We introduce an implicit solvent Molecular Dynamics approach for calculating ionic fluxes through narrow nano-pores and transmembrane channels. The method relies on a dual-control- volume grand-canonical molecular dynamics (DCV-GCMD) simulation and the analytical solution for the electrostatic potential inside a cylindrical nano-pore recently obtained by Levin [Europhys. Lett., 76, 163 (2006)]. The theory is used to calculate the ionic fluxes through an artificial trans-membrane c hannel which mimics the antibacterial gramicidin A channel. Both current-voltage and current-concentration relations are calculated under various experimental conditions. We show that our results are comparable to the characteristics associated to the gramicidin A pore, specially the existence of two binding sites inside the pore and the observed saturation in the current-concentration profiles.
Aquaporins (AQPs) are a family of transmembrane channels that are found from archaea, eubacteria, and fungi kingdoms to plants and animals. These proteins play a major role in water and small solutes transport across biological cell membranes and maintain the osmotic balance of living cells. In this sense, many works in recent years have been devoted to understanding their behavior, including in plants, where 5 major groups of AQPs have been identified, whose physiological function details still have open questions waiting for an answer. In this direction, we observed in the literature very fe…
The optical polarimetry technique is used to explore molecular ordering of nematic liquid crystals 5FPFFPP3 embedded in parallel cylindrical channels of alumina membranes with pore walls covered by a SE-1211 polymer film enhancing normal anchoring. A chemical film deposition from organic solution apparently results in inhomogeneous coverage with local islands on the channels walls. Accordingly, a coexistence of differently ordered LC regions (nanodomains), characterized by positive and negative anisotropy, results in a weak effective (average) optical birefringence. Repeated polymer deposition…
Mixed surfactant systems with strongly bound counterions show many interesting phases such as the random mesh phase consisting of a disordered array of defects (water-filled nano-pores in the bilayers). The present study addresses the non-equilibrium phase transition of the random mesh phase under shear to an ordered mesh phase with a high degree of coherence between nano-pores in three-dimension. In-situ small-angle synchrotron X-ray study under different shear stress conditions shows sharp Bragg peaks in the X-ray diffraction, successfully indexed to the rhombohedral lattice with R$\bar{3}$m…
We review recent progress on the theory of dynamics of polymer translocation through a nanopore based on the iso-flux tension propagation (IFTP) theory. We investigate both pore-driven translocation of flexible and a semi-flexible polymers, and the end-pulled case of flexible chains by means of the IFTP theory and extensive molecular dynamics (MD) simulations. The validity of the IFTP theory can be quantified by the waiting time distributions of the monomers which reveal the details of the dynamics of the translocation process. The IFTP theory allows a parameter-free description of the translo…
In this work, molecular dynamics simulations are performed to estimate the equilibrium pressure of liquid confined in nanopores. The simulations show that the pressure is highly sensitive to the pore size and can significantly change from absolute positive to negative values for a very small (0.1 nm) change in pore size. The contribution from the solid-liquid interaction always dominates the pressure in the first liquid layer adjacent to the surface and the sensitiveness of pressure on the pore size is due to the atom distribution in the liquid layers. A surface influence number S is introduce…
Molecular Dynamics simulations of glycerol confined in $γ$-Al$_2$O$_3$ slit nanopores are used to explain controversial and inconsistent observations reported in the literature regarding the dynamics of viscous fluids in confined geometries. Analysing the effects of the degree of confinement and pore saturation in this system, we found that the presence of the solid/liquid interface and the liquid/gas interface in partially saturated pores are the main contributors for the disruption of the hydrogen bond network of glycerol. Despite the reduction of hydrogen bonds between glycerol molecules ca…
Rectification properties of conically shaped nanopores: consequences of miniaturization
TU Darmstadt（达姆施塔特工业大学）；University of Vienna（维也纳大学）；Materials Science, TU Darmstadt（达姆施塔特工业大学材料科学系）；Department of Physics and Astronomy, University of California, Irvine（加州大学欧文分校物理与天文系）；GSI Helmholtz Center（德国重离子研究中心）
Ion transport through nanopores permeates through many areas of science and technology, from cell behavior to sensing and separation to catalysis and batteries. Two-dimensional materials, such as graphene, molybdenum disulfide (MoS$_2$), and hexagonal boron nitride (hBN), are recent additions to these fields. Low-dimensional materials present new opportunities to develop filtration, sensing, and power technologies, encompassing ion exclusion membranes, DNA sequencing, single molecule detection, osmotic power generation, and beyond. Moreover, the physics of ionic transport through pores and con…
Using molecular dynamic simulations we show that single-layers of molybdenum disulfide (MoS$_2$) and graphene can effectively reject ions and allow high water permeability. Solutions of water and three cations with different valence (Na$^+$, Zn$^{2+}$ and Fe$^{3+}$) were investigated in the presence of the two types of membranes and the results indicate a high dependence of the ion rejection on the cation charge. The associative characteristic of ferric chloride leads to a high rate of ion rejection by both nanopores, while the monovalent sodium chloride induces lower rejection rates. Particul…
We use molecular dynamics simulations to investigate the displacement of a simple butterfly-like molecular motor inside nanopores of various radii filled with a viscous medium. The medium is modeled with a versatile potential that may be adjusted to represent a large number of materials. It was found previously that the motor folding not only increases its displacement but also creates elementary diffusion processes inside the medium, related to the opening angle of the motor folding. The presence of these processes changes the medium dynamics and in turn affects the motor displacement. Theref…
We have investigated the dynamics of water confined in mesostructured porous silicas (SBA-15, MCM-41) and four periodic mesoporous organosilicas (PMOs) by dielectric relaxation spectroscopy. The influence of water-surface interaction has been controlled by the carefully designed surface chemistry of PMOs that involved organic bridges connecting silica moieties with different repetition lengths, hydrophilicity and H-bonding capability. Relaxation processes attributed to the rotational motions of non-freezable water located in the vicinity of the pore surface were studied in the temperature rang…
Single nanopores have attracted much scientific interest due to their versatile applications. The majority of experiments have been performed with nanopores being in contact with the same electrolyte on both sides of the membrane, while solution gradients across semi-permeable membranes are omnipresent in natural systems. In this manuscript, we studied ionic and fluidic movement through thin nanopores under viscosity gradients both experimentally and using simulations. Ionic current rectification was observed under these conditions, due to solutions with different conductivities filled across …
The influence of spatial confinement on the thermally excited stochastic cation dynamics of the room-temperature ionic liquid 1-N-butylpyridinium bis-((trifluoromethyl)sulfonyl)imide ([BuPy][Tf_2N]) inside porous carbide-derived carbons with various pore sizes in the sub- to a few nanometer range are investigated by quasi-elastic neutron spectroscopy. Using the potential of fixed window scans, i.e. scanning a sample parameter, while observing solely one specific energy transfer value, an overview of the dynamic landscape within a wide temperature range is obtained. It is shown that already the…
We investigate a model nanopore sensor that is able to detect analyte ions that are present in the electrolyte solution in very small concentrations. The nanopore selectively binds the analyte ions with which the local concentrations of the ions of the background electrolyte (KCl), and, thus, the ionic current flowing through the pore is changed. Analyte concentration can be determined from calibration curves. In our previous study (Mádai et al. J. Chem. Phys., 147(24):244702, 2017.), we proposed a symmetric model (surface charge is negative all along the pore). The mechanism of sensing was a …
Asymptotic models for transport in large aspect ratio nanopores
University of Warwick（华威大学）；Osnabrück University, Institute of Mathematics（奥斯纳布吕克大学数学研究所）；Radon Institute for Computational and Applied Mathematics, Austrian Academy of Sciences（奥地利科学院拉德诺计算与应用数学研究所）
The recent measurement of a very low dielectric constant, $ε$, of water confined in nanometric slit pores leads us to reconsider the physical basis of ion partitioning into nanopores. For confined ions in chemical equilibrium with a bulk of dielectric constant $ε_b>ε$, three physical mechanisms, at the origin of ion exclusion in nanopores, are expected to be modified due to this dielectric mismatch: dielectric exclusion at the water-pore interface (with membrane dielectric constant, $ε_m<ε$), the solvation energy related to the difference in Debye-Hückel screening parameters in the pore, $κ$, …
A model system is proposed to investigate the chemical equilibrium and mechanical stability of biological spherical-like nanoshells in contact with an aqueous solution with added dissociated electrolyte of a given concentration. The ionic chemical equilibrium across the permeable shell is investigated in the framework of an accurate Density Functional Theory (DFT) that incorporates electrostatic and hardcore correlations beyond the traditional mean-field ({\it e. g.}, Poisson-Boltzmann) limit. The accuracy of the theory is tested by a direct comparison with Monte Carlo (MC) simulations. A simp…
We present a modeling study of a nanopore-based transistor computed by a mean-field continuum theory (Poisson-Nernst-Planck, PNP) and a hybrid method including particle simulation (Local Equilibrium Monte Carlo, LEMC) that is able to take ionic correlations into account including finite size of ions. The model is composed of three regions along the pore axis with the left and right regions determining the ionic species that is the main charge carrier, and the central region tuning the concentration of that species and, thus, the current flowing through the nanopore. We consider a model of smal…
We present gravimetrical and optical imaging experiments on the capillarity-driven imbibition of silicone oils in monolithic silica glasses traversed by 3D networks of pores (mesoporous Vycor glass with 6.5 nm or 10 nm pore diameters). As evidenced by a robust square-root-of-time Lucas-Washburn (L-W) filling kinetics, the capillary rise is governed by a balance of capillarity and viscous drag forces in the absence of inertia and gravitational effects over the entire experimental times studied, ranging from a few seconds up to 10 days. A video on the infiltration process corroborates a collecti…
Capillary rise dynamics of liquid hydrocarbons in mesoporous silica as explored by gravimetry, optical and neutron imaging: Nano-rheology and determination of pore size distributions from the shape of imbibition fronts
