Separation of long DNA molecules in a microfabricated entropic trap array

Manipulation and analysis of large DNA molecules by controlling their dynamics using micro and nanogaps

Manipulation and analysis methods for large DNAs are critical for epidemiological, clinical, diagnostic, and fundamental research on bacteria, membrane vesicles, plants, yeast, and human cells. However, the physical properties of large DNAs often challenge their manipulation and analysis with high accuracy and speed using conventional methods such as gel electrophoresis and column-based methods. This review presents the approaches that leverage micrometer- and nanometer-sized gaps within microchannels to control the dynamics and conformations of large DNAs, thereby overcoming these challenges. By designing gap structures and migration conditions based on the relationship between gap parameters and the physical characteristics of large DNAs-such as diameter and persistence length-these methods enable swifter and more precise manipulation and analysis of large DNAs, including size separation, concentration, purification, and single-molecule analysis.

Channel-facilitated transport under resetting dynamics

The transport of particles through channels holds immense significance in physics, chemistry, and biological sciences. For instance, the motion of solutes through biological membranes is facilitated by specialized proteins that create water-filled channels. Valuable insights can be obtained by studying the transition paths of particles through a channel and gathering information on their lifetimes inside the channel as well as their exit probabilities. In a similar vein, we consider a one-dimensional model of channel-facilitated transport where a diffusive particle is subject to attractive interactions with the walls of the channel. We study the statistics of conditional and unconditional escape times in the presence of resetting-an intermittent dynamics that brings the particle back to its initial coordinate stochastically. We determine analytically the physical conditions under which such a resetting mechanism becomes beneficial for the faster escape of the particles from the channel, thus enhancing transport. Our theory has been verified with the aid of Brownian dynamics simulations for various interaction strengths and extents. The overall results presented herein highlight the scope of resetting-based strategies to be universally promising for complex transport processes of single or long molecules through biological membranes.

Electrokinetic transport phenomena in nanofluidics and their applications

Much progress has been made in the electrokinetic phenomena inside nanochannels in the last decades. As the dimensions of the nanochannels are compatible to that of the electric double layer (EDL), the electrokinetics inside nanochannels indicate many unexpected behaviors, which show great potential in the fields of material science, biology, and chemistry. This review summarizes the recent development of nanofluidic electrokinetics in both fundamental and applied research. First, the techniques for constructing nanochannels are introduced to give a guideline for choosing the optimal fabrication technique based on the specific feature of the nanochannel. Then, the theories and experimental investigations of the EDL, electroosmotic flow, and electrophoresis of nanoparticles inside the nanochannels are discussed. Furthermore, the applications of nanofluidic electrokinetics in iontronics, sensing, and biomolecule separation fields are summarized. In Section 5, some critical challenges and the perspective on the future development of nanofluidic electrokinetics are briefly proposed.

A superstable, flexible, and scalable nanofluidic ion regulation composite membrane

Two-dimensional layered membranes with high and stable ion transport properties have various applications in nanofluidic devices; however, their construction remains a considerable challenge. Herein, we develop a superstable aramid nanofiber/graphite composite membrane with numerous one-dimensional and two-dimensional nano-confined interspaces for ultrafast ion transport. The fabricated flexible and scalable membrane exhibits high tensile strength (∼115.3 MPa) even after immersion in water for 90 days. Further, the aramid nanofiber/graphite conductor features the surface-charge-governed ion transport behavior. The ionic conductivity of the membrane at a low potassium chloride concentration of 10-4 mol/L can be enhanced by 16 times that of the bulk counterpart. More importantly, its structure and ionic conductivity remain unchanged even after immersion in different harsh solutions (e.g., acid, base, and ethanol) for over 30 days. Molecular dynamics simulations reveal that the superstability of the membrane is attributable to the robust interchain interactions within the aramid nanofibers and the strong interfacial interactions between the aramid nanofibers and graphite nanosheets. This study highlights the superior structural stability of the proposed flexible and scalable aramid nanofiber/graphite composite membrane, which could be employed in advanced nanofluidic devices for application under extreme working environments.

Continuous-flow macromolecular sieving in slanted nanofilter array: stochastic model and coupling effect of electrostatic and steric hindrance

Microfabricated slanted nanofilter arrays are a promising technology for integrated biomolecule analysis systems such as online monitoring and point-of-care quality validation, due to their continuous-flow and one-step operation capability. However, an incomplete understanding of the system limits the performance and wider applications of slanted nanofilter arrays. In this paper, we present rigorous theoretical and experimental studies on macromolecule sieving in a slanted nanofilter array. From both stochastic and kinetic models, an explicit theoretical solution describing size-dependent molecule sieving was derived, which was validated using experimental sieving results obtained for various sieving conditions. Our results not only detail the relationship between sieving conditions and sieving efficiency but also demonstrate that sieving is affected by multiple hindrance effects (electrostatic hindrance), not steric hindrance alone. There is an optimal sieving condition for achieving the greatest separation efficiency for DNAs of a certain size range. Small DNA has great size selectivity in small nanofilters and in weak electric fields, whereas large DNA is present in large nanofilters and in strong electric fields. This study provides insights into designing a slanted nanofilter array for particular target applications and understanding the sieving principles in the nanofilter array.

Observation of a Large Slip Effect in the Nanoscale Flow of Highly Viscous Supercooled Liquid Metals

Understanding and controlling the flow of materials confined in channels play important roles in science and engineering. The general no-slip boundary condition will result in it being more challenging to drive the flow as the channel size decreases to the nanoscale, especially for highly viscous liquids. Here, we report the observation of a large boundary slip in the nanoscale flow of highly viscous supercooled liquid metals (with viscosities of ≲108 Pa s), enabled by the hydrophobic treatment of smooth nanochannels. The slip length significantly depends on the pressure, which can be rationalized by the shear-dependent viscosity. Our findings provide not only new insights into the field of nanofluidics but also a practical technique for resolving the challenge in the net formation of highly viscous supercooled liquid metals at the nanoscale.

Nonmonotonous Translocation Time of Polymers across Pores

Polymers confined in corrugated channels, i.e., channels of varying amplitude, display multiple local maxima and minima of the diffusion coefficient upon increasing their degree of polymerization N. We propose a theoretical effective free energy for linear polymers based on a Fick-Jacobs approach. We validate the predictions against numerical data, obtaining quantitative agreement for the effective free energy, the diffusion coefficient, and the mean first passage time. Finally, we employ the effective free energy to compute the polymer lengths N_{min} at which the diffusion coefficient presents a minimum: we find a scaling expression that we rationalize with a blob model. Our results could be useful to design porous adsorbers, that separate polymers of different sizes without the action of an external flow.

Compression of a confined semiflexible polymer under direct and oscillating fields

The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long biopolymers tend to collapse under an external field, which is contrary to the previously reported stretching of the chain. In this work, we capture the compression of a confined semiflexible polymer under direct and oscillating fields using a coarse-grained computer simulation model in the presence of long-range hydrodynamics. In the case of a semiflexible polymer chain, the inhomogeneous hydrodynamic drag from the center to the periphery of the coil couples with the chain bending to cause a swirling movement of the chain segments, leading to structural intertwining and compaction. Contrarily, a flexible chain of the same length lacks such structural deformation and forms a well-established tadpole structure. While bending rigidity profoundly influences the chain's folding favorability, we also found that subject to the direct field, chains in stronger confinements exhibit substantial compaction, contrary to the one in moderate confinements or bulk where such compaction is absent. However, an alternating field within an optimum frequency can effectuate this compression even in moderate or no confinement. This field-induced collapse is a quintessential hydrodynamic phenomenon, resulting in intertwined knotted structures even for shorter chains, unlike other spontaneous knotting experiments where it happens exclusively for longer chains.

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

Optical trapping of two different microparticles by a double-tapered fiber probe

We theoretically and experimentally study the optical trapping of two different microparticles by a double-tapered optical fiber probe (DOFP) which is fabricated by the interfacial etching method. A SiO₂ microsphere and a yeast, or two SiO₂ microspheres with different diameters, are trapped. We calculate and measure the trapping forces on the two microparticles, discuss the impacts of the geometrical size and refractive index on the trapping forces. Both the theoretical calculation and experimental measurements indicate that if the two particles have the same refractive index, the larger the second particle is, the larger the trapping force is. Whereas, if the two particles have the same geometrical size, the smaller the refractive index is, the lager trapping force is. Trapping and manipulation of different multiple microparticles by a DOFP enhance the application of optical tweezers, especially in biomedical engineering and material science.

Fick-Jacobs description and first passage dynamics for diffusion in a channel under stochastic resetting

The transport of particles through channels is of paramount importance in physics, chemistry, and surface science due to its broad real world applications. Much insight can be gained by observing the transition paths of a particle through a channel and collecting statistics on the lifetimes in the channel or the escape probabilities from the channel. In this paper, we consider the diffusive transport through a narrow conical channel of a Brownian particle subject to intermittent dynamics, namely, stochastic resetting. As such, resetting brings the particle back to a desired location from where it resumes its diffusive phase. To this end, we extend the Fick-Jacobs theory of channel-facilitated diffusive transport to resetting-induced transport. Exact expressions for the conditional mean first passage times, escape probabilities, and the total average lifetime in the channel are obtained, and their behavior as a function of the resetting rate is highlighted. It is shown that resetting can expedite the transport through the channel-rigorous constraints for such conditions are then illustrated. Furthermore, we observe that a carefully chosen resetting rate can render the average lifetime of the particle inside the channel minimal. Interestingly, the optimal rate undergoes continuous and discontinuous transitions as some relevant system parameters are varied. The validity of our one-dimensional analysis and the corresponding theoretical predictions is supported by three-dimensional Brownian dynamics simulations. We thus believe that resetting can be useful to facilitate particle transport across biological membranes-a phenomenon that can spearhead further theoretical and experimental studies.

First-passage times in conical varying-width channels biased by a transverse gravitational force: Comparison of analytical and numerical results

We study the crossing time statistic of diffusing point particles between the two ends of expanding and narrowing two-dimensional conical channels under a transverse external gravitational field. The theoretical expression for the mean first-passage time for such a system is derived under the assumption that the axial diffusion in a two-dimensional channel of smoothly varying geometry can be approximately described as a one-dimensional diffusion in an entropic potential with position-dependent effective diffusivity in terms of the modified Fick-Jacobs equation. We analyze the channel crossing dynamics in terms of the mean first-passage time, combining our analytical results with extensive two-dimensional Brownian dynamics simulations, allowing us to find the range of applicability of the one-dimensional approximation. We find that the effective particle diffusivity decreases with increasing amplitude of the external potential. Remarkably, the mean first-passage time for crossing the channel is shown to assume a minimum at finite values of the potential amplitude.

Nanofluidic devices for the separation of biomolecules

Over the last 30-years, microchip electrophoresis and its applications have expanded due to the benefits it offers. Nanochip electrophoresis, on the other hand, is viewed as an evolving area of electrophoresis because it offers some unique advantages not associated with microchip electrophoresis. These advantages arise from unique phenomena that occur in the nanometer domain not readily apparent in the microscale domain due to scale-dependent effects. Scale-dependent effects associated with nanochip electrophoresis includes high surface area-to-volume ratio, electrical double layer overlap generating parabolic flow even for electrokinetic pumping, concentration polarization, transverse electromigration, surface charge dominating flow, and surface roughness. Nanochip electrophoresis devices consist of channels with dimensions ranging from 1 to 1000 nm including classical (1-100 nm) and extended (100 nm - 1000 nm) nanoscale devices. In this review, we highlight scale-dependent phenomena associated with nanochip electrophoresis and the utilization of those phenomena to provide unique biomolecular separations that are not possible with microchip electrophoresis. We will also review the range of materials used for nanoscale separations and the implication of material choice for the top-down fabrication and operation of these devices. We will also provide application examples of nanochip electrophoresis for biomolecule separations with an emphasis on nano-electrophoresis (nEP) and nano-electrochromatography (nEC).

Unraveling the liquid gliding on vibrating solid liquid interfaces with dynamic nanoslip enactment

Slip length describes the classical no-slip boundary condition violation of Newtonian fluid mechanics, where fluids glide on the solid surfaces. Here, we propose a new analytical model validated by experiments for characterization of the liquid slip using vibrating solid surfaces. Essentially, we use a microfluidic system integrated with quartz crystal microbalance (QCM) to investigate the relationship between the slip and the mechanical response of a vibrating solid for a moving fluid. We discover a liquid slip that emerges especially at high flow rates, which is independent of the surface wetting condition, having significant contributions to the changes in resonant frequency of the vibrating solid and energy dissipation on its surface. Overall, our work will lead to consideration of ‘missing slip’ in the vibrating solid-liquid systems such as the QCM-based biosensing where traditionally frequency changes are interpreted exclusively with mass change on the sensor surface, irrespective of the flow conditions.

A fluid flowing in solid confinement will glide, rather than stick to, the solid’s surfaces. This is usually described by introducing a concept known as slip length. The liquid slip concept is now extended for the situation of a vibrating solid–liquid interface.

High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays

Length-based separation of DNA remains as relevant today as when gel electrophoresis was introduced almost 100 years ago. While new, long-read genomics technologies have revolutionised accessibility to powerful genomic data, the preparation of samples has not proceeded at the same pace, with sample preparation often constituting a considerable bottleneck, both in time and difficulty. Microfluidics holds great potential for automated, sample-to-answer analysis via the integration of preparatory and analytical steps, but for this to be fully realised, more versatile, powerful and integrable unit operations, such as separation, are essential. We demonstrate the displacement and separation of DNA with a throughput that is one to five orders of magnitude greater than other microfluidic techniques. Using a device with a small footprint (23 mm × 0.5 mm), and with feature sizes in the micrometre range, it is considerably easier to fabricate than parallelized nano-array-based approaches. We show the separation of 48.5 kbp and 166 kbp DNA strands achieving a significantly improved throughput of 760 ng/h, compared to previous work and the separation of low concentrations of 48.5 kbp DNA molecules from a massive background of sub 10 kbp fragments. We show that the extension of DNA molecules at high flow velocities, generally believed to make the length-based separation of long DNA difficult, does not place the ultimate limitation on our method. Instead, we explore the effects of polymer rotations and intermolecular interactions at extremely high DNA concentrations and postulate that these may have both negative and positive influences on the separation depending on the detailed experimental conditions.

Parallel computing for mobilities in periodic geometries

We examine methods for calculating the effective mobilities of molecules driven through periodic geometries in the context of particle-based simulation. The standard formulation of the mobility, based on the long-time limit of the mean drift velocity, is compared to a formulation based on the mean first-passage time of molecules crossing a single period of the system geometry. The equivalence of the two definitions is derived under weaker assumptions than similar conclusions obtained previously, requiring only that the state of the system at subsequent period crossings satisfy the Markov property. Approximate theoretical analyses of the computational costs of estimating these two mobility formulations via particle simulations suggest that the definition based on first-passage times may be substantially better suited to exploiting parallel computation hardware. This claim is investigated numerically on an example system modeling the passage of nanoparticles through the slit-well device. In this case, the traditional mobility formulation is found to perform best when the Péclet number is small, whereas the mean first-passage time formulation is found to converge much more quickly when the Péclet number is moderate or large. The results suggest that, given relatively modest access to modern GPU hardware, this alternative mobility formulation may be an order of magnitude faster than the standard technique for computing effective mobilities of biomolecules through periodic geometries.

Micro/nanofluidic devices for DNA/RNA detection and separation

The development and research have ramped up at a greater speed than ever in the field of diseases diagnosis. Still there is struggle in developing early detection techniques which uses complex biomolecules like RNA, DNA and proteins in order to detect diseases caused by bacteria, viruses or fungi. Until now separation techniques used before detection rely on traditional techniques like electrophoresis etc. which often require centralized services. Although efforts are made in developing devices that is capable enough on carrying out separation and detection based on microfluidic (MF) and nanofluidic (NF) or lab on chip. Hence, in this chapter, we have discussed about the advancement, limitations and future steps that needs to be taken to flourish the field of NF and MF for the detection and separation of nucleic acid.

Two-dimensional diffusion biased by a transverse gravitational force in an asymmetric channel: Reduction to an effective one-dimensional description

We focus on the derivation of a general position-dependent effective diffusion coefficient to describe two-dimensional (2D) diffusion in a narrow and smoothly asymmetric channel of varying width under a transverse gravitational external field, a generalization of the symmetric channel case using the projection method introduced earlier by Kalinay and Percus [P. Kalinay and J. K. Percus, J. Chem. Phys. 122, 204701 (2005)10.1063/1.1899150]. To this end, we project the 2D Smoluchowski equation into an effective one-dimensional generalized Fick-Jacobs equation in the presence of constant force in the transverse direction. The expression for the diffusion coefficient given in Eq. (34) is our main result. This expression is a more general effective diffusion coefficient for narrow 2D channels in the presence of constant transverse force, which contains the well-known previous results for a symmetric channel obtained by Kalinay, as well as the limiting cases when the transverse gravitational external field goes to zero and infinity. Finally, we show that diffusivity can be described by the interpolation formula proposed by Kalinay, D_{0}/[1+(1/4)w^{'2}(x)]^{-η}, where spatial confinement, asymmetry, and the presence of a constant transverse force can be encoded in η, which is a function of channel width (w), channel centerline, and transverse force. The interpolation formula also reduces to well-known previous results, namely, those obtained by Reguera and Rubi [D. Reguera and J. M. Rubi, Phys. Rev. E 64, 061106 (2001)10.1103/PhysRevE.64.061106] and by Kalinay [P. Kalinay, Phys. Rev. E 84, 011118 (2011)10.1103/PhysRevE.84.011118].

Ion transport in electrolytes of dielectric nanodevices

Ion transport in electrolytes with nanoscale confinements is of great importance in many fields such as nanofluidics and electrochemical energy devices. The mobility and conductance for ions are often described by the classical Debye-Hückel-Onsager (DHO) theory but this theory fails for ions near dielectric interfaces. We propose a generalized DHO theory by using the Wentzel-Kramers-Brillouin techniques for the solution of the Onsager-Fuoss equation with variable coefficients. The theory allows to quantitatively measure physical quantities of ion transport in nanodevices and is demonstrated to well explain the abnormal increase or decrease of the ionic mobility tuned via the dielectric mismatch. By numerical calculations, our theory unravels the crucial role of the size of confinements and the ionic concentration on the ion transport, and demonstrates that the dielectric polarization can provide a giant enhancement on the conductance of electrolytes in nanodevices. This mechanism provides a practical guide for related nanoscale technologies with controllable transport properties.

Shear-Thinning in Oligomer Melts-Molecular Origins and Applications

We investigate the molecular origin of shear-thinning in melts of flexible, semiflexible and rigid oligomers with coarse-grained simulations of a sheared melt. Entanglements, alignment, stretching and tumbling modes or suppression of the latter all contribute to understanding how macroscopic flow properties emerge from the molecular level. In particular, we identify the rise and decline of entanglements with increasing chain stiffness as the major cause for the non-monotonic behaviour of the viscosity in equilibrium and at low shear rates, even for rather small oligomeric systems. At higher shear rates, chains align and disentangle, contributing to shear-thinning. By performing simulations of single chains in shear flow, we identify which of these phenomena are of collective nature and arise through interchain interactions and which are already present in dilute systems. Building upon these microscopic simulations, we identify by means of the Irving-Kirkwood formula the corresponding macroscopic stress tensor for a non-Newtonian polymer fluid. Shear-thinning effects in oligomer melts are also demonstrated by macroscopic simulations of channel flows. The latter have been obtained by the discontinuous Galerkin method approximating macroscopic polymer flows. Our study confirms the influence of microscopic details in the molecular structure of short polymers such as chain flexibility on macroscopic polymer flows.

Exploring an In-Plane Graphene and Hexagonal Boron Nitride Array for Separation of Single Nucleotides

Regular nanofluidic sieving structures are emerging as rapid and compatible on-chip techniques for biomolecular separation. Although the current nanofluidic sieving devices, mostly based on three-dimensional nanostructures, have achieved a separation resolution of ∼20 nm, it is still far away from single-nucleotide resolution. Using all-atom molecular dynamics simulations, here we demonstrate a two-dimensional (2D) nanofluidic sieve consisting of an in-plane graphene (GRA)/hexagonal boron nitride (h-BN) nanoarray, which enables ultrahigh resolution in the successful separation of four types of single nucleotides. The alternating GRA and h-BN stripes can create size-dependent energy barriers for adsorbed nucleotides, which provide a strong modulation for their mobility, thus causing distinct band separations on the 2D surface. We further show that this 2D sieve is particularly sensitive when the sample dimensions are within the range from a half period to one period of the nanoarray. This 2D sieving structure may shed light on the development of lab-on-a-chip sequencing in the future.

Detection and Separation of Single-Stranded DNA Fragments Using Solid-State Nanopores

Many biological assays require effectively and sensitively sorting DNA fragments. Here, we demonstrate a solid-state nanopore platform for label-free detection and separation of short single-stranded DNA (ssDNA) fragments (<100 nt), based on their length-dependent translocation behaviors. Our experimental data show that each sized pore has a passable length threshold. The negative charged ssDNA fragments with length smaller than the threshold can be electrically facilitated driven through the correspondingly sized nanopore along the direction of electric field. In addition, the passable length threshold increases with the pore size enlarging. As a result, this phenomenon is able to be applicable for the controllable selectivity of ssDNA by tuning nanopore size, and the selectivity limitation is up to 30nt. Numerical simulation results indicate the translocation direction of ssDNA is governed by the competition of electroosmosis and electrophoresis effects on the ssDNA and offer the relationship between passable length threshold and pore size.

Pulsed electric field-assisted overlimiting current enhancement through a perm-selective membrane

Overlimiting current through a perm-selective membrane has been actively researched not only for the fundamental advancement of electrokinetics but also for energy/environmental applications such as electrodialysis, fuel cells, etc. In particular, various strategies were reported for the enhancement of overlimiting current because these applications demand efficient mass transport through the membrane. In this work, we presented in operando visualization and rigorous numerical study for the overlimiting current density enhancement using a pulsed electric field which is one of the most cost-effective parameters to be externally controlled. We clearly demonstrated that the current density had a peak value as a function of the pulse frequency and would suggest its correlation to a concentration profile and diffusion relaxation time ([small tau, Greek, tilde]diff). As the pulse frequency was chosen which is similar to ([small tau, Greek, tilde]diff)-1, the concentration profiles (i.e. established current paths) were maintained even in off-state due to remnant current paths helping the fast ion transportation. The fundamental evidence presented in this work would provide a strategical design of a perm-selective membrane system for a higher mass transportation efficiency.

Effective diffusivity of a Brownian particle in a two-dimensional periodic channel of abruptly alternating width

We study diffusion of a Brownian particle in a two-dimensional periodic channel of abruptly alternating width. Our main result is a simple approximate analytical expression for the particle effective diffusivity, which shows how the diffusivity depends on the geometric parameters of the channel: lengths and widths of its wide and narrow segments. The result is obtained in two steps: first, we introduce an approximate one-dimensional description of particle diffusion in the channel, and second, we use this description to derive the expression for the effective diffusivity. While the reduction to the effective one-dimensional description is standard for systems of smoothly varying geometry, such a reduction in the case of abruptly changing geometry requires a new methodology used here, which is based on the boundary homogenization approach to the trapping problem. To test the accuracy of our analytical expression and thus establish the range of its applicability, we compare analytical predictions with the results obtained from Brownian dynamics simulations. The comparison shows excellent agreement between the two, on condition that the length of the wide segment of the channel is equal to or larger than its width.

Entropic stochastic resonance induced by a transverse driving force

The phenomenon of entropic stochastic resonance (ESR) is investigated with the presence of a time-periodic force in the transverse direction. Simulation results manifest that the ESR can survive even if there is no static bias force in any direction, just if a transverse driving field is applied. In the weak noise region, the transverse driving force leads to a giant-suppression of the escape rate from one well to another, i.e. the entropic trapping. The increase in noise intensity will eliminate this suppression and induce the ESR phenomenon. An alternative quantity, called the mean free flying time, is also proposed to characterize the ESR as well as the conventional spectral power amplification. The ESR can be modulated conveniently by the transverse periodic force, which implies an alternative method for controlling the dynamics of small-scale systems. This article is part of the theme issue 'Vibrational and stochastic resonance in driven nonlinear systems (part 2)'.

Integration of sequential analytical processes into sub-100 nm channels: volumetric sampling, chromatographic separation, and label-free molecule detection

The progress of nanotechnology has developed nanofluidic devices utilizing nanochannels with a width and/or depth of sub-100 nm (10¹ nm channels), and several experiments have been implemented in ultra-small spaces comparable to DNAs and proteins. However, current experiments utilizing 10¹ nm channels focus on a single function or operation; integration of multiple analytical operations into 10¹ nm channels using nanofluidic circuits and fluidic control has yet to be realized despite the advantage of nanochannels. Herein, we report the establishment of a label-free molecule detection method for 10¹ nm channels and demonstration of sequential analytical processes using integrated nanofluidic devices. Our absorption-based detection method called photothermal optical diffraction (POD) enables non-invasive label-free molecule detection in 10¹ nm channels for the first time, and the limit of detection (LOD) of 1.8 μM is achieved in 70 nm wide and deep nanochannels, which corresponds to 7.5 molecules in the detection volume of 7 aL. As a demonstration of sampling in 10¹ nm channels, aL-fL volumetric sampling is performed using 90 nm deep cross-shaped nanochannels and pressure-driven fluidic control from three directions. Finally, the POD and volumetric sampling are combined with nanochannel chromatography, and separation analysis in 10¹ nm channels is demonstrated. The experimental results reported in this paper will contribute to the advances in 10¹ nm fluidic devices which have the potential to provide a novel platform for chemical/biological analyses.

Brownian Sieving Effect for Boosting the Performance of Microcapillary Hydrodynamic Chromatography. Proof of Concept

Microcapillary hydrodynamic chromatography (MHDC) is a well-established technique for the size-based separation of suspensions and colloids, where the characteristic size of the dispersed phase ranges from tens of nanometers to micrometers. It is based on hindrance effects which prevent relatively large particles from experiencing the low velocity region near the walls of a pressure-driven laminar flow through an empty microchannel. An improved device design is here proposed, where the relative extent of the low velocity region is made tunable by exploiting a two-channel annular geometry. The geometry is designed so that the core and the annular channel are characterized by different average flow velocities when subject to one and the same pressure drop. The channels communicate through openings of assigned cut-off length, say A. As they move downstream the channel, particles of size bigger than A are confined to the core region, whereas smaller particles can diffuse through the openings and spread throughout the entire cross section, therein attaining a spatially uniform distribution. By using a classical excluded-volume approach for modeling particle transport, we perform Lagrangian-stochastic simulations of particle dynamics and compare the separation performance of the two-channel and the standard (single-channel) MHDC. Results suggest that a quantitative (up to thirtyfold) performance enhancement can be obtained at operating conditions and values of the transport parameters commonly encountered in practical implementations of MHDC. The separation principle can readily be extended to a multistage geometry when the efficient fractionation of an arbitrary size distribution of the suspension is sought.

Thermoplastic nanofluidic devices for identifying abasic sites in single DNA molecules

DNA damage can take many forms such as double-strand breaks and/or the formation of abasic (apurinic/apyrimidinic; AP) sites. The presence of AP sites can be used to determine therapeutic efficacy of many drugs, such as doxorubicin. While there are different assays to search for DNA damage, they are fraught with limitations, such as the need for large amounts of DNA secured from millions of cells. This is challenging due to the growing importance of using liquid biopsies as a source of biomarkers for many in vitro diagnostic assays. To accommodate the mass limits imposed by the use of liquid biopsies, we report a single-molecule DNA damage assay that uses plastic nanofluidic chips to stretch DNA to near its full contour length when the channel dimensions (width and depth) are near the persistence length (∼50 nm) of double-stranded (ds) DNA. The nanofluidic chip consisted of input funnels for high loading efficiency of single DNA molecules, entropic traps to store the DNA and simultaneously load a series of nanochannels for high throughput processing, and an array of stretching nanochannels to read the AP sites. Single dsDNA molecules, which were labeled with an intercalating dye and a biotinylated aldehyde reactive probe (bARP), could be parked in the stretching nanochannels, where the AP sites were read directly using a dual-color fluorescence microscope equipped with an EMCCD camera. One color of the microscope was used to read the DNA length and the second color detected the AP sites. The nanofluidic chip was made from thermoplastics via nanoimprint lithography, which obviated the need for direct writing the devices in glass or quartz using focused ion beam milling. We show that we can read the frequency of AP sites in single dsDNA molecules with the frequency of AP sites determined by associating fluorescently-labeled streptavidin with bARP through a biotin/streptavidin complex.

Driven Transport of Dilute Polymer Solutions through Porous Media Comprising Interconnected Cavities

Driven transport of dilute polymer solutions through porous media has been simulated using a recently proposed novel dissipative particle dynamics method satisfying the no-penetration and no-slip boundary conditions. The porous media is an array of overlapping spherical cavities arranged in a simple cubic lattice. Simulations were performed for linear, ring, and star polymers with 12 arms for two cases with the external force acting on (I) both polymer and solvent beads to model a pressure-driven flow; (II) polymer beads only, similar to electrophoresis. When the external force is in the direction of a principal axis, the extent of change in the polymers’ conformation and their alignment with the driving force is more significant for case I. These effects are most pronounced for linear chains, followed by rings and stars at the same molecular weight. Moreover, the polymer mean velocity is affected by its molecular weight and architecture as well as the direction and strength of the imposed force.

Diffusion of colloidal particles in model porous media

Using video microscopy and simulations, we study the long-time diffusion of colloidal tracers in a wide range of model porous media composed of frozen colloidal matrices with different structures. We found that the diffusion coefficient of a tracer can be quantitatively determined by the structures of porous media. In particular, a universal scaling relation exists between the dimensionless diffusion coefficient of the tracer and the structural entropy of the system. This universal scaling relation is an extension of the scaling law previously discovered for the diffusion of colloidal particles in fluctuating media.

The translocation dynamics of the polymer through a conical pore: Non-stuck, weak-stuck, and strong-stuck modes

The external voltage-driven polymer translocation through a conical pore (with a large opening at the entry and a small tip at the exit) is studied by using the Langevin dynamics simulation in this paper. The entire translocation process is divided into an approaching stage and a threading stage. First, the approaching stage starts from the polymer entering the large opening and ends up at a terminal monomer reaching the pore tip. In this stage, the polymer will undergo the conformation adjustment to fit the narrowed cross-sectional area of the pore, leading to three approaching modes: the non-stuck mode with a terminal monomer arriving at the pore tip smoothly, the weak-stuck mode for the polymer stuck inside the pore for a short duration with minor conformational adjustments, and the strong-stuck mode with major conformational changes and a long duration. The approaching times (the duration of the approaching stage) of the three approaching modes show different behavior as a function of the pore apex angle. Second, the threading stage describes that the polymer threads through the pore tip with a linear fashion. In this stage, an increase in the apex angle causes the reduction of the threading time (the duration of the threading stage) due to the increase in the driving force with the apex angle at the tip. Moreover, we also find that with the increase in the apex angle or the polymer length, the polymer threading dynamics will change from the quasi-equilibrium state to the non-equilibrium state.

Free energy and segregation dynamics of two channel-confined polymers of different lengths

Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere polymers under confinement in a cylindrical channel. We focus on the effects of using polymers of different lengths. We measure the variation of the conformational free energy, F, with the center-of-mass separation distance, λ. The simulations reveal four different separation regimes, characterized by different scaling properties of the free energy with respect to the polymer lengths and the channel diameter, D. We propose a regime map in which the state of the system is determined by the values of the quantities N_{2}/N_{1} and λ/(N_{1}+N_{2})D^{-β}, where N_{1} and N_{2} are the polymer lengths, and where β≈0.64. The observed scaling behavior of F(λ) in each regime is in reasonable agreement with predictions using a simple theoretical model. In addition, we use MC dynamics simulations to study the segregation dynamics of initially overlapping polymers by measurement of the incremental mean first-passage time with respect to λ. For systems characterized by a wide range of λ in which a short polymer is nested within a longer one, the segregation dynamics are close to that expected for two noninteracting one-dimensional random walkers undergoing unbiased diffusion. When the free-energy gradient is large, segregation is rapid and characterized by out-of-equilibrium effects.

Dynamics of a driven confined polyelectrolyte solution

The transport of polyelectrolytes confined by oppositely charged surfaces and driven by a constant electric field is of interest in studies of DNA separation according to size. Using molecular dynamics simulations that include the surface polarization effect, we find that the mobilities of the polyelectrolytes and their counterions change non-monotonically with the confinement surface charge density. For an optimum value of the confinement charge density, efficient separation of polyelectrolytes can be achieved over a wide range of polyelectrolyte charge due to the differential friction imparted by oppositely charged confinement on the polyelectrolyte chains. Furthermore, by altering the placement of the charged confinement counterions, enhanced polyelectrolyte separation can be achieved by utilizing the surface polarization effect due to dielectric mismatch between the media inside and outside the confinement.

Continuous and spontaneous nanoparticle separation by diffusiophoresis

The separation of nanoparticles has drawn critical attention in various microfluidic applications including chemical analysis, diagnostics and environmental monitoring. Thus, a number of nanoparticle separation methods have been extensively proposed. However, most of the conventional methods require complicated structured devices, expensive manufacturing processes, and external power sources. While a spontaneous diffusiophoretic separation device based on an ion exchange mechanism could overcome such drawbacks, the recovery of separated particles and the inevitable development of an acidic environment due to the release of H+ from the cation exchange membrane limit its practical applicability. Therefore, in this work, we present a simple but robust nanoparticle separation method based on spontaneously induced diffusiophoresis, which is operated in a continuous manner to overcome the limitations of conventional methods. First, we confirmed that the particle exclusion distance followed the previously developed scaling law of diffusiophoresis. Consequently, we demonstrated the separation of nanoparticles of 40 nm, 200 nm and 2 μm diameter by utilizing the fact that the exclusion distances of various particles were proportional to their diffusiophoretic mobility. Furthermore, the use of Tris buffer increased the diffusiophoretic migration of nanoparticles due to the enhanced concentration gradient, and enabled the produced solution to be compatible with pH-sensitive bio-samples. Therefore, we expect this continuous and spontaneous diffusiophoretic separation platform to be useful in practical applications for analyzing various nano-meter scale bio-particles.

Advanced Top-Down Fabrication for a Fused Silica Nanofluidic Device

Nanofluidics have recently attracted significant attention with regard to the development of new functionalities and applications, and producing new functional devices utilizing nanofluidics will require the fabrication of nanochannels. Fused silica nanofluidic devices fabricated by top-down methods are a promising approach to realizing this goal. Our group previously demonstrated the analysis of a living single cell using such a device, incorporating nanochannels having different sizes (102-103 nm) and with branched and confluent structures and surface patterning. However, fabrication of geometrically-controlled nanochannels on the 101 nm size scale by top-down methods on a fused silica substrate, and the fabrication of micro-nano interfaces on a single substrate, remain challenging. In the present study, the smallest-ever square nanochannels (with a size of 50 nm) were fabricated on fused silica substrates by optimizing the electron beam exposure time, and the absence of channel breaks was confirmed by streaming current measurements. In addition, micro-nano interfaces between 103 nm nanochannels and 101 μm microchannels were fabricated on a single substrate by controlling the hydrophobicity of the nanochannel surfaces. A micro-nano interface for a single cell analysis device, in which a nanochannel was connected to a 101 μm single cell chamber, was also fabricated. These new fabrication procedures are expected to advance the basic technologies employed in the field of nanofluidics.

Advances in Label-Free Detections for Nanofluidic Analytical Devices

Nanofluidics, a discipline of science and engineering of fluids confined to structures at the 1-1000 nm scale, has experienced significant growth over the past decade. Nanofluidics have offered fascinating platforms for chemical and biological analyses by exploiting the unique characteristics of liquids and molecules confined in nanospaces; however, the difficulty to detect molecules in extremely small spaces hampers the practical applications of nanofluidic devices. Laser-induced fluorescence microscopy with single-molecule sensitivity has been so far a major detection method in nanofluidics, but issues arising from labeling and photobleaching limit its application. Recently, numerous label-free detection methods have been developed to identify and determine the number of molecules, as well as provide chemical, conformational, and kinetic information of molecules. This review focuses on label-free detection techniques designed for nanofluidics; these techniques are divided into two groups: optical and electrical/electrochemical detection methods. In this review, we discuss on the developed nanofluidic device architectures, elucidate the mechanisms by which the utilization of nanofluidics in manipulating molecules and controlling light-matter interactions enhances the capabilities of biological and chemical analyses, and highlight new research directions in the field of detections in nanofluidics.

pH-regulated thermo-driven nanofluidics for nanoconfined mass transport and energy conversion

Bioinspired nanochannels whose functions are similar to those of the biological prototypes attract increasing attention due to their potential applications in signal transmission, mass transport, energy conversion, etc. Up to now, however, it is still a challenge to extract low-grade waste heat from the ambient environment in an aqueous solution. Herein, a thermo-driven nanofluidic system was developed to extract low-grade waste heat efficiently based on directed ionic transport at a micro-/nanoscale. A steady streaming current increases linearly with the temperature gradient, achieving as high as 14 nA at a temperature gradient of 47.5 °C (δT = 47.5 °C) through a 0.5 cm2 porous membrane (106 cm-2). And an unexpected theoretical power of 25.48 pW using a single nanochannel at a temperature difference of 40 °C has been achieved. This bioinspired multifunctional system broadens thermal energy recovery and will accelerate the evolution of nanoconfined mass transport for practical applications.

Single-step electrohydrodynamic separation of 1-150 kbp in less than 5 min using homogeneous glass/adhesive/glass microchips

Electrohydrodynamic migration, which is based on hydrodynamic actuation with an opposing electrophoretic force, enables the separation of DNA molecules of 3-100 kbp in glass capillary within 1 h. Here, we wish to enhance these performances using microchip technologies. This study starts with the fabrication of microchips with uniform surfaces, as motivated by our observation that band splitting occurs in microchannels made out of heterogeneous materials such as glass and silicon. The resulting glass-adhesive-glass microchips feature the highest reported bonding strength of 11 MPa for such materials (115 kgf/cm²), a high lateral resolution of critical dimension 5 μm, and minimal auto-fluorescence. These devices enable us to report the separation of 13 DNA bands in the size range of 1-150 kbp in one experiment of 5 min, i.e. 13 times faster than with capillary. In turn, we observe that bands split during electrohydrodynamic migration in heterogeneous glass-silicon but not in homogeneous glass-adhesive-glass microchips. We suggest that this effect arises from differential Electro-Osmotic Flow (EOF) in between the upper and lower walls of heterogeneous channels, and provide evidence that this phenomenon of differential EOF causes band broadening in electrophoresis during microchip electrophoresis. We finally prove that our electrohydrodynamic separation compares very favorably to microchip technologies in terms of resolution length and features the broadest analytical range reported so far.

Confined diffusion in a random Lorentz gas environment

We study the diffusive behavior of biased Brownian particles in a two dimensional confined geometry filled with the freezing obstacles. The transport properties of these particles are investigated for various values of the obstacle density η and the scaling parameter f, which is the ratio of work done to the particles to available thermal energy. We show that, when the thermal fluctuations dominate over the external force, i.e., small f regime, particles get trapped in the given environment when the system percolates at the critical obstacle density η_{c}≈1.2. However, as f increases, we observe that particle trapping occurs prior to η_{c}. In particular, we find a relation between η and f which provides an estimate of the minimum η up to a critical scaling parameter f_{c} beyond which the Fick-Jacobs description is invalid. Prominent transport features like nonmonotonic behavior of the nonlinear mobility, anomalous diffusion, and greatly enhanced effective diffusion coefficient are explained for various strengths of f and η. Also, it is interesting to observe that particles exhibit different kinds of diffusive behaviors, i.e., subdiffusion, normal diffusion, and superdiffusion. These findings, which are genuine to the confined and random Lorentz gas environment, can be useful to understand the transport of small particles or molecules in systems such as molecular sieves and porous media, which have a complex heterogeneous environment of the freezing obstacles.

On interfacial viscosity in nanochannels

Capillary driven transport of liquids in nanoscopic channels is an omnipresent phenomenon in nature and technology including fluid flow in the human body and plants, drug delivery, nanofluidic devices, and energy/water systems. However, the kinetics of this mass transport mechanism remains in question as the well-known Lucas-Washburn (LW) model predicts significantly faster flow rates compared to the experimental observations. We here showed the role of interfacial viscosity in capillary motion slowdown in nanochannels through a combination of experimental, analytical and molecular dynamics techniques. We showed that the slower liquid flow is due to the formation of a thin liquid layer adjacent to the channel walls with a viscosity substantially greater than the bulk liquid. By incorporating the effect of the interfacial layer, we presented a theoretical model that accurately predicts the capillarity kinetics in nanochannels of different heights. Non-equilibrium molecular dynamics simulation confirmed the obtained interfacial viscosities. The viscosities of isopropanol and ethanol within the interfacial layer were 9.048 mPa s and 4.405 mPa s, respectively (i.e. 279% and 276% greater than their bulk values). We also showed that the interfacial layers are 6.4 nm- and 5.3 nm-thick for isopropanol and ethanol, respectively.

Trapping, gliding, vaulting: transport of semiflexible polymers in periodic post arrays

The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the dynamics of semiflexible polymers under the influence of an imposed flow in a structured two-dimensional lattice serving as an idealization of a porous medium. This problem has received much attention in the limit of reptation and for long-chain polymer molecules such as DNA that are transported through micropost arrays for electrophoretic chromatographic separation. In contrast to long entropic molecules, the dynamics of elastic polymers results from a combination of scattering with the obstacles and flow-induced buckling instabilities. We identify three dominant modes of transport that involve trapping, gliding and vaulting of the polymers around the obstacles, and we reveal their essential features using tools from dynamical systems theory. The interplay of these scattering dynamics with transport and deformations in the imposed flow results in the long-time asymptotic dispersion of the center of mass, which we quantify in terms of a hydrodynamic dispersion tensor. We then discuss a simple yet efficient chromatographic device that exploits the competition between different modes of transport to sort filaments in a dilute suspension according to their lengths.

Three-Dimensional Single Particle Tracking and Its Applications in Confined Environments

Single particle tracking (SPT) has proven to be a powerful technique in studying molecular dynamics in complicated systems. We review its recent development, including three-dimensional (3D) SPT and its applications in probing nanostructures and molecule-surface interactions that are important to analytical chemical processes. Several frequently used 3D SPT techniques are introduced. Especially of interest are those based on point spread function engineering, which are simple in instrumentation and can be easily adapted and used in analytical labs. Corresponding data analysis methods are briefly discussed. We present several important case studies, with a focus on probing mass transport and molecule-surface interactions in confined environments. The presented studies demonstrate the great potential of 3D SPT for understanding fundamental phenomena in confined space, which will enable us to predict basic principles involved in chemical recognition, separation, and analysis, and to optimize mass transport and responses by structural design and optimization.

Direct Fabrication of Freestanding and Patterned Nanoporous Junctions in a 3D Micro-Nanofluidic Device for Ion-Selective Transport

In the field of micro-nanofluidics, a freestanding configuration of a nanoporous junction is highly demanded to increase the design flexibility of the microscale device and the interfacial area between the nanoporous junction and microchannels, thereby improving the functionality and performance. This work first reports direct fabrication and incorporation of a freestanding nanoporous junction in a microfluidic device by performing an electrolyte-assisted electrospinning process to fabricate a freestanding nanofiber membrane and subsequently impregnating the nanofiber membrane with a nanoporous precursor material followed by a solidification process. This process also enables to readily control the geometry of the nanoporous junction depending on its application. By these advantages, vertically stacked 3D micro-nanofluidic devices with complex configurations are easily achieved. To demonstrate the broad applicability of this process in various research fields, a reverse electrodialysis-based energy harvester and an ion concentration polarization-based preconcentrator are produced. The freestanding Nafion-polyvinylidene fluoride nanofiber membrane (F-NPNM) energy harvester generates a high power (59.87 nW) owing to the enlarged interfacial area. Besides, 3D multiplexed and multi-stacked F-NPNM preconcentrators accumulate multiple preconcentrated plugs that can increase the operating sample volume and the degree of freedom of handling. Hence, the proposed process is expected to contribute to numerous research fields related to micro-nanofluidics in the future.