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1.  Nanoporous membranes for medical and biological applications 
Synthetic nanoporous materials have numerous potential biological and medical applications that involve sorting, sensing, isolating and releasing biological molecules. Nanoporous systems engineered to mimic natural filtration systems are actively being developed for use in smart implantable drug delivery systems, bioartificial organs, and other novel nano-enabled medical devices. Recent advances in nanoscience have made it possible to precisely control the morphology as well as physical and chemical properties of the pores in nanoporous materials that make them increasingly attractive for regulating and sensing transport at the molecular level. In this work, an overview of nanoporous membranes for biomedical applications is given. Various in vivo and in vitro membrane applications, including biosensing, biosorting, immunoisolation and drug delivery, are presented. Different types of nanoporous materials and their fabrication techniques are discussed with an emphasis on membranes with ordered pores. Desirable properties of membranes used in implantable devices, including biocompatibility and antibiofouling behavior, are discussed. The use of surface modification techniques to improve the function of nanoporous membranes is reviewed. Despite the extensive research carried out in fabrication, characterization, and modeling of nanoporous materials, there are still several challenges that must be overcome in order to create synthetic nanoporous systems that behave similarly to their biological counterparts.
doi:10.1002/wnan.50
PMCID: PMC3684197  PMID: 20049818
Biosensing; Drug delivery; Implantable materials; Nanopores; Nano-scale membranes
2.  Ordered nanoporous silica as carriers for improved delivery of water insoluble drugs: a comparative study between three dimensional and two dimensional macroporous silica 
The goal of the present study was to compare the drug release properties and stability of the nanoporous silica with different pore architectures as a matrix for improved delivery of poorly soluble drugs. For this purpose, three dimensional ordered macroporous (3DOM) silica with 3D continuous and interconnected macropores of different sizes (200 nm and 500 nm) and classic mesoporous silica (ie, Mobil Composition of Matter [MCM]-41 and Santa Barbara Amorphous [SBA]-15) with well-ordered two dimensional (2D) cylindrical mesopores were successfully fabricated and then loaded with the model drug indomethacin (IMC) via the solvent deposition method. Scanning electron microscopy (SEM), N2 adsorption, differential scanning calorimetry (DSC), and X-ray diffraction (XRD) were applied to systematically characterize all IMC-loaded nanoporous silica formulations, evidencing the successful inclusion of IMC into nanopores, the reduced crystallinity, and finally accelerated dissolution of IMC. It was worth mentioning that, in comparison to 2D mesoporous silica, 3DOM silica displayed a more rapid release profile, which may be ascribed to the 3D interconnected pore networks and the highly accessible surface areas. The results obtained from the stability test indicated that the amorphous state of IMC entrapped in the 2D mesoporous silica (SBA-15 and MCM-41) has a better physical stability than in that of 3DOM silica. Moreover, the dissolution rate and stability of IMC loaded in 3DOM silica was closely related to the pore size of macroporous silica. The colorimetric 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and Cell Counting Kit (CCK)-8 assays in combination with direct morphology observations demonstrated the good biocompatibility of nanoporous silica, especially for 3DOM silica and SBA-15. The present work encourages further study of the drug release properties and stability of drug entrapped in different pore architecture of silica in order to realize their potential in oral drug delivery.
doi:10.2147/IJN.S52605
PMCID: PMC3808157  PMID: 24174875
3D ordered macroporous silica; mesoporous silica; poorly soluble drugs; in vitro dissolution; stability test; in vitro cytotoxicity
3.  Lipid bilayer coated Al2O3 nanopore sensors: towards a hybrid biological solid-state nanopore 
Biomedical microdevices  2011;13(4):671-682.
Solid-state nanopore sensors are highly versatile platforms for the rapid, label-free electrical detection and analysis of single molecules, applicable to next generation DNA sequencing. The versatility of this technology allows for both large scale device integration and interfacing with biological systems. Here we report on the development of a hybrid biological solid-state nanopore platform that incorporates a highly mobile lipid bilayer on a single solid-state Al2O3 nanopore sensor, for the potential reconstitution of ion channels and biological nanopores. Such a system seeks to combine the superior electrical, thermal, and mechanical stability of Al2O3 solid-state nanopores with the chemical specificity of biological nanopores. Bilayers on Al2O3 exhibit higher diffusivity than those formed on TiO2 and SiO2 substrates, attributed to the presence of a thick hydration layer on Al2O3, a key requirement to preserving the biological functionality of reconstituted membrane proteins. Molecular dynamics simulations demonstrate that the electrostatic repulsion between the dipole of the DOPC headgroup and the positively charged Al2O3 surface may be responsible for the enhanced thickness of this hydration layer. Lipid bilayer coated Al2O3 nanopore sensors exhibit excellent electrical properties and enhanced mechanical stability (GΩ seals for over 50 h), making this technology ideal for use in ion channel electrophysiology, the screening of ion channel active drugs and future integration with biological nanopores such as α-hemolysin and MspA for rapid single molecule DNA sequencing. This technology can find broad application in bio-nanotechnology.
doi:10.1007/s10544-011-9537-3
PMCID: PMC3175492  PMID: 21487665
Nanopore; Al2O3; Lipid bilayer; Hybrid biological solid-state Nanopore
4.  Development of a nanoporous and multilayer drug-delivery platform for medical implants 
Biodegradable polymers can be applied to a variety of implants for controlled and local drug delivery. The aim of this study is to develop a biodegradable and nanoporous polymeric platform for a wide spectrum of drug-eluting implants with special focus on stent-coating applications. It was synthesized by poly(DL-lactide-co-glycolide) (PLGA 65:35, PLGA 75:25) and polycaprolactone (PCL) in a multilayer configuration by means of a spin-coating technique. The antiplatelet drug dipyridamole was loaded into the surface nanopores of the platform. Surface characterization was made by atomic force microscopy (AFM) and spectroscopic ellipsometry (SE). Platelet adhesion and drug-release kinetic studies were then carried out. The study revealed that the multilayer films are highly nanoporous, whereas the single layers of PLGA are atomically smooth and spherulites are formed in PCL. Their nanoporosity (pore diameter, depth, density, surface roughness) can be tailored by tuning the growth parameters (eg, spinning speed, polymer concentration), essential for drug-delivery performance. The origin of pore formation may be attributed to the phase separation of polymer blends via the spinodal decomposition mechanism. SE studies revealed the structural characteristics, film thickness, and optical properties even of the single layers in the triple-layer construct, providing substantial information for drug loading and complement AFM findings. Platelet adhesion studies showed that the dipyridamole-loaded coatings inhibit platelet aggregation that is a prerequisite for clotting. Finally, the films exhibited sustained release profiles of dipyridamole over 70 days. These results indicate that the current multilayer phase therapeutic approach constitutes an effective drug-delivery platform for drug-eluting implants and especially for cardiovascular stent applications.
doi:10.2147/IJN.S31185
PMCID: PMC3469098  PMID: 23071394
drug delivery; implants; stents; polymers; spin-coating; atomic force microscopy
5.  Nanoporous Anodic Alumina Platforms: Engineered Surface Chemistry and Structure for Optical Sensing Applications 
Sensors (Basel, Switzerland)  2014;14(7):11878-11918.
Electrochemical anodization of pure aluminum enables the growth of highly ordered nanoporous anodic alumina (NAA) structures. This has made NAA one of the most popular nanomaterials with applications including molecular separation, catalysis, photonics, optoelectronics, sensing, drug delivery, and template synthesis. Over the past decades, the ability to engineer the structure and surface chemistry of NAA and its optical properties has led to the establishment of distinctive photonic structures that can be explored for developing low-cost, portable, rapid-response and highly sensitive sensing devices in combination with surface plasmon resonance (SPR) and reflective interference spectroscopy (RIfS) techniques. This review article highlights the recent advances on fabrication, surface modification and structural engineering of NAA and its application and performance as a platform for SPR- and RIfS-based sensing and biosensing devices.
doi:10.3390/s140711878
PMCID: PMC4168464  PMID: 25004150
nanoporous anodic alumina; surface modification; optical biosensor; plasmon resonance; reflective interferometry
6.  Calcified Nanostructured Silicon Wafer Surfaces for Biosensing: Effects of Surface Modification on Bioactivity 
Disease Markers  2003;18(4):159-165.
The growth of known biologically-relevant mineral phases on semiconducting surfaces is one strategy to explicitly induce bioactivity in such materials, either for sensing or drug delivery applications. In this work, we describe the use of a spark ablation process to fabricate deliberate patterns of Ca10(PO4)6(OH)2 on crystalline Si (calcified nanoporous silicon). These patterns have been principally characterized by scanning electron microscopy in conjunction with elemental characterization by energy dispersive x-ray analysis. This is followed by a detailed comparison of the effects of fibroblast adhesion and proliferation onto calcified nanoporous Si, calcified nanoporous Si derivatized with alendronate, as well as control samples of an identical surface area containing porous SiO2. Fibroblast adhesion and proliferation assays demonstrate that a higher density of cells grow on the Ca3(PO4)2 /porous Si/ SiO2 structures relative to the alendronate-modified surfaces and porous Si/SiOM2 samples.
doi:10.1155/2002/727014
PMCID: PMC3850822  PMID: 12590169
Calcium phosphate; silicon; fibroblasts; biosensor
7.  Electrically facilitated translocation of protein through solid nanopore 
Nanoscale Research Letters  2014;9(1):140.
Nanopores have been proven as versatile single-molecule sensors for individual unlabeled biopolymer detection and characterization. In the present work, a relative large nanopore with a diameter of about 60 nm has been used to detect protein translocation driven by a series of applied voltages. Compared with previous studied small nanopores, a distinct profile of protein translocation through a larger nanopore has been characterized. First, a higher threshold voltage is required to drive proteins into the large nanopore. With the increase of voltages, the capture frequency of protein into the nanopore has been markedly enhanced. And the distribution of current blockage events is characterized as a function of biased voltages. Due to the large dimension of the nanopore, the adsorption and desorption phenomenon of proteins observed with a prolonged dwell time has been weakened in our work. Nevertheless, the protein can still be stretched into an unfolded state by increased electric forces at high voltages. In consideration of the high throughput of the large nanopore, a couple of proteins passing through the nanopore simultaneously occur at high voltage. As a new feature, the feasibility and specificity of a nanopore with distinct geometry have been demonstrated for sensing protein translocation, which broadly expand the application of nanopore devices.
doi:10.1186/1556-276X-9-140
PMCID: PMC3976542  PMID: 24661490
Protein translocation; Solid state nanopore; Current blockage; Translocation time
8.  Use of a nanoporous biodegradable miniature device to regulate cytokine release for cancer treatment 
The clinical management of locally recurrent or unresectable malignant melanoma continues to pose a significant challenge. These lesions are typically painful and currently available treatments, such as repeated intratumoral injections of interferon-alpha (IFN-α), are costly and inconvenient. Nanotechnology offers promise as a novel means of drug delivery. A capsule-like nanoporous miniature device (NMD) based on a biodegradable polymer, poly(polycaprolactone) (PCL) was developed for controlling the local delivery of immunological agents to the tumor microenvironment. The device consists of a nanoporous release gate, a fabricated drug reservoir loaded with IFN-α and a protective layer. To improve the biocompatibility of the device, a hydrophilic poly(ethylene glycol) monoacrylate was applied to the outside wall of the device via covalent bonding techniques. Microscopic visualization of the nanoporous gate from in vitro experiments exhibited good pore stability over a two-month period. In vitro experiments demonstrated a constant release rate of IFN-α from the NMD and showed that the release rate could be regulated by the gate area. The released IFN-α was biologically functional. Cytokine-containing supernatants from release experiments phosphorylated signal transducer and activator of transcription (STAT1) in peripheral blood mononuclear cells. Subcutaneous implantation of the NMDs was well tolerated and associated with an anti-tumor effect in a human xenograft model of melanoma. There was no evidence of a significant inflammatory response to the NMD or encapsulation of the NMD by fibrosis. These experiments show that the NMD can be fabricated and employed in vivo as a versatile drug delivery platform.
doi:10.1016/j.jconrel.2011.02.020
PMCID: PMC4076956  PMID: 21362447
Biodegradable nanoporous miniature device (NMD); PCL; Nanoporous membrane; Interferon-alpha release; Malignant melanoma
9.  Directly Observing the Motion of DNA Molecules near Solid-State Nanopores 
ACS nano  2012;6(11):10090-10097.
We investigate the diffusion and the drift motion of λ DNA molecules near solid-state nanopores prior to their translocation though the nanopores using fluorescence microscopy. The radial dependence of the electric field near a nanopore generated by an applied voltage in ionic solution can be estimated quantitatively in 3D by analyzing the motion of negatively charged DNA molecules. We find that the electric field is approximately spherically symmetric around the nanopore under the conditions investigated. In addition, DNA clogging at the nanopore was directly observed. Surprisingly, the probability of the clogging event increases with increasing external bias voltage. We also find that DNA molecules clogging the nanopore reduce the electric field amplitude at the nanopore membrane surface. To better understand these experimental results, analytical method with Ohm’s law and computer simulation with Poisson and Nernst-Planck (PNP) equations are used to calculate the electric field near the nanopore. These results are of great interest in both experimental and theoretical considerations of the motion of DNA molecules near voltage-biased nanopores. These findings will also contribute to the development of solid-state nanopore based DNA sensing devices.
doi:10.1021/nn303816w
PMCID: PMC3508321  PMID: 23046052
single-molecule; sensing; nanopore; DNA
10.  Coarse-Grained Molecular Dynamics Simulation of DNA Translocation in Chemically-Modified Nanopores 
The journal of physical chemistry. B  2011;115(19):6138-6148.
Solid-state nanopores provide a direct mean to detect and analyze DNA and proteins. In a typical setup, the DNA molecules travel through a nanopore under electrophoretic voltage bias. The nanopore is sandwiched between two chambers that are filled with ionic solution. A major challenge in using solid-state nanopores for DNA sequencing and gene detection is to improve their selectivity and detection sensitivity. To achieve these goals, one solution is to functionalize the nanopores by chemically modifying the pore walls with silanes or nucleic acids. However, little is known about molecular interactions in functionalized nanopores. This paper presents DNA translocation dynamics and the mechanism of DNA sequencing in a functionalized nanopore through a coarse-grained molecular dynamics model.
The DNA nucleotide is coarse-grained into two interaction sites, one site corresponds to the base group, and the other encompasses the phosphate and sugar group. The water molecules are included into the model implicitly through Langevin dynamics. The coarse-grained model immensely improves the computational efficiency while still capturing the essential translocation dynamics. The model characterizes important physical properties of functionalized nanopores such as the effective pore diameter and effect of biasing voltage on the DNA translocation dynamics. The model reveals a nonlinear relationship between translocation speed of DNA and applied voltage. Moreover, DNA translocation in nanopores functionalized with hairpin loop (HPL) DNA and single stranded DNA (ssDNA) shows significant differences; a target DNA is found to translocate through a ssDNA coated nanopore nine times faster than through an HPL coated one at a bias of 100 mV, putatively from lower stiffness of ssDNA than that for HPL. The DNA translocation speed is also largely influenced by interaction potential between the DNA and surface-tethered molecules. The results reveal that such selective translocation, distinctly different translocation dynamics of target DNAs largely stem from the flexibility and orientation of the surface-tethered molecules. These findings can significantly impact the rational design of DNA transport experiments leading to rapid molecule-level diagnostics.
doi:10.1021/jp101052x
PMCID: PMC3148180  PMID: 21526788
Molecular Dynamics; Coarse-grained Simulations; DNA sequencing; Functionalized Nanopore
11.  Direct Prototyping of Patterned Nanoporous Carbon: A Route from Materials to On-chip Devices 
Scientific Reports  2013;3:2294.
Prototyping of nanoporous carbon membranes with three-dimensional microscale patterns is significant for integration of such multifunctional materials into various miniaturized systems. Incorporating nano material synthesis into microelectronics technology, we present a novel approach to direct prototyping of carbon membranes with highly nanoporous structures inside. Membranes with significant thicknesses (1 ~ 40 μm) are rapidly prototyped at wafer level by combining nano templating method with readily available microfabrication techniques, which include photolithography, high-temperature annealing and etching. In particular, the high-surface-area membranes are specified as three-dimensional electrodes for micro supercapacitors and show high performance compared to reported ones. Improvements in scalability, compatibility and cost make the general strategy promising for batch fabrication of operational on-chip devices or full integration of three-dimensional nanoporous membranes with existing micro systems.
doi:10.1038/srep02294
PMCID: PMC3724177  PMID: 23887486
12.  Characterization of Protein Unfolding with Solid-state Nanopores 
Protein and peptide letters  2014;21(3):256-265.
In this work, we review the process of protein unfolding characterized by a solid-state nanopore based device. The occupied or excluded volume of a protein molecule in a nanopore depends on the protein’s conformation or shape. A folded protein has a larger excluded volume in a nanopore thus it blocks more ionic current flow than its unfolded form and produces a greater current blockage amplitude. The time duration a protein stays in a pore also depends on the protein’s folding state. We use Bovine Serum Albumin (BSA) as a model protein to discuss this current blockage amplitude and the time duration associated with the protein unfolding process. BSA molecules were measured in folded, partially unfolded, and completely unfolded conformations in solid-state nanopores. We discuss experimental results, data analysis, and theoretical considerations of BSA protein unfolding measured with silicon nitride nanopores. We show this nanopore method is capable of characterizing a protein’s unfolding process at single molecule level. Problems and future studies in characterization of protein unfolding using a solid-state nanopore device will also be discussed.
PMCID: PMC4188535  PMID: 24370259
Bovine Serum Albumin (BSA); current blockage; excluded volume; protein unfolding; solid-state nanopore; translocation time
13.  Ocular Biocompatibility and Structural Integrity of Micro- and Nanostructured Poly(caprolactone) Films 
Abstract
The identification of biomaterials that are well tolerated in the eye is important for the development of new ocular drug delivery devices and implants, and the application of micro- and nanoengineered devices to biomedical treatments is predicated on the long-term preservation within the target organ or tissue of the very small functional design elements. This study assesses the ocular tolerance and durability of micro- and nanostructured biopolymer thin films injected or implanted into the rabbit eye. Structured poly(caprolactone) (PCL) thin films were placed in adult rabbit eyes for survival studies, with serial ophthalmic examinations over 6 months. Morphologic abnormalities and device/tissue reactions were evaluated by histologic studies, and scanning electron microscopy (SEM) of films was used to determine the structural integrity. Structured PCL thin films (20- to 40-μm thick) were constructed to design specifications with 50-μm linear microgrooves or arrays of nanopores with ∼30-nm diameters. After up to 9 months of ocular residency, SEM on devices retrieved from the eye showed preservation of micro- and nanostructural features. In ocular safety evaluations carried out over 6 months, serial examinations in 18 implanted eyes showed no evidence of chronic inflammation, cataractogenesis, or retinal toxicity. Postoperative ocular inflammation was seen in 67% of eyes for 1 week, and persistent corneal edema occurred in 1 eye. Histology revealed no ocular inflammation or morphologic abnormalities of ocular tissues. Thin-film/tissue responses such as cellular reaction, fibrosis, or surface biodeposits were not seen. Micro- and nanostructured PCL thin films exhibited acceptable ocular tolerance and maintained the structural integrity of design features while residing in the eye. Thin-film micro- and nanostructured PCL appears to be a feasible biomaterial for intraocular therapeutic applications.
doi:10.1089/jop.2012.0152
PMCID: PMC3601720  PMID: 23391326
14.  Regulating the Transport of DNA through Biofriendly Nanochannels in a Thin Solid Membrane 
Scientific Reports  2014;4:3985.
Channels formed by membrane proteins regulate the transport of water, ions or nutrients that are essential to cells' metabolism. Recent advances in nanotechnology allow us to fabricate solid-state nanopores for transporting and analyzing biomolecules. However, uncontrollable surface properties of a fabricated nanopore cause irregular transport of biomolecules, limiting potential biomimetic applications. Here we show that a nanopore functionalized with a self-assembled monolayer (SAM) can potentially regulate the transport of a DNA molecule by changing functional groups of the SAM. We found that an enhanced interaction between DNA and a SAM-coated nanopore can slow down the translocation speed of DNA molecules and increase the DNA capture-rate. Our results demonstrate that the transport of DNA molecules inside nanopores could be modulated by coating a SAM on the pore surface. Our method to control the DNA motion inside a nanopore may find its applications in nanopore-based DNA sequencing devices.
doi:10.1038/srep03985
PMCID: PMC3914175  PMID: 24496378
15.  Anodization of nanoporous alumina on impurity-induced hemisphere curved surface of aluminum at room temperature 
Nanoscale Research Letters  2011;6(1):596.
Nanoporous alumina which was produced by a conventional direct current anodization [DCA] process at low temperatures has received much attention in various applications such as nanomaterial synthesis, sensors, and photonics. In this article, we employed a newly developed hybrid pulse anodization [HPA] method to fabricate the nanoporous alumina on a flat and curved surface of an aluminum [Al] foil at room temperature [RT]. We fabricate the nanopores to grow on a hemisphere curved surface and characterize their behavior along the normal vectors of the hemisphere curve. In a conventional DCA approach, the structures of branched nanopores were grown on a photolithography-and-etched low-curvature curved surface with large interpore distances. However, a high-curvature hemisphere curved surface can be obtained by the HPA technique. Such a curved surface by HPA is intrinsically induced by the high-resistivity impurities in the aluminum foil and leads to branching and bending of nanopore growth via the electric field mechanism rather than the interpore distance in conventional approaches. It is noted that by the HPA technique, the Joule heat during the RT process has been significantly suppressed globally on the material, and nanopores have been grown along the normal vectors of a hemisphere curve. The curvature is much larger than that in other literatures due to different fabrication methods. In theory, the number of nanopores on the hemisphere surface is two times of the conventional flat plane, which is potentially useful for photocatalyst or other applications.
PACS: 81.05.Rm; 81.07.-b; 82.45.Cc.
doi:10.1186/1556-276X-6-596
PMCID: PMC3235325  PMID: 22087646
anodic aluminum oxide; porous alumina; nanoporous template
16.  Influence of Anodic Conditions on Self-ordered Growth of Highly Aligned Titanium Oxide Nanopores 
Nanoscale Research Letters  2007;2(7):355-363.
Self-aligned nanoporous TiO2templates synthesized via dc current electrochemical anodization have been carefully analyzed. The influence of environmental temperature during the anodization, ranging from 2 °C to ambient, on the structure and morphology of the nanoporous oxide formation has been investigated, as well as that of the HF electrolyte chemical composition, its concentration and their mixtures with other acids employed for the anodization. Arrays of self-assembled titania nanopores with inner pores diameter ranging between 50 and 100 nm, wall thickness around 20–60 nm and 300 nm in length, are grown in amorphous phase, vertical to the Ti substrate, parallel aligned to each other and uniformly disordering distributed over all the sample surface. Additional remarks about the photoluminiscence properties of the titania nanoporous templates and the magnetic behavior of the Ni filled nanoporous semiconductor Ti oxide template are also included.
doi:10.1007/s11671-007-9073-5
PMCID: PMC3246376
Titanium oxides; Nanoporous materials; Electrochemical anodization
17.  A Single-Molecule Nanopore Device Detects DNA Polymerase Activity With Single-Nucleotide Resolution 
The ability to monitor DNA polymerase activity with single-nucleotide resolution has been the cornerstone of a number of advanced single-molecule DNA sequencing concepts. Toward this goal, we report the first spatially-resolved observation of DNA polymerase activity with single-base resolution at the single-molecule level. We describe the design and characterization of a single-species supramolecular nanopore device capable of detecting up to nine consecutive DNA polymerase-catalyzed single nucleotide primer extensions with high sensitivity and spatial resolution (≤ 2.4 Å). The device is assembled in a suspended lipid membrane by threading and mechanically capturing a single strand of DNA-PEG copolymer inside an α-hemolysin protein pore. Single nucleotide primer extensions result in successive displacements of the template DNA strand within the protein pore, which can be monitored by the corresponding stepped changes in the ion current flowing through the pore under an applied transmembrane potential. The system described thus represents a promising advance toward nanopore-mediated single-molecule DNA sequencing concept, and in addition might be applicable to studying a number of other biopolymer-protein interactions and dynamics.
doi:10.1021/ja077082c
PMCID: PMC2453067  PMID: 18166054
18.  Modeling Transport Through Synthetic Nanopores 
IEEE nanotechnology magazine  2009;3(1):20-28.
Nanopores in thin synthetic membranes have emerged as convenient tools for high-throughput single-molecule manipulation and analysis. Because of their small sizes and their ability to selectively transport solutes through otherwise impermeable membranes, nanopores have numerous potential applications in nanobiotechnology. For most applications, properties of the nanopore systems have to be characterize at the atomic level, which is currently beyond the limit of experimental methods. Molecular dynamics (MD) simulations can provide the desired information, however several technical challenges have to be met before this method can be applied to synthetic nanopore systems. Here, we highlight our recent work on modeling synthetic nanopores of the most common types. First, we describe a novel graphical tool for setting up all-atom systems incorporating inorganic materials and biomolecules. Next, we illustrate the application of the MD method for silica, silicon nitride, and polyethylene terephthalate nanopores. Following that, we describe a method for modeling synthetic surfaces using a bias potential. Future directions for tool development and nanopore modeling are briefly discussed at the end of this article.
doi:10.1109/MNANO.2008.931112
PMCID: PMC3168529  PMID: 21909347
19.  Assessing Graphene Nanopores for Sequencing DNA 
Nano letters  2012;12(8):4117-4123.
Using all-atom molecular dynamics and atomic-resolution Brownian dynamics, we simulate the translocation of single-stranded DNA through graphene nanopores and characterize the ionic current blockades produced by DNA nucleotides. We find that transport of single DNA strands through graphene nanopores may occur in single nucleotide steps. For certain pore geometries, hydrophobic interactions with the graphene membrane lead to a dramatic reduction in the conformational fluctuations of the nucleotides in the nanopores. Furthermore, we show that ionic current blockades produced by different DNA nucleotides are, in general, indicative of the nucleotide type, but very sensitive to the orientation of the nucleotides in the nanopore. Taken together, our simulations suggest that strand sequencing of DNA by measuring the ionic current blockades in graphene nanopores may be possible, given that the conformation of DNA nucleotides in the nanopore can be controlled through precise engineering of the nanopore surface.
doi:10.1021/nl301655d
PMCID: PMC3434709  PMID: 22780094
Nanopore; graphene; molecular dynamics; biosensors; nucleic acids; ionic current
20.  Synthesis and Characterization of Polydiacetylene Films and Nanotubes 
We report here the synthesis and characterization of polydiacetylene (PDA) films and nanotubes using layer-by-layer (LBL) chemistry. 10,12-Docosadiyndioic acid (DCDA) monomer was self-assembled on flat surfaces and inside of nanoporous alumina templates. UV irradiation of DCDA provided polymerized-DCDA (PDCDA) films and nanotubes. We have used zirconium-carboxylate interlayer chemistry to synthesize PDCDA multilayers on flat surfaces and in nanoporous template. PDCDA multilayers were characterized using optical (UV–vis, fluorescence, ellipsometry, FTIR) spectroscopies, ionic current–voltage (I–V) analysis, and scanning electron microscopy. Ellipsometry, FTIR, electronic absorption and emission spectroscopies showed a uniform DCDA deposition at each deposition cycle. Our optical spectroscopic analysis indicates that carboxylate-zirconium interlinking chemistry is robust. To explain the disorganization in the alkyl portion of PDCDA multilayer films, we propose carboxylate-zirconium interlinkages act as “locks” in between PDCDA layers which restrict the movement of alkyl portion in the films. Because of this locking, the induced-stresses in the polymer chains can not be efficiently relieved. Our ionic resistance data from I–V analysis correlate well with calculated resistance at smaller number of PDCDA layers but significantly deviated for thicker PDCDA nanotubes. These differences were attributed to ion-blocking because some of the PDCDA nanotubes were totally closed and the nonohmic and permselective ionic behaviors when the diameter of the pores approaches the double-layer thickness of the solution inside of the nanotubes.
doi:10.1021/la801948z
PMCID: PMC2683165  PMID: 18823090
21.  Automated Forward and Reverse Ratcheting of DNA in a Nanopore at Five Angstrom Precision1 
Nature biotechnology  2012;30(4):344-348.
Single-molecule techniques have been developed for commercial DNA sequencing1,2. One emerging strategy uses a nanopore to analyze DNA molecules as they are driven electrophoretically in single file order past a sensor3-5. However, uncontrolled DNA strand electrophoresis through nanopores is too fast for accurate base reads6. A proposed solution would employ processive enzymes to deliver DNA through the pore at a slower average rate7. Here, we describe forward and reverse ratcheting of DNA templates through the α–hemolysin (α-HL) nanopore controlled by wild-type phi29 DNA polymerase (phi29 DNAP). DNA strands were examined in single file order at one nucleotide spatial precision in real time. The registry error probability (either an insertion or deletion during one pass along a template strand) ranged from 10% to 24.5% absent optimization. This general strategy facilitates multiple reads of individual template strands and is transferrable to other nanopore devices for implementation of DNA sequence analysis.
doi:10.1038/nbt.2147
PMCID: PMC3408072  PMID: 22334048
22.  Nanopore-based Sensors for Multi-parameter Characterization of Nanoparticles and Viruses 
Nanopore-based instrumentation has been developed for improved multi-parameter characterization of the physical properties of nano- and micro-sized particles. Accurate measurement, with individual particle resolution, of a range of biological and synthetic sample types, i.e. liposomes, PLGA, lipids, micelles, virus-like-particles, polymers, viruses, bacteria, protein-conjugates, exosomes, and vesicles will be presented.
Particles are transported through a size-tunable pore via electric field and/or with pressure, for rapid and detailed determination of particle concentration (particles/mL for dosage), accurate size, aggregation levels, size distribution and relative surface charge distribution, all determined simultaneously.
Experimental parameters are adjusted in real-time for mapping how different populations within particle mixtures respond to externally applied conditions for high-resolution and powerful analysis of particle physical properties and their dynamic behaviour, i.e. to assess the level of surface modification (PEG-lyation) of drug delivery carriers.
The ability to individually interrogate each particle addresses the shortcomings of ensemble systems such as dynamic light-scattering and also of static systems using electron microscopy. This also enables the quantification of the dynamic behaviour of particle mixtures, such as aggregation and fragmentation of particles, and surface modification changes to particles.
Research work utilizing tunable pore sensors in virus quantification, pathogen interaction dynamics, medical diagnostics and drug delivery systems are presented.
PMCID: PMC3630705
23.  Infuence of Microstructure in Drug Release Behavior of Silica Nanocapsules 
Journal of Drug Delivery  2013;2013:803585.
Meso- and nanoporous structures are adequate matrices for controlled drug delivery systems, due to their large surface areas and to their bioactive and biocompatibility properties. Mesoporous materials of type SBA-15, synthesized under different pH conditions, and zeolite beta were studied in order to compare the different intrinsic morphological characteristics as pore size, pore connectivity, and pore geometry on the drug loading and release process. These materials were characterized by X-ray diffraction, nitrogen adsorption, scanning and transmission electron microscopy, and calorimetric measurements. Ibuprofen (IBU) was chosen as a model drug for the formulation of controlled-release dosage forms; it was impregnated into these two types of materials by a soaking procedure during different periods. Drug loading and release studies were followed by UV-Vis spectrophotometry. All nano- and mesostructured materials showed a similar loading behavior. It was found that the pore size and Al content strongly influenced the release process. These results suggest that the framework structure and architecture affect the drug adsorption and release properties of these materials. Both materials offer a good potential for a controlled delivery system of ibuprofen.
doi:10.1155/2013/803585
PMCID: PMC3748776  PMID: 23986870
24.  Conductance-Based Determination of Solid-State Nanopore Size and Shape: An Exploration of Performance Limits 
Knowledge of nanopore size and shape is critical for many implementations of these single-molecule sensing elements. Geometry determination by fitting the electrolyte-concentration-dependence of the conductance of surface-charged, solid-state nanopores has been proposed to replace demanding electron microscope-based methods. The functional form of the conductance poses challenges for this method by restricting the number of free parameters used to characterize the nanopore. We calculated the electrolyte-dependent conductance of nanopores with an exponential-cylindrical radial profile using three free geometric parameters; this profile, itself, could not be uniquely geometry-optimized by the conductance. Several different structurally simplified models, however, generated quantitative agreement with the conductance, but with errors exceeding 40% for estimates of key geometrical parameters. A tractable conical-cylindrical model afforded a good characterization of the nanopore size and shape, with errors of less than 1% for the limiting radius. Understanding these performance limits provides a basis for using and extending analytical nanopore conductance models.
doi:10.1021/jp305381j
PMCID: PMC3673737  PMID: 23750286
Electric double layer; nanopore surface charge; nanopore conductance; nanopore shape; silicon nitride nanopore; silicon oxide nanopore
25.  Preparation and characterization of superhydrophobic surfaces based on hexamethyldisilazane-modified nanoporous alumina 
Nanoscale Research Letters  2011;6(1):487.
Superhydrophobic nanoporous anodic aluminum oxide (alumina) surfaces were prepared using treatment with vapor-phase hexamethyldisilazane (HMDS). Nanoporous alumina substrates were first made using a two-step anodization process. Subsequently, a repeated modification procedure was employed for efficient incorporation of the terminal methyl groups of HMDS to the alumina surface. Morphology of the surfaces was characterized by scanning electron microscopy, showing hexagonally ordered circular nanopores with approximately 250 nm in diameter and 300 nm of interpore distances. Fourier transform infrared spectroscopy-attenuated total reflectance analysis showed the presence of chemically bound methyl groups on the HMDS-modified nanoporous alumina surfaces. Wetting properties of these surfaces were characterized by measurements of the water contact angle which was found to reach 153.2 ± 2°. The contact angle values on HMDS-modified nanoporous alumina surfaces were found to be significantly larger than the average water contact angle of 82.9 ± 3° on smooth thin film alumina surfaces that underwent the same HMDS modification steps. The difference between the two cases was explained by the Cassie-Baxter theory of rough surface wetting.
doi:10.1186/1556-276X-6-487
PMCID: PMC3212001  PMID: 21827683
superhydrophobic surfaces; surface modification; hexamethyldisilazane; nanoporous alumina

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