Search Results (11)

Simulations of the Brownian dynamics of diffusing particles in complex environments provide important information about the characteristics of the medium and the properties of biological processes. Notable examples include the diffusion of ions and macromolecular solutes through channels of varying cross-section, such as pores in biological membranes, living tissues, zeolites, carbon nanotubes, and synthetic porous materials. In these systems, the observed diffusion can exhibit anomalous behavior characterized by a nonlinear increase in the mean squared displacement. In this article, we present a toy model of the diffusion of rod-shaped particles through a narrowing, conical pore with a trapezoidal longitudinal cross-section. Particles of different sizes undergo a random walk due to interactions with the environment (modeled as noise). We study how the diffusion properties change with particle size as a function of pore width. The numerical analysis of diffusion-driven transport through narrowing conical channels reveals its effective subdiffusive, i.e., anomalous, character. Full article

Cardiolipin is one of the main phospholipid components of Staphylococcus aureus membranes. This lipid is found at varying concentrations in the bilayer, depending on the growth stage of the bacteria, and as a response to environmental stress. Cardiolipin is an anionic phospholipid with four acyl chains, which modulates the bending properties of the membrane due to its inverted conical shape. It has been shown to inhibit the pore forming activity of several antimicrobial peptides, in general doubling the peptide concentration needed to induce leakage. Here we find that the short snake-derived antimicrobial peptide ATRA-1 is inhibited by several orders of magnitude in the presence of cardiolipin in saturated membranes (DMPG) compared to the human cathelicidin LL-37, which is only inhibited two-fold in its leakage-inducing concentration. The ATRA-1 is too short to span the membrane and its leakage activity is likely related to detergent-like alterations of bilayer structure. Fluorescence spectroscopy shows only a minor effect on ATRA-1 binding to DMPG membranes due to the presence of cardiolipin. However, FTIR spectroscopy shows that the acyl chain structure of DMPG membranes, containing cardiolipin, become more organized in the presence of ATRA-1, as reflected by an increase in the gel to liquid-crystalline phase transition temperature. Instead, a depression in the melting temperature is induced by ATRA-1 in DMPG in the absence of cardiolipin. In comparison, LL-37 induces a depression of the main phase transition of DMPG even in the presence of cardiolipin. These data suggest that cardiolipin inhibits the penetration of ATRA-1 into the membrane core, impeding its capacity to disrupt lipid packing. Full article

Routinely, in membrane technology, the decay from radioactive particles or the bombardment of ions with MeV energy per nucleon have been employed for the production of narrow and long pores in membranes. Presently, the ion lithography is proposed to make the fabrication cost more affordable. It is prospective for the use of medium capacity accelerators making more feasible the fabrication of customized membranes. Thin polyethylene terephthalate foils have been patterned using 12 MeV O⁵⁺ ions and then processed to obtain good aspect ratio ion track pores in membranes. Pores of micrometric diameter with the following profiles were fabricated in the membranes: truncated cone, double conical, ideal cone, and cylindrical. Monitoring of the shape and size of pores has been attempted with a combination of Scanning Transmission Ion Microscope and a newly designed simulation program. This study is focused on the use of low-energy ions, accomplished in all laboratories, for the fabrication of membranes where the pores are not randomly traced and exhibit higher surface density and negligible overlapping than in membranes commonly manufactured. The good reproducibility and the ordered pore locations can be potentially utilized in applications such as microfluidics and organ-on-chip microsystems, where cells growing over porous substrates are used in simulation of biological barriers and transport processes. Full article

A simultaneous analytical method, which used LC/MSMS for imidazolinone herbicides from livestock products (egg, milk, beef, pork, and chicken) for monitoring, was developed with a QuEChERS preparation. A weighed sample (5 g) in a 50 mL conical tube was added to 0.1 M potassium phosphate dibasic solution (5 mL) and shaken for 10 min. After shaking, 0.5 mL of 6 N HCl and 5 mL of acetonitrile were added, and this solution was shaken for 10 min. Additionally, QuEChERS extraction salts (original method, 4 g MgSO₄, 1 g NaCl) were added to the sample in a 50 mL conical tube. The mixture was strongly shaken for 1 min and centrifuged at 3000× g for 10 min. The acetonitrile layer was purified with dSPE (150 mg MgSO₄, 25 mg C₁₈) and was centrifuged at 13,000× g for 5 min. The supernatant was filtered with a membrane filter (pore size: 0.2 μm) before analysis. The ME (%, matrix effect) range for almost all analytes was −6.56 to 7.11%. MLOD (method limit of detection) and MLOQ (method limit of quantitative) values were calculated by the S/N ratio. MLOQs were 0.01 mg/kg. The linear correlation coefficients (R²) were >0.99 with the range of 0.5~25 μg/kg for all of the imidazolinone herbicides. The recoveries (of imidazolinone herbicides) were in the range of 76.1~110.6% (0.01 mg/kg level), 89.2~97.1% (0.1 mg/kg level), and 94.4~104.4% (0.5 mg/kg level). These are within the validation criteria (to recover 70–120% with RSD <20%). The method demonstrated the simple, rapid, high throughput screening and quantitative analysis of imidazolinone herbicide residues for monitoring in livestock products. Full article

Artificial membranes with conical pores and controllable thickness reveal ionic-transport capabilities that are superior compared with those offered by cylindrical pores. By simulating the translocation of an abstract chain-like body through a conical pore in a membrane with a variable thickness, we formulate a statistical model of the translocation time $\tau$. Our rough model encodes the biochemical details of a given real chain-like molecule as evolving sequences of the allowed chain-like body’s conformations. In our simulation experiments, we focus primarily on pore geometry and kinetic aspects of the translocation process. We study the impact of the membrane thickness L, and both conical-pore diameters ${\varphi }_{cis},{\varphi }_{trans}$ on the probability distribution of $\tau$. We have found that for all considered simulation setups, the randomness of $\tau$ is accurately described by the family of Moyal distributions while its expected value $⟨\tau ⟩$ is proportional to $L^{\xi }$, with $\xi$ being dependent on ${\varphi }_{cis},{\varphi }_{trans}$. Full article

The micro/nanocone structures of noble metals play a critical role as heterogeneous electrocatalysts that provide excellent activity. We successfully fabricated platinum cones by electrodeposition using non-penetrated porous membranes as templates. This method involved the preparation of template membranes by the swift-heavy-ion irradiation of commercially available polycarbonate films and subsequent chemical etching in an aqueous NaOH solution. The surface diameter, depth, aspect ratio and cone angle of the resulting conical pores were controlled in the ranges of approximately 70–1500 nm, 0.7–11 μm, 4–12 and 5–13°, respectively, by varying the etching conditions, which finally produced size- and shape-controlled platinum cones with nanotips. In order to demonstrate the electrocatalytic activity, electrochemical measurements were performed for the ethanol oxidation reaction. The oxidation activity was found to be up to 3.2 times higher for the platinum cone arrays than for the platinum plate. Ion-track etching combined with electrodeposition has the potential to be an effective method for the fabrication of micro/nanocones with high electrocatalytic performance. Full article

Synthetic membranes containing asymmetrically shaped pores have been shown to rectify the ionic current flowing through the membrane. Ion-current rectification means that such membranes produce nonlinear current–voltage curves analogous to those observed with solid-state diode rectifiers. In order to observe this ion-current rectification phenomenon, the asymmetrically shaped pores must have pore-wall surface charge. Pore-wall surface charge also allows for electroosmotic flow (EOF) to occur through the membrane. We have shown that, because ion-current is rectified, EOF is likewise rectified in such membranes. This means that flow through the membrane depends on the polarity of the voltage applied across the membrane, one polarity producing a higher, and the opposite producing a lower, flow rate. As is reviewed here, these ion-current and EOF rectification phenomena are being used to develop new sensing technologies. Results obtained from an ion-current-based sensor for hydrophobic cations are reviewed. In addition, ion-current and EOF rectification can be combined to make a new type of device—a chemoresponsive nanofluidic pump. This is a pump that either turns flow on or turns flow off, when a specific chemical species is detected. Results from a prototype Pb²⁺ chemoresponsive pump are also reviewed here. Full article

A biosensor formed by a combination of silicon (Si) micropore and graphene nanohole technology is expected to act as a promising device structure to interrogate single molecule biopolymers, such as deoxyribonucleic acid (DNA). This paper reports a novel technique of using a focused ion beam (FIB) as a tool for direct fabrication of both conical-shaped micropore in Si₃N₄/Si and a nanohole in graphene to act as a fluidic channel and sensing membrane, respectively. The thinning of thick Si substrate down to 50 µm has been performed prior to a multi-step milling of the conical-shaped micropore with final pore size of 3 µm. A transfer of graphene onto the fabricated conical-shaped micropore with little or no defect was successfully achieved using a newly developed all-dry transfer method. A circular shape graphene nanohole with diameter of about 30 nm was successfully obtained at beam exposure time of 0.1 s. This study opens a breakthrough in fabricating an integrated graphene nanohole and conical-shaped Si micropore structure for biosensor applications. Full article

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

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

Water transport through aquaporin water channels occurs extensively in cell membranes. Hourglass-shaped (biconical) pores resemble the geometry of these aquaporin channels and therefore attract much research attention. We assumed that hourglass-shaped nanopores are capable of high water permeation like biological aquaporins. In order to prove the assumption, we investigated nanoscale water transport through a model hourglass-shaped pore using molecular dynamics simulations while varying the angle of the conical entrance and the total nanopore length. The results show that a minimal departure from optimized cone angle (e.g., 9° for 30 Å case) significantly increases the osmotic permeability and that there is a non-linear relationship between permeability and the cone angle. The analysis of hydrodynamic resistance proves that the conical entrance helps to reduce the hydrodynamic entrance hindrance. Our numerical and analytical results thus confirm our initial assumption and suggest that fast water transport can be achieved by adjusting the cone angle and length of an hourglass-shaped nanopore. Full article