Describing the diffusion of particles through crowded, confined environments with which they can interact is of considerable biological and technological interest. Under conditions where the confinement dimensions become comparable to the particle dimensions, steric interactions between particles, as well as particle-wall interactions, will play a crucial role in determining transport properties. To elucidate the effects of these interactions on particle transport, we consider the diffusion and binding of finite-size particles within a channel whose diameter is comparable to the size of the particles. Using a simple lattice model of this process, we calculate the steady-state current and density profiles of both bound and free particles in the channel. We show that the system can exhibit qualitatively different behavior depending on the ratio of the channel width to the particle size. We also perform simulations of this system, and find excellent agreement with our analytic results.
We consider a random walk in confined geometry, starting from a site and eventually reaching a target site. We calculate analytically the distribution of the occupation time on a third site, before reaching the target site. The obtained distribution is exact, and completely explicit in the case or parallepipedic confining domains. We discuss implications of these results in two different fields: The mean first passage time for the random trap model is computed in dimensions greater than 1, and is shown to display a non-trivial dependence with the source and target positions ; The probability o…
This review introduces the elasticity theory of two-dimensional crystals and nematic liquid crystals on curved surfaces, the energetics of topological defects (disclinations, dislocations and pleats) in these ordered phases, and the interaction of defects with the underlying curvature. This chapter concludes with two cases of three-dimensional nematic phases confined to spaces with curved boundaries, namely a torus and a spherical shell.
Motivated by subdiffusive motion of bio-molecules observed in living cells we study the stochastic properties of a non-Brownian particle whose motion is governed by either fractional Brownian motion or the fractional Langevin equation and restricted to a finite domain. We investigate by analytic calculations and simulations how time-averaged observables (e.g., the time averaged mean squared displacement and displacement correlation) are affected by spatial confinement and dimensionality. In particular we study the degree of weak ergodicity breaking and scatter between different single trajecto…
We identify problems with the standard complex order parameter formalism for smectic-A (SmA) liquid crystals, and discuss possible alternative descriptions of smectic order. In particular, we suggest an approach based on the real smectic density variation rather than a complex order parameter. This approach gives reasonable numerical results for the smectic layer configuration and director field in sample geometries, and can be used to model smectic liquid crystals under nanoscale confinement for technological applications.
This article gives an overview of recent theoretical and experimental findings concerning the hydrodynamic interaction between liquid-embedded particles in various confined geometries. A simple unifying description emerges, which accounts for the various findings based on the effect of confinement on conserved fields of the embedding liquid. It shows, in particular, that the hydrodynamic interaction under confinement remains long-ranged, decaying algebraically with inter-particle distance, except for the case of confinement in a rigid linear channel.
Previously, we developed a minimal model based on random cooperative strings for the relaxation of supercooled liquids in the bulk and near free interfaces, and we recovered some key experimental observations. In this article, after recalling the main ingredients of the cooperative string model, we study the effective glass transition and surface mobility of various experimentally-relevant confined geometries: freestanding films, supported films, spherical particles, and cylindrical particles, with free interfaces and/or passive substrates. Finally, we introduce a novel way to account for a pu…
We studied the crystallization of a globular protein, lysozyme, in the cubic phase of the lipid monoolein. The solubility of lysozyme in salt solution decreased by a factor of $\sim 4$ when confined in cubic phase. Calculations and Monte Carlo simulations show that this can be explained by the {\it confinement} of lysozyme molecules to the narrow water cells in the cubic phase.
Two-dimensional nematics possess peculiar properties that have been studied recently using computer simulation and various theoretical models. Here we review our own contribution to the field using density-functional theory, and present some preliminary simulation results on confined two-dimensional nematics. First we discuss the possible stable bulk phases and phase diagrams and the relation between phases and particle geometry. We then explore the adsorption properties on a single substrate and the confinement effects that arise when the fluid is confined between parallel walls. Next, confin…
The massive field theory approach in fixed space dimensions $d=3$ is applied to investigate a dilute solution of long-flexible polymer chains in a good solvent between two parallel repulsive walls, two inert walls and for the mixed case of one inert and one repulsive wall. The well known correspondence between the field theoretical $ϕ^4$ O(n)-vector model in the limit $n\to 0$ and the behavior of long-flexible polymer chains in a good solvent is used to calculate the depletion interaction potential and the depletion force up to one-loop order. Our investigations include modification of renorma…
Studies of random close packing of spheres have advanced our knowledge about the structure of systems such as liquids, glasses, emulsions, granular media, and amorphous solids. When these systems are confined their structural properties change. To understand these changes we study random close packing in finite-sized confined systems, in both two and three dimensions. Each packing consists of a 50-50 binary mixture with particle size ratio 1.4. The presence of confining walls significantly lowers the overall maximum area fraction (or volume fraction in three dimensions). A simple model is pres…
In both nature and engineering, loosely packed granular materials are often compacted inside confined geometries. Here, we explore such behaviour in a quasi-two dimensional geometry, where parallel rigid walls provide the confinement. We use the discrete element method to investigate the stress distribution developed within the granular packing as a result of compaction due to the displacement of a rigid piston. We observe that the stress within the packing increases exponentially with the length of accumulated grains, and show an extension to current analytic models which fits the measured st…
Motivated by recent experiments on the rod-like virus bacteriophage fd, confined to circular and annular domains, we present a theoretical study of structural transitions in these geometries. Using the continuum theory of nematic liquid crystals, we examine the competition between bulk elasticity and surface anchoring, mediated by the formation of topological defects. We show analytically that bulk defects are unstable with respect to defects sitting at the boundary. Moreover, in case of an annulus, whose topology does not require the presence of topological defects, under weak anchoring condi…
The universal density-force relation is analyzed and the correspondent universal amplitude ratio $B_{real}$ is obtained using the massive field theory approach in fixed space dimensions d=3 up to one-loop order. The layer monomer density profiles of ideal chains and real polymer chains with excluded volume interaction in a good solvent between two parallel repulsive walls, one repulsive and one inert wall are obtained. Besides, taking into account the Derjaguin approximation the layer monomer density profiles for dilute polymer solution confined in semi-infinite space containing mesoscopic sph…
Transport of ions in molecular-scale confined spaces is central to all aspects of life and technology: into a crack, it may break steel within days; through a membrane separator, it determines the efficiency of electrochemical energy conversion devices; or through lipid membranes, it steers neural communication. Yet, the direct observation of ion mobility and structuring in sub-nanometer confinement is experimentally challenging and, so far, solely accessible to molecular simulations. Here, we show quantitative, 3D molecularly-resolved ion transportation of aqueous ionic liquid and s-block met…
We apply a hybrid Molecular Dynamics and mesoscopic simulation technique to study the dynamics of two dimensional colloidal discs in confined geometries. We calculate the velocity autocorrelation functions, and observe the predicted $t^{-1}$ long time hydrodynamic tail that characterizes unconfined fluids, as well as more complex oscillating behavior and negative tails for strongly confined geometries. Because the $t^{-1}$ tail of the velocity autocorrelation function is cut off for longer times in finite systems, the related diffusion coefficient does not diverge, but instead depends logarith…
When a Coulombic fluid is confined between two parallel charged plates, an exact relation links the difference of ionic densities at contact with the plates, to the surface charges of these boundaries. It no longer applies when the boundaries are curved, and we work out how it generalizes when the fluid is confined between two concentric spheres (or cylinders), in two and in three space dimensions. The analysis is thus performed within the cell model picture. The generalized contact relation opens the possibility to derive new exact expressions, of particular interest in the regime of strong c…
The paper presents a short overview of the theoretical, numerical and experimental works on the critical behavior of a dilute polymer solution of long-flexible polymer chains confined in semi-infinite space restricted by a surface or in a slit geometry of two parallel walls with different adsorbing or repelling properties in respect for polymers as well as in a solution of mesoscopic spherical colloidal particles of one sort or two different sorts. We discuss the application of the massive field theory approach in a fixed space dimensions d=3 up to one loop order for such topics as:(a) the inv…
The investigation of a dilute solution of phantom ideal ring polymers and ring polymers with excluded volume interactions (EVI) in a good solvent confined in a slit geometry of two parallel repulsive walls and in a solution of colloidal particles of big size was performed. Taking into account the correspondence between the field theoretical $ϕ^4$ $O(n)$-vector model in the limit $n\to 0$ and the behaviour of long-flexible polymers in a good solvent, the correspondent depletion forces and the forces which exert phantom ideal ring polymers and ring polymers with EVI on the walls were obtained in…
Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the polymer, and from these functions we extract the free energy of the hairpin fold, as well as the entropic force arising from interactions between the portions of the polymer that overlap along the channel. We consider the scaling of the free energies with respect to varying the persistence length of the polymer, as well as the channel dimensions for confineme…
We propose numerical simulations of viscoelastic fluids based on a hybrid algorithm combining Lattice-Boltzmann models (LBM) and Finite Differences (FD) schemes, the former used to model the macroscopic hydrodynamic equations, and the latter used to model the polymer dynamics. The kinetics of the polymers is introduced using constitutive equations for viscoelastic fluids with finitely extensible non-linear elastic dumbbells with Peterlin's closure (FENE-P). The numerical model is first benchmarked by characterizing the rheological behaviour of dilute homogeneous solutions in various configurat…
When the motion of a motile cell is observed closely, it appears erratic, and yet the combination of nonequilibrium forces and surfaces can produce striking examples of organization in microbial systems. While most of our current understanding is based on bulk systems or idealized geometries, it remains elusive how and at which length scale self-organization emerges in complex geometries. Here, using experiments, analytical and numerical calculations we study the motion of motile cells under controlled microfluidic conditions, and demonstrate that probability flux loops organize active motion …
Thin elastic solids are easily deformed into a myriad of three-dimensional shapes, which may contain sharp localized structures as in a crumpled candy wrapper, or have smooth and diffuse features like the undulating edge of a flower. Anticipating and controlling these morphologies is crucial to a variety of applications involving textiles, synthetic skins, and inflatable structures. Here we show that a "wrinkle-to-crumple" transition, previously observed in specific settings, is a ubiquitous response for confined sheets. This unified picture is borne out of a suite of model experiments on poly…
The interaction energy and minimum energy structure for different geometries of the benzene dimer has been calculated using the recently developed nonlocal correlation energy functional for calculating dispersion interactions. The comparison of this straightforward and relatively quick density functional based method with recent calculations can elucidate how the former, quicker method might be exploited in larger more complicated biological, organic, aromatic, and even infinite systems such as molecules physisorbed on surfaces, and van der Waals crystals.
Nano-scale confinement of polymer in cone-shaped geometries occurs in many experimental situations. A flexible polymer confined in a cone-shaped nano-channel is studied theoretically and using molecular dynamics simulations. Distribution of the monomers inside the channel, configuration of the confined polymer, entropic force acting on the polymer, and their dependence on the channel and the polymer parameters are investigated. The theory and the simulation results are in very good agreement. The entropic force on the polymer that results from the asymmetric shape of the channel is measured in…
The collective diffusion of dense fluids in spatial confinement was studied by combining high-energy (21 keV) x-ray photon correlation spectroscopy and small-angle x-ray scattering from colloid-filled microfluidic channels. We found the structural relaxation in confinement to be slower compared to bulk. The collective dynamics is wave vector dependent, akin to de Gennes narrowing typically observed in bulk fluids. However, in stark contrast to bulk, the structure factor and de Gennes narrowing in confinement are anisotropic. These experimental observations are essential in order to develop a m…
We study bidisperse colloidal suspensions confined within glass microcapillary tubes to model the glass transition in confined cylindrical geometries. We use high speed three-dimensional confocal microscopy to observe particle motions for a wide range of volume fractions and tube radii. Holding volume fraction constant, we find that particles move slower in thinner tubes. The tube walls induce a gradient in particle mobility: particles move substantially slower near the walls. This suggests that the confinement-induced glassiness may be due to an interfacial effect.
In biology, there are several processes in which unfolded protein chains are transported along narrow-tube channels. Normally, without such a severe configurational constraint, unfolded polypeptides would not bind to each other. However, when chain entropy is much reduced in the narrow channel, we find that polypeptide chains have a propensity to bind, even if there is no great potential energy gain in doing so. We find the average length of binding m* (the number of monomers at the chain ends that form bonds) and the critical tube diameter at which such constrained binding occurs. We carry ou…
We study the effects of the optical binding force on wavelength sized colloidal particles free to move in a counter-propagating beam. This work is motivated by the concept of using optical binding to direct the assembly of large numbers of colloidal particles; previous work has used small numbers of particles and/or 1D or 2D restricted geometries. Utilizing a novel experimental scheme, we describe the general static and dynamic self-organization behaviors for 20--100 particles free to move in 3-dimensional space. We observe the self-organization of the colloids into large optically bound struc…
Computing stable configurations of confined smectic liquid crystals with a deep variational framework
School of Mathematical Sciences, Peking University（北京大学数学科学学院）；Columbia University（哥伦比亚大学）；Center for Applied Mathematics, Renmin University of China（中国人民大学应用数学中心）；School of Mathematical Sciences, Beijing International Center for Mathematical Research, Center for Quantitative Biology, Center for Machine Learning Research, Peking University（北京大学数学科学学院、北京国际数学研究中心、定量生物学中心、机器学习研究中心）
