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Analytical Model for Particle Capture in Nanopores Elucidates Competition among Electrophoresis, Electroosmosis, and Dielectrophoresis.

ABSTRACT: The interaction between nanoparticles dispersed in a fluid and nanopores is governed by the interplay of hydrodynamical, electrical, and chemical effects. We developed a theory for particle capture in nanopores and derived analytical expressions for the capture rate under the concurrent action of electrical forces, fluid advection, and Brownian motion. Our approach naturally splits the average capture time in two terms, an approaching time due to the migration of particles from the bulk to the pore mouth and an entrance time associated with a free-energy barrier at the pore entrance. Within this theoretical framework, we described the standard experimental condition where a particle concentration is driven into the pore by an applied voltage, with specific focus on different capture mechanisms: under pure electrophoretic force, in the presence of a competition between electrophoresis and electroosmosis, and finally under dielectrophoretic reorientation of dipolar particles. Our theory predicts that dielectrophoresis is able to induce capture for both positive and negative voltages. We performed a dedicated experiment involving a biological nanopore (α-hemolysin) and a rigid dipolar dumbbell (realized with a β-hairpin peptide) that confirms the theoretically proposed capture mechanism.

SUBMITTER: Chinappi M

PROVIDER: S-EPMC8016366 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Geometrically Induced Selectivity and Unidirectional Electroosmosis in Uncharged Nanopores.

Project description:Selectivity toward positive and negative ions in nanopores is often associated with electroosmotic flow, the control of which is pivotal in several micro-nanofluidic technologies. Selectivity is traditionally understood to be a consequence of surface charges that alter the ion distribution in the pore lumen. Here we present a purely geometrical mechanism to induce ionic selectivity and electroosmotic flow in uncharged nanopores, and we tested it via molecular dynamics simulations. Our approach exploits the accumulation of charges, driven by an external electric field, in a coaxial cavity that decorates the membrane close to the pore entrance. The selectivity was shown to depend on the applied voltage and becomes completely inverted when reversing the voltage. The simultaneous inversion of ionic selectivity and electric field direction causes a unidirectional electroosmotic flow. We developed a quantitatively accurate theoretical model for designing pore geometry to achieve the desired electroosmotic velocity. Finally, we show that unidirectional electroosmosis also occurs in much more complex scenarios, such as a biological pore whose structure presents a coaxial cavity surrounding the pore constriction as well as a complex surface charge pattern. The capability to induce ion selectivity without altering the pore lumen shape or the surface charge may be useful for a more flexible design of selective membranes.

| S-EPMC9245180 | biostudies-literature

Electroosmosis Dominates Electrophoresis of Antibiotic Transport Across the Outer Membrane Porin F.

Project description:We report that the dynamics of antibiotic capture and transport across a voltage-biased OmpF nanopore is dominated by the electroosmotic flow rather than the electrophoretic force. By reconstituting an OmpF porin in an artificial lipid bilayer and applying an electric field across it, we are able to elucidate the permeation of molecules and their mechanism of transport. This field gives rise to an electrophoretic force acting directly on a charged substrate but also indirectly via coupling to all other mobile ions, causing an electroosmotic flow. The directionality and magnitude of this flow depends on the selectivity of the channel. Modifying the charge state of three different substrates (norfloxacin, ciprofloxacin, and enoxacin) by varying the pH between 6 and 9 while the charge and selectivity of OmpF is conserved allows us to work under conditions in which electroosmotic flow and electrophoretic forces add or oppose. This configuration allows us to identify and distinguish the contributions of the electroosmotic flow and the electrophoretic force on translocation. Statistical analysis of the resolvable dwell times reveals rich kinetic details regarding the direction and the stochastic movement of antibiotics inside the nanopore. We quantitatively describe the electroosmotic velocity component experienced by the substrates and their diffusion coefficients inside the porin with an estimate of the energy barrier experienced by the molecules caused by the interaction with the channel wall, which slows down the permeation by several orders of magnitude.

| S-EPMC7264812 | biostudies-literature

Individual Microparticle Manipulation Using Combined Electroosmosis and Dielectrophoresis through a Si3N4 Film with a Single Micropore.

Project description:Porous dielectric membranes that perform insulator-based dielectrophoresis or electroosmotic pumping are commonly used in microchip technologies. However, there are few fundamental studies on the electrokinetic flow patterns of single microparticles around a single micropore in a thin dielectric film. Such a study would provide fundamental insights into the electrokinetic phenomena around a micropore, with practical applications regarding the manipulation of single cells and microparticles by focused electric fields. We have fabricated a device around a silicon nitride film with a single micropore (2-4 µm in diameter) which has the ability to locally focus electric fields on the micropore. Single microscale polystyrene beads were used to study the electrokinetic flow patterns. A mathematical model was developed to support the experimental study and evaluate the electric field distribution, fluid motion, and bead trajectories. Good agreement was found between the mathematic model and the experimental data. We show that the combination of electroosmotic flow and dielectrophoretic force induced by direct current through a single micropore can be used to trap, agglomerate, and repel microparticles around a single micropore without an external pump. The scale of our system is practically relevant for the manipulation of single mammalian cells, and we anticipate that our single-micropore approach will be directly employable in applications ranging from fundamental single cell analyses to high-precision single cell electroporation or cell fusion.

| S-EPMC8708253 | biostudies-literature

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Understanding Electrophoresis and Electroosmosis in Nanopore Sensing with the Help of the Nanopore Electro-Osmotic Trap.

Project description:Nanopore technology is widely used for sequencing DNA, RNA, and peptides with single-molecule resolution, for fingerprinting single proteins, and for detecting metabolites. However, the molecular driving forces controlling the analyte capture, its residence time, and its escape have remained incompletely understood. The recently developed Nanopore Electro-Osmotic trap (NEOtrap) is well fit to study these basic physical processes in nanopore sensing, as it reveals previously missed events. Here, we use the NEOtrap to quantitate the electro-osmotic and electrophoretic forces that act on proteins inside the nanopore. We establish a physical model to describe the capture and escape processes, including the trapping energy potential. We verified the model with experimental data on CRISPR dCas9-RNA-DNA complexes, where we systematically screened crucial modeling parameters such as the size and net charge of the complex. Tuning the balance between electrophoretic and electro-osmotic forces in this way, we compare the trends in the kinetic parameters with our theoretical models. The result is a comprehensive picture of the major physical processes in nanopore trapping, which helps to guide the experiment design and signal interpretation in nanopore experiments.

| S-EPMC11308919 | biostudies-literature

Modulation of electrophoresis, electroosmosis and diffusion for electrical transport of proteins through a solid-state nanopore.

Project description:Nanopore probing of molecular level transport of proteins is strongly influenced by electrolyte type, concentration, and solution pH. As a result, electrolyte chemistry and applied voltage are critical for protein transport and impact, for example, capture rate (C R), transport mechanism (i.e., electrophoresis, electroosmosis or diffusion), and 3D conformation (e.g., chaotropic vs. kosmotropic effects). In this study, we explored these using 0.5-4 M LiCl and KCl electrolytes with holo-human serum transferrin (hSTf) protein as the model protein in both low (±50 mV) and high (±400 mV) electric field regimes. Unlike in KCl, where events were purely electrophoretic, the transport in LiCl transitioned from electrophoretic to electroosmotic with decreasing salt concentration while intermediate concentrations (i.e., 2 M and 2.5 M) were influenced by diffusion. Segregating diffusion-limited capture rate (R diff) into electrophoretic (R diff,EP) and electroosmotic (R diff,EO) components provided an approach to calculate the zeta-potential of hSTf (ζ hSTf) with the aid of C R and zeta potential of the nanopore surface (ζ pore) with (ζ pore-ζ hSTf) governing the transport mechanism. Scrutinization of the conventional excluded volume model revealed its shortcomings in capturing surface contributions and a new model was then developed to fit the translocation characteristics of proteins.

| S-EPMC8285365 | biostudies-literature

Blood Particle Separation Using Dielectrophoresis in A Novel Microchannel: A Numerical Study.

Project description:ObjectiveWe present a four-branch model of the dielectrophoresis (DEP) method that takes into consideration the inherent properties of particles, including size, electrical conductivity, and permittivity coefficient. By using this model, bioparticles can be continuously separated by the application of only a one-stage separation process.Materials and methodsIn this numerical study, we based the separation process on the differences in the particle sizes. We used the various negative DEP forces on the particles caused by the electrodes to separate them with a high efficiency. The particle separator could separate blood cells because of their different sizes.ResultsBlood cells greater than 12 μm were guided to a special branch, which improved separation efficiency because it prevented the deposition of particles in other branches. The designed device had the capability to separate blood cells with diameters of 2.0 μm, 6.2 μm, 10.0 μm, and greater than 12.0 μm. The applied voltage to the electrodes was 50 V with a frequency of 100 kHz.ConclusionThe proposed device is a simple, efficient DEP-based continuous cell separator. This capability makes it ideal for use in various biomedical applications, including cell therapy and cell separation, and results in a throughput increment of microfluidics devices.

| S-EPMC6874797 | biostudies-literature

An Experimental Study of 3D Electrode-Facilitated Particle Traffic Flow-Focusing Driven by Induced-Charge Electroosmosis.

Project description:In this paper we present a novel microfluidic approach for continuous, rapid and switchable particle concentration, using induced-charge electroosmosis (ICEO) in 3D electrode layouts. Field-effect control on non-linear electroosmosis in the transverse direction greatly facilitates a selective concentration of biological yeast cells from a straight main microchannel into one of the three downstream branch channels in our microfluidic device. For the geometry configuration of 3D driving electrode plates on sidewalls and a 2D planar gate electrode strip on the channel bottom surface, we briefly describe the underlying physics of an ICEO-based particle flow-focusing method, and provide relevant simulation results to show how gate voltage amplitude can be used to guide the motion trajectory of the concentrated particle stream. With a relatively simple geometrical configuration, the proposed microfluidic device provides new possibilities to controllably concentrate micro/nanoparticles in continuous flow by using ICEO, and is suitable for a high-throughput front-end cell concentrator interfacing with various downstream biosensors.

| S-EPMC6412237 | biostudies-literature

Comparison of Capture Hi-C Analytical Pipelines.

Project description:It is now evident that DNA forms an organized nuclear architecture, which is essential to maintain the structural and functional integrity of the genome. Chromatin organization can be systematically studied due to the recent boom in chromosome conformation capture technologies (e.g., 3C and its successors 4C, 5C and Hi-C), which is accompanied by the development of computational pipelines to identify biologically meaningful chromatin contacts in such data. However, not all tools are applicable to all experimental designs and all structural features. Capture Hi-C (CHi-C) is a method that uses an intermediate hybridization step to target and select predefined regions of interest in a Hi-C library, thereby increasing effective sequencing depth for those regions. It allows researchers to investigate fine chromatin structures at high resolution, for instance promoter-enhancer loops, but it introduces additional biases with the capture step, and therefore requires specialized pipelines. Here, we compare multiple analytical pipelines for CHi-C data analysis. We consider the effect of retaining multi-mapping reads and compare the efficiency of different statistical approaches in both identifying reproducible interactions and determining biologically significant interactions. At restriction fragment level resolution, the number of multi-mapping reads that could be rescued was negligible. The number of identified interactions varied widely, depending on the analytical method, indicating large differences in type I and type II error rates. The optimal pipeline depends on the project-specific tolerance level of false positive and false negative chromatin contacts.

| S-EPMC8859814 | biostudies-literature

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