Hard Rod Fluid Research Articles

Bridging electronic and classical density-functional theory using universal machine-learned functional approximations.

The accuracy of density-functional theory (DFT) calculations is ultimately determined by the quality of the underlying approximate functionals, namely the exchange-correlation functional in electronic DFT and the excess functional in the classical DFT formalism of fluids. For both electrons and fluids, the exact functional is highly nonlocal, yet most calculations employ approximate functionals that are semi-local or nonlocal in a limited weighted-density form. Machine-learned (ML) nonlocal density-functional approximations show promise in advancing applications of both electronic and classical DFTs, but so far these two distinct research areas have implemented disparate approaches with limited generality. Here, we formulate a universal ML framework and training protocol to learn nonlocal functionals that combine features of equivariant convolutional neural networks and the weighted-density approximation. We prototype this new approach for several 1D and quasi-1D problems and demonstrate that functionals with exactly the same hyperparameters achieve excellent accuracy for a diverse set of systems, including the hard-rod fluid, the inhomogeneous Ising model, the exact exchange energy of electrons, the electron kinetic energy for orbital-free DFT, as well as for liquid water with 1D inhomogeneities. These results lay the foundation for a universal ML approach to approximate exact 3D functionals spanning electronic and classical DFTs.

Thermalization and Hydrodynamics in an Interacting Integrable System: The Case of Hard Rods

We consider the relaxation of an initial non-equilibrium state in a one-dimensional fluid of hard rods. Since it is an interacting integrable system, we expect it to reach the Generalized Gibbs Ensemble (GGE) at long times for generic initial conditions. Here we show that there exist initial conditions for which the system does not reach GGE even at very long times and in the thermodynamic limit. In particular, we consider an initial condition of uniformly distributed hard-rods in a box with the left half having particles with a singular velocity distribution (all moving with unit velocity) and the right half particles in thermal equilibrium. We find that the density profile for the singular component does not spread to the full extent of the box and keeps moving with a fixed effective speed at long times. We show that such density profiles can be well described by the solution of the Euler equations almost everywhere except at the location of the shocks, where we observe slight discrepancies due to dissipation arising from the initial fluctuations of the thermal background. To demonstrate this effect of dissipation analytically, we consider a second initial condition with a single particle at the origin with unit velocity in a thermal background. We find that the probability distribution of the position of the unit velocity quasi-particle has diffusive spreading which can be understood from the solution of the Navier–Stokes (NS) equation of the hard rods. Finally, we consider an initial condition with a spread in velocity distribution for which we show convergence to GGE. Our conclusions are based on molecular dynamics simulations supported by analytical arguments.

Two-temperature activity induces liquid-crystal phases inaccessible in equilibrium.

In equilibrium hard-rod fluids, and in effective hard-rod descriptions of anisotropic soft-particle systems, the transition from the isotropic (I) phase to the nematic phase (N) is observed above the rod aspect ratio L/D=3.70 as predicted by Onsager. We examine the fate of this criterion in a molecular dynamics study of a system of soft repulsive spherocylinders rendered active by coupling half the particles to a heat bath at a higher temperature than that imposed on the other half. We show that the system phase-separates and self-organizes into various liquid-crystalline phases that are not observed in equilibrium for the respective aspect ratios. In particular, we find a nematic phase for L/D=3 and a smectic phase for L/D=2 above a critical activity.

Structure and Interfacial Tension of a Hard-Rod Fluid in Planar Confinement.

The structural properties and interfacial tension of a fluid of rodlike hard-spherocylinder particles in contact with hard structureless flat walls are studied by means of Monte Carlo simulation. The calculated surface tension between the rod fluid and the substrate is characterized by a nonmonotonic trend as a function of the bulk concentration (density) over the range of isotropic bulk concentrations. As suggested by earlier theoretical studies, a surface-ordering scenario is confirmed by our simulations: the local orientational order close to the wall changes from uniaxial to biaxial nematic when the bulk concentration reaches about 85% of the value at the onset of the isotropic-nematic phase transition. The surface ordering coincides with a wetting transition whereby the hard wall is wetted by a nematic film. Accurate values of the fluid-solid surface tension, the adsorption, and the average particle-wall contact distance are reported (over a broad range of densities into the dense nematic region for the first time), which can serve as a useful benchmark for future theoretical and experimental studies on confined rod fluids. The simulation data are supplemented with predictions from second-virial density functional theory, which are in good qualitative agreement with the simulation results.

Dynamics of hard rods with initial domain wall state

Inspired by recent results on the non-equilibrium dynamics of many-body quantum systems, we study the classical hard rod problem in one dimension with initial domain wall condition. Hard rods are an integrable system, in the sense that for each velocity the density of particles is locally conserved. It was proven by Boldrighini et al (1983 J. Stat. Phys. 31 577) that on the hydrodynamic space-time scale, the fluid of hard rods satisfies Euler-type equations which comprise all conservation laws. We provide the general solution to these equations on the line, with an initial condition where the left and right halves are, asymptotically, in different states. The solution is interpreted as being composed of a continuum of contact discontinuities, one for each velocity. This is a classical counterpart of the transport problem solved recently in quantum integrable systems. We also discuss the Navier–Stokes (viscous) corrections, and study its effect on the broadening of the contact discontinuity and on entropy production.

Radial distribution function for hard spheres in fractal dimensions: A heuristic approximation

Analytic approximations for the radial distribution function, the structure factor, and the equation of state of hard-core fluids in fractal dimension d(1≤d≤3) are developed as heuristic interpolations from the knowledge of the exact and Percus-Yevick results for the hard-rod and hard-sphere fluids, respectively. In order to assess their value, such approximate results are compared with those of recent Monte Carlo simulations and numerical solutions of the Percus-Yevick equation for a fractal dimension [M. Heinen et al., Phys. Rev. Lett. 115, 097801 (2015)PRLTAO0031-900710.1103/PhysRevLett.115.097801], a good agreement being observed.

Solvation force in hard ellipsoid fluids with HNW interaction

In present work, using density functional theory and extended restricted orientation model, the one particle density of hard Gaussian overlap fluid near the colloid walls is calculated. The hard needle–wall interaction between molecules and colloids are considered. Using non-linear equation, proposed by Grimson–Rickyazen, the solvation force of hard ellipsoidal molecular fluid with hard Gaussian overlap interaction is calculated. We could not find the exact or simulation results for comparison. The results in the case k = 2.0 are compared with the solvation force of one-dimensional hard rod fluids. The results are corresponded, qualitatively.

Domain walls in two-dimensional nematics confined in a small circular cavity

Using Monte Carlo simulation, we study a fluid of two-dimensional hard rods inside a small circular cavity bounded by a hard wall, from the dilute regime to the high-density, layering regime. Both planar and homeotropic anchoring of the nematic director can be induced at the walls through a free-energy penalty. The circular geometry creates frustration in the nematic phase and a polar-symmetry configuration with a distorted director field plus two +1/2 disclinations is created. At higher densities, a quasi-uniform structure is observed with a (minimal) director distortion which is relaxed via the formation of orientational domain walls. This novel structure is not predicted by elasticity theory and is similar to the step-like structures observed in three-dimensional hybrid slit pores. We speculate that the formation of domain walls is a general mechanism to relax elastic stresses under the conditions of strong surface anchoring and severe spatial confinement.

One-dimensional hard rod fluid in a disordered porous medium: scaled particle theory

The scaled particle theory is applied to a description of thermodynamic properties of one-dimensional hard rod fluid in disordered porous media. To this end, we extended the SPT2 approach, which had been developed previously. Analytical expressions are obtained for the chemical potential and pressure of a hard-rod fluid in hard rod and overlapping hard rod matrices. A series of new approximations for SPT2 are proposed. It is shown that apart from two well known porosities such as geometrical porosity and specific probe particle porosity, a new type of porosity defined by the maximum value of packing fraction of fluid particles in porous medium should be taken into account. The grand canonical Monte-Carlo simulations are performed to verify the accuracy of the SPT2 approach in combination with the new approximations. It is observed that the theoretical description proposed in this study essentially improves the results up to the highest values of fluid densities.

Thermally induced directed currents in hard rod systems

We study the non equilibrium statistical properties of a one dimensional hard-rod fluid undergoing collisions and subject to a spatially non uniform Gaussian heat-bath and periodic potential. The system is able to sustain finite currents when the spatially inhomogeneous heat-bath and the periodic potential profile display an appropriate relative phase shift, $\phi$. By comparison with the collisionless limit, we determine the conditions for the most efficient transport among inelastic, elastic and non interacting rods. We show that the situation is complex as, depending on shape of the temperature profile, the current of one system may outperform the others.

Glassy Dynamics, Spinodal Fluctuations, and the Kinetic Limit of Nucleation in Suspensions of Colloidal Hard Rods

Using simulations we identify three dynamic regimes in supersaturated isotropic fluid states of short hard rods: (i) for moderate supersaturations, we observe nucleation of multilayered crystalline clusters; (ii) at higher supersaturation, we find nucleation of small crystallites which arrange into long-lived locally favored structures that get kinetically arrested; and (iii) at even higher supersaturation, the dynamic arrest is due to the conventional cage-trapping glass transition. For longer rods we find that the formation of the (stable) smectic phase out of a supersaturated isotropic state is strongly suppressed by an isotropic-nematic spinodal instability that causes huge spinodal-like orientation fluctuations with nematic clusters diverging in size. Our results show that glassy dynamics and spinodal instabilities set kinetic limits to nucleation in highly supersaturated hard-rod fluids.

Can the isotropic-smectic transition of colloidal hard rods occur via nucleation and growth?

We investigate the isotropic-to-smectic transformation in a fluid of colloidal hard rods using computer simulations. At high supersaturation, we observe spinodal decomposition: many small clusters are formed at the initial stage of the phase transformation, which form a percolating network that eventually transforms into a stable bulk smectic phase. At low supersaturation, we find that nucleation and growth of the smectic phase is hampered by the pre-smectic ordering in the supersaturated isotropic fluid phase. As the system evolves mainly via cooperative motion of these smectic domains, the diffusion and attachment of single particles to the nucleation site is largely hindered.

Thermodynamics of Intragenic Nucleosome Ordering

The nucleosome ordering observed in vivo along yeast genes is described by a thermodynamical model of nonuniform fluid of 1D hard rods confined by two excluding energy barriers at gene extremities. For interbarrier distances L less than or approximately equal to 1.5 kbp, nucleosomes equilibrate into a crystal-like configuration with a nucleosome repeat length (NRL) L/n approximately 165 bp, where n is the number of regularly positioned nucleosomes. We also observe "bistable" genes with a fuzzy chromatin resulting from a statistical mixing of two crystal states, one with an expanded chromatin (NRL approximately L/n) and the other with a compact one (NRL approximately L/(n+1)). By means of single nucleosome switching, bistable genes may drastically alter their expression level as suggested by their higher transcriptional plasticity. These results enlighten the role of the intragenic chromatin on gene expression regulation.

Active dynamics of filaments in motility assays

We study the active dynamics of single and interacting cytoskeletal filaments in motility assays, in which immobilized motor proteins bind the filaments to a surface and actively pull them along this surface. We present a model which couples the overdamped dynamics of filaments, the active dynamics of motor heads, and the elasticity of motor stalks and which can be used for Langevin dynamics simulations. Single filaments perform a persistent random walk, which we characterize by several simulation results. For interacting filaments with a repulsive interaction of filaments, the motor-driven dynamics of filaments leads to a non-equilibrium phase transition which generalizes the isotropic-nematic phase transition of the corresponding equilibrium system, the hard-rod fluid. Langevin dynamics simulations and analytical theory show that the motor activity enhances the tendency for nematic ordering.

Isotropic-to-nematic nucleation in suspensions of colloidal rods.

Using computer simulations, we study the isotropic-to-nematic nucleation in a fluid of colloidal hard rods as well as in a mixture of colloidal rods and non-adsorbing polymer. In order to follow the transformation of the system from the isotropic to the nematic phase, we use a new cluster criterion that enables us to distinguish the nematic clusters from the isotropic fluid phase. Applying this criterion in Monte Carlo simulations, we find two different regimes depending on the supersaturation. At low supersaturation we find nucleation and growth, while at higher supersaturation spinodal decomposition is observed. We determine the height of the nucleation barrier, and we study the structure as well as the shape of the nematic clusters. We discuss our simulation results in the light of classical nucleation theory.

Exact bulk correlation functions in one-dimensional nonadditive hard-core mixtures

In a recent paper [Phys. Rev. E 76, 031202 (2007)], Schmidt proposed a fundamental measure density functional theory for one-dimensional nonadditive hard-rod fluid mixtures and compared its predictions for the bulk structural properties with Monte Carlo simulations. The aim of this Brief Report is to recall that the problem admits an exact solution in the bulk, which is briefly summarized in a self-contained way.

Density functional theory for molecular orientation of hard rod fluids in hard slits

A density functional theory (DFT) is used to investigate molecular orientation of hard rod fluids in a hard slit. The DFT approach combines a modified fundamental measure theory (MFMT) for excluded-volume effect with the first order thermodynamics perturbation theory for chain connectivity. In the DFT approach, the intra-molecular bonding orientation function is introduced. We consider the effects of molecular length (i.e. aspect ratio of rod) and packing fraction on the orientations of hard rod fluids and flexible chains. For the flexible chains, the chain length has no significant effect while the packing fraction shows slight effect on the molecular orientation distribution. In contrast, for the hard rod fluids, the chain length determines the molecular orientation distribution, while the packing fraction has no significant effect on the molecular orientation distribution. By making a comparison between molecular orientations of the flexible chain and the hard rod fluid, we find that the molecular stiffness distinctly affects the molecular orientation. In addition, partitioning coefficient indicates that the longer rodlike molecule is more difficult to enter the confined phase, especially at low bulk packing fractions.

Capillary ordering and layering transitions in two-dimensional hard-rod fluids

We calculate the surface phase diagram of a two-dimensional hard-rod fluid confined between two hard lines. In the first stage we study a semi-infinite system consisting of an isotropic fluid in contact with a single hard line. We have found complete wetting by the columnar phase at the wall-isotropic fluid interface. When the fluid is confined between two hard walls, capillary columnar ordering occurs via a first-order phase transition. For higher chemical potentials the system exhibits layering transitions even for very narrow slits (near the one-dimensional limit). The theoretical model used was a density-functional theory based on the fundamental-measure functional applied to a fluid of hard rectangles in the restricted-orientation approximation (Zwanzig model). The results presented here can be checked experimentally in two-dimensional granular media made of rods, where vertical motions induced by an external source and excluded volume interactions between the grains allow the system to explore those stationary states which entropically maximize packing configurations. We claim that some of the surface phenomena found here can be present in two-dimensional granular-media fluids.

Theory of thermostatted inhomogeneous granular fluids: A self-consistent density functional description

The authors present a study of the nonequilibrium statistical properties of a one dimensional hard-rod fluid dissipating energy via inelastic collisions and subject to the action of a Gaussian heat bath, simulating an external driving mechanism. They show that the description of the fluid based on the one-particle phase-space reduced distribution function, in principle necessary because of the presence of velocity dependent collisional dissipation, can be contracted to a simpler description in configurational space. Indeed, by means of a multiple-time-scale method the authors derive a self-consistent governing equation for the particle density distribution function. This equation is similar to the dynamic density functional equation employed in the study of colloids, but contains additional terms taking into account the inelastic nature of the fluid. Such terms cannot be derived from a Liapunov generating functional and contribute not only to the relaxational properties, but also to the nonequilibrium steady state properties. A validation of the theory against molecular dynamics simulations is presented in a series of cases, and good agreement is found.

Kinetic Pathways for the Isotropic-Nematic Phase Transition in a System of Colloidal Hard Rods: A Simulation Study

We study the kinetic pathways for the isotropic-to-nematic transition in a fluid of colloidal hard rods. In order to follow the formation of the nematic phase, we develop a new cluster criterion that distinguishes nematic clusters from the isotropic phase. Applying this criterion in Monte Carlo simulations, we find spinodal decomposition as well as nucleation and growth depending on the supersaturation. We determine the height of the nucleation barrier and we study the shape and structure of the cluster. More specifically, we find ellipsoidal nematic clusters with an aspect ratio of about 1.7 and a homogeneous nematic director field. Our results are consistent with theoretical predictions on the shape and director field of nematic tactoids. Classical nucleation theory gives reasonable predictions for the height of the nucleation barrier and the critical nucleus size.