chip structure. By increasing the temporal and spatial resolution of nanopore sensors, studies of shorter molecules are now possible. Nanopore sensors are beginning to be used for the study and characterization of nanoparticles. Nanoparticles have found many uses from biomedical imaging to next-generation solar cells. However, further insights into the formation and characterization of nanoparticles would aid in developing improved synthesis methods leading to more effective and customizable nanoparticles. This dissertation presents two methods of employing nanopore sensors to benet nanoparticle characterization and fabrication. Nanopores were used to study the formation of individual nanoparticles and serve as nanoparticle growth templates that could be exploited to create custom nanoparticle arrays. Additionally, nanopore sensors were used to characterize the surface charge density of anisotropic nanopores, which previously could not be reliably measured. Current nanopore sensor resolution levels have facilitated innovative research on nanoscale systems, including studies of DNA and nanoparticle characterization. Further nanopore system improvements will enable vastly improved DNA sequencing capabilities and open the door to additional nanopore sensing applications.

Optical Sensors for Biomolecules Using Nanoporous Sol-Gel Materials

NASA Technical Reports Server (NTRS)

Fang, Jonathan; Zhou, Jing C.; Lan, Esther H.; Dunn, Bruce; Gillman, Patricia L.; Smith, Scott M.

2004-01-01

An important consideration for space missions to Mars is the ability to detect biosignatures. Solid-state sensing elements for optical detection of biological entities are possible using sol-gel based biologically active materials. We have used these materials as optical sensing elements in a variety of bioassays, including immunoassays and enzyme assays. By immobilizing an appropriate biomolecule in the sol-gel sensing element, we have successfully detected analytes such as amino acids and hormones. In the case of the amino acid glutamate, the enzyme glutamate dehydrogenase was the immobilized molecule, whereas in the case of the hormone cortisol, an anti-cortisol antibody was immobilized in the sensing element. In this previous work with immobilized enzymes and antibodies, excellent sensitivity and specificity were demonstrated in a variety of formats including bulk materials, thin films and fibers. We believe that the sol-gel approach is an attractive platform for bioastronautics sensing applications because of the ability to detect a wide range of entities such as amino acids, fatty acids, hopanes, porphyrins, etc. The sol-gel approach produces an optically transparent 3D silica matrix that forms around the biomolecule of interest, thus stabilizing its structure and functionality while allowing for optical detection. This encapsulation process protects the biomolecule and leads to a more "rugged" sensor. The nanoporous structure of the sol-gel matrix allows diffusion of small target molecules but keeps larger, biomolecules immobilized in the pores. We are currently developing these biologically active sol-gel materials into small portable devices for on-orbit cortisol detection

Formation of self-organized nanoporous anodic oxide from metallic gallium.

PubMed

Pandey, Bipin; Thapa, Prem S; Higgins, Daniel A; Ito, Takashi

2012-09-25

This paper reports the formation of self-organized nanoporous gallium oxide by anodization of solid gallium metal. Because of its low melting point (ca. 30 °C), metallic gallium can be shaped into flexible structures, permitting the fabrication of nanoporous anodic oxide monoliths within confined spaces like the inside of a microchannel. Here, solid gallium films prepared on planar substrates were employed to investigate the effects of anodization voltage (1, 5, 10, 15 V) and H(2)SO(4) concentration (1, 2, 4, 6 M) on anodic oxide morphology. Self-organized nanopores aligned perpendicular to the film surface were obtained upon anodization of gallium films in ice-cooled 4 and 6 M aqueous H(2)SO(4) at 10 and 15 V. Nanopore formation could be recognized by an increase in anodic current after a current decrease reflecting barrier oxide formation. The average pore diameter was in the range of 18-40 nm with a narrow diameter distribution (relative standard deviation ca. 10-20%), and was larger at lower H(2)SO(4) concentration and higher applied voltage. The maximum thickness of nanoporous anodic oxide was ca. 2 μm. In addition, anodic formation of self-organized nanopores was demonstrated for a solid gallium monolith incorporated at the end of a glass capillary. Nanoporous anodic oxide monoliths formed from a fusible metal will lead to future development of unique devices for chemical sensing and catalysis.

Resistive-pulse and rectification sensing with glass and carbon nanopipettes

PubMed Central

Wang, Yixian; Wang, Dengchao

2017-01-01

Along with more prevalent solid-state nanopores, glass or quartz nanopipettes have found applications in resistive-pulse and rectification sensing. Their advantages include the ease of fabrication, small physical size and needle-like geometry, rendering them useful for local measurements in small spaces and delivery of nanoparticles/biomolecules. Carbon nanopipettes fabricated by depositing a thin carbon layer on the inner wall of a quartz pipette provide additional means for detecting electroactive species and fine-tuning the current rectification properties. In this paper, we discuss the fundamentals of resistive-pulse sensing with nanopipettes and our recent studies of current rectification in carbon pipettes. PMID:28413354

Resistive-pulse and rectification sensing with glass and carbon nanopipettes.

PubMed

Wang, Yixian; Wang, Dengchao; Mirkin, Michael V

2017-03-01

Along with more prevalent solid-state nanopores, glass or quartz nanopipettes have found applications in resistive-pulse and rectification sensing. Their advantages include the ease of fabrication, small physical size and needle-like geometry, rendering them useful for local measurements in small spaces and delivery of nanoparticles/biomolecules. Carbon nanopipettes fabricated by depositing a thin carbon layer on the inner wall of a quartz pipette provide additional means for detecting electroactive species and fine-tuning the current rectification properties. In this paper, we discuss the fundamentals of resistive-pulse sensing with nanopipettes and our recent studies of current rectification in carbon pipettes.

Brownian dynamics simulation of a polymer chain in a solid-state nanopore attached to a molecular stop

NASA Astrophysics Data System (ADS)

Wells, Craig; Hulings, Zachery; Melnikov, Dmitriy; Gracheva, Maria

We study a nanopore inside a silicon dioxide membrane submerged in a KCl solution with a negatively charged polymer chain of varying lengths whose movement is described using Brownian dynamics. The polymer is attached to a molecule with a radius larger than that of the nanopore's which acts as a molecular stop, allowing the chain to thread the nanopore but preventing it from translocating. We found that the polymer chain's variation of movement along the nanopore decreased when increasing applied biases and chain lengths for portions of the chain closest to the molecular stop. The chain displacement within the pore is also compared to a freely translocating polymer where preliminary results show the free polymer having a greater variation in the radial direction. Overall, our preliminary results indicate that the radial direction of the polymer chain is dominated by the confinement in the narrow nanopore with restrictions imposed by the molecular stop and bias playing a lesser role. Understanding the interaction behavior of the polymer chain-stop molecule may lead to methods that decrease movement variation, facilitating an improvement on characterizing and identification of molecules. NSF DMR and CBET Grant No. 1352218.

Reversible Immobilization of Proteins in Sensors and Solid-State Nanopores.

PubMed

Ananth, Adithya; Genua, María; Aissaoui, Nesrine; Díaz, Leire; Eisele, Nico B; Frey, Steffen; Dekker, Cees; Richter, Ralf P; Görlich, Dirk

2018-05-01

The controlled functionalization of surfaces with proteins is crucial for many analytical methods in life science research and biomedical applications. Here, a coating for silica-based surfaces is established which enables stable and selective immobilization of proteins with controlled orientation and tunable surface density. The coating is reusable, retains functionality upon long-term storage in air, and is applicable to surfaces of complex geometry. The protein anchoring method is validated on planar surfaces, and then a method is developed to measure the anchoring process in real time using silicon nitride solid-state nanopores. For surface attachment, polyhistidine tags that are site specifically introduced into recombinant proteins are exploited, and the yeast nucleoporin Nsp1 is used as model protein. Contrary to the commonly used covalent thiol chemistry, the anchoring of proteins via polyhistidine tag is reversible, permitting to take proteins off and replace them by other ones. Such switching in real time in experiments on individual nanopores is monitored using ion conductivity. Finally, it is demonstrated that silica and gold surfaces can be orthogonally functionalized to accommodate polyhistidine-tagged proteins on silica but prevent protein binding to gold, which extends the applicability of this surface functionalization method to even more complex sensor devices. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Top-down solid-phase fabrication of nanoporous cadmium oxide architectures.

PubMed

Yu, Haidong; Wang, Deshen; Han, Ming-Yong

2007-02-28

In this article, we have demonstrated one-step solid-phase transformation from high-quality cadmium carbonate microcrystals into highly nanoporous cadmium oxide. The high crystal quality of cadmium carbonate is critical for the successful fabrication of porous nanoarchitectures with predetermined morphology and well-controlled internal structure. This novel strategy has a good potential to prepare nanoporous materials at a large scale by using perfect monolithic carbonate crystals, and it is also useful to synthesize different nanoporous materials on metal-oxide-coated substrates. Meanwhile, this simple thermal transformation of cadmium carbonate into porous structures has further been extended to convert calcium carbonate into such porous structures.

Solid-state devices for detection of DNA, protein biomarkers and cells

NASA Astrophysics Data System (ADS)

Asghar, Waseem

Nanobiotechnology and BioMEMS have had tremendous impact on biosensing in the areas of cancer cell detection and therapeutics, disease diagnostics, proteomics and DNA analysis. Diseases are expressed on all levels including DNA, protein, cell and tissue. Therefore it is very critical to develop biosensors at each level. The power of the nanotechnology lies in the fact that we can fabricate devices on all scales from micro to nano. This dissertation focuses on four areas: 1) Development of nanopore sensors for DNA analysis; 2) Development of micropore sensors for early detection of circulating tumor cells (CTCs) from whole blood; 3) Synthesis of nano-textured substrates for cancer isolation and tissue culture applications; 4) Fabrication of nanoscale break-junctions. All of these sensors are fabricated using standard silicon processing techniques. Pulsed plasma polymer deposition is also utilized to control the density of the biosensor surface charges. These devices are then used for efficient detection of DNA, proteins and cells, and can be potentially used in point-of-care systems. Overall, our designed biosensing platforms offer improved selectivity, yield and reliability. Novel approaches to nanopore shrinking are simple, reliable and do not change the material composition around the pore boundary. The micropores provide a direct interface to distinguish CTCs from normal cell without requiring fluorescent dyes and surface functionalization. Nano-textured surfaces and break-junctions can be used for enhanced adhesion of cells and selective detection of proteins respectively.

Direct Evidence for Solid-like Hydrogen in a Nanoporous Carbon Hydrogen Storage Material at Supercritical Temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ting, Valeska P.; Ramirez-Cuesta, Anibal J.; Bimbo, Nuno

Here in this paper we report direct physical evidence that confinement of molecular hydrogen (H 2) in an optimized nanoporous carbon results in accumulation of hydrogen with characteristics commensurate with solid H 2 at temperatures up to 67 K above the liquid vapor critical temperature of bulk H 2. This extreme densification is attributed to confinement of 112 molecules in the optimally sized micropores, and occurs at pressures as low as 0.02 MPa. The quantities of contained, solid-like H 2 increased with pressure and were directly evaluated using in situ inelastic neutron scattering and confirmed by analysis of gas sorptionmore » isotherms. The demonstration of the existence of solid-like H 2 challenges the existing assumption that supercritical hydrogen confined in nanopores has an upper limit of liquid H 2 density. Thus, this insight offers opportunities for the development of more accurate models for the evaluation and design of nanoporous materials for high capacity adsorptive hydrogen storage.« less

Direct Evidence for Solid-like Hydrogen in a Nanoporous Carbon Hydrogen Storage Material at Supercritical Temperatures

DOE PAGES

Ting, Valeska P.; Ramirez-Cuesta, Anibal J.; Bimbo, Nuno; ...

2015-07-14

Here in this paper we report direct physical evidence that confinement of molecular hydrogen (H 2) in an optimized nanoporous carbon results in accumulation of hydrogen with characteristics commensurate with solid H 2 at temperatures up to 67 K above the liquid vapor critical temperature of bulk H 2. This extreme densification is attributed to confinement of 112 molecules in the optimally sized micropores, and occurs at pressures as low as 0.02 MPa. The quantities of contained, solid-like H 2 increased with pressure and were directly evaluated using in situ inelastic neutron scattering and confirmed by analysis of gas sorptionmore » isotherms. The demonstration of the existence of solid-like H 2 challenges the existing assumption that supercritical hydrogen confined in nanopores has an upper limit of liquid H 2 density. Thus, this insight offers opportunities for the development of more accurate models for the evaluation and design of nanoporous materials for high capacity adsorptive hydrogen storage.« less

Growing large columnar grains of CH3NH3PbI3 using the solid-state reaction method enhanced by less-crystallized nanoporous PbI2 films

NASA Astrophysics Data System (ADS)

Zheng, Huifeng; Wang, Weiqi; Liu, Yangqiao; Sun, Jing

2017-03-01

Compact, pinhole-free and PbI2-free perovskite films, are desirable for high-performance perovskite solar cells (PSCs), especially if large columnar grains are obtained in which the adverse effects of grain boundaries will be minimized. However, the conventional solid-state reaction methods, originated from the two-step method, failed to grow columnar grains of CH3NH3PbI3 in a facile way. Here, we demonstrate a strategy for growing large columnar grains of CH3NH3PbI3, by less-crystallized nanoporous PbI2 (ln-PbI2) film enhanced solid-state reaction method. We demonstrated columnar grains were obtainable only when ln-PbI2 films were applied. Therefore, the replacement of compact PbI2 by ln-PbI2 in the solid-sate reaction, leads to higher power conversion efficiency, better reproducibility, better stability and less hysteresis. Furthermore, by systematically investigating the effects of annealing temperature and duration, we found that an annealing temperature ≥120 °C was also critical for growing columnar grains. With the optimal process, a champion efficiency of 16.4% was obtained and the average efficiency reached 14.2%. Finally, the mechanism of growing columnar grains was investigated, in which a VPb″ -assisted hooping model was proposed. This work reveals the origins of grain growth in the solid-state reaction method, which will contribute to preparing high quality perovskite films with much larger columnar grains.

Gassmann Theory Applies to Nanoporous Media

NASA Astrophysics Data System (ADS)

Gor, Gennady Y.; Gurevich, Boris

2018-01-01

Recent progress in extraction of unconventional hydrocarbon resources has ignited the interest in the studies of nanoporous media. Since many thermodynamic and mechanical properties of nanoscale solids and fluids differ from the analogous bulk materials, it is not obvious whether wave propagation in nanoporous media can be described using the same framework as in macroporous media. Here we test the validity of Gassmann equation using two published sets of ultrasonic measurements for a model nanoporous medium, Vycor glass, saturated with two different fluids, argon, and n-hexane. Predictions of the Gassmann theory depend on the bulk and shear moduli of the dry samples, which are known from ultrasonic measurements and the bulk moduli of the solid and fluid constituents. The solid bulk modulus can be estimated from adsorption-induced deformation or from elastic effective medium theory. The fluid modulus can be calculated according to the Tait-Murnaghan equation at the solvation pressure in the pore. Substitution of these parameters into the Gassmann equation provides predictions consistent with measured data. Our findings set up a theoretical framework for investigation of fluid-saturated nanoporous media using ultrasonic elastic wave propagation.

Transport mechanisms in nanopores and nanochannels: Can we mimic nature?

DOE PAGES

Tagliazucchi, Mario; Szleifer, Igal

2014-11-03

The last few years have witnessed major advancements in the synthesis, modification, characterization and modeling of nanometer-size solid-state channels and pores. Future applications in sensing, energy conversion and purification technologies will critically rely on qualitative improvements in the control over the selectivity, directionality and responsiveness of these nanochannels and nanopores. It is not surprising, therefore, that researchers in the field seek inspiration in biological ion channels and ion pumps, paradigmatic examples of transport selectivity. This work reviews our current fundamental understanding of the mechanisms of transport of ions and larger cargoes through nanopores and nanochannels by examining recent experimental andmore » theoretical work. It is argued that that structure and transport in biological channels and polyelectrolyte-modified synthetic nanopores are strongly coupled: the structure dictates transport and transport affects the structure. We compare synthetic and biological systems throughout this review to conclude that while they present interesting similarities, they also have striking differences.« less

Brownian dynamics of a protein-polymer chain complex in a solid-state nanopore

NASA Astrophysics Data System (ADS)

Wells, Craig C.; Melnikov, Dmitriy V.; Gracheva, Maria E.

2017-08-01

We study the movement of a polymer attached to a large protein inside a nanopore in a thin silicon dioxide membrane submerged in an electrolyte solution. We use Brownian dynamics to describe the motion of a negatively charged polymer chain of varying lengths attached to a neutral protein modeled as a spherical bead with a radius larger than that of the nanopore, allowing the chain to thread the nanopore but preventing it from translocating. The motion of the protein-polymer complex within the pore is also compared to that of a freely translocating polymer. Our results show that the free polymer's standard deviations in the direction normal to the pore axis is greater than that of the protein-polymer complex. We find that restrictions imposed by the protein, bias, and neighboring chain segments aid in controlling the position of the chain in the pore. Understanding the behavior of the protein-polymer chain complex may lead to methods that improve molecule identification by increasing the resolution of ionic current measurements.

Brownian dynamics of a protein-polymer chain complex in a solid-state nanopore.

PubMed

Wells, Craig C; Melnikov, Dmitriy V; Gracheva, Maria E

2017-08-07

We study the movement of a polymer attached to a large protein inside a nanopore in a thin silicon dioxide membrane submerged in an electrolyte solution. We use Brownian dynamics to describe the motion of a negatively charged polymer chain of varying lengths attached to a neutral protein modeled as a spherical bead with a radius larger than that of the nanopore, allowing the chain to thread the nanopore but preventing it from translocating. The motion of the protein-polymer complex within the pore is also compared to that of a freely translocating polymer. Our results show that the free polymer's standard deviations in the direction normal to the pore axis is greater than that of the protein-polymer complex. We find that restrictions imposed by the protein, bias, and neighboring chain segments aid in controlling the position of the chain in the pore. Understanding the behavior of the protein-polymer chain complex may lead to methods that improve molecule identification by increasing the resolution of ionic current measurements.

Application of 1-(2-pyridylazo)-2-naphthol-modified nanoporous silica as a technique in simultaneous trace monitoring and removal of toxic heavy metals in food and water samples.

PubMed

Abolhasani, Jafar; Behbahani, Mohammad

2015-01-01

Solid-phase extraction is one the most useful and efficient techniques for sample preparation, purification, cleanup, preconcentration, and determination of heavy metals at trace levels. In this paper, functionalized MCM-48 nanoporous silica with 1-(2-pyridylazo)-2-naphthol was applied for trace determination of copper, lead, cadmium, and nickel in water and seafood samples. The experimental conditions such as pH, sample and eluent flow rate, type, concentration and volume of the eluent, breakthrough volume, and effect of coexisting ions were optimized for efficient solid-phase extraction of trace heavy metals in different water and seafood samples. The content of solutions containing the mentioned heavy metals was determined by flame atomic absorption spectrometry (FAAS), and the limits of detection were 0.3, 0.4, 0.6, and 0.9 ng mL(-1) for cadmium, copper, nickel, and lead, respectively. Recoveries and precisions were >98.0 and <4%, respectively. The adsorption capacity of the modified nanoporous silica was 178 mg g(-1) for cadmium, 110 mg g(-1) for copper, 98 mg g(-1) for nickel, and 210 mg g(-1) for lead, respectively. The functionalized MCM-48 nanoporous silica with 1-(2-pyridylazo)-2-naphthol was characterized by thermogravimetry analysis (TGA), differential thermal analysis (DTA), transmission electron microscopy (TEM), Fourier transform infrared spectrometry (FT-IR), X-ray diffraction (XRD), elemental analysis (CHN), and N2 adsorption surface area measurement.

Resizing metal-coated nanopores using a scanning electron microscope.

PubMed

Chansin, Guillaume A T; Hong, Jongin; Dusting, Jonathan; deMello, Andrew J; Albrecht, Tim; Edel, Joshua B

2011-10-04

Electron beam-induced shrinkage provides a convenient way of resizing solid-state nanopores in Si(3) N(4) membranes. Here, a scanning electron microscope (SEM) has been used to resize a range of different focussed ion beam-milled nanopores in Al-coated Si(3) N(4) membranes. Energy-dispersive X-ray spectra and SEM images acquired during resizing highlight that a time-variant carbon deposition process is the dominant mechanism of pore shrinkage, although granular structures on the membrane surface in the vicinity of the pores suggest that competing processes may occur. Shrinkage is observed on the Al side of the pore as well as on the Si(3) N(4) side, while the shrinkage rate is observed to be dependent on a variety of factors. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preparation of 3D nanoporous copper-supported cuprous oxide for high-performance lithium ion battery anodes.

PubMed

Liu, Dequan; Yang, Zhibo; Wang, Peng; Li, Fei; Wang, Desheng; He, Deyan

2013-03-07

Three-dimensional (3D) nanoporous architectures can provide efficient and rapid pathways for Li-ion and electron transport as well as short solid-state diffusion lengths in lithium ion batteries (LIBs). In this work, 3D nanoporous copper-supported cuprous oxide was successfully fabricated by low-cost selective etching of an electron-beam melted Cu(50)Al(50) alloy and subsequent in situ thermal oxidation. The architecture was used as an anode in lithium ion batteries. In the first cycle, the sample delivered an extremely high lithium storage capacity of about 2.35 mA h cm(-2). A high reversible capacity of 1.45 mA h cm(-2) was achieved after 120 cycles. This work develops a promising approach to building reliable 3D nanostructured electrodes for high-performance lithium ion batteries.

Nanotechnology Based Materials and Devices for Health Care

NASA Technical Reports Server (NTRS)

Srivastava, Deepaka; Cho, K.; Brenner, Don; Menon, Madhu; Andriotis, Antonis; Sagman, Uri; Biegel, Bryan A. (Technical Monitor)

2002-01-01

This viewgraph presentation provides information on trends in NASA nanotechnology research and development, and future biotechnological applications for that nanotechnology. The presentation covers nanoelectronics, nanosensors, and nanomaterials, biomimetics, devices and materials for health care, carbon nanotubes, biosensors for astrobiology, solid-state nanopores for DNA sequencing, and protein nanotubes.

Spontaneous Transport of Single-Stranded DNA through Graphene-MoS2 Heterostructure Nanopores.

PubMed

Luan, Binquan; Zhou, Ruhong

2018-04-24

The effective transport of a single-stranded DNA (ssDNA) molecule through a solid-state nanopore is essential to the future success of high-throughput and low-cost DNA sequencing. Compatible with current electric sensing technologies, here, we propose and demonstrate by molecular dynamics simulations the ssDNA transport through a quasi-two-dimensional nanopore in a heterostructure stacked together with different 2D materials, such as graphene and molybdenum disulfide (MoS 2 ). Due to different chemical potentials, U, of DNA bases on different 2D materials, it is energetically favorable for a ssDNA molecule to move from the low- U MoS 2 surface to the high- U graphene surface through a nanopore. With the proper attraction between the negatively charged phosphate group in each nucleotide and the positively charged Mo atoms exposed on the pore surface, the ssDNA molecule can be temporarily seized and released thereafter through a thermal activation, that is, a slow and possible nucleotide-by-nucleotide transport. A theoretical formulation is then developed for the free energy of the ssDNA transiting a heterostructure nanopore to properly characterize the non-equilibrium stick-slip-like motion of a ssDNA molecule.

Nanoporous Au structures by dealloying Au/Ag thermal- or laser-dewetted bilayers on surfaces

NASA Astrophysics Data System (ADS)

Ruffino, F.; Torrisi, V.; Grillo, R.; Cacciato, G.; Zimbone, M.; Piccitto, G.; Grimaldi, M. G.

2017-03-01

Nanoporous Au attracts great technological interest and it is a promising candidate for optical and electrochemical sensors. In addition to nanoporous Au leafs and films, recently, interest was focused on nanoporous Au micro- and nano-structures on surfaces. In this work we report on the study of the characteristics of nanoporous Au structures produced on surfaces. We developed the following procedures to fabricate the nanoporous Au structures: we deposited thin Au/Ag bilayers on SiO2 or FTO (fluorine-doped tin oxide) substrates with thickness xAu and xAg of the Au and Ag layers; we induced the alloying and dewetting processes of the bilayers by furnace annealing processes of the bilayers deposited on SiO2 and by laser irradiations of the bilayers deposited on FTO; the alloying and dewetting processes result in the formation of AuxAgy alloy sub-micron particles being x and y tunable by xAu and xAg. These particles are dealloyed in HNO3 solution to remove the Ag atoms. We obtain, so, nanoporous sub-micron Au particles on the substrates. Analyzing the characteristics of these particles we find that: a) the size and shape of the particles depend on the nature of the dewetting process (solid-state dewetting on SiO2, molten-state dewetting on FTO); b) the porosity fraction of the particles depends on how the alloying process is reached: about 32% of porosity for the particles fabricated by the furnace annealing at 900 °C, about 45% of porosity for the particles fabricated by the laser irradiation at 0.5 J/cm2, in both cases independently on the Ag concentration in the alloy; c) After the dealloying process the mean volume of the Au particles shrinks of about 39%; d) After an annealing at 400 °C the nanoporous Au particles reprise their initial volume while the porosity fraction is reduced. Arguments to justify these behaviors are presented.

Development of sensing techniques for weaponry health monitoring

NASA Astrophysics Data System (ADS)

Edwards, Eugene; Ruffin, Paul B.; Walker, Ebonee A.; Brantley, Christina L.

2013-04-01

Due to the costliness of destructive evaluation methods for assessing the aging and shelf-life of missile and rocket components, the identification of nondestructive evaluation methods has become increasingly important to the Army. Verifying that there is a sufficient concentration of stabilizer is a dependable indicator that the missile's double-based solid propellant is viable. The research outlined in this paper summarizes the Army Aviation and Missile Research, Development, and Engineering Center's (AMRDEC's) comparative use of nanoporous membranes, carbon nanotubes, and optical spectroscopic configured sensing techniques for detecting degradation in rocket motor propellant. The first sensing technique utilizes a gas collecting chamber consisting of nanoporous structures that trap the smaller solid propellant particles for measurement by a gas analysis device. In collaboration with NASA-Ames, sensing methods are developed that utilize functionalized single-walled carbon nanotubes as the key sensing element. The optical spectroscopic sensing method is based on a unique light collecting optical fiber system designed to detect the concentration of the propellant stabilizer. Experimental setups, laboratory results, and overall effectiveness of each technique are presented in this paper. Expectations are for the three sensing mechanisms to provide nondestructive evaluation methods that will offer cost-savings and improved weaponry health monitoring.

Excitation of luminescence of the nanoporous bioactive nanocrystalline carbonate-substituted hydroxyapatite for early tooth disease detection

NASA Astrophysics Data System (ADS)

Goloshchapov, D. L.; Minakov, D. A.; Domashevskaya, E. P.; Seredin, P. V.

This paper deals with the luminescence characteristics of an analogue of the mineral component of dental enamel of the nanocrystalline B-type carbonate-substituted hydroxyapatite (CHAP) with 3D defects (i.e. nanopores of ∼2-5 nm) on the nanocrystalline surface. The laser-induced luminescence (LIL) of the synthesized CHAP samples was in the range of ∼515 nm (∼2.4 eV) and is due to CO3 groups replacing the PO4 group. It was found that the intensity of the luminescence of the CHAP is caused by structurally incorporated CO3 groups in the HAP structure. Furthermore, the intensity of the luminescence also decreases as the number of the above intracentre defects (CO3) in the apatite structure declines. These results are potentially promising for developing the foundations for precise methods for the early detection of caries in human solid dental tissue.

Study of the nanoporous CHAP photoluminiscence for developing the precise methods of early caries detection

NASA Astrophysics Data System (ADS)

Goloshchapov, D.; Seredin, P.; Minakov, D.; Domashevskaya, E.

2018-02-01

This paper deals with the luminescence characteristics of an analogue of the mineral component of dental enamel of the nanocrystalline B-type carbonate-substituted hydroxyapatite (CHAP) with 3D defects (i.e. nanopores of ∼2-5 nm) on the nanocrystalline surface. The laser-induced luminescence of the synthesized CHAP samples was in the range of ∼515 nm (∼2.4 eV) and is due to CO3 groups replacing the PO4 group. It was found that the intensity of the luminescence of the CHAP is caused by structurally incorporated CO3 groups in the HAP structure. Furthermore, the intensity of the luminescence also decreases as the number of the above intracentre defects (CO3) in the apatite structure declines. These results are potentially promising for developing the foundations for precise methods for the early detection of caries in human solid dental tissue.

Simultaneous Ionic Current and Potential Detection of Nanoparticles by a Multifunctional Nanopipette.

PubMed

Panday, Namuna; Qian, Gongming; Wang, Xuewen; Chang, Shuai; Pandey, Popular; He, Jin

2016-12-27

Nanopore sensing-based technologies have made significant progress for single molecule and single nanoparticle detection and analysis. In recent years, multimode sensing by multifunctional nanopores shows the potential to greatly improve the sensitivity and selectivity of traditional resistive-pulse sensing methods. In this paper, we showed that two label-free electric sensing modes could work cooperatively to detect the motion of 40 nm diameter spherical gold nanoparticles (GNPs) in solution by a multifunctional nanopipette. The multifunctional nanopipettes containing both nanopore and nanoelectrode (pyrolytic carbon) at the tip were fabricated quickly and cheaply. We demonstrated that the ionic current and local electrical potential changes could be detected simultaneously during the translocation of individual GNPs. We also showed that the nanopore/CNE tip geometry enabled the CNE not only to detect the translocation of single GNP but also to collectively detect several GNPs outside the nanopore entrance. The dynamic accumulation of GNPs near the nanopore entrance resulted in no detectable current changes, but was detected by the potential changes at the CNE. We revealed the motions of GNPs both outside and inside the nanopore, individually and collectively, with the combination of ionic current and potential measurements.

Microsecond Simulations of DNA and Ion Transport in Nanopores with Novel Ion-Ion and Ion-Nucleotides Effective Potentials

PubMed Central

De Biase, Pablo M.; Markosyan, Suren; Noskov, Sergei

2014-01-01

We developed a novel scheme based on the Grand-Canonical Monte-Carlo/Brownian Dynamics (GCMC/BD) simulations and have extended it to studies of ion currents across three nanopores with the potential for ssDNA sequencing: solid-state nanopore Si3N4, α-hemolysin, and E111N/M113Y/K147N mutant. To describe nucleotide-specific ion dynamics compatible with ssDNA coarse-grained model, we used the Inverse Monte-Carlo protocol, which maps the relevant ion-nucleotide distribution functions from an all-atom MD simulations. Combined with the previously developed simulation platform for Brownian Dynamic (BD) simulations of ion transport, it allows for microsecond- and millisecond-long simulations of ssDNA dynamics in nanopore with a conductance computation accuracy that equals or exceeds that of all-atom MD simulations. In spite of the simplifications, the protocol produces results that agree with the results of previous studies on ion conductance across open channels and provide direct correlations with experimentally measured blockade currents and ion conductances that have been estimated from all-atom MD simulations. PMID:24738152

Stiff Filamentous Viruses Probe the Mobility of Counterions During Nanopore Translocations

NASA Astrophysics Data System (ADS)

McMullen, Angus; Tang, Jay; Stein, Derek

2015-03-01

We study the electrophoresis of two different filamentous viruses and double-stranded DNA through solid-state nanopores. The two viruses we examine, fd and M13, are both 880 nm in length, 6.6 nm in diameter, very stiff, and monodisperse. They only differ in their linear charge density, which is 30 % lower for M13 than for fd. Filamentous viruses are therefore ideal for testing transport models and for comparisons with DNA dynamics. We find that the mean translocation speed of fd virus is related to the nanopore diameter, D, and the virus diameter, d, as ln(D / d) - 1 , in agreement with the conventional electrokinetic model of translocations. In order to obtain quantitative agreement between that electrokinetic model and the measured translocation dynamics, however, one must conclude that the mobility of counterions within a few Angstroms of the polymer surface is strongly reduced from the bulk value. Similar reductions in counterion mobility near fd, M13, and dsDNA explain their dynamics over a wide range of ionic strengths. This work was supported by NSF Grant CBET0846505, NSF Grant PHYS1058375 and Oxford Nanopore Technologies.

Flow-through lipid nanotube arrays for structure-function studies of membrane proteins by solid-state NMR spectroscopy.

PubMed

Chekmenev, Eduard Y; Gor'kov, Peter L; Cross, Timothy A; Alaouie, Ali M; Smirnov, Alex I

2006-10-15

A novel method for studying membrane proteins in a native lipid bilayer environment by solid-state NMR spectroscopy is described and tested. Anodic aluminum oxide (AAO) substrates with flow-through 175 nm wide and 60-mum-long nanopores were employed to form macroscopically aligned peptide-containing lipid bilayers that are fluid and highly hydrated. We demonstrate that the surfaces of both leaflets of such bilayers are fully accessible to aqueous solutes. Thus, high hydration levels as well as pH and desirable ion and/or drug concentrations could be easily maintained and modified as desired in a series of experiments with the same sample. The method allows for membrane protein NMR experiments in a broad pH range that could be extended to as low as 1 and as high as 12 units for a period of up to a few hours and temperatures as high as 70 degrees C without losing the lipid alignment or bilayers from the nanopores. We demonstrate the utility of this method by a solid-state 19.6 T (17)O NMR study of reversible binding effects of mono- and divalent ions on the chemical shift properties of the Leu(10) carbonyl oxygen of transmembrane pore-forming peptide gramicidin A (gA). We further compare the (17)O shifts induced by binding metal ions to the binding of protons in the pH range from 1 to 12 and find a significant difference. This unexpected result points to a difference in mechanisms for ion and proton conduction by the gA pore. We believe that a large number of solid-state NMR-based studies, including structure-function, drug screening, proton exchange, pH, and other titration experiments, will benefit significantly from the method described here.

A novel input-parasitic compensation technique for a nanopore-based CMOS DNA detection sensor

NASA Astrophysics Data System (ADS)

Kim, Jungsuk

2016-12-01

This paper presents a novel input-parasitic compensation (IPC) technique for a nanopore-based complementary metal-oxide-semiconductor (CMOS) DNA detection sensor. A resistive-feedback transimpedance amplifier is typically adopted as the headstage of a DNA detection sensor to amplify the minute ionic currents generated from a nanopore and convert them to a readable voltage range for digitization. But, parasitic capacitances arising from the headstage input and the nanopore often cause headstage saturation during nanopore sensing, thereby resulting in significant DNA data loss. To compensate for the unwanted saturation, in this work, we propose an area-efficient and automated IPC technique, customized for a low-noise DNA detection sensor, fabricated using a 0.35- μm CMOS process; we demonstrated this prototype in a benchtop test using an α-hemolysin ( α-HL) protein nanopore.

Investigation of thermal conduction in symmetric and asymmetric nanoporous structures

NASA Astrophysics Data System (ADS)

Yu, Ziqi; Ferrer-Argemi, Laia; Lee, Jaeho

2017-12-01

Nanoporous structures with a critical dimension comparable to or smaller than the phonon mean free path have demonstrated significant thermal conductivity reductions that are attractive for thermoelectric applications, but the presence of various geometric parameters complicates the understanding of governing mechanisms. Here, we use a ray tracing technique to investigate phonon boundary scattering phenomena in Si nanoporous structures of varying pore shapes, pore alignments, and pore size distributions, and identify mechanisms that are primarily responsible for thermal conductivity reductions. Our simulation results show that the neck size, or the smallest distance between nearest pores, is the key parameter in understanding nanoporous structures of varying pore shapes and the same porosities. When the neck size and the porosity are both identical, asymmetric pore shapes provide a lower thermal conductivity compared with symmetric pore shapes, due to localized heat fluxes. Asymmetric nanoporous structures show possibilities of realizing thermal rectification even with fully diffuse surface boundaries, in which optimal arrangements of triangular pores show a rectification ratio up to 13 when the injection angles are optimally controlled. For symmetric nanoporous structures, hexagonal-lattice pores achieve larger thermal conductivity reductions than square-lattice pores due to the limited line of sight for phonons. We also show that nanoporous structures of alternating pore size distributions from large to small pores yield a lower thermal conductivity compared with those of uniform pore size distributions in the given porosity. These findings advance the understanding of phonon boundary scattering phenomena in complex geometries and enable optimal designs of artificial nanostructures for thermoelectric energy harvesting and solid-state cooling systems.

Cost-efficient magnetic nanoporous carbon derived from citrus peel for the selective adsorption of seven insecticides.

PubMed

Zhou, Yuantao; Cao, Shurui; Xi, Cunxian; Chen, Jiuyan; Zhang, Lei; Li, Xianliang; Wang, Guomin; Chen, Zhiqiong

2018-05-18

A magnetic solid-phase extraction adsorbent that consisted of citrus peel-derived nanoporous carbon and silica-coated Fe 3 O 4 microspheres (C/SiO 2 @Fe 3 O 4 ) was successfully fabricated by co-precipitation. As a modifier for magnetic microspheres, citrus peel-derived nanoporous carbon was not only economical and renewable for its raw material, but exerted enormous nanosized pore structure, which could directly influence the type of adsorbed analytes. The C/SiO 2 @Fe 3 O 4 also possessed the advantages of Fe 3 O 4 microspheres like superparamagnetism, that could be easily separated magnetically after adsorption. Integrating the superior of biomass-derived nanoporous carbon and Fe 3 O 4 microspheres, the as-prepared C/SiO 2 @Fe 3 O 4 showed high extraction efficiency for target analytes. The obtained material was characterized by scanning electron microscopy, FTIR spectroscopy, X-ray photoelectron spectroscopy and the Brunauer-Emmett-Teller method, which demonstrated that C/SiO 2 @Fe 3 O 4 was successfully synthesized. Under the optimal conditions, the adsorbent was selected for the selective adsorption of seven insecticides before gas chromatography with mass spectrometry detection, good linearity was obtained in the concentration range of 2-200 μg/kg with the correlation coefficient ranging from 0.9952 to 0.9997. The limits of detection were in the range of 0.03-0.39 μg/kg. The proposed method has been successfully applied to the enrichment and detection of seven insecticides in real vegetable samples. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Nanopore arrays in a silicon membrane for parallel single-molecule detection: DNA translocation

NASA Astrophysics Data System (ADS)

Zhang, Miao; Schmidt, Torsten; Jemt, Anders; Sahlén, Pelin; Sychugov, Ilya; Lundeberg, Joakim; Linnros, Jan

2015-08-01

Optical nanopore sensing offers great potential in single-molecule detection, genotyping, or DNA sequencing for high-throughput applications. However, one of the bottle-necks for fluorophore-based biomolecule sensing is the lack of an optically optimized membrane with a large array of nanopores, which has large pore-to-pore distance, small variation in pore size and low background photoluminescence (PL). Here, we demonstrate parallel detection of single-fluorophore-labeled DNA strands (450 bps) translocating through an array of silicon nanopores that fulfills the above-mentioned requirements for optical sensing. The nanopore array was fabricated using electron beam lithography and anisotropic etching followed by electrochemical etching resulting in pore diameters down to ∼7 nm. The DNA translocation measurements were performed in a conventional wide-field microscope tailored for effective background PL control. The individual nanopore diameter was found to have a substantial effect on the translocation velocity, where smaller openings slow the translocation enough for the event to be clearly detectable in the fluorescence. Our results demonstrate that a uniform silicon nanopore array combined with wide-field optical detection is a promising alternative with which to realize massively-parallel single-molecule detection.

3D nanoporous graphene films converted from liquid-crystalline holey graphene oxide for thin and high-performance supercapacitors

NASA Astrophysics Data System (ADS)

Wang, Bin; Liu, Jinzhang; Zhao, Yi; Zheng, Dezhi; Li, Yan; Sha, Jiangbo

2018-01-01

Holey graphene oxide (HGO) is prepared and its liquid crystal (LC) formation in water is investigated. The blade-coated LC-HGO hydrogel is hydrothermally reduced to form 3D nanoporous films used as supercapacitor electrodes. Holey graphene sheets are rumpled and interconnected to form a cellular structure with pore size around 100 nm during the reduction process. Reduced HGO films with different thicknesses are integrated into solid-state symmetric supercapacitors and their electrochemical performances are studied. High specific capacitance up to 304 F g-1 and high volumetric capacitance around 400 F cm-3 are achieved from our thin and flexible devices.

Multicomponent Transport through Realistic Zeolite Membranes: Characterization & Transport in Nanoporous Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

William C. Conner

These research studies focused on the characterization and transport for porous solids which comprise both microporosity and mesoporosity. Such materials represent membranes made from zeolites as well as for many new nanoporous solids. Several analytical sorption techniques were developed and evaluated by which these multi-dimensional porous solids could be quantitatively characterized. Notably an approach by which intact membranes could be studied was developed and applied to plate-like and tubular supported zeolitic membranes. Transport processes were studied experimentally and theoretically based on the characterization studies.

Mechanical, Thermal, and Electrical Energy Storage in a Single Working Body: Electrification and Thermal Effects upon Pressure-Induced Water Intrusion-Extrusion in Nanoporous Solids.

PubMed

Grosu, Yaroslav; Mierzwa, Michał; Eroshenko, Valentine A; Pawlus, Sebastian; Chorażewski, Mirosław; Nedelec, Jean-Marie; Grolier, Jean-Pierre E

2017-03-01

This paper presents the first experimental evidence of pronounced electrification effects upon reversible cycle of forced water intrusion-extrusion in nanoporous hydrophobic materials. Recorded generation of electricity combined with high-pressure calorimetric measurements improves the energy balance of {nanoporous solid + nonwetting liquid} systems by compensating mechanical and thermal energy hysteresis in the cycle. Revealed phenomena provide a novel way of "mechanical to electrical" and/or "thermal to electrical" energy transformation with unprecedented efficiency and additionally open a perspective to increase the efficiency of numerous energy applications based on such systems taking advantage of electricity generation during operational cycle.

Polarization-induced local pore-wall functionalization for biosensing: from micropore to nanopore.

PubMed

Liu, Jie; Pham, Pascale; Haguet, Vincent; Sauter-Starace, Fabien; Leroy, Loïc; Roget, André; Descamps, Emeline; Bouchet, Aurélie; Buhot, Arnaud; Mailley, Pascal; Livache, Thierry

2012-04-03

The use of biological-probe-modified solid-state pores in biosensing is currently hindered by difficulties in pore-wall functionalization. The surface to be functionalized is small and difficult to target and is usually chemically similar to the bulk membrane. Herein, we demonstrate the contactless electrofunctionalization (CLEF) approach and its mechanism. This technique enables the one-step local functionalization of the single pore wall fabricated in a silica-covered silicon membrane. CLEF is induced by polarization of the pore membrane in an electric field and requires a sandwich-like composition and a conducting or semiconducting core for the pore membrane. The defects in the silica layer of the micropore wall enable the creation of an electric pathway through the silica layer, which allows electrochemical reactions to take place locally on the pore wall. The pore diameter is not a limiting factor for local wall modification using CLEF. Nanopores with a diameter of 200 nm fabricated in a silicon membrane and covered with native silica layer have been successfully functionalized with this method, and localized pore-wall modification was obtained. Furthermore, through proof-of-concept experiments using ODN-modified nanopores, we show that functionalized nanopores are suitable for translocation-based biosensing.

Soft matter in hard confinement: phase transition thermodynamics, structure, texture, diffusion and flow in nanoporous media.

PubMed

Huber, Patrick

2015-03-18

Spatial confinement in nanoporous media affects the structure, thermodynamics and mobility of molecular soft matter often markedly. This article reviews thermodynamic equilibrium phenomena, such as physisorption, capillary condensation, crystallisation, self-diffusion, and structural phase transitions as well as selected aspects of the emerging field of spatially confined, non-equilibrium physics, i.e. the rheology of liquids, capillarity-driven flow phenomena, and imbibition front broadening in nanoporous materials. The observations in the nanoscale systems are related to the corresponding bulk phenomenologies. The complexity of the confined molecular species is varied from simple building blocks, like noble gas atoms, normal alkanes and alcohols to liquid crystals, polymers, ionic liquids, proteins and water. Mostly, experiments with mesoporous solids of alumina, gold, carbon, silica, and silicon with pore diameters ranging from a few up to 50 nm are presented. The observed peculiarities of nanopore-confined condensed matter are also discussed with regard to applications. A particular emphasis is put on texture formation upon crystallisation in nanoporous media, a topic both of high fundamental interest and of increasing nanotechnological importance, e.g. for the synthesis of organic/inorganic hybrid materials by melt infiltration, the usage of nanoporous solids in crystal nucleation or in template-assisted electrochemical deposition of nano structures.

Soft matter in hard confinement: phase transition thermodynamics, structure, texture, diffusion and flow in nanoporous media

NASA Astrophysics Data System (ADS)

Huber, Patrick

2015-03-01

Spatial confinement in nanoporous media affects the structure, thermodynamics and mobility of molecular soft matter often markedly. This article reviews thermodynamic equilibrium phenomena, such as physisorption, capillary condensation, crystallisation, self-diffusion, and structural phase transitions as well as selected aspects of the emerging field of spatially confined, non-equilibrium physics, i.e. the rheology of liquids, capillarity-driven flow phenomena, and imbibition front broadening in nanoporous materials. The observations in the nanoscale systems are related to the corresponding bulk phenomenologies. The complexity of the confined molecular species is varied from simple building blocks, like noble gas atoms, normal alkanes and alcohols to liquid crystals, polymers, ionic liquids, proteins and water. Mostly, experiments with mesoporous solids of alumina, gold, carbon, silica, and silicon with pore diameters ranging from a few up to 50 nm are presented. The observed peculiarities of nanopore-confined condensed matter are also discussed with regard to applications. A particular emphasis is put on texture formation upon crystallisation in nanoporous media, a topic both of high fundamental interest and of increasing nanotechnological importance, e.g. for the synthesis of organic/inorganic hybrid materials by melt infiltration, the usage of nanoporous solids in crystal nucleation or in template-assisted electrochemical deposition of nano structures.

From Ion Current to Electroosmotic Flow Rectification in Asymmetric Nanopore Membranes

PubMed Central

Wu, Xiaojian

2017-01-01

Asymmetrically shaped nanopores have been shown to rectify the ionic current flowing through pores in a fashion similar to a p-n junction in a solid-state diode. Such asymmetric nanopores include conical pores in polymeric membranes and pyramidal pores in mica membranes. We review here both theoretical and experimental aspects of this ion current rectification phenomenon. A simple intuitive model for rectification, stemming from previously published more quantitative models, is discussed. We also review experimental results on controlling the extent and sign of rectification. It was shown that ion current rectification produces a related rectification of electroosmotic flow (EOF) through asymmetric pore membranes. We review results that show how to measure and modulate this EOF rectification phenomenon. Finally, EOF rectification led to the development of an electroosmotic pump that works under alternating current (AC), as opposed to the currently available direct current EOF pumps. Experimental results on AC EOF rectification are reviewed, and advantages of using AC to drive EOF are discussed. PMID:29240676

From Ion Current to Electroosmotic Flow Rectification in Asymmetric Nanopore Membranes.

PubMed

Experton, Juliette; Wu, Xiaojian; Martin, Charles R

2017-12-14

Asymmetrically shaped nanopores have been shown to rectify the ionic current flowing through pores in a fashion similar to a p-n junction in a solid-state diode. Such asymmetric nanopores include conical pores in polymeric membranes and pyramidal pores in mica membranes. We review here both theoretical and experimental aspects of this ion current rectification phenomenon. A simple intuitive model for rectification, stemming from previously published more quantitative models, is discussed. We also review experimental results on controlling the extent and sign of rectification. It was shown that ion current rectification produces a related rectification of electroosmotic flow (EOF) through asymmetric pore membranes. We review results that show how to measure and modulate this EOF rectification phenomenon. Finally, EOF rectification led to the development of an electroosmotic pump that works under alternating current (AC), as opposed to the currently available direct current EOF pumps. Experimental results on AC EOF rectification are reviewed, and advantages of using AC to drive EOF are discussed.

Atomic Layer Deposition for the Conformal Coating of Nanoporous Materials

DOE PAGES

Elam, Jeffrey W.; Xiong, Guang; Han, Catherine Y.; ...

2006-01-01

Amore » tomic layer deposition ( LD ) is ideal for applying precise and conformal coatings over nanoporous materials. We have recently used LD to coat two nanoporous solids: anodic aluminum oxide ( O ) and silica aerogels. O possesses hexagonally ordered pores with diameters d ∼ 40 nm and pore length L ∼ 70 microns. The O membranes were coated by LD to fabricate catalytic membranes that demonstrate remarkable selectivity in the oxidative dehydrogenation of cyclohexane. dditional O membranes coated with LD Pd films show promise as hydrogen sensors. Silica aerogels have the lowest density and highest surface area of any solid material. Consequently, these materials serve as an excellent substrate to fabricate novel catalytic materials and gas sensors by LD .« less

Controlling the orientation of spin-correlated radical pairs by covalent linkage to nanoporous anodic aluminum oxide membranes.

PubMed

Chen, Hsiao-Fan; Gardner, Daniel M; Carmieli, Raanan; Wasielewski, Michael R

2013-10-07

Ordered multi-spin assemblies are required for developing solid-state molecule-based spintronics. A linear donor-chromophore-acceptor (D-C-A) molecule was covalently attached inside the 150 nm diam. nanopores of an anodic aluminum oxide (AAO) membrane. Photoexcitation of D-C-A in a 343 mT magnetic field results in sub-nanosecond, two-step electron transfer to yield the spin-correlated radical ion pair (SCRP) (1)(D(+)˙-C-A(-)˙), which then undergoes radical pair intersystem crossing (RP-ISC) to yield (3)(D(+)˙-C-A(-)˙). RP-ISC results in S-T0 mixing to selectively populate the coherent superposition states |S'> and |T'>. Microwave-induced transitions between these states and the unpopulated |T(+1)> and |T(-1)> states result in spin-polarized time-resolved EPR (TREPR) spectra. The dependence of the electron spin polarization (ESP) phase of the TREPR spectra on the orientation of the AAO membrane pores relative to the externally applied magnetic field is used to determine the overall orientation of the SCRPs within the pores at room temperature.

Multifunctional nanopipette for simultaneous ionic current and potential detection of nanoparticles

NASA Astrophysics Data System (ADS)

Panday, Namuna; He, Jin

Nanopipette has been demonstrated as a nanopore type biosensor for DNA, protein, nanoparticle and virus analysis. In the last two decades, nanopore based technologies have made remarkable progress for single entity detection and analysis. Multifunctional nanopipette for multi-parameter detection is a new trend for nanopore based technique. We have developed a technique to fabricate multifunctional nanopipette which contains both nanopore and carbon nanoelectrode (CNE) at the nanopipette tip. It can be quickly, cheaply and reproducibly fabricated from theta pipettes. We have been able to use this multifunctional nanopieptte for simultaneous detection of ionic current and local electrical potential changes during translocation of charged gold nanoparticles (GNPs) which is used as a model experiment. The CNE functions as a local potential probe. We have demonstrated that it can detect the local potential change during translocation of a single GNP as well as collective potential change due to cluster of GNPs outside the nanopore entrance. From the potential change, we can also have insight of motion of GNPs before entering the nanopore. We have also tested insulating and biological NPs with various size and charge. Observed results have shown correlations between ionic current and potential change during translocation of these NPs. Florida International University.

Ultrathin NiCo2O4 nanowalls supported on a 3D nanoporous gold coated needle for non-enzymatic amperometric sensing of glucose.

PubMed

Li, Weiwei; Qi, Hui; Wang, Baogang; Wang, Qiyu; Wei, Shuting; Zhang, Xiaolin; Wang, Ying; Zhang, Lei; Cui, Xiaoqiang

2018-01-24

A disposable needle-type of hybrid electrode was prepared from a core of stainless steel needle whose surface was modified with a 3D nanoporous gold/NiCo 2 O 4 nanowall hybrid structure for electrochemical non-enzymatic glucose detection. This hybrid electrode, best operated at 0.45 V (vs. SCE) in solutions of pH 13 has a linear response in the 0.01 to 21 mM glucose concentration range, a response time of <1 s, and a 1 μM detection limit (at an S/N ratio of 3). The remarkable enhancement compared to the solid gold/NiCo 2 O 4 and stainless steel/NiCo 2 O 4 hybrid electrodes in electrochemical performance is assumed to originate from the good electrical conductivity and large surface area of the hybrid electrode, which enhance the transport of mass and charge during electrochemical reactions. This biosensor was also applied to real sample analysis with little interferences. The electrode is disposable and considered to be a promising tool for non-enzymatic sensing of glucose in a variety of practical situations. Graphical abstract Ultrathin NiCo 2 O 4 nanowalls supported on nanoporous gold that is coated on a stainless steel needle was fabricated for sensitive non-enzymatic amperometric sensing of glucose.

The role of nanopore shape in surface-induced crystallization

NASA Astrophysics Data System (ADS)

Diao, Ying; Harada, Takuya; Myerson, Allan S.; Alan Hatton, T.; Trout, Bernhardt L.

2011-11-01

Crystallization of a molecular liquid from solution often initiates at solid-liquid interfaces, and nucleation rates are generally believed to be enhanced by surface roughness. Here we show that, on a rough surface, the shape of surface nanopores can also alter nucleation kinetics. Using lithographic methods, we patterned polymer films with nanopores of various shapes and found that spherical nanopores 15-120 nm in diameter hindered nucleation of aspirin crystals, whereas angular nanopores of the same size promoted it. We also show that favourable surface-solute interactions are required for angular nanopores to promote nucleation, and propose that pore shape affects nucleation kinetics through the alteration of the orientational order of the crystallizing molecule near the angles of the pores. Our findings have clear technological implications, for instance in the control of pharmaceutical polymorphism and in the design of ‘seed’ particles for the regulation of crystallization of fine chemicals.

The Upper Limit of Energy Density of Nanoporous Materials Functionalized Liquid

NASA Astrophysics Data System (ADS)

Han, Aijie; Punyamurtula, Venkata K.; Kim, Taewan; Qiao, Yu

2008-06-01

In this article, we report the experimental result of energy dissipation of a mobil crystalline material (MCM) 41 in mercury. The MCM41 contains a large volume fraction of nanometer-sized pores. As the applied pressure is relatively high, the nanopore surfaces are exposed to mercury. Due to the large nanopore surface area and the large solid-liquid interfacial tension, the energy dissipation effectiveness of this system is ultrahigh, representing the upper limit that can be achieved by the pressure-induced infiltration technique.

High-performance solid state supercapacitors assembling graphene interconnected networks in porous silicon electrode by electrochemical methods using 2,6-dihydroxynaphthalen.

PubMed

Romanitan, Cosmin; Varasteanu, Pericle; Mihalache, Iuliana; Culita, Daniela; Somacescu, Simona; Pascu, Razvan; Tanasa, Eugenia; Eremia, Sandra A V; Boldeiu, Adina; Simion, Monica; Radoi, Antonio; Kusko, Mihaela

2018-06-25

The challenge for conformal modification of the ultra-high internal surface of nanoporous silicon was tackled by electrochemical polymerisation of 2,6-dihydroxynaphthalene using cyclic voltammetry or potentiometry and, notably, after the thermal treatment (800 °C, N 2 , 4 h) an assembly of interconnected networks of graphene strongly adhering to nanoporous silicon matrix resulted. Herein we demonstrate the achievement of an easy scalable technology for solid state supercapacitors on silicon, with excellent electrochemical properties. Accordingly, our symmetric supercapacitors (SSC) showed remarkable performance characteristics, comparable to many of the best high-power and/or high-energy carbon-based supercapacitors, their figures of merit matching under battery-like supercapacitor behaviour. Furthermore, the devices displayed high specific capacity values along with enhanced capacity retention even at ultra-high rates for voltage sweep, 5 V/s, or discharge current density, 100 A/g, respectively. The cycling stability tests performed at relatively high discharge current density of 10 A/g indicated good capacity retention, with a superior performance demonstrated for the electrodes obtained under cyclic voltammetry approach, which may be ascribed on the one hand to a better coverage of the porous silicon substrate and, on the other hand, to an improved resilience of the hybrid electrode to pore clogging.

Transient effects of drying creep in nanoporous solids: understanding the effects of nanoscale energy barriers

NASA Astrophysics Data System (ADS)

Sinko, Robert; Vandamme, Matthieu; Bažant, Zdeněk P.; Keten, Sinan

2016-07-01

The Pickett effect is the phenomenon of creep enhancement during transient drying. It has been observed for many nanoporous solids, including concrete, wood and Kevlar. While the existing micromechanical models can partially explain this effect, they have yet to consider nanoscale dynamic effects of water in nanopores, which are believed to be of paramount importance. Here, we examine how creep deformations in a slit pore are accelerated by the motion of water due to drying forces using coarse-grained molecular dynamics simulations. We find that the drying that drives water flow in the nanopores lowers both the activation energy of pore walls sliding past one another and the apparent viscosity of confined water molecules. This lowering can be captured with an analytical Arrhenius relationship accounting for the role of water flow in overcoming the energy barriers. Notably, we use this model and simulation results to demonstrate that the drying creep strain is not linearly dependent on the applied creep stress at the nanopore level. Our findings establish the scaling relationships that explain how the creep driving force, drying force and fluid properties are related. Thus, we establish the nanoscale origins of the Pickett effect and provide strategies for minimizing the additional displacements arising from this effect.

Transient effects of drying creep in nanoporous solids: understanding the effects of nanoscale energy barriers

PubMed Central

Sinko, Robert; Vandamme, Matthieu; Keten, Sinan

2016-01-01

The Pickett effect is the phenomenon of creep enhancement during transient drying. It has been observed for many nanoporous solids, including concrete, wood and Kevlar. While the existing micromechanical models can partially explain this effect, they have yet to consider nanoscale dynamic effects of water in nanopores, which are believed to be of paramount importance. Here, we examine how creep deformations in a slit pore are accelerated by the motion of water due to drying forces using coarse-grained molecular dynamics simulations. We find that the drying that drives water flow in the nanopores lowers both the activation energy of pore walls sliding past one another and the apparent viscosity of confined water molecules. This lowering can be captured with an analytical Arrhenius relationship accounting for the role of water flow in overcoming the energy barriers. Notably, we use this model and simulation results to demonstrate that the drying creep strain is not linearly dependent on the applied creep stress at the nanopore level. Our findings establish the scaling relationships that explain how the creep driving force, drying force and fluid properties are related. Thus, we establish the nanoscale origins of the Pickett effect and provide strategies for minimizing the additional displacements arising from this effect. PMID:27493584

Transient effects of drying creep in nanoporous solids: understanding the effects of nanoscale energy barriers.

PubMed

Sinko, Robert; Vandamme, Matthieu; Bažant, Zdeněk P; Keten, Sinan

2016-07-01

The Pickett effect is the phenomenon of creep enhancement during transient drying. It has been observed for many nanoporous solids, including concrete, wood and Kevlar. While the existing micromechanical models can partially explain this effect, they have yet to consider nanoscale dynamic effects of water in nanopores, which are believed to be of paramount importance. Here, we examine how creep deformations in a slit pore are accelerated by the motion of water due to drying forces using coarse-grained molecular dynamics simulations. We find that the drying that drives water flow in the nanopores lowers both the activation energy of pore walls sliding past one another and the apparent viscosity of confined water molecules. This lowering can be captured with an analytical Arrhenius relationship accounting for the role of water flow in overcoming the energy barriers. Notably, we use this model and simulation results to demonstrate that the drying creep strain is not linearly dependent on the applied creep stress at the nanopore level. Our findings establish the scaling relationships that explain how the creep driving force, drying force and fluid properties are related. Thus, we establish the nanoscale origins of the Pickett effect and provide strategies for minimizing the additional displacements arising from this effect.

Study on the Characteristics of Gas Molecular Mean Free Path in Nanopores by Molecular Dynamics Simulations

PubMed Central

Liu, Qixin; Cai, Zhiyong

2014-01-01

This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale. PMID:25046745

Eco-friendly synthesis for MCM-41 nanoporous materials using the non-reacted reagents in mother liquor.

PubMed

Ng, Eng-Poh; Goh, Jia-Yi; Ling, Tau Chuan; Mukti, Rino R

2013-03-04

Nanoporous materials such as Mobil composite material number 41 (MCM-41) are attractive for applications such as catalysis, adsorption, supports, and carriers. Green synthesis of MCM-41 is particularly appealing because the chemical reagents are useful and valuable. We report on the eco-friendly synthesis of MCM-41 nanoporous materials via multi-cycle approach by re-using the non-reacted reagents in supernatant as mother liquor after separating the solid product. This approach was achieved via minimal requirement of chemical compensation where additional fresh reactants were added into the mother liquor followed by pH adjustment after each cycle of synthesis. The solid product of each successive batch was collected and characterized while the non-reacted reagents in supernatant can be recovered and re-used to produce subsequent cycle of MCM-41. The multi-cycle synthesis is demonstrated up to three times in this research. This approach suggests a low cost and eco-friendly synthesis of nanoporous material since less waste is discarded after the product has been collected, and in addition, product yield can be maintained at the high level.

Eco-friendly synthesis for MCM-41 nanoporous materials using the non-reacted reagents in mother liquor

PubMed Central

2013-01-01

Nanoporous materials such as Mobil composite material number 41 (MCM-41) are attractive for applications such as catalysis, adsorption, supports, and carriers. Green synthesis of MCM-41 is particularly appealing because the chemical reagents are useful and valuable. We report on the eco-friendly synthesis of MCM-41 nanoporous materials via multi-cycle approach by re-using the non-reacted reagents in supernatant as mother liquor after separating the solid product. This approach was achieved via minimal requirement of chemical compensation where additional fresh reactants were added into the mother liquor followed by pH adjustment after each cycle of synthesis. The solid product of each successive batch was collected and characterized while the non-reacted reagents in supernatant can be recovered and re-used to produce subsequent cycle of MCM-41. The multi-cycle synthesis is demonstrated up to three times in this research. This approach suggests a low cost and eco-friendly synthesis of nanoporous material since less waste is discarded after the product has been collected, and in addition, product yield can be maintained at the high level. PMID:23497184

Eco-friendly synthesis for MCM-41 nanoporous materials using the non-reacted reagents in mother liquor

NASA Astrophysics Data System (ADS)

Ng, Eng-Poh; Goh, Jia-Yi; Ling, Tau Chuan; Mukti, Rino R.

2013-03-01

Nanoporous materials such as Mobil composite material number 41 (MCM-41) are attractive for applications such as catalysis, adsorption, supports, and carriers. Green synthesis of MCM-41 is particularly appealing because the chemical reagents are useful and valuable. We report on the eco-friendly synthesis of MCM-41 nanoporous materials via multi-cycle approach by re-using the non-reacted reagents in supernatant as mother liquor after separating the solid product. This approach was achieved via minimal requirement of chemical compensation where additional fresh reactants were added into the mother liquor followed by pH adjustment after each cycle of synthesis. The solid product of each successive batch was collected and characterized while the non-reacted reagents in supernatant can be recovered and re-used to produce subsequent cycle of MCM-41. The multi-cycle synthesis is demonstrated up to three times in this research. This approach suggests a low cost and eco-friendly synthesis of nanoporous material since less waste is discarded after the product has been collected, and in addition, product yield can be maintained at the high level.

Detection and interrogation of biomolecules via nanoscale probes: From fundamental physics to DNA sequencing

NASA Astrophysics Data System (ADS)

Zwolak, Michael

2013-03-01

A rapid and low-cost method to sequence DNA would revolutionize personalized medicine, where genetic information is used to diagnose, treat, and prevent diseases. There is a longstanding interest in nanopores as a platform for rapid interrogation of single DNA molecules. I will discuss a sequencing protocol based on the measurement of transverse electronic currents during the translocation of single-stranded DNA through nanopores. Using molecular dynamics simulations coupled to quantum mechanical calculations of the tunneling current, I will show that the DNA nucleotides are predicted to have distinguishable electronic signatures in experimentally realizable systems. Several recent experiments support our theoretical predictions. In addition to their possible impact in medicine and biology, the above methods offer ideal test beds to study open scientific issues in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. http://mike.zwolak.org

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

DOEpatents

Sansinena, Jose-Maria [Los Alamos, NM; Redondo, Antonio [Los Alamos, NM; Olazabal, Virginia [Los Alamos, NM; Hoffbauer, Mark A [Los Alamos, NM; Akhadov, Elshan A [Los Alamos, NM

2009-12-29

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia

2017-09-12

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia

2017-07-18

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Nanopores and nucleic acids: prospects for ultrarapid sequencing

NASA Technical Reports Server (NTRS)

Deamer, D. W.; Akeson, M.

2000-01-01

DNA and RNA molecules can be detected as they are driven through a nanopore by an applied electric field at rates ranging from several hundred microseconds to a few milliseconds per molecule. The nanopore can rapidly discriminate between pyrimidine and purine segments along a single-stranded nucleic acid molecule. Nanopore detection and characterization of single molecules represents a new method for directly reading information encoded in linear polymers. If single-nucleotide resolution can be achieved, it is possible that nucleic acid sequences can be determined at rates exceeding a thousand bases per second.

Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping

NASA Astrophysics Data System (ADS)

Freedman, Kevin J.; Otto, Lauren M.; Ivanov, Aleksandar P.; Barik, Avijit; Oh, Sang-Hyun; Edel, Joshua B.

2016-01-01

Single-molecule techniques are being developed with the exciting prospect of revolutionizing the healthcare industry by generating vast amounts of genetic and proteomic data. One exceptionally promising route is in the use of nanopore sensors. However, a well-known complexity is that detection and capture is predominantly diffusion limited. This problem is compounded when taking into account the capture volume of a nanopore, typically 108-1010 times smaller than the sample volume. To rectify this disproportionate ratio, we demonstrate a simple, yet powerful, method based on coupling single-molecule dielectrophoretic trapping to nanopore sensing. We show that DNA can be captured from a controllable, but typically much larger, volume and concentrated at the tip of a metallic nanopore. This enables the detection of single molecules at concentrations as low as 5 fM, which is approximately a 103 reduction in the limit of detection compared with existing methods, while still maintaining efficient throughput.

Integrated Solid/Nanoporous Copper/Oxide Hybrid Bulk Electrodes for High-performance Lithium-Ion Batteries

PubMed Central

Hou, Chao; Lang, Xing-You; Han, Gao-Feng; Li, Ying-Qi; Zhao, Lei; Wen, Zi; Zhu, Yong-Fu; Zhao, Ming; Li, Jian-Chen; Lian, Jian-She; Jiang, Qing

2013-01-01

Nanoarchitectured electroactive materials can boost rates of Li insertion/extraction, showing genuine potential to increase power output of Li-ion batteries. However, electrodes assembled with low-dimensional nanostructured transition metal oxides by conventional approach suffer from dramatic reductions in energy capacities owing to sluggish ion and electron transport kinetics. Here we report that flexible bulk electrodes, made of three-dimensional bicontinuous nanoporous Cu/MnO2 hybrid and seamlessly integrated with Cu solid current collector, substantially optimizes Li storage behavior of the constituent MnO2. As a result of the unique integration of solid/nanoporous hybrid architecture that simultaneously enhances the electron transport of MnO2, facilitates fast ion diffusion and accommodates large volume changes on Li insertion/extraction of MnO2, the supported MnO2 exhibits a stable capacity of as high as ~1100 mA h g−1 for 1000 cycles, and ultrahigh charge/discharge rates. It makes the environmentally friendly and low-cost electrode as a promising anode for high-performance Li-ion battery applications. PMID:24096928

Probing the size of proteins with glass nanopores

NASA Astrophysics Data System (ADS)

Steinbock, L. J.; Krishnan, S.; Bulushev, R. D.; Borgeaud, S.; Blokesch, M.; Feletti, L.; Radenovic, A.

2014-11-01

Single molecule studies using nanopores have gained attention due to the ability to sense single molecules in aqueous solution without the need to label them. In this study, short DNA molecules and proteins were detected with glass nanopores, whose sensitivity was enhanced by electron reshaping which decreased the nanopore diameter and created geometries with a reduced sensing length. Further, proteins having molecular weights (MW) ranging from 12 kDa to 480 kDa were detected, which showed that their corresponding current peak amplitude changes according to their MW. In the case of the 12 kDa ComEA protein, its DNA-binding properties to an 800 bp long DNA molecule was investigated. Moreover, the influence of the pH on the charge of the protein was demonstrated by showing a change in the translocation direction. This work emphasizes the wide spectrum of detectable molecules using nanopores from glass nanocapillaries, which stand out because of their inexpensive, lithography-free, and rapid manufacturing process.Single molecule studies using nanopores have gained attention due to the ability to sense single molecules in aqueous solution without the need to label them. In this study, short DNA molecules and proteins were detected with glass nanopores, whose sensitivity was enhanced by electron reshaping which decreased the nanopore diameter and created geometries with a reduced sensing length. Further, proteins having molecular weights (MW) ranging from 12 kDa to 480 kDa were detected, which showed that their corresponding current peak amplitude changes according to their MW. In the case of the 12 kDa ComEA protein, its DNA-binding properties to an 800 bp long DNA molecule was investigated. Moreover, the influence of the pH on the charge of the protein was demonstrated by showing a change in the translocation direction. This work emphasizes the wide spectrum of detectable molecules using nanopores from glass nanocapillaries, which stand out because of their inexpensive, lithography-free, and rapid manufacturing process. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr05001k

The kinetics and mechanism of nanoconfined molten salt reactions: trimerization of potassium and rubidium dicyanamide.

PubMed

Yancey, Benjamin; Vyazovkin, Sergey

2015-04-21

This study highlights the effect of the aggregate state of a reactant on the reaction kinetics under the conditions of nanoconfinement. Our previous work (Phys. Chem. Chem. Phys., 2014, 16, 11409) has demonstrated considerable deceleration of the solid state trimerization of sodium dicyanamide in organically modified silica nanopores. In the present study we use FTIR, NMR, pXRD, TGA and DSC to analyze the kinetics and mechanism of the liquid state trimerization of potassium and rubidium dicyanamide under similar conditions of nanoconfinement. It is found that nanoconfinement accelerates dramatically the kinetics of the liquid state trimerization, whereas it does not appear to affect the reaction mechanism. Kinetic analysis indicates that the acceleration is associated with an increase in the preexponential factor. Although nanoconfinement has the opposite effects on the respective kinetics of solid and liquid state trimerization, both effects are linked to a change in the preexponential factor. The results obtained are consistent with our hypothesis that the effects differ because nanoconfinement may promote disordering of the solid and ordering of the liquid reaction media.

Liquid-solid phase transition of hydrogen and deuterium in silica aerogel

NASA Astrophysics Data System (ADS)

Van Cleve, E.; Worsley, M. A.; Kucheyev, S. O.

2014-10-01

Behavior of hydrogen isotopes confined in disordered low-density nanoporous solids remains essentially unknown. Here, we use relaxation calorimetry to study freezing and melting of H2 and D2 in an ˜85%-porous base-catalyzed silica aerogel. We find that liquid-solid transition temperatures of both isotopes inside the aerogel are depressed. The phase transition takes place over a wide temperature range of ˜4 K and non-trivially depends on the liquid filling fraction, reflecting the broad pore size distribution in the aerogel. Undercooling is observed for both H2 and D2 confined inside the aerogel monolith. Results for H2 and D2 are extrapolated to tritium-containing hydrogens with the quantum law of corresponding states.

Resistive-pulse measurements with nanopipettes: detection of Au nanoparticles and nanoparticle-bound anti-peanut IgY.

PubMed

Wang, Yixian; Kececi, Kaan; Mirkin, Michael V; Mani, Vigneshwaran; Sardesai, Naimish; Rusling, James F

2013-02-01

Solid-state nanopores have been widely employed in sensing applications from Coulter counters to DNA sequencing devices. The analytical signal in such experiments is the change in ionic current flowing through the orifice caused by the large molecule or nanoparticle translocation through the pore. Conceptually similar nanopipette-based sensors can offer several advantages including the ease of fabrication and small physical size essential for local measurements and experiments in small spaces. This paper describes the first evaluation of nanopipettes with well characterized geometry for resistive-pulse sensing of Au nanoparticles (AuNP), nanoparticles coated with an allergen epitope peptide layer, and AuNP-peptide particles with bound antipeanut antibodies (IgY) on the peptide layer. The label-free signal produced by IgY-conjugated particles was strikingly different from those obtained with other analytes, thus suggesting the possibility of selective and sensitive resistive-pulse sensing of antibodies.

Resistive-pulse measurements with nanopipettes: detection of Au nanoparticles and nanoparticle-bound anti-peanut IgY†

PubMed Central

Wang, Yixian; Kececi, Kaan; Mani, Vigneshwaran; Sardesai, Naimish

2013-01-01

Solid-state nanopores have been widely employed in sensing applications from Coulter counters to DNA sequencing devices. The analytical signal in such experiments is the change in ionic current flowing through the orifice caused by the large molecule or nanoparticle translocation through the pore. Conceptually similar nanopipette-based sensors can offer several advantages including the ease of fabrication and small physical size essential for local measurements and experiments in small spaces. This paper describes the first evaluation of nanopipettes with well characterized geometry for resistive-pulse sensing of Au nanoparticles (AuNP), nanoparticles coated with an allergen epitope peptide layer, and AuNP–peptide particles with bound antipeanut antibodies (IgY) on the peptide layer. The label-free signal produced by IgY-conjugated particles was strikingly different from those obtained with other analytes, thus suggesting the possibility of selective and sensitive resistive-pulse sensing of antibodies. PMID:23991282

Applications of Nanoporous Materials in Agriculture

USDA-ARS?s Scientific Manuscript database

Nanoporous materials possess organized pore distributions and increased surface areas. Advances in the systematic design of nanoporous materials enable incorporation of functionality for better sensitivity in detection methods, increased capacity of sorbents, and improved selectivity and yield in ca...

A Protein Nanopore-Based Approach for Bacteria Sensing

NASA Astrophysics Data System (ADS)

Apetrei, Aurelia; Ciuca, Andrei; Lee, Jong-kook; Seo, Chang Ho; Park, Yoonkyung; Luchian, Tudor

2016-11-01

We present herein a first proof of concept demonstrating the potential of a protein nanopore-based technique for real-time detection of selected Gram-negative bacteria ( Pseudomonas aeruginosa or Escherichia coli) at a concentration of 1.2 × 108 cfu/mL. The anionic charge on the bacterial outer membrane promotes the electrophoretically driven migration of bacteria towards a single α-hemolysin nanopore isolated in a lipid bilayer, clamped at a negative electric potential, and followed by capture at the nanopore's mouth, which we found to be described according to the classical Kramers' theory. By using a specific antimicrobial peptide as a putative molecular biorecognition element for the bacteria used herein, we suggest that the detection system can combine the natural sensitivity of the nanopore-based sensing techniques with selective biological recognition, in aqueous samples, and highlight the feasibility of the nanopore-based platform to provide portable, sensitive analysis and monitoring of bacterial pathogens.

Inkjet printing of nanoporous gold electrode arrays on cellulose membranes for high-sensitive paper-like electrochemical oxygen sensors using ionic liquid electrolytes.

PubMed

Hu, Chengguo; Bai, Xiaoyun; Wang, Yingkai; Jin, Wei; Zhang, Xuan; Hu, Shengshui

2012-04-17

A simple approach to the mass production of nanoporous gold electrode arrays on cellulose membranes for electrochemical sensing of oxygen using ionic liquid (IL) electrolytes was established. The approach, combining the inkjet printing of gold nanoparticle (GNP) patterns with the self-catalytic growth of these patterns into conducting layers, can fabricate hundreds of self-designed gold arrays on cellulose membranes within several hours using an inexpensive inkjet printer. The resulting paper-based gold electrode arrays (PGEAs) had several unique properties as thin-film sensor platforms, including good conductivity, excellent flexibility, high integration, and low cost. The porous nature of PGEAs also allowed the addition of electrolytes from the back cellulose membrane side and controllably produced large three-phase electrolyte/electrode/gas interfaces at the front electrode side. A novel paper-based solid-state electrochemical oxygen (O(2)) sensor was therefore developed using an IL electrolyte, 1-butyl-3-methylimidazolium hexafluorophosphate (BMIMPF(6)). The sensor looked like a piece of paper but possessed high sensitivity for O(2) in a linear range from 0.054 to 0.177 v/v %, along with a low detection limit of 0.0075% and a short response time of less than 10 s, foreseeing its promising applications in developing cost-effective and environment-friendly paper-based electrochemical gas sensors.

Electrolysis-induced protonation of VO2 thin film transistor for the metal-insulator phase modulation

NASA Astrophysics Data System (ADS)

Katase, Takayoshi; Endo, Kenji; Ohta, Hiromichi

2016-02-01

Compared to state-of-the-art modulation techniques, protonation is the most ideal to control the electrical and optical properties of transition metal oxides (TMOs) due to its intrinsic non-volatile operation. However, the protonation of TMOs is not typically utilized for solid-state devices because of imperative high-temperature annealing treatment in hydrogen source. Although one solution for room temperature (RT) protonation of TMOs is liquid-phase electrochemistry, it is unsuited for practical purposes due to liquid-leakage problem. Herein we demonstrate solid-state RT-protonation of vanadium dioxide (VO2), which is a well-known thermochromic TMO. We fabricated the three terminal thin-film-transistor structure on an insulating VO2 film using a water-infiltrated nanoporous glass, which serves as a solid electrolyte. For gate voltage application, water electrolysis and protonation/deprotonation of VO2 film surface occurred, leading to reversible metal-insulator phase conversion of ~11-nm-thick VO2 layer. The protonation was clearly accompanied by the structural change from an insulating monoclinic to a metallic tetragonal phase. Present results offer a new route for the development of electro-optically active solid-state devices with TMO materials by engineering RT protonation.

11% efficiency solid-state dye-sensitized solar cells with copper(II/I) hole transport materials

PubMed Central

Cao, Yiming; Saygili, Yasemin; Ummadisingu, Amita; Teuscher, Joël; Luo, Jingshan; Pellet, Norman; Giordano, Fabrizio; Zakeeruddin, Shaik Mohammed; Moser, Jacques -E.; Freitag, Marina; Hagfeldt, Anders; Grätzel, Michael

2017-01-01

Solid-state dye-sensitized solar cells currently suffer from issues such as inadequate nanopore filling, low conductivity and crystallization of hole-transport materials infiltrated in the mesoscopic TiO2 scaffolds, leading to low performances. Here we report a record 11% stable solid-state dye-sensitized solar cell under standard air mass 1.5 global using a hole-transport material composed of a blend of [Cu (4,4′,6,6′-tetramethyl-2,2′-bipyridine)2](bis(trifluoromethylsulfonyl)imide)2 and [Cu (4,4′,6,6′-tetramethyl-2,2′-bipyridine)2](bis(trifluoromethylsulfonyl)imide). The amorphous Cu(II/I) conductors that conduct holes by rapid hopping infiltrated in a 6.5 μm-thick mesoscopic TiO2 scaffold are crucial for achieving such high efficiency. Using time-resolved laser photolysis, we determine the time constants for electron injection from the photoexcited sensitizers Y123 into the TiO2 and regeneration of the Y123 by Cu(I) to be 25 ps and 3.2 μs, respectively. Our work will foster the development of low-cost solid-state photovoltaic based on transition metal complexes as hole conductors. PMID:28598436

Using Synthetic Nanopores for Single-Molecule Analyses: Detecting SNPs, Trapping DNA Molecules, and the Prospects for Sequencing DNA

ERIC Educational Resources Information Center

Dimitrov, Valentin V.

2009-01-01

This work focuses on studying properties of DNA molecules and DNA-protein interactions using synthetic nanopores, and it examines the prospects of sequencing DNA using synthetic nanopores. We have developed a method for discriminating between alleles that uses a synthetic nanopore to measure the binding of a restriction enzyme to DNA. There exists…

Tunable graphene quantum point contact transistor for DNA detection and characterization

PubMed Central

Girdhar, Anuj; Sathe, Chaitanya; Schulten, Klaus; Leburton, Jean-Pierre

2015-01-01

A graphene membrane conductor containing a nanopore in a quantum point contact (QPC) geometry is a promising candidate to sense, and potentially sequence, DNA molecules translocating through the nanopore. Within this geometry, the shape, size, and position of the nanopore as well as the edge configuration influences the membrane conductance caused by the electrostatic interaction between the DNA nucleotides and the nanopore edge. It is shown that the graphene conductance variations resulting from DNA translocation can be enhanced by choosing a particular geometry as well as by modulating the graphene Fermi energy, which demonstrates the ability to detect conformational transformations of a double-stranded DNA, as well as the passage of individual base pairs of a single-stranded DNA molecule through the nanopore. PMID:25765702

Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping

PubMed Central

Freedman, Kevin J.; Otto, Lauren M.; Ivanov, Aleksandar P.; Barik, Avijit; Oh, Sang-Hyun; Edel, Joshua B.

2016-01-01

Single-molecule techniques are being developed with the exciting prospect of revolutionizing the healthcare industry by generating vast amounts of genetic and proteomic data. One exceptionally promising route is in the use of nanopore sensors. However, a well-known complexity is that detection and capture is predominantly diffusion limited. This problem is compounded when taking into account the capture volume of a nanopore, typically 108–1010 times smaller than the sample volume. To rectify this disproportionate ratio, we demonstrate a simple, yet powerful, method based on coupling single-molecule dielectrophoretic trapping to nanopore sensing. We show that DNA can be captured from a controllable, but typically much larger, volume and concentrated at the tip of a metallic nanopore. This enables the detection of single molecules at concentrations as low as 5 fM, which is approximately a 103 reduction in the limit of detection compared with existing methods, while still maintaining efficient throughput. PMID:26732171

Science of Nanofluidics and Energy Conversion

NASA Astrophysics Data System (ADS)

Xu, Baoxing

The emerging subject of nanofluidics, where solids and fluids interact closely at the nanoscale, has exhibited radically different from their macroscopic counterparts (and sometimes counterintuitive), and yet relatively less explored. On the other hand, the resulting unique properties may contribute to a number of innovative functions with fascinating applications. Among various exciting potential applications, an important and ever expanding one is to provide alternative solutions to energy conversion with high efficiency, including energy absorption, actuation and harvesting. In this dissertation, we first report a novel protection mechanism of energy capture through which an intensive impact or blast energy can be effectively mitigated based on a nonwetting liquid-nanoporous material system. The captured energy is stored in nanopores in the form of potential energy of intercalated water molecules for a while, and not necessarily converted to other forms of energy (e.g. heat). At unloading stage, the captured energy will be released gradually due to the hydrophobic inner surfaces of nanopores through the diffusion of water molecules out of nanopores, thus making this system reusable. Several key controlling factors including impacting velocity, nanopore size, nanopore structure, and liquid phase have been investigated on the capacity of energy capture. The molecular mechanism is elucidated through the study of water molecular distributions inside nanpores. These molecular dynamic (MD) findings are quantitatively verified by a parallel blast experiment on a zeolite/water system. During the transport of confined liquid molecules, the friction resistance exerted by solid atoms of nanopores to liquid molecules will dissipate part of energy, and is highly dependent of temperature of liquid molecules and wall morphology of nanopores. Using MD simulations, the effects of temperature and wall roughness on the transport resistance of water molecules inside nanopores are investigated in Chapter 3. The effective shear stress and nominal viscosity that dominate the nanofluidic transport resistance are extracted and coupled with the nanopore size, transport rate, and liquid property. The molecular-level mechanisms are revealed through the study of the density profile and hydrogen bonding of confined liquid molecules. A parallel experiment on a nanoporous carbon-liquid system is carried out and qualitatively verifies MD findings. Motived by the well-known thermo- and electro-capillary effect, Chapter 4 and Chapter 5 present a conceptual design of thermal and electric actuation system by adjusting the relative hydrophobicity of a liquid-nanoporous system through a thermal and electric field, respectively. The thermally and electrically dependent infiltration behaviors of liquids into nanopores are analyzed by using MD simulations. The fundamental molecular characteristics, including the density profile, contact angle, and surface tension of the confined liquid molecules, are examined to reveal underlying mechanisms. The energy density, power density, and efficiency of both thermal and electric actuation systems are explored and their variations with pore size, solid phase, and liquid phase are evaluated. Thermally and electrically controlled infiltration experiments on a zeolite-water /electrolyte solution system are performed accordingly to qualitatively validate these findings. These energy actuation systems can also become high density thermal or electric storage devices with proper designs. Energy harvesting by the flow of a hydrochloric acid-water solution through a nanopore is explored using atomistic simulations in the last chapter. Through ion configurations near the pore wall, an averaged ion drifting velocity is determined, and the induced voltage along the axial direction is obtained as a function of key material parameters, including the applied flow rate, environmental temperature, solution concentration and nanopore size. The molecular mechanism of ion hopping and motion is revealed. This study shed light on harvesting wasted thermal and mechanical energy from ambient environmental sources such as wasted heat in power plants. Nanofluidics is a novel and thriving research area, whose couplings with other disciplines such as material, mechanical, physical, chemical, electrical engineering are open.

Nanopore extended field-effect transistor for selective single-molecule biosensing.

PubMed

Ren, Ren; Zhang, Yanjun; Nadappuram, Binoy Paulose; Akpinar, Bernice; Klenerman, David; Ivanov, Aleksandar P; Edel, Joshua B; Korchev, Yuri

2017-09-19

There has been a significant drive to deliver nanotechnological solutions to biosensing, yet there remains an unmet need in the development of biosensors that are affordable, integrated, fast, capable of multiplexed detection, and offer high selectivity for trace analyte detection in biological fluids. Herein, some of these challenges are addressed by designing a new class of nanoscale sensors dubbed nanopore extended field-effect transistor (nexFET) that combine the advantages of nanopore single-molecule sensing, field-effect transistors, and recognition chemistry. We report on a polypyrrole functionalized nexFET, with controllable gate voltage that can be used to switch on/off, and slow down single-molecule DNA transport through a nanopore. This strategy enables higher molecular throughput, enhanced signal-to-noise, and even heightened selectivity via functionalization with an embedded receptor. This is shown for selective sensing of an anti-insulin antibody in the presence of its IgG isotype.Efficient detection of single molecules is vital to many biosensing technologies, which require analytical platforms with high selectivity and sensitivity. Ren et al. combine a nanopore sensor and a field-effect transistor, whereby gate voltage mediates DNA and protein transport through the nanopore.

Study of polymer molecules and conformations with a nanopore

DOEpatents

Golovchenko, Jene A.; Li, Jiali; Stein, Derek; Gershow, Marc H.

2013-03-12

The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

Study of polymer molecules and conformations with a nanopore

DOEpatents

Golovchenko, Jene A.; Li, Jiali; Stein, Derek; Gershow, Marc H.

2010-12-07

The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

Study of polymer molecules and conformations with a nanopore

DOEpatents

Golovchenko, Jene A; Li, Jiali; Stein, Derek; Gershow, Marc H

2015-03-03

The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

Hydrodynamic flow in the vicinity of a nanopore induced by an applied voltage

PubMed Central

Mao, Mao; Ghosal, Sandip; Hu, Guohui

2013-01-01

Continuum simulation is employed to study ion transport and fluid flow through a nanopore in a solid-state membrane under an applied potential drop. Results show the existence of concentration polarization layers on the surfaces of the membrane. The nonuniformity of the ionic distribution gives rise to an electric pressure that drives vortical motion in the fluid. There is also a net hydrodynamic flow through the nanopore due to an asymmetry induced by the membrane surface charge. The qualitative behavior is similar to that observed in a previous study using molecular dynamic simulations. The current–voltage characteristics show some nonlinear features but are not greatly affected by the hydrodynamic flow in the parameter regime studied. In the limit of thin Debye layers, the electric resistance of the system can be characterized using an equivalent circuit with lumped parameters. Generation of vorticity can be understood qualitatively from elementary considerations of the Maxwell stresses. However, the flow strength is a strongly nonlinear function of the applied field. Combination of electrophoretic and hydrodynamic effects can lead to ion selectivity in terms of valences and this could have some practical applications in separations. PMID:23689946

Functionalized nanoporous silicas for the immobilization of penicillin acylase

NASA Astrophysics Data System (ADS)

Maria Chong, A. S.; Zhao, X. S.

2004-10-01

Nanoporous silica materials with uniform pore size and ordered structure have drawn growing interest of researchers since 1990s. A large-pore nanoporous material, SBA-15, was functionalized with organosilanes by co-condensation method in the presence of nonionic triblock copolymer P123 as a template under acidic conditions. The functionalization was demonstrated by using five organosilanes, namely 3-aminopropyltriethoxysilane (APTES), 3-mercaptopropyltrimethoxysilane (MPTMS), phenyltrimethoxysilane (PTMS), vinyltriethoxysilane (VTES), and 4-(triethoxysilyl)butyronitrile (TSBN), which modified the surface properties of the silica materials, enabling the materials to be a promising support for immobilization of biological molecules. The functionalized SBA-15 materials exhibited long-range ordering of two-dimensional hexagonal pore arrays of size ranging from 66 to 90 Å as demonstrated by small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), and physical adsorption techniques. A variety of organosilane density in the range of 0.5-2.6 mmol/g was achieved as revealed by elemental analysis and solid-state nuclear magnetic resonance (NMR) techniques. The functionalized materials displayed improved properties for immobilization of penicillin acylase (PA) in comparison with pure-silica SBA-15. Such improvement is believed to be due to the enhanced surface hydrophobicity and electrostatic interactions of the functional groups with the enzyme.

Single molecule unfolding and stretching of protein domains inside a solid-state nanopore by electric field.

PubMed

Freedman, Kevin J; Haq, S Raza; Edel, Joshua B; Jemth, Per; Kim, Min Jun

2013-01-01

Single molecule methods have provided a significantly new look at the behavior of biomolecules in both equilibrium and non-equilibrium conditions. Most notable are the stretching experiments performed by atomic force microscopes and laser tweezers. Here we present an alternative single molecule method that can unfold a protein domain, observed at electric fields greater than 10(6) V/m, and is fully controllable by the application of increasing voltages across the membrane of the pore. Furthermore this unfolding mechanism is characterized by measuring both the residence time of the protein within the nanopore and the current blockade. The unfolding data supports a gradual unfolding mechanism rather than the cooperative transition observed by classical urea denaturation experiments. Lastly it is shown that the voltage-mediated unfolding is a function of the stability of the protein by comparing two mutationally destabilized variants of the protein.

Phase diagram of supercooled water confined to hydrophilic nanopores

NASA Astrophysics Data System (ADS)

Limmer, David T.; Chandler, David

2012-07-01

We present a phase diagram for water confined to cylindrical silica nanopores in terms of pressure, temperature, and pore radius. The confining cylindrical wall is hydrophilic and disordered, which has a destabilizing effect on ordered water structure. The phase diagram for this class of systems is derived from general arguments, with parameters taken from experimental observations and computer simulations and with assumptions tested by computer simulation. Phase space divides into three regions: a single liquid, a crystal-like solid, and glass. For large pores, radii exceeding 1 nm, water exhibits liquid and crystal-like behaviors, with abrupt crossovers between these regimes. For small pore radii, crystal-like behavior is unstable and water remains amorphous for all non-zero temperatures. At low enough temperatures, these states are glasses. Several experimental results for supercooled water can be understood in terms of the phase diagram we present.

Protein separation using an electrically tunable membrane

NASA Astrophysics Data System (ADS)

Jou, Ining; Melnikov, Dmitriy; Gracheva, Maria

Separation of small proteins by charge with a solid-state porous membrane requires control over the protein's movement. Semiconductor membrane has this ability due to the electrically tunable electric potential profile inside the nanopore. In this work we investigate the possibility to separate the solution of two similar sized proteins by charge. As an example, we consider two small globular proteins abundant in humans: insulin (negatively charged) and ubiquitin (neutral). We find that the localized electric field inside the pore either attracts or repels the charged protein to or from the pore wall which affects the delay time before a successful translocation of the protein through the nanopore. However, the motion of the uncharged ubiquitin is unaffected. The difference in the delay time (and hence the separation) can be further increased by the application of the electrolyte bias which induces an electroosmotic flow in the pore. NSF DMR and CBET Grant No. 1352218.

Layered double hydroxide films on nanoporous anodic aluminum oxide/aluminum wire: a new fiber for rapid analysis of Origanum vulgare essential oils.

PubMed

Piryaei, Marzieh

2018-01-01

Zn/Al layered double hydroxide (LDH) films were fabricated in situ with anodic aluminium oxide aluminium as both the substrate and the sole aluminium source by means of urea hydrolysis. Headspace solid phase microextraction using LDH fibre in combination with capillary GC-MS was utilised as a monitoring technique for the collection and detection of the volatile compounds of Origanum vulgare. Experimental parameters, including the sample weight, microwave power, extraction time and humidity effect, were examined and optimised.

Liquid–solid phase transition of hydrogen and deuterium in silica aerogel

DOE PAGES

Van Cleve, E.; Worsley, M. A.; Kucheyev, S. O.

2014-10-30

Behavior of hydrogen isotopes confined in disordered low-density nanoporous solids remains essentially unknown. Here, we use relaxation calorimetry to study freezing and melting of H 2 and D 2 in an ~85%-porous base-catalyzed silica aerogel. In this work, we find that liquid–solid transition temperatures of both isotopes inside the aerogel are depressed. The phase transition takes place over a wide temperature range of ~4 K and non-trivially depends on the liquid filling fraction, reflecting the broad pore size distribution in the aerogel. Undercooling is observed for both H 2 and D 2 confined inside the aerogel monolith. Lastly, results formore » H 2 and D 2 are extrapolated to tritium-containing hydrogens with the quantum law of corresponding states.« less

Nanolock-Nanopore Facilitated Digital Diagnostics of Cancer Driver Mutation in Tumor Tissue.

PubMed

Wang, Yong; Tian, Kai; Shi, Ruicheng; Gu, Amy; Pennella, Michael; Alberts, Lindsey; Gates, Kent S; Li, Guangfu; Fan, Hongxin; Wang, Michael X; Gu, Li-Qun

2017-07-28

Cancer driver mutations are clinically significant biomarkers. In precision medicine, accurate detection of these oncogenic changes in patients would enable early diagnostics of cancer, individually tailored targeted therapy, and precise monitoring of treatment response. Here we investigated a novel nanolock-nanopore method for single-molecule detection of a serine/threonine protein kinase gene BRAF V600E mutation in tumor tissues of thyroid cancer patients. The method lies in a noncovalent, mutation sequence-specific nanolock. We found that the nanolock formed on the mutant allele/probe duplex can separate the duplex dehybridization procedure into two sequential steps in the nanopore. Remarkably, this stepwise unzipping kinetics can produce a unique nanopore electric marker, with which a single DNA molecule of the cancer mutant allele can be unmistakably identified in various backgrounds of the normal wild-type allele. The single-molecule sensitivity for mutant allele enables both binary diagnostics and quantitative analysis of mutation occurrence. In the current configuration, the method can detect the BRAF V600E mutant DNA lower than 1% in the tumor tissues. The nanolock-nanopore method can be adapted to detect a broad spectrum of both transversion and transition DNA mutations, with applications from diagnostics to targeted therapy.

A novel adenine-based metal organic framework derived nitrogen-doped nanoporous carbon for flexible solid-state supercapacitor.

PubMed

Li, Haowen; Fu, Dongying; Zhang, Xian-Ming

2018-01-01

In this article, we have synthesized a series of nitrogen-doped nanoporous carbon (NPC) from metal organic framework of UiO-66 with different ratios of adenine and 1,4-benzendicarboxylate (H 2 BDC) coated on carbon nanotube film (CNTF) to obtain a flexible porous electrode (NPC/CNTF). It is worth noting that the introduction of adenine at different ratios did not change the structure of UiO-66. We also investigated the effect of carbonization temperature from 800 to 1000°C on the electrochemical properties of the NPC. The ratio (H 2 BDC:adenine) 9 : 1 and the NPC carbonized at 900°C (denoted as NPC-1-900) exhibits better electrochemical properties. The results show that NPC-1-900/CNTF electrode exhibits an exceptional areal capacitance of 121.5 mF cm -2 compared to that of PC-900/CNTF electrode (22.8 mF cm -2 ) at 5 mV s -1 in a three-electrode system, indicating that the incorporation of nitrogen is beneficial to the electrochemical properties of nanoporous carbon. A symmetric flexible solid-state supercapacitor of NPC-1-900/CNTF has also been assembled and tested. Electrochemical data show that the device exhibited superior areal capacitance (43.2 mF cm -2 ) at the scan rate of 5 mV s -1 ; the volumetric energy density is 57.3 µWh cm -3 and the volumetric power density is 2.4 mW cm -3 at the current density of 0.5 mA cm -2 based on poly(vinyl alcohol)/H 3 PO 4 gel electrolyte. For practical application, we have also studied the bending tests of the device, which show that the device exhibits outstanding mechanical stability under different bending angles. Furthermore, the flexible device shows excellent cyclic stability, which can retain 91.5% of the initial capacitance after 2000 cycles.

A novel adenine-based metal organic framework derived nitrogen-doped nanoporous carbon for flexible solid-state supercapacitor

PubMed Central

Li, Haowen; Zhang, Xian-Ming

2018-01-01

In this article, we have synthesized a series of nitrogen-doped nanoporous carbon (NPC) from metal organic framework of UiO-66 with different ratios of adenine and 1,4-benzendicarboxylate (H2BDC) coated on carbon nanotube film (CNTF) to obtain a flexible porous electrode (NPC/CNTF). It is worth noting that the introduction of adenine at different ratios did not change the structure of UiO-66. We also investigated the effect of carbonization temperature from 800 to 1000°C on the electrochemical properties of the NPC. The ratio (H2BDC:adenine) 9 : 1 and the NPC carbonized at 900°C (denoted as NPC-1-900) exhibits better electrochemical properties. The results show that NPC-1-900/CNTF electrode exhibits an exceptional areal capacitance of 121.5 mF cm−2 compared to that of PC-900/CNTF electrode (22.8 mF cm−2) at 5 mV s−1 in a three-electrode system, indicating that the incorporation of nitrogen is beneficial to the electrochemical properties of nanoporous carbon. A symmetric flexible solid-state supercapacitor of NPC-1-900/CNTF has also been assembled and tested. Electrochemical data show that the device exhibited superior areal capacitance (43.2 mF cm−2) at the scan rate of 5 mV s−1; the volumetric energy density is 57.3 µWh cm−3 and the volumetric power density is 2.4 mW cm−3 at the current density of 0.5 mA cm−2 based on poly(vinyl alcohol)/H3PO4 gel electrolyte. For practical application, we have also studied the bending tests of the device, which show that the device exhibits outstanding mechanical stability under different bending angles. Furthermore, the flexible device shows excellent cyclic stability, which can retain 91.5% of the initial capacitance after 2000 cycles. PMID:29410815

Amphotericin B channels in phospholipid membrane-coated nanoporous silicon surfaces: implications for photovoltaic driving of ions across membranes.

PubMed

Yilma, Solomon; Liu, Nangou; Samoylov, Alexander; Lo, Ting; Brinker, C Jeffrey; Vodyanoy, Vitaly

2007-03-15

The antimycotic agent amphotericin B (AmB) functions by forming complexes with sterols to form ion channels that cause membrane leakage. When AmB and cholesterol mixed at 2:1 ratio were incorporated into phospholipid bilayer membranes formed on the tip of patch pipettes, ion channel current fluctuations with characteristic open and closed states were observed. These channels were also functional in phospholipid membranes formed on nanoporous silicon surfaces. Electrophysiological studies of AmB-cholesterol mixtures that were incorporated into phospholipid membranes formed on the surface of nanoporous (6.5 nm pore diameter) silicon plates revealed large conductance ion channels ( approximately 300 pS) with distinct open and closed states. Currents through the AmB-cholesterol channels on nanoporous silicon surfaces can be driven by voltage applied via conventional electrical circuits or by photovoltaic electrical potential entirely generated when the nanoporous silicon surface is illuminated with a narrow laser beam. Electrical recordings made during laser illumination of AmB-cholesterol containing membrane-coated nanoporous silicon surfaces revealed very large conductance ion channels with distinct open and closed states. Our findings indicate that nanoporous silicon surfaces can serve as mediums for ion-channel-based biosensors. The photovoltaic properties of nanoporous silicon surfaces show great promise for making such biosensors addressable via optical technologies.

Effect of Minor Alloying Elements on Localized Corrosion Behavior of Aluminum-Copper-Magnesium based Solid Solution Alloys

NASA Astrophysics Data System (ADS)

Aburada, Tomohiro

2011-12-01

The effects and mechanistic roles of a minor alloying element, Ni, on the localized corrosion behavior were explored by studying (Al75Cu 17Mg8)97Ni3 and Al70Cu 18Mg12 amorphous alloys. To explore the minor alloying element limited to the outer surface layers, the corrosion behavior of Al70Cu 18Mg12 amorphous alloy in solutions with and without Ni 2+ was also studied. Both Ni alloying and Ni2+ in solution improved the localized corrosion resistance of the alloys by ennobling the pitting and repassivation potentials. Pit growth by the selective dissolution of Al and Mg was also suppressed by Ni alloying. Remaining Cu and Ni reorganized into a Cu-rich polycrystalline nanoporous structure with continuous ligaments in pits. The minor Ni alloying and Ni2+ in solution suppressed the coarsening of the ligaments in the dealloyed nanoporous structure. The presence of relatively immobile Ni atoms at the surface suppressed the surface diffusion of Cu, which reduced the coarsening of the nanoporous structure, resulting in the formation of 10 to 30 nm wide Cu ligaments. Two mechanistic roles of minor alloying elements in the improvement of the pitting corrosion resistance of the solid solution alloys are elucidated. The first role is the suppression of active dissolution by altering the atomic structure. Ni in solid solution formed stronger bonds with Al, and reduces the probability of weaker Al-Al bonds. The second role is to hinder dissolution by producing a greater negative shift of the true interfacial potential at the dissolution front under the dealloyed layer due to the greater Ohmic resistance through the finer porous structure. These effects contributed to the elevation of pitting potentials by ennobling the applied potential required to produce enough dissolution for the stabilization of pits. Scientifically, this thesis advances the state of understanding of alloy dissolution, particularly the role of minor alloying elements on preferential oxidation at the atomic, nanometer, and micrometer scales. Technological implementations of the findings of the research are also discussed, including a new route to synthesize nanoporous materials with tunable porosity and new corrosion mitigation strategies for commercial Al-based alloys containing the detrimental Al2CuMg phase.

Surface-Directed Synthesis of Erbium-Doped Yttrium Oxide Nanoparticles within Organosilane Zeptoliter Containers

PubMed Central

2015-01-01

We introduce an approach to synthesize rare earth oxide nanoparticles using high temperature without aggregation of the nanoparticles. The dispersity of the nanoparticles is controlled at the nanoscale by using small organosilane molds as reaction containers. Zeptoliter reaction vessels prepared from organosilane self-assembled monolayers (SAMs) were used for the surface-directed synthesis of rare earth oxide (REO) nanoparticles. Nanopores of octadecyltrichlorosilane were prepared on Si(111) using particle lithography with immersion steps. The nanopores were filled with a precursor solution of erbium and yttrium salts to confine the crystallization step to occur within individual zeptoliter-sized organosilane reaction vessels. Areas between the nanopores were separated by a matrix film of octadecyltrichlorosilane. With heating, the organosilane template was removed by calcination to generate a surface array of erbium-doped yttria nanoparticles. Nanoparticles synthesized by the surface-directed approach retain the periodic arrangement of the nanopores formed from mesoparticle masks. While bulk rare earth oxides can be readily prepared by solid state methods at high temperature (>900 °C), approaches for preparing REO nanoparticles are limited. Conventional wet chemistry methods are limited to low temperatures according to the boiling points of the solvents used for synthesis. To achieve crystallinity of REO nanoparticles requires steps for high-temperature processing of samples, which can cause self-aggregation and dispersity in sample diameters. The facile steps for particle lithography address the problems of aggregation and the requirement for high-temperature synthesis. PMID:25163977

Low frequency sonochemical synthesis of nanoporous amorphous manganese dioxide (MnO2) and adsorption of remazol reactive dye

NASA Astrophysics Data System (ADS)

Hasan, Siti Zubaidah; Yusop, Muhammad Rahimi; Othman, Mohamed Rozali

2015-09-01

Nanoporous amorphous-MnO2 was synthesized by sonochemical process (sonication) on the solid manganese (II) acetate tetrahydrate (Mn(CH3COO)2.4H2O) in 0.1 M KMnO4. The product was characterized by X-ray diffraction (XRD), morphology of the material was scanned by Field Emission Scanning Electron Microscopy (FE-SEM) and absorptions of MnO2 bonding was characterized by Fourier Transform Infra-Red Spectrometer (FT-IR). Remazol reactive dye or Red 3BS, was used in the adsorption study using nanoporous amorphous-MnO2. In batch experiment, 10 ppm of Remazol reactive dye was used and experiment was carried out at room temperature. Adsorption of Remazol dye on 0.2g synthesized nanoporous amorphous-MnO2 showed 99 - 100% decolorization.

Selectively Sized Graphene-Based Nanopores for in Situ Single Molecule Sensing

PubMed Central

2015-01-01

The use of nanopore biosensors is set to be extremely important in developing precise single molecule detectors and providing highly sensitive advanced analysis of biological molecules. The precise tailoring of nanopore size is a significant step toward achieving this, as it would allow for a nanopore to be tuned to a corresponding analyte. The work presented here details a methodology for selectively opening nanopores in real-time. The tunable nanopores on a quartz nanopipette platform are fabricated using the electroetching of a graphene-based membrane constructed from individual graphene nanoflakes (ø ∼30 nm). The device design allows for in situ opening of the graphene membrane, from fully closed to fully opened (ø ∼25 nm), a feature that has yet to be reported in the literature. The translocation of DNA is studied as the pore size is varied, allowing for subfeatures of DNA to be detected with slower DNA translocations at smaller pore sizes, and the ability to observe trends as the pore is opened. This approach opens the door to creating a device that can be target to detect specific analytes. PMID:26204996

Advanced Nanoporous Materials for Micro-Gravimetric Sensing to Trace-Level Bio/Chemical Molecules

PubMed Central

Xu, Pengcheng; Li, Xinxin; Yu, Haitao; Xu, Tiegang

2014-01-01

Functionalized nanoporous materials have been developed recently as bio/chemical sensing materials. Due to the huge specific surface of the nano-materials for molecular adsorption, high hopes have been placed on gravimetric detection with micro/nano resonant cantilevers for ultra-sensitive sensing of low-concentration bio/chemical substances. In order to enhance selectivity of the gravimetric resonant sensors to the target molecules, it is crucial to modify specific groups onto the pore-surface of the nano-materials. By loading the nanoporous sensing material onto the desired region of the mass-type transducers like resonant cantilevers, the micro-gravimetric bio/chemical sensors can be formed. Recently, such micro-gravimetric bio/chemical sensors have been successfully applied for rapid or on-the-spot detection of various bio/chemical molecules at the trace-concentration level. The applicable nanoporous sensing materials include mesoporous silica, zeolite, nanoporous graphene oxide (GO) and so on. This review article focuses on the recent achievements in design, preparation, functionalization and characterization of advanced nanoporous sensing materials for micro-gravimetric bio/chemical sensing. PMID:25313499

Detecting a single molecule using a micropore-nanopore hybrid chip

PubMed Central

2013-01-01

Nanopore-based DNA sequencing and biomolecule sensing have attracted more and more attention. In this work, novel sensing devices were built on the basis of the chips containing nanopore arrays in polycarbonate (PC) membranes and micropores in Si3N4 films. Using the integrated chips, the transmembrane ionic current induced by biomolecule's translocation was recorded and analyzed, which suggested that the detected current did not change linearly as commonly expected with increasing biomolecule concentration. On the other hand, detailed translocation information (such as translocation gesture) was also extracted from the discrete current blockages in basic current curves. These results indicated that the nanofluidic device based on the chips integrated by micropores and nanopores possessed comparative potentials in biomolecule sensing. PMID:24261484

Detecting a single molecule using a micropore-nanopore hybrid chip.

PubMed

Liu, Lei; Zhu, Lizhong; Ni, Zhonghua; Chen, Yunfei

2013-11-21

Nanopore-based DNA sequencing and biomolecule sensing have attracted more and more attention. In this work, novel sensing devices were built on the basis of the chips containing nanopore arrays in polycarbonate (PC) membranes and micropores in Si3N4 films. Using the integrated chips, the transmembrane ionic current induced by biomolecule's translocation was recorded and analyzed, which suggested that the detected current did not change linearly as commonly expected with increasing biomolecule concentration. On the other hand, detailed translocation information (such as translocation gesture) was also extracted from the discrete current blockages in basic current curves. These results indicated that the nanofluidic device based on the chips integrated by micropores and nanopores possessed comparative potentials in biomolecule sensing.

Signal and Noise in FET-Nanopore Devices.

PubMed

Parkin, William M; Drndić, Marija

2018-02-23

The combination of a nanopore with a local field-effect transistor (FET-nanopore), like a nanoribbon, nanotube, or nanowire, in order to sense single molecules translocating through the pore is promising for DNA sequencing at megahertz bandwidths. Previously, it was experimentally determined that the detection mechanism was due to local potential fluctuations that arise when an analyte enters a nanopore and constricts ion flow through it, rather than the theoretically proposed mechanism of direct charge coupling between the DNA and nanowire. However, there has been little discussion on the experimentally observed detection mechanism and its relation to the operation of real devices. We model the intrinsic signal and noise in such an FET-nanopore device and compare the results to the ionic current signal. The physical dimensions of DNA molecules limit the change in gate voltage on the FET to below 40 mV. We discuss the low-frequency flicker noise (<10 kHz), medium-frequency thermal noise (<100 kHz), and high-frequency capacitive noise (>100 kHz) in FET-nanopore devices. At bandwidths dominated by thermal noise, the signal-to-noise ratio in FET-nanopore devices is lower than in the ionic current signal. At high frequencies, where noise due to parasitic capacitances in the amplifier and chip is the dominant source of noise in ionic current measurements, high-transconductance FET-nanopore devices can outperform ionic current measurements.

Liquid–solid phase transition of hydrogen and deuterium in silica aerogel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Cleve, E.; Worsley, M. A.; Kucheyev, S. O., E-mail: kucheyev@llnl.gov

2014-10-28

Behavior of hydrogen isotopes confined in disordered low-density nanoporous solids remains essentially unknown. Here, we use relaxation calorimetry to study freezing and melting of H{sub 2} and D{sub 2} in an ∼85%-porous base-catalyzed silica aerogel. We find that liquid–solid transition temperatures of both isotopes inside the aerogel are depressed. The phase transition takes place over a wide temperature range of ∼4 K and non-trivially depends on the liquid filling fraction, reflecting the broad pore size distribution in the aerogel. Undercooling is observed for both H{sub 2} and D{sub 2} confined inside the aerogel monolith. Results for H{sub 2} and D{sub 2}more » are extrapolated to tritium-containing hydrogens with the quantum law of corresponding states.« less

Silicon deposition in nanopores using a liquid precursor.

PubMed

Masuda, Takashi; Tatsuda, Narihito; Yano, Kazuhisa; Shimoda, Tatsuya

2016-11-22

Techniques for depositing silicon into nanosized spaces are vital for the further scaling down of next-generation devices in the semiconductor industry. In this study, we filled silicon into 3.5-nm-diameter nanopores with an aspect ratio of 70 by exploiting thermodynamic behaviour based on the van der Waals energy of vaporized cyclopentasilane (CPS). We originally synthesized CPS as a liquid precursor for semiconducting silicon. Here we used CPS as a gas source in thermal chemical vapour deposition under atmospheric pressure because vaporized CPS can fill nanopores spontaneously. Our estimation of the free energy of CPS based on Lifshitz van der Waals theory clarified the filling mechanism, where CPS vapour in the nanopores readily undergoes capillary condensation because of its large molar volume compared to those of other vapours such as water, toluene, silane, and disilane. Consequently, a liquid-specific feature was observed during the deposition process; specifically, condensed CPS penetrated into the nanopores spontaneously via capillary force. The CPS that filled the nanopores was then transformed into solid silicon by thermal decomposition at 400 °C. The developed method is expected to be used as a nanoscale silicon filling technology, which is critical for the fabrication of future quantum scale silicon devices.

Silicon deposition in nanopores using a liquid precursor

NASA Astrophysics Data System (ADS)

Masuda, Takashi; Tatsuda, Narihito; Yano, Kazuhisa; Shimoda, Tatsuya

2016-11-01

Techniques for depositing silicon into nanosized spaces are vital for the further scaling down of next-generation devices in the semiconductor industry. In this study, we filled silicon into 3.5-nm-diameter nanopores with an aspect ratio of 70 by exploiting thermodynamic behaviour based on the van der Waals energy of vaporized cyclopentasilane (CPS). We originally synthesized CPS as a liquid precursor for semiconducting silicon. Here we used CPS as a gas source in thermal chemical vapour deposition under atmospheric pressure because vaporized CPS can fill nanopores spontaneously. Our estimation of the free energy of CPS based on Lifshitz van der Waals theory clarified the filling mechanism, where CPS vapour in the nanopores readily undergoes capillary condensation because of its large molar volume compared to those of other vapours such as water, toluene, silane, and disilane. Consequently, a liquid-specific feature was observed during the deposition process; specifically, condensed CPS penetrated into the nanopores spontaneously via capillary force. The CPS that filled the nanopores was then transformed into solid silicon by thermal decomposition at 400 °C. The developed method is expected to be used as a nanoscale silicon filling technology, which is critical for the fabrication of future quantum scale silicon devices.

A Nanoporous Alumina Membrane Based Electrochemical Biosensor for Histamine Determination with Biofunctionalized Magnetic Nanoparticles Concentration and Signal Amplification

PubMed Central

Ye, Weiwei; Xu, Yifan; Zheng, Lihao; Zhang, Yu; Yang, Mo; Sun, Peilong

2016-01-01

Histamine is an indicator of food quality and indispensable in the efficient functioning of various physiological systems. Rapid and sensitive determination of histamine is urgently needed in food analysis and clinical diagnostics. Traditional histamine detection methods require qualified personnel, need complex operation processes, and are time-consuming. In this study, a biofunctionalized nanoporous alumina membrane based electrochemical biosensor with magnetic nanoparticles (MNPs) concentration and signal amplification was developed for histamine determination. Nanoporous alumina membranes were modified by anti-histamine antibody and integrated into polydimethylsiloxane (PDMS) chambers. The specific antibody modified MNPs were used to concentrate histamine from samples and transferred to the antibody modified nanoporous membrane. The MNPs conjugated to histamine were captured in the nanopores via specific reaction between histamine and anti-histamine antibody, resulting in a blocking effect that was amplified by MNPs in the nanopores. The blockage signals could be measured by electrochemical impedance spectroscopy across the nanoporous alumina membrane. The sensing platform had great sensitivity and the limit of detection (LOD) reached as low as 3 nM. This biosensor could be successfully applied for histamine determination in saury that was stored in frozen conditions for different hours, presenting a potentially novel, sensitive, and specific sensing system for food quality assessment and safety support. PMID:27782087

Fabrication of nanoporous thin-film working electrodes and their biosensing applications.

PubMed

Li, Tingjie; Jia, Falong; Fan, Yaxi; Ding, Zhifeng; Yang, Jun

2013-04-15

Electrochemical detection for point-of-care diagnostics is of great interest due to its high sensitivity, fast analysis time and ability to operate on a small scale. Herein, we report the fabrication of a nanoporous thin-film electrode and its application in the configuration of a simple and robust enzymatic biosensor. The nanoporous thin-film was formed in a planar gold electrode through an alloying/dealloying process. The nanoporous electrode has an electroactive surface area up to 40 times higher than that of a flat gold electrode of the same size. The nanoporous electrode was used as a substrate to build an enzymatic electrochemical biosensor for the detection of glucose in standard samples and control serum samples. The example glucose biosensor has a linear response up to 30 mM, with a high sensitivity of 0.50 μA mM⁻¹ mm⁻², and excellent anti-interference ability against lactate, uric acid and ascorbic acid. Abundant catalyst and enzyme were stably entrapped in the nanoporous structure, leading to high stability and reproducibility of the biosensor. Development of such nanoporous structure enables the miniaturization of high-performance electrochemical biosensors for point-of-care diagnostics or environmental field testing. Copyright © 2012 Elsevier B.V. All rights reserved.

Low frequency sonochemical synthesis of nanoporous amorphous manganese dioxide (MnO{sub 2}) and adsorption of remazol reactive dye

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasan, Siti Zubaidah; Yusop, Muhammad Rahimi; Othman, Mohamed Rozali, E-mail: rozali@ukm.edu.my

2015-09-25

Nanoporous amorphous-MnO{sub 2} was synthesized by sonochemical process (sonication) on the solid manganese (II) acetate tetrahydrate (Mn(CH{sub 3}COO){sub 2}.4H{sub 2}O) in 0.1 M KMnO{sub 4}. The product was characterized by X-ray diffraction (XRD), morphology of the material was scanned by Field Emission Scanning Electron Microscopy (FE-SEM) and absorptions of MnO{sub 2} bonding was characterized by Fourier Transform Infra-Red Spectrometer (FT-IR). Remazol reactive dye or Red 3BS, was used in the adsorption study using nanoporous amorphous-MnO{sub 2}. In batch experiment, 10 ppm of Remazol reactive dye was used and experiment was carried out at room temperature. Adsorption of Remazol dye onmore » 0.2g synthesized nanoporous amorphous-MnO{sub 2} showed 99 – 100% decolorization.« less

Rapid detection of a cocaine-binding aptamer using biological nanopores on a chip.

PubMed

Kawano, Ryuji; Osaki, Toshihisa; Sasaki, Hirotaka; Takinoue, Masahiro; Yoshizawa, Satoko; Takeuchi, Shoji

2011-06-08

This paper describes a methodology for the rapid and highly selective detection of cocaine using a membrane protein channel combined with a DNA aptamer. The DNA aptamer recognizes the cocaine molecule with high selectivity. We successfully detected a low concentration of cocaine (300 ng/mL, the drug test cutoff limit) within 60 s using a biological nanopore embedded in a microchip.

Improved Analysis of Nanopore Sequence Data and Scanning Nanopore Techniques

NASA Astrophysics Data System (ADS)

Szalay, Tamas

The field of nanopore research has been driven by the need to inexpensively and rapidly sequence DNA. In order to help realize this goal, this thesis describes the PoreSeq algorithm that identifies and corrects errors in real-world nanopore sequencing data and improves the accuracy of de novo genome assembly with increasing coverage depth. The approach relies on modeling the possible sources of uncertainty that occur as DNA advances through the nanopore and then using this model to find the sequence that best explains multiple reads of the same region of DNA. PoreSeq increases nanopore sequencing read accuracy of M13 bacteriophage DNA from 85% to 99% at 100X coverage. We also use the algorithm to assemble E. coli with 30X coverage and the lambda genome at a range of coverages from 3X to 50X. Additionally, we classify sequence variants at an order of magnitude lower coverage than is possible with existing methods. This thesis also reports preliminary progress towards controlling the motion of DNA using two nanopores instead of one. The speed at which the DNA travels through the nanopore needs to be carefully controlled to facilitate the detection of individual bases. A second nanopore in close proximity to the first could be used to slow or stop the motion of the DNA in order to enable a more accurate readout. The fabrication process for a new pyramidal nanopore geometry was developed in order to facilitate the positioning of the nanopores. This thesis demonstrates that two of them can be placed close enough to interact with a single molecule of DNA, which is a prerequisite for being able to use the driving force of the pores to exert fine control over the motion of the DNA. Another strategy for reading the DNA is to trap it completely with one pore and to move the second nanopore instead. To that end, this thesis also shows that a single strand of immobilized DNA can be captured in a scanning nanopore and examined for a full hour, with data from many scans at many different voltages obtained in order to detect a bound protein placed partway along the molecule.

Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation

NASA Astrophysics Data System (ADS)

Mereuta, Loredana; Roy, Mahua; Asandei, Alina; Lee, Jong Kook; Park, Yoonkyung; Andricioaei, Ioan; Luchian, Tudor

2014-01-01

The microscopic details of how peptides translocate one at a time through nanopores are crucial determinants for transport through membrane pores and important in developing nano-technologies. To date, the translocation process has been too fast relative to the resolution of the single molecule techniques that sought to detect its milestones. Using pH-tuned single-molecule electrophysiology and molecular dynamics simulations, we demonstrate how peptide passage through the α-hemolysin protein can be sufficiently slowed down to observe intermediate single-peptide sub-states associated to distinct structural milestones along the pore, and how to control residence time, direction and the sequence of spatio-temporal state-to-state dynamics of a single peptide. Molecular dynamics simulations of peptide translocation reveal the time- dependent ordering of intermediate structures of the translocating peptide inside the pore at atomic resolution. Calculations of the expected current ratios of the different pore-blocking microstates and their time sequencing are in accord with the recorded current traces.

A nanoporous gold membrane for sensing applications

PubMed Central

Oo, Swe Zin; Silva, Gloria; Carpignano, Francesca; Noual, Adnane; Pechstedt, Katrin; Mateos, Luis; Grant-Jacob, James A.; Brocklesby, Bill; Horak, Peter; Charlton, Martin; Boden, Stuart A.; Melvin, Tracy

2016-01-01

Design and fabrication of three-dimensionally structured, gold membranes containing hexagonally close-packed microcavities with nanopores in the base, are described. Our aim is to create a nanoporous structure with localized enhancement of the fluorescence or Raman scattering at, and in the nanopore when excited with light of approximately 600 nm, with a view to provide sensitive detection of biomolecules. A range of geometries of the nanopore integrated into hexagonally close-packed assemblies of gold micro-cavities was first evaluated theoretically. The optimal size and shape of the nanopore in a single microcavity were then considered to provide the highest localized plasmon enhancement (of fluorescence or Raman scattering) at the very center of the nanopore for a bioanalyte traversing through. The optimized design was established to be a 1200 nm diameter cavity of 600 nm depth with a 50 nm square nanopore with rounded corners in the base. A gold 3D-structured membrane containing these sized microcavities with the integrated nanopore was successfully fabricated and ‘proof of concept’ Raman scattering experiments are described. PMID:26973809

The Utility of Nanopore Technology for Protein and Peptide Sensing.

PubMed

Robertson, Joseph W F; Reiner, Joseph E

2018-06-28

Resistive-pulse nanopore sensing enables label-free single-molecule analysis of a wide range of analytes. An increasing number of studies have demonstrated the feasibility and usefulness of nanopore sensing for protein and peptide characterization. Nanopores offer the potential to study a variety of protein-related phenomena that includes unfolding kinetics, differences in unfolding pathways, protein structure stability and free energy profiles of DNA-protein and RNA-protein binding. In addition to providing a tool for fundamental protein characterization, nanopores have also been used as highly selective protein detectors in various solution mixtures and conditions. This review highlights these and other developments in the area of nanopore-based protein and peptide detection. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Nanoporous impedemetric biosensor for detection of trace atrazine from water samples.

PubMed

Pichetsurnthorn, Pie; Vattipalli, Krishna; Prasad, Shalini

2012-02-15

Trace contamination of ground water sources has been a problem ever since the introduction of high-soil-mobility pesticides, one such example is atrazine. In this paper we present a novel nanoporous portable bio-sensing device that can identify trace contamination of atrazine through a label-free assay. We have designed a pesticide sensor comprising of a nanoporous alumina membrane integrated with printed circuit board platform. Nanoporous alumina in the biosensor device generates a high density array of nanoscale confined spaces. By leveraging the size based immobilization of atrazine small molecules we have designed electrochemical impedance spectroscopy based biosensor to detect trace amounts of atrazine. We have calibrated the sensor using phosphate buffered saline and demonstrated trace detection from river and bottled drinking water samples. The limit of detection in all the three cases was in the femtogram/mL (fg/mL) (parts-per-trillion) regime with a dynamic range of detection spanning from 10 fg/mL to 1 ng/mL (0.01 ppt to 1 ppm). The selectivity of the device was tested using a competing pesticide; malathion and selectivity in detection was observed in the fg/mL regime in all the three cases. Copyright © 2011 Elsevier B.V. All rights reserved.

Spatial structure of disordered proteins dictates conductance and selectivity in nuclear pore complex mimics

PubMed Central

Frey, Steffen; Dwarkasing, Arvind; Versloot, Roderick; van der Giessen, Erik

2018-01-01

Nuclear pore complexes (NPCs) lined with intrinsically disordered FG-domains act as selective gatekeepers for molecular transport between the nucleus and the cytoplasm in eukaryotic cells. The underlying physical mechanism of the intriguing selectivity is still under debate. Here, we probe the transport of ions and transport receptors through biomimetic NPCs consisting of Nsp1 domains attached to the inner surface of solid-state nanopores. We examine both wildtype FG-domains and hydrophilic SG-mutants. FG-nanopores showed a clear selectivity as transport receptors can translocate across the pore whereas other proteins cannot. SG mutant pores lack such selectivity. To unravel this striking difference, we present coarse-grained molecular dynamics simulations that reveal that FG-pores exhibit a high-density, nonuniform protein distribution, in contrast to a uniform and significantly less-dense protein distribution in the SG-mutant. We conclude that the sequence-dependent density distribution of disordered proteins inside the NPC plays a key role for its conductivity and selective permeability. PMID:29442997

Pore Diameter Dependence and Segmental Dynamics of Poly-Z-L-lysine and Poly-L-alanine Confined in 1D Nanocylindrical Geometry

NASA Astrophysics Data System (ADS)

Tuncel, Eylul; Suzuki, Yasuhito; Iossifidis, Agathaggelos; Steinhart, Martin; Butt, Hans-Jurgen; Floudas, George; Duran, Hatice

Structure formation, thermodynamic stability, phase and dynamic behaviors of polypeptides are strongly affected by confinement. Since understanding the changes in these behaviors will allow their rational design as functional devices with tunable properties, herein we investigated Poly-Z-L-lysine (PZLL) and Poly-L-alanine (PAla) homopolypeptides confined in nanoporous alumina containing aligned cylindrical nanopores as a function of pore size by differential scanning calorimetry (DSC), Fourier Transform Infrared Spectroscopy, Solid-state NMR, X-ray diffraction, Dielectric spectroscopy(DS). Bulk PZLL exhibits a glass transition temperature (Tg) at about 301K while PZLL nanorods showed slightly lower Tg (294K). The dynamic investigation by DS also revealed a decrease (4K) in Tg between bulk and PZLL nanorods. DS is a very sensitive probe of the local and global secondary structure relaxation through the large dipole to study effect of confinement. The results revealed that the local segmental dynamics, associated with broken hydrogen bonds, and segmental dynamics speed-up on confinement.

Nanoporous array anodic titanium-supported co-polymeric ionic liquids as high performance solid-phase microextraction sorbents for hydrogen bonding compounds.

PubMed

Jia, Jing; Liang, Xiaojing; Wang, Licheng; Guo, Yong; Liu, Xia; Jiang, Shengxiang

2013-12-13

A nanoporous array anodic titanium-supported co-polymeric ionic liquids (NAAT/PILs) solid-phase microextraction (SPME) fiber was prepared in situ on the titanium wire. NAAT was selected as the substrate, in view of its high surface-to-volume ratio, easy preparation, mechanical stability, and rich titanol groups on its surface which can anchor silica coupling agent containing vinyl and then introduce ionic liquid copolymers as sorbents. In this work, 1-vinyl-3-nonanol imidazolium bromide ([C9OHVIm]Br) and 1,4-di(3-vinylimidazolium) butane dibromide ([(VIM)2C4]2[Br]) were synthesized and used as monomer and crosslinker, respectively. Extraction properties of the NAAT/PILs fiber for polar alcohols and volatile fatty acids (VFAs) in aqueous matrix were examined using gaseous sampling-SPME (GS-SPME) and headspace SPME (HS-SPME) mode, respectively. Combining the superior properties of NAAT substrate and the strong hydrogen bond interaction of PILs to polar compounds, the NAAT/PILs SPME fiber showed much higher adsorption affinity to aliphatic alcohols than bare NAAT and pure PILs fibers. The detection limits (LOD) of established GS-SPME-GC-FID method are in the range of 0.35-17.30ngL(-1) with a linear range from 0.01 to 500ngmL(-1). Also, it showed high extraction performance toward volatile fatty acids (VFAs) compounds from aqueous matrix. Under the optimized SPME conditions, wide linear ranges were obtained with correlation coefficients (R(2)) greater than 0.99 and limits of detection were in the range of 0.85-8.74ngL(-1). Moreover, real-world samples were analyzed and good results were obtained. Copyright © 2013. Published by Elsevier B.V.

Electrochemically-Driven Insertion of Biological Nanodiscs into Solid State Membrane Pores as a Basis for "Pore-In-Pore" Membranes.

PubMed

Farajollahi, Farid; Seidenstücker, Axel; Altintoprak, Klara; Walther, Paul; Ziemann, Paul; Plettl, Alfred; Marti, Othmar; Wege, Christina; Gliemann, Hartmut

2018-04-13

Nanoporous membranes are of increasing interest for many applications, such as molecular filters, biosensors, nanofluidic logic and energy conversion devices. To meet high-quality standards, e.g., in molecular separation processes, membranes with well-defined pores in terms of pore diameter and chemical properties are required. However, the preparation of membranes with narrow pore diameter distributions is still challenging. In the work presented here, we demonstrate a strategy, a "pore-in-pore" approach, where the conical pores of a solid state membrane produced by a multi-step top-down lithography procedure are used as a template to insert precisely-formed biomolecular nanodiscs with exactly defined inner and outer diameters. These nanodiscs, which are the building blocks of tobacco mosaic virus-deduced particles, consist of coat proteins, which self-assemble under defined experimental conditions with a stabilizing short RNA. We demonstrate that the insertion of the nanodiscs can be driven either by diffusion due to a concentration gradient or by applying an electric field along the cross-section of the solid state membrane. It is found that the electrophoresis-driven insertion is significantly more effective than the insertion via the concentration gradient.

Electrochemically-Driven Insertion of Biological Nanodiscs into Solid State Membrane Pores as a Basis for “Pore-In-Pore” Membranes

PubMed Central

Farajollahi, Farid; Seidenstücker, Axel; Altintoprak, Klara; Walther, Paul; Ziemann, Paul; Plettl, Alfred; Wege, Christina; Gliemann, Hartmut

2018-01-01

Nanoporous membranes are of increasing interest for many applications, such as molecular filters, biosensors, nanofluidic logic and energy conversion devices. To meet high-quality standards, e.g., in molecular separation processes, membranes with well-defined pores in terms of pore diameter and chemical properties are required. However, the preparation of membranes with narrow pore diameter distributions is still challenging. In the work presented here, we demonstrate a strategy, a “pore-in-pore” approach, where the conical pores of a solid state membrane produced by a multi-step top-down lithography procedure are used as a template to insert precisely-formed biomolecular nanodiscs with exactly defined inner and outer diameters. These nanodiscs, which are the building blocks of tobacco mosaic virus-deduced particles, consist of coat proteins, which self-assemble under defined experimental conditions with a stabilizing short RNA. We demonstrate that the insertion of the nanodiscs can be driven either by diffusion due to a concentration gradient or by applying an electric field along the cross-section of the solid state membrane. It is found that the electrophoresis-driven insertion is significantly more effective than the insertion via the concentration gradient. PMID:29652841

An ultrasensitive bio-surrogate for nanoporous filter membrane performance metrology directed towards contamination control in microlithography applications

NASA Astrophysics Data System (ADS)

Ahmad, Farhan; Mish, Barbara; Qiu, Jian; Singh, Amarnauth; Varanasi, Rao; Bedford, Eilidh; Smith, Martin

2016-03-01

Contamination tolerances in semiconductor manufacturing processes have changed dramatically in the past two decades, reaching below 20 nm according to the guidelines of the International Technology Roadmap for Semiconductors. The move to narrower line widths drives the need for innovative filtration technologies that can achieve higher particle/contaminant removal performance resulting in cleaner process fluids. Nanoporous filter membrane metrology tools that have been the workhorse over the past decade are also now reaching limits. For example, nanoparticle (NP) challenge testing is commonly applied for assessing particle retention performance of filter membranes. Factors such as high NP size dispersity, low NP detection sensitivity, and high NP particle-filter affinity impose challenges in characterizing the next generation of nanoporous filter membranes. We report a novel bio-surrogate, 5 nm DNA-dendrimer conjugate for evaluating particle retention performance of nanoporous filter membranes. A technique capable of single molecule detection is employed to detect sparse concentration of conjugate in filter permeate, providing >1000- fold higher detection sensitivity than any existing 5 nm-sized particle enumeration technique. This bio-surrogate also offers narrow size distribution, high stability and chemical tunability. This bio-surrogate can discriminate various sub-15 nm pore-rated nanoporous filter membranes based on their particle retention performance. Due to high bio-surrogate detection sensitivity, a lower challenge concentration of bio-surrogate (as compared to other NPs of this size) can be used for filter testing, providing a better representation of customer applications. This new method should provide better understanding of the next generation filter membranes for removing defect-causing contaminants from lithography processes.

Ionic Conductivity, Structural Deformation and Programmable Anisotropy of DNA Origami in Electric Field

PubMed Central

Li, Chen-Yu; Hemmig, Elisa A.; Kong, Jinglin; Yoo, Jejoong; Hernández-Ainsa, Silvia

2015-01-01

The DNA origami technique can enable functionalization of inorganic structures for single-molecule electric current recordings. Experiments have shown that several layers of DNA molecules—a DNA origami plate— placed on top of a solid-state nanopore is permeable to ions. Here, we report a comprehensive characterization of the ionic conductivity of DNA origami plates by means of all-atom molecular dynamics (MD) simulations and nanocapillary electric current recordings. Using the MD method, we characterize the ionic conductivity of several origami constructs, revealing the local distribution of ions, the distribution of the electrostatic potential and contribution of different molecular species to the current. The simulations determine the dependence of the ionic conductivity on the applied voltage, the number of DNA layers, the nucleotide content and the lattice type of the plates. We demonstrate that increasing the concentration of Mg2+ ions makes the origami plates more compact, reducing their conductivity. The conductance of a DNA origami plate on top of a solid-state nanopore is determined by the two competing effects: bending of the DNA origami plate that reduces the current and separation of the DNA origami layers that increases the current. The latter is produced by the electro-osmotic flow and is reversible at the time scale of a hundred nanoseconds. The conductance of a DNA origami object is found to depend on its orientation, reaching maximum when the electric field aligns with the direction of the DNA helices. Our work demonstrates feasibility of programming the electrical properties of a self-assembled nanoscale object using DNA. PMID:25623807

Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field.

PubMed

Li, Chen-Yu; Hemmig, Elisa A; Kong, Jinglin; Yoo, Jejoong; Hernández-Ainsa, Silvia; Keyser, Ulrich F; Aksimentiev, Aleksei

2015-02-24

The DNA origami technique can enable functionalization of inorganic structures for single-molecule electric current recordings. Experiments have shown that several layers of DNA molecules, a DNA origami plate, placed on top of a solid-state nanopore is permeable to ions. Here, we report a comprehensive characterization of the ionic conductivity of DNA origami plates by means of all-atom molecular dynamics (MD) simulations and nanocapillary electric current recordings. Using the MD method, we characterize the ionic conductivity of several origami constructs, revealing the local distribution of ions, the distribution of the electrostatic potential and contribution of different molecular species to the current. The simulations determine the dependence of the ionic conductivity on the applied voltage, the number of DNA layers, the nucleotide content and the lattice type of the plates. We demonstrate that increasing the concentration of Mg(2+) ions makes the origami plates more compact, reducing their conductivity. The conductance of a DNA origami plate on top of a solid-state nanopore is determined by the two competing effects: bending of the DNA origami plate that reduces the current and separation of the DNA origami layers that increases the current. The latter is produced by the electro-osmotic flow and is reversible at the time scale of a hundred nanoseconds. The conductance of a DNA origami object is found to depend on its orientation, reaching maximum when the electric field aligns with the direction of the DNA helices. Our work demonstrates feasibility of programming the electrical properties of a self-assembled nanoscale object using DNA.

Nanofluidic Device with Embedded Nanopore

NASA Astrophysics Data System (ADS)

Zhang, Yuning; Reisner, Walter

2014-03-01

Nanofluidic based devices are robust methods for biomolecular sensing and single DNA manipulation. Nanopore-based DNA sensing has attractive features that make it a leading candidate as a single-molecule DNA sequencing technology. Nanochannel based extension of DNA, combined with enzymatic or denaturation-based barcoding schemes, is already a powerful approach for genome analysis. We believe that there is revolutionary potential in devices that combine nanochannels with nanpore detectors. In particular, due to the fast translocation of a DNA molecule through a standard nanopore configuration, there is an unfavorable trade-off between signal and sequence resolution. With a combined nanochannel-nanopore device, based on embedding a nanopore inside a nanochannel, we can in principle gain independent control over both DNA translocation speed and sensing signal, solving the key draw-back of the standard nanopore configuration. We demonstrate that we can detect - using fluorescent microscopy - successful translocation of DNA from the nanochannel out through the nanopore, a possible method to 'select' a given barcode for further analysis. We also show that in equilibrium DNA will not escape through an embedded sub-persistence length nanopore until a certain voltage bias is added.

Effect of ultraviolet illumination and ambient gases on the photoluminescence and electrical properties of nanoporous silicon layer for organic vapor sensor.

PubMed

Atiwongsangthong, Narin

2012-08-01

The purpose of this research, the nanoporous silicon layer were fabricated and investigated the physical properties such as photoluminescence and the electrical properties in order to develop organic vapor sensor by using nanoporous silicon. The Changes in the photoluminescence intensity of nanoporous silicon samples are studied during ultraviolet illumination in various ambient gases such as nitrogen, oxigen and vacuum. In this paper, the nanoporous silicon layer was used as organic vapor adsorption and sensing element. The advantage of this device are simple process compatible in silicon technology and usable in room temperature. The structure of this device consists of nanoporous silicon layer which is formed by anodization of silicon wafer in hydrofluoric acid solution and aluminum electrode which deposited on the top of nanoporous silicon layer by evaporator. The nanoporous silicon sensors were placed in a gas chamber with various organic vapor such as ethanol, methanol and isopropyl alcohol. From studying on electrical characteristics of this device, it is found that the nanoporous silicon layer can detect the different organic vapor. Therefore, the nanoporous silicon is important material for organic vapor sensor and it can develop to other applications about gas sensors in the future.

Logic Gate Operation by DNA Translocation through Biological Nanopores.

PubMed

Yasuga, Hiroki; Kawano, Ryuji; Takinoue, Masahiro; Tsuji, Yutaro; Osaki, Toshihisa; Kamiya, Koki; Miki, Norihisa; Takeuchi, Shoji

2016-01-01

Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs "1" and "0" as single-stranded DNA (ssDNA) that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND) operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment.

Logic Gate Operation by DNA Translocation through Biological Nanopores

PubMed Central

Takinoue, Masahiro; Tsuji, Yutaro; Osaki, Toshihisa; Kamiya, Koki; Miki, Norihisa; Takeuchi, Shoji

2016-01-01

Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs “1” and “0” as single-stranded DNA (ssDNA) that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND) operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment. PMID:26890568

DNA origami nanopores: developments, challenges and perspectives

NASA Astrophysics Data System (ADS)

Hernández-Ainsa, Silvia; Keyser, Ulrich F.

2014-11-01

DNA nanotechnology has enabled the construction of DNA origami nanopores; synthetic nanopores that present improved capabilities for the area of single molecule detection. Their extraordinary versatility makes them a new and powerful tool in nanobiotechnology for a wide range of important applications beyond molecular sensing. In this review, we briefly present the recent developments in this emerging field of research. We discuss the current challenges and possible solutions that would enhance the sensing capabilities of DNA origami nanopores. Finally, we anticipate novel avenues for future research and highlight a range of exciting ideas and applications that could be explored in the near future.

Ultrananocrystalline diamond-coated nanoporous membranes support SK-N-SH neuroblastoma endothelial cell attachment.

PubMed

Yang, Kai-Hung; Nguyen, Alexander K; Goering, Peter L; Sumant, Anirudha V; Narayan, Roger J

2018-06-06

Ultrananocrystalline diamond (UNCD) has been demonstrated to have attractive features for biomedical applications and can be combined with nanoporous membranes for applications in drug delivery systems, biosensing, immunoisolation and single molecule analysis. In this study, free-standing nanoporous UNCD membranes with pore sizes of 100 or 400 nm were fabricated by directly depositing ultrathin UNCD films on nanoporous silicon nitride membranes and then etching away silicon nitride using reactive ion etching. Successful deposition of UNCD on the substrate with a novel process was confirmed with Raman spectroscopy, X-ray photoelectron spectroscopy, cross-section scanning electron microscopy (SEM) and transmission electron microscopy. Both sample types exhibited uniform geometry and maintained a clear hexagonal pore arrangement. Cellular attachment of SK-N-SH neuroblastoma endothelial cells was examined using confocal microscopy and SEM. Attachment of SK-N-SH cells onto UNCD membranes on both porous regions and solid surfaces was shown, indicating the potential use of UNCD membranes in biomedical applications such as biosensors and tissue engineering scaffolds.

Three-Dimensional Morphological and Chemical Evolution of Nanoporous Stainless Steel by Liquid Metal Dealloying [3D Morphological and Chemical Evolution of Nanoporous Stainless Steel by Liquid Metal Dealloying

DOE PAGES

Zhao, Chonghang; Wada, Takeshi; De Andrade, Vincent; ...

2017-09-04

Nanoporous materials, especially those fabricated by liquid metal dealloying processes, possess great potential in a wide range of applications due to their high surface area, bicontinuous structure with both open pores for transport and solid phase for conductivity or support, and low material cost. Here, we used X-ray nanotomography and X-ray fluorescence microscopy to reveal the three-dimensional (3D) morphology and elemental distribution within materials. Focusing on nanoporous stainless steel, we evaluated the 3D morphology of the dealloying front and established a quantitative processing-structure-property relationship at a later stage of dealloying. The morphological differences of samples created by liquid metal dealloyingmore » and aqueous dealloying methods were also discussed. Here, we concluded that it is particularly important to consider the dealloying, coarsening, and densification mechanisms in influencing the performance-determining, critical 3D parameters, such as tortuosity, pore size, porosity, curvature, and interfacial shape.« less

Three-Dimensional Morphological and Chemical Evolution of Nanoporous Stainless Steel by Liquid Metal Dealloying [3D Morphological and Chemical Evolution of Nanoporous Stainless Steel by Liquid Metal Dealloying

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Chonghang; Wada, Takeshi; De Andrade, Vincent

Nanoporous materials, especially those fabricated by liquid metal dealloying processes, possess great potential in a wide range of applications due to their high surface area, bicontinuous structure with both open pores for transport and solid phase for conductivity or support, and low material cost. Here, we used X-ray nanotomography and X-ray fluorescence microscopy to reveal the three-dimensional (3D) morphology and elemental distribution within materials. Focusing on nanoporous stainless steel, we evaluated the 3D morphology of the dealloying front and established a quantitative processing-structure-property relationship at a later stage of dealloying. The morphological differences of samples created by liquid metal dealloyingmore » and aqueous dealloying methods were also discussed. Here, we concluded that it is particularly important to consider the dealloying, coarsening, and densification mechanisms in influencing the performance-determining, critical 3D parameters, such as tortuosity, pore size, porosity, curvature, and interfacial shape.« less

Optical detection of two-color-fluorophore barcode for nanopore DNA sensing

NASA Astrophysics Data System (ADS)

Zhang, M.; Sychugov, I.; Schmidt, T.; Linnros, J.

2015-06-01

A simple schematic on parallel optical detection of two-fluorophore barcode for single-molecule nanopore sensing is presented. The chosen two fluorophores, ATTO-532 and DY-521-XL, emitting in well-separated spectrum range can be excited at the same wavelength. A beam splitter was employed to separate signals from the two fluorophores and guide them to the same CCD camera. Based on a conventional microscope, sources of background in the nanopore sensing system, including membranes, compounds in buffer solution, and a detection cell was characterized. By photoluminescence excitation measurements, it turned out that silicon membrane has a negligible photoluminescence under the examined excitation from 440 nm to 560 nm, in comparison with a silicon nitrite membrane. Further, background signals from the detection cell were suppressed. Brownian motion of 450 bps DNA labelled with single ATTO-532 or DY-521-XL was successfully recorded by our optical system.

Thermally stable solids based on endohedrally doped ZnS clusters.

PubMed

Matxain, Jon M; Piris, Mario; Lopez, Xabier; Ugalde, Jesus M

2009-01-01

The existence of inorganic, hollow, fullerene-like ZnS clusters has been theoretically predicted and then recently confirmed experimentally. These clusters were observed to trap alkali metals and halogens because the ionization energies (IE) of alkali metals are very similar to the electron affinities (EA) of halogens. This opens the possibility of forming molecular solids composed of these fullerene building blocks because the energy released due to the difference between the IE and EA would be very small. Herein we have focused on assembling bare Zn(12)S(12) and endohedral X@Zn(12)S(12)-Y@Zn(12)S(12) dimers (X = Na, K; Y = Cl, Br) by considering the square-faces-square orientation of every two adjacent clusters, which leads to a fcc cubic crystal structure in the solid. The structures were fully optimized in all cases, and their thermal stability was confirmed by ab initio thermal molecular dynamics calculations. The optimum lattice parameter of the solids was found to be around 13.8 A, which corresponds to distances of about 2.5 A between monomers, which is typical of covalent Zn-S bonds. The resulting solids are nanoporous materials similar to B(12)N(12). Due to their nanoporous structure, these zeolite-shaped solids could be used in heterogeneous catalysis and as storage materials and molecular sieves.

Tailoring the hydrophobicity of graphene for its use as nanopores for DNA translocation

NASA Astrophysics Data System (ADS)

Schneider, Grégory F.; Xu, Qiang; Hage, Susanne; Luik, Stephanie; Spoor, Johannes N. H.; Malladi, Sairam; Zandbergen, Henny; Dekker, Cees

2013-10-01

Graphene nanopores are potential successors to biological and silicon-based nanopores. For sensing applications, it is however crucial to understand and block the strong nonspecific hydrophobic interactions between DNA and graphene. Here we demonstrate a novel scheme to prevent DNA-graphene interactions, based on a tailored self-assembled monolayer. For bare graphene, we encounter a paradox: whereas contaminated graphene nanopores facilitated DNA translocation well, clean crystalline graphene pores very quickly exhibit clogging of the pore. We attribute this to strong interactions between DNA nucleotides and graphene, yielding sticking and irreversible pore closure. We develop a general strategy to noncovalently tailor the hydrophobic surface of graphene by designing a dedicated self-assembled monolayer of pyrene ethylene glycol, which renders the surface hydrophilic. We demonstrate that this prevents DNA to adsorb on graphene and show that single-stranded DNA can now be detected in graphene nanopores with excellent nanopore durability and reproducibility.

Anomalous low strain induced by surface charge in nanoporous gold with low relative density.

PubMed

Liu, Feng; Ye, Xing-Long; Jin, Hai-Jun

2017-07-26

The surface stress induced axial strain in a fiber-like solid is larger than its radical strain, and is also greater than the radical strain in similar-sized spherical solids. It is thus envisaged that the surface-induced macroscopic dimension change (i.e., actuation strain) in nanoporous gold (NPG) increases with decreasing relative density, or alternatively, with an increasing ratio between volumes of fiber-like ligaments and sphere-like nodes. In this study, electrochemical actuations of NPG with similar structure sizes, same (oxide-covered) surface state but different relative densities were characterized in situ in response to surface charging/discharging. We found that the actuation strain amplitude did not increase, but decreased dramatically with decreasing relative density of NPG, in contrast to the above prediction. The actuation strain decreased abruptly when the relative density of NPG was decreased to below 0.25, when the Au content in the AuAg precursor was below 20 at%. Further studies indicate that this anomalous behavior cannot be explained by potential- or size-dependences of the elasticity, the structure difference arising from different dealloying rates, or additional strain induced by the external load during dilatometry experiments. In NPG with low relative density, mutual movements of nano-ligaments may occur in the pore space and disconnected regions, which may compensate the local strain in ligaments and account for the anomalous low actuation strain in macroscopic NPG samples.

Plasmon-assisted radiolytic energy conversion in aqueous solutions

PubMed Central

Kim, Baek Hyun; Kwon, Jae W.

2014-01-01

The field of conventional energy conversion using radioisotopes has almost exclusively focused on solid-state materials. Herein, we demonstrate that liquids can be an excellent media for effective energy conversion from radioisotopes. We also show that free radicals in liquid, which are continuously generated by beta radiation, can be utilized for electrical energy generation. Under beta radiation, surface plasmon obtained by the metallic nanoporous structures on TiO2 enhanced the radiolytic conversion via the efficient energy transfer between plasmons and free radicals. This work introduces a new route for the development of next-generation power sources. PMID:24918356

Asymmetric ion transport through ion-channel-mimetic solid-state nanopores.

PubMed

Guo, Wei; Tian, Ye; Jiang, Lei

2013-12-17

Both scientists and engineers are interested in the design and fabrication of synthetic nanofluidic architectures that mimic the gating functions of biological ion channels. The effort to build such structures requires interdisciplinary efforts at the intersection of chemistry, materials science, and nanotechnology. Biological ion channels and synthetic nanofluidic devices have some structural and chemical similarities, and therefore, they share some common features in regulating the traverse ionic flow. In the past decade, researchers have identified two asymmetric ion transport phenomena in synthetic nanofluidic structures, the rectified ionic current and the net diffusion current. The rectified ionic current is a diode-like current-voltage response that occurs when switching the voltage bias. This phenomenon indicates a preferential direction of transport in the nanofluidic system. The net diffusion current occurs as a direct product of charge selectivity and is generated from the asymmetric diffusion through charged nanofluidic channels. These new ion transport phenomena and the elaborate structures that occur in biology have inspired us to build functional nanofluidic devices for both fundamental research and practical applications. In this Account, we review our recent progress in the design and fabrication of biomimetic solid-state nanofluidic devices with asymmetric ion transport behavior. We demonstrate the origin of the rectified ionic current and the net diffusion current. We also identify several influential factors and discuss how to build these asymmetric features into nanofluidic systems by controlling (1) nanopore geometry, (2) surface charge distribution, (3) chemical composition, (4) channel wall wettability, (5) environmental pH, (6) electrolyte concentration gradient, and (7) ion mobility. In the case of the first four features, we build these asymmetric features directly into the nanofluidic structures. With the final three, we construct different environmental conditions in the electrolyte solutions on either side of the nanochannel. The novel and well-controlled nanofluidic phenomena have become the foundation for many promising applications, and we have highlighted several representative examples. Inspired by the electrogenic cell of the electric eel, we have demonstrated a proof-of-concept nanofluidic reverse electrodialysis system (NREDS) that converts salinity gradient energy into electricity by means of net diffusion current. We have also constructed chirality analysis systems into nanofluidic architectures and monitored these sensing events as the change in the degree of ionic current rectification. Moreover, we have developed a biohybrid nanosystem, in which we reconstituted the F0F1-ATPase on a liposome-coated, solid-state nanoporous membrane. By applying a transmembrane proton concentration gradient, the biohybrid nanodevice can synthesize ATP in vitro. These findings have improved our understanding of the asymmetric ion transport phenomena in synthetic nanofluidic systems and offer innovative insights into the design of functional nanofluidic devices.

Nanochannel Device with Embedded Nanopore: a New Approach for Single-Molecule DNA Analysis and Manipulation

NASA Astrophysics Data System (ADS)

Zhang, Yuning; Reisner, Walter

2013-03-01

Nanopore and nanochannel based devices are robust methods for biomolecular sensing and single DNA manipulation. Nanopore-based DNA sensing has attractive features that make it a leading candidate as a single-molecule DNA sequencing technology. Nanochannel based extension of DNA, combined with enzymatic or denaturation-based barcoding schemes, is already a powerful approach for genome analysis. We believe that there is revolutionary potential in devices that combine nanochannels with embedded pore detectors. In particular, due to the fast translocation of a DNA molecule through a standard nanopore configuration, there is an unfavorable trade-off between signal and sequence resolution. With a combined nanochannel-nanopore device, based on embedding a pore inside a nanochannel, we can in principle gain independent control over both DNA translocation speed and sensing signal, solving the key draw-back of the standard nanopore configuration. We demonstrate that we can optically detect successful translocation of DNA from the nanochannel out through the nanopore, a possible method to 'select' a given barcode for further analysis. In particular, we show that in equilibrium DNA will not escape through an embedded sub-persistence length nanopore, suggesting that the pore could be used as a nanoscale window through which to interrogate a nanochannel extended DNA molecule. Furthermore, electrical measurements through the nanopore are performed, indicating that DNA sensing is feasible using the nanochannel-nanopore device.

Ion-beam-induced planarization, densification, and exfoliation of low-density nanoporous silica

NASA Astrophysics Data System (ADS)

Kucheyev, S. O.; Shin, S. J.

2017-09-01

Planarization of low-density nanoporous solids is challenging. Here, we demonstrate that ion bombardment to doses of ˜1015 cm-2 results in significant smoothing of silica aerogels, yielding mirror-like surfaces after metallization. The surface smoothing efficiency scales with the ion energy loss component leading to local lattice heating. Planarization is accompanied by sub-surface monolith densification, resulting in surface exfoliation with increasing ion dose. These findings have implications for the fabrication of graded-density nanofoams, aerogel-based lightweight optical components, and meso-origami.

Modeling electrochemical deposition inside nanotubes to obtain metal-semiconductor multiscale nanocables or conical nanopores.

PubMed

Lebedev, Konstantin; Mafé, Salvador; Stroeve, Pieter

2005-08-04

Nanocables with a radial metal-semiconductor heterostructure have recently been prepared by electrochemical deposition inside metal nanotubes. First, a bare nanoporous polycarbonate track-etched membrane is coated uniformly with a metal film by electroless deposition. The film forms a working electrode for further deposition of a semiconductor layer that grows radially inside the nanopore when the deposition rate is slow. We propose a new physical model for the nanocable synthesis and study the effects of the deposited species concentration, potential-dependent reaction rate, and nanopore dimensions on the electrochemical deposition. The problem involves both axial diffusion through the nanopore and radial transport to the nanopore surface, with a surface reaction rate that depends on the axial position and the time. This is so because the radial potential drop across the deposited semiconductor layer changes with the layer thickness through the nanopore. Since axially uniform nanocables are needed for most applications, we consider the relative role of reaction and axial diffusion rates on the deposition process. However, in those cases where partial, empty-core deposition should be desirable (e.g., for producing conical nanopores to be used in single nanoparticle detection), we give conditions where asymmetric geometries can be experimentally realized.

Slow DNA Transport through Nanopores in Hafnium Oxide Membranes

PubMed Central

Bell, David C.; Cohen-Karni, Tzahi; Rosenstein, Jacob K.; Wanunu, Meni

2016-01-01

We present a study of double- and single-stranded DNA transport through nanopores fabricated in ultrathin (2–7 nm thick) free-standing hafnium oxide (HfO2) membranes. The high chemical stability of ultrathin HfO2 enables long-lived experiments with <2 nm diameter pores that last several hours, in which we observe >50 000 DNA translocations with no detectable pore expansion. Mean DNA velocities are slower than velocities through comparable silicon nitride pores, providing evidence that HfO2 nanopores have favorable physicochemical interactions with nucleic acids that can be leveraged to slow down DNA in a nanopore. PMID:24083444

Nanoporous palladium anode for direct ethanol solid oxide fuel cells with nanoscale proton-conducting ceramic electrolyte

NASA Astrophysics Data System (ADS)

Li, Yong; Wong, Lai Mun; Xie, Hanlin; Wang, Shijie; Su, Pei-Chen

2017-02-01

In this work, we demonstrate the operation of micro-solid oxide fuel cells (μ-SOFCs) with nanoscale proton-conducting Y-BaZrO3 (BZY) electrolyte to avoid the fuel crossover problem for direct ethanol fuel cells (DEFCs). The μ-SOFCs are operated with the direct utilisation of ethanol vapour as a fuel and Pd as anode at the temperature range of 300-400 °C. The nanoporous Pd anode is achieved by DC sputtering at high Ar pressure of 80 mTorr. The Pd-anode/BYZ-electrolyte/Pt-cathode cell show peak power densities of 72.4 mW/cm2 using hydrogen and 15.3 mW/cm2 using ethanol at 400 °C. No obvious carbon deposition is seen from XPS analysis after fuel cell test with ethanol fuel.

Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis.

PubMed

Cao, Chan; Long, Yi-Tao

2018-02-20

Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis, we develop an integrated current measurement system and an accurate data processing method for nanopore sensing. The unique geometric structure of a biological nanopore offers a distinct advantage as a nanosensor for single-molecule sensing. The construction of the pore entrance is responsible for capturing the target molecule, while the lumen region determines the translocation process of the single molecule. Since the capture of the target molecule is predominantly diffusion-limited, it is expected that the capture ability of the nanopore toward the target analyte could be effectively enhanced by site-directed mutations of key amino acids with desirable groups. Additionally, changing the side chains inside the wall of the biological nanopore could optimize the geometry of the pore and realize an optimal interaction between the single-molecule interface and the analyte. These improvements would allow for high spatial and current resolution of nanopore sensors, which would ensure the possibility of dynamic study of single biomolecules, including their metastable conformations, charge distributions, and interactions. In the future, data analysis with powerful algorithms will make it possible to automatically and statistically extract detailed information while an analyte translocates through the pore. We conclude that these improvements could have tremendous potential applications for nanopore sensing in the near future.

Multiply Surface-Functionalized Nanoporous Carbon for Vehicular Hydrogen Storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pfeifer, Peter; Gillespie, Andrew; Stalla, David

The purpose of the project “Multiply Surface-Functionalized Nanoporous Carbon for Vehicular Hydrogen Storage” is the development of materials that store hydrogen (H 2) by adsorption in quantities and at conditions that outperform current compressed-gas H 2 storage systems for electric power generation from hydrogen fuel cells (HFCs). Prominent areas of interest for HFCs are light-duty vehicles (“hydrogen cars”) and replacement of batteries with HFC systems in a wide spectrum of applications, ranging from forklifts to unmanned areal vehicles to portable power sources. State-of-the-art compressed H 2 tanks operate at pressures between 350 and 700 bar at ambient temperature and storemore » 3-4 percent of H 2 by weight (wt%) and less than 25 grams of H 2 per liter (g/L) of tank volume. Thus, the purpose of the project is to engineer adsorbents that achieve storage capacities better than compressed H 2 at pressures less than 350 bar. Adsorption holds H 2 molecules as a high-density film on the surface of a solid at low pressure, by virtue of attractive surface-gas interactions. At a given pressure, the density of the adsorbed film is the higher the stronger the binding of the molecules to the surface is (high binding energies). Thus, critical for high storage capacities are high surface areas, high binding energies, and low void fractions (high void fractions, such as in interstitial space between adsorbent particles, “waste” storage volume by holding hydrogen as non-adsorbed gas). Coexistence of high surface area and low void fraction makes the ideal adsorbent a nanoporous monolith, with pores wide enough to hold high-density hydrogen films, narrow enough to minimize storage as non-adsorbed gas, and thin walls between pores to minimize the volume occupied by solid instead of hydrogen. A monolith can be machined to fit into a rectangular tank (low pressure, conformable tank), cylindrical tank (high pressure), or other tank shape without any waste of volume.« less

Porous Silica-Supported Solid Lipid Particles for Enhanced Solubilization of Poorly Soluble Drugs.

PubMed

Yasmin, Rokhsana; Rao, Shasha; Bremmell, Kristen E; Prestidge, Clive A

2016-07-01

Low dissolution of drugs in the intestinal fluid can limit their effectiveness in oral therapies. Here, a novel porous silica-supported solid lipid system was developed to optimize the oral delivery of drugs with limited aqueous solubility. Using lovastatin (LOV) as the model poorly water-soluble drug, two porous silica-supported solid lipid systems (SSL-A and SSL-S) were fabricated from solid lipid (glyceryl monostearate, GMS) and nanoporous silica particles Aerosil 380 (silica-A) and Syloid 244FP (silica-S) via immersion/solvent evaporation. SSL particles demonstrated significantly higher rate and extent of lipolysis in comparison with the pure solid lipid, depending on the lipid loading levels and the morphology. The highest lipid digestion was observed when silica-S was loaded with 34% (w/w) solid lipid, and differential scanning calorimeter (DSC) analysis confirmed the encapsulation of up to 2% (w/w) non-crystalline LOV in this optimal SSL-S formulation. Drug dissolution under non-digesting intestinal conditions revealed a three- to sixfold increase in dissolution efficiencies when compared to the unformulated drug and a LOV-lipid suspension. Furthermore, the SSL-S provided superior drug solubilization under simulated intestinal digesting condition in comparison with the drug-lipid suspension and drug-loaded silica. Therefore, solid lipid and nanoporous silica provides a synergistic effect on optimizing the solubilization of poorly water-soluble compound and the solid lipid-based porous carrier system provides a promising delivery approach to overcome the oral delivery challenges of poorly water-soluble drugs.

An aptamer nanopore-enabled microsensor for detection of theophylline.

PubMed

Feng, Silu; Chen, Changtian; Wang, Wei; Que, Long

2018-05-15

This paper reports an aptamer-based nanopore thin film sensor for detecting theophylline in the buffer solution and complex fluids including plant extracts and serum samples. Compared to antibody-based detection, aptamer-based detection offers many advantages such as low cost and high stability at elevated temperatures. Experiments found that this type of sensor can readily detect theophylline at a concentration as low as 0.05µM, which is much lower than the detection limit of current lab-based equipment such as liquid chromatography (LC). Experiments also found that the aptamer-based sensor has good specificity, selectivity, and reasonable reusability with a significantly improved dynamic detection range. By using the same nanopore thin film sensors as the reference sensors to further mitigate the non-specific binding effect, the theophylline in plant extracts and serum has been detected. Only a small amount (~1μL) of plant extracts or serum samples is required to measure theophylline. Its low cost and ease-of-operation make this type of sensor suitable for point-of-care application to monitor the theophylline level of patients in real time. Copyright © 2018 Elsevier B.V. All rights reserved.

A transparent electrochromic metal-insulator switching device with three-terminal transistor geometry

NASA Astrophysics Data System (ADS)

Katase, Takayoshi; Onozato, Takaki; Hirono, Misako; Mizuno, Taku; Ohta, Hiromichi

2016-05-01

Proton and hydroxyl ion play an essential role for tuning functionality of oxides because their electronic state can be controlled by modifying oxygen off-stoichiometry and/or protonation. Tungsten trioxide (WO3), a well-known electrochromic (EC) material for smart window, is a wide bandgap insulator, whereas it becomes a metallic conductor HxWO3 by protonation. Although one can utilize electrochromism together with metal-insulator (MI) switching for one device, such EC-MI switching cannot be utilized in current EC devices because of their two-terminal structure with parallel-plate configuration. Here we demonstrate a transparent EC-MI switchable device with three-terminal TFT-type structure using amorphous (a-) WO3 channel layer, which was fabricated on glass substrate at room temperature. We used water-infiltrated nano-porous glass, CAN (calcium aluminate with nano-pores), as a liquid-leakage-free solid gate insulator. At virgin state, the device was fully transparent in the visible-light region. For positive gate voltage, the active channel became dark blue, and electrical resistivity of the a-WO3 layer drastically decreased with protonation. For negative gate voltage, deprotonation occurred and the active channel returned to transparent insulator. Good cycleability of the present transparent EC-MI switching device would have potential for the development of advanced smart windows.

Adsorption-induced deformation of nanoporous materials—A review

NASA Astrophysics Data System (ADS)

Gor, Gennady Y.; Huber, Patrick; Bernstein, Noam

2017-03-01

When a solid surface accommodates guest molecules, they induce noticeable stresses to the surface and cause its strain. Nanoporous materials have high surface area and, therefore, are very sensitive to this effect called adsorption-induced deformation. In recent years, there has been significant progress in both experimental and theoretical studies of this phenomenon, driven by the development of new materials as well as advanced experimental and modeling techniques. Also, adsorption-induced deformation has been found to manifest in numerous natural and engineering processes, e.g., drying of concrete, water-actuated movement of non-living plant tissues, change of permeation of zeolite membranes, swelling of coal and shale, etc. In this review, we summarize the most recent experimental and theoretical findings on adsorption-induced deformation and present the state-of-the-art picture of thermodynamic and mechanical aspects of this phenomenon. We also reflect on the existing challenges related both to the fundamental understanding of this phenomenon and to selected applications, e.g., in sensing and actuation, and in natural gas recovery and geological CO2 sequestration.

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.

PubMed

Cretu Stancu, Mircea; van Roosmalen, Markus J; Renkens, Ivo; Nieboer, Marleen M; Middelkamp, Sjors; de Ligt, Joep; Pregno, Giulia; Giachino, Daniela; Mandrile, Giorgia; Espejo Valle-Inclan, Jose; Korzelius, Jerome; de Bruijn, Ewart; Cuppen, Edwin; Talkowski, Michael E; Marschall, Tobias; de Ridder, Jeroen; Kloosterman, Wigard P

2017-11-06

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications.

Nanoporous polymeric nanofibers based on selectively etched PS-b-PDMS block copolymers.

PubMed

Demirel, Gokcen B; Buyukserin, Fatih; Morris, Michael A; Demirel, Gokhan

2012-01-01

One-dimensional nanoporous polymeric nanofibers have been fabricated within an anodic aluminum oxide (AAO) membrane by a facile approach based on selective etching of poly(dimethylsiloxane) (PDMS) domains in polystyrene-block-poly(dimethylsiloxane) (PS-b-PDMS) block copolymers that had been formed within the AAO template. It was observed that prior to etching, the well-ordered PS-b-PDMS nanofibers are solid and do not have any porosity. The postetched PS nanofibers, on the other hand, had a highly porous structure having about 20-50 nm pore size. The nanoporous polymeric fibers were also employed as a drug carrier for the native, continuous, and pulsatile drug release using Rhodamine B (RB) as a model drug. These studies showed that enhanced drug release and tunable drug dosage can be achieved by using ultrasound irradiation. © 2011 American Chemical Society

Tailoring uniform gold nanoparticle arrays and nanoporous films for next-generation optoelectronic devices

NASA Astrophysics Data System (ADS)

Farid, Sidra; Kuljic, Rade; Poduri, Shripriya; Dutta, Mitra; Darling, Seth B.

2018-06-01

High-density arrays of gold nanodots and nanoholes on indium tin oxide (ITO)-coated glass surfaces are fabricated using a nanoporous template fabricated by the self-assembly of diblock copolymers of poly (styrene-block-methyl methacrylate) (PS-b-PMMA) structures. By balancing the interfacial interactions between the polymer blocks and the substrate using random copolymer, cylindrical block copolymer microdomains oriented perpendicular to the plane of the substrate have been obtained. Nanoporous PS films are created by selectively etching PMMA cylinders, a straightforward route to form highly ordered nanoscale porous films. Deposition of gold on the template followed by lift off and sonication leaves a highly dense array of gold nanodots. These materials can serve as templates for the vapor-liquid-solid (VLS) growth of semiconductor nanorod arrays for next generation hybrid optoelectronic applications.

Nonfaradaic nanoporous electrochemistry for conductometry at high electrolyte concentration.

PubMed

Bae, Je Hyun; Kang, Chung Mu; Choi, Hyoungseon; Kim, Beom Jin; Jang, Woohyuk; Lim, Sung Yul; Kim, Hee Chan; Chung, Taek Dong

2015-02-17

Nanoporous electrified surfaces create a unique nonfaradaic electrochemical behavior that is sensitively influenced by pore size, morphology, ionic strength, and electric field modulation. Here, we report the contributions of ion concentration and applied ac frequency to the electrode impedance through an electrical double layer overlap and ion transport along the nanopores. Nanoporous Pt with uniform pore size and geometry (L2-ePt) responded more sensitively to conductivity changes in aqueous solutions than Pt black with poor uniformity despite similar real surface areas and enabled the previously difficult quantitative conductometry measurements at high electrolyte concentrations. The nanopores of L2-ePt were more effective in reducing the electrode impedance and exhibited superior linear responses to not only flat Pt but also Pt black, leading to successful conductometric detection in ion chromatography without ion suppressors and at high ionic strengths.

Selective and reversible ammonia gas detection with nanoporous film functionalized silicon photonic micro-ring resonator.

PubMed

Yebo, Nebiyu A; Sree, Sreeprasanth Pulinthanathu; Levrau, Elisabeth; Detavernier, Christophe; Hens, Zeger; Martens, Johan A; Baets, Roel

2012-05-21

Portable, low cost and real-time gas sensors have a considerable potential in various biomedical and industrial applications. For such applications, nano-photonic gas sensors based on standard silicon fabrication technology offer attractive opportunities. Deposition of high surface area nano-porous coatings on silicon photonic sensors is a means to achieve selective, highly sensitive and multiplexed gas detection on an optical chip. Here we demonstrate selective and reversible ammonia gas detection with functionalized silicon-on-insulator optical micro-ring resonators. The micro-ring resonators are coated with acidic nano-porous aluminosilicate films for specific ammonia sensing, which results in a reversible response to NH(3)with selectivity relative to CO(2). The ammonia detection limit is estimated at about 5 ppm. The detectors reach a steady response to NH(3) within 30 and return to their base level within 60 to 90 seconds. The work opens perspectives on development of nano-photonic sensors for real-time, non-invasive, low cost and light weight biomedical and industrial sensing applications.

Next Generation Epigenetic Detection Technique: Identifying Methylated DNA using Graphene Nanopore

NASA Astrophysics Data System (ADS)

Ahmed, Towfiq; Haraldsen, Jason T.; Zhu, Jian-Xin; Balatsky, A. V.

2014-03-01

DNA methylation plays a pivotal role in the genetic evolution of both embryonic and adult cells.Unusual methylation on CPG islands are identified as the prime causes for silencing the tumor suppressant genes. Early detection of such methylation can diagnose the potentially harmful oncogenic evolution of cells, and provide a promising guideline for cancer prevention.We propose a detection technique and calculate the transport current through punctured graphene as the cytosine and methylated cytosine translocate through the nanopore. We also calculate the transport properties for uracil and cyano-cytosine to compare. Our calculations of transmission, current and tunneling conductance show distinct signatures in their spectrum for each molecular type. Our theoretical study provides a next generation detection technique for identifying DNA methylation using graphene based nanopore device. This work was supported by U.S. DOE Office of Basic Energy Sciences, and by VR 621-2012-2983 and ERC 321031-DM. This work was, in part, supported by the Center for Integrated Nanotechnologies, a U.S. DOE BES user facility.

Nanoporous Monolithic Microsphere Arrays Have Anti-Adhesive Properties Independent of Humidity

PubMed Central

Eichler-Volf, Anna; Xue, Longjian; Kovalev, Alexander; Gorb, Elena V.; Gorb, Stanislav N.; Steinhart, Martin

2016-01-01

Bioinspired artificial surfaces with tailored adhesive properties have attracted significant interest. While fibrillar adhesive pads mimicking gecko feet are optimized for strong reversible adhesion, monolithic microsphere arrays mimicking the slippery zone of the pitchers of carnivorous plants of the genus Nepenthes show anti-adhesive properties even against tacky counterpart surfaces. In contrast to the influence of topography, the influence of relative humidity (RH) on adhesion has been widely neglected. Some previous works deal with the influence of RH on the adhesive performance of fibrillar adhesive pads. Commonly, humidity-induced softening of the fibrils enhances adhesion. However, little is known on the influence of RH on solid anti-adhesive surfaces. We prepared polymeric nanoporous monolithic microsphere arrays (NMMAs) with microsphere diameters of a few 10 µm to test their anti-adhesive properties at RHs of 2% and 90%. Despite the presence of continuous nanopore systems through which the inner nanopore walls were accessible to humid air, the topography-induced anti-adhesive properties of NMMAs on tacky counterpart surfaces were retained even at RH = 90%. This RH-independent robustness of the anti-adhesive properties of NMMAs significantly contrasts the adhesion enhancement by humidity-induced softening on nanoporous fibrillar adhesive pads made of the same material. PMID:28773497

Electroactive Nanoporous Metal Oxides and Chalcogenides by Chemical Design

PubMed Central

2017-01-01

The archetypal silica- and aluminosilicate-based zeolite-type materials are renowned for wide-ranging applications in heterogeneous catalysis, gas-separation and ion-exchange. Their compositional space can be expanded to include nanoporous metal chalcogenides, exemplified by germanium and tin sulfides and selenides. By comparison with the properties of bulk metal dichalcogenides and their 2D derivatives, these open-framework analogues may be viewed as three-dimensional semiconductors filled with nanometer voids. Applications exist in a range of molecule size and shape discriminating devices. However, what is the electronic structure of nanoporous metal chalcogenides? Herein, materials modeling is used to describe the properties of a homologous series of nanoporous metal chalcogenides denoted np-MX2, where M = Si, Ge, Sn, Pb, and X = O, S, Se, Te, with Sodalite, LTA and aluminum chromium phosphate-1 structure types. Depending on the choice of metal and anion their properties can be tuned from insulators to semiconductors to metals with additional modification achieved through doping, solid solutions, and inclusion (with fullerene, quantum dots, and hole transport materials). These systems form the basis of a new branch of semiconductor nanochemistry in three dimensions. PMID:28572706

Synthesis of Hierarchical Nanoporous Microstructures via the Kirkendall Effect in Chemical Reduction Process

NASA Astrophysics Data System (ADS)

Gao, Ling; Pang, Chao; He, Dafang; Shen, Liming; Gupta, Arunava; Bao, Ningzhong

2015-11-01

A series of novel hierarchical nanoporous microstructures have been synthesized through one-step chemical reduction of micron size Cu2O and Co3O4 particles. By controlling the reduction time, non-porous Cu2O microcubes sequentially transform to nanoporous Cu/Cu2O/Cu dented cubic composites and hollow eightling-like Cu microparticles. The mechanism involved in the complex structural evolution is explained based on oxygen diffusion and Kirkendall effect. The nanoporous Cu/Cu2O/Cu dented cubic composites exhibit superior electrochemical performance as compared to solid Cu2O microcubes. The reduction of nonporous Co3O4 also exhibits a uniform sequential reduction process from nonporous Co3O4 to porous Co3O4/CoO composites, porous CoO, porous CoO/Co composites, and porous foam-like Co particles. Nanoscale channels originate from the particle surface and eventually develop inside the entire product, resulting in porous foam-like Co microparticles. The Kirkendall effect is believed to facilitate the formation of porous structures in both processes.

Mechanisms of water infiltration into conical hydrophobic nanopores.

PubMed

Liu, Ling; Zhao, Jianbing; Yin, Chun-Yang; Culligan, Patricia J; Chen, Xi

2009-08-14

Fluid channels with inclined solid walls (e.g. cone- and slit-shaped pores) have wide and promising applications in micro- and nano-engineering and science. In this paper, we use molecular dynamics (MD) simulations to investigate the mechanisms of water infiltration (adsorption) into cone-shaped nanopores made of a hydrophobic graphene sheet. When the apex angle is relatively small, an external pressure is required to initiate infiltration and the pressure should keep increasing in order to further advance the water front inside the nanopore. By enlarging the apex angle, the pressure required for sustaining infiltration can be effectively lowered. When the apex angle is sufficiently large, under ambient condition water can spontaneously infiltrate to a certain depth of the nanopore, after which an external pressure is still required to infiltrate more water molecules. The unusual involvement of both spontaneous and pressure-assisted infiltration mechanisms in the case of blunt nanocones, as well as other unique nanofluid characteristics, is explained by the Young's relation enriched with the size effects of surface tension and contact angle in the nanoscale confinement.

Nanochannel Device with Embedded Nanopore: a New Approach for Single-Molecule DNA Analysis and Manipulation

NASA Astrophysics Data System (ADS)

Zhang, Yuning; Reisner, Walter

2012-02-01

Nanopore and nanochannel based devices are robust methods for biomolecular sensing and single DNA manipulation. Nanopore-based DNA sensing has attractive features that make it a leading candidate as a single-molecule DNA sequencing technology. Nanochannel based extension of DNA, combined with enzymatic or denaturation-based barcoding schemes, is already a powerful approach for genome analysis. We believe that there is revolutionary potential in devices that combine nanochannels with nanpore detectors. In particular, due to the fast translocation of a DNA molecule through a standard nanopore configuration, there is an unfavorable trade-off between signal and sequence resolution. With a combined nanochannel-nanopore device, based on embedding a nanopore inside a nanochannel, we can in principle gain independent control over both DNA translocation speed and sensing signal, solving the key draw-back of the standard nanopore configuration. We will discuss our recent progress on device fabrication and characterization. In particular, we demonstrate that we can detect - using fluorescent microscopy - successful translocation of DNA from the nanochannel out through the nanopore, a possible method to 'select' a given barcode for further analysis. In particular, we show that in equilibrium DNA will not escape through an embedded sub-persistence length nanopore, suggesting that the embedded pore could be used as a nanoscale window through which to interrogate a nanochannel extended DNA molecule.

Real-time detection of BRAF V600E mutation from archival hairy cell leukemia FFPE tissue by nanopore sequencing.

PubMed

Vacca, Davide; Cancila, Valeria; Gulino, Alessandro; Lo Bosco, Giosuè; Belmonte, Beatrice; Di Napoli, Arianna; Florena, Ada Maria; Tripodo, Claudio; Arancio, Walter

2018-02-01

The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirable, but their adoption for molecular assays is hurdled by the high degree of fragmentation and by the chemical-induced mutations stemming from the fixation protocols. In order to investigate the suitability of MinION sequencing on formalin-fixed paraffin-embedded samples, the presence and frequency of BRAF c.1799T > A mutation was investigated in two archival tissue specimens of Hairy cell leukemia and Hairy cell leukemia Variant. Despite the poor quality of the starting DNA, BRAF mutation was successfully detected in the Hairy cell leukemia sample with around 50% of the reads obtained within 2 h of the sequencing start. Notably, the mutational burden of the Hairy cell leukemia sample as derived from nanopore sequencing proved to be comparable to a sensitive method for the detection of point mutations, namely the Digital PCR, using a validated assay. Nanopore sequencing can be adopted for targeted sequencing of genetic lesions on critical DNA samples such as those extracted from archival routine formalin-fixed paraffin-embedded samples. This result let speculating about the possibility that the nanopore sequencing could be trustably adopted for the real-time targeted sequencing of genetic lesions. Our report opens the window for the adoption of nanopore sequencing in molecular pathology for research and diagnostics.

Nanopore with Transverse Nanoelectrodes for Electrical Characterization and Sequencing of DNA

PubMed Central

Gierhart, Brian C.; Howitt, David G.; Chen, Shiahn J.; Zhu, Zhineng; Kotecki, David E.; Smith, Rosemary L.; Collins, Scott D.

2009-01-01

A DNA sequencing device which integrates transverse conducting electrodes for the measurement of electrode currents during DNA translocation through a nanopore has been nanofabricated and characterized. A focused electron beam (FEB) milling technique, capable of creating features on the order of 1 nm in diameter, was used to create the nanopore. The device was characterized electrically using gold nanoparticles as an artificial analyte with both DC and AC measurement methods. Single nanoparticle/electrode interaction events were recorded. A low-noise, high-speed transimpedance current amplifier for the detection of nano to picoampere currents at microsecond time scales was designed, fabricated and tested for future integration with the nanopore device. PMID:19584949

Nanopore with Transverse Nanoelectrodes for Electrical Characterization and Sequencing of DNA.

PubMed

Gierhart, Brian C; Howitt, David G; Chen, Shiahn J; Zhu, Zhineng; Kotecki, David E; Smith, Rosemary L; Collins, Scott D

2008-06-16

A DNA sequencing device which integrates transverse conducting electrodes for the measurement of electrode currents during DNA translocation through a nanopore has been nanofabricated and characterized. A focused electron beam (FEB) milling technique, capable of creating features on the order of 1 nm in diameter, was used to create the nanopore. The device was characterized electrically using gold nanoparticles as an artificial analyte with both DC and AC measurement methods. Single nanoparticle/electrode interaction events were recorded. A low-noise, high-speed transimpedance current amplifier for the detection of nano to picoampere currents at microsecond time scales was designed, fabricated and tested for future integration with the nanopore device.

Some properties of electrolyte solutions in nanoconfinement revealed by the measurement of transient filtration potential after pressure switch off.

PubMed

Yaroshchuk, Andriy E; Boiko, Yuriy P; Makovetskiy, Alexandre L

2005-08-16

We have demonstrated that with a composite nanoporous ceramic membrane in a batch membrane cell it is technically feasible to switch off the trans-membrane hydrostatic pressure difference within tens of milliseconds. That enabled us to resolve practically the whole time evolution of transient filtration potential. Measurements of the latter have been complemented by measurements of steady-state salt rejection by the composite membrane and by measurements of the streaming potential and hydraulic permeability of membrane supports available separately. A theory has been developed in terms of network thermodynamics for the electrical response of a bilayer membrane to a pressure perturbation. In combination with the results of salt rejection measurements, from the time transients of filtration potential we could determine the ion transport numbers within the nanoporous layer. Besides that, from the dependence of steady-state salt rejection on the trans-membrane volume flow, we have determined the diffusion permeability of and the salt reflection coefficient in the nanoporous layer. This has enabled us to estimate the contributions of Donnan and non-Donnan mechanisms to the rejection of ions by the nanoporous membrane used in this study. It has been unexpectedly found that the Donnan exclusion played only a secondary role. Our hypothesis is that the non-Donnan exclusion of ions from the nanopores might be caused by changes in water properties in nanoconfinement. Proceeding from the results of steady-state filtration experiments with the membrane and the support, we also concluded that the nanoporous layer was imperfection-free and had a quite narrow pore size distribution, which made it a suitable object for fundamental studies of ion transfer mechanisms in nanopores.

Applications of biological pores in nanomedicine, sensing, and nanoelectronics

PubMed Central

Majd, Sheereen; Yusko, Erik C; Billeh, Yazan N; Macrae, Michael X; Yang, Jerry; Mayer, Michael

2011-01-01

Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated – often regulated – functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics. PMID:20561776

Investigation of nanoporous platinum thin films fabricated by reactive sputtering: Application as micro-SOFC electrode

NASA Astrophysics Data System (ADS)

Jung, WooChul; Kim, Jae Jin; Tuller, Harry L.

2015-02-01

Highly porous Pt thin films, with nano-scale porosity, were fabricated by reactive sputtering. The strategy involved deposition of thin film PtOx at room temperature, followed by the subsequent decomposition of the oxide by rapid heat treatment. The resulting films exhibited percolating Pt networks infiltrated with interconnected nanosized pores, critical for superior solid oxide fuel cell cathode performance. This approach is particularly attractive for micro-fabricated solid oxide fuel cells, since it enables fabrication of the entire cell stack (anode/electrolyte/cathode) within the sputtering chamber, without breaking vacuum. In this work, the morphological, crystallographic and chemical properties of the porous electrode were systematically varied by control of deposition conditions. Oxygen reduction reaction kinetics were investigated by means of electrochemical impedance spectroscopy, demonstrating the critical role of nano-pores in achieving satisfactory micro-SOFC cathode performance.

Quantitative secondary electron detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agrawal, Jyoti; Joy, David C.; Nayak, Subuhadarshi

Quantitative Secondary Electron Detection (QSED) using the array of solid state devices (SSD) based electron-counters enable critical dimension metrology measurements in materials such as semiconductors, nanomaterials, and biological samples (FIG. 3). Methods and devices effect a quantitative detection of secondary electrons with the array of solid state detectors comprising a number of solid state detectors. An array senses the number of secondary electrons with a plurality of solid state detectors, counting the number of secondary electrons with a time to digital converter circuit in counter mode.

Asymmetric Nanopore Electrode-Based Amplification for Electron Transfer Imaging in Live Cells.

PubMed

Ying, Yi-Lun; Hu, Yong-Xu; Gao, Rui; Yu, Ru-Jia; Gu, Zhen; Lee, Luke P; Long, Yi-Tao

2018-04-25

Capturing real-time electron transfer, enzyme activity, molecular dynamics, and biochemical messengers in living cells is essential for understanding the signaling pathways and cellular communications. However, there is no generalizable method for characterizing a broad range of redox-active species in a single living cell at the resolution of cellular compartments. Although nanoelectrodes have been applied in the intracellular detection of redox-active species, the fabrication of nanoelectrodes to maximize the signal-to-noise ratio of the probe remains challenging because of the stringent requirements of 3D fabrication. Here, we report an asymmetric nanopore electrode-based amplification mechanism for the real-time monitoring of NADH in a living cell. We used a two-step 3D fabrication process to develop a modified asymmetric nanopore electrode with a diameter down to 90 nm, which allowed for the detection of redox metabolism in living cells. Taking advantage of the asymmetric geometry, the above 90% potential drop at the two terminals of the nanopore electrode converts the faradaic current response into an easily distinguishable bubble-induced transient ionic current pattern. Therefore, the current signal was amplified by at least 3 orders of magnitude, which was dynamically linked to the presence of trace redox-active species. Compared to traditional wire electrodes, this wireless asymmetric nanopore electrode exhibits a high signal-to-noise ratio by increasing the current resolution from nanoamperes to picoamperes. The asymmetric nanopore electrode achieves the highly sensitive and selective probing of NADH concentrations as low as 1 pM. Moreover, it enables the real-time nanopore monitoring of the respiration chain (i.e., NADH) in a living cell and the evaluation of the effects of anticancer drugs in an MCF-7 cell. We believe that this integrated wireless asymmetric nanopore electrode provides promising building blocks for the future imaging of electron transfer dynamics in live cells.

Theory for polymer analysis using nanopore-based single-molecule mass spectrometry

PubMed Central

Reiner, Joseph E.; Kasianowicz, John J.; Nablo, Brian J.; Robertson, Joseph W. F.

2010-01-01

Nanometer-scale pores have demonstrated potential for the electrical detection, quantification, and characterization of molecules for biomedical applications and the chemical analysis of polymers. Despite extensive research in the nanopore sensing field, there is a paucity of theoretical models that incorporate the interactions between chemicals (i.e., solute, solvent, analyte, and nanopore). Here, we develop a model that simultaneously describes both the current blockade depth and residence times caused by individual poly(ethylene glycol) (PEG) molecules in a single α-hemolysin ion channel. Modeling polymer-cation binding leads to a description of two significant effects: a reduction in the mobile cation concentration inside the pore and an increase in the affinity between the polymer and the pore. The model was used to estimate the free energy of formation for K+-PEG inside the nanopore (≈-49.7 meV) and the free energy of PEG partitioning into the nanopore (≈0.76 meV per ethylene glycol monomer). The results suggest that rational, physical models for the analysis of analyte-nanopore interactions will develop the full potential of nanopore-based sensing for chemical and biological applications. PMID:20566890

EDITORIAL: Nanotechnological selection Nanotechnological selection

NASA Astrophysics Data System (ADS)

Demming, Anna

2013-01-01

At the nanoscale measures can move from a mass-scale analogue calibration to counters of discrete units. The shift redefines the possible levels of control that can be achieved in a system if adequate selectivity can be imposed. As an example as ionic substances pass through nanoscale pores, the quantity of ions is low enough that the pore can contain either negative or positive ions. Yet precise control over this selectivity still raises difficulties. In this issue researchers address the challenge of how to regulate the ionic selectivity of negative and positive charges with the use of an external charge. The approach may be useful for controlling the behaviour, properties and chemical composition of liquids and has possible technical applications for nanofluidic field effect transistors [1]. Selectivity is a critical advantage in the administration of drugs. Nanoparticles functionalized with targeting moieties can allow delivery of anti-cancer drugs to tumour cells, whilst avoiding healthy cells and hence reducing some of the debilitating side effects of cancer treatments [2]. Researchers in Belarus and the US developed a new theranostic approach—combining therapy and diagnosis—to support the evident benefits of cellular selectivity that can be achieved when nanoparticles are applied in medicine [3]. Their process uses nanobubbles of photothermal vapour, referred to as plasmonic nanobubbles, generated by plasmonic excitations in gold nanoparticles conjugated to diagnosis-specific antibodies. The intracellular plasmonic nanobubbles are controlled by laser fluence so that the response can be tuned in individual living cells. Lower fluence allows non-invasive high-sensitive imaging for diagnosis and higher fluence can disrupt the cellular membrane for treatments. The selective response of carbon nanotubes to different gases has leant them to be used within various different types of sensors, as summarized in a review by researchers at the University of California, Riverside [4]. Mangu et al in the US have developed highly sensitive and selective room temperature gas sensors made from composites of multiwalled carbon nanotubes and polymers [5]. They report sensitivities as high as 28% when exposed to 100 ppm of NH3 and 29.8% to 100 ppm of NO2. Nanopore structures are also showing increasing promise for sensing and biophysical characterization applications, in particular DNA [6]. An applied potential drives negatively charged DNA molecules through nanopores in a membrane and gives rise to current blockage pulses that are characteristic of specific analytes. Solid-state nanopore structures hold advantages over biological pores, such as those in α-haemolysin protein, as they are more resilient to experimental conditions, and ideally should also allow control of the nanopore diameter, channel length and surface composition. Asghar and colleagues have now reported a method that enables just that, 'a rapid solid-state nanopore fabrication and controlled pore shrinking process which does provide simultaneous in situ control of surface properties' [7]. In addition, they demonstrate the viability of the approach for single molecule sensor applications using double-stranded DNA. In this issue, researchers in China report on a different approach which allows control over the transport of ionic fluids through nanopore-type structures. They describe the rapid field effect control of electrical conductance in single nanotube nanofluidic transistors [1]. Rather than seeking to control the charge of thenanotube inner surface, Gong and colleagues control polarity switching based on negative and positive ion selectivity using an external charge. 'The polarity of the nanotube can be reversed and tuned by the external field, which could find interesting applications in the field of ion separation and energy conversion', they explain, adding that the system may also find a use as a voltage sensor through the detection of the type of ions across the channel. The aim of achieving selectivity encompasses a huge range of fields in nanotechnology research, from sensing and medicine to nanoelectronics and self-assembly. As our understanding of how nanosystems behave deepens, so too does the hunger to improve our capabilities, allowing greater precision and control in manipulating these systems. Selectivity is far from trivial when shrinking to systems of nanoscale dimensions, but the range of opportunities it brings just keeps on growing. References [1] Gong X, Li J, Guo C, Xu K and Hui Y 2012 Molecular switch for tuning ions across nanopores by an external electric field Nanotechnology 24 025502 [2] Brannon-Peppas L and Blanchette J O 2004 Nanoparticle and targeted systems for cancer therapy Adv. Drug Deliv. Rev 56 1649-59 [3] Lukianova-Hleb E Y, Hanna E Y, Hafner J H and Lapotko D O 2010 Tunable plasmonic nanobubbles for cell theranostics Nanotechnology 21 085102 [4] Zhang T, Mubeen S, Myung N V and Deshusses M A 2008 Recent progress in carbon nanotube-based gas sensors Nanotechnology 19 332001 [5] Mangu R, Rajaputra S and Singh V P 2011 MWCNT-polymer composites as highly sensitive and selective room temperature gas sensors Nanotechnology 22 215502 [6]Meller A, Nivon L, Brandin E, Golovchenko J and Branton D 2000 Rapid nanopore discrimination between single polynucleotide molecules Proc. Natl Acad. Sci. 97 1079-84 [7] Asghar W, Ilyas A, Deshmukh R R, Sumitsawan S, Timmons R B and Iqbal S M 2011 Pulsed plasma polymerization for controlling shrinkage and surface composition of nanopores Nanotechnology 22 285304

Long cycle life microporous spherical carbon anodes for sodium-ion batteries derived from furfuryl alcohol

DOE PAGES

Zhou, Dehua; Peer, Maryam; Yang, Zhenzhen; ...

2016-04-11

Spherical micron-sized carbon powders were synthesized from feedstock furfuryl alcohol and tested as anodes in sodium ion batteries (SIBs). A long cycle life of 1000 cycles is achievable with this carbon at C rate (3–4 mg cm –2 loading and i = 200 mA g –1) yielding a steady capacity of ca. 115 mA h g –1. Furthermore, the results from solid-state 23Na MAS NMR analyses of cycled electrodes indicate no correlation in voltage profiles with sodium site nature (graphene or nanopores), which is a new observation in SIB carbon anodes.

Phase-field based Multiscale Modeling of Heterogeneous Solid Electrolytes: Applications to Nanoporous Li 3 PS 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Jia-Mian; Wang, Bo; Ji, Yanzhou

Modeling the effective ion conductivities of heterogeneous solid electrolytes typically involves the use of a computer-generated microstructure consisting of randomly or uniformly oriented fillers in a matrix. But, the structural features of the filler/matrix interface, which critically determine the interface ion conductivity and the microstructure morphology, have not been considered during the microstructure generation. In using nanoporous β-Li 3PS 4 electrolyte as an example, we develop a phase-field model that enables generating nanoporous microstructures of different porosities and connectivity patterns based on the depth and the energy of the surface (pore/electrolyte interface), both of which are predicted through density functionalmore » theory (DFT) calculations. Room-temperature effective ion conductivities of the generated microstructures are then calculated numerically, using DFT-estimated surface Li-ion conductivity (3.14×10 -3 S/cm) and experimentally measured bulk Li-ion conductivity (8.93×10 -7 S/cm) of β-Li 3PS 4 as the inputs. We also use the generated microstructures to inform effective medium theories to rapidly predict the effective ion conductivity via analytical calculations. Furthemore, when porosity approaches the percolation threshold, both the numerical and analytical methods predict a significantly enhanced Li-ion conductivity (1.74×10 -4 S/cm) that is in good agreement with experimental data (1.64×10 -4 S/cm). The present phase-field based multiscale model is generally applicable to predict both the microstructure patterns and the effective properties of heterogeneous solid electrolytes.« less

Phase-field based Multiscale Modeling of Heterogeneous Solid Electrolytes: Applications to Nanoporous Li 3 PS 4

DOE PAGES

Hu, Jia-Mian; Wang, Bo; Ji, Yanzhou; ...

2017-09-07

Modeling the effective ion conductivities of heterogeneous solid electrolytes typically involves the use of a computer-generated microstructure consisting of randomly or uniformly oriented fillers in a matrix. But, the structural features of the filler/matrix interface, which critically determine the interface ion conductivity and the microstructure morphology, have not been considered during the microstructure generation. In using nanoporous β-Li 3PS 4 electrolyte as an example, we develop a phase-field model that enables generating nanoporous microstructures of different porosities and connectivity patterns based on the depth and the energy of the surface (pore/electrolyte interface), both of which are predicted through density functionalmore » theory (DFT) calculations. Room-temperature effective ion conductivities of the generated microstructures are then calculated numerically, using DFT-estimated surface Li-ion conductivity (3.14×10 -3 S/cm) and experimentally measured bulk Li-ion conductivity (8.93×10 -7 S/cm) of β-Li 3PS 4 as the inputs. We also use the generated microstructures to inform effective medium theories to rapidly predict the effective ion conductivity via analytical calculations. Furthemore, when porosity approaches the percolation threshold, both the numerical and analytical methods predict a significantly enhanced Li-ion conductivity (1.74×10 -4 S/cm) that is in good agreement with experimental data (1.64×10 -4 S/cm). The present phase-field based multiscale model is generally applicable to predict both the microstructure patterns and the effective properties of heterogeneous solid electrolytes.« less

Label-Free Nanopore Biosensor for Rapid and Highly Sensitive Cocaine Detection in Complex Biological Fluids.

PubMed

Rauf, Sana; Zhang, Ling; Ali, Asghar; Liu, Yang; Li, Jinghong

2017-02-24

Detection of very low amounts of illicit drugs such as cocaine in clinical fluids like serum continues to be important for many areas in the fight against drug trafficking. Herein, we constructed a label-free nanopore biosensor for rapid and highly sensitive detection of cocaine in human serum and saliva samples based on target-induced strand release strategy. In this bioassay, an aptamer for cocaine was prehybridized with a short complementary DNA. Owing to cocaine specific binding with aptamer, the short DNA strand was displaced from aptamer and translocation of this output DNA through α-hemolysin nanopore generated distinct spike-like current blockages. When plotted in double-logarithmic scale, a linear relationship between target cocaine concentration and output DNA event frequency was obtained in a wide concentration range from 50 nM to 100 μM of cocaine, with the limit of detection down to 50 nM. In addition, this aptamer-based sensor method was successfully applied for cocaine detection in complex biological fluids like human saliva and serum samples with great selectivity. Simple preparation, low cost, rapid, label-free, and real sample detection are the motivating factors for practical application of the proposed biosensor.

The use of nanomaterials for mass spectrometry can be uplifting for analyte detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, J.; Lipson, R. H.

2014-03-31

Surface-Assisted Laser Desorption Ionization (SALDI) involves desorbing and ionizing analyte molecules from a nanoporous substrate by laser irradiation for detection in a mass spectrometer. In this work experiments were designed to better understand the mechanisms governing desorption and ionization for Desorption Ionization On Silicon (DIOS), a variant of SALDI which uses porous silicon (pSi) as a substrate. Experiments are also reported for other nanoporous semiconducting materials (WO{sub 3}, TiO{sub 2}) which exhibit very similar behaviors; specifically, that both protonated analyte ions and analyte radical cations can be generated with relative intensities that depend on the position of the incident lasermore » focus relative to substrate surface. While thermal desorption appears to be important, preliminary evidence suggests that the ionization mechanism leading to protonated analytes involves in part electrons and holes formed when photoexciting the substrate above its electronic band gap, and the presence of defect states within the band gap. Radical cation formation appears to be driven in part by electron transfer due to the large electron affinity of each substrate used in this work.« less

Photoluminescence emission of nanoporous anodic aluminum oxide films prepared in phosphoric acid

PubMed Central

2012-01-01

The photoluminescence emission of nanoporous anodic aluminum oxide films formed in phosphoric acid is studied in order to explore their defect-based subband electronic structure. Different excitation wavelengths are used to identify most of the details of the subband states. The films are produced under different anodizing conditions to optimize their emission in the visible range. Scanning electron microscopy investigations confirm pore formation in the produced layers. Gaussian analysis of the emission data indicates that subband states change with anodizing parameters, and various point defects can be formed both in the bulk and on the surface of these nanoporous layers during anodizing. PMID:23272786

Silver-halide photographic materials based on nanoporous glasses

NASA Astrophysics Data System (ADS)

Andreeva, O. V.; Obyknovennaya, I. E.; Gavrilyuk, E. R.; Paramonov, A. A.; Kushnarenko, A. P.

2005-12-01

This paper discusses the results of an investigation of the recording of composite nanoporous photographic materials with a photosensitive composite made from silver halide in gelatin, developed and created at S. I. Vavilov State Optical Institute.

DETECTION OF TWO ISOMERIC BINDING CONFIGURATIONS IN A PROTEIN-APTAMER COMPLEX WITH A BIOLOGICAL NANOPORE

PubMed Central

Van Meervelt, Veerle; Soskine, Misha; Maglia, Giovanni

2015-01-01

Protein-DNA interactions play critical roles in biological systems, and they often involve complex mechanisms and dynamics that are not easily measured by ensemble experiments. Recently, we have shown that folded proteins can be internalised inside ClyA nanopores and studied by ionic current recordings at the single-molecule level. Here, we use ClyA nanopores to sample the interaction between the G-quadruplex fold of the thrombin binding aptamer (TBA) and human thrombin (HT). Surprisingly, the internalisation of the HT:TBA complex inside the nanopore induced two types of current blockades with distinguished residual current and lifetime. Using single nucleobase substitutions to TBA we showed that these two types of blockades originate from TBA binding to thrombin with two isomeric orientations. Voltage dependencies and the use of ClyA nanopores with two different diameters allowed assessing the effect of the applied potential and confinement, and revealed that the two binding configurations of TBA to HT display different lifetimes. These results show that the ClyA nanopores might provide a new approach to probe conformational heterogeneity in protein:DNA interactions. PMID:25493908

Nanowire-nanopore transistor sensor for DNA detection during translocation

NASA Astrophysics Data System (ADS)

Xie, Ping; Xiong, Qihua; Fang, Ying; Qing, Quan; Lieber, Charles

2011-03-01

Nanopore sequencing, as a promising low cost, high throughput sequencing technique, has been proposed more than a decade ago. Due to the incompatibility between small ionic current signal and fast translocation speed and the technical difficulties on large scale integration of nanopore for direct ionic current sequencing, alternative methods rely on integrated DNA sensors have been proposed, such as using capacitive coupling or tunnelling current etc. But none of them have been experimentally demonstrated yet. Here we show that for the first time an amplified sensor signal has been experimentally recorded from a nanowire-nanopore field effect transistor sensor during DNA translocation. Independent multi-channel recording was also demonstrated for the first time. Our results suggest that the signal is from highly localized potential change caused by DNA translocation in none-balanced buffer condition. Given this method may produce larger signal for smaller nanopores, we hope our experiment can be a starting point for a new generation of nanopore sequencing devices with larger signal, higher bandwidth and large-scale multiplexing capability and finally realize the ultimate goal of low cost high throughput sequencing.

Building solids inside nano-space: from confined amorphous through confined solvate to confined 'metastable' polymorph.

PubMed

Nartowski, K P; Tedder, J; Braun, D E; Fábián, L; Khimyak, Y Z

2015-10-14

The nanocrystallisation of complex molecules inside mesoporous hosts and control over the resulting structure is a significant challenge. To date the largest organic molecule crystallised inside the nano-pores is a known pharmaceutical intermediate - ROY (259.3 g mol(-1)). In this work we demonstrate smart manipulation of the phase of a larger confined pharmaceutical - indomethacin (IMC, 357.8 g mol(-1)), a substance with known conformational flexibility and complex polymorphic behaviour. We show the detailed structural analysis and the control of solid state transformations of encapsulated molecules inside the pores of mesoscopic cellular foam (MCF, pore size ca. 29 nm) and controlled pore glass (CPG, pore size ca. 55 nm). Starting from confined amorphous IMC we drive crystallisation into a confined methanol solvate, which upon vacuum drying leads to the stabilised rare form V of IMC inside the MCF host. In contrast to the pure form, encapsulated form V does not transform into a more stable polymorph upon heating. The size of the constraining pores and the drug concentration within the pores determine whether the amorphous state of the drug is stabilised or it recrystallises into confined nanocrystals. The work presents, in a critical manner, an application of complementary techniques (DSC, PXRD, solid-state NMR, N2 adsorption) to confirm unambiguously the phase transitions under confinement and offers a comprehensive strategy towards the formation and control of nano-crystalline encapsulated organic solids.

DNA Physical Mapping via the Controlled Translocation of Single Molecules through a 5-10nm Silicon Nitride Nanopore

NASA Astrophysics Data System (ADS)

Stein, Derek; Reisner, Walter; Jiang, Zhijun; Hagerty, Nick; Wood, Charles; Chan, Jason

2009-03-01

The ability to map the binding position of sequence-specific markers, including transcription-factors, protein-nucleic acids (PNAs) or deactivated restriction enzymes, along a single DNA molecule in a nanofluidic device would be of key importance for the life-sciences. Such markers could give an indication of the active genes at particular stage in a cell's transcriptional cycle, pinpoint the location of mutations or even provide a DNA barcode that could aid in genomics applications. We have developed a setup consisting of a 5-10 nm nanopore in a 20nm thick silicon nitride film coupled to an optical tweezer setup. The translocation of DNA across the nanopore can be detected via blockades in the electrical current through the pore. By anchoring one end of the translocating DNA to an optically trapped microsphere, we hope to stretch out the molecule in the nanopore and control the translocation speed, enabling us to slowly scan across the genome and detect changes in the baseline current due to the presence of bound markers.

Hybrid Circuits with Nanofluidic Diodes and Load Capacitors

NASA Astrophysics Data System (ADS)

Ramirez, P.; Garcia-Morales, V.; Gomez, V.; Ali, M.; Nasir, S.; Ensinger, W.; Mafe, S.

2017-06-01

The chemical and physical input signals characteristic of micro- and nanofluidic devices operating in ionic solutions should eventually be translated into output electric currents and potentials that are monitored with solid-state components. This crucial step requires the design of hybrid circuits showing robust electrical coupling between ionic solutions and electronic elements. We study experimentally and theoretically the connectivity of the nanofluidic diodes in single-pore and multipore membranes with conventional capacitor systems for the cases of constant, periodic, and white-noise input potentials. The experiments demonstrate the reliable operation of these hybrid circuits over a wide range of membrane resistances, electrical capacitances, and solution p H values. The model simulations are based on empirical equations that have a solid physical basis and provide a convenient description of the electrical circuit operation. The results should contribute to advance signal transduction and processing using nanopore-based biosensors and bioelectronic interfaces.

Biomimetic Mineralization of Gold Nanoclusters as Multifunctional Thin Films for Glass Nanopore Modification, Characterization, and Sensing.

PubMed

Cao, Sumei; Ding, Shushu; Liu, Yingzi; Zhu, Anwei; Shi, Guoyue

2017-08-01

Hurdles of nanopore modification and characterization restrain the development of glass capillary-based nanopore sensing platforms. In this article, a simple but effective biomimetic mineralization method was developed to decorate glass nanopore with a thin film of bovine serum albumin-protected Au nanocluster (BSA-Au NC). The BSA-Au NC film emitted a strong red fluorescence whereby nondestructive characterization of Au film decorated at the inner surface of glass nanopore can be facilely achieved by a fluorescence microscopy. Besides, the BSA molecules played dual roles in the fabrication of functionalized Au thin film in glass nanopore: they not only directed the synthesis of fluorescent Au thin film but also provided binding sites for recognition, thus achieving synthesis-modification integration. This occurred due to the ionized carboxyl groups (-COO - ) of a BSA coating layer on Au NCs which can interacted with arginine (Arg) via guanidinium groups. The added Arg selectively led to the change in the charge and ionic current of BSA-Au NC film-decorated glass nanopore. Such ionic current responses can be used for quantifying Arg with a detection limit down to 1 fM, which was more sensitive than that of previous sensing systems. Together, the designed method exhibited great promise in providing a facile and controllable solution for glass nanopore modification, characterization, and sensing.

Surface effects on ionic Coulomb blockade in nanometer-size pores

NASA Astrophysics Data System (ADS)

Tanaka, Hiroya; Iizuka, Hideo; Pershin, Yuriy V.; Di Ventra, Massimiliano

2018-01-01

Ionic Coulomb blockade in nanopores is a phenomenon that shares some similarities but also differences with its electronic counterpart. Here, we investigate this phenomenon extensively using all-atom molecular dynamics of ionic transport through nanopores of about one nanometer in diameter and up to several nanometers in length. Our goal is to better understand the role of atomic roughness and structure of the pore walls in the ionic Coulomb blockade. Our numerical results reveal the following general trends. First, the nanopore selectivity changes with its diameter, and the nanopore position in the membrane influences the current strength. Second, the ionic transport through the nanopore takes place in a hopping-like fashion over a set of discretized states caused by local electric fields due to membrane atoms. In some cases, this creates a slow-varying ‘crystal-like’ structure of ions inside the nanopore. Third, while at a given voltage, the resistance of the nanopore depends on its length, the slope of this dependence appears to be independent of the molarity of ions. An effective kinetic model that captures the ionic Coulomb blockade behavior observed in MD simulations is formulated.

Surface effects on ionic Coulomb blockade in nanometer-size pores.

PubMed

Tanaka, Hiroya; Iizuka, Hideo; Pershin, Yuriy V; Ventra, Massimiliano Di

2018-01-12

Ionic Coulomb blockade in nanopores is a phenomenon that shares some similarities but also differences with its electronic counterpart. Here, we investigate this phenomenon extensively using all-atom molecular dynamics of ionic transport through nanopores of about one nanometer in diameter and up to several nanometers in length. Our goal is to better understand the role of atomic roughness and structure of the pore walls in the ionic Coulomb blockade. Our numerical results reveal the following general trends. First, the nanopore selectivity changes with its diameter, and the nanopore position in the membrane influences the current strength. Second, the ionic transport through the nanopore takes place in a hopping-like fashion over a set of discretized states caused by local electric fields due to membrane atoms. In some cases, this creates a slow-varying 'crystal-like' structure of ions inside the nanopore. Third, while at a given voltage, the resistance of the nanopore depends on its length, the slope of this dependence appears to be independent of the molarity of ions. An effective kinetic model that captures the ionic Coulomb blockade behavior observed in MD simulations is formulated.

Two-Dimensional Nanoporous Networks Formed by Liquid-to-Solid Transfer of Hydrogen-Bonded Macrocycles Built from DNA Bases.

PubMed

Bilbao, Nerea; Destoop, Iris; De Feyter, Steven; González-Rodríguez, David

2016-01-11

We present an approach that makes use of DNA base pairing to produce hydrogen-bonded macrocycles whose supramolecular structure can be transferred from solution to a solid substrate. A hierarchical assembly process ultimately leads to two-dimensional nanostructured porous networks that are able to host size-complementary guests. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Applications of biological pores in nanomedicine, sensing, and nanoelectronics.

PubMed

Majd, Sheereen; Yusko, Erik C; Billeh, Yazan N; Macrae, Michael X; Yang, Jerry; Mayer, Michael

2010-08-01

Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated - often regulated - functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics. Copyright © 2010 Elsevier Ltd. All rights reserved.

Selective-area nanoheteroepitaxy for light emitting diode (LED) applications

NASA Astrophysics Data System (ADS)

Wildeson, Isaac H.

Over 20% of the electricity in the United States is consumed for lighting, and the majority of this energy is wasted as heat during the lighting process. A solid-state (or light emitting diode (LED)-based) light source has the potential of saving the United States billions of dollars in electricity and reducing megatons of global CO2 emissions annually. While white light LEDs are currently on the market with efficiencies that are superior to incandescent and fluorescent light sources, their high up-front cost is inhibiting mass adoption. One reason for the high cost is the inefficiency of green and amber LEDs that can used to make white light. The inefficiency of green and amber LEDs results in more of these chips being required, and thus a higher cost. Improvements in the performance of green and amber LEDs is also required in order to realize the full potential of solid-state lighting. Nanoheteroepitaxy is an interesting route towards achieving efficient green and amber LEDs as it resolves major challenges that are currently plaguing III-nitride LEDs such as high dislocation densities and limited active region critical thicknesses. A method for fabricating III-nitride nanopyramid LEDs is presented that employs conventional processing used in industry. The present document begins with an overview of the current challenges in III-nitride LEDs and the benefits of nanoheteroepitaxy. A process for controlled selective-area growth of nanopyramid LEDs by organometallic vapor phase epitaxy has been developed throughout the course of this work. Dielectric templates used for the selective-area growth are patterned by two methods, namely porous anodic alumina and electron-beam lithography. The dielectric templates serve as efficient dislocation filters; however, planar defects are initiated during lower temperature growth on the nanopyramids. The quantum wells outline six semipolar planes that form each hexagonal pyramid. Quantum wells grown on these semipolar planes generate built-in electric fields with magnitudes that are one-tenth those on the polar c-plane with the same (In,Ga)N composition. The lateral strain relaxation innate in the nanoheterostructures allows greater coherent InN incorporation in the nanopyramids as compared to thin-film heterostructures, as confirmed by electroluminescence and transmission electron microscopy. In addition to applications for light emitting diodes, selective area growth of GaN nanostructures is also important for biological and sensing applications. A process for fabricating porous GaN nanorods is presented that also relies on selective-area organometallic vapor phase epitaxy. The nanopore walls are primarily outlined by nonpolar planes, and the diameter of the nanopore can be controlled by the diameter of the opening in the dielectric template and the growth time. The lining of the nanopore walls is comprised of crystalline GaN, which makes these structures interesting for sensing, electrical and optical applications.

Impedimetric DNA biosensor based on a nanoporous alumina membrane for the detection of the specific oligonucleotide sequence of dengue virus.

PubMed

Deng, Jiajia; Toh, Chee-Seng

2013-06-17

A novel and integrated membrane sensing platform for DNA detection is developed based on an anodic aluminum oxide (AAO) membrane. Platinum electrodes (~50-100 nm thick) are coated directly on both sides of the alumina membrane to eliminate the solution resistance outside the nanopores. The electrochemical impedance technique is employed to monitor the impedance changes within the nanopores upon DNA binding. Pore resistance (Rp) linearly increases in response towards the increasing concentration of the target DNA in the range of 1 × 10⁻¹² to 1 × 10⁻⁶ M. Moreover, the biosensor selectively differentiates the complementary sequence from single base mismatched (MM-1) strands and non-complementary strands. This study reveals a simple, selective and sensitive method to fabricate a label-free DNA biosensor.

Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array

PubMed Central

Stranges, P. Benjamin; Palla, Mirkó; Kalachikov, Sergey; Nivala, Jeff; Dorwart, Michael; Trans, Andrew; Kumar, Shiv; Porel, Mintu; Chien, Minchen; Tao, Chuanjuan; Morozova, Irina; Li, Zengmin; Shi, Shundi; Aberra, Aman; Arnold, Cleoma; Yang, Alexander; Aguirre, Anne; Harada, Eric T.; Korenblum, Daniel; Pollard, James; Bhat, Ashwini; Gremyachinskiy, Dmitriy; Bibillo, Arek; Chen, Roger; Davis, Randy; Russo, James J.; Fuller, Carl W.; Roever, Stefan; Ju, Jingyue; Church, George M.

2016-01-01

Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to an α-hemolysin (αHL) heptamer using the SpyCatcher/SpyTag conjugation approach. These porin–polymerase conjugates were inserted into lipid bilayers on a complementary metal oxide semiconductor (CMOS)-based electrode array for high-throughput electrical recording of DNA synthesis. The designed nanopore construct successfully detected the capture of tagged nucleotides complementary to a DNA base on a provided template. We measured over 200 tagged-nucleotide signals for each of the four bases and developed a classification method to uniquely distinguish them from each other and background signals. The probability of falsely identifying a background event as a true capture event was less than 1.2%. In the presence of all four tagged nucleotides, we observed sequential additions in real time during polymerase-catalyzed DNA synthesis. Single-polymerase coupling to a nanopore, in combination with the Nanopore-SBS approach, can provide the foundation for a low-cost, single-molecule, electronic DNA-sequencing platform. PMID:27729524

Osmylated DNA, a novel concept for sequencing DNA using nanopores

NASA Astrophysics Data System (ADS)

Kanavarioti, Anastassia

2015-03-01

Saenger sequencing has led the advances in molecular biology, while faster and cheaper next generation technologies are urgently needed. A newer approach exploits nanopores, natural or solid-state, set in an electrical field, and obtains base sequence information from current variations due to the passage of a ssDNA molecule through the pore. A hurdle in this approach is the fact that the four bases are chemically comparable to each other which leads to small differences in current obstruction. ‘Base calling’ becomes even more challenging because most nanopores sense a short sequence and not individual bases. Perhaps sequencing DNA via nanopores would be more manageable, if only the bases were two, and chemically very different from each other; a sequence of 1s and 0s comes to mind. Osmylated DNA comes close to such a sequence of 1s and 0s. Osmylation is the addition of osmium tetroxide bipyridine across the C5-C6 double bond of the pyrimidines. Osmylation adds almost 400% mass to the reactive base, creates a sterically and electronically notably different molecule, labeled 1, compared to the unreactive purines, labeled 0. If osmylated DNA were successfully sequenced, the result would be a sequence of osmylated pyrimidines (1), and purines (0), and not of the actual nucleobases. To solve this problem we studied the osmylation reaction with short oligos and with M13mp18, a long ssDNA, developed a UV-vis assay to measure extent of osmylation, and designed two protocols. Protocol A uses mild conditions and yields osmylated thymidines (1), while leaving the other three bases (0) practically intact. Protocol B uses harsher conditions and effectively osmylates both pyrimidines, but not the purines. Applying these two protocols also to the complementary of the target polynucleotide yields a total of four osmylated strands that collectively could define the actual base sequence of the target DNA.

Probing DNA in nanopores via tunneling: from sequencing to ``quantum'' analogies

NASA Astrophysics Data System (ADS)

di Ventra, Massimiliano

2012-02-01

Fast and low-cost DNA sequencing methods would revolutionize medicine: a person could have his/her full genome sequenced so that drugs could be tailored to his/her specific illnesses; doctors could know in advance patients' likelihood to develop a given ailment; cures to major diseases could be found faster [1]. However, this goal of ``personalized medicine'' is hampered today by the high cost and slow speed of DNA sequencing methods. In this talk, I will discuss the sequencing protocol we suggest which requires the measurement of the distributions of transverse currents during the translocation of single-stranded DNA into nanopores [2-5]. I will support our conclusions with a combination of molecular dynamics simulations coupled to quantum mechanical calculations of electrical current in experimentally realizable systems [2-5]. I will also discuss recent experiments that support these theoretical predictions. In addition, I will show how this relatively unexplored area of research at the interface between solids, liquids, and biomolecules at the nanometer length scale is a fertile ground to study quantum phenomena that have a classical counterpart, such as ionic quasi-particles, ionic ``quantized'' conductance [6,7] and Coulomb blockade [8]. Work supported in part by NIH. [4pt] [1] M. Zwolak, M. Di Ventra, Physical Approaches to DNA Sequencing and Detection, Rev. Mod. Phys. 80, 141 (2008).[0pt] [2] M. Zwolak and M. Di Ventra, Electronic signature of DNA nucleotides via transverse transport, Nano Lett. 5, 421 (2005).[0pt] [3] J. Lagerqvist, M. Zwolak, and M. Di Ventra, Fast DNA sequencing via transverse electronic transport, Nano Lett. 6, 779 (2006).[0pt] [4] J. Lagerqvist, M. Zwolak, and M. Di Ventra, Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport, Biophys. J. 93, 2384 (2007).[0pt] [5] M. Krems, M. Zwolak, Y.V. Pershin, and M. Di Ventra, Effect of noise on DNA sequencing via transverse electronic transport, Biophys. J. 97, 1990, (2009).[0pt] [6] M. Zwolak, J. Lagerqvist, and M. Di Ventra, Ionic conductance quantization in nanopores, Phys. Rev.Lett. 103, 128102 (2009).[0pt] [7] M. Zwolak, J. Wilson, and M. Di Ventra, Dehydration and ionic conductance quantization in nanopores, J. Phys. Cond. Matt. 22 454126 (2011). [0pt] [8] M. Krems and M. Di Ventra, Ionic Coulomb blockade in nanopores arXiv:1103.2749.

Development of a DNA Sensor Based on Nanoporous Pt-Rich Electrodes

NASA Astrophysics Data System (ADS)

Van Hao, Pham; Thanh, Pham Duc; Xuan, Chu Thi; Hai, Nguyen Hoang; Tuan, Mai Anh

2017-06-01

Nanoporous Pt-rich electrodes with 72 at.% Pt composition were fabricated by sputtering a Pt-Ag alloy, followed by an electrochemical dealloying process to selectively etch away Ag atoms. The surface properties of nanoporous membranes were investigated by energy-dispersive x-ray spectroscopy (EDS), scanning electron microscopy (SEM), atomic force microscopy (AFM), a documentation system, and a gel image system (Gel Doc Imager). A single strand of probe deoxyribonucleic acid (DNA) was immobilized onto the electrode surface by physical adsorption. The DNA probe and target hybridization were measured using a lock-in amplifier and an electrochemical impedance spectroscope (EIS). The nanoporous Pt-rich electrode-based DNA sensor offers a fast response time of 3.7 s, with a limit of detection (LOD) of 4.35 × 10-10 M of DNA target.

Electrostatic Interactions between OmpG Nanopore and Analyte Protein Surface Can Distinguish between Glycosylated Isoforms.

PubMed

Fahie, Monifa A; Chen, Min

2015-08-13

The flexible loops decorating the entrance of OmpG nanopore move dynamically during ionic current recording. The gating caused by these flexible loops changes when a target protein is bound. The gating is characterized by parameters including frequency, duration, and open-pore current, and these features combine to reveal the identity of a specific analyte protein. Here, we show that OmpG nanopore equipped with a biotin ligand can distinguish glycosylated and deglycosylated isoforms of avidin by their differences in surface charge. Our studies demonstrate that the direct interaction between the nanopore and analyte surface, induced by the electrostatic attraction between the two molecules, is essential for protein isoform detection. Our technique is remarkably sensitive to the analyte surface, which may provide a useful tool for glycoprotein profiling.

Capture, Unfolding, and Detection of Individual tRNA Molecules Using a Nanopore Device

PubMed Central

Smith, Andrew M.; Abu-Shumays, Robin; Akeson, Mark; Bernick, David L.

2015-01-01

Transfer RNAs (tRNA) are the most common RNA molecules in cells and have critical roles as both translators of the genetic code and regulators of protein synthesis. As such, numerous methods have focused on studying tRNA abundance and regulation, with the most widely used methods being RNA-seq and microarrays. Though revolutionary to transcriptomics, these assays are limited by an inability to encode tRNA modifications in the requisite cDNA. These modifications are abundant in tRNA and critical to their function. Here, we describe proof-of-concept experiments where individual tRNA molecules are examined as linear strands using a biological nanopore. This method utilizes an enzymatically ligated synthetic DNA adapter to concentrate tRNA at the lipid bilayer of the nanopore device and efficiently denature individual tRNA molecules, as they are pulled through the α-hemolysin (α-HL) nanopore. Additionally, the DNA adapter provides a loading site for ϕ29 DNA polymerase (ϕ29 DNAP), which acts as a brake on the translocating tRNA. This increases the dwell time of adapted tRNA in the nanopore, allowing us to identify the region of the nanopore signal that is produced by the translocating tRNA itself. Using adapter-modified Escherichia coli tRNAfMet and tRNALys, we show that the nanopore signal during controlled translocation is dependent on the identity of the tRNA. This confirms that adapter-modified tRNA can translocate end-to-end through nanopores and provide the foundation for future work in direct sequencing of individual transfer RNA with a nanopore-based device. PMID:26157798

Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array

PubMed Central

Fuller, Carl W.; Kumar, Shiv; Porel, Mintu; Chien, Minchen; Bibillo, Arek; Stranges, P. Benjamin; Dorwart, Michael; Tao, Chuanjuan; Li, Zengmin; Guo, Wenjing; Shi, Shundi; Korenblum, Daniel; Trans, Andrew; Aguirre, Anne; Liu, Edward; Harada, Eric T.; Pollard, James; Bhat, Ashwini; Cech, Cynthia; Yang, Alexander; Arnold, Cleoma; Palla, Mirkó; Hovis, Jennifer; Chen, Roger; Morozova, Irina; Kalachikov, Sergey; Russo, James J.; Kasianowicz, John J.; Davis, Randy; Roever, Stefan; Church, George M.; Ju, Jingyue

2016-01-01

DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5′-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods. PMID:27091962

Microscale solid-state thermal diodes enabling ambient temperature thermal circuits for energy applications.

PubMed

Wang, Song; Cottrill, Anton L; Kunai, Yuichiro; Toland, Aubrey R; Liu, Pingwei; Wang, Wen-Jun; Strano, Michael S

2017-05-24

Thermal diodes, or devices that transport thermal energy asymmetrically, analogous to electrical diodes, hold promise for thermal energy harvesting and conservation, as well as for phononics or information processing. The junction of a phase change material and phase invariant material can form a thermal diode; however, there are limited constituent materials available for a given target temperature, particularly near ambient. In this work, we demonstrate that a micro and nanoporous polystyrene foam can house a paraffin-based phase change material, fused to PMMA, to produce mechanically robust, solid-state thermal diodes capable of ambient operation with Young's moduli larger than 11.5 MPa and 55.2 MPa above and below the melting transition point, respectively. Moreover, the composites show significant changes in thermal conductivity above and below the melting point of the constituent paraffin and rectification that is well-described by our previous theory and the Maxwell-Eucken model. Maximum thermal rectifications range from 1.18 to 1.34. We show that such devices perform reliably enough to operate in thermal diode bridges, dynamic thermal circuits capable of transforming oscillating temperature inputs into single polarity temperature differences - analogous to an electrical diode bridge with widespread implications for transient thermal energy harvesting and conservation. Overall, our approach yields mechanically robust, solid-state thermal diodes capable of engineering design from a mathematical model of phase change and thermal transport, with implications for energy harvesting.

A Hybrid Semi-Digital Transimpedance Amplifier With Noise Cancellation Technique for Nanopore-Based DNA Sequencing.

PubMed

Hsu, Chung-Lun; Jiang, Haowei; Venkatesh, A G; Hall, Drew A

2015-10-01

Over the past two decades, nanopores have been a promising technology for next generation deoxyribonucleic acid (DNA) sequencing. Here, we present a hybrid semi-digital transimpedance amplifier (HSD-TIA) to sense the minute current signatures introduced by single-stranded DNA (ssDNA) translocating through a nanopore, while discharging the baseline current using a semi-digital feedback loop. The amplifier achieves fast settling by adaptively tuning a DC compensation current when a step input is detected. A noise cancellation technique reduces the total input-referred current noise caused by the parasitic input capacitance. Measurement results show the performance of the amplifier with 31.6 M Ω mid-band gain, 950 kHz bandwidth, and 8.5 fA/ √Hz input-referred current noise, a 2× noise reduction due to the noise cancellation technique. The settling response is demonstrated by observing the insertion of a protein nanopore in a lipid bilayer. Using the nanopore, the HSD-TIA was able to measure ssDNA translocation events.

Gold/silver coated nanoporous ceramic membranes: a new substrate for SERS studies

NASA Astrophysics Data System (ADS)

Kassu, A.; Robinson, P.; Sharma, A.; Ruffin, P. B.; Brantley, C.; Edwards, E.

2010-08-01

Surface Enhanced Raman Scattering (SERS) is a recently discovered powerful technique which has demonstrated sensitivity and selectivity for detecting single molecules of certain chemical species. This is due to an enhancement of Raman scattered light by factors as large as 1015. Gold and Silver-coated substrates fabricated by electron-beam lithography on Silicon are widely used in SERS technique. In this paper, we report the use of nanoporous ceramic membranes for SERS studies. Nanoporous membranes are widely used as a separation membrane in medical devices, fuel cells and other studies. Three different pore diameter sizes of commercially available nanoporous ceramic membranes: 35 nm, 55nm and 80nm are used in the study. To make the membranes SERS active, they are coated with gold/silver using sputtering techniques. We have seen that the membranes coated with gold layer remain unaffected even when immersed in water for several days. The results show that gold coated nanoporous membranes have sensitivity comparable to substrates fabricated by electron-beam lithography on Silicon substrates.

A nanoscale perspective on the effects of transverse microprestress on drying creep of nanoporous solids

NASA Astrophysics Data System (ADS)

Sinko, Robert; Bažant, Zdeněk P.; Keten, Sinan

2018-01-01

The Pickett effect describes the excess non-additive strain developed during drying of a nanoporous solid material under creep. One explanation for its origins, developed using micromechanical models, is the progressive relaxation of internally developed microprestress. However, these models have not explicitly considered the effects of this microprestress on nanoscale energy barriers that govern the relative motion and displacement between nanopore walls during deformation. Here, we evaluate the nanoscale effects of transverse microprestresses on the drying creep behaviour of a nanoscale slit pore using coarse-grained molecular dynamics. We find that the underlying energy barrier depends exponentially on the transverse microprestress, which is attributed to changes in the effective viscosity and degree of nanoconfinement of molecules in the water interlayer. Specifically, as the transverse microprestress is relaxed (i.e. its magnitude decreases), the activation energy barrier is reduced, thereby leading to an acceleration of the creep behaviour and a stronger Pickett effect. Based on our simulation results, we introduce a new microprestress-dependent energy term into our existing Arrhenius model, which describes the relative displacement of pore walls as a function of the underlying activation energy barriers. Our findings further verify the existing micromechanical theories for the origin of the Pickett effect and establish a quantitative relationship between the transverse microprestress and the intensity of the Pickett effect.

High-speed event detector for embedded nanopore bio-systems.

PubMed

Huang, Yiyun; Magierowski, Sebastian; Ghafar-Zadeh, Ebrahim; Wang, Chengjie

2015-08-01

Biological measurements of microscopic phenomena often deal with discrete-event signals. The ability to automatically carry out such measurements at high-speed in a miniature embedded system is desirable but compromised by high-frequency noise along with practical constraints on filter quality and sampler resolution. This paper presents a real-time event-detection method in the context of nanopore sensing that helps to mitigate these drawbacks and allows accurate signal processing in an embedded system. Simulations show at least a 10× improvement over existing on-line detection methods.

Recording ion channels across soy-extracted lecithin bilayer generated by water-soluble quantum dots

NASA Astrophysics Data System (ADS)

Sarma, Runjun; Mohanta, Dambarudhar

2014-02-01

We report on the quantum dot (QD)-induced ion channels across a soya-derived lecithin bilayer supported on a laser drilled of ~100 μm aperture of cellulose acetate substrate that separates two electrolytic chambers. Adequate current bursts were observed when the bilayer was subjected to a gating voltage. The voltage-dependent current fluctuation, across the bilayer, was attributed to the insertion of ~20 nm sized water-soluble CdSe QDs, forming nanopores due to their spontaneous aggregation. Apart from a closed state, the first observable conductance levels were found as 6.3 and 11 nS, as for the respective biasing voltages of -10 and -20 mV. The highest observable conductance states, at corresponding voltages were ~14.3 and 21.1 nS. Considering two simplified models, we predict that the non-spherical pores (dnspore) can be a better approximation over spherical nanopores (dspore) for exhibiting a definite conductance level. At times, even dnspore ≤ 4dspore and that the non-spherical nanopores were associated with a smaller No. of QDs than the case for spherical nanopores, for a definite conductance state. It seems like the current events are partly stochastic, possibly due to thermal effects on the aggregated QDs that would form nanopores. The dwell time of the states was predicted in the range of 384-411 μs. The ion channel mechanism in natural phospholipid bilayers over artificial ones will provide a closer account to understand ion transport mechanism in live cells and signaling activity including labelling with fluorescent QDs.

Instrumentation for low noise nanopore-based ionic current recording under laser illumination

NASA Astrophysics Data System (ADS)

Roelen, Zachary; Bustamante, José A.; Carlsen, Autumn; Baker-Murray, Aidan; Tabard-Cossa, Vincent

2018-01-01

We describe a nanopore-based optofluidic instrument capable of performing low-noise ionic current recordings of individual biomolecules under laser illumination. In such systems, simultaneous optical measurements generally introduce significant parasitic noise in the electrical signal, which can severely reduce the instrument sensitivity, critically hindering the monitoring of single-molecule events in the ionic current traces. Here, we present design rules and describe simple adjustments to the experimental setup to mitigate the different noise sources encountered when integrating optical components to an electrical nanopore system. In particular, we address the contributions to the electrical noise spectra from illuminating the nanopore during ionic current recording and mitigate those effects through control of the illumination source and the use of a PDMS layer on the SiNx membrane. We demonstrate the effectiveness of our noise minimization strategies by showing the detection of DNA translocation events during membrane illumination with a signal-to-noise ratio of ˜10 at 10 kHz bandwidth. The instrumental guidelines for noise minimization that we report are applicable to a wide range of nanopore-based optofluidic systems and offer the possibility of enhancing the quality of synchronous optical and electrical signals obtained during single-molecule nanopore-based analysis.

N-(L-2-aminopentanoyl)-L-phenylalanine dihydrate, a hydrophobic dipeptide with a nonproteinogenic residue.

PubMed

Görbitz, Carl Henrik; Yadav, Vitthal N

2013-09-01

The title dipeptide, better known as L-norvalyl-L-phenylalanine {systematic name: (S)-2-[(S)-2-aminopentanamido]-3-phenylpropanoic acid dihydrate}, C14H20N2O3·2H2O, has a nonproteinogenic N-terminal residue. In the solid state, it takes on a molecular conformation typical for one of the three classes of nanoporous dipeptides, but like two related compounds with a hydrophobic N-terminal residue and a C-terminal L-phenylalanine, it fails to form channels or pores. Instead, the crystal structure is divided into distinct hydrophobic and hydrophilic layers, the latter encompassing cocrystallized water molecules connecting the charged N- and C-terminal groups.

Nanoporous gold as a solid support for protein immobilization and development of an electrochemical immunoassay for prostate specific antigen and carcinoembryonic antigen

PubMed Central

Pandey, Binod; Demchenko, Alexei V.; Stine, Keith J.

2013-01-01

Nanoporous gold (NPG) was utilized as a support for immobilizing alkaline phosphatase (ALP) conjugated to monoclonal antibodies against either prostate specific antigen (PSA) or carcinoembryonic antigen (CEA). The antibody-ALP conjugates were coupled to self-assembled monolayers of lipoic acid and used in direct kinetic assays. Using the enzyme substrate p-aminophenylphosphate, the product p-aminophenol was detected by its oxidation near 0.1 V (vs. Ag|AgCl) using square wave voltammetry. The difference in peak current arising from oxidation of p-aminophenol before and after incubation with biomarker increased with biomarker concentration. The response to these two biomarkers was linear up to 10 ng mL-1 for CEA and up to 30 ng mL-1 for PSA. The effect of interference on the PSA assay was studied using bovine serum albumin (BSA) as a model albumin protein. The effect of interference from a serum matrix was examined for the PSA assay using newborn calf serum. A competitive version of the immunoassay using antigen immobilized onto the NPG surface was highly sensitive at lower antigen concentration. Estimates of the surface coverage of the antibody-ALP conjugates on the NPG surface are presented. PMID:23935216

Solid phase extraction and trace monitoring of cadmium ions in environmental water and food samples based on modified magnetic nanoporous silica

NASA Astrophysics Data System (ADS)

Omidi, Fariborz; Behbahani, Mohammad; Kalate Bojdi, Majid; Shahtaheri, Seyed Jamaleddin

2015-12-01

A new method has been developed for trace separation/preconcentration of cadmium ions using pyridine-functionalized magnetic nanoporous silica material (called Py-Fe3O4@MCM-41) as a new magnetic sorbent and their determination by flame atomic absorption spectrometry (FAAS). The Py-Fe3O4@MCM-41 sorbent was characterized by thermogravimetric analysis, differential thermal analysis, transmission electron microscopy, Fourier transform infrared spectrometry and X-ray diffraction. The modified Fe3O4@MCM-41 can be easily separated from an aqueous solution by applying an external magnetic field. Effects of pH, amount of functionalized Fe3O4@MCM-41, extraction time, type and quantity of eluent, desorption time, and interfering ions on the extraction efficiency were evaluated and optimized. Under the optimized conditions, the detection limit and relative standard deviation was 0.04 μg L-1 and 2.9%, respectively and the maximum adsorption capacity of the synthesized sorbent for cadmium ions was 154 mg g-1. The proposed method has been applied to the determination of Cd ions at trace levels in real samples such as, rice, onion, carrot, lettuce, parsley, basil, tap water, river water and seawater with satisfactory results.

Analyte-Triggered DNA-Probe Release from a Triplex Molecular Beacon for Nanopore Sensing.

PubMed

Guo, Bingyuan; Sheng, Yingying; Zhou, Ke; Liu, Quansheng; Liu, Lei; Wu, Hai-Chen

2018-03-26

A new nanopore sensing strategy based on triplex molecular beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex-forming molecular beacon and a stem-forming DNA component that is modified with a host-guest complex. Upon target DNA hybridizing with the molecular beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α-hemolysin. The frequency of current signatures can be used to quantify the concentrations of the target molecules. This sensing approach provides a simple, quick, and modular tool for the detection of specific macromolecules with high sensitivity and excellent selectivity. It may find useful applications in point-of-care diagnostics with a portable nanopore kit in the future. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomic layer deposition modified track-etched conical nanochannels for protein sensing.

PubMed

Wang, Ceming; Fu, Qibin; Wang, Xinwei; Kong, Delin; Sheng, Qian; Wang, Yugang; Chen, Qiang; Xue, Jianming

2015-08-18

Nanopore-based devices have recently become popular tools to detect biomolecules at the single-molecule level. Unlike the long-chain nucleic acids, protein molecules are still quite challenging to detect, since the protein molecules are much smaller in size and usually travel too fast through the nanopore with poor signal-to-noise ratio of the induced transport signals. In this work, we demonstrate a new type of nanopore device based on atomic layer deposition (ALD) Al2O3 modified track-etched conical nanochannels for protein sensing. These devices show very promising properties of high protein (bovine serum albumin) capture rate with well time-resolved transport signals and excellent signal-to-noise ratio for the transport events. Also, a special mechanism involving transient process of ion redistribution inside the nanochannel is proposed to explain the unusual biphasic waveshapes of the current change induced by the protein transport.

A study on modification of nanoporous rice husk silica for hydrophobic nano filter.

PubMed

Kim, Hee Jin; So, Soo Jeong; Han, Chong Soo

2010-05-01

Nanoporous rice husk silica (RHS) was modified with alkylsilylation reagents, hexamethyldisilazane, diethoxydiphenylsilane, dichlorodimethylsilane and n-octodecyltrimethoxysilane. The silica samples were characterized with Raman spectrometer, thermal gravimetric analyzer, scanning electron microscope, nitrogen adsorption measurement and solid state nuclear magnetic resonance spectrometer. Raman spectra of the modified silica showed growth of the peaks of C-H stretching and CH3 bending at approximateluy 3000 cm(-1) and approximately 1500 cm(-1), respectively. Weight losses of 3 approximately 5% were observed in thermo gravimetric profiles of the modified silica. The microscopic shape of RHS, approximately 20 nm primary particles and their aggregates was almost not changed by the modification but there were colligations of the silica particles in the sample treated with dichlorodimethylsilane or diethoxydiphenylsilane. BET adsorption experiment showed the modification significantly decreased the mean pore size of the silica from approximately 5 nm to approximately 4 nm as well as the pore volume from 0.5 cm3/g to 0.4 cm3/g except the case of treatment with n-octodecyltrimethoxysilane. 29Si Solid NMR Spectra of the silica samples showed that there were decrease in the relative intensities of Q2 and Q3 peaks and large increments in Q4 after the modification except for the case of bulky n-octodecyltrimethoxysilane. From the results, it was concluded that the alkylsilylation reagents reacted with hydroxyl groups on the silica particles as well as in the nano pores while the size of the reagent molecule affected its diffusion and reaction with the hydroxyl groups in the pores.

Plasmonic activity on gold nanoparticles embedded in nanopores formed in a surface layer of silica glass by swift-heavy-ion irradiation.

PubMed

Nomura, Ken-ichi; Ohki, Yoshimichi; Fujimaki, Makoto; Wang, Xiaomin; Awazu, Koichi; Komatsubara, Tetsuro

2009-11-25

Silica glass was irradiated by swift heavy ions by selecting the ion species and its energy in order to induce the largest damaged regions. These regions were then selectively etched by hydrofluoric acid vapour to form nanopores on the glass surface. Subsequently, gold nanoparticles were embedded into the nanopores by vacuum evaporation, followed by thermal treatment. In the new plasmonic structure obtained with these procedures, the localized surface plasmon excitation wavelength induced around the gold nanoparticles was found to show a redshift, which agreed well with the theoretical calculation, when water was introduced into the nanopores. This indicates that the fabricated structure can be used as a sensing element to detect the adhesion of substances such as biomolecules to the nanoparticles by measuring the redshift.

Ultrasensitive Detection of Ebola Virus Oligonucleotide Based on Upconversion Nanoprobe/Nanoporous Membrane System.

PubMed

Tsang, Ming-Kiu; Ye, WeiWei; Wang, Guojing; Li, Jingming; Yang, Mo; Hao, Jianhua

2016-01-26

Ebola outbreaks are currently of great concern, and therefore, development of effective diagnosis methods is urgently needed. The key for lethal virus detection is high sensitivity, since early-stage detection of virus may increase the probability of survival. Here, we propose a luminescence scheme of assay consisting of BaGdF5:Yb/Er upconversion nanoparticles (UCNPs) conjugated with oligonucleotide probe and gold nanoparticles (AuNPs) linked with target Ebola virus oligonucleotide. As a proof of concept, a homogeneous assay was fabricated and tested, yielding a detection limit at picomolar level. The luminescence resonance energy transfer is ascribed to the spectral overlapping of upconversion luminescence and the absorption characteristics of AuNPs. Moreover, we anchored the UCNPs and AuNPs on a nanoporous alumina (NAAO) membrane to form a heterogeneous assay. Importantly, the detection limit was greatly improved, exhibiting a remarkable value at the femtomolar level. The enhancement is attributed to the increased light-matter interaction throughout the nanopore walls of the NAAO membrane. The specificity test suggested that the nanoprobes were specific to Ebola virus oligonucleotides. The strategy combining UCNPs, AuNPs, and NAAO membrane provides new insight into low-cost, rapid, and ultrasensitive detection of different diseases. Furthermore, we explored the feasibility of clinical application by using inactivated Ebola virus samples. The detection results showed great potential of our heterogeneous design for practical application.

Functional reconstitution of rhodopsin into tubular lipid bilayers supported by nanoporous media.

PubMed

Soubias, Olivier; Polozov, Ivan V; Teague, Walter E; Yeliseev, Alexei A; Gawrisch, Klaus

2006-12-26

We report on a novel reconstitution method for G-protein-coupled receptors (GPCRs) that yields detergent-free, single, tubular membranes in porous anodic aluminum oxide (AAO) filters at concentrations sufficient for structural studies by solid-state NMR. The tubular membranes line the inner surface of pores that traverse the filters, permitting easy removal of detergents during sample preparation as well as delivery of ligands for functional studies. Reconstitution of bovine rhodopsin into AAO filters did not interfere with rhodopsin function. Photoactivation of rhodopsin in AAO pores, monitored by UV-vis spectrophotometry, was indistinguishable from rhodopsin in unsupported unilamellar liposomes. The rhodopsin in AAO pores is G-protein binding competent as shown by a [35S]GTPgammaS binding assay. The lipid-rhodopsin interaction was investigated by 2H NMR on sn-1- or sn-2-chain perdeuterated 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phospholine as a matrix lipid. Rhodopsin incorporation increased mosaic spread of bilayer orientations and contributed to spectral density of motions with correlation times in the range of nano- to microseconds, detected as a significant reduction in spin-spin relaxation times. The change in lipid chain order parameters due to interaction with rhodopsin was insignificant.

Pore structure and function of synthetic nanopores with fixed charges: tip shape and rectification properties

NASA Astrophysics Data System (ADS)

Ramírez, Patricio; Apel, Pavel Yu; Cervera, Javier; Mafé, Salvador

2008-08-01

We present a complete theoretical study of the relationship between the structure (tip shape and dimensions) and function (selectivity and rectification) of asymmetric nanopores on the basis of previous experimental studies. The theoretical model uses a continuum approach based on the Nernst-Planck equations. According to our results, the nanopore transport properties, such as current-voltage (I-V) characteristics, conductance, rectification ratio, and selectivity, are dictated mainly by the shape of the pore tip (we have distinguished bullet-like, conical, trumpet-like, and hybrid shapes) and the concentration of pore surface charges. As a consequence, the nanopore performance in practical applications will depend not only on the base and tip openings but also on the pore shape. In particular, we show that the pore opening dimensions estimated from the pore conductance can be very different, depending on the pore shape assumed. The results obtained can also be of practical relevance for the design of nanopores, nanopipettes, and nanoelectrodes, where the electrical interactions between the charges attached to the nanostructure and the mobile charges confined in the reduced volume of the inside solution dictate the device performance in practical applications. Because single tracks are the elementary building blocks for nanoporous membranes, the understanding and control of their individual properties should also be crucial in protein separation, water desalination, and bio-molecule detection using arrays of identical nanopores.

Pore structure and function of synthetic nanopores with fixed charges: tip shape and rectification properties.

PubMed

Ramírez, Patricio; Apel, Pavel Yu; Cervera, Javier; Mafé, Salvador

2008-08-06

We present a complete theoretical study of the relationship between the structure (tip shape and dimensions) and function (selectivity and rectification) of asymmetric nanopores on the basis of previous experimental studies. The theoretical model uses a continuum approach based on the Nernst-Planck equations. According to our results, the nanopore transport properties, such as current-voltage (I-V) characteristics, conductance, rectification ratio, and selectivity, are dictated mainly by the shape of the pore tip (we have distinguished bullet-like, conical, trumpet-like, and hybrid shapes) and the concentration of pore surface charges. As a consequence, the nanopore performance in practical applications will depend not only on the base and tip openings but also on the pore shape. In particular, we show that the pore opening dimensions estimated from the pore conductance can be very different, depending on the pore shape assumed. The results obtained can also be of practical relevance for the design of nanopores, nanopipettes, and nanoelectrodes, where the electrical interactions between the charges attached to the nanostructure and the mobile charges confined in the reduced volume of the inside solution dictate the device performance in practical applications. Because single tracks are the elementary building blocks for nanoporous membranes, the understanding and control of their individual properties should also be crucial in protein separation, water desalination, and bio-molecule detection using arrays of identical nanopores.

Flexible nanoporous tunable electrical double layer biosensors for sweat diagnostics.

PubMed

Munje, Rujuta D; Muthukumar, Sriram; Panneer Selvam, Anjan; Prasad, Shalini

2015-09-30

An ultra-sensitive and highly specific electrical double layer (EDL) modulated biosensor, using nanoporous flexible substrates for wearable diagnostics is demonstrated with the detection of the stress biomarker cortisol in synthetic and human sweat. Zinc oxide thin film was used as active region in contact with the liquid i.e. synthetic and human sweat containing the biomolecules. Cortisol detection in sweat was accomplished by measuring and quantifying impedance changes due to modulation of the double layer capacitance within the electrical double layer through the application of a low orthogonally directed alternating current (AC) electric field. The EDL formed at the liquid-semiconductor interface was amplified in the presence of the nanoporous flexible substrate allowing for measuring the changes in the alternating current impedance signal due to the antibody-hormone interactions at diagnostically relevant concentrations. High sensitivity of detection of 1 pg/mL or 2.75 pmol cortisol in synthetic sweat and 1 ng/mL in human sweat is demonstrated with these novel biosensors. Specificity in synthetic sweat was demonstrated using a cytokine IL-1β. Cortisol detection in human sweat was demonstrated over a concentration range from 10-200 ng/mL.

Flexible nanoporous tunable electrical double layer biosensors for sweat diagnostics

NASA Astrophysics Data System (ADS)

Munje, Rujuta D.; Muthukumar, Sriram; Panneer Selvam, Anjan; Prasad, Shalini

2015-09-01

An ultra-sensitive and highly specific electrical double layer (EDL) modulated biosensor, using nanoporous flexible substrates for wearable diagnostics is demonstrated with the detection of the stress biomarker cortisol in synthetic and human sweat. Zinc oxide thin film was used as active region in contact with the liquid i.e. synthetic and human sweat containing the biomolecules. Cortisol detection in sweat was accomplished by measuring and quantifying impedance changes due to modulation of the double layer capacitance within the electrical double layer through the application of a low orthogonally directed alternating current (AC) electric field. The EDL formed at the liquid-semiconductor interface was amplified in the presence of the nanoporous flexible substrate allowing for measuring the changes in the alternating current impedance signal due to the antibody-hormone interactions at diagnostically relevant concentrations. High sensitivity of detection of 1 pg/mL or 2.75 pmol cortisol in synthetic sweat and 1 ng/mL in human sweat is demonstrated with these novel biosensors. Specificity in synthetic sweat was demonstrated using a cytokine IL-1β. Cortisol detection in human sweat was demonstrated over a concentration range from 10-200 ng/mL.

Au particle formation on the electron beam induced membrane

NASA Astrophysics Data System (ADS)

Choi, Seong Soo; Park, Myoung Jin; Han, Chul Hee; Oh, Sae-Joong; Kim, Sung-In; Park, Nam Kyou; Park, Doo-Jae; Choi, Soo Bong; Kim, Yong-Sang

2017-02-01

Recently the single molecules such as protein and deoxyribonucleic acid (DNA) have been successfully characterized by using a portable solidstate nanopore (MinION) with an electrical detection technique. However, there have been several reports about the high error rates of the fabricated nanopore device, possibly due to an electrical double layer formed inside the pore channel. The current DNA sequencing technology utilized is based on the optical detection method. In order to utilize the current optical detection technique, we will present the formation of the Au nano-pore with Au particle under the various electron beam irradiations. In order to provide the diffusion of Au atoms, a 2 keV electron beam irradiation has been performed During electron beam irradiations by using field emission scanning electron microscopy (FESEM), Au and C atoms would diffuse together and form the binary mixture membrane. Initially, the Au atoms diffused in the membrane are smaller than 1 nm, below the detection limit of the transmission electron microscopy (TEM), so that we are unable to observe the Au atoms in the formed membrane. However, after several months later, the Au atoms became larger and larger with expense of the smaller particles: Ostwald ripening. Furthermore, we also observe the Au crystalline lattice structure on the binary Au-C membrane. The formed Au crystalline lattice structures were constantly changing during electron beam imaging process due to Spinodal decomposition; the unstable thermodynamic system of Au-C binary membrane. The fabricated Au nanopore with an Au nanoparticle can be utilized as a single molecule nanobio sensor.

Polygons and Faceted Polyhedra and Nanoporous Networks.

PubMed

Lu, Jianjiang; Mondal, Arunendu; Moulton, Brian; Zaworotko, Michael J

2001-06-01

Small rhombihexahedra and small cubicuboctahedra, namely faceted polyhedra, form the basis of two novel low-density framework solids that are afforded by the self-assembly of molecular squares only or molecular squares and triangles, respectively. © 2001 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.

An Innovative Metal Ions Sensitive “Test Paper” Based on Virgin Nanoporous Silicon Wafer: Highly Selective to Copper(II)

NASA Astrophysics Data System (ADS)

Li, Shaoyuan; Chen, Xiuhua; Ma, Wenhui; Ding, Zhao; Zhang, Cong; Chen, Zhengjie; He, Xiao; Shang, Yudong; Zou, Yuxin

2016-11-01

Developing an innovative “Test Paper” based on virgin nanoporous silicon (NPSi) which shows intense visible emission and excellent fluorescence stability. The visual fluorescence quenching “Test Paper” was highly selective and sensitive recognizing Cu2+ at μmol/L level. Within the concentration range of 5 × 10-7 ~50 × 10-7mol/L, the linear regression equation of IPL = 1226.3-13.6[CCu2+] (R = 0.99) was established for Cu2+ quantitative detection. And finally, Cu2+ fluorescence quenching mechanism of NPSi prober was proposed by studying the surface chemistry change of NPSi and metal ions immersed-NPSi using XPS characterization. The results indicate that SiHx species obviously contribute to the PL emission of NPSi, and the introduce of oxidization state and the nonradiative recombination center are responsible for the PL quenching. These results demonstrate how virgin NPSi wafer can serve as Cu2+ sensor. This work is of great significant to promote the development of simple instruments that could realize rapid, visible and real-time detection of various toxic metal ions.

Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

PubMed Central

Roever, Stefan

2012-01-01

A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

Detection of low-level PTFE contamination: An application of solid-state NMR to structure elucidation in the pharmaceutical industry.

PubMed

Pham, Tran N; Day, Caroline J; Edwards, Andrew J; Wood, Helen R; Lynch, Ian R; Watson, Simon A; Bretonnet, Anne-Sophie Z; Vogt, Frederick G

2011-01-25

We report a novel use of solid-state ¹⁹F nuclear magnetic resonance to detect and quantify polytetrafluoroethylene contamination from laboratory equipment, which due to low quantity (up to 1% w/w) and insolubility remained undetected by standard analytical techniques. Solid-state ¹⁹F NMR is shown to be highly sensitive to such fluoropolymers (detection limit 0.02% w/w), and is demonstrated as a useful analytical tool for structure elucidation of unknown solid materials. Copyright © 2010 Elsevier B.V. All rights reserved.

FITC-modified PPy nanotubes embedded in nanoporous AAO membrane can detect trace PCB20 via fluorescence ratiometric measurement.

PubMed

Wang, Meiling; Meng, Guowen; Huang, Qing; Xu, Qiaoling; Chu, Zhaoqin; Zhu, Chuhong

2011-04-07

A highly sensitive and selective fluorescence ratiometric sensor membrane for 2,3,3'-trichlorobiphenyl has been achieved, via depositing polypyrrole nanotubes (PPyNTs, the fluorescence indicator) in nano-porous anodic aluminium oxide (NPAAO) template and subsequently immobilizing fluorescein isothiocyanate (as an internal reference) onto the inner walls of the PPyNTs embedded in the NPAAO.

High-Performance Flexible Solid-State Supercapacitor with an Extended Nanoregime Interface through in Situ Polymer Electrolyte Generation.

PubMed

Anothumakkool, Bihag; Torris A T, Arun; Veeliyath, Sajna; Vijayakumar, Vidyanand; Badiger, Manohar V; Kurungot, Sreekumar

2016-01-20

Here, we report an efficient strategy by which a significantly enhanced electrode-electrolyte interface in an electrode for supercapacitor application could be accomplished by allowing in situ polymer gel electrolyte generation inside the nanopores of the electrodes. This unique and highly efficient strategy could be conceived by judiciously maintaining ultraviolet-triggered polymerization of a monomer mixture in the presence of a high-surface-area porous carbon. The method is very simple and scalable, and a prototype, flexible solid-state supercapacitor could even be demonstrated in an encapsulation-free condition by using the commercial-grade electrodes (thickness = 150 μm, area = 12 cm(2), and mass loading = 7.3 mg/cm(2)). This prototype device shows a capacitance of 130 F/g at a substantially reduced internal resistance of 0.5 Ω and a high capacitance retention of 84% after 32000 cycles. The present system is found to be clearly outperforming a similar system derived by using the conventional polymer electrolyte (PVA-H3PO4 as the electrolyte), which could display a capacitance of only 95 F/g, and this value falls to nearly 50% in just 5000 cycles. The superior performance in the present case is credited primarily to the excellent interface formation of the in situ generated polymer electrolyte inside the nanopores of the electrode. Further, the interpenetrated nature of the polymer also helps the device to show a low electron spin resonance and power rate and, most importantly, excellent shelf-life in the unsealed flexible conditions. Because the nature of the electrode-electrolyte interface is the major performance-determining factor in the case of many electrochemical energy storage/conversion systems, along with the supercapacitors, the developed process can also find applications in preparing electrodes for the devices such as lithium-ion batteries, metal-air batteries, polymer electrolyte membrane fuel cells, etc.

Nanopore Confinement of C-O-H Fluids Relevant to Subsurface Energy Systems

NASA Astrophysics Data System (ADS)

Cole, D. R.

2016-12-01

Complex intermolecular interactions of C-O-H fluids (e.g., H2O, CO2, CH4) result in their unique thermophysical properties, including large deviations in the volumetric properties from ideality, vapor-liquid equilibria, and critical phenomena as these fluids encounter different pressure-temperature-pore network conditions in the crust. Development of a comprehensive understanding of the structures, dynamics, and reactivity at multiple length scales (molecular to macroscopic) over wide ranges of state conditions and composition is foundational to advances in quantifying geochemical processes involving mineral-fluid interfaces. The size, distribution and connectivity of these confined geometries dictate how fluids migrate into and through these micro- and nano-environments, wet and react with the solid. This presentation will provide an overview of the application of state-of-the-art experimental, analytical and computational tools to assess key features of the fluid-matrix interaction. The multidisciplinary approaches highlighted will include neutron scattering and NMR experiments, thermodynamic measurements and molecular-level simulations to quantitatively assess molecular properties of different mixtures of C-O-H fluids in nanpores. Key results include: (1) The addition of a second carbon-bearing phase or water has a profound effect on the competition for sorption sites, phase chemistry and the dynamical properties of all phases present in the pore. (2) Low solubility phases such as methane may exhibit profound increases in concentration in nanopores in the presence of water at elevated pressures and ambient temperature compared to bulk values. (3) Methane permeability through the hydrated pores is strongly dependent on the solid substrate and local properties of confined water, including its structure and, more importantly, evolution of solvation free energy and hydrogen bond structure. (4) Under certain conditions preferential adsorption of the fluids in the narrow pores can produce a shift in the equilibrium distribution of mixed volatiles present in adjoining fractures (aka the bulk portion of the system).

DNA Base-Calling from a Nanopore Using a Viterbi Algorithm

PubMed Central

Timp, Winston; Comer, Jeffrey; Aksimentiev, Aleksei

2012-01-01

Nanopore-based DNA sequencing is the most promising third-generation sequencing method. It has superior read length, speed, and sample requirements compared with state-of-the-art second-generation methods. However, base-calling still presents substantial difficulty because the resolution of the technique is limited compared with the measured signal/noise ratio. Here we demonstrate a method to decode 3-bp-resolution nanopore electrical measurements into a DNA sequence using a Hidden Markov model. This method shows tremendous potential for accuracy (∼98%), even with a poor signal/noise ratio. PMID:22677395

Nanoporous Microsphere Assembly of Iodine-Functionalised Silver Nanoparticles as a Novel Mini-Substrate for Enriching and Sensing

NASA Astrophysics Data System (ADS)

Wu, X.-L.; Wu, H.; Wang, Z.-M.; Aizawa, H.; Guo, J.; Chu, Y.-H.

2017-04-01

Herein, debris particulates of nanoporous silver (np-Ag) were synthesised by a dealloying method, and their integration behaviour and surface-enhanced Raman scattering (SERS) properties during iodine functionalisation were examined. It was found that the dealloyed np-Ag debris particulates gradually assembled to form rigid nanoporous microspheres comprising Ag nano-ligaments due to mechanical collisions during iodine treatment. High-resolution transmission electron microscopy and X-ray photoelectron microscopy clearly showed the iodide surface of np-Ag, which was dotted with iodine or iodide ‘nanoislands’. The exceptional, and unexpected, integration and surface structures result in a highly enhanced localised surface plasmon resonance. Furthermore, the robust nanoporous microspheres can be employed individually as as-produced miniaturised electrodes to electrically enrich target molecules at parts-per-trillion levels, so as to achieve charge selectivity and superior detectability compared with the ordinary SERS effect.

Mapping DNA Methylation with High Throughput Nanopore Sequencing

PubMed Central

Rand, Arthur C.; Jain, Miten; Eizenga, Jordan M.; Musselman-Brown, Audrey; Olsen, Hugh E.; Akeson, Mark

2017-01-01

Chemical modifications to DNA regulate its biological function. We present a framework for mapping methylation to cytosine and adenosine with the Oxford Nanopore Technologies MinION using its ionic current signal. We map three cytosine variants and two adenine variants. The results show that our model is sensitive enough to detect changes in genomic DNA methylation levels as a function of growth phase in E. coli. PMID:28218897

Using a nanopore for single molecule detection and single cell transfection.

PubMed

Nelson, Edward M; Kurz, Volker; Shim, Jiwook; Timp, Winston; Timp, Gregory

2012-07-07

We assert that it is possible to trap and identify proteins, and even (conceivably) manipulate proteins secreted from a single cell (i.e. the secretome) through transfection via electroporation by exploiting the exquisite control over the electrostatic potential available in a nanopore. These capabilities may be leveraged for single cell analysis and transfection with single molecule resolution, ultimately enabling a careful scrutiny of tissue heterogeneity.

Nanopore Force Spectroscopy of Aptamer–Ligand Complexes

PubMed Central

Arnaut, Vera; Langecker, Martin; Simmel, Friedrich C.

2013-01-01

The stability of aptamer–ligand complexes is probed in nanopore-based dynamic force spectroscopy experiments. Specifically, the ATP-binding aptamer is investigated using a backward translocation technique, in which the molecules are initially pulled through an α-hemolysin nanopore from the cis to the trans side of a lipid bilayer membrane, allowed to refold and interact with their target, and then translocated back in the trans–cis direction. From these experiments, the distribution of bound and unbound complexes is determined, which in turn allows determination of the dissociation constant Kd ≈ 0.1 mM of the aptamer and of voltage-dependent unfolding rates. The experiments also reveal differences in binding of the aptamer to AMP, ADP, or ATP ligands. Investigation of an aptamer variant with a stabilized ATP-binding site indicates fast conformational switching of the original aptamer before ATP binding. Nanopore force spectroscopy is also used to study binding of the thrombin-binding aptamer to its target. To detect aptamer–target interactions in this case, the stability of the ligand-free aptamer—containing G-quadruplexes—is tuned via the potassium content of the buffer. Although the presence of thrombin was detected, limitations of the method for aptamers with strong secondary structures and complexes with nanomolar Kd were identified. PMID:24010663

Bilayer membrane interactions with nanofabricated scaffolds

DOE PAGES

Collier, C. Patrick

2015-07-29

Membrane function is facilitated by lateral organization within the lipid bilayer, including phase-separation of lipids into more ordered domains (lipid rafts) and anchoring of the membrane to a cytoskeleton. These features have proven difficult to reproduce in model membrane systems such as black lipid membranes, unilamellar vesicles and supported bilayers. However, advances in micro/nanofabrication have resulted in more realistic synthetic models of membrane-cytoskeleton interactions that can help uncover the design rules responsible for biological membrane formation and organization. This review will focus on describing micro-/nanostructured scaffolds that can emulate the connections of a cellular membrane to an underlying “cytoskeleton”. Thismore » includes molecular-based scaffolds anchored to a solid substrate through surface chemistry, solid-state supports modified by material deposition, lithography and etching, the creation of micro/nanoporous arrays, integration with microfluidics, and droplet-based bilayers at interfaces. Lastly, model systems such as these are increasing our understanding of structure and organization in cell membranes, and how they result in the emergence of functionality at the nanoscale.« less

Label-free histamine detection with nanofluidic diodes through metal ion displacement mechanism.

PubMed

Ali, Mubarak; Ramirez, Patricio; Duznovic, Ivana; Nasir, Saima; Mafe, Salvador; Ensinger, Wolfgang

2017-02-01

We design and characterize a nanofluidic device for the label-free specific detection of histamine neurotransmitter based on a metal ion displacement mechanism. The sensor consists of an asymmetric polymer nanopore fabricated via ion track-etching technique. The nanopore sensor surface having metal-nitrilotriacetic (NTA-Ni 2+ ) chelates is obtained by covalent coupling of native carboxylic acid groups with N α ,N α -bis(carboxymethyl)-l-lysine (BCML), followed by exposure to Ni 2+ ion solution. The BCML immobilization and subsequent Ni 2+ ion complexation with NTA moieties change the surface charge concentration, which has a significant impact on the current-voltage (I-V) curve after chemical modification of the nanopore. The sensing mechanism is based on the displacement of the metal ion from the NTA-Ni 2+ chelates. When the modified pore is exposed to histamine solution, the Ni 2+ ion in NTA-Ni 2+ chelate recognizes histamine through a metal ion coordination displacement process and formation of stable Ni-histamine complexes, leading to the regeneration of metal-free NTA groups on the pore surface, as shown in the current-voltage characteristics. Nanomolar concentrations of the histamine in the working electrolyte can be detected. On the contrary, other neurotransmitters such as glycine, serotonin, gamma-aminobutyric acid, and dopamine do not provoke significant changes in the nanopore electronic signal due to their inability to displace the metal ion and form a stable complex with Ni 2+ ion. The nanofluidic sensor exhibits high sensitivity, specificity and reusability towards histamine detection and can then be used to monitor the concentration of biological important neurotransmitters. Copyright © 2016 Elsevier B.V. All rights reserved.

High performance SERS on nanoporous gold substrates synthesized by chemical de-alloying a Au-based metallic glass

NASA Astrophysics Data System (ADS)

Xue, Yanpeng; Scaglione, Federico; Rizzi, Paola; Battezzati, Livio

2017-12-01

A Au20Cu48Ag7Pd5Si20 metallic glass precursor has been used to synthesize nanoporous gold by chemical de-alloying in a mixture of HNO3 and HF. Gold ligaments of size ranging from 45 to 100 nm were obtained as a function of HNO3 concentration, electrolyte temperature and de-alloying time. The as-prepared nanoporous gold exhibited strong surface enhanced Raman scattering (SERS) effect using 4,4‧-bi-pyridine as probe molecule. For application in melamine sensing, the detection limit of 10-6 M was achieved, which indicated that this biocompatible material has great potential as SERS active substrate.

Micropore and nanopore fabrication in hollow antiresonant reflecting optical waveguides

PubMed Central

Holmes, Matthew R.; Shang, Tao; Hawkins, Aaron R.; Rudenko, Mikhail; Measor, Philip; Schmidt, Holger

2011-01-01

We demonstrate the fabrication of micropore and nanopore features in hollow antiresonant reflecting optical waveguides to create an electrical and optical analysis platform that can size select and detect a single nanoparticle. Micropores (4 μm diameter) are reactive-ion etched through the top SiO2 and SiN layers of the waveguides, leaving a thin SiN membrane above the hollow core. Nanopores are formed in the SiN membranes using a focused ion-beam etch process that provides control over the pore size. Openings as small as 20 nm in diameter are created. Optical loss measurements indicate that micropores did not significantly alter the loss along the waveguide. PMID:21922035

Micropore and nanopore fabrication in hollow antiresonant reflecting optical waveguides.

PubMed

Holmes, Matthew R; Shang, Tao; Hawkins, Aaron R; Rudenko, Mikhail; Measor, Philip; Schmidt, Holger

2010-01-01

We demonstrate the fabrication of micropore and nanopore features in hollow antiresonant reflecting optical waveguides to create an electrical and optical analysis platform that can size select and detect a single nanoparticle. Micropores (4 μm diameter) are reactive-ion etched through the top SiO(2) and SiN layers of the waveguides, leaving a thin SiN membrane above the hollow core. Nanopores are formed in the SiN membranes using a focused ion-beam etch process that provides control over the pore size. Openings as small as 20 nm in diameter are created. Optical loss measurements indicate that micropores did not significantly alter the loss along the waveguide.

Real-time monitoring of H2O2 release from single cells using nanoporous gold microelectrodes decorated with platinum nanoparticles.

PubMed

Xiao, Chong; Liu, Yan-Ling; Xu, Jia-Quan; Lv, Song-Wei; Guo, Shan; Huang, Wei-Hua

2015-06-07

Here, we report a self-supported nanoporous gold microelectrode decorated with well-dispersed and tiny platinum nanoparticles as an electrochemical nonenzymatic hydrogen peroxide biosensor. Nanoporous gold was fabricated by electrochemical alloying/dealloying and then small-sized platinum nanoparticles were electrodeposited uniformly on them. This novel hybrid nanostructure endows the sensor with high sensitivity and selectivity towards the reduction of hydrogen peroxide with a low detection limit of 0.3 nM. The sensor has been successfully applied for the measurement of H2O2 release from a single isolated human breast cancer cell, demonstrating its great potential for further physiological and pathological applications.

A nanoporous alumina microelectrode array for functional cell-chip coupling.

PubMed

Wesche, Manuel; Hüske, Martin; Yakushenko, Alexey; Brüggemann, Dorothea; Mayer, Dirk; Offenhäusser, Andreas; Wolfrum, Bernhard

2012-12-14

The design of electrode interfaces has a strong impact on cell-based bioelectronic applications. We present a new type of microelectrode array chip featuring a nanoporous alumina interface. The chip is fabricated in a combination of top-down and bottom-up processes using state-of-the-art clean room technology and self-assembled generation of nanopores by aluminum anodization. The electrode characteristics are investigated in phosphate buffered saline as well as under cell culture conditions. We show that the modified microelectrodes exhibit decreased impedance compared to planar microelectrodes, which is caused by a nanostructuring effect of the underlying gold during anodization. The stability and biocompatibility of the device are demonstrated by measuring action potentials from cardiomyocyte-like cells growing on top of the chip. Cross sections of the cell-surface interface reveal that the cell membrane seals the nanoporous alumina layer without bending into the sub-50 nm apertures. The nanoporous microelectrode array device may be used as a platform for combining extracellular recording of cell activity with stimulating topographical cues.

Sputtering from a Porous Material by Penetrating Ions

NASA Technical Reports Server (NTRS)

Rodriguez-Nieva, J. F.; Bringa, E. M.; Cassidy, T. A.; Johnson, R. E.; Caro, A.; Fama, M.; Loeffler, M.; Baragiola, R. A.; Farkas, D.

2012-01-01

Porous materials are ubiquitous in the universe and weathering of porous surfaces plays an important role in the evolution of planetary and interstellar materials. Sputtering of porous solids in particular can influence atmosphere formation, surface reflectivity, and the production of the ambient gas around materials in space, Several previous studies and models have shown a large reduction in the sputtering of a porous solid compared to the sputtering of the non-porous solid. Using molecular dynamics simulations we study the sputtering of a nanoporous solid with 55% of the solid density. We calculate the electronic sputtering induced by a fast, penetrating ion, using a thermal spike representation of the deposited energy. We find that sputtering for this porous solid is, surprisingly, the same as that for a full-density solid, even though the sticking coefficient is high.

Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations.

PubMed

Tian, Kai; Chen, Xiaowei; Luan, Binquan; Singh, Prashant; Yang, Zhiyu; Gates, Kent S; Lin, Mengshi; Mustapha, Azlin; Gu, Li-Qun

2018-05-22

Accurate and rapid detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for many fields such as food safety regulation and disease diagnostics. Current detection methods involve laborious sample preparations and expensive characterizations. Here, we investigated a single locked nucleic acid (LNA) approach, facilitated by a nanopore single-molecule sensor, to accurately determine SNPs for detection of Shiga toxin producing Escherichia coli (STEC) serotype O157:H7, and cancer-derived EGFR L858R and KRAS G12D driver mutations. Current LNA applications that require incorporation and optimization of multiple LNA nucleotides. But we found that in the nanopore system, a single LNA introduced in the probe is sufficient to enhance the SNP discrimination capability by over 10-fold, allowing accurate detection of the pathogenic mutant DNA mixed in a large amount of the wild-type DNA. Importantly, the molecular mechanistic study suggests that such a significant improvement is due to the effect of the single-LNA that both stabilizes the fully matched base-pair and destabilizes the mismatched base-pair. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, could be generalized for various applications that need rapid and accurate identification of single-nucleotide variations.

Evaluation of elastic properties of nanoporous silicon oxide thin films by picosecond laser ultrasonics

NASA Astrophysics Data System (ADS)

Mechri, C.; Ruello, P.; Gusev, V.; Breteau, J. M.; Mounier, D.; Henderson, M.; Gibaud, A.; Dourdain, S.

2008-01-01

Picosecond laser ultrasonics uses femtosecond laser pulses for the generation and detection of acoustic pulses with a typical duration between few picoseconds and few hundreds of pico seconds. The shorter the duration of the acoustic pulse is, the more precisely could be made the measurements of the film thickness [C. Thomsen et al., Phys. Rev. B 34, 4129 (1986)] and the elastic modulus by pulse-echo method or through Brillouin scattering detection. In this short communication we report the results of the evaluation of the properties of nanoporous silicon oxide thin films which present potential low-k and thermal barrier properties and are also of great interest for the microelectronic industry to replace the traditional silicate glass films in order to decrease the resistance-capacitance transition delay in the VLSI circuits. Most of the studies that have been carried so far have treated the optical properties of such structures. We report the results of the evaluation of acoustic properties of nanoporous thin films.

Screen-printed SnO2/CNT quasi-solid-state gel-electrolyte supercapacitor

NASA Astrophysics Data System (ADS)

Kuok, Fei-Hong; Liao, Chen-Yu; Chen, Chieh-Wen; Hao, Yu-Chuan; Yu, Ing-Song; Chen, Jian-Zhang

2017-11-01

This study investigates a quasi-solid-state gel-electrolyte supercapacitor fabricated with nanoporous SnO2/CNT nanocomposite electrodes and a polyvinyl alcohol/sulfuric acid (PVA/H2SO4) gel electrolyte. First, pastes containing SnO2 nanoparticles, CNTs, ethyl cellulose, and terpineol are screen-printed onto carbon cloth. A tube furnace is then used for calcining the SnO2/CNT electrodes on carbon cloth. After furnace-calcination, the wettability of SnO2/CNT significantly improved; furthermore, the XPS analysis shows that number of C-O bond and oxygen content significantly decrease after furnace-calcination owing to the burnout of the ethyl cellulose by the furnace calcination processes. The furnace-calcined SnO2/CNT electrodes sandwich the PVA/H2SO4 gel electrolyte to form a supercapacitor. The fabricated supercapacitor exhibits an areal capacitance of 5.61 mF cm-2 when flat and 5.68 mF cm-2 under bending with a bending radius (R) of 1.0 cm. After a 1000 cycle stability test, the capacitance retention rates of the supercapacitor are 96% and 97% when flat and under bending (R  =  1.0 cm), respectively.

High-power direct ethylene glycol fuel cell (DEGFC) based on nanoporous proton-conducting membrane (NP-PCM)

NASA Astrophysics Data System (ADS)

Peled, E.; Livshits, V.; Duvdevani, T.

We recently reported the development of a new nanoporous proton-conducting membrane (NP-PCM) and have applied it in a direct methanol fuel cell (DMFC) and in other direct oxidation fuel cells. The use of the NP-PCM in the DMFC offers several advantages over the Nafion-based DMFC including lower membrane cost, lower methanol crossover which leads to a much higher fuel utilization and higher conductivity. In this work, we found that the 90 °C swelling of the NP-PCM is only 5-8% and that the diffusion constant of methanol at 80-130 °C is higher by a factor of 1.5-3 than that of ethylene glycol (EG). The maximum power density of methanol/oxygen and EG/oxygen FCs equipped with a 100 μm thick NP-PCMs is 400 and 300 mW/cm 2 respectively, higher than that for a DMFC based on Nafion 115 (260 mW/cm 2 [Eletrochem. Solid-State Lett. 4 (4) (2001) A31]. This puts the DEGFC in direct competition with both DMFC and indirect methanol FC. Ethylene glycol (EG) is well known in the automobile industry and in contrast to methanol, its distribution infrastructure already exists, thus it is a promising candidate for practical electric vehicles.

A reference electrode based on polyvinyl butyral (PVB) polymer for decentralized chemical measurements.

PubMed

Guinovart, Tomàs; Crespo, Gastón A; Rius, F Xavier; Andrade, Francisco J

2014-04-22

A new solid-state reference electrode using a polymeric membrane of polyvinyl butyral (PVB), Ag/AgCl and NaCl to be used in decentralized chemical measurements is presented. The electrode is made by drop-casting the membrane cocktail onto a glassy carbon (GC) substrate. A stable potential (less than 1 mV dec(-1)) over a wide range of concentrations for the several chemical species tested is obtained. No significant influence to changes in redox potential, light and pH are observed. The response of this novel electrode shows good correlation when compared with a conventional double-junction reference electrode. Also good long-term stability (90±33 μV/h) and a lifetime of approximately 4 months are obtained. Aspects related to the working mechanisms are discussed. Atomic Force Microscopy (AFM) studies reveal the presence of nanopores and channels on the surface, and electrochemical impedance spectroscopy (EIS) of optimized electrodes show low bulk resistances, usually in the kΩ range, suggesting that a nanoporous polymeric structure is formed in the interface with the solution. Future applications of this electrode as a disposable device for decentralized measurements are discussed. Examples of the utilization on wearable substrates (tattoos, fabrics, etc) are provided. Copyright © 2014 Elsevier B.V. All rights reserved.

DNA base-calling from a nanopore using a Viterbi algorithm.

PubMed

Timp, Winston; Comer, Jeffrey; Aksimentiev, Aleksei

2012-05-16

Nanopore-based DNA sequencing is the most promising third-generation sequencing method. It has superior read length, speed, and sample requirements compared with state-of-the-art second-generation methods. However, base-calling still presents substantial difficulty because the resolution of the technique is limited compared with the measured signal/noise ratio. Here we demonstrate a method to decode 3-bp-resolution nanopore electrical measurements into a DNA sequence using a Hidden Markov model. This method shows tremendous potential for accuracy (~98%), even with a poor signal/noise ratio. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Electrically Conductive and Optically Active Porous Silicon Nanowires

PubMed Central

Qu, Yongquan; Liao, Lei; Li, Yujing; Zhang, Hua; Huang, Yu; Duan, Xiangfeng

2009-01-01

We report the synthesis of vertical silicon nanowire array through a two-step metal-assisted chemical etching of highly doped n-type silicon (100) wafers in a solution of hydrofluoric acid and hydrogen peroxide. The morphology of the as-grown silicon nanowires is tunable from solid nonporous nanowires, nonporous/nanoporous core/shell nanowires, and entirely nanoporous nanowires by controlling the hydrogen peroxide concentration in the etching solution. The porous silicon nanowires retain the single crystalline structure and crystallographic orientation of the starting silicon wafer, and are electrically conductive and optically active with visible photoluminescence. The combination of electronic and optical properties in the porous silicon nanowires may provide a platform for the novel optoelectronic devices for energy harvesting, conversion and biosensing. PMID:19807130

Article coated with flash bonded superhydrophobic particles

DOEpatents

Simpson, John T [Clinton, TN; Blue, Craig A [Knoxville, TN; Kiggans, Jr., James O [Oak Ridge, TN

2010-07-13

A method of making article having a superhydrophobic surface includes: providing a solid body defining at least one surface; applying to the surface a plurality of diatomaceous earth particles and/or particles characterized by particle sizes ranging from at least 100 nm to about 10 .mu.m, the particles being further characterized by a plurality of nanopores, wherein at least some of the nanopores provide flow through porosity, the particles being further characterized by a plurality of spaced apart nanostructured features that include a contiguous, protrusive material; flash bonding the particles to the surface so that the particles are adherently bonded to the surface; and applying a hydrophobic coating layer to the surface and the particles so that the hydrophobic coating layer conforms to the nanostructured features.

Control of both particle and pore size in nanoporous palladium alloy powders

DOE PAGES

Jones, Christopher G.; Cappillino, Patrick J.; Stavila, Vitalie; ...

2014-07-15

Energy storage materials often involve chemical reactions with bulk solids. Porosity within the solids can enhance reaction rates. The porosity can be either within or between individual particles of the material. Greater control of the size and uniformity of both types of pore should lead to enhancements of charging and discharging rates in energy storage systems. Furthermore, to control both particle and pore size in nanoporous palladium (Pd)-based hydrogen storage materials, first we created uniformly sized copper particles of about 1 μm diameter by the reduction of copper sulfate with ascorbic acid. In turn, these were used as reducing agentsmore » for tetrachloropalladate in the presence of a block copolymer surfactant. The copper reductant particles are geometrically self-limiting, so the resulting Pd particles are of similar size. The surfactant induces formation of 10 nm-scale pores within the particles. Some residual copper is alloyed with the Pd, reducing hydrogen storage capacity; use of a more reactive Pd salt can mitigate this. The reaction is conveniently performed in gram-scale batches.« less

In situ solid-state electrochemistry of mass-selected ions at well-defined electrode–electrolyte interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prabhakaran, Venkateshkumar; Johnson, Grant E.; Wang, Bingbing

2016-11-07

Molecular-level understanding of electrochemical processes occurring at electrode-electrolyte interfaces (EEI) is key to the rational development of high-performance and sustainable electrochemical technologies. This article reports the development and first application of solid-state in situ electrochemical probes to study redox and catalytic processes occurring at well-defined EEI generated using soft-landing of mass- and charge-selected cluster ions (SL). In situ electrochemical probes with excellent mass transfer properties are fabricated using carefully-designed nanoporous ionic liquid membranes. SL enables deposition of pure active species that are not obtainable with other techniques onto electrode surfaces with precise control over charge state, composition, and kinetic energy.more » SL is, therefore, a unique tool for studying fundamental processes occurring at EEI. For the first time using an aprotic electrochemical probe, the effect of charge state (PMo12O403-/2-) and the contribution of building blocks of Keggin polyoxometalate (POM) clusters to redox processes are characterized by populating EEI with novel POM anions generated by electrospray ionization and gas phase dissociation. Additionally, a proton conducting electrochemical probe has been developed to characterize the reactive electrochemistry (oxygen reduction activity) of bare Pt clusters (Pt40 ~1 nm diameter), thus demonstrating the capability of the probe for studying reactions in controlled gaseous environments. The newly developed in situ electrochemical probes combined with ion SL provide a versatile method to characterize the EEI in solid-state redox systems and reactive electrochemistry at precisely-defined conditions. This capability will advance molecular-level understanding of processes occurring at EEI that are critical to many energy-related technologies.« less

Quantifying short-lived events in multistate ionic current measurements.

PubMed

Balijepalli, Arvind; Ettedgui, Jessica; Cornio, Andrew T; Robertson, Joseph W F; Cheung, Kin P; Kasianowicz, John J; Vaz, Canute

2014-02-25

We developed a generalized technique to characterize polymer-nanopore interactions via single channel ionic current measurements. Physical interactions between analytes, such as DNA, proteins, or synthetic polymers, and a nanopore cause multiple discrete states in the current. We modeled the transitions of the current to individual states with an equivalent electrical circuit, which allowed us to describe the system response. This enabled the estimation of short-lived states that are presently not characterized by existing analysis techniques. Our approach considerably improves the range and resolution of single-molecule characterization with nanopores. For example, we characterized the residence times of synthetic polymers that are three times shorter than those estimated with existing algorithms. Because the molecule's residence time follows an exponential distribution, we recover nearly 20-fold more events per unit time that can be used for analysis. Furthermore, the measurement range was extended from 11 monomers to as few as 8. Finally, we applied this technique to recover a known sequence of single-stranded DNA from previously published ion channel recordings, identifying discrete current states with subpicoampere resolution.

Gas adsorption and capillary condensation in nanoporous alumina films.

PubMed

Casanova, Fèlix; Chiang, Casey E; Li, Chang-Peng; Roshchin, Igor V; Ruminski, Anne M; Sailor, Michael J; Schuller, Ivan K

2008-08-06

Gas adsorption and capillary condensation of organic vapors are studied by optical interferometry, using anodized nanoporous alumina films with controlled geometry (cylindrical pores with diameters in the range of 10-60 nm). The optical response of the film is optimized with respect to the geometric parameters of the pores, for potential performance as a gas sensor device. The average thickness of the adsorbed film at low relative pressures is not affected by the pore size. Capillary evaporation of the liquid from the nanopores occurs at the liquid-vapor equilibrium described by the classical Kelvin equation with a hemispherical meniscus. Due to the almost complete wetting, we can quantitatively describe the condensation for isopropanol using the Cohan model with a cylindrical meniscus in the Kelvin equation. This model describes the observed hysteresis and allows us to use the adsorption branch of the isotherm to calculate the pore size distribution of the sample in good agreement with independent structural measurements. The condensation for toluene lacks reproducibility due to incomplete surface wetting. This exemplifies the relevant role of the fluid-solid (van der Waals) interactions in the hysteretic behavior of capillary condensation.

Nanoporous Hybrid Electrolytes for High-Energy Batteries Based on Reactive Metal Anodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tu, Zhengyuan; Zachman, Michael J.; Choudhury, Snehashis

2017-01-06

Successful strategies for stabilizing electrodeposition of reactive metals, including lithium, sodium, and aluminum are a requirement for safe, high-energy electrochemical storage technologies that utilize these metals as anodes. Unstable deposition produces high-surface area dendritic structures at the anode/electrolyte interface, which causes premature cell failure by complex physical and chemical processes that have presented formidable barriers to progress. Here, it is reported that hybrid electrolytes created by infusing conventional liquid electrolytes into nanoporous membranes provide exceptional ability to stabilize Li. Electrochemical cells based on γ-Al2O3 ceramics with pore diameters below a cut-off value above 200 nm exhibit long-term stability even atmore » a current density of 3 mA cm-2. The effect is not limited to ceramics; similar large enhancements in stability are observed for polypropylene membranes with less monodisperse pores below 450 nm. These findings are critically assessed using theories for ion rectification and electrodeposition reactions in porous solids and show that the source of stable electrodeposition in nanoporous electrolytes is fundamental.« less

Sensing small neurotransmitter-enzyme interaction with nanoporous gated ion-sensitive field effect transistors.

PubMed

Kisner, Alexandre; Stockmann, Regina; Jansen, Michael; Yegin, Ugur; Offenhäusser, Andreas; Kubota, Lauro Tatsuo; Mourzina, Yulia

2012-01-15

Ion-sensitive field effect transistors with gates having a high density of nanopores were fabricated and employed to sense the neurotransmitter dopamine with high selectivity and detectability at micromolar range. The nanoporous structure of the gates was produced by applying a relatively simple anodizing process, which yielded a porous alumina layer with pores exhibiting a mean diameter ranging from 20 to 35 nm. Gate-source voltages of the transistors demonstrated a pH-dependence that was linear over a wide range and could be understood as changes in surface charges during protonation and deprotonation. The large surface area provided by the pores allowed the physical immobilization of tyrosinase, which is an enzyme that oxidizes dopamine, on the gates of the transistors, and thus, changes the acid-base behavior on their surfaces. Concentration-dependent dopamine interacting with immobilized tyrosinase showed a linear dependence into a physiological range of interest for dopamine concentration in the changes of gate-source voltages. In comparison with previous approaches, a response time relatively fast for detecting dopamine was obtained. Additionally, selectivity assays for other neurotransmitters that are abundantly found in the brain were examined. These results demonstrate that the nanoporous structure of ion-sensitive field effect transistors can easily be used to immobilize specific enzyme that can readily and selectively detect small neurotransmitter molecule based on its acid-base interaction with the receptor. Therefore, it could serve as a technology platform for molecular studies of neurotransmitter-enzyme binding and drugs screening. Copyright © 2011 Elsevier B.V. All rights reserved.

Bilayer-Spanning DNA Nanopores with Voltage-Switching between Open and Closed State

PubMed Central

2014-01-01

Membrane-spanning nanopores from folded DNA are a recent example of biomimetic man-made nanostructures that can open up applications in biosensing, drug delivery, and nanofluidics. In this report, we generate a DNA nanopore based on the archetypal six-helix-bundle architecture and systematically characterize it via single-channel current recordings to address several fundamental scientific questions in this emerging field. We establish that the DNA pores exhibit two voltage-dependent conductance states. Low transmembrane voltages favor a stable high-conductance level, which corresponds to an unobstructed DNA pore. The expected inner width of the open channel is confirmed by measuring the conductance change as a function of poly(ethylene glycol) (PEG) size, whereby smaller PEGs are assumed to enter the pore. PEG sizing also clarifies that the main ion-conducting path runs through the membrane-spanning channel lumen as opposed to any proposed gap between the outer pore wall and the lipid bilayer. At higher voltages, the channel shows a main low-conductance state probably caused by electric-field-induced changes of the DNA pore in its conformation or orientation. This voltage-dependent switching between the open and closed states is observed with planar lipid bilayers as well as bilayers mounted on glass nanopipettes. These findings settle a discrepancy between two previously published conductances. By systematically exploring a large space of parameters and answering key questions, our report supports the development of DNA nanopores for nanobiotechnology. PMID:25338165

Bilayer-spanning DNA nanopores with voltage-switching between open and closed state.

PubMed

Seifert, Astrid; Göpfrich, Kerstin; Burns, Jonathan R; Fertig, Niels; Keyser, Ulrich F; Howorka, Stefan

2015-02-24

Membrane-spanning nanopores from folded DNA are a recent example of biomimetic man-made nanostructures that can open up applications in biosensing, drug delivery, and nanofluidics. In this report, we generate a DNA nanopore based on the archetypal six-helix-bundle architecture and systematically characterize it via single-channel current recordings to address several fundamental scientific questions in this emerging field. We establish that the DNA pores exhibit two voltage-dependent conductance states. Low transmembrane voltages favor a stable high-conductance level, which corresponds to an unobstructed DNA pore. The expected inner width of the open channel is confirmed by measuring the conductance change as a function of poly(ethylene glycol) (PEG) size, whereby smaller PEGs are assumed to enter the pore. PEG sizing also clarifies that the main ion-conducting path runs through the membrane-spanning channel lumen as opposed to any proposed gap between the outer pore wall and the lipid bilayer. At higher voltages, the channel shows a main low-conductance state probably caused by electric-field-induced changes of the DNA pore in its conformation or orientation. This voltage-dependent switching between the open and closed states is observed with planar lipid bilayers as well as bilayers mounted on glass nanopipettes. These findings settle a discrepancy between two previously published conductances. By systematically exploring a large space of parameters and answering key questions, our report supports the development of DNA nanopores for nanobiotechnology.

Single-Molecule Titration in a Protein Nanoreactor Reveals the Protonation/Deprotonation Mechanism of a C:C Mismatch in DNA.

PubMed

Ren, Hang; Cheyne, Cameron G; Fleming, Aaron M; Burrows, Cynthia J; White, Henry S

2018-04-18

Measurement of single-molecule reactions can elucidate microscopic mechanisms that are often hidden from ensemble analysis. Herein, we report the acid-base titration of a single DNA duplex confined within the wild-type α-hemolysin (α-HL) nanopore for up to 3 h, while monitoring the ionic current through the nanopore. Modulation between two states in the current-time trace for duplexes containing the C:C mismatch in proximity to the latch constriction of α-HL is attributed to the base flipping of the C:C mismatch. As the pH is lowered, the rate for the C:C mismatch to flip from the intra-helical state to the extra-helical state ( k intra-extra ) decreases, while the rate for base flipping from the extra-helical state to the intra-helical state ( k extra-intra ) remains unchanged. Both k intra-extra and k extra-intra are on the order of 1 × 10 -2 s -1 to 1 × 10 -1 s -1 and remain stable over the time scale of the measurement (several hours). Analysis of the pH-dependent kinetics of base flipping using a hidden Markov kinetic model demonstrates that protonation/deprotonation occurs while the base pair is in the intra-helical state. We also demonstrate that the rate of protonation is limited by transport of H + into the α-HL nanopore. Single-molecule kinetic isotope experiments exhibit a large kinetic isotope effect (KIE) for k intra-extra ( k H / k D ≈ 5) but a limited KIE for k extra-intra ( k H / k D ≈ 1.3), supporting our model. Our experiments correspond to the longest single-molecule measurements performed using a nanopore, and demonstrate its application in interrogating mechanisms of single-molecule reactions in confined geometries.

Microimaging of transient guest profiles to monitor mass transfer in nanoporous materials

NASA Astrophysics Data System (ADS)

Kärger, Jörg; Binder, Tomas; Chmelik, Christian; Hibbe, Florian; Krautscheid, Harald; Krishna, Rajamani; Weitkamp, Jens

2014-04-01

The intense interactions of guest molecules with the pore walls of nanoporous materials is the subject of continued fundamental research. Stimulated by their thermal energy, the guest molecules in these materials are subject to a continuous, irregular motion, referred to as diffusion. Diffusion, which is omnipresent in nature, influences the efficacy of nanoporous materials in reaction and separation processes. The recently introduced techniques of microimaging by interference and infrared microscopy provide us with a wealth of information on diffusion, hitherto inaccessible from commonly used techniques. Examples include the determination of surface barriers and the sticking coefficient's analogue, namely the probability that, on colliding with the particle surface, a molecule may continue its diffusion path into the interior. Microimaging is further seen to open new vistas in multicomponent guest diffusion (including the detection of a reversal in the preferred diffusion pathways), in guest-induced phase transitions in nanoporous materials and in matching the results of diffusion studies under equilibrium and non-equilibrium conditions.

Solid-liquid critical behavior of water in nanopores.

PubMed

Mochizuki, Kenji; Koga, Kenichiro

2015-07-07

Nanoconfined liquid water can transform into low-dimensional ices whose crystalline structures are dissimilar to any bulk ices and whose melting point may significantly rise with reducing the pore size, as revealed by computer simulation and confirmed by experiment. One of the intriguing, and as yet unresolved, questions concerns the observation that the liquid water may transform into a low-dimensional ice either via a first-order phase change or without any discontinuity in thermodynamic and dynamic properties, which suggests the existence of solid-liquid critical points in this class of nanoconfined systems. Here we explore the phase behavior of a model of water in carbon nanotubes in the temperature-pressure-diameter space by molecular dynamics simulation and provide unambiguous evidence to support solid-liquid critical phenomena of nanoconfined water. Solid-liquid first-order phase boundaries are determined by tracing spontaneous phase separation at various temperatures. All of the boundaries eventually cease to exist at the critical points and there appear loci of response function maxima, or the Widom lines, extending to the supercritical region. The finite-size scaling analysis of the density distribution supports the presence of both first-order and continuous phase changes between solid and liquid. At around the Widom line, there are microscopic domains of two phases, and continuous solid-liquid phase changes occur in such a way that the domains of one phase grow and those of the other evanesce as the thermodynamic state departs from the Widom line.

Method and apparatus for acoustic plate mode liquid-solid phase transition detection

DOEpatents

Blair, Dianna S.; Freye, Gregory C.; Hughes, Robert C.; Martin, Stephen J.; Ricco, Antonio J.

1993-01-01

A method and apparatus for sensing a liquid-solid phase transition event is provided which comprises an acoustic plate mode detecting element placed in contact with a liquid or solid material which generates a high-frequency acoustic wave that is attenuated to an extent based on the physical state of the material is contact with the detecting element. The attenuation caused by the material in contact with the acoustic plate mode detecting element is used to determine the physical state of the material being detected. The method and device are particularly suited for detecting conditions such as the icing and deicing of wings of an aircraft. In another aspect of the present invention, a method is provided wherein the adhesion of a solid material to the detecting element can be measured using the apparatus of the invention.

Nanoscale Investigation of Generation 1 PAMAM Dendrimers Interaction with a Protein Nanopore.

PubMed

Asandei, Alina; Ciuca, Andrei; Apetrei, Aurelia; Schiopu, Irina; Mereuta, Loredana; Seo, Chang Ho; Park, Yoonkyung; Luchian, Tudor

2017-07-21

Herein, we describe at uni-molecular level the interactions between poly(amidoamine) (PAMAM) dendrimers of generation 1 and the α-hemolysin protein nanopore, at acidic and neutral pH, and ionic strengths of 0.5 M and 1 M KCl, via single-molecule electrical recordings. The results indicate that kinetics of dendrimer-α-hemolysin reversible interactions is faster at neutral as compared to acidic pH, and we propose as a putative explanation the fine interplay among conformational and rigidity changes on the dendrimer structure, and the ionization state of the dendrimer and the α-hemolysin. From the analysis of the dendrimer's residence time inside the nanopore, we posit that the pH- and salt-dependent, long-range electrostatic interactions experienced by the dendrimer inside the ion-selective α-hemolysin, induce a non-Stokesian diffusive behavior of the analyte inside the nanopore. We also show that the ability of dendrimer molecules to adapt their structure to nanoscopic spaces, and control the flow of matter through the α-hemolysin nanopore, depends non-trivially on the pH- and salt-induced conformational changes of the dendrimer.

Novel nanoporous sorbent for solid-phase extraction in petroleum fingerprinting

NASA Astrophysics Data System (ADS)

Alayande, S. Oluwagbemiga; Hlengilizwe, Nyoni; Dare, E. Olugbenga; Msagati, Titus A. M.; Akinlabi, A. Kehinde; Aiyedun, P. O.

2016-04-01

Sample preparation is crucial in the analysis of petroleum and its derivatives. In this study, developing affordable sorbent for petroleum fingerprinting analysis using polymer waste such expanded polystyrene was explored. The potential of electrospun expanded polystyrene (EPS) as a sorbent for the solid-phase extraction (SPE) technique was investigated, and its efficiency was compared with commercial cartridges such as alumina, silica and alumina/silica hybrid commercial for petroleum fingerprinting analysis. The chromatograms showed that the packed electrospun EPS fibre demonstrated excellent properties for SPE applications relative to the hybrid cartridges.

Advances in nanopore sensing promises to transform healthcare.

PubMed

Haque, Farzin; Wang, Shaoying; Wu, Taoxiang; Guo, Peixuan

2017-08-01

International Conference on Nanopore Technology (Shenzhen), 30 March-1 April 2017, Shenzhen, China The International Conference on Nanopore Technology (Shenzhen) was held from 30 March to 1 April 2017 in Shenzhen, China. The goal of the meeting was threefold: leverage the unique properties of nanopore technology to promote transformative advances in medicine, encourage cross-disciplinary collaborations in the research community within China and abroad; and discuss critical challenges that need to be addressed to rapidly advance the field. The meeting was chaired by Peixuan Guo, Endowed chair professor and Director of The Center for RNA Nanobiotechnology & Nanomedicine at The Ohio State University, USA and co-chaired by Xian-En Zhang, distinguished professor of the Institute of Biophysics, Chinese Academy of Sciences, China. The conference was attended by more than 300 academic researchers, hospital administrators, government leaders and scientists from many disciplines across the country from both academic institutions and industry.

Nanoporous-Gold-Based Electrode Morphology Libraries for Investigating Structure-Property Relationships in Nucleic Acid Based Electrochemical Biosensors.

PubMed

Matharu, Zimple; Daggumati, Pallavi; Wang, Ling; Dorofeeva, Tatiana S; Li, Zidong; Seker, Erkin

2017-04-19

Nanoporous gold (np-Au) electrode coatings significantly enhance the performance of electrochemical nucleic acid biosensors because of their three-dimensional nanoscale network, high electrical conductivity, facile surface functionalization, and biocompatibility. Contrary to planar electrodes, the np-Au electrodes also exhibit sensitive detection in the presence of common biofouling media due to their porous structure. However, the pore size of the nanomatrix plays a critical role in dictating the extent of biomolecular capture and transport. Small pores perform better in the case of target detection in complex samples by filtering out the large nonspecific proteins. On the other hand, larger pores increase the accessibility of target nucleic acids in the nanoporous structure, enhancing the detection limits of the sensor at the expense of more interference from biofouling molecules. Here, we report a microfabricated np-Au multiple electrode array that displays a range of electrode morphologies on the same chip for identifying feature sizes that reduce the nonspecific adsorption of proteins but facilitate the permeation of target DNA molecules into the pores. We demonstrate the utility of the electrode morphology library in studying DNA functionalization and target detection in complex biological media with a special emphasis on revealing ranges of electrode morphologies that mutually enhance the limit of detection and biofouling resilience. We expect this technique to assist in the development of high-performance biosensors for point-of-care diagnostics and facilitate studies on the electrode structure-property relationships in potential applications ranging from neural electrodes to catalysts.

Asymmetric nanopore membranes: Single molecule detection and unique transport properties

NASA Astrophysics Data System (ADS)

Bishop, Gregory William

Biological systems rely on the transport properties of transmembrane channels. Such pores can display selective transport by allowing the passage of certain ions or molecules while rejecting others. Recent advances in nanoscale fabrication have allowed the production of synthetic analogs of such channels. Synthetic nanopores (pores with a limiting dimension of 1--100 nm) can be produced in a variety of materials by several different methods. In the Martin group, we have been exploring the track-etch method to produce asymmetric nanopores in thin films of polymeric or crystalline materials. Asymmetric nanopores are of particular interest due to their ability to serve as ion-current rectifiers. This means that when a membrane that contains such a pore or collection of pores is used to separate identical portions of electrolyte solution, the magnitude of the ionic current will depend not only on the magnitude of the applied potential (as expected) but also the polarity. Ion-current rectification is characterized by an asymmetric current--potential response. Here, the interesting transport properties of asymmetric nanopores (ion-current rectification and the related phenomenon of electroosmotic flow rectification) are explored. The effects of pore shape and pore density on these phenomena are investigated. Membranes that contain a single nanopore can serve as platforms for the single-molecule sensing technique known as resistive pulse sensing. The resistive-pulse sensing method is based on the Coulter principle. Thus, the selectivity of the technique is based largely upon size, making the analysis of mixtures by this method difficult in many cases. Here, the surface of a single nanopore membrane is modified with a molecular recognition agent in an attempt to obtain a more selective resistive-pulse sensor for a specific analyte.

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer.

PubMed

Istace, Benjamin; Friedrich, Anne; d'Agata, Léo; Faye, Sébastien; Payen, Emilie; Beluche, Odette; Caradec, Claudia; Davidas, Sabrina; Cruaud, Corinne; Liti, Gianni; Lemainque, Arnaud; Engelen, Stefan; Wincker, Patrick; Schacherer, Joseph; Aury, Jean-Marc

2017-02-01

Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive; it has the potential to revolutionize genomic applications due to its portability, low cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed. Here, we resequenced the genome of the Saccharomyces cerevisiae S288C strain to evaluate the performance of nanopore-only assemblers. Then we de novo sequenced and assembled the genomes of 21 isolates representative of the S. cerevisiae genetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65 % of the chromosomes. This high contiguity allowed us to accurately detect large structural variations across the 21 studied genomes. Because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy. Our analyses show that the Oxford Nanopore technology is already usable for de novo sequencing and assembly; however, non-random errors in homopolymers require polishing the consensus using an alternate sequencing technology. © The Author 2017. Published by Oxford University Press.

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

PubMed Central

Istace, Benjamin; Friedrich, Anne; d'Agata, Léo; Faye, Sébastien; Payen, Emilie; Beluche, Odette; Caradec, Claudia; Davidas, Sabrina; Cruaud, Corinne; Liti, Gianni; Lemainque, Arnaud; Engelen, Stefan; Wincker, Patrick; Schacherer, Joseph

2017-01-01

Abstract Background: Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive; it has the potential to revolutionize genomic applications due to its portability, low cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome. Combined with existing assembler algorithms, near complete genome assemblies can be generated and comprehensive population genomic analyses can be performed. Results: Here, we resequenced the genome of the Saccharomyces cerevisiae S288C strain to evaluate the performance of nanopore-only assemblers. Then we de novo sequenced and assembled the genomes of 21 isolates representative of the S. cerevisiae genetic diversity using the MinION platform. The contiguity of our assemblies was 14 times higher than the Illumina-only assemblies and we obtained one or two long contigs for 65 % of the chromosomes. This high contiguity allowed us to accurately detect large structural variations across the 21 studied genomes. Conclusion: Because of the high completeness of the nanopore assemblies, we were able to produce a complete cartography of transposable elements insertions and inspect structural variants that are generally missed using a short-read sequencing strategy. Our analyses show that the Oxford Nanopore technology is already usable for de novo sequencing and assembly; however, non-random errors in homopolymers require polishing the consensus using an alternate sequencing technology. PMID:28369459

Vapor-Phase Deposition and Modification of Metal-Organic Frameworks: State-of-the-Art and Future Directions.

PubMed

Stassen, Ivo; De Vos, Dirk; Ameloot, Rob

2016-10-04

Materials processing, and thin-film deposition in particular, is decisive in the implementation of functional materials in industry and real-world applications. Vapor processing of materials plays a central role in manufacturing, especially in electronics. Metal-organic frameworks (MOFs) are a class of nanoporous crystalline materials on the brink of breakthrough in many application areas. Vapor deposition of MOF thin films will facilitate their implementation in micro- and nanofabrication research and industries. In addition, vapor-solid modification can be used for postsynthetic tailoring of MOF properties. In this context, we review the recent progress in vapor processing of MOFs, summarize the underpinning chemistry and principles, and highlight promising directions for future research. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

New Electrochemical Methods for Studying Nanoparticle Electrocatalysis and Neuronal Exocytosis

NASA Astrophysics Data System (ADS)

Cox, Jonathan T.

This dissertation presents the construction and application of micro and nanoscale electrodes for electroanalytical analysis. The studies presented herein encompass two main areas: electrochemical catalysis, and studies of the dynamics of single cell exocytosis. The first portion of this dissertation engages the use of Pt nanoelectrodes to study the stability and electrocatalytic properties of materials. A single nanoparticle electrode (SNPE) was fabricated by immobilizing a single Au nanoparticle on a Pt disk nanoelectrode via an amine-terminated silane cross linker. In this manner we were able to effectively study the electrochemistry and electrocatalytic activity of single Au nanoparticles and found that the electrocatalytic activity is dependent on nanoparticle size. This study can further the understanding of the structure-function relationship in nanoparticle based electrocatalysis. Further work was conducted to probe the stability of Pt nanoelectrodes under conditions of potential cycling. Pt based catalysts are known to deteriorate under such conditions due to losses in electrochemical surface area and Pt dissolution. By using Pt disk nanoelectrodes we were able to study Pt dissolution via steady-state voltammetry. We observed an enhanced dissolution rate and higher charge density on nanoelectrodes than that previously found on macro scale electrodes. The goal of the second portion of this dissertation is to develop new analytical methods to study the dynamics of exocytosis from single cells. The secretion of neurotransmitters plays a key role in neuronal communication, and our studies highlight how bipolar electrochemistry can be employed to enhance detection of neurotransmitters from single cells. First, we developed a theory to quantitatively characterize the voltammetric behavior of bipolar carbon fiber microelectrodes and secondly applied those principles to single cell detection. We showed that by simply adding an additional redox mediator to the back-fill solution of a carbon fiber microelectrode, there is a significant enhancement in detection. Additionally we used solid state nanopores to detect individual phospholipid vesicles in solution. Vesicles are key cellular components that play essential biological roles especially in neurotransmission. This work represents preliminary studies in detection and size determination from vesicles isolated from individual cells.

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

PubMed

Senol Cali, Damla; Kim, Jeremie S; Ghose, Saugata; Alkan, Can; Mutlu, Onur

2018-04-02

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. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs 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, to overcome the high error rates of the nanopore sequencing technology.

Nanoporous Anodic Alumina: A Versatile Platform for Optical Biosensors

PubMed Central

Santos, Abel; Kumeria, Tushar; Losic, Dusan

2014-01-01

Nanoporous anodic alumina (NAA) has become one of the most promising nanomaterials in optical biosensing as a result of its unique physical and chemical properties. Many studies have demonstrated the outstanding capabilities of NAA for developing optical biosensors in combination with different optical techniques. These results reveal that NAA is a promising alternative to other widely explored nanoporous platforms, such as porous silicon. This review is aimed at reporting on the recent advances and current stage of development of NAA-based optical biosensing devices. The different optical detection techniques, principles and concepts are described in detail along with relevant examples of optical biosensing devices using NAA sensing platforms. Furthermore, we summarise the performance of these devices and provide a future perspective on this promising research field. PMID:28788678

Rational Design of Photonic Dust from Nanoporous Anodic Alumina Films: A Versatile Photonic Nanotool for Visual Sensing

PubMed Central

Chen, Yuting; Santos, Abel; Wang, Ye; Kumeria, Tushar; Ho, Daena; Li, Junsheng; Wang, Changhai; Losic, Dusan

2015-01-01

Herein, we present a systematic study on the development, optimisation and applicability of interferometrically coloured distributed Bragg reflectors based on nanoporous anodic alumina (NAA-DBRs) in the form of films and nanoporous microparticles as visual/colorimetric analytical tools. Firstly, we synthesise a complete palette of NAA-DBRs by galvanostatic pulse anodisation approach, in which the current density is altered in a periodic fashion in order to engineer the effective medium of the resulting photonic films in depth. NAA-DBR photonic films feature vivid colours that can be tuned across the UV-visible-NIR spectrum by structural engineering. Secondly, the effective medium of the resulting photonic films is assessed systematically by visual analysis and reflectometric interference spectroscopy (RIfS) in order to establish the most optimal nanoporous platforms to develop visual/colorimetric tools. Then, we demonstrate the applicability of NAA-DBR photonic films as a chemically selective sensing platform for visual detection of mercury(II) ions. Finally, we generate a new nanomaterial, so-called photonic dust, by breaking down NAA-DBRs films into nanoporous microparticles. The resulting microparticles (μP-NAA-DBRs) display vivid colours and are sensitive towards changes in their effective medium, opening new opportunities for developing advanced photonic nanotools for a broad range of applications. PMID:26245759

Nanoporous membranes enable concentration and transport in fully wet paper-based assays.

PubMed

Gong, Max M; Zhang, Pei; MacDonald, Brendan D; Sinton, David

2014-08-19

Low-cost paper-based assays are emerging as the platform for diagnostics worldwide. Paper does not, however, readily enable advanced functionality required for complex diagnostics, such as analyte concentration and controlled analyte transport. That is, after the initial wetting, no further analyte manipulation is possible. Here, we demonstrate active concentration and transport of analytes in fully wet paper-based assays by leveraging nanoporous material (mean pore diameter ≈ 4 nm) and ion concentration polarization. Two classes of devices are developed, an external stamp-like device with the nanoporous material separate from the paper-based assay, and an in-paper device patterned with the nanoporous material. Experimental results demonstrate up to 40-fold concentration of a fluorescent tracer in fully wet paper, and directional transport of the tracer over centimeters with efficiencies up to 96%. In-paper devices are applied to concentrate protein and colored dye, extending their limits of detection from ∼10 to ∼2 pmol/mL and from ∼40 to ∼10 μM, respectively. This approach is demonstrated in nitrocellulose membrane as well as paper, and the added cost of the nanoporous material is very low at ∼0.015 USD per device. The result is a major advance in analyte concentration and manipulation for the growing field of low-cost paper-based assays.

Rational Design of Photonic Dust from Nanoporous Anodic Alumina Films: A Versatile Photonic Nanotool for Visual Sensing

NASA Astrophysics Data System (ADS)

Chen, Yuting; Santos, Abel; Wang, Ye; Kumeria, Tushar; Ho, Daena; Li, Junsheng; Wang, Changhai; Losic, Dusan

2015-08-01

Herein, we present a systematic study on the development, optimisation and applicability of interferometrically coloured distributed Bragg reflectors based on nanoporous anodic alumina (NAA-DBRs) in the form of films and nanoporous microparticles as visual/colorimetric analytical tools. Firstly, we synthesise a complete palette of NAA-DBRs by galvanostatic pulse anodisation approach, in which the current density is altered in a periodic fashion in order to engineer the effective medium of the resulting photonic films in depth. NAA-DBR photonic films feature vivid colours that can be tuned across the UV-visible-NIR spectrum by structural engineering. Secondly, the effective medium of the resulting photonic films is assessed systematically by visual analysis and reflectometric interference spectroscopy (RIfS) in order to establish the most optimal nanoporous platforms to develop visual/colorimetric tools. Then, we demonstrate the applicability of NAA-DBR photonic films as a chemically selective sensing platform for visual detection of mercury(II) ions. Finally, we generate a new nanomaterial, so-called photonic dust, by breaking down NAA-DBRs films into nanoporous microparticles. The resulting microparticles (μP-NAA-DBRs) display vivid colours and are sensitive towards changes in their effective medium, opening new opportunities for developing advanced photonic nanotools for a broad range of applications.

Single-molecule study of thymidine glycol and i-motif through the alpha-hemolysin ion channel

NASA Astrophysics Data System (ADS)

He, Lidong

Nanopore-based devices have emerged as a single-molecule detection and analysis tool for a wide range of applications. Through electrophoretically driving DNA molecules across a nanosized pore, a lot of information can be received, including unfolding kinetics and DNA-protein interactions. This single-molecule method has the potential to sequence kilobase length DNA polymers without amplification or labeling, approaching "the third generation" genome sequencing for around $1000 within 24 hours. alpha-Hemolysin biological nanopores have the advantages of excellent stability, low-noise level, and precise site-directed mutagenesis for engineering this protein nanopore. The first work presented in this thesis established the current signal of the thymidine glycol lesion in DNA oligomers through an immobilization experiment. The thymidine glycol enantiomers were differentiated from each other by different current blockage levels. Also, the effect of bulky hydrophobic adducts to the current blockage was investigated. Secondly, the alpha-hemolysin nanopore was used to study the human telomere i-motif and RET oncogene i-motif at a single-molecule level. In Chapter 3, it was demonstrated that the alpha-hemolysin nanopore can differentiate an i-motif form and single-strand DNA form at different pH values based on the same sequence. In addition, it shows potential to differentiate the folding topologies generated from the same DNA sequence.

Single-molecule DNA detection with an engineered MspA protein nanopore

PubMed Central

Butler, Tom Z.; Pavlenok, Mikhail; Derrington, Ian M.; Niederweis, Michael; Gundlach, Jens H.

2008-01-01

Nanopores hold great promise as single-molecule analytical devices and biophysical model systems because the ionic current blockades they produce contain information about the identity, concentration, structure, and dynamics of target molecules. The porin MspA of Mycobacterium smegmatis has remarkable stability against environmental stresses and can be rationally modified based on its crystal structure. Further, MspA has a short and narrow channel constriction that is promising for DNA sequencing because it may enable improved characterization of short segments of a ssDNA molecule that is threaded through the pore. By eliminating the negative charge in the channel constriction, we designed and constructed an MspA mutant capable of electronically detecting and characterizing single molecules of ssDNA as they are electrophoretically driven through the pore. A second mutant with additional exchanges of negatively-charged residues for positively-charged residues in the vestibule region exhibited a factor of ≈20 higher interaction rates, required only half as much voltage to observe interaction, and allowed ssDNA to reside in the vestibule ≈100 times longer than the first mutant. Our results introduce MspA as a nanopore for nucleic acid analysis and highlight its potential as an engineerable platform for single-molecule detection and characterization applications. PMID:19098105

Detection of target-probe oligonucleotide hybridization using synthetic nanopore resistive pulse sensing.

PubMed

Booth, Marsilea Adela; Vogel, Robert; Curran, James M; Harbison, SallyAnn; Travas-Sejdic, Jadranka

2013-07-15

Despite the plethora of DNA sensor platforms available, a portable, sensitive, selective and economic sensor able to rival current fluorescence-based techniques would find use in many applications. In this research, probe oligonucleotide-grafted particles are used to detect target DNA in solution through a resistive pulse nanopore detection technique. Using carbodiimide chemistry, functionalized probe DNA strands are attached to carboxylated dextran-based magnetic particles. Subsequent incubation with complementary target DNA yields a change in surface properties as the two DNA strands hybridize. Particle-by-particle analysis with resistive pulse sensing is performed to detect these changes. A variable pressure method allows identification of changes in the surface charge of particles. As proof-of-principle, we demonstrate that target hybridization is selectively detected at micromolar concentrations (nanomoles of target) using resistive pulse sensing, confirmed by fluorescence and phase analysis light scattering as complementary techniques. The advantages, feasibility and limitations of using resistive pulse sensing for sample analysis are discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

High density group IV semiconductor nanowire arrays fabricated in nanoporous alumina templates

NASA Astrophysics Data System (ADS)

Redwing, Joan M.; Dilts, Sarah M.; Lew, Kok-Keong; Cranmer, Alexana E.; Mohney, Suzanne E.

2005-11-01

The fabrication of high density arrays of semiconductor nanowires is of interest for nanoscale electronics, chemical and biological sensing and energy conversion applications. We have investigated the synthesis, intentional doping and electrical characterization of Si and Ge nanowires grown by the vapor-liquid-solid (VLS) method in nanoporous alumina membranes. Nanoporous membranes provide a convenient platform for nanowire growth and processing, enabling control of wire diameter via pore size and the integration of contact metals for electrical testing. For VLS growth in nanoporous materials, reduced pressures and temperatures are required in order to promote the diffusion of reactants into the pore without premature decomposition on the membrane surface or pore walls. The effect of growth conditions on the growth rate of Si and Ge nanowires from SiH 4 and GeH 4 sources, respectively, was investigated and compared. In both cases, the measured activation energies for nanowire growth were substantially lower than activation energies typically reported for Si and Ge thin film deposition under similar growth conditions, suggesting that gold plays a catalytic role in the VLS growth process. Intentionally doped SiNW arrays were also prepared using trimethylboron (TMB) and phosphine (PH 3) as p-type and n-type dopant sources, respectively. Nanowire resistivities were calculated from plots of the array resistance as a function of nanowire length. A decrease in resistivity was observed for both n-type and p-type doped SiNW arrays compared to those grown without the addition of a dopant source.

Characterization of nanoporous shales with gas sorption

NASA Astrophysics Data System (ADS)

Joewondo, N.; Prasad, M.

2017-12-01

The understanding of the fluid flow in porous media requires the knowledge of the pore system involved. Fluid flow in fine grained shales falls under different regime than transport regime in conventional reservoir due to the different average pore sizes in the two materials; the average pore diameter of conventional sandstones is on the micrometer scale, while of shales can be as small as several nanometers. Mercury intrusion porosimetry is normally used to characterize the pores of conventional reservoir, however with increasingly small pores, the injection pressure required to imbibe the pores becomes infinitely large due to surface tension. Characterization of pores can be expressed by a pore size distribution (PSD) plot, which reflects distribution of pore volume or surface area with respect to pore size. For the case of nanoporous materials, the surface area, which serves as the interface between the rock matrix and fluid, becomes increasingly large and important. Physisorption of gas has been extensively studied as a method of nanoporous solid characterization (particularly for the application of catalysis, metal organic frameworks, etc). The PSD is obtained by matching the experimental result to the calculated theoretical result (using Density Functional Theory (DFT), a quantum mechanics based modelling method for molecular scale interactions). We present the challenges and experimental result of Nitrogen and CO2 gas sorption on shales with various mineralogy and the interpreted PSD obtained by DFT method. Our result shows significant surface area contributed by the nanopores of shales, hence the importance of surface area measurements for the characterization of shales.

Crystallographic structure refinement with quadrupolar nuclei: a combined solid-state NMR and GIPAW DFT example using MgBr(2).

PubMed

Widdifield, Cory M; Bryce, David L

2009-09-07

Solid-state NMR spectroscopy and GIPAW DFT calculations reveal the pronounced sensitivity of (79/81)Br and (25)Mg quadrupolar coupling constants to subtle aspects of solid state structure which were not previously detected by pXRD methods.

Ionic-Liquid-Infused Nanostructures as Repellent Surfaces.

PubMed

Galvan, Yaraset; Phillips, Katherine R; Haumann, Marco; Wasserscheid, Peter; Zarraga, Ramon; Vogel, Nicolas

2018-06-12

In order to prepare lubricant-infused repellent coatings on silica nanostructures using low vapor pressure ionic liquids as lubricants, we study the wetting behavior of a set of imidazolium-based ionic liquids with different alkyl side chains as a function of the applied surface functionalities. We take advantage of the structural color of inverse opals prepared from a colloidal coassembly technique to study the infiltration of ionic liquids into these nanoporous structures. We find that the more hydrophobic ionic liquids with butyl and hexyl side chains can completely infiltrate inverse opals functionalized with mixed self-assembled monolayers composed of imidazole groups and aliphatic hydrocarbon chains, which we introduce via silane chemistry. These molecular species reflect the chemical nature of the ionic liquid, thereby increasing the affinity between the liquid and solid surface. The mixed surface chemistry provides sufficiently small contact angles with the ionic liquid to infiltrate the nanopores while maximizing the contact angle with water. As a result, the mixed monolayers enable the design of a stable ionic liquid/solid interface that is able to repel water as a test liquid. Our results underline the importance of matching chemical affinities to predict and control the wetting behavior in complex, multiphase systems.

Hydroxyl-Exchanged Nanoporous Ionic Copolymer toward Low-Temperature Cycloaddition of Atmospheric Carbon Dioxide into Carbonates.

PubMed

Guo, Zengjing; Cai, Xiaochun; Xie, Jingyan; Wang, Xiaochen; Zhou, Yu; Wang, Jun

2016-05-25

An ionic copolymer catalyst with nanopores, large surface area, high ionic density, and superior basicity was prepared via the radical copolymerization of amino-functionalized ionic liquid bromide and divinylbenzene, followed with a hydroxyl exchange for removing bromonium. Evaluated in chemical fixation of CO2 with epoxides into cyclic carbonates in the absence of any solvent and basic additive, the nanoporous copolymer catalyst showed high and stable activity, superior to various control catalysts including the halogen-containing analogue. Further, high yields were obtained over a wide scope of substrates including aliphatic long carbon-chain alkyl epoxides and internal epoxide, even under atmospheric pressure and less than 100 °C for the majority of the substrates. On the basis of in situ Fourier transform infrared (FT-IR) investigation and density functional theory (DFT) calculation for the reaction intermediates, we proposed a possible reaction mechanism accounting for the superior catalytic activity of the ionic copolymer. The specifically prepared ionic copolymer material of this work features highly stable, noncorrosive, and sustainable catalysis and, thus, may be a new possibility for efficient chemical fixation of CO2 since it is an environmentally friendly, metal-free solid catalyst.

Three dimensional analysis of nanoporous silicon particles for Li-ion batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roiban, Lucian, E-mail: lucian.roiban@insa-lyon.fr

2017-02-15

Bulk nanoporous silicon prepared by top-down method form Li-ion batteries was investigated combining different conventional technique such as nitrogen physisorption and high resolution electron microscopy with electron tomography. It was found that the Si nanorods are forming porous aggregates with a half of the volume of the particle occupied by pores. The nanorods are preferentially oriented along the main axis of the aggregate. The porosity and the lack of compaction between the aggregates provide space for the Si expansion during the lithiation process. It was found that the Si nanorods mainly expose the (111) family plane as an external faces.more » The size distributions of the porous and solid phases in a granule were found to be similar. The pores represent 50% of the total volume of an aggregate. The shape orientation of the particles was quantified and it was found to exhibit a narrow distribution. - Highlights: •Bulk nanoporous silicon for Li-ion batteries is studied by HRTEM and electron tomography. •The crystalline facets of Si nanorods are formed by (111) plains. •The lack of compactness between Si nanorods provides 50% of porous volume. •The Si nanorods are oriented along a preferential axis.« less

Detecting single-abasic residues within a DNA strand immobilized in a biological nanopore using an integrated CMOS sensor.

PubMed

Kim, Jungsuk; Maitra, Raj D; Pedrotti, Ken; Dunbar, William B

2013-02-01

In this paper, we demonstrate the application of a novel current-measuring sensor (CMS) customized for nanopore applications. The low-noise CMS is fabricated in a 0.35μm CMOS process and is implemented in experiments involving DNA captured in an α-hemolysin (α-HL) nanopore. Specifically, the CMS is used to build a current amplitude map as a function of varying positions of a single-abasic residue within a homopolymer cytosine single-stranded DNA (ssDNA) that is captured and held in the pore. Each ssDNA is immobilized using a biotin-streptavidin linkage. Five different DNA templates are measured and compared: one all-cytosine ssDNA, and four with a single-abasic residue substitution that resides in or near the ~1.5nm aperture of the α-HL channel when the strand is immobilized. The CMOS CMS is shown to resolves the ~5Å displacements of the abasic residue within the varying templates. The demonstration represents an advance in application-specific circuitry that is optimized for small-footprint nanopore applications, including genomic sequencing.

Resolved single-molecule detection of individual species within a mixture of anti-biotin antibodies using an engineered monomeric nanopore.

PubMed

Fahie, Monifa; Chisholm, Christina; Chen, Min

2015-02-24

Oligomeric protein nanopores with rigid structures have been engineered for the purpose of sensing a wide range of analytes including small molecules and biological species such as proteins and DNA. We chose a monomeric β-barrel porin, OmpG, as the platform from which to derive the nanopore sensor. OmpG is decorated with seven flexible loops that move dynamically to create a distinct gating pattern when ionic current passes through the pore. Biotin was chemically tethered to the most flexible one of these loops. The gating characteristic of the loop's movement in and out of the porin was substantially altered by analyte protein binding. The gating characteristics of the pore with bound targets were remarkably sensitive to molecular identity, even providing the ability to distinguish between homologues within an antibody mixture. A total of five gating parameters were analyzed for each analyte to create a unique fingerprint for each biotin-binding protein. Our exploitation of gating noise as a molecular identifier may allow more sophisticated sensor design, while OmpG's monomeric structure greatly simplifies nanopore production.

Micro-engineered first wall tungsten armor for high average power laser fusion energy systems

NASA Astrophysics Data System (ADS)

Sharafat, Shahram; Ghoniem, Nasr M.; Anderson, Michael; Williams, Brian; Blanchard, Jake; Snead, Lance; HAPL Team

2005-12-01

The high average power laser program is developing an inertial fusion energy demonstration power reactor with a solid first wall chamber. The first wall (FW) will be subject to high energy density radiation and high doses of high energy helium implantation. Tungsten has been identified as the candidate material for a FW armor. The fundamental concern is long term thermo-mechanical survivability of the armor against the effects of high temperature pulsed operation and exfoliation due to the retention of implanted helium. Even if a solid tungsten armor coating would survive the high temperature cyclic operation with minimal failure, the high helium implantation and retention would result in unacceptable material loss rates. Micro-engineered materials, such as castellated structures, plasma sprayed nano-porous coatings and refractory foams are suggested as a first wall armor material to address these fundamental concerns. A micro-engineered FW armor would have to be designed with specific geometric features that tolerate high cyclic heating loads and recycle most of the implanted helium without any significant failure. Micro-engineered materials are briefly reviewed. In particular, plasma-sprayed nano-porous tungsten and tungsten foams are assessed for their potential to accommodate inertial fusion specific loads. Tests show that nano-porous plasma spray coatings can be manufactured with high permeability to helium gas, while retaining relatively high thermal conductivities. Tungsten foams where shown to be able to overcome thermo-mechanical loads by cell rotation and deformation. Helium implantation tests have shown, that pulsed implantation and heating releases significant levels of implanted helium. Helium implantation and release from tungsten was modeled using an expanded kinetic rate theory, to include the effects of pulsed implantations and thermal cycles. Although, significant challenges remain micro-engineered materials are shown to constitute potential candidate FW armor materials.

EDITORIAL: Nanopores—the 'Holey Grail' in nanotechnology research Nanopores—the 'Holey Grail' in nanotechnology research

NASA Astrophysics Data System (ADS)

Demming, Anna

2012-06-01

'Negative space' may be as important in the development of nanomaterials as it is in creating works of art. The term refers to the space around and between objects, an important aspect in artistic composition. In nanotechnology, while nanoposts and nanowires have been assiduously studied and exploited for enhancing the performance of solar cells [1], real-time chemical sensors [2], UV emitters [3] and many other applications, nanopore structures have also yielded important advances in a wide range of fields. In this issue Melnikov, Leburton and Gracheva report on the electrostatic properties of nanopores in a layered semiconductor, and show how they allow a more accurate characterization of DNA than pores in other membranes [4]. Nanoporous materials have been applied to a diverse range of technological challenges. In recognition of its potential in high-efficiency solar cells, Prakasam and colleagues in the US reported the first ever synthesis of self-aligned nanoporous haematite [5]. Haematite is abundant, stable, non-toxic and has a band gap in the visible region and, as their work demonstrates, the photoresponse of nanoporous haematite is very promising for energy harvesting applications. Nanoporous aluminum oxide has also proved to be a particularly valuable material in applications ranging from liquid display panels to biosensor microchips. A collaboration of researchers in Taiwan demonstrated that porous aluminum oxide on an indium tin oxide surface could act as an alignment layer in liquid crystal display panels that have a transmittance of 60-80%, and switch from black to bright with a response time of 62.5 ms [6]. In Korea, Chung, Son and Min investigated the effect of nanostructural parameters of porous aluminum oxide on cell adhesion and proliferation for cell-based microchips [7]. While aluminum oxide without any modifications is not favourable for adherent cell culture, the proliferation of cells dramatically increased in porous aluminum oxide, particularly when the aspect ratio of the nanopore was near unity. In the mid 1990s a collaboration of researchers in the US demonstrated that nanopores could be used to characterize DNA [8]. They showed that as an electric field drove DNA molecules through a pore in a lipid bilayer membrane, the decrease in ionic current due to the partially blocked channel allowed measurement of the polynucleotide length. 'With further improvements, the method could in principle provide direct, high-speed detection of the sequence of bases in single molecules of DNA or RNA', suggested the authors. The idea inspired a catalogue of further research. Gracheva and colleagues in Illinois described a modified approach to detecting DNA using a nanopore in a membrane fabricated from a metal-oxide-semiconductor (MOS) capacitor [9]. The use of semiconductor materials allows the direct integration of high-sensitivity nanoscale MOS amplifiers on the nanopore layer structure to improve the signal. Researchers in the Netherlands have investigated ways of refining geometrical control of nanopores in SiN membranes for more accurate molecular characterization [10]. They reported the fabrication of nanopores using transmission electron microscope beams of different sizes. They found that the stability of small nanopores is related to their geometry, which could be controlled by the size of the beam used in fabrication. One challenge for accurate DNA characterization has been the speed of translocation through the pore. In a collaboration between the University of Illinois and the University of Notre-Dame in Indiana, researchers used a time-varying electric field to slow down the molecule's passage in the pore [11]. In this issue, researchers in Illinois have studied the translocation and stretching of DNA in a pore in a semiconductor membrane consisting of doped p- and n-layers of Si forming a p-n-junction [4]. Control over the stretching of the DNA is important, as is controlling the speed of translocation. Interference between the secondary structure of the probed molecule can interfere with the recorded signal, muddling measurements of the molecule's charge. According to Gracheva and her colleagues, 'the results indicate that the tunable local electric field inside the membrane can effectively control dynamics of a DNA in the channel to either momentarily trap, slow down or allow the biomolecule to translocate at will'. The fertility of research based on nanopores complements well the interest in nanowires and nanoposts. This may largely be a symptom of the comprehensive rigour in scientific enquiry which encourages the investigation of all approaches to a solution. It was once suggested that 'art and science have their meeting point in method' [12]. One might also argue that the creative and inspired ingenuity that is evident in the application of nanopores to such wide-ranging technological challenges demonstrates how the development of scientific methods is in itself a fine art. References [1] Qiu J et al 2010 Solution-derived 40 μm vertically aligned ZnO nanowire arrays as photoelectrodes in dye-sensitized solar cells Nanotechnology 21 195602 [2] Park I, Li Z, Pisano A P and Williams R S 2010 Top-down fabricated silicon nanowire sensors for real-time chemical detection Nanotechnology 21 015501 [3] Gao J et al 2011 UV light emitting transparent conducting tin-doped indium oxide (ITO) nanowires Nanotechnology 22 195706 [4] Melnikov D V, Leburton J-P and Gracheva M E 2012 Slowing down and stretching DNA with an electrically tunable nanopore in a p-n semiconductor membrane Nanotechnology 23 255501 [5] Prakasam H E, Varghese O K, Paulose M, Mor G K and Grimes C A 2006 Synthesis and photoelectrochemical properties of nanoporous iron (III) oxide by potentiostatic anodization Nanotechnology 17 4285-91 [6] Hong C, Tang T-T, Hung C-Y, Pan R-P and Fang W 2010 Liquid crystal alignment in nanoporous anodic aluminum oxide layer for LCD panel applications Nanotechnology 21 285201 [7] Chung S H, Son S J and Min J 2010 The nanostructure effect on the adhesion and growth rates of epithelial cells with well-defined nanoporous alumina s substrates Nanotechnology 21 125104 [8] Kasianowicz J J, Brandin E, Branton D and Deamer D W 1996 Characterization of individual polynucleotide molecules using a membrane channel Proc. Natl Acad. Sci. 93 13770-3 [9] Gracheva M E, Xiong A, Aksimentiev A, Schulten K, Timp G and Leburton J-P 2006 Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor Nanotechnology 17 622-33 [10] Van Den Hout M, Hall A R, Wu M Y, Zandbergen H W, Dekker C and Dekker N H 2010 Controlling nanopore size, shape and stability Nanotechnology 21 115304 [11] Mirsaidov U, Comer J, Dimitrov V, Aksimentiev A and Timp G 2010 Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix Nanotechnology 21 395501 [12] Baron E and Bulwer L L 1864 Caxtoniana vol 2 (Leipzig: Bernard Tauchnits) p 122

Nanoporous membranes with electrochemically switchable, chemically stabilized ionic selectivity

NASA Astrophysics Data System (ADS)

Small, Leo J.; Wheeler, David R.; Spoerke, Erik D.

2015-10-01

Nanopore size, shape, and surface charge all play important roles in regulating ionic transport through nanoporous membranes. The ability to control these parameters in situ provides a means to create ion transport systems tunable in real time. Here, we present a new strategy to address this challenge, utilizing three unique electrochemically switchable chemistries to manipulate the terminal functional group and control the resulting surface charge throughout ensembles of gold plated nanopores in ion-tracked polycarbonate membranes 3 cm2 in area. We demonstrate the diazonium mediated surface functionalization with (1) nitrophenyl chemistry, (2) quinone chemistry, and (3) previously unreported trimethyl lock chemistry. Unlike other works, these chemistries are chemically stabilized, eliminating the need for a continuously applied gate voltage to maintain a given state and retain ionic selectivity. The effect of surface functionalization and nanopore geometry on selective ion transport through these functionalized membranes is characterized in aqueous solutions of sodium chloride at pH = 5.7. The nitrophenyl surface allows for ionic selectivity to be irreversibly switched in situ from cation-selective to anion-selective upon reduction to an aminophenyl surface. The quinone-terminated surface enables reversible changes between no ionic selectivity and a slight cationic selectivity. Alternatively, the trimethyl lock allows ionic selectivity to be reversibly switched by up to a factor of 8, approaching ideal selectivity, as a carboxylic acid group is electrochemically revealed or hidden. By varying the pore shape from cylindrical to conical, it is demonstrated that a controllable directionality can be imparted to the ionic selectivity. Combining control of nanopore geometry with stable, switchable chemistries facilitates superior control of molecular transport across the membrane, enabling tunable ion transport systems.Nanopore size, shape, and surface charge all play important roles in regulating ionic transport through nanoporous membranes. The ability to control these parameters in situ provides a means to create ion transport systems tunable in real time. Here, we present a new strategy to address this challenge, utilizing three unique electrochemically switchable chemistries to manipulate the terminal functional group and control the resulting surface charge throughout ensembles of gold plated nanopores in ion-tracked polycarbonate membranes 3 cm2 in area. We demonstrate the diazonium mediated surface functionalization with (1) nitrophenyl chemistry, (2) quinone chemistry, and (3) previously unreported trimethyl lock chemistry. Unlike other works, these chemistries are chemically stabilized, eliminating the need for a continuously applied gate voltage to maintain a given state and retain ionic selectivity. The effect of surface functionalization and nanopore geometry on selective ion transport through these functionalized membranes is characterized in aqueous solutions of sodium chloride at pH = 5.7. The nitrophenyl surface allows for ionic selectivity to be irreversibly switched in situ from cation-selective to anion-selective upon reduction to an aminophenyl surface. The quinone-terminated surface enables reversible changes between no ionic selectivity and a slight cationic selectivity. Alternatively, the trimethyl lock allows ionic selectivity to be reversibly switched by up to a factor of 8, approaching ideal selectivity, as a carboxylic acid group is electrochemically revealed or hidden. By varying the pore shape from cylindrical to conical, it is demonstrated that a controllable directionality can be imparted to the ionic selectivity. Combining control of nanopore geometry with stable, switchable chemistries facilitates superior control of molecular transport across the membrane, enabling tunable ion transport systems. Electronic supplementary information (ESI) available: Experimental procedures, synthesis, and characterization of molecules 1, 2 and 3. Explanation of the electrochemical method for approximating nanopore diameter. Additional XPS spectra. See DOI: 10.1039/C5NR02939B

A Nanopore Structured High Performance Toluene Gas Sensor Made by Nanoimprinting Method

PubMed Central

Kim, Kwang-Su; Baek, Woon-Hyuk; Kim, Jung-Min; Yoon, Tae-Sik; Lee, Hyun Ho; Kang, Chi Jung; Kim, Yong-Sang

2010-01-01

Toluene gas was successfully measured at room temperature using a device microfabricated by a nanoimprinting method. A highly uniform nanoporous thin film was produced with a dense array of titania (TiO2) pores with a diameter of 70∼80 nm using this method. This thin film had a Pd/TiO2 nanoporous/SiO2/Si MIS layered structure with Pd-TiO2 as the catalytic sensing layer. The nanoimprinting method was useful in expanding the TiO2 surface area by about 30%, as confirmed using AFM and SEM imaging. The measured toluene concentrations ranged from 50 ppm to 200 ppm. The toluene was easily detected by changing the Pd/TiO2 interface work function, resulting in a change in the I–V characteristics. PMID:22315567

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnakumar, Raga; Sinha, Anupama; Bird, Sara W.

Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed themore » quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.« less

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

DOE PAGES

Krishnakumar, Raga; Sinha, Anupama; Bird, Sara W.; ...

2018-02-16

Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed themore » quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.« less

Methane storage in nanoporous material at supercritical temperature over a wide range of pressures

PubMed Central

Wu, Keliu; Chen, Zhangxin; Li, Xiangfang; Dong, Xiaohu

2016-01-01

The methane storage behavior in nanoporous material is significantly different from that of a bulk phase, and has a fundamental role in methane extraction from shale and its storage for vehicular applications. Here we show that the behavior and mechanisms of the methane storage are mainly dominated by the ratio of the interaction between methane molecules and nanopores walls to the methane intermolecular interaction, and a geometric constraint. By linking the macroscopic properties of the methane storage to the microscopic properties of a system of methane molecules-nanopores walls, we develop an equation of state for methane at supercritical temperature over a wide range of pressures. Molecular dynamic simulation data demonstrates that this equation is able to relate very well the methane storage behavior with each of the key physical parameters, including a pore size and shape and wall chemistry and roughness. Moreover, this equation only requires one fitted parameter, and is simple, reliable and powerful in application. PMID:27628747

Study of reversible magnetization in FeCoNi alloy nanowires with different diameters by first order reversal curve (FORC) diagrams

NASA Astrophysics Data System (ADS)

Samanifar, S.; Kashi, M. Almasi; Ramazani, A.

2018-05-01

Magnetic nanowires electrodeposited into solid templates are of high interest due to their tunable properties which are required for magnetic recording media and spintronic devices. Here, highly ordered arrays of FeCoNi NWs with varied diameters (between 60 and 150 nm) were fabricated into nanopores of hard-anodized aluminum oxide templates using pulsed ac electrodeposition technique. X-ray diffraction patterns indicated the formation of FeCoNi NWs with fcc FeNi and bcc FeCo alloy phases, being highly textured along the bcc [110] direction. Magnetic properties were studied by hysteresis loop measurements at room temperature and they showed reductions in coercivity and squareness values by increasing diameter. First-order reversal curve measurements revealed that, with increasing diameter from 60 to 150 nm, besides a transition from a single domain (SD) state to a pseudo SD state, an increase in the reversible magnetization component of the NWs from 11% to 24% occurred.

Rapid antibiotic efficacy screening with aluminum oxide nanoporous membrane filter-chip and optical detection system.

PubMed

Tsou, Pei-Hsiang; Sreenivasappa, Harini; Hong, Sungmin; Yasuike, Masayuki; Miyamoto, Hiroshi; Nakano, Keiyo; Misawa, Takeyuki; Kameoka, Jun

2010-09-15

We have developed a filter-chip and optical detection system for rapid antibiotic efficacy screening. The filter-chip consisted of a 1-mL reservoir and an anodic aluminum oxide (AAO) nanoporous membrane. Sample solution with liquid growth media, bacteria, and antibiotics was incubated in the reservoir for a specific period of time. The number of live bacteria on the surface of membrane was counted after the incubation with antibiotics and filtration. Using this biosensing system, we have demonstrated a 1-h antibiotic screening for patients' clinical samples, significantly faster than the conventional antibiotic susceptibility tests that typically take more than 24h. This rapid screening nature makes the filter-chip and detection system ideal for tailoring antibiotic treatment to individual patients by reducing the microbial antibiotic resistance, and improving the survival rate for patients suffering from postoperative infections. Published by Elsevier B.V.

Nanosecond pulsed electric field thresholds for nanopore formation in neural cells

NASA Astrophysics Data System (ADS)

Roth, Caleb C.; Tolstykh, Gleb P.; Payne, Jason A.; Kuipers, Marjorie A.; Thompson, Gary L.; DeSilva, Mauris N.; Ibey, Bennett L.

2013-03-01

The persistent influx of ions through nanopores created upon cellular exposure to nanosecond pulse electric fields (nsPEF) could be used to modulate neuronal function. One ion, calcium (Ca), is important to action potential firing and regulates many ion channels. However, uncontrolled hyper-excitability of neurons leads to Ca overload and neurodegeneration. Thus, to prevent unintended consequences of nsPEF-induced neural stimulation, knowledge of optimum exposure parameters is required. We determined the relationship between nsPEF exposure parameters (pulse width and amplitude) and nanopore formation in two cell types: rodent neuroblastoma (NG108) and mouse primary hippocampal neurons (PHN). We identified thresholds for nanoporation using Annexin V and FM1-43, to detect changes in membrane asymmetry, and through Ca influx using Calcium Green. The ED50 for a single 600 ns pulse, necessary to cause uptake of extracellular Ca, was 1.76 kV/cm for NG108 and 0.84 kV/cm for PHN. At 16.2 kV/cm, the ED50 for pulse width was 95 ns for both cell lines. Cadmium, a nonspecific Ca channel blocker, failed to prevent Ca uptake suggesting that observed influx is likely due to nanoporation. These data demonstrate that moderate amplitude single nsPEF exposures result in rapid Ca influx that may be capable of controllably modulating neurological function.

Computational modeling of ion transport through nanopores.

PubMed

Modi, Niraj; Winterhalter, Mathias; Kleinekathöfer, Ulrich

2012-10-21

Nanoscale pores are ubiquitous in biological systems while artificial nanopores are being fabricated for an increasing number of applications. Biological pores are responsible for the transport of various ions and substrates between the different compartments of biological systems separated by membranes while artificial pores are aimed at emulating such transport properties. As an experimental method, electrophysiology has proven to be an important nano-analytical tool for the study of substrate transport through nanopores utilizing ion current measurements as a probe for the detection. Independent of the pore type, i.e., biological or synthetic, and objective of the study, i.e., to model cellular processes of ion transport or electrophysiological experiments, it has become increasingly important to understand the dynamics of ions in nanoscale confinements. To this end, numerical simulations have established themselves as an indispensable tool to decipher ion transport processes through biological as well as artificial nanopores. This article provides an overview of different theoretical and computational methods to study ion transport in general and to calculate ion conductance in particular. Potential new improvements in the existing methods and their applications are highlighted wherever applicable. Moreover, representative examples are given describing the ion transport through biological and synthetic nanopores as well as the high selectivity of ion channels. Special emphasis is placed on the usage of molecular dynamics simulations which already have demonstrated their potential to unravel ion transport properties at an atomic level.

Molecular understanding of osmosis in semipermeable membranes.

PubMed

Raghunathan, A V; Aluru, N R

2006-07-14

We investigate single-file osmosis of water through a semipermeable membrane with an uncharged, a positively and a negatively charged nanopore. Molecular dynamics simulations indicate that the osmotic flux through a negatively charged pore (J_) is higher compared to the osmotic flux in a positively charged pore (J+) followed by the osmotic flux in the uncharged pore (J(0)), i.e., J_ > J+ > J(0). The molecular mechanisms governing osmosis, steady state osmosis, and the observed osmotic flux dependence on the nanopore charge are explained by computing all the molecular interactions involved and identifying the molecular interactions that play an important role during and after osmosis. This study helps in a fundamental understanding of osmosis and in the design of advanced nanoporous membranes for various applications of osmosis.

Single molecule detection with graphene and other two-dimensional materials: nanopores and beyond

PubMed Central

Arjmandi-Tash, Hadi; Belyaeva, Liubov A.

2016-01-01

Graphene and other two dimensional (2D) materials are currently integrated into nanoscaled devices that may – one day – sequence genomes. The challenge to solve is conceptually straightforward: cut a sheet out of a 2D material and use the edge of the sheet to scan an unfolded biomolecule from head to tail. As the scan proceeds – and because 2D materials are atomically thin – the information provided by the edge might be used to identify different segments – ideally single nucleotides – in the biomolecular strand. So far, the most efficient approach was to drill a nano-sized pore in the sheet and use this pore as a channel to guide and detect individual molecules by measuring the electrochemical ionic current. Nanoscaled gaps between two electrodes in 2D materials recently emerged as powerful alternatives to nanopores. This article reviews the current status and prospects of integrating 2D materials in nanopores, nanogaps and similar devices for single molecule biosensing applications. We discuss the pros and cons, the challenges, and the latest achievements in the field. To achieve high-throughput sequencing with 2D materials, interdisciplinary research is essential. PMID:26612268

Real-time monitoring of ischemia inside stomach.

PubMed

Tahirbegi, Islam Bogachan; Mir, Mònica; Samitier, Josep

2013-02-15

The low pH in the gastric juice of the stomach makes it difficult to fabricate stable and functional all-solid-state pH ISE sensors to sense ischemia, mainly because of anion interference and adhesion problem between the ISE membrane and the electrode surface. In this work, the adhesion of ISE membrane on solid surface at low pH was improved by modifying the surface with a conductive substrate containing hydrophilic and hydrophobic groups. This creates a stable and robust candidate for low pH applications. Moreover, anion interference problem at low pH was solved by integration of all-solid-state ISE and internal reference electrodes on an array. So, the same tendencies of anion interferences for all-solid-state ISE and all-solid-state reference electrodes cancel each other in differential potentiometric detection. The developed sensor presents a novel all-solid-state potentiometric, miniaturized and mass producible pH ISE sensor for detecting ischemia on the stomach tissue on an array designed for endoscopic applications. Copyright © 2012 Elsevier B.V. All rights reserved.

Structure and transport properties of nanostructured materials.

PubMed

Sonwane, C G; Li, Q

2005-03-31

In the present manuscript, we have presented the simulation of nanoporous aluminum oxide using a molecular-dynamics approach with recently developed dynamic charge transfer potential using serial/parallel programming techniques (Streitz and Mintmire Phys. Rev. B 1994, 50, 11996). The structures resembling recently invented ordered nanoporous crystalline material, MCM-41/SBA-15 (Kresge et al. Nature 1992, 359, 710), and inverted porous solids (hollow nanospheres) with up to 10 000 atoms were fabricated and studied in the present work. These materials have been used for separation of gases and catalysis. On several occasions including the design of the reactor, the knowledge of surface diffusion is necessary. In the present work, a new method for estimating surface transport of gases based on a hybrid Monte Carlo method with unbiased random walk of tracer atom on the pore surface has been introduced. The nonoverlapping packings used in the present work were fabricated using an algorithm of very slowly settling rigid spheres from a dilute suspension into a randomly packed bed. The algorithm was modified to obtain unimodal, homogeneous Gaussian and segregated bimodal porous solids. The porosity of these solids was varied by densification using an arbitrary function or by coarsening from a highly densified pellet. The surface tortuosity for the densified solids indicated an inverted bell shape curve consistent with the fact that at very high porosities there is a reduction in the connectivity while at low porosities the pores become inaccessible or dead-end. The first passage time distribution approach was found to be more efficient in terms of computation time (fewer tracer atoms needed for the linearity of Einstein's plot). Results by hybrid discrete-continuum simulations were close to the discrete simulations for a boundary layer thickness of 5lambda.

Interferometric nanoporous anodic alumina photonic coatings for optical sensing

NASA Astrophysics Data System (ADS)

Chen, Yuting; Santos, Abel; Wang, Ye; Kumeria, Tushar; Wang, Changhai; Li, Junsheng; Losic, Dusan

2015-04-01

Herein, we present a systematic study on the development, optical optimization and sensing applicability of colored photonic coatings based on nanoporous anodic alumina films grown on aluminum substrates. These optical nanostructures, so-called distributed Bragg reflectors (NAA-DBRs), are fabricated by galvanostatic pulse anodization process, in which the current density is altered in a periodic manner in order to engineer the effective medium of the resulting photonic coatings. As-prepared NAA-DBR photonic coatings present brilliant interference colors on the surface of aluminum, which can be tuned at will within the UV-visible spectrum by means of the anodization profile. A broad library of NAA-DBR colors is produced by means of different anodization profiles. Then, the effective medium of these NAA-DBR photonic coatings is systematically assessed in terms of optical sensitivity, low limit of detection and linearity by reflectometric interference spectroscopy (RIfS) in order to optimize their nanoporous structure toward optical sensors with enhanced sensing performance. Finally, we demonstrate the applicability of these photonic nanostructures as optical platforms by selectively detecting gold(iii) ions in aqueous solutions. The obtained results reveal that optimized NAA-DBR photonic coatings can achieve an outstanding sensing performance for gold(iii) ions, with a sensitivity of 22.16 nm μM-1, a low limit of detection of 0.156 μM (i.e. 30.7 ppb) and excellent linearity within the working range (0.9983).Herein, we present a systematic study on the development, optical optimization and sensing applicability of colored photonic coatings based on nanoporous anodic alumina films grown on aluminum substrates. These optical nanostructures, so-called distributed Bragg reflectors (NAA-DBRs), are fabricated by galvanostatic pulse anodization process, in which the current density is altered in a periodic manner in order to engineer the effective medium of the resulting photonic coatings. As-prepared NAA-DBR photonic coatings present brilliant interference colors on the surface of aluminum, which can be tuned at will within the UV-visible spectrum by means of the anodization profile. A broad library of NAA-DBR colors is produced by means of different anodization profiles. Then, the effective medium of these NAA-DBR photonic coatings is systematically assessed in terms of optical sensitivity, low limit of detection and linearity by reflectometric interference spectroscopy (RIfS) in order to optimize their nanoporous structure toward optical sensors with enhanced sensing performance. Finally, we demonstrate the applicability of these photonic nanostructures as optical platforms by selectively detecting gold(iii) ions in aqueous solutions. The obtained results reveal that optimized NAA-DBR photonic coatings can achieve an outstanding sensing performance for gold(iii) ions, with a sensitivity of 22.16 nm μM-1, a low limit of detection of 0.156 μM (i.e. 30.7 ppb) and excellent linearity within the working range (0.9983). Electronic supplementary information (ESI) available: The Supporting Information file provides further information about real-time monitoring of ΔOTeff with changes in the refractive index of the medium filling the nanopores, demonstration of visual red shift in a NAA-DBR sample after infiltration with isopropanol and calculations of linearity (R2) for each NAA-DBR coating. See DOI: 10.1039/c5nr00369e

Nanopore tweezers: voltage-controlled trapping and releasing of analytes.

PubMed

Chinappi, Mauro; Luchian, Tudor; Cecconi, Fabio

2015-09-01

Several devices for single-molecule detection and analysis employ biological and artificial nanopores as core elements. The performance of such devises strongly depends on the amount of time the analytes spend into the pore. This residence time needs to be long enough to allow the recording of a high signal-to-noise ratio analyte-induced blockade. We propose a simple approach, dubbed nanopore tweezing, for enhancing the trapping time of molecules inside the pore via a proper tuning of the applied voltage. This method requires the creation of a strong dipole that can be generated by adding a positive and a negative tail at the two ends of the molecules to be analyzed. Capture rate is shown to increase with the applied voltage while escape rate decreases. In this paper we rationalize the essential ingredients needed to control the residence time and provide a proof of principle based on atomistic simulations.

A Comprehensive Numerical Model for Simulating Fluid Transport in Nanopores

PubMed Central

Zhang, Yuan; Yu, Wei; Sepehrnoori, Kamy; Di, Yuan

2017-01-01

Since a large amount of nanopores exist in tight oil reservoirs, fluid transport in nanopores is complex due to large capillary pressure. Recent studies only focus on the effect of nanopore confinement on single-well performance with simple planar fractures in tight oil reservoirs. Its impacts on multi-well performance with complex fracture geometries have not been reported. In this study, a numerical model was developed to investigate the effect of confined phase behavior on cumulative oil and gas production of four horizontal wells with different fracture geometries. Its pore sizes were divided into five regions based on nanopore size distribution. Then, fluid properties were evaluated under different levels of capillary pressure using Peng-Robinson equation of state. Afterwards, an efficient approach of Embedded Discrete Fracture Model (EDFM) was applied to explicitly model hydraulic and natural fractures in the reservoirs. Finally, three fracture geometries, i.e. non-planar hydraulic fractures, non-planar hydraulic fractures with one set natural fractures, and non-planar hydraulic fractures with two sets natural fractures, are evaluated. The multi-well performance with confined phase behavior is analyzed with permeabilities of 0.01 md and 0.1 md. This work improves the analysis of capillarity effect on multi-well performance with complex fracture geometries in tight oil reservoirs. PMID:28091599

A New Approach to the Computer Modeling of Amorphous Nanoporous Structures of Semiconducting and Metallic Materials: A Review

PubMed Central

Romero, Cristina; Noyola, Juan C.; Santiago, Ulises; Valladares, Renela M.; Valladares, Alexander; Valladares, Ariel A.

2010-01-01

We review our approach to the generation of nanoporous materials, both semiconducting and metallic, which leads to the existence of nanopores within the bulk structure. This method, which we have named as the expanding lattice method, is a novel transferable approach which consists first of constructing crystalline supercells with a large number of atoms and a density close to the real value and then lowering the density by increasing the volume. The resulting supercells are subjected to either ab initio or parameterized—Tersoff-based—molecular dynamics processes at various temperatures, all below the corresponding bulk melting points, followed by geometry relaxations. The resulting samples are essentially amorphous and display pores along some of the “crystallographic” directions without the need of incorporating ad hoc semiconducting atomic structural elements such as graphene-like sheets and/or chain-like patterns (reconstructive simulations) or of reproducing the experimental processes (mimetic simulations). We report radial (pair) distribution functions, nanoporous structures of C and Si, and some computational predictions for their vibrational density of states. We present numerical estimates and discuss possible applications of semiconducting materials for hydrogen storage in potential fuel tanks. Nanopore structures for metallic elements like Al and Au also obtained through the expanding lattice method are reported.

A Comprehensive Numerical Model for Simulating Fluid Transport in Nanopores

NASA Astrophysics Data System (ADS)

Zhang, Yuan; Yu, Wei; Sepehrnoori, Kamy; di, Yuan

2017-01-01

Since a large amount of nanopores exist in tight oil reservoirs, fluid transport in nanopores is complex due to large capillary pressure. Recent studies only focus on the effect of nanopore confinement on single-well performance with simple planar fractures in tight oil reservoirs. Its impacts on multi-well performance with complex fracture geometries have not been reported. In this study, a numerical model was developed to investigate the effect of confined phase behavior on cumulative oil and gas production of four horizontal wells with different fracture geometries. Its pore sizes were divided into five regions based on nanopore size distribution. Then, fluid properties were evaluated under different levels of capillary pressure using Peng-Robinson equation of state. Afterwards, an efficient approach of Embedded Discrete Fracture Model (EDFM) was applied to explicitly model hydraulic and natural fractures in the reservoirs. Finally, three fracture geometries, i.e. non-planar hydraulic fractures, non-planar hydraulic fractures with one set natural fractures, and non-planar hydraulic fractures with two sets natural fractures, are evaluated. The multi-well performance with confined phase behavior is analyzed with permeabilities of 0.01 md and 0.1 md. This work improves the analysis of capillarity effect on multi-well performance with complex fracture geometries in tight oil reservoirs.

Facile fabrication of nanofluidic diode membranes using anodic aluminium oxide

NASA Astrophysics Data System (ADS)

Wu, Songmei; Wildhaber, Fabien; Vazquez-Mena, Oscar; Bertsch, Arnaud; Brugger, Juergen; Renaud, Philippe

2012-08-01

Active control of ion transport plays important roles in chemical and biological analytical processes. Nanofluidic systems hold the promise for such control through electrostatic interaction between ions and channel surfaces. Most existing experiments rely on planar geometry where the nanochannels are generally very long and shallow with large aspect ratios. Based on this configuration the concepts of nanofluidic gating and rectification have been successfully demonstrated. However, device minimization and throughput scaling remain significant challenges. We report here an innovative and facile realization of hetero-structured Al2O3/SiO2 (Si) nanopore array membranes by using pattern transfer of self-organized nanopore structures of anodic aluminum oxide (AAO). Thanks to the opposite surface charge states of Al2O3 (positive) and SiO2 (negative), the membrane exhibits clear rectification of ion current in electrolyte solutions with very low aspect ratios compared to previous approaches. Our hetero-structured nanopore arrays provide a valuable platform for high throughput applications such as molecular separation, chemical processors and energy conversion.Active control of ion transport plays important roles in chemical and biological analytical processes. Nanofluidic systems hold the promise for such control through electrostatic interaction between ions and channel surfaces. Most existing experiments rely on planar geometry where the nanochannels are generally very long and shallow with large aspect ratios. Based on this configuration the concepts of nanofluidic gating and rectification have been successfully demonstrated. However, device minimization and throughput scaling remain significant challenges. We report here an innovative and facile realization of hetero-structured Al2O3/SiO2 (Si) nanopore array membranes by using pattern transfer of self-organized nanopore structures of anodic aluminum oxide (AAO). Thanks to the opposite surface charge states of Al2O3 (positive) and SiO2 (negative), the membrane exhibits clear rectification of ion current in electrolyte solutions with very low aspect ratios compared to previous approaches. Our hetero-structured nanopore arrays provide a valuable platform for high throughput applications such as molecular separation, chemical processors and energy conversion. Electronic supplementary information (ESI) available: Pattern transfer of local AAO mask into Si layers of different thickness; characterization of the Ag/AgCl electrodes and the cell constant; control experiments of mono-charged nanopore membranes; and simulation of ionic transport in nanofluidic diodes. See DOI: 10.1039/c2nr31243c

Molecular dynamics study of ionic liquid confined in silicon nanopore

NASA Astrophysics Data System (ADS)

Liu, Y. S.; Sha, M. L.; Cai, K. Y.

2017-05-01

Molecular dynamics simulations was carried to investigate the structure and dynamics of [BMIM][PF6] ionic liquid (IL) confined inside a slit-like silicon nanopore with pore size of 5.5 nm. It is clearly shown that the mass and number densities of the confined ILs are oscillatory, high density layers are also formed in the vicinity of the silicon surface, which indicates the existence of solid-like high density IL layers. The orientational investigation shows that the imidazolium ring of [BMIM] cation lies preferentially flat on the surface of the silicon pore walls. Furthermore, the mean squared displacement (MSD) calculation indicates that the dynamics of confined ILs are significantly slower than those observed in bulk systems. Our results suggest that the interactions between the pore walls and the ILs can strongly affect the structural and dynamical properties of the confined ILs.

Nanoporous Metallic Networks: Fabrication, Optical Properties, and Applications.

PubMed

Ron, Racheli; Haleva, Emir; Salomon, Adi

2018-05-17

Nanoporous metallic networks are a group of porous materials made of solid metals with suboptical wavelength sizes of both particles and voids. They are characterized by unique optical properties, as well as high surface area and permeability of guest materials. As such, they attract a great focus as novel materials for photonics, catalysis, sensing, and renewable energy. Their properties together with the ability for scaling-up evoke an increased interest also in the industrial field. Here, fabrication techniques of large-scale metallic networks are discussed, and their interesting optical properties as well as their applications are considered. In particular, the focus is on disordered systems, which may facilitate the fabrication technique, yet, endow the three-dimensional (3D) network with distinct optical properties. These metallic networks bridge the nanoworld into the macroscopic world, and therefore pave the way to the fabrication of innovative materials with unique optoelectronic properties. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of Adsorption on Gas Transport in Nanopores.

PubMed

Wu, Tianhao; Zhang, Dongxiao

2016-03-29

Given the complex nature of the interaction between gas and solid atoms, the development of nanoscale science and technology has engendered a need for further understanding of gas transport behavior through nanopores and more tractable models for large-scale simulations. In the present paper, we utilize molecular dynamic simulations to demonstrate the behavior of gas flow under the influence of adsorption in nano-channels consisting of illite and graphene, respectively. The results indicate that velocity oscillation exists along the cross-section of the nano-channel, and the total mass flow could be either enhanced or reduced depending on variations in adsorption under different conditions. The mechanisms can be explained by the extra average perturbation stress arising from density oscillation via the novel perturbation model for micro-scale simulation, and approximated via the novel dual-region model for macro-scale simulation, which leads to a more accurate permeability correction model for industrial applications than is currently available.

Translocation of double strand DNA into a biological nanopore

NASA Astrophysics Data System (ADS)

Chatkaew, Sunita; Mlayeh, Lamia; Leonetti, Marc; Homble, Fabrice

2009-03-01

Translocation of double strand DNA across a unique mitochondrial biological nanopore (VDAC) is observed by an electrophysiological method. Characteristics of opened and sub-conductance states of VDAC are studied. When the applied electric potential is beyond ± 20 mV, VDAC transits to a sub-conductance state. Plasmids (circular double strand DNA) with a diameter greater than that of the channel shows the current reduction into the channel during the interaction but the state with zero-current is not observed. On the contrary, the interaction of linear double strand DNA with the channel shows the current reduction along with the zero-current state. These show the passages of linear double strand DNA across the channel and the electrostatic effect due to the surface charges of double strand DNA and channel for circular and linear double strand DNA.

Amplified solid-state electrochemiluminescence detection of cholesterol in near-infrared range based on CdTe quantum dots decorated multiwalled carbon nanotubes@reduced graphene oxide nanoribbons.

PubMed

Huan, Juan; Liu, Qian; Fei, Airong; Qian, Jing; Dong, Xiaoya; Qiu, Baijing; Mao, Hanping; Wang, Kun

2015-11-15

An amplified solid-state electrochemiluminescence (ECL) biosensor for detection of cholesterol in near-infrared (NIR) range was constructed based on CdTe quantum dots (QDs) decorated multiwalled carbon nanotubes@reduced graphene nanoribbons (CdTe-MWCNTs@rGONRs), which were prepared by electrostatic interactions. The CdTe QDs decorated on the MWCNTs@rGONRs resulted in the amplified ECL intensity by ~4.5 fold and decreased onset potential by ~100 mV. By immobilization of the cholesterol oxidase (ChOx) and NIR CdTe-MWCNTs@rGONRs on the electrode surface, a solid-state ECL biosensor for cholesterol detection was constructed. When cholesterol was added to the detection solution, the immobilized ChOx catalyzed the oxidation of cholesterol to generate H2O2, which could be used as the co-reactant in the ECL system of CdTe-MWCNTs@rGONRs. The as-prepared biosensor exhibited good performance for cholesterol detection including good reproducibility, selectivity, and acceptable linear range from 1 μM to 1mM with a relative low detection limit of 0.33 μM (S/N=3). The biosensor was successfully applied to the determination of cholesterol in biological fluid and food sample, which would open a new possibility for development of solid-state ECL biosensors with NIR emitters. Copyright © 2015 Elsevier B.V. All rights reserved.

Instrumental Analysis in Environmental Chemistry - Liquid and Solid Phase Detection Systems

ERIC Educational Resources Information Center

Stedman, Donald H.; Meyers, Philip A.

1974-01-01

This is the second of two reviews dealing with analytical methods applicable to environmental chemistry. Methods are discussed under gas, liquid, or solid depending upon the state of the analyte during detection. (RH)

Detection of pulsed neutrons with solid-state electronics

NASA Astrophysics Data System (ADS)

Chatzakis, J.; Rigakis, I.; Hassan, S. M.; Clark, E. L.; Lee, P.

2016-09-01

Measurements of the spatial and time-resolved characteristics of pulsed neutron sources require large area detection materials and fast circuitry that can process the electronic pulses readout from the active region of the detector. In this paper, we present a solid-state detector based on the nuclear activation of materials by neutrons, and the detection of the secondary particle emission of the generated radionuclides’ decay. The detector utilizes a microcontroller that communicates using a modified SPI protocol. A solid-state, pulse shaping filter follows a charge amplifier, and it is designed as an inexpensive, low-noise solution for measuring pulses measured by a digital counter. An imaging detector can also be made by using an array of these detectors. The system can communicate with an interface unit and pass an image to a personal computer.

Emerging solid-state laser technology by lidar/DIAL remote sensing

NASA Technical Reports Server (NTRS)

Killinger, Dennis

1992-01-01

Significant progress has been made in recent years in the development of new, solid-state laser sources. This talk will present an overview of some of the new developments in solid-state lasers, and their application toward lidar/DIAL measurements of the atmosphere. Newly emerging lasers such as Ho:YAG, Tm:YAG, OPO, and Ti:Sapphire will be covered, along with the spectroscopic parameters required for differential operational modes of atmospheric remote sensing including Doppler-Windshear lidar, Tunable laser detection of water/CO2, and broad linewidth OPO's for open path detection of pollutant hydrocarbon gases. Additional considerations of emerging laser technology for lidar/DIAL will also be covered.

Quantitative differentiation of multiple virus in blood using nanoporous silicon oxide immunosensor and artificial neural network.

PubMed

Chakraborty, W; Ray, R; Samanta, N; RoyChaudhuri, C

2017-12-15

In spite of the rapid developments in various nanosensor technologies, it still remains challenging to realize a reliable ultrasensitive electrical biosensing platform which will be able to detect multiple viruses in blood simultaneously with a fairly high reproducibility without using secondary labels. In this paper, we have reported quantitative differentiation of Hep-B and Hep-C viruses in blood using nanoporous silicon oxide immunosensor array and artificial neural network (ANN). The peak frequency output (f p ) from the steady state sensitivity characteristics and the first cut off frequency (f c ) from the transient characteristics have been considered as inputs to the multilayer ANN. Implementation of several classifier blocks in the ANN architecture and coupling them with both the sensor chips, functionalized with Hep-B and Hep-C antibodies have enabled the quantification of the viruses with an accuracy of around 95% in the range of 0.04fM-1pM and with an accuracy of around 90% beyond 1pM and within 25nM in blood serum. This is the most sensitive report on multiple virus quantification using label free method. Copyright © 2017 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prabhakaran, Venkateshkumar; Johnson, Grant E.; Wang, Bingbing

Molecular-level understanding of electrochemical processes occurring at electrode-electrolyte interfaces (EEI) is key to the rational development of high-performance and sustainable electrochemical technologies. This article reports the development and first application of solid-state in situ electrochemical probes to study redox and catalytic processes occurring at well-defined EEI generated using soft-landing of mass- and charge-selected cluster ions (SL). In situ electrochemical probes with excellent mass transfer properties are fabricated using carefully-designed nanoporous ionic liquid membranes. SL enables deposition of pure active species that are not obtainable with other techniques onto electrode surfaces with precise control over charge state, composition, and kinetic energy.more » SL is, therefore, a unique tool for studying fundamental processes occurring at EEI. For the first time using an aprotic electrochemical probe, the effect of charge state (PMo12O403-/2-) and the contribution of building blocks of Keggin polyoxometalate (POM) clusters to redox processes are characterized by populating EEI with novel POM anions generated by electrospray ionization and gas phase dissociation. Additionally, a proton conducting electrochemical probe has been developed to characterize the reactive electrochemistry (oxygen reduction activity) of bare Pt clusters (Pt40 ~1 nm diameter), thus demonstrating the capability of the probe for studying reactions in controlled gaseous environments. The newly developed in situ electrochemical probes combined with ion SL provide a versatile method to characterize the EEI in solid-state redox systems and reactive electrochemistry at precisely-defined conditions. This capability will advance molecular-level understanding of processes occurring at EEI that are critical to many energy-related technologies.« less

Nanopore DNA sensors based on dendrimer-modified nanopipettes.

PubMed

Fu, Yaqin; Tokuhisa, Hideo; Baker, Lane A

2009-08-28

A dendrimer-modified nanopipette is used to detect hybridization of a specific DNA sequence through evaluation of the extent of rectification of ion currents observed in the measured current-voltage response.

Molecular Sensing by Nanoporous Crystalline Polymers

PubMed Central

Pilla, Pierluigi; Cusano, Andrea; Cutolo, Antonello; Giordano, Michele; Mensitieri, Giuseppe; Rizzo, Paola; Sanguigno, Luigi; Venditto, Vincenzo; Guerra, Gaetano

2009-01-01

Chemical sensors are generally based on the integration of suitable sensitive layers and transducing mechanisms. Although inorganic porous materials can be effective, there is significant interest in the use of polymeric materials because of their easy fabrication process, lower costs and mechanical flexibility. However, porous polymeric absorbents are generally amorphous and hence present poor molecular selectivity and undesired changes of mechanical properties as a consequence of large analyte uptake. In this contribution the structure, properties and some possible applications of sensing polymeric films based on nanoporous crystalline phases, which exhibit all identical nanopores, will be reviewed. The main advantages of crystalline nanoporous polymeric materials with respect to their amorphous counterparts are, besides a higher selectivity, the ability to maintain their physical state as well as geometry, even after large guest uptake (up to 10–15 wt%), and the possibility to control guest diffusivity by controlling the orientation of the host polymeric crystalline phase. The final section of the review also describes the ability of suitable polymeric films to act as chirality sensors, i.e., to sense and memorize the presence of non-racemic volatile organic compounds. PMID:22303150

Recognition Tunneling of Canonical and Modified RNA Nucleotides for Their Identification with the Aid of Machine Learning.

PubMed

Im, JongOne; Sen, Suman; Lindsay, Stuart; Zhang, Peiming

2018-06-28

In the present study, we demonstrate a tunneling nanogap technique to identify individual RNA nucleotides, which can be used as a mechanism to read the nucleobases for direct sequencing of RNA in a solid-state nanopore. The tunneling nanogap is composed of two electrodes separated by a distance of <3 nm and functionalized with a recognition molecule. When a chemical entity is captured in the gap, it generates electron tunneling currents, a process we call recognition tunneling (RT). Using RT nanogaps created in a scanning tunneling microscope (STM), we acquired the electron tunneling signals for the canonical and two modified RNA nucleotides. To call the individual RNA nucleotides from the RT data, we adopted a machine learning algorithm, support vector machine (SVM), for the data analysis. Through the SVM, we were able to identify the individual RNA nucleotides and distinguish them from their DNA counterparts with reasonably high accuracy. Since each RNA nucleoside contains a hydroxyl group at the 2'-position of its sugar ring in an RNA strand, it allows for the formation of a tunneling junction at a larger nanogap compared to the DNA nucleoside in a DNA strand, which lacks the 2' hydroxyl group. It also proves advantageous for the manufacture of RT devices. This study is a proof-of-principle demonstration for the development of an RT nanopore device for directly sequencing single RNA molecules, including those bearing modifications.

Thermodynamics of water intrusion in nanoporous hydrophobic solids.

PubMed

Cailliez, Fabien; Trzpit, Mickael; Soulard, Michel; Demachy, Isabelle; Boutin, Anne; Patarin, Joël; Fuchs, Alain H

2008-08-28

We report a joint experimental and molecular simulation study of water intrusion in silicalite-1 and ferrerite zeolites. The main conclusion of this study is that water condensation takes place through a genuine first-order phase transition, provided that the interconnected pores structure is 3-dimensional. In the extreme confinement situation (ferrierite zeolite), condensation takes place through a continuous transition, which is explained by a shift of both the first-order transition line and the critical point with increasing confinement. The present findings are at odds with the common belief that conventional phase transitions cannot take place in microporous solids such as zeolites. The most important features of the intrusion/extrusion process can be understood in terms of equilibrium thermodynamics considerations. We believe that these findings are very general for hydrophobic solids, i.e. for both nonwetting as well as wetting water-solid interface systems.

Solid-State Multimission Magnetometer (SSM(3)): Application to Groundwater Exploration on Mars

NASA Technical Reports Server (NTRS)

Grimm, Robert E.

2002-01-01

This report describes work to develop solid-state magnetometers using magnetoresistive thin films, low-frequency electric-field measurements, and methods for electromagnetic detection of water and ice in the subsurface of Mars.

Nanoporous Anodic Alumina Surface Modification by Electrostatic, Covalent, and Immune Complexation Binding Investigated by Capillary Filling.

PubMed

Eckstein, Chris; Acosta, Laura K; Pol, Laura; Xifré-Pérez, Elisabet; Pallares, Josep; Ferré-Borrull, Josep; Marsal, Lluis F

2018-03-28

The fluid imbibition-coupled laser interferometry (FICLI) technique has been applied to detect and quantify surface changes and pore dimension variations in nanoporous anodic alumina (NAA) structures. FICLI is a noninvasive optical technique that permits the determination of the NAA average pore radius with high accuracy. In this work, the technique is applied after each step of different surface modification paths of the NAA pores: (i) electrostatic immobilization of bovine serum albumin (BSA), (ii) covalent attachment of streptavidin via (3-aminipropyl)-triethoxysilane and glutaraldehyde grafting, and (iii) immune complexation. Results show that BSA attachment can be detected as a reduction in estimated radius from FICLI with high accuracy and reproducibility. In the case of the covalent attachment of streptavidin, FICLI is able to recognize a multilayer formation of the silane and the protein. For immune complexation, the technique is able to detect different antibody-antigen bindings and distinguish different dynamics among different immune species.

Transcriptome amplification coupled with nanopore sequencing as a surveillance tool for plant pathogens in plant and insect tissues

USDA-ARS?s Scientific Manuscript database

There are many plant pathogen-specific diagnostic assays, based on PCR and immune-detection. However, the ability to test for large numbers of pathogens simultaneously is lacking. Next generation sequencing (NGS) allows one to detect all organisms within a given sample, but has computational limitat...

Detection of benzo[a]pyrene-guanine adducts in single-stranded DNA using the α-hemolysin nanopore

NASA Astrophysics Data System (ADS)

Perera, Rukshan T.; Fleming, Aaron M.; Johnson, Robert P.; Burrows, Cynthia J.; White, Henry S.

2015-02-01

The carcinogenic precursor benzo[a]pyrene (BP), a polycyclic aromatic hydrocarbon, is released into the environment through the incomplete combustion of hydrocarbons. Metabolism of BP in the human body yields a potent alkylating agent (benzo[a]pyrene diol epoxide, BPDE) that reacts with guanine (G) in DNA to form an adduct implicated in cancer initiation. We report that the α-hemolysin (αHL) nanopore platform can be used to detect a BPDE adduct to G in synthetic oligodeoxynucleotides. Translocation of a 41-mer poly-2‧-deoxycytidine strand with a centrally located BPDE adduct to G through αHL in 1 M KCl produces a unique multi-level current signature allowing the adduct to be detected. This readily distinguishable current modulation was observed when the BPDE-adducted DNA strand translocated from either the 5‧ or 3‧ directions. This study suggests that BPDE adducts and other large aromatic biomarkers can be detected with αHL, presenting opportunities for the monitoring, quantification, and sequencing of mutagenic compounds from cellular DNA samples.

Membranes with highly ordered straight nanopores by selective swelling of fast perpendicularly aligned block copolymers.

PubMed

Yin, Jun; Yao, Xueping; Liou, Jiun-You; Sun, Wei; Sun, Ya-Sen; Wang, Yong

2013-11-26

Membranes with uniform, straight nanopores have important applications in diverse fields, but their application is limited by the lack of efficient producing methods with high controllability. In this work, we reported on an extremely simple and efficient strategy to produce such well-defined membranes. We demonstrated that neutral solvents were capable of annealing amphiphilic block copolymer (BCP) films of polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP) with thicknesses up to 600 nm to the perpendicular orientation within 1 min. Annealing in neutral solvents was also effective to the perpendicular alignment of block copolymers with very high molecular weights, e.g., 362 000 Da. Remarkably, simply by immersing the annealed BCP films in hot ethanol followed by drying in air, the originally dense BCP films were nondestructively converted into porous membranes containing highly ordered, straight nanopores traversing the entire thickness of the membrane (up to 1.1 μm). Grazing incident small-angle X-ray spectroscopy confirmed the hexagonal ordering of the nanopores over large areas. We found that the overflow of P2VP chains from their reservoir P2VP cylinders and the deformation of the PS matrix in the swelling process contributed to the transformation of the solid P2VP cylinders to empty straight pores. The pore diameters can be tuned by either changing the swelling temperatures or depositing thin layers of metal oxides on the preformed membranes via atomic layer deposition with a subnanometer accuracy. To demonstrate the application of the obtained porous membranes, we used them as templates and produced centimeter-scale arrays of aligned nanotubes of metal oxides with finely tunable wall thicknesses.

Protein-nucleotide contacts in motor proteins detected by DNP-enhanced solid-state NMR.

PubMed

Wiegand, Thomas; Liao, Wei-Chih; Ong, Ta Chung; Däpp, Alexander; Cadalbert, Riccardo; Copéret, Christophe; Böckmann, Anja; Meier, Beat H

2017-11-01

DNP (dynamic nuclear polarization)-enhanced solid-state NMR is employed to directly detect protein-DNA and protein-ATP interactions and identify the residue type establishing the intermolecular contacts. While conventional solid-state NMR can detect protein-DNA interactions in large oligomeric protein assemblies in favorable cases, it typically suffers from low signal-to-noise ratios. We show here, for the oligomeric DnaB helicase from Helicobacter pylori complexed with ADP and single-stranded DNA, that this limitation can be overcome by using DNP-enhanced spectroscopy. Interactions are established by DNP-enhanced 31 P- 13 C polarization-transfer experiments followed by the recording of a 2D 13 C- 13 C correlation experiment. The NMR spectra were obtained in less than 2 days and allowed the identification of residues of the motor protein involved in nucleotide binding.

Planar Solid-Oxide Fuel Cell System Demonstration at UT SimCenter

DTIC Science & Technology

2015-12-09

including metals, carbon, and zeolites , have been proposed for sulfur adsorption performances [9-13]. Nickel and copper supported on activated carbon and... zeolite exhibited effective desulfurization effects for jet fuels [14,15]. Muzic et al. [16] examined the adsorptive desulfurization of three...sulfur by using a nanoporous Ni loaded, Y-type zeolite at ambient conditions. The adsorption capacity of Ni-Y zeolite was 0.84 and 2.31 mg S/g

Evaluation of Chemically-Sensitive Field-Effect Transistors for Detection of Organophosphorus Compounds

DTIC Science & Technology

1989-12-05

during past decade. In order to understand the basic operation of these sensors, especially of the CHEMFET, the appropriate background information will...during the past decade for detecting organophosphorus compounds, the chemically- sensitive thin films investigated in this thesis, and finally, the...reactivate the phosphorylated cholinesterase enzyme. Solid State Chemical Sensors During the past decade, a number of solid state chemical sensors have been

Applying graphene oxide nano-film over a polycarbonate nanoporous membrane to monitor E. coli by infrared spectroscopy

NASA Astrophysics Data System (ADS)

Singh, Krishna Pal; Dhek, Neeraj Singh; Nehra, Anuj; Ahlawat, Sweeti; Puri, Anu

2017-01-01

Nano-biosensors are excellent monitoring tools for rapid, specific, sensitive, inexpensive, in-field, on-line, and/or real-time detection of pathogens in foods, soil, air, and water samples. A variety of nano-materials (metallic, polymeric, and/or carbon-based) were employed to enhance the efficacy, efficiency, and sensitivity of these nano-biosensors, including graphene-based materials, especially graphene oxide (GO)-based materials. GO bears many oxygen-bearing groups, enabling ligand conjugation at the high density critical for sensitive detection. We have fabricated GO-modified nano-porous polycarbonate track-etched (PCTE) membranes that were conjugated to an Escherichia coli-specific antibody (Ab) and used to detect E. coli. The random distribution of nanopores on the PCTE membrane surface and the bright coating of the GO onto the membrane were confirmed by scanning electron microscope. Anti-E. coli β-gal Abs were conjugated to the GO surface via 1-ethyl-3,3-dimethylaminopropyl carbodiimide hydrochloride-N-hydroxysuccinimide chemistry; antibody coating was confirmed by the presence of a characteristic IR peak near 1600 cm- 1. A non-corresponding Ab (anti-Pseudomonas) was used as a negative control under identical conditions. When E. coli interacted anti-E.coli β-gal with Ab-coated GO-nano-biosensor units, we observed a clear shift in the IR peak from 3373.14 to 3315 cm- 1; in contrast, we did not observe any shift in IR peaks when the GO unit was coated with the non-corresponding Ab (anti-Pseudomonas). Therefore, the detection of E. coli using the described GO-nano-sensor unit is highly specific, is highly selective and can be applied for real-time monitoring of E. coli with a detection limit between 100 μg/mL and 10 μg/mL, similar to existing detection systems.

Applying graphene oxide nano-film over a polycarbonate nanoporous membrane to monitor E. coli by infrared spectroscopy.

PubMed

Singh, Krishna Pal; Dhek, Neeraj Singh; Nehra, Anuj; Ahlawat, Sweeti; Puri, Anu

2017-01-05

Nano-biosensors are excellent monitoring tools for rapid, specific, sensitive, inexpensive, in-field, on-line, and/or real-time detection of pathogens in foods, soil, air, and water samples. A variety of nano-materials (metallic, polymeric, and/or carbon-based) were employed to enhance the efficacy, efficiency, and sensitivity of these nano-biosensors, including graphene-based materials, especially graphene oxide (GO)-based materials. GO bears many oxygen-bearing groups, enabling ligand conjugation at the high density critical for sensitive detection. We have fabricated GO-modified nano-porous polycarbonate track-etched (PCTE) membranes that were conjugated to an Escherichia coli-specific antibody (Ab) and used to detect E. coli. The random distribution of nanopores on the PCTE membrane surface and the bright coating of the GO onto the membrane were confirmed by scanning electron microscope. Anti-E. coli β-gal Abs were conjugated to the GO surface via 1-ethyl-3,3-dimethylaminopropyl carbodiimide hydrochloride-N-hydroxysuccinimide chemistry; antibody coating was confirmed by the presence of a characteristic IR peak near 1600cm(-1). A non-corresponding Ab (anti-Pseudomonas) was used as a negative control under identical conditions. When E. coli interacted anti-E.coli β-gal with Ab-coated GO-nano-biosensor units, we observed a clear shift in the IR peak from 3373.14 to 3315cm(-1); in contrast, we did not observe any shift in IR peaks when the GO unit was coated with the non-corresponding Ab (anti-Pseudomonas). Therefore, the detection of E. coli using the described GO-nano-sensor unit is highly specific, is highly selective and can be applied for real-time monitoring of E. coli with a detection limit between 100μg/mL and 10μg/mL, similar to existing detection systems. Copyright © 2016 Elsevier B.V. All rights reserved.

Dendritic copper phthalocyanine with aggregation induced blue emission and solid-state fluorescence

NASA Astrophysics Data System (ADS)

Wang, Jiayi; Pan, Lin; Zhou, Xuefei; Jia, Kun; Liu, Xiaobo

2016-09-01

In this work, dendritic copper phthalocyanine (CuPc) showing obvious aggregation induced emission (AIE) and strong solid-state fluorescence was synthesized. It was found that synthesized CuPc can be easily solubilized in polar aprotic solvent, where no fluorescence signal was detected. Interestingly, both the CuPc aggregates in solution and solid-state powder exhibited strong fluorescence emission around 480 nm, which should be attributed to the restriction of intramolecular rotation as rationalized in aggregation induced emission framework. Meanwhile the obvious crystalline enhanced solid-state fluorescent emission is observed for CuPc powder.

Host-Guest Chemistry in Integrated Porous Space Formed by Molecular Self-Assembly at Liquid-Solid Interfaces.

PubMed

Iritani, Kohei; Tahara, Kazukuni; De Feyter, Steven; Tobe, Yoshito

2017-05-16

Host-guest chemistry in two-dimensional (2D) space, that is, physisorbed monolayers of a single atom or a single molecular thickness on surfaces, has become a subject of intense current interest because of perspectives for various applications in molecular-scale electronics, selective sensors, and tailored catalysis. Scanning tunneling microscopy has been used as a powerful tool for the visualization of molecules in real space on a conducting substrate surface. For more than a decade, we have been investigating the self-assembly of a series of triangle-shaped phenylene-ethynylene macrocycles called dehydrobenzo[12]annulenes (DBAs). These molecules are substituted with six alkyl chains and are capable of forming hexagonal porous 2D molecular networks via van der Waals interactions between interdigitated alkyl chains at the interface of organic solvents and graphite. The dimension of the nanoporous space or nanowell formed by the self-assembly of DBAs can be controlled from 1.6 to 4.7 nm by simply changing the alkyl chain length from C 6 to C 20 . Single molecules as well as homoclusters and heteroclusters are capable of coadsorbing within the host matrix using shape- and size-complementarity principles. Moreover, on the basis of the versatility of the DBA molecules that allows chemical modification of the alkyl chain terminals, we were able to decorate the interior space of the nanoporous networks with functional groups such as azobenzenedicarboxylic acid for photoresponsive guest adsorption/desorption or fluoroalkanes and tetraethylene glycol groups for selective guest binding by electrostatic interactions and zinc-porphyrin units for complexation with a guest by charge-transfer interactions. In this Feature Article, we describe the general aspects of molecular self-assembly at liquid/solid interfaces, followed by the formation of programmed porous molecular networks using rationally designed molecular building blocks. We focus on our own work involving host-guest chemistry in integrated nanoporous space that is modified for specific purposes.

Influence of Nanopore Shapes on Thermal Conductivity of Two-Dimensional Nanoporous Material.

PubMed

Huang, Cong-Liang; Huang, Zun; Lin, Zi-Zhen; Feng, Yan-Hui; Zhang, Xin-Xin; Wang, Ge

2016-12-01

The influence of nanopore shapes on the electronic thermal conductivity (ETC) was studied in this paper. It turns out that with same porosity, the ETC will be quite different for different nanopore shapes, caused by the different channel width for different nanopore shapes. With same channel width, the influence of different nanopore shapes can be approximately omitted if the nanopore is small enough (smaller than 0.5 times EMFP in this paper). The ETC anisotropy was discovered for triangle nanopores at a large porosity with a large nanopore size, while there is a similar ETC for small pore size. It confirmed that the structure difference for small pore size may not be seen by electrons in their moving.

Two-step fabrication of nanoporous copper films with tunable morphology for SERS application

NASA Astrophysics Data System (ADS)

Diao, Fangyuan; Xiao, Xinxin; Luo, Bing; Sun, Hui; Ding, Fei; Ci, Lijie; Si, Pengchao

2018-01-01

It is important to design and fabricate nanoporous metals (NPMs) with optimized microstructures for specific applications. In this contribution, nanoporous coppers (NPCs) with controllable thicknesses and pore sizes were fabricated via the combination of a co-sputtering of Cu/Ti with a subsequent dealloying process. The effect of dealloying time on porous morphology and the corresponding surface enhanced Raman scattering (SERS) behaviors were systematically investigated. Transmission electron microscopy (TEM) identified the presences of the gaps formed between ligaments and also the nanobumps on the nanoparticle-aggregated ligament surface, which were likely to contribute as the ;hot spots; for electromagnetic enhancement. The optimal NPC film exhibited excellent SERS performance towards Rhodamine 6G (R6G) with a low limiting detection (10-9 M), along with good uniformity and reproducibility. The calculated enhancement factor of ca. 4.71 × 107 was over Au substrates and comparable to Ag systems, promising the proposed NPC as a cheap candidate for high-performance SERS substrate.

Assessment of in vivo systemic toxicity and biodistribution of iron-doped silica nanoshells.

PubMed

Mendez, Natalie; Liberman, Alexander; Corbeil, Jacqueline; Barback, Christopher; Viveros, Robert; Wang, James; Wang-Rodriguez, Jessica; Blair, Sarah L; Mattrey, Robert; Vera, David; Trogler, William; Kummel, Andrew C

2017-04-01

Silica nanoparticles are an emerging class of biomaterials which may be used as diagnostic and therapeutic tools for biomedical applications. In particular, hollow silica nanoshells are attractive due to their hollow core. Approximately 70% of a 500 nm nanoshell is hollow, therefore more particles can be administered on a mg/kg basis compared to solid nanoparticles. Additionally, their nanoporous shell permits influx/efflux of gases and small molecules. Since the size, shape, and composition of a nanoparticle can dramatically alter its toxicity and biodistribution, the toxicology of these nanomaterials was assessed. A single dose toxicity study was performed in vivo to assess the toxicity of 500 nm iron-doped silica nanoshells at clinically relevant doses of 10-20 mg/kg. This study showed that only a trace amount of silica was detected in the body 10 weeks post-administration. The hematology, biochemistry and pathological results show that the nanoshells exhibit no acute or chronic toxicity in mice. Copyright © 2016 Elsevier Inc. All rights reserved.

Uncovering a reconstructive solid-solid phase transition in a metal-organic framework.

PubMed

Longley, L; Li, N; Wei, F; Bennett, T D

2017-11-01

A nanoporous three-dimensional metal-organic framework (MOF), ZnPurBr undergoes a transition to a previously unreported high-temperature phase, ZnPurBr-ht. The transition, which proceeds without mass loss, is uncovered through the use of differential scanning calorimetry (DSC). The new crystal structure was solved using single-crystal X-ray diffraction, and the mechanical properties of both phases investigated by nanoindentation and density functional theory. The anisotropy of the calculated Young's moduli showed good agreement with the crystallographic alignment of the stiff purinate organic linker. The results provide a prototypical example of the importance of the use of DSC in the MOF field, where its use is not currently standard in characterization.

Highly sensitive surface-enhanced Raman scattering substrate made from superaligned carbon nanotubes.

PubMed

Sun, Yinghui; Liu, Kai; Miao, Jiao; Wang, Zheyao; Tian, Baozhong; Zhang, Lina; Li, Qunqing; Fan, Shoushan; Jiang, Kaili

2010-05-12

Surface-enhanced Raman scattering (SERS) has attracted wide attention because it can enhance normally weak Raman signal by several orders of magnitude and facilitate the sensitive detection of molecules. Conventional SERS substrates are constructed by placing metal nanoparticles on a planar surface. Here we show that, if the planar surface was substituted by a unique nanoporous surface, the enhancement effect can be dramatically improved. The nanoporous surface can be easily fabricated in batches and at low costs by cross stacking superaligned carbon nanotube films. The as-prepared transparent and freestanding SERS substrate is capable of detecting ambient trinitrotoluene vapor, showing much higher Raman enhancement than ordinary planar substrates because of the extremely large surface area and the unique zero-dimensional at one-dimensional nanostructure. These results not only provide a new approach to ultrasensitive SERS substrates, but also are helpful for improving the fundamental understanding of SERS phenomena.

Effect of film thickness on localized surface plasmon enhanced chemical sensor

NASA Astrophysics Data System (ADS)

Kassu, Aschalew; Farley, Carlton; Sharma, Anup; Kim, Wonkyu; Guo, Junpeng

2014-05-01

A highly-sensitive, reliable, simple and inexpensive chemical detection and identification platform is demonstrated. The sensing technique is based on localized surface plasmon enhanced Raman scattering measurements from gold-coated highly-ordered symmetric nanoporous ceramic membranes fabricated from anodic aluminum oxide. To investigate the effects of the thickness of the sputter-coated gold films on the sensitivity of sensor, and optimize the performance of the substrates, the geometry of the nanopores and the film thicknesses are varied in the range of 30 nm to 120 nm. To characterize the sensing technique and the detection limits, surface enhanced Raman scatterings of low concentrations of a standard chemical adsorbed on the gold coated substrates are collected and analyzed. The morphology of the proposed substrates is characterized by atomic force microscopy and the optical properties including transmittance, reflectance and absorbance of each substrate are also investigated.

Mapping Base Modifications in DNA by Transverse-Current Sequencing

NASA Astrophysics Data System (ADS)

Alvarez, Jose R.; Skachkov, Dmitry; Massey, Steven E.; Kalitsov, Alan; Velev, Julian P.

2018-02-01

Sequencing DNA modifications and lesions, such as methylation of cytosine and oxidation of guanine, is even more important and challenging than sequencing the genome itself. The traditional methods for detecting DNA modifications are either insensitive to these modifications or require additional processing steps to identify a particular type of modification. Transverse-current sequencing in nanopores can potentially identify the canonical bases and base modifications in the same run. In this work, we demonstrate that the most common DNA epigenetic modifications and lesions can be detected with any predefined accuracy based on their tunneling current signature. Our results are based on simulations of the nanopore tunneling current through DNA molecules, calculated using nonequilibrium electron-transport methodology within an effective multiorbital model derived from first-principles calculations, followed by a base-calling algorithm accounting for neighbor current-current correlations. This methodology can be integrated with existing experimental techniques to improve base-calling fidelity.

Self-induced redox cycling coupled luminescence on nanopore recessed disk-multiscale bipolar electrodes

DOE PAGES

Ma, Chaoxiong; Zaino III, Lawrence P.; Bohn, Paul W.

2015-03-25

Self-induced redox cycling at nanopore ring-disk electrodes is coupled, through a bipolar electrode, to a remote fluorigenic reporter reaction. We present a new configuration for coupling fluorescence microscopy and voltammetry using self-induced redox cycling for ultrasensitive electrochemical measurements. An array of nanopores, each supporting a recessed disk electrode separated by 100 nm in depth from a planar multiscale bipolar top electrode, was fabricated using multilayer deposition, nanosphere lithography, and reactive-ion etching. Self-induced redox cycling was induced on the disk electrode producing ~30× current amplification, which was independently confirmed by measuring induced electrogenerated chemiluminescence from Ru(bpy) 3 2/3+/tri-n-propylamine on the floatingmore » bipolar electrode. In this design, redox cycling occurs between the recessed disk and the top planar portion of a macroscopic thin film bipolar electrode in each nanopore. Electron transfer also occurs on a remote (mm-distance) portion of the planar bipolar electrode to maintain electroneutrality. This couples the electrochemical reactions of the target redox pair in the nanopore array with a reporter, such as a potential-switchable fluorescent indicator, in the cell at the distal end of the bipolar electrode. Oxidation or reduction of reversible analytes on the disk electrodes were accompanied by reduction or oxidation, respectively, on the nanopore portion of the bipolar electrode and then monitored by the accompanying oxidation of dihydroresorufin or reduction of resorufin at the remote end of the bipolar electrode, respectively. In both cases, changes in fluorescence intensity were triggered by the reaction of the target couple on the disk electrode, while recovery was largely governed by diffusion of the fluorescent indicator. Reduction of 1 nM of Ru(NH 3) 6 3+ on the nanoelectrode array was detected by monitoring the fluorescence intensity of resorufin, demonstrating high sensitivity fluorescence-mediated electrochemical sensing coupled to self-induced redox cycling.« less

Self-induced redox cycling coupled luminescence on nanopore recessed disk-multiscale bipolar electrodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Chaoxiong; Zaino III, Lawrence P.; Bohn, Paul W.

Self-induced redox cycling at nanopore ring-disk electrodes is coupled, through a bipolar electrode, to a remote fluorigenic reporter reaction. We present a new configuration for coupling fluorescence microscopy and voltammetry using self-induced redox cycling for ultrasensitive electrochemical measurements. An array of nanopores, each supporting a recessed disk electrode separated by 100 nm in depth from a planar multiscale bipolar top electrode, was fabricated using multilayer deposition, nanosphere lithography, and reactive-ion etching. Self-induced redox cycling was induced on the disk electrode producing ~30× current amplification, which was independently confirmed by measuring induced electrogenerated chemiluminescence from Ru(bpy) 3 2/3+/tri-n-propylamine on the floatingmore » bipolar electrode. In this design, redox cycling occurs between the recessed disk and the top planar portion of a macroscopic thin film bipolar electrode in each nanopore. Electron transfer also occurs on a remote (mm-distance) portion of the planar bipolar electrode to maintain electroneutrality. This couples the electrochemical reactions of the target redox pair in the nanopore array with a reporter, such as a potential-switchable fluorescent indicator, in the cell at the distal end of the bipolar electrode. Oxidation or reduction of reversible analytes on the disk electrodes were accompanied by reduction or oxidation, respectively, on the nanopore portion of the bipolar electrode and then monitored by the accompanying oxidation of dihydroresorufin or reduction of resorufin at the remote end of the bipolar electrode, respectively. In both cases, changes in fluorescence intensity were triggered by the reaction of the target couple on the disk electrode, while recovery was largely governed by diffusion of the fluorescent indicator. Reduction of 1 nM of Ru(NH 3) 6 3+ on the nanoelectrode array was detected by monitoring the fluorescence intensity of resorufin, demonstrating high sensitivity fluorescence-mediated electrochemical sensing coupled to self-induced redox cycling.« less

Oxygen Reduction at Very Low Overpotential on Nanoporous Ag Catalysts

DOE PAGES

Zhou, Yang; Lu, Qi; Zhuang, Zhongbin; ...

2015-05-07

Here we report a monolithic nanoporous Ag (np-Ag) material, synthesized using the dealloying method, as high-performance catalysts for ORR in alkaline media. As shown in Scheme 1, when there is insufficient potential input, the O 2 molecules are more likely to rebound off from a planar electrode surface (i.e. bulk polycrystalline metal, films made from nanoparticles or nanowires) before they could be reduced. In contrast, they are more likely to be trapped inside the monolithic nanoporous structure, contacting with catalytic surface for multiple time, which greatly enhances the chance for them to be fully reduced. As a result, the np-Agmore » catalyst is able to achieve an equivalent or better ORR performance than the state-of the-art Pt/C catalyst at low overpotentials, which is most desired in electrochemical energy applications for maximizing efficiency.« less

Ultra-sensitive flow measurement in individual nanopores through pressure--driven particle translocation.

PubMed

Gadaleta, Alessandro; Biance, Anne-Laure; Siria, Alessandro; Bocquet, Lyderic

2015-05-07

A challenge for the development of nanofluidics is to develop new instrumentation tools, able to probe the extremely small mass transport across individual nanochannels. Such tools are a prerequisite for the fundamental exploration of the breakdown of continuum transport in nanometric confinement. In this letter, we propose a novel method for the measurement of the hydrodynamic permeability of nanometric pores, by diverting the classical technique of Coulter counting to characterize a pressure-driven flow across an individual nanopore. Both the analysis of the translocation rate, as well as the detailed statistics of the dwell time of nanoparticles flowing across a single nanopore, allow us to evaluate the permeability of the system. We reach a sensitivity for the water flow down to a few femtoliters per second, which is more than two orders of magnitude better than state-of-the-art alternative methods.

Bottom-up synthesis of multifunctional nanoporous graphene

NASA Astrophysics Data System (ADS)

Moreno, César; Vilas-Varela, Manuel; Kretz, Bernhard; Garcia-Lekue, Aran; Costache, Marius V.; Paradinas, Markos; Panighel, Mirko; Ceballos, Gustavo; Valenzuela, Sergio O.; Peña, Diego; Mugarza, Aitor

2018-04-01

Nanosize pores can turn semimetallic graphene into a semiconductor and, from being impermeable, into the most efficient molecular-sieve membrane. However, scaling the pores down to the nanometer, while fulfilling the tight structural constraints imposed by applications, represents an enormous challenge for present top-down strategies. Here we report a bottom-up method to synthesize nanoporous graphene comprising an ordered array of pores separated by ribbons, which can be tuned down to the 1-nanometer range. The size, density, morphology, and chemical composition of the pores are defined with atomic precision by the design of the molecular precursors. Our electronic characterization further reveals a highly anisotropic electronic structure, where orthogonal one-dimensional electronic bands with an energy gap of ∼1 electron volt coexist with confined pore states, making the nanoporous graphene a highly versatile semiconductor for simultaneous sieving and electrical sensing of molecular species.

Cellular telephone-based radiation sensor and wide-area detection network

DOEpatents

Craig, William W [Pittsburg, CA; Labov, Simon E [Berkeley, CA

2006-12-12

A network of radiation detection instruments, each having a small solid state radiation sensor module integrated into a cellular phone for providing radiation detection data and analysis directly to a user. The sensor module includes a solid-state crystal bonded to an ASIC readout providing a low cost, low power, light weight compact instrument to detect and measure radiation energies in the local ambient radiation field. In particular, the photon energy, time of event, and location of the detection instrument at the time of detection is recorded for real time transmission to a central data collection/analysis system. The collected data from the entire network of radiation detection instruments are combined by intelligent correlation/analysis algorithms which map the background radiation and detect, identify and track radiation anomalies in the region.

Cellular telephone-based radiation detection instrument

DOEpatents

Craig, William W [Pittsburg, CA; Labov, Simon E [Berkeley, CA

2011-06-14

A network of radiation detection instruments, each having a small solid state radiation sensor module integrated into a cellular phone for providing radiation detection data and analysis directly to a user. The sensor module includes a solid-state crystal bonded to an ASIC readout providing a low cost, low power, light weight compact instrument to detect and measure radiation energies in the local ambient radiation field. In particular, the photon energy, time of event, and location of the detection instrument at the time of detection is recorded for real time transmission to a central data collection/analysis system. The collected data from the entire network of radiation detection instruments are combined by intelligent correlation/analysis algorithms which map the background radiation and detect, identify and track radiation anomalies in the region.

Cellular telephone-based wide-area radiation detection network

DOEpatents

Craig, William W [Pittsburg, CA; Labov, Simon E [Berkeley, CA

2009-06-09

A network of radiation detection instruments, each having a small solid state radiation sensor module integrated into a cellular phone for providing radiation detection data and analysis directly to a user. The sensor module includes a solid-state crystal bonded to an ASIC readout providing a low cost, low power, light weight compact instrument to detect and measure radiation energies in the local ambient radiation field. In particular, the photon energy, time of event, and location of the detection instrument at the time of detection is recorded for real time transmission to a central data collection/analysis system. The collected data from the entire network of radiation detection instruments are combined by intelligent correlation/analysis algorithms which map the background radiation and detect, identify and track radiation anomalies in the region.

Structural evolution of nanoporous ultra-low k dielectrics under voltage stress

NASA Astrophysics Data System (ADS)

Raja, Archana; Shaw, Thomas; Grill, Alfred; Laibowitz, Robert; Heinz, Tony

2013-03-01

High speed interconnects in advanced integrated circuits require ultra-low-k dielectrics. Reduction of the dielectric constant is achieved via incorporation of nanopores in structures containing silicon, carbon, oxygen and hydrogen (SiCOH). We study nanoporous SiCOH films of k=2.5 and thicknesses of 40 - 400 nm. Leakage currents develop in the films under long-term voltage stress, eventually leading to breakdown and chip failure. Previous work* has shown the build-up of trap states as dielectric breakdown progresses. Using FTIR spectroscopy we have tracked the reorganization of the bonds in the SiCOH networks induced by voltage stress. Our results indicate that the cleavage of the Si-C and SiC-O bonds contribute toward increase in the density of bulk trapping states as breakdown is approached. AC conductance and capacitance measurements have also been carried out to describe interfacial and bulk traps and mechanisms. Comparison of breakdown properties of films with differing carbon content will also be presented to further delineate the role of carbon. *Atkin, J.M.; Shaw, T.M.; Liniger, E.; Laibowitz, R.B.; Heinz, T.F. Reliability Physics Symposium (IRPS), 2012 IEEE International Supported by the Semiconductor Research Corporation

Experimental investigation on a colloidal damper rendered controllable under the variable magnetic field generated by moving permanent magnets

NASA Astrophysics Data System (ADS)

Suciu, B.

2016-09-01

In this work, a colloidal damper rendered controllable under variable magnetic fields is proposed and its controllability is experimentally evaluated. This absorber employs a water- based ferrofluid (FERROTEC MSGW10) in association with a liquid-repellent nanoporous solid matrix, consisted of particles of gamma alumina or/and silica gel. Control of the dynamic characteristics is obtained by moving permanent neodymium annular magnets, which are placed either on the piston head (axial magnetic field) or on the external surface of the cylinder (radial magnetic field). In order to properly select these magnets, flow visualizations inside of a transparent model damper were performed, and the quantity of the displaced liquid by the magnets through the damper's filter and through the nanoporous solid matrix was determined. Experimental data concerning variation of the magnetic flux density at the magnet surface versus the height of the magnet, and versus the target distance was collected. Based on such data, the suitable magnet geometry was decided. Then, the 3D structural model of the trial colloidal damper obtained by using Solidworks, and the excitation test rig are presented. From excitation tests on a ball-screw shaker, one confirmed larger damping abilities of the proposed absorber relative to the traditional colloidal damper, and also the possibility to adjust the damping coefficient according to the excitation type.

Reversible switch between the nanoporous and the nonporous state of amphiphilic block copolymer films regulated by selective swelling.

PubMed

Yan, Nina; Wang, Yong

2015-09-21

Switchable nanoporous films, which can repeatedly alternate their porosities, are of great interest in a diversity of fields. Currently these intelligent materials are mostly based on polyelectrolytes and their porosities can change only in relatively narrow ranges, typically under wet conditions, severely limiting their applications. Here we develop a new system, which is capable of reversibly switching between a highly porous state and a nonporous state dozens of times regulated simply by exposure to selective solvents. In this system nanopores are created or reversibly eliminated in films of a block copolymer, polystyrene-block-poly(2-vinyl pyridine) (PS-b-P2VP), by exposing the films to P2VP-selective or PS-selective solvents, respectively. The mechanism of the switch is based on the selective swelling of the constituent blocks in corresponding solvents, which is a nondestructive and easily controllable process enabling the repeatable and ample switch between the open and the closed state. Systematic microscopic and ellipsometric characterization methods are performed to elucidate the pore-closing course induced by nonsolvents and the cycling between the pore-open and the pore-closed state up to 20 times. The affinity of the solvent for PS blocks is found to play a dominating role in determining the pore-closing process and the porosities of the pore-open films increase with the cycling numbers as a result of loose packing conditions of the polymer chains. We finally demonstrate the potential applications of these films as intelligent antireflection coatings and drug carriers.

Threading DNA through nanopores for biosensing applications

NASA Astrophysics Data System (ADS)

Fyta, Maria

2015-07-01

This review outlines the recent achievements in the field of nanopore research. Nanopores are typically used in single-molecule experiments and are believed to have a high potential to realize an ultra-fast and very cheap genome sequencer. Here, the various types of nanopore materials, ranging from biological to 2D nanopores are discussed together with their advantages and disadvantages. These nanopores can utilize different protocols to read out the DNA nucleobases. Although, the first nanopore devices have reached the market, many still have issues which do not allow a full realization of a nanopore sequencer able to sequence the human genome in about a day. Ways to control the DNA, its dynamics and speed as the biomolecule translocates the nanopore in order to increase the signal-to-noise ratio in the reading-out process are examined in this review. Finally, the advantages, as well as the drawbacks in distinguishing the DNA nucleotides, i.e., the genetic information, are presented in view of their importance in the field of nanopore sequencing.

Zeolitic imidazolate framework-coated acoustic sensors for room temperature detection of carbon dioxide and methane

DOE PAGES

Devkota, Jagannath; Kim, Ki-Joong; Ohodnicki, Paul R.; ...

2018-01-01

The integration of nanoporous materials such as metal organic frameworks (MOFs) with sensitive transducers can result in robust sensing platforms for monitoring gases and chemical vapors for a range of applications.

A novel material screening platform for nanoporous gold-based neural electrodes

NASA Astrophysics Data System (ADS)

Chapman, Christopher Abbott Reece

Neural-electrical interfaces have emerged in the past decades as a promising modality to facilitate the understanding of the electropathophysiology of neurological disorders as well as the normal functioning of the central nervous system, and enable the treatment of neurological defects through electrical stimulation or electrically-controlled drug delivery. However, chronically implanted electrodes face a myriad of design challenges, including their coupling to neural tissue (biocompatibility), small form factor requirement, and their electrical properties (maintaining a low electrical impedance). Planar electrode materials such as planar platinum and gold experience a large increase in electrical impedance when electrode dimensions are reduced to increase spatial resolution of neural recordings. A decrease in electrode surface area reduces the total capacitance of the electrode double layer resulting in an increase in electrode impedance. This high impedance can reduce the signal amplitude and increase the thermal noise, resulting in degradation of signal-to-noise ratio. Conventionally, this increase in electrical impedance at small electrode dimensions has been mitigated by coatings with rough morphologies such as platinum black, conducting polymers, and titanium nitride. Porous surfaces have high effective surface area enabling low impedance at small electrode dimensions. However, achieving long-term stability of cellular coupling to the electrode surface has remained difficult. Designing electrodes that can physically couple with neurons successfully and maintain low impedance at small electrode dimensions necessitates consideration of novel electrode coatings, such as carbon nanotubes and gold nanopillars. Another promising material, and focus of this proposal, is thin film nanoporous gold (np-Au). Nanoporous gold is a promising material for addressing these limitations because of its inherently large effective surface area allows for lower impedances at small form factors, and its modifiable surface morphology can be used to control cell-electrode coupling. Additionally, thin film nanoporous gold is fabricated by traditional microfabrication methods, and thus can be directly adopted by the current state-of-the-art neural electrode fabrication processes. All these properties make thin film nanoporous gold a promising candidate for use in neural electrode surfaces. This dissertation seeks to characterize both the morphological and the electrical response of neural cells to thin film nanoporous gold morphologies using an in vitro electrode morphology screening platform. The specific aims for this proposal are to: (i) develop a electrode morphology library that displays varying topographies to study structure-property relationships of thin film nanoporous gold and cellular response, (ii) characterize neural cell response to identified nanoporous gold topographies that reduce adverse tissue response in vitro, and (iii) develop an electrophysiology platform to characterize neural coupling to each identified nanoporous gold topography.

An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer.

PubMed

Imai, Kazuo; Tarumoto, Norihito; Runtuwene, Lucky Ronald; Sakai, Jun; Hayashida, Kyoko; Eshita, Yuki; Maeda, Ryuichiro; Tuda, Josef; Ohno, Hideaki; Murakami, Takashi; Maesaki, Shigefumi; Suzuki, Yutaka; Yamagishi, Junya; Maeda, Takuya

2018-05-29

The recent spread of artemisinin (ART)-resistant Plasmodium falciparum represents an emerging global threat to public health. In Southeast Asia, the C580Y mutation of kelch13 (k13) is the dominant mutation of ART-resistant P. falciparum. Therefore, a simple method for the detection of C580Y mutation is urgently needed to enable widespread routine surveillance in the field. The aim of this study is to develop a new diagnostic procedure for the C580Y mutation using loop-mediated isothermal amplification (LAMP) combined with the MinION nanopore sequencer. A LAMP assay for the k13 gene of P. falciparum to detect the C580Y mutation was successfully developed. The detection limit of this procedure was 10 copies of the reference plasmid harboring the k13 gene within 60 min. Thereafter, amplicon sequencing of the LAMP products using the MinION nanopore sequencer was performed to clarify the nucleotide sequences of the gene. The C580Y mutation was identified based on the sequence data collected from MinION reads 30 min after the start of sequencing. Further, clinical evaluation of the LAMP assay in 34 human blood samples collected from patients with P. falciparum malaria in Indonesia revealed a positive detection rate of 100%. All LAMP amplicons of up to 12 specimens were simultaneously sequenced using MinION. The results of sequencing were consistent with those of the conventional PCR and Sanger sequencing protocol. All procedures from DNA extraction to variant calling were completed within 3 h. The C580Y mutation was not found among these 34 P. falciparum isolates in Indonesia. An innovative method combining LAMP and MinION will enable simple, rapid, and high-sensitivity detection of the C580Y mutation of P. falciparum, even in resource-limited situations in developing countries.

Immobilization of glucose oxidase into a nanoporous TiO₂ film layered on metallophthalocyanine modified vertically-aligned carbon nanotubes for efficient direct electron transfer.

PubMed

Cui, Hui-Fang; Zhang, Kuan; Zhang, Yong-Fang; Sun, Yu-Long; Wang, Jia; Zhang, Wei-De; Luong, John H T

2013-08-15

Glucose oxidase (GOD) was adsorbed into a nanoporous TiO₂ film layered on the surface of an iron phthalocyanine (FePc) vertically-aligned carbon nanotube (CNT) modified electrode. A Nafion film was then dropcast on the electrode's surface to improve operational and storage stabilities of the GOD-based electrode. Scanning electron microscopy (SEM) micrographs revealed the formation of FePc and nanoporous TiO₂ nanoparticles along the sidewall and the tip of CNTs. Cyclic voltammograms of the GOD electrode in neutral PBS exhibited a pair of well-defined redox peaks, attesting the direct electron transfer of GOD (FAD/FADH₂) with the underlying electrode. The potential of glucose electro-oxidation under nitrogen was ∼+0.12 V with an oxidation current density of 65.3 μA cm(-2) at +0.77 V. Voltammetric and amperometric responses were virtually unaffected by oxygen, illustrating an efficient and fast direct electron transfer. The modification of the CNT surface with FePc resulted in a biosensor with remarkable detection sensitivity with an oxygen-independent bioelectrocatalysis. In deaerated PBS, the biosensor displayed average response time of 12 s, linearity from 50 μM to 4 mM, and a detection limit of 30 μM (S/N=3) for glucose. Copyright © 2013 Elsevier B.V. All rights reserved.

Diffusion of Supercritical Fluids through Single-Layer Nanoporous Solids: Theory and Molecular Simulations.

PubMed

Oulebsir, Fouad; Vermorel, Romain; Galliero, Guillaume

2018-01-16

With the advent of graphene material, membranes based on single-layer nanoporous solids appear as promising devices for fluid separation, be it liquid or gaseous mixtures. The design of such architectured porous materials would greatly benefit from accurate models that can predict their transport and separation properties. More specifically, there is no universal understanding of how parameters such as temperature, fluid loading conditions, or the ratio of the pore size to the fluid molecular diameter influence the permeation process. In this study, we address the problem of pure supercritical fluids diffusing through simplified models of single-layer porous materials. Basically, we investigate a toy model that consists of a single-layer lattice of Lennard-Jones interaction sites with a slit gap of controllable width. We performed extensive equilibrium and biased molecular dynamics simulations to document the physical mechanisms involved at the molecular scale. We propose a general constitutive equation for the diffusional transport coefficient derived from classical statistical mechanics and kinetic theory, which can be further simplified in the ideal gas limit. This transport coefficient relates the molecular flux to the fluid density jump across the single-layer membrane. It is found to be proportional to the accessible surface porosity of the single-layer porous solid and to a thermodynamic factor accounting for the inhomogeneity of the fluid close to the pore entrance. Both quantities directly depend on the potential of mean force that results from molecular interactions between solid and fluid atoms. Comparisons with the simulations data show that the kinetic model captures how narrowing the pore size below the fluid molecular diameter lowers dramatically the value of the transport coefficient. Furthermore, we demonstrate that our general constitutive equation allows for a consistent interpretation of the intricate effects of temperature and fluid loading conditions on the permeation process.

Single-molecule nanopore enzymology

PubMed Central

Wloka, Carsten; Maglia, Giovanni

2017-01-01

Biological nanopores are a class of membrane proteins that open nanoscale water-conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. More recently, proteins and enzymes have started being analysed with nanopores. Monitoring enzymatic reactions with nanopores, i.e. nanopore enzymology, has the unique advantage that it allows long-timescale observations of native proteins at the single-molecule level. Here we describe the approaches and challenges in nanopore enzymology. PMID:28630164

Nanopore thin film enabled optical platform for drug loading and release.

PubMed

Song, Chao; Che, Xiangchen; Que, Long

2017-08-07

In this paper, a drug loading and release device fabricated using nanopore thin film and layer-by-layer (LbL) nanoassembly is reported. The nanopore thin film is a layer of anodic aluminum oxide (AAO), consisting of honeycomb-shape nanopores. Using the LbL nanoassembly process, the drug, using gentamicin sulfate (GS) as the model, can be loaded into the nanopores and the stacked layers on the nanopore thin film surface. The drug release from the device is achieved by immersing it into flowing DI water. Both the loading and release processes can be monitored optically. The effect of the nanopore size/volume on drug loading and release has also been evaluated. Further, the neuron cells have been cultured and can grow normally on the nanopore thin film, verifying its bio-compatibility. The successful fabrication of nanopore thin film device on silicon membrane render it as a potential implantable controlled drug release device.

Ion transport in a pH-regulated nanopore.

PubMed

Yeh, Li-Hsien; Zhang, Mingkan; Qian, Shizhi

2013-08-06

Fundamental understanding of ion transport phenomena in nanopores is crucial for designing the next-generation nanofluidic devices. Due to surface reactions of dissociable functional groups on the nanopore wall, the surface charge density highly depends upon the proton concentration on the nanopore wall, which in turn affects the electrokinetic transport of ions, fluid, and particles within the nanopore. Electrokinetic ion transport in a pH-regulated nanopore, taking into account both multiple ionic species and charge regulation on the nanopore wall, is theoretically investigated for the first time. The model is verified by the experimental data of nanopore conductance available in the literature. The results demonstrate that the spatial distribution of the surface charge density at the nanopore wall and the resulting ion transport phenomena, such as ion concentration polarization (ICP), ion selectivity, and conductance, are significantly affected by the background solution properties, such as the pH and salt concentration.

Nanoporous Silicon Combustion: Observation of Shock Wave and Flame Synthesis of Nanoparticle Silica.

PubMed

Becker, Collin R; Gillen, Greg J; Staymates, Matthew E; Stoldt, Conrad R

2015-11-18

The persistent hydrogen termination present in nanoporous silicon (nPS) is unique compared to other forms of nanoscale silicon (Si) which typically readily form a silicon dioxide passivation layer. The hydrogen terminated surface combined with the extremely high surface area of nPS yields a material capable of powerful exothermic reactions when combined with strong oxidizers. Here, a galvanic etching mechanism is used to produce nPS both in bulk Si wafers as well as in patterned regions of Si wafers with microfabricated ignition wires. An explosive composite is generated by filling the pores with sodium perchlorate (NaClO4). Using high-speed video including Schlieren photography, a shock wave is observed to propagate through air at 1127 ± 116 m/s. Additionally, a fireball is observed above the region of nPS combustion which persists for nearly 3× as long when reacted in air compared to N2, indicating that highly reactive species are generated that can further combust with excess oxygen. Finally, reaction products from either nPS-NaClO4 composites or nPS alone combusted with only high pressure O2 (400 psig) gas as an oxidizer are captured in a calorimeter bomb. The products in both cases are similar and verified by transmission electron microscopy (TEM) to include nano- to micrometer scale SiOx particles. This work highlights the complex oxidation mechanism of nPS composites and demonstrates the ability to use a solid state reaction to create a secondary gas phase combustion.

In vitro proliferation and osteogenic differentiation of mesenchymal stem cells on nanoporous alumina

PubMed Central

Song, Yuanhui; Ju, Yang; Song, Guanbin; Morita, Yasuyuki

2013-01-01

Cell adhesion, migration, and proliferation are significantly affected by the surface topography of the substrates on which the cells are cultured. Alumina is one of the most popular implant materials used in orthopedics, but few data are available concerning the cellular responses of mesenchymal stem cells (MSCs) grown on nanoporous structures. MSCs were cultured on smooth alumina substrates and nanoporous alumina substrates to investigate the interaction between surface topographies of nanoporous alumina and cellular behavior. Nanoporous alumina substrates with pore sizes of 20 nm and 100 nm were used to evaluate the effect of pore size on MSCs as measured by proliferation, morphology, expression of integrin β1, and osteogenic differentiation. An MTT assay was used to measure cell viability of MSCs on different substrates, and determined that cell viability decreased with increasing pore size. Scanning electron microscopy was used to investigate the effect of pore size on cell morphology. Extremely elongated cells and prominent cell membrane protrusions were observed in cells cultured on alumina with the larger pore size. The expression of integrin β1 was enhanced in MSCs cultured on porous alumina, revealing that porous alumina substrates were more favorable for cell growth than smooth alumina substrates. Higher levels of osteoblastic differentiation markers such as alkaline phosphatase, osteocalcin, and mineralization were detected in cells cultured on alumina with 100 nm pores compared with cells cultured on alumina with either 20 nm pores or smooth alumina. This work demonstrates that cellular behavior is affected by variation in pore size, providing new insight into the potential application of this novel biocompatible material for the developing field of tissue engineering. PMID:23935364

AAO-CNTs electrode on microfluidic flow injection system for rapid iodide sensing.

PubMed

Phokharatkul, Ditsayut; Karuwan, Chanpen; Lomas, Tanom; Nacapricha, Duangjai; Wisitsoraat, Anurat; Tuantranont, Adisorn

2011-06-15

In this work, carbon nanotubes (CNTs) nanoarrays in anodized aluminum oxide (AAO-CNTs) nanopore is integrated on a microfluidic flow injection system for in-channel electrochemical detection of iodide. The device was fabricated from PDMS (polydimethylsiloxane) microchannel bonded on glass substrates that contains three-electrode electrochemical system, including AAO-CNTs as a working electrode, silver as a reference electrode and platinum as an auxiliary electrode. Aluminum, stainless steel catalyst, silver and platinum layers were sputtered on the glass substrate through shadow masks. Aluminum layer was then anodized by two-step anodization process to form nanopore template. CNTs were then grown in AAO template by thermal chemical vapor deposition. The amperometric detection of iodide was performed in 500-μm-wide and 100-μm-deep microchannels on the microfluidic chip. The influences of flow rate, injection volume and detection potential on the current response were optimized. From experimental results, AAO-CNTs electrode on chip offers higher sensitivity and wider dynamic range than CNTs electrode with no AAO template. Copyright © 2011 Elsevier B.V. All rights reserved.

Tunable Impedance Spectroscopy Sensors via Selective Nanoporous Materials.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nenoff, Tina M.; Small, Leo J

Impedance spectroscopy was leveraged to directly detect the sorption of I 2 by selective adsorption into nanoporous metal organic frameworks (MOF). Films of three different types of MOF frameworks, respectively, were drop cast onto platinum interdigitated electrodes, dried, and exposed to gaseous I 2 at 25, 40, or 70 C. The MOF frameworks varied in topology from small pores (equivalent to I 2 diameter) to large pore frameworks. The combination of the chemistry of the framework and pore size dictated quantity and kinetics of I 2 adsorption. Air, argon, methanol, and water were found to produce minimal changes in ZIF-8more » impedance. Independent of MOF framework characteristics, all resultant sensors showed high response to I 2 in air. As an example of sensor output, I 2 was readily detected at 25 C in air within 720 s of exposure, using an un-optimized sensor geometry with a small pored MOF. Further optimization of sensor geometry, decreasing MOF film thicknesses and maximizing sensor capacitance, will enable faster detection of trace I 2 .« less

Nanoporous Au-based chronocoulometric aptasensor for amplified detection of Pb(2+) using DNAzyme modified with Au nanoparticles.

PubMed

Zhang, Chen; Lai, Cui; Zeng, Guangming; Huang, Danlian; Tang, Lin; Yang, Chunping; Zhou, Yaoyu; Qin, Lei; Cheng, Min

2016-07-15

The authors herein described an amplified detection strategy employing nanoporous Au (NPG) and gold nanoparticles (AuNPs) to detect Pb(2+) ions in aqueous solution. The thiol modified Pb(2+)-specific DNAzyme was self-assembled onto the surface of the NPG modified electrode for hybridizing with the AuNPs labeled oligonucleotide and for forming the DNA double helix structure. Electrochemical signal, redox charge of hexaammineruthenium(III) chloride (RuHex), was measured by chronocoulometry. Taking advantage of amplification effects of the NPG electrode for increasing the reaction sites of capture probe and DNA-AuNPs complexes for bringing about the adsorption of large numbers of RuHex molecules, this electrochemical sensor could detect Pb(2+) quantitatively, in the range of 0.05-100nM, with a limit of detection as low as 0.012nM. Selectivity measurements revealed that the sensor was specific for Pb(2+) even with interference by high concentrations of other metal ions. This sensor was also used to detect Pb(2+) ions from samples of tap water, river water, and landfill leachate samples spiked with Pb(2+) ions, and the results showed good agreement with the found values determined by an atomic fluorescence spectrometer. This simple aptasensor represented a promising potential for on-site detecting Pb(2+) in drinking water. Copyright © 2016 Elsevier B.V. All rights reserved.

Nanopore Electrochemistry: A Nexus for Molecular Control of Electron Transfer Reactions

PubMed Central

2018-01-01

Pore-based structures occur widely in living organisms. Ion channels embedded in cell membranes, for example, provide pathways, where electron and proton transfer are coupled to the exchange of vital molecules. Learning from mother nature, a recent surge in activity has focused on artificial nanopore architectures to effect electrochemical transformations not accessible in larger structures. Here, we highlight these exciting advances. Starting with a brief overview of nanopore electrodes, including the early history and development of nanopore sensing based on nanopore-confined electrochemistry, we address the core concepts and special characteristics of nanopores in electron transfer. We describe nanopore-based electrochemical sensing and processing, discuss performance limits and challenges, and conclude with an outlook for next-generation nanopore electrode sensing platforms and the opportunities they present. PMID:29392173

Nanopore Logic Operation with DNA to RNA Transcription in a Droplet System.

PubMed

Ohara, Masayuki; Takinoue, Masahiro; Kawano, Ryuji

2017-07-21

This paper describes an AND logic operation with amplification and transcription from DNA to RNA, using T7 RNA polymerase. All four operations, (0 0) to (1 1), with an enzyme reaction can be performed simultaneously, using four-droplet devices that are directly connected to a patch-clamp amplifier. The output RNA molecule is detected using a biological nanopore with single-molecule translocation. Channel current recordings can be obtained using the enzyme solution. The integration of DNA logic gates into electrochemical devices is necessary to obtain output information in a human-recognizable form. Our method will be useful for rapid and confined DNA computing applications, including the development of programmable diagnostic devices.

Detecting trihalomethanes using nanoporous-carbon coated surface-acoustic-wave sensors

DOE PAGES

Siegal, Michael P.; Mowry, Curtis D.; Pfeifer, Kent B.; ...

2015-03-07

We study nanoporous-carbon (NPC) grown via pulsed laser deposition (PLD) as a sorbent coating on 96.5-MHz surface-acoustic-wave (SAW) devices to detect trihalomethanes (THMs), regulated byproducts from the chemical treatment of drinking water. Using both insertion-loss and isothermal-response measurements from known quantities of chloroform, the highest vapor pressure THM, we optimize the NPC mass-density at 1.05 ± 0.08 g/cm3 by controlling the background argon pressure during PLD. Precise THM quantities in a chlorobenzene solvent are directly injected into a separation column and detected as the phase-angle shift of the SAW device output compared to the drive signal. Using optimized NPC-coated SAWs,more » we study the chloroform response as a function of operating temperatures ranging from 10–50°C. Finally, we demonstrate individual responses from complex mixtures of all four THMs, with masses ranging from 10–2000 ng, after gas chromatography separation. As a result, estimates for each THM detection limit using a simple peak-height response evaluation are 4.4 ng for chloroform and 1 ng for bromoform; using an integrated-peak area response analysis improves the detection limits to 0.73 ng for chloroform and 0.003 ng bromoform.« less

General introduction: Liquid and solid (materials, main properties and applications …)

NASA Astrophysics Data System (ADS)

Zabler, Simon

2014-10-01

A general introduction about the diversity of foam structures is given with focus onto the structural, mechanical and dynamical properties at hand. Two classes of materials are addressed: liquid and semi-solid foams, on the one hand, solid foams, on the other hand. The latter can be subdivided into metallic, ceramic and organic foams, depending on the nature of the solid skeleton that supports the overall cell structure. Solid foams generally stem from the concept of mechanical light-weight structures, but they can just as well be employed for their large surface area as well as for their acoustic and thermal properties. Modern biomaterials use tailored ceramic or organo-ceramic foams as bone scaffolds, whereas hierarchically micro- and nanoporous structures are being used by chemistry to control catalytic reactions. Future materials design and development is going to rely increasingly on natural and synthetic foam structures and properties, be it food, thermal insulators or car frames, thus giving a promising outlook onto the foam research and development that is about to come. xml:lang="fr"

The role of nanosecond electric pulse-induced mechanical stress in cellular nanoporation

NASA Astrophysics Data System (ADS)

Roth, Caleb C.

Background: Exposures of cells to very short (less than 1 microsecond) electric pulses in the megavolt/meter range have been shown to cause a multitude of effects, both physical and molecular in nature. Physically, nanosecond electrical pulse exposure can disrupt the plasma membrane, leading to a phenomenon known as nanoporation. Nanoporation is the production of nanometer sized holes (less than 2 nanometers in diameter) that can persist for up to fifteen minutes, allowing the flow of ions into and out of the cell. Nanoporation can lead to secondary physical effects, such as cellular swelling, shrinking and blebbing. Molecularly, nanosecond electrical pulses have been shown to activate signaling pathways, produce oxidative stress, stimulate hormone secretion and induce both apoptotic and necrotic death. The mechanism by which nanosecond electrical pulses cause molecular changes is unknown; however, it is thought the flow of ions, such as calcium, into the cell via nanopores, could be a major cause. The ability of nanosecond electrical pulses to cause membranes to become permeable and to induce apoptosis makes the technology a desirable modality for cancer research; however, the lack of understanding regarding the mechanisms by which nanosecond electrical pulses cause nanoporation impedes further development of this technology. This dissertation documents the genomic and proteomic responses of cells exposed to nanosecond electrical pulses and describes in detail the biophysical effects of these electrical pulses, including the demonstration for the first time of the generation of acoustic pressure transients capable of disrupting plasma membranes and possibly contributing to nanoporation. Methods: Jurkat, clone E6-1 (human lymphocytic cell line), U937 (human lymphocytic cell line), Chinese hamster ovarian cells and adult primary human dermal fibroblasts exposed to nanosecond electrical pulses were subjected to a variety of molecular assays, including flow cytometry, fluorescent confocal microscopy, microarray analysis and or real time polymerase chain reaction. To investigate the physical interaction(s) of the electrical pulse with the aqueous environment, optical techniques such as pump-probe imaging, schlieren imaging, and probe beam deflection were used. Finally, electrochemistry was employed to modify the electrical parameters of the exposures such that different biophysical phenomena could be detected. Results: Approximately 500 genes were selectively up-regulated in each of the assayed cells. Validation of the microarray data indicated genes such as the putative transforming gene of avian sarcoma virus 17, commonly known as jun proto-oncogene, and the Finkel--Biskis--Jinkins murine osteosarcoma viral oncogene homolog were significantly up-regulated in response to the exposure. Many of the genes selectively up-regulated in each cell type are biomarkers of mechanical stress. Proteomic analysis indicated proteins responsible for mitigation of reactive oxygen species were produced in response to nanosecond electrical pulse exposure. Analysis using the Probe Beam Deflection Technique identified the generation of an acoustic pressure transient emanating from the electrodes immediately after the application of the pulse. This acoustic pressure transient traveled at approximately 1500 meters per second, had a frequency bandwidth of 2.5 megahertz and was capable of delivering 13 kilopascals of pressure at 5 millimeters distance from the generating electrodes. Visual confirmation of the acoustic pressure transients was accomplished using pump-probe, schlieren and ultrasonic imaging techniques. Modification of the bathing media in which the cells were exposed indicated that acoustic pressure transient formation was directly dependent on the amount of electrical current induced by the exposure. Confocal microscopy revealed that, in the absence of the acoustic pressure transients, nanoporation, as detected by a green fluorescent carbocyanine nucleic acid stain, was greatly enhanced. Conclusions: We found several genes, some of which are mechanosensitive, were selectively up-regulated due to nanosecond electrical pulse exposure. The source of this apparent mechanical stress was likely the acoustic pressure transients generated by the nanosecond electrical pulse exposure interacting with the plasma membrane of exposed cells. Contrary to our original hypothesis that these acoustic pressure transients enhance nanoporation, it appears that the opposite is true. Acoustic pressure transients generated by nanosecond electrical pulses inhibit nanoporation (or at least are negatively correlated with nanopore formation). This finding is substantiated by other reports in the literature, which indicate shock waves produced by electrical exposures inhibit gene transfection. General Significance: This work provides strong evidence that cells exposed to nanosecond electrical pulses experience a mechanical stress which by some unknown mechanism inhibits nanoporation. The findings in this dissertation are not only poised to cause a paradigm shift in how researchers understand electrical pulses cause electropermeabilization, but also will help fill in a gap in the knowledge concerning this technology, thus enabling its further development as a potential cancer therapy.

Single cigar-shaped nanopores functionalized with amphoteric amino acid chains: experimental and theoretical characterization.

PubMed

Ali, Mubarak; Ramirez, Patricio; Nguyen, Hung Quoc; Nasir, Saima; Cervera, Javier; Mafe, Salvador; Ensinger, Wolfgang

2012-04-24

We present an experimental and theoretical characterization of single cigar-shaped nanopores with pH-responsive carboxylic acid and lysine chains functionalized on the pore surface. The nanopore characterization includes (i) optical images of the nanostructure obtained by FESEM; (ii) different chemical procedures for the nanopore preparation (etching time and functionalizations; pH and electrolyte concentration of the external solution) allowing externally tunable nanopore responses monitored by the current-voltage (I-V) curves; and (iii) transport simulations obtained with a multilayer nanopore model. We show that a single, approximately symmetric nanopore can be operated as a reconfigurable diode showing different rectifying behaviors by applying chemical and electrical signals. The remarkable characteristics of the new nanopore are the sharp response observed in the I-V curves, the improved tunability (with respect to previous designs of symmetric nanopores) which is achieved because of the direct external access to the nanostructure mouths, and the broad range of rectifying properties. The results concern both fundamental concepts useful for the understanding of transport processes in biological systems (ion channels) and applications relevant for tunable nanopore technology (information processing and drug controlled release).

Controlled formation of closed-edge nanopores in graphene

NASA Astrophysics Data System (ADS)

He, Kuang; Robertson, Alex W.; Gong, Chuncheng; Allen, Christopher S.; Xu, Qiang; Zandbergen, Henny; Grossman, Jeffrey C.; Kirkland, Angus I.; Warner, Jamie H.

2015-07-01

Dangling bonds at the edge of a nanopore in monolayer graphene make it susceptible to back-filling at low temperatures from atmospheric hydrocarbons, leading to potential instability for nanopore applications, such as DNA sequencing. We show that closed edge nanopores in bilayer graphene are robust to back-filling under atmospheric conditions for days. A controlled method for closed edge nanopore formation starting from monolayer graphene is reported using an in situ heating holder and electron beam irradiation within an aberration-corrected transmission electron microscopy. Tailoring of closed-edge nanopore sizes is demonstrated from 1.4-7.4 nm. These results should provide mechanisms for improving the stability of nanopores in graphene for a wide range of applications involving mass transport.Dangling bonds at the edge of a nanopore in monolayer graphene make it susceptible to back-filling at low temperatures from atmospheric hydrocarbons, leading to potential instability for nanopore applications, such as DNA sequencing. We show that closed edge nanopores in bilayer graphene are robust to back-filling under atmospheric conditions for days. A controlled method for closed edge nanopore formation starting from monolayer graphene is reported using an in situ heating holder and electron beam irradiation within an aberration-corrected transmission electron microscopy. Tailoring of closed-edge nanopore sizes is demonstrated from 1.4-7.4 nm. These results should provide mechanisms for improving the stability of nanopores in graphene for a wide range of applications involving mass transport. Electronic supplementary information (ESI) available: Low magnification images, image processing techniques employed, modelling and simulation of closed edge nanoribbon, comprehensive AC-TEM dataset, and supporting analysis. See DOI: 10.1039/c5nr02277k

The radiation gas detectors with novel nanoporous converter for medical imaging applications

NASA Astrophysics Data System (ADS)

Zarei, H.; Saramad, S.

2018-02-01

For many reason it is tried to improve the quantum efficiency (QE) of position sensitive gas detectors. For energetic X-rays, the imaging systems usually consist of a bulk converter and gas amplification region. But the bulk converters have their own limitation. For X-rays, the converter thickness should be increased to achieve a greater detection efficiency, however in this case, the chance of escaping the photoelectrons is reduced. To overcome this limitation, a new type of converter, called a nanoporous converter such as Anodizing Aluminum Oxide (AAO) membrane with higher surface to volume ratio is proposed. According to simulation results with GATE code, for this nanoporous converter with the 1 mm thickness and inter pore distance of 627 nm, for 20-100 keV X-ray energies with a reasonable gas pressure and different pore diameters, the QE can be one order of magnitude greater than the bulk ones, which is a new approach for proposing high QE position sensitive gas detectors for medical imaging application and also high energy physics.

Towards efficient chemical synthesis via engineering enzyme catalysis in biomimetic nanoreactors.

PubMed

Liu, Jia; Yang, Qihua; Li, Can

2015-09-18

Biocatalysis with immobilized enzymes as catalysts holds enormous promise in developing more efficient and sustainable processes for the synthesis of fine chemicals, chiral pharmaceuticals and biomass feedstocks. Despite the appealing potentials, nowadays the industrial-scale application of biocatalysts is still quite modest in comparison with that of traditional chemical catalysts. A critical issue is that the catalytic performance of enzymes, the sophisticated and vulnerable catalytic machineries, strongly depends on their intracellular working environment; however the working circumstances provided by the support matrix are radically different from those in cells. This often leads to various adverse consequences on enzyme conformation and dynamic properties, consequently decreasing the overall performance of immobilized enzymes with regard to their activity, selectivity and stability. Engineering enzyme catalysis in support nanopores by mimicking the physiological milieu of enzymes in vivo and investigating how the interior microenvironment of nanopores imposes an influence on enzyme behaviors in vitro are of paramount significance to modify and improve the catalytic functions of immobilized enzymes. In this feature article, we have summarized the recent advances in mimicking the working environment and working patterns of intracellular enzymes in nanopores of mesoporous silica-based supports. Especially, we have demonstrated that incorporation of polymers into silica nanopores could be a valuable approach to create the biomimetic microenvironment for enzymes in the immobilized state.

Responsive nanoporous metals: recoverable modulations on strength and shape by watering

NASA Astrophysics Data System (ADS)

Ye, Xing-Long; Liu, Ling-Zhi; Jin, Hai-Jun

2016-08-01

Many biological materials can readily modulate their mechanical properties and shape by interacting with water in the surrounding environment, which is essential to their high performance in application. In contrast, typical inorganic materials (such as the metals) cannot change their strength and shape without involving thermal/mechanical treatments. By introducing nano-scale porous structure and exploiting a simple physical concept—the water-capillarity in nanopores, here we report that a ‘dead’ metal can be transformed into a ‘smart’ material with water-responsive properties. We demonstrate that the apparent strength, volume and shape of nanoporous Au and Au(Pt) can be modulated in situ, dramatically and recoverably, in response to water-dipping and partial-drying. The amplitude of strength-modulation reaches 20 MPa, which is nearly 50% of the yield strength at initial state. This approach also leads to reversible length change up to 1.3% in nanoporous Au and a large reversible bending motion of a bi-layer strip with tip displacement of ˜20 mm, which may be used for actuation. This method is simple and effective, occurring in situ under ambient conditions and requiring no external power, analogous to biological materials. The findings may open up novel applications in many areas such as micro-robotics and bio-medical devices.

Direct detection and characterization of bioinorganic peroxo moieties in a vanadium complex by 17O solid-state NMR and density functional theory.

PubMed

Gupta, Rupal; Stringer, John; Struppe, Jochem; Rehder, Dieter; Polenova, Tatyana

2018-07-01

Electronic and structural properties of short-lived metal-peroxido complexes, which are key intermediates in many enzymatic reactions, are not fully understood. While detected in various enzymes, their catalytic properties remain elusive because of their transient nature, making them difficult to study spectroscopically. We integrated 17 O solid-state NMR and density functional theory (DFT) to directly detect and characterize the peroxido ligand in a bioinorganic V(V) complex mimicking intermediates non-heme vanadium haloperoxidases. 17 O chemical shift and quadrupolar tensors, measured by solid-state NMR spectroscopy, probe the electronic structure of the peroxido ligand and its interaction with the metal. DFT analysis reveals the unusually large chemical shift anisotropy arising from the metal orbitals contributing towards the magnetic shielding of the ligand. The results illustrate the power of an integrated approach for studies of oxygen centers in enzyme reaction intermediates. Copyright © 2018 Elsevier Inc. All rights reserved.

Microwave-aided synthesis and applications of gold and nickel nanoporous metal foams

NASA Astrophysics Data System (ADS)

Lu, Zhifeng

In the field of nanoscience, nanoporous metal foams are a representative type of nanostructured materials, representing the ultimate form factor of a metal. They possess the hybrid properties of metal and nanoarchitectures, including the following properties such as good electrical and thermal conductivity, catalytic activity and high surface area, ultralow density, high strength-to-weight ratio. The outstanding properties bring the nanoporous metal foams to a wide range of applications, especially in the field of sensor system, energy storage and chemical catalyst. A new method of synthesis developed recently is presented for nanoporous metal foams of gold and nickel. The goal of this study is for the synthesis process of NMFs of and some applications in research and realistic life. Gold NMFs were produced by mixing gold chloride with ethylene glycol, ethanol, and reducing agent, and heating at 150 °C for 5 min with a CEM microwave. Both hydrazine and sodium borohydride were applied as the reducing agent for this redox reaction. Nickel NMFs were produced through the similar procedure with a little difference in the heating condition of 50 W, instead of 150 °C, with either hydrazine or sodium borohydride as the reducing agent. Gold NMFs were applied in surface-enhanced Raman spectroscopy (SERS) as a substrate. It is presented that with the presence of gold NMFs, the detection of the rhodamine 6G (R6G), a model analyte, can be enhanced significantly. The limit of detection for rhodamine 6G was found to be 5.2 x 10 -7 M in this research. Nickel NMFs was applied to degrade methyl orange (MO). An aqueous MO solution will turn nearly colorless after only 10 h of mixing with 0.025 g of nickel NMFs at room temperature under dark condition. In order to study the kinetics of the degradation reaction, MO solution with different initial concentration were used. This application of Ni NMFs is applicable as waste treatment of industrial water and to protect the environment.

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

PubMed Central

Sanz, Yolanda

2017-01-01

Abstract The miniaturized and portable DNA sequencer MinION™ has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION™ platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION™ device using R9 and R9.4 chemistries were sufficient to study 2 mock microbial communities in a multiplex manner and to almost completely reconstruct the microbial diversity contained in the HM782D and D6305 mock communities. Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, we presented a novel approach consisting of multi-locus and long amplicon sequencing using the MinION™ MkIb DNA sequencer and R9 and R9.4 chemistries that help to overcome the main disadvantage of this portable sequencing platform. Furthermore, the nanopore sequencing library, constructed with the last releases of pore chemistry (R9.4) and sequencing kit (SQK-LSK108), permitted the retrieval of the higher level of 1D read accuracy sufficient to characterize the microbial species present in each mock community analysed. Improvements in nanopore chemistry, such as minimizing base-calling errors and new library protocols able to produce rapid 1D libraries, will provide more reliable information in the near future. Such data will be useful for more comprehensive and faster specific detection of microbial species and strains in complex ecosystems. PMID:28605506

Directly and indirectly detected through-bond heteronuclear correlation solid-state NMR spectroscopy under fast MAS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mao, Kanmi; Pruski, Marek

Two-dimensional through-bond {sup 1}H({sup 13}C) solid-state NMR experiments utilizing fast magic angle spinning (MAS) and homonuclear multipulse {sup 1}H decoupling are presented. Remarkable efficiency of polarization transfer can be achieved at MAS rates exceeding 40 kHz, which is instrumental in these measurements. Schemes utilizing direct and indirect detection of heteronuclei are compared in terms of resolution and sensitivity. A simple procedure for optimization of {sup 1}H homonuclear decoupling sequences under these conditions is proposed. The capabilities of these techniques were confirmed on two naturally abundant solids, tripeptide N-formyl-l-methionyl-l-leucyl-l-phenylalanine (f-MLF-OH) and brown coal.

Directly and indirectly detected through-bond heteronuclear correlation solid-state NMR spectroscopy under fast MAS

NASA Astrophysics Data System (ADS)

Mao, Kanmi; Pruski, Marek

2009-12-01

Two-dimensional through-bond 1H{ 13C} solid-state NMR experiments utilizing fast magic angle spinning (MAS) and homonuclear multipulse 1H decoupling are presented. Remarkable efficiency of polarization transfer can be achieved at MAS rates exceeding 40 kHz, which is instrumental in these measurements. Schemes utilizing direct and indirect detection of heteronuclei are compared in terms of resolution and sensitivity. A simple procedure for optimization of 1H homonuclear decoupling sequences under these conditions is proposed. The capabilities of these techniques were confirmed on two naturally abundant solids, tripeptide N- formyl- L-methionyl- L-leucyl- L-phenylalanine (f-MLF-OH) and brown coal.

Atomic layer deposition of nanoporous biomaterials.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Narayan, R. J.; Adiga, S. P.; Pellin, M. J.

2010-03-01

Due to its chemical stability, uniform pore size, and high pore density, nanoporous alumina is being investigated for use in biosensing, drug delivery, hemodialysis, and other medical applications. In recent work, we have examined the use of atomic layer deposition for coating the surfaces of nanoporous alumina membranes. Zinc oxide coatings were deposited on nanoporous alumina membranes using atomic layer deposition. The zinc oxide-coated nanoporous alumina membranes demonstrated antimicrobial activity against Escherichia coli and Staphylococcus aureus bacteria. These results suggest that atomic layer deposition is an attractive technique for modifying the surfaces of nanoporous alumina membranes and other nanostructured biomaterials.more » Nanoporous alumina, also known as anodic aluminum oxide (AAO), is a nanomaterial that exhibits several unusual properties, including high pore densities, straight pores, small pore sizes, and uniform pore sizes. In 1953, Keller et al. showed that anodizing aluminum in acid electrolytes results in a thick layer of nearly cylindrical pores, which are arranged in a close-packed hexagonal cell structure. More recently, Matsuda & Fukuda demonstrated preparation of highly ordered platinum and gold nanohole arrays using a replication process. In this study, a negative structure of nanoporous alumina was initially fabricated and a positive structure of a nanoporous metal was subsequently fabricated. Over the past fifteen years, nanoporous alumina membranes have been used as templates for growth of a variety of nanostructured materials, including nanotubes, nanowires, nanorods, and nanoporous membranes.« less

Engineering the internal surfaces of three-dimensional nanoporous catalysts by surfactant-modified dealloying.

PubMed

Wang, Zhili; Liu, Pan; Han, Jiuhui; Cheng, Chun; Ning, Shoucong; Hirata, Akihiko; Fujita, Takeshi; Chen, Mingwei

2017-10-20

Tuning surface structures by bottom-up synthesis has been demonstrated as an effective strategy to improve the catalytic performances of nanoparticle catalysts. Nevertheless, the surface modification of three-dimensional nanoporous metals, fabricated by a top-down dealloying approach, has not been achieved despite great efforts devoted to improving the catalytic performance of three-dimensional nanoporous catalysts. Here we report a surfactant-modified dealloying method to tailor the surface structure of nanoporous gold for amplified electrocatalysis toward methanol oxidation and oxygen reduction reactions. With the assistance of surfactants, {111} or {100} faceted internal surfaces of nanoporous gold can be realized in a controllable manner by optimizing dealloying conditions. The surface modified nanoporous gold exhibits significantly enhanced electrocatalytic activities in comparison with conventional nanoporous gold. This study paves the way to develop high-performance three-dimensional nanoporous catalysts with a tunable surface structure by top-down dealloying for efficient chemical and electrochemical reactions.

Flexible, transparent and highly sensitive SERS substrates with cross-nanoporous structures for fast on-site detection.

PubMed

Wang, Yingcheng; Jin, Yuanhao; Xiao, Xiaoyang; Zhang, Tianfu; Yang, Haitao; Zhao, Yudan; Wang, Jiaping; Jiang, Kaili; Fan, Shoushan; Li, Qunqing

2018-05-30

A flexible and transparent film assembled from the cross-nanoporous structures of Au on PET (CNS of Au@PET) is developed as a versatile and effective SERS substrate for rapid, on-site trace analysis with high sensitivity. The fabrication of the CNS of Au can be achieved on a large scale at low cost by employing an etching process with super-aligned carbon nanotubes as a mask, followed by metal deposition. A strongly enhanced Raman signal with good uniformity can be obtained, which is attributed to the excitation of "hot spots" around the metal nanogaps and sharp edges. Using the CNS of Au@PET film as a SERS platform, real-time and on-site SERS detection of the food contaminant crystal violet (CV) is achieved, with a detection limit of CV solution on a tomato skin of 10-7 M. Owing to its ability to efficiently extract trace analytes, the resulting substrate also achieves detection of 4-ATP contaminants and thiram pesticides by swabbing the skin of an apple. A SERS detection signal for 4-ATP has a relative standard deviation of less than 10%, revealing the excellent reproducibility of the substrate. The flexible, transparent and highly sensitive substrates fabricated using this simple and cost-effective strategy are promising for practical application in rapid, on-site SERS-based detection.

Gas-phase detection of solid-state fission product complexes for post-detonation nuclear forensic analysis

DOE PAGES

Stratz, S. Adam; Jones, Steven A.; Oldham, Colton J.; ...

2016-06-27

This study presents the first known detection of fission products commonly found in post-detonation nuclear debris samples using solid sample introduction and a uniquely coupled gas chromatography inductively-coupled plasma time-of-flight mass spectrometer. Rare earth oxides were chemically altered to incorporate a ligand that enhances the volatility of the samples. These samples were injected (as solids) into the aforementioned instrument and detected for the first time. Repeatable results indicate the validity of the methodology, and this capability, when refined, will prove to be a valuable asset for rapid post-detonation nuclear forensic analysis.

Gas-phase detection of solid-state fission product complexes for post-detonation nuclear forensic analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stratz, S. Adam; Jones, Steven A.; Oldham, Colton J.

This study presents the first known detection of fission products commonly found in post-detonation nuclear debris samples using solid sample introduction and a uniquely coupled gas chromatography inductively-coupled plasma time-of-flight mass spectrometer. Rare earth oxides were chemically altered to incorporate a ligand that enhances the volatility of the samples. These samples were injected (as solids) into the aforementioned instrument and detected for the first time. Repeatable results indicate the validity of the methodology, and this capability, when refined, will prove to be a valuable asset for rapid post-detonation nuclear forensic analysis.

Recent Advances in Nanoporous Membranes for Water Purification

PubMed Central

Wang, Zhuqing; Colombi Ciacchi, Lucio

2018-01-01

Nanoporous materials exhibit wide applications in the fields of electrocatalysis, nanodevice fabrication, energy, and environmental science, as well as analytical science. In this review, we present a summary of recent studies on nanoporous membranes for water purification application. The types and fabrication strategies of various nanoporous membranes are first introduced, and then the fabricated nanoporous membranes for removing various water pollutants, such as salt, metallic ions, anions, nanoparticles, organic chemicals, and biological substrates, are demonstrated and discussed. This work will be valuable for readers to understand the design and fabrication of various nanoporous membranes, and their potential purification mechanisms towards different water pollutants. In addition, it will be helpful for developing new nanoporous materials for quick, economic, and high-performance water purification. PMID:29370128

Pore spanning lipid bilayers on silanised nanoporous alumina membranes

NASA Astrophysics Data System (ADS)

Md Jani, Abdul M.; Zhou, Jinwen; Nussio, Matthew R.; Losic, Dusan; Shapter, Joe G.; Voelcker, Nicolas H.

2008-12-01

The preparation of bilayer lipid membranes (BLMs) on solid surfaces is important for many studies probing various important biological phenomena including the cell barrier properties, ion-channels, biosensing, drug discovery and protein/ligand interactions. In this work we present new membrane platforms based on suspended BLMs on nanoporous anodic aluminium oxide (AAO) membranes. AAO membranes were prepared by electrochemical anodisation of aluminium foil in 0.3 M oxalic acid using a custom-built etching cell and applying voltage of 40 V, at 1oC. AAO membranes with controlled diameter of pores from 30 - 40 nm (top of membrane) and 60 -70 nm (bottom of membrane) were fabricated. Pore dimensions have been confirmed by scanning electron microscopy (SEM) and atomic force microscopy (AFM). AAO membranes were chemically functionalised with 3-aminopropyltriethoxysilane (APTES). Confirmation of the APTES attachment to the AAO membrane was achieved by means of infrared spectroscopy, X-ray photoelectron spectroscopy and contact angle measurements. The Fourier transform infrared (FTIR) spectra of functionalised membranes show several peaks from 2800 to 3000 cm-1 which were assigned to symmetric and antisymmetric CH2 bands. XPS data of the membrane showed a distinct increase in C1s (285 eV), N1s (402 eV) and Si2p (102 eV) peaks after silanisation. The water contact angle of the functionalised membrane was 80o as compared to 20o for the untreated membrane. The formation of BLMs comprising dioleoyl-phosphatidylserine (DOPS) on APTESmodified AAO membranes was carried using the vesicle spreading technique. AFM imaging and force spectroscopy was used to characterise the structural and nanomechanical properties of the suspended membrane. This technique also confirmed the stability of bilayers on the nanoporous alumina support for several days. Fabricated suspended BLMs on nanoporous AAO hold promise for the construction of biomimetic membrane architectures with embedded transmembrane proteins.

Facile fabrication of nanofluidic diode membranes using anodic aluminium oxide.

PubMed

Wu, Songmei; Wildhaber, Fabien; Vazquez-Mena, Oscar; Bertsch, Arnaud; Brugger, Juergen; Renaud, Philippe

2012-09-21

Active control of ion transport plays important roles in chemical and biological analytical processes. Nanofluidic systems hold the promise for such control through electrostatic interaction between ions and channel surfaces. Most existing experiments rely on planar geometry where the nanochannels are generally very long and shallow with large aspect ratios. Based on this configuration the concepts of nanofluidic gating and rectification have been successfully demonstrated. However, device minimization and throughput scaling remain significant challenges. We report here an innovative and facile realization of hetero-structured Al(2)O(3)/SiO(2) (Si) nanopore array membranes by using pattern transfer of self-organized nanopore structures of anodic aluminum oxide (AAO). Thanks to the opposite surface charge states of Al(2)O(3) (positive) and SiO(2) (negative), the membrane exhibits clear rectification of ion current in electrolyte solutions with very low aspect ratios compared to previous approaches. Our hetero-structured nanopore arrays provide a valuable platform for high throughput applications such as molecular separation, chemical processors and energy conversion.

A general melt-injection-decomposition route to oriented metal oxide nanowire arrays

NASA Astrophysics Data System (ADS)

Han, Dongqiang; Zhang, Xinwei; Hua, Zhenghe; Yang, Shaoguang

2016-12-01

In this manuscript, a general melt-injection-decomposition (MID) route has been proposed and realized for the fabrication of oriented metal oxide nanowire arrays. Nitrate was used as the starting materials, which was injected into the nanopores of the anodic aluminum oxide (AAO) membrane through the capillarity action in its liquid state. At higher temperature, the nitrate decomposed into corresponding metal oxide within the nanopores of the AAO membrane. Oriented metal oxide nanowire arrays were formed within the AAO membrane as a result of the confinement of the nanopores. Four kinds of metal oxide (CuO, Mn2O3, Co3O4 and Cr2O3) nanowire arrays are presented here as examples fabricated by this newly developed process. X-ray diffraction, scanning electron microscopy and transmission electron microscopy studies showed clear evidence of the formations of the oriented metal oxide nanowire arrays. Formation mechanism of the metal oxide nanowire arrays is discussed based on the Thermogravimetry and Differential Thermal Analysis measurement results.

1H-detected MAS solid-state NMR experiments enable the simultaneous mapping of rigid and dynamic domains of membrane proteins

NASA Astrophysics Data System (ADS)

Gopinath, T.; Nelson, Sarah E. D.; Veglia, Gianluigi

2017-12-01

Magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy is emerging as a unique method for the atomic resolution structure determination of native membrane proteins in lipid bilayers. Although 13C-detected ssNMR experiments continue to play a major role, recent technological developments have made it possible to carry out 1H-detected experiments, boosting both sensitivity and resolution. Here, we describe a new set of 1H-detected hybrid pulse sequences that combine through-bond and through-space correlation elements into single experiments, enabling the simultaneous detection of rigid and dynamic domains of membrane proteins. As proof-of-principle, we applied these new pulse sequences to the membrane protein phospholamban (PLN) reconstituted in lipid bilayers under moderate MAS conditions. The cross-polarization (CP) based elements enabled the detection of the relatively immobile residues of PLN in the transmembrane domain using through-space correlations; whereas the most dynamic region, which is in equilibrium between folded and unfolded states, was mapped by through-bond INEPT-based elements. These new 1H-detected experiments will enable one to detect not only the most populated (ground) states of biomacromolecules, but also sparsely populated high-energy (excited) states for a complete characterization of protein free energy landscapes.

Measurements of electron detection efficiencies in solid state detectors.

NASA Technical Reports Server (NTRS)

Lupton, J. E.; Stone, E. C.

1972-01-01

Detailed laboratory measurement of the electron response of solid state detectors as a function of incident electron energy, detector depletion depth, and energy-loss discriminator threshold. These response functions were determined by exposing totally depleted silicon surface barrier detectors with depletion depths between 50 and 1000 microns to the beam from a magnetic beta-ray spectrometer. The data were extended to 5000 microns depletion depth using the results of previously published Monte Carlo electron calculations. When the electron counting efficiency of a given detector is plotted as a function of energy-loss threshold for various incident energies, the efficiency curves are bounded by a smooth envelope which represents the upper limit to the detection efficiency. These upper limit curves, which scale in a simple way, make it possible to easily estimate the electron sensitivity of solid-state detector systems.

Atomic layer deposition-based functionalization of materials for medical and environmental health applications

PubMed Central

Narayan, Roger J.; Adiga, Shashishekar P.; Pellin, Michael J.; Curtiss, Larry A.; Hryn, Alexander J.; Stafslien, Shane; Chisholm, Bret; Shih, Chun-Che; Shih, Chun-Ming; Lin, Shing-Jong; Su, Yea-Yang; Jin, Chunming; Zhang, Junping; Monteiro-Riviere, Nancy A.; Elam, Jeffrey W.

2010-01-01

Nanoporous alumina membranes exhibit high pore densities, well-controlled and uniform pore sizes, as well as straight pores. Owing to these unusual properties, nanoporous alumina membranes are currently being considered for use in implantable sensor membranes and water purification membranes. Atomic layer deposition is a thin-film growth process that may be used to modify the pore size in a nanoporous alumina membrane while retaining a narrow pore distribution. In addition, films deposited by means of atomic layer deposition may impart improved biological functionality to nanoporous alumina membranes. In this study, zinc oxide coatings and platinum coatings were deposited on nanoporous alumina membranes by means of atomic layer deposition. PEGylated nanoporous alumina membranes were prepared by self-assembly of 1-mercaptoundec-11-yl hexa(ethylene glycol) on platinum-coated nanoporous alumina membranes. The pores of the PEGylated nanoporous alumina membranes remained free of fouling after exposure to human platelet-rich plasma; protein adsorption, fibrin networks and platelet aggregation were not observed on the coated membrane surface. Zinc oxide-coated nanoporous alumina membranes demonstrated activity against two waterborne pathogens, Escherichia coli and Staphylococcus aureus. The results of this work indicate that nanoporous alumina membranes may be modified using atomic layer deposition for use in a variety of medical and environmental health applications. PMID:20308114

Detection of tannins in modern and fossil barks and in plant residues by high-resolution solid-state 13C nuclear magnetic resonance

USGS Publications Warehouse

Wilson, M.A.; Hatcher, P.G.

1988-01-01

Bark samples isolated from brown coal deposits in Victoria, Australia, and buried wood from Rhizophora mangle have been studies by high-resolution solid-state nuclear magnetic resonance (NMR) techniques. Dipolar dephasing 13C NMR appears to be a useful method of detecting the presence of tannins in geochemical samples including barks, buried woods, peats and leaf litter. It is shown that tannins are selectively preserved in bark during coalification to the brown coal stage. ?? 1988.

Characterization of resonant tunneling diodes for microwave and millimeter-wave detection

NASA Technical Reports Server (NTRS)

Mehdi, I.; East, J. R.; Haddad, G. I.

1991-01-01

The authors report on the direct detection capabilities of resonant tunneling diodes in the 10-100 GHz range. An open circuit voltage sensitivity of 1750 mV/mW (in Ka-band) was measured. This is higher than the sensitivity of comparatively based commercially available solid-state detectors. The detector properties are a strong function of diode bias and the measured tangential signal sensitivity (-32 dBm at Ka-band with 1-MHz bandwidth) and the dynamic range (25 dB) of the diode are smaller compared to other solid-state detectors.

Fast and accurate de novo genome assembly from long uncorrected reads

PubMed Central

Vaser, Robert; Sović, Ivan; Nagarajan, Niranjan

2017-01-01

The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource-intensive error-correction and consensus-generation steps to obtain high-quality assemblies. We show that the error-correction step can be omitted and that high-quality consensus sequences can be generated efficiently with a SIMD-accelerated, partial-order alignment–based, stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore data sets, we show that Racon coupled with miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster. PMID:28100585

Structure-dependent water transport across nanopores of carbon nanotubes: toward selective gating upon temperature regulation.

PubMed

Zhao, Kuiwen; Wu, Huiying

2015-04-28

Determining water structure in nanopores and its influence on water transport behaviour is of great importance for understanding and regulating the transport across nanopores. Here we report an ultrafast-slow flow transition phenomenon for water transport across nanopores of carbon nanotubes owing to the change in water structure in nanopores induced by temperature. By performing extensive molecular dynamics simulations, we show the dependence of water transport behaviours on water structures. Our results indicate that owing to the change in water structure in nanopores, water flux across nanopores with certain pore sizes decreases sharply (nearly 3 orders of magnitude) with the decreasing temperature. This phenomenon is very sensitive to the pore size. The threshold temperatures for the occurrence of the ultrafast-slow flow transition for water transport are also determined for various pore sizes. These findings suggest a novel protocol for selective gating of water and proton conduction across nanopores and temperature-controlled drug release.