We calculate the first passage time distribution for diffusion through a cylindrical pore with sticky walls. A particle diffusively explores the interior of the pore through a series of binding and unbinding events with the cylinder wall. Through a diagrammatic expansion we obtain first passage time statistics for the particle's exit from the pore. Connections between the model and nucleocytoplasmic transport in cells are discussed.
A cylindrical nanopore immersed in a non-additive hard sphere binary fluid is studied by means of integral equation theories and Monte Carlo simulations. It is found that at low and intermediate values of the bulk total number density the more concentrated bulk species is preferentially absorbed by the pore, as expected. However, further increments of the bulk number density lead to an abrupt population inversion in the confined fluid and an entropy driven prewetting transition at the outside wall of the pore. These phenomena are a function of the pore size, the non-additivity parameter, the b…
The effect of cylindrical confinement on the phase behaviour of a system of parallel hard rods is studied using Onsager's second virial theory. The hard rods are represented as hard cylinders of diameter $D$ and length $L$, while the cylindrical pore is infinite with diameter $W$. The interaction between the wall and the rods is hard repulsive, and it is assumed that molecules are parallel to the surface of the pore (planar anchoring). In very narrow pores ($D<W<2 D$), the structure is homogeneous and the system behaves as a one-dimensional Tonks gas. For wider pores, inhomogeneous fluid struc…
We present results of molecular dynamics simulations of water confined in a silica pore. A cylindrical cavity is created inside a vitreous silica cell with geometry and size similar to the pores of real Vycor glass. The simulations are performed at different hydration levels. At all hydration levels water adsorbs strongly on the Vycor surface; a double layer structure is evident at higher hydrations. At almost full hydration the modifications of the confinement-induced site-site pair distribution functions are in qualitative agreement with neutron diffraction experiment. A decrease in the numb…
The structure of flexible polymers endgrafted in cylindrical pores of diameter D is studied as a function of chain length N and grafting density σ, assuming good solvent conditions. A phenomenological scaling theory, describing the variation of the linear dimensions of the chains with σ, is developed and tested by Molecular Dynamics simulations of a bead-spring model.
The collision dynamics of hard spheres and cylindrical pores is solved exactly, which is the minimal model for a regularly porous membrane. Nonequilibrium event-driven molecular dynamics simulations are used to show that the permeability $P$ of hard spheres of size $σ$ through cylinderical pores of size $d$ follow the hindered diffusion mechanism due to size exclusion as $P \propto (1-σ/d)^2$. Under this law, the separation of binary mixtures of large and small particles exhibits a linear relationship between $α^{-1/2}$ and $P^{-1/2}$, where $α$ and $P$ are the selectivity and permeability of …
We present a neutron scattering analysis of the density and the static structure factor of confined methanol at various temperatures. Confinement is performed in the cylindrical pores of MCM-41 silicates with pore diameters D=24 angstrom and D=35 angstrom. A change of the thermal expansivity of confined methanol at low temperature is the signature of a glass transition, which occurs at higher temperature for the smallest pore. This is an evidence of a surface induced slowing down of the dynamics of the fluid. The structure factor presents a systematic evolution with the pore diameter, which ha…
Understanding how electrolyte-filled porous electrodes respond to an applied potential is important to many electrochemical technologies. Here, we consider a model supercapacitor of two blocking cylindrical pores on either side of a cylindrical electrolyte reservoir. A stepwise potential difference $2Φ$ between the pores drives ionic fluxes in the setup, which we study through the modified Poisson-Nernst-Planck equations, solved with finite elements. We focus our discussion on the dominant timescales with which the pores charge and how these timescales depend on three dimensionless numbers. Ne…
Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $σ$ are varied over a wide range and the crossover from ``mushroom'' to ``brush'' behavior is studied for three pore diameters. The monomer density profile and the distribution of the free chain ends are computed and compared to the corresponding model of polymer brushes at flat substrates. It is found that there exists a regime of $N$ and $σ$ for large enough pore diameter where the brush…
The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic hydrodynamic method of lattice Boltzmann facilitates coarse-grained simulations that are on the order of microseconds and hundreds of nanometers for the study of diffusive transport of protein-like colloid particles. The raspberry model reproduces linearity in resistance to motion versus particle size and correct enhanced drag within cylindrical pores at off-c…
We use Metropolis Monte Carlo and umbrella sampling to calculate the free energies of interaction of two methane molecules and their charged derivatives in cylindrical water-filled pores. Confinement strongly alters the interactions between the nonpolar solutes, and completely eliminates the solvent separated minimum (SSM) that is seen in bulk water. The free energy profiles show that the methane molecules are either in contact or at separations corresponding to the diameter and the length of the cylindrical pore. Analytic calculations that estimate the entropy of the solutes, which are solvat…
We investigate the effect of cylindrical nano-confinement on the phase behaviour of a rigid model of carbon dioxide using both molecular dynamics and well tempered metadynamics. To this aim we study a simplified pore model across a parameter space comprising pore diameter, CO2-pore wall potential and CO2 density. In order to systematically identify ordering events within the pore model we devise a generally applicable approach based on the analysis of the distribution of intermolecular orientations. Our simulations suggest that, while confinement in nano-pores inhibits the formation of known c…
A field theoretic variational approach is introduced to study ion penetration into water-filled cylindrical nanopores in equilibrium with a bulk reservoir. It is shown that (i) an ion located in a neutral pore undergoes two opposing mechanisms: the deformation of its surrounding ionic cloud of opposite charge, with respect to the reservoir, which increases the surface tension and tends to exclude ions form the pore, and (ii) the attractive contribution to the ion self-energy of the repulsive image forces associated with the dielectric jump between the solvent and the pore wall, which becomes m…
Using an algorithm for simulating equilibrium configurations, we study a fluctuating helical polymer either (i) contained in a cylindrical pore or (ii) wound around a cylindrical rod. We work in the regime where both the contour length and the persistence length of the helical polymer are much larger than the diameter of the cylinder. In case (i) we calculate the free energy of confinement and interpret it in terms of a worm-like chain in a pore with an effective diameter that depends on the parameters of the helix. In case (ii) we consider the possibility that one end of the helical polymer e…
We calculate the mean end-to-end distance ($R$) of a self-avoiding polymer encapsulated in an infinitely long cylinder with radius $D$. A self-consistent perturbation theory is used to calculate $R$ as a function of $D$ for impenetrable hard walls and soft walls. In both cases, $R$ obeys the predicted scaling behavior in the limit of large and small $D$. The crossover from the three dimensional behavior ($D\to\infty$) to the fully stretched one dimensional case ($D\to 0$) is non-monotonic. The minimum value of $R$ is found at $D\sim 0.46 R_F$, where $R_F$ is the Flory radius of $R$ at $D \to \…
We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation time of the chain, t, with the chain length N and pore diameter D. An earlier scaling analysis based on the de Gennes blob picture led to t ~ N^2D^(1/3). Our numerical effort that combines molecular dynamics and Monte Carlo simulations, however, consistently produces different t-results for N up to 2000. We argue that the previous scaling prediction is only as…
Ion transport in porous media is present in a wealth of technologies, e.g., energy storage devices such as batteries and supercapacitors, and environmental technologies such as electrochemical carbon capture and capacitive deionization. Recent studies on flat-plate electrodes have demonstrated that asymmetries in ion properties, such as valences and diffusivities, lead to intriguing and counter-intuitive physical phenomena. Yet, the consequences of such asymmetries to ion transport have seldom been explored in porous geometries. To bridge this knowledge gap, we conduct a perturbation expansion…
We extensively study the phase diagram of a diblock copolymer melt confined in a cylindrical nanopore using real-space self-consistent mean-field theory. We discover a rich variety of new two-dimensional equilibrium structures that have no analog in the unconfined system. These include non-hexagonally coordinated cylinder phases and structures intermediate between lamellae and cylinders. We map the stability regions and phase boundaries for all the structures we find. As the pore radius is decreased, the pore accommodates fewer cylindrical domains and structural transitions occur as cylinders …
Using grand canonical Monte Carlo simulations, we have explored the phenomenon of capillary condensation (CC) of Ar at the triple temperature inside infinitely long, cylindrical pores. Pores of radius R= 1 nm, 1.7 nm and 2.5 nm have been investigated, using a gas-surface interaction potential parameterized by the well-depth D of the gas on a planar surface made of the same material as that comprising the porous host. For strongly attractive situations, i.e., large D, one or more (depending on R) Ar layers adsorb successively before liquid fills the pore. For very small values of D, in contrast…
Nuclear pores have an approximately uniform distribution in the nuclear envelope of most living cells. Hence, the morphology of the nuclear envelope is a spherical stomatocyte with a high genus. We have investigated the morphology of high-genus vesicles under pore-size constraint using dynamically triangulated membrane simulations. Bending-energy minimization without volume or other constraints produces a circular-cage stomatocyte, where the pores are aligned in a circular line on an oblate bud. As the pore radius is reduced, the circular-pore alignment is more stabilized than a random pore di…
The phase behaviour and structural properties of a monolayer of hard particles is examined in such a confinement, where the adsorbed particles are constrained to the surface of a narrow hard cylindrical pore. The diameter of the pore is chosen such that only first and second neighbour interactions occur between the hard particles. The transfer operator method of Percus and Zhang [Mol. Phys., 69, 347 (1990)] is reformulated to obtain information about the structure of the monolayer. We have found that a true phase transition is not possible in the examined range of pore diameters. The monolayer…
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…
We consider the translocation of a neutral (uncharged) nanoparticle through a pore in a thin membrane with constant surface charge density. If the concomitant Debye screening layer is sufficiently thin, the resulting forces experienced by the particle on its way through the pore are negligible. But when the Debye length becomes comparable to the pore diameter, the particle encounters a quite significant potential barrier while approaching and entering the pore, and symmetrically upon exiting the pore. The main reason is an increasing pressure which acts on the particle when it intrudes into th…
Understanding how colloidal suspensions behave in confined environments has a striking relevance in practical applications. Despite the fact that the behaviour of colloids in the bulk is key to identify the main elements affecting their equilibrium and dynamics, it is only by studying their response under confinement that one can ponder the use of colloids in formulation technology. In particular, confining fluids of anisotropic particles in nanopores provides the opportunity to control their phase behaviour and stabilise a spectrum of morphologies that cannot form in the bulk. By properly sel…
The orientational and translational order of a thermotropic ferroelectric liquid crystal (2MBOCBC) imbibed in self-organized, parallel, cylindrical pores with radii of 10, 15, or 20 nm in anodic aluminium oxide monoliths (AAO) are explored by high-resolution linear and circular optical birefringence as well as neutron diffraction texture analysis. The results are compared to experiments on the bulk system. The native oxidic pore walls do not provide a stable smectogen wall anchoring. By contrast, a polymeric wall grafting enforcing planar molecular anchoring results in a thermal-history indepe…
The confinement of liquid crystals inside curved geometries leads to exotic structures, with applications ranging from bio-sensors to optical switches and privacy windows. Here we study how curvature affects the alignment of a cholesteric liquid crystal. We model the system on the mesoscale using the Landau-de Gennes model. Our study was performed in three stages, analysing different curved geometries from cylindrical walls and pores, to toroidal domains, in order to isolate the curvature effects. Our results show that the stresses introduced by the curvature influence the orientation of the l…
Based on a coarse-grained model, we carry out molecular dynamics simulations to analyze the diffusion of a small tracer particle inside a cylindrical channel whose inner wall is covered with randomly grafted short polymeric chains. We observe an interesting transient subdiffusive behavior along the cylindrical axis at high attraction between the tracer and the chains, however, the long time diffusion is always normal. This process is found to be enhanced for the case that we immobilize the grafted chains, i.e. the sub-diffusive behavior sets in at an earlier time and spans over a longer time p…
We consider elongated cylindrical particles, modeling e.g. DNA fragments or nano-rods, while translocating under the action of an externally applied voltage through a solid state nanopore. Particular emphasis is put on the concomitant potential energy landscape, encountered by the particle on its passage through the pore due to the complex interplay of various electrohydrodynamic effects beyond the realm of small Debye lengths. We find that the net potential energy difference across the membrane may be of opposite sign for short and long particles of equal diameters and charge densities (e.g. …
Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium. The system is modeled as a flexible hard-sphere chain that translocates through a cylindrical hole in a hard flat wall. In some calculations, the nanopore is connected at one end to a spherical cavity. Translocation times are measured directly using MC dynamics simulations. For sufficiently narrow pores, translocation is sufficiently slow that the mean transl…
