Silicon Nanochannels Research Articles

Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays.

Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Hence, chromatin accessibility is a central regulator of gene expression, and its genomic profile holds essential information on the cell type and state. We utilized the E. coli Dam methyltransferase in combination with a fluorescent cofactor analogue to generate fluorescent tags in accessible DNA regions within the cell nucleus. The accessible portions of the genome are then detected by single-molecule optical genome mapping in nanochannel arrays. This method allowed us to characterize long-range structural variations and their associated chromatin structure. We show the ability to create whole-genome, allele-specific chromatin accessibility maps composed of long DNA molecules extended in silicon nanochannels.

The electrophoretic motion of cylindrical macroions inside a nanochannel using molecular dynamics simulation

This paper examines the electrophoretic motion of a cylindrical macroion floating in a solution of water and NaCl inside a silicon nanochannel using molecular dynamics simulation. The aim is to investigate the effects of parameters like free movement, initial orientation, shape, aspect ratio, surface charge density and initial electrical charge of macroion on the electrophoretic motion. Findings suggest that any increase in surface charge density could give a rise to electrophoretic velocity of the solution. Considering the macroion free to move around, initial orientation does not play significant role in final results. Results also imply that macroion’s velocity does not change steadily by variations in surface charge density which is because of the multilayer structure of the Stern layer. Finally, average electrophoretic velocity of the solution for all scenarios in this study is witnessed to be the same. However, maximum electrophoretic velocity could be four times greater than average values. This must be taken into account in applications with limited maximum velocity.

Classical modeling of positronium cooling in silicon nanochannel plates

Silicon nanochannel plates (NCPs) are employed in a variety of experiments as sources of cold positronium (Ps) via positron to Ps conversion. Despite the widespread use of NCPs, no comprehensive model of the dynamics of the cooling process of Ps within the nanochannels has been provided yet. In this work, we present a classical Monte Carlo model of Ps cooling produced in NCPs and validate it against experimental values present in the literature. Our model allows us to estimate crucial characteristics such as the cooling time in NCPs, the angular distribution of emitted Ps, and the fraction of Ps annihilating into three gamma quanta. The simulated energy spectra of emitted Ps closely match experimental results for NCPs held at room temperature. At cryogenic temperature the classical thermalization model does not accurately reproduce the measured spectra, which we attribute to a transition in the cooling process towards a regime where quantum effects play a significant role.

Nanoengineered nanochannels for thermally ionic nanofluidic energy harvesting

This work demonstrates thermal-to-electric energy conversion based on ionic nanofluidic transport in nanochannels inducted by a temperature gradient. Two types of highly periodic and high aspect ratio nanochannels have been fabricated in a silicon (Si) substrate and in an aluminium oxide (Al2O3) membrane. Silicon nanochannels with diameter of 100 nm and height of 300 μm have been produced by metal-assisted chemical etching process (MACE), while nanochannels with the dimensions of the 10 nm and 3 μm respectively, were fabricated in a Al2O3 membrane by the anodic aluminum oxidation (AAO) process. Moreover, a novel approach of thermally nanofluidic energy harvesting was proposed and conducted. The performance of the thermally ionic nanofluidic energy harvesting system in cases with and without nanochannels has been evaluated and compared. The advantage of the presence nanochannels on energy conversion has been confirmed. The electrolyte concentration dependence on the output power has been determined. Also, the effect of nanochannel materials, including alumina and silicon materials, on the power density has been verified. The ionic Seebeck coefficient was enhanced by 7.3 times when the nanochannels were present. The silicon substrate with nanochannels demonstrated the highest performance for energy harvesting. Its power density reaches approximately 1.47 mW/m2, which was 13.3 times larger than the case without nanochannels. This investigation may open new opportunities for the future thermoelectric generators based on ionic transport in nanochannels.

Time-of-flight apparatus for the measurement of slow positronium emitted by nanochannel converters at cryogenic temperatures

Silicon nanochannel plates (NCPs) are efficient positron to positronium converters and are employed as sources of abundant cold positronium. Characterization of the emitted positronium energy spectrum is crucial to assess the NCP performance and support their further optimization. We present here a Time-of-Flight (ToF) system optimized to measure the energy spectrum of positronium produced by NCP converters held at cryogenic temperatures. The ToF-apparatus was tested by implanting 7keV positrons into NCPs at room temperature before performing ToF experiments using positron implantation energies of 7 and 11keV into NCPs held at 20K. At these conditions we succeeded in determining the energy spectrum of the positronium escaping from the nanochannels into the vacuum down to an energy of 10meV.

Investigating the effect of single-walled carbon nanotubes chirality on the electrokinetics transport of water and ions: A molecular dynamics study

The effect of carbon nanotubes (CNTs) chirality on the water electrokinetics transport through CNTs while embedded in silicon nanochannels is studied using molecular dynamics simulation. Voltage difference across the CNTs changed from 0 V to 3.2 V that resulted in a shift in water transport rate from ~8 to ~140 H2O/ns, 4 to ~120 H2O/ns, 15 to ~300 H2O/ns and 10 to ~285 H2O/ns for CNT (8,8), CNT (14,0), CNT (16,16) and CNT (28,0), respectively. In comparison to zigzag CNTs, armchair CNTs showed higher flux for all kind of cations (Na+, K+, Zn2+). It has been shown that water flux through CNTs are not linearly dependent on electric field, yet it faces a peak. Interestingly, zigzag CNTs showed a tendency to retard this maximum voltage to higher values of electric field than armchair CNTs. This work highlights the importance of CNTs chirality effect in future CNT-nanofluidic systems design.

Direct investigation of methane nanofluidic microstructure and system dynamics in rough silicon nanochannel

The microstructure and system dynamics of methane nanofluidic are important to determine the flow properties. In this study, we use non-equilibrium multiscale molecular dynamics simulation (NEMSMD) to investigate the microstructure and system dynamics of methane nanofluidic confined by rough silicon atomic walls. To capture the detailed atomic microstructure of methane moving in rough nanochannel accurately, the modification of OPLS methane fully atomic model is employed. The average number density distributions of C (H) atom, average velocity profile, velocity autocorrelation function and projection radial distribution function (XOY-, XOZ- and YOZ planes) plots give a clear observation of the impacts of different conditions (roughness, body driving force, fluid–wall interaction strength and cutoff radius) on the methane Poiseuille flow in nanochannel. The projection radial distribution functions and diffusivity appear anisotropic, and seem to be affected more significantly by roughness, fluid–wall interaction strength and cutoff radius than body driving force in the whole channel region. Moreover, the body driving force and cutoff radius also play an important role in methane nanofluidic simulation using NEMSMD. The present simulation results are very meaningful for the design of energy-saving emission reduction nanofluidic devices.

Label-Free Bacterial Toxin Detection in Water Supplies Using Porous Silicon Nanochannel Sensors.

Lipopolysaccharides (LPS) are the major component of the outer membrane of all Gram-negative bacteria and some cyanobacteria and are released during growth and cell death. LPS pose a potential health risk in water, causing acute respiratory illnesses, inhalation fever, and gastrointestinal disorders. The need for rapid and accurate detection of LPS has become a major priority to facilitate more timely and efficacious intervention and, hence, avoid unsafe water distribution. In this context, a porous silicon membrane (pSiM)-based electrochemical biosensor was developed for direct and sensitive detection of LPS. pSiM, featuring arrays of nanochannels, was modified with polymyxin B (PmB), an antimicrobial peptide with strong affinity to LPS. Detection of LPS was based on measuring the changes in the diffusion through the nanochannels of an electroactive species added in solution, caused by the nanochannel blockage upon LPS binding to PmB. Results showed a limit of detection of 1.8 ng/mL, and a linear response up to 10,000 ng/mL spiked in buffer. Selectivity of the sensor toward potential interfering species in water supplies was also assessed. Sensor performance was then evaluated in water samples from a water treatment plant (WTP), and detection of LPS well below the levels encountered in episodes of water contamination and in humidifiers was demonstrated. The same platform was also tested for bacterial detection including Pseudomonas aeruginosa and Escherichia coli spiked in water samples from a WTP. Considering its performance characteristics, this platform represents a promising screening tool to identify the presence of LPS in water supplies and provide early warning of contamination events.

Molecular and Continuum Transport Perspectives on Electroosmotic Slip Flows

Velocity slip in electroosmotic flows (EOF) is investigated using an analytical solution of Poisson–Boltzmann and Stokes (PB-S) equations with slip correction, and the results are compared with the predictions from molecular dynamics (MD) simulations. Particularly, EOFs of NaCl solution in silicon nanochannels are simulated, and channel dimensions are picked to exhibit plug flow behavior in the bulk region. Electrochemical conditions are specified within the validity region of PB theory to avoid charge inversion and flow reversal effects. The analytical model shows normalization of the slip length (an interfacial property) with the Debye length determined by the ionic concentration, implying that the slip enhancement in EOFs is independent of the channel height. MD results are compared with the analytical solution using the apparent viscosity and slip lengths determined by force-driven flow simulations in charged silicon nanochannels. Onset of slip velocity within the electrical double layer and its effec...

Nanostructured Electrochemical Biosensors for Label-Free Detection of Water- and Food-Borne Pathogens.

The emergence of nanostructured materials has opened new horizons in the development of next generation biosensors. Being able to control the design of the electrode interface at the nanoscale combined with the intrinsic characteristics of the nanomaterials engenders novel biosensing platforms with improved capabilities. The purpose of this review is to provide a comprehensive and critical overview of the latest trends in emerging nanostructured electrochemical biosensors. A detailed description and discussion of recent approaches to construct label-free electrochemical nanostructured electrodes is given with special focus on pathogen detection for environmental monitoring and food safety. This includes the use of nanoscale materials such as nanotubes, nanowires, nanoparticles, and nanosheets as well as porous nanostructured materials including nanoporous anodic alumina, mesoporous silica, porous silicon, and polystyrene nanochannels. These platforms may pave the way toward the development of point-of-care portable electronic devices for applications ranging from environmental analysis to biomedical diagnostics.

Plasmonic nanochannel structure for narrow-band selective thermal emitter

A plasmonic structure consisting of a periodic arrangement of vertical silicon nanochannels connected by U-shaped gold layers is demonstrated as a spectrally selective thermal emitter. The plasmonic nanochannel structure sustains a coupled mode between a surface plasmon polariton and a stationary surface plasmon resonance, which induces a strong and sharp resonance observed in the form of a reflectance dip in the far field. Upon heating the structure, a strong and narrow-bandwidth thermal emittance peak is observed with a maximum emittance value of 0.72 and a full-width-at-half-maximum of 248 nm at a wavelength of 5.66 μm, which corresponds to the reflectance dip wavelength. Moreover, we demonstrate the control of the emission peak wavelength by varying the period of the structure. The plasmonic nanochannel structure realizes a small-size and selective infrared thermal emitter, which is expected to be applicable as an infrared light source.

The effects of wall roughness on the methane flow in nano-channels using non-equilibrium multiscale molecular dynamics simulation

This paper presents a non-equilibrium multiscale molecular dynamics simulation method to investigate the effects of periodic wall surface roughness on the structure and mass transfer of methane fluid through the silicon nano-channels. In order to accurately capture the trajectories and microstructure of methane nano-fluidics, the present modification of OPLS fully atomic model is employed. Meanwhile, we introduce the corresponding coarse-grained model to solve the problem of wall–fluid interaction for methane Poiseuille flow within silicon atomic walls using the classical Lorentz–Berthelot mixing rules. The geometries of the upper wall roughness are modeled by rectangular waves with different amplitudes and wavelengths. The three-dimensional number densities of C (H) atom and kinetic energy distribution plots give a clear observation of the impacts of surface roughness on the localization micro-information of methane fluid. Moreover, the slip length of fluid over rough surface decreases with the increase in amplitude. The diffusion coefficients appear anisotropic, and the radial distribution functions decrease with the increase in the amplitude. These properties should be taken into account in the design of energy-saving emission reduction nano-fluidic devices. All numerical results also indicate that the presented method not only can well solve the issue of wall–fluid interactions, but also could accurately predict the micro-information and dynamic properties of methane Poiseuille flow.

Transport properties and structure of dense methane fluid in the rough nano-channels using non-equilibrium multiscale molecular dynamics simulation

In this paper, non-equilibrium multiscale molecular dynamics simulation is applied to investigate the transport properties (shear viscosity, diffusion coefficient and thermal conductivity) and structural properties of dense methane for Poiseuille flow within rough silicon nano-channel. In this simulation, the recently modified OPLS model is used to capture the micro-information of dense methane nanofluidics, as well as its coarse-grained model to solve the problem of wall-fluid interactions via the classical Lorentz-Berthelot mixing rule. In order to calculate the local shear viscosity in fluid layers accurately, the fitted local velocity profile method is introduced to determine the viscosity value by fitting the local velocity profile based on the Navier-Stokes equations. Additionally, the Green-Kubo formula is employed to compute the diffusion coefficient and thermal conductivity of methane nanofluidics. From the simulation, we conclude that atom number density, transport and structural properties of methane nanofluidics present significant variations near the rough nano-channel walls, and the obtained data in the central part of the nano-channel is close to experiment value of bulk system. Moreover, the streamlines are distorted near rough nano-channel walls. The results above are significant in understanding of the nanoscale hydrodynamics, and should be taken into account in fluid dynamics theory and the design of nanofluidic devices.

Studying the viscosity of methane fluid for different resolution levels models using Poiseuille flow in a nano-channel

In this work, the viscosity–temperature–density relationship of methane is investigated for three fully atomistic models (RISM, OPLS and MOPLS) and the corresponding coarse-grained models (CGRISM, CGOPLS and CGMOPLS) by studying the Poiseuille flow inside a silicon nano-channel using molecular dynamic simulation. In order to solve the interaction problem of nano-channel atom and methane molecule, the coarse-grained methane model and the classical Berthelot–Lorentz mixing rules are employed. The optimized coarse-grained methane models are determined using the relative entropy minimization method. The density distribution, stress force profile and velocity profile of coarse-grained models are compared with the fully atomistic models for different nano-channel widths. It is concluded that the results of coarse-grained model are in reasonable agreement with those of the corresponding fully atomistic model. Furthermore, the value of viscosity is calculated by fitting the velocity profile to the continuum solution from the Navier–Stokes equations and then compared to experimental value. The results show that the MOPLS and CGMOPLS models could well predict the viscosity of methane fluid, while the OPLS model performed worst. All simulation results indicate that the coarse-grained models can be used to predict the viscosity of methane fluid accurately.

Super-Resolution Genome Mapping in Silicon Nanochannels

Optical genome mapping in nanochannels is a powerful genetic analysis method, complementary to deoxyribonucleic acid (DNA) sequencing. The method is based on detecting a pattern of fluorescent labels attached along individual DNA molecules. When such molecules are extended in nanochannels, the labels create a fluorescent genetic barcode that is used for mapping the DNA molecule to its genomic locus and identifying large-scale variation from the genome reference. Mapping resolution is currently limited by two main factors: the optical diffraction limit and the thermal fluctuations of DNA molecules suspended in the nanochannels. Here, we utilize single-molecule tracking and super-resolution localization in order to improve the mapping accuracy and resolving power of this genome mapping technique and achieve a 15-fold increase in resolving power compared to currently practiced methods. We took advantage of a naturally occurring genetic repeat array and labeled each repeat with custom-designed Trolox conjugated fluorophores for enhanced photostability. This model system allowed us to acquire extremely long image sequences of the equally spaced fluorescent markers along DNA molecules, enabling detailed characterization of nanoconfined DNA dynamics and quantitative comparison to the Odijk theory for confined polymer chains. We present a simple method to overcome the thermal fluctuations in the nanochannels and exploit single-step photobleaching to resolve subdiffraction spaced fluorescent markers along fluctuating DNA molecules with ∼100 bp resolution. In addition, we show how time-averaging over just ∼50 frames of 40 ms enhances mapping accuracy, improves mapping P-value scores by 3 orders of magnitude compared to nonaveraged alignment, and provides a significant advantage for analyzing structural variations between DNA molecules with similar sequence composition.

Hydrodynamic slip in silicon nanochannels.

Equilibrium and nonequilibrium molecular dynamics simulations were performed to better understand the hydrodynamic behavior of water flowing through silicon nanochannels. The water-silicon interaction potential was calibrated by means of size-independent molecular dynamics simulations of silicon wettability. The wettability of silicon was found to be dependent on the strength of the water-silicon interaction and the structure of the underlying surface. As a result, the anisotropy was found to be an important factor in the wettability of these types of crystalline solids. Using this premise as a fundamental starting point, the hydrodynamic slip in nanoconfined water was characterized using both equilibrium and nonequilibrium calculations of the slip length under low shear rate operating conditions. As was the case for the wettability analysis, the hydrodynamic slip was found to be dependent on the wetted solid surface atomic structure. Additionally, the interfacial water liquid structure was the most significant parameter to describe the hydrodynamic boundary condition. The calibration of the water-silicon interaction potential performed by matching the experimental contact angle of silicon led to the verification of the no-slip condition, experimentally reported for silicon nanochannels at low shear rates.

Wettability transparency and the quasiuniversal relationship between hydrodynamic slip and contact angle

The universality of the scaling laws that correlate the hydrodynamic slip length and static contact angle was investigated by introducing the concept of the wettability transparency of graphene-coated surfaces. Equilibrium molecular dynamics simulations of droplet wettability for Si(111), Si(100), and graphene-coated silicon surfaces were performed to determine the conditions required to obtain similar contact angles between bare and graphene-coated surfaces (wettability transparency). The hydrodynamic slip length was determined by means of equilibrium calculations for silicon and graphene-coated silicon nanochannels. The results indicate that the slip-wettability scaling laws can be used to describe the slip behavior of the bare silicon nanochannels in general terms; however, clear departures from a general universal description were observed for hydrophobic conditions. In addition, a significant difference in the hydrodynamic slippage was observed under wettability transparency conditions. Alternatively, the hydrodynamic boundary condition for silicon and graphene-coated silicon nanochannels was more accurately predicted by observing the density depletion length, posing this parameter as a better alternative than the contact angle to correlate with the slip length.

Silicon nanochannel platforms for tightly controlled therapeutic release and immunoisolated cell transplantation

Silicon nanochannel platforms for tightly controlled therapeutic release and immunoisolated cell transplantation

Counterions and water molecules in charged silicon nanochannels: the influence of surface charge discreteness

In order to detect the effect of the surface charge discreteness on the properties at the solid–liquid interface, a molecular dynamics simulation model considering the vibration of wall atoms was used to investigate the performance of ion and water under different charge distributions. Through the comparison between simulation results and the theoretical prediction, it was found that, with the increasing degree of discreteness, much more counterions were attracted to the surface. These ions formed a denser accumulating layer which was located much nearer to the surface and caused charge inversion. The ions in this layer were non-hydrated or partially hydrated. When a voltage was applied across the nanochannel, this dense accumulating layer did not move unlike the ions near the uniformly charged surface. From the water density profiles obtained in nanochannels with different surface charge distributions, the influence of the surface charge discreteness on water distributions could be neglected.

Investigation of charge inversion in silicon nanochannels with molecular dynamics simulation

Through molecular dynamics simulation, the ionic distributions in NaCl and CaCl2 solutions confined in 3-nm-high nanochannels were investigated. Different from the previous simulation model with artificial electrical neutrality, our model would reach equilibrium and electrical neutrality through ion exchange among the nanochannel region and the bulk sinks. It is observed that when the surface charge density is −0.101 C/m2, charge inversion occurs at 1.0 M concentration of CaCl2 solution, but not in NaCl solution due to the stronger correlation effect between Ca2+ ions near the charged surface, which is not considered in the mean field Poisson–Boltzmann equation. Our simulation results agree well with the experimental results by F.H.J. Van Der Heyden et al. In addition, with the increase in the surface charge density, the charge inversion can be induced in the monovalent solution and be strengthened in the divalent ionic solution.