Orientational Degrees Of Freedom Research Articles

Boltzmann's H-function for molecules with orientational degrees of freedom: Emergence of unique features.

Boltzmann's H-function H(t), often regarded as an analog of time-dependent entropy, holds a venerable place in the history of science. However, accurate numerical evaluation of H(t) for particles other than atoms is rare. To remove this lacuna, we generalize Boltzmann's H-function to a gas of molecules with orientational degrees of freedom and evaluate H(t) from the time-dependent joint probability distribution function f(p, L, t) for linear (p) and angular (L) momenta, evolving from an initial nonequilibrium state, by molecular dynamics simulations. We consider both prolate- and oblate-shaped particles, interacting via the well-known Gay-Berne potential and obtain the relaxation of the generalized molecular H(t) from initial (t = 0) nonequilibrium states. In the long-time limit, the H function saturates to its exact equilibrium value, which is the sum of translational and rotational contributions to the respective entropies. Both the translational and rotational components of H(t) decay nearly exponentially with time; the rotational component is more sensitive to the molecular shape that enters through the aspect ratio. A remarkable rapid decrease in the rotational relaxation time is observed as the spherical limit is approached, in a way tantalizingly reminiscent of Hu-Zwanzig hydrodynamic prediction with the slip boundary condition. In addition, we obtain H(t) analytically by solving the appropriate translational and rotational Fokker-Planck equation and obtain a modest agreement with simulations. We observe a remarkable signature of translation-rotation coupling as a function of molecular shape, captured through a physically meaningful differential term that quantifies the magnitude of translation-rotation coupling.

Impact of ageing on structure of random sequential adsorption packings of discorectangles

The ageing processes in the systems of elongated particles (discorectangles) adsorbed on a plane was studied numerically. An off-lattice model with continuous positional and orientational degrees of freedom was tested. The initial jammed state was produced using the random sequential adsorption (RSA) model. The transition from the jammed to equilibrium states were performed via translational and rotational Brownian motions. An aspect ratio of the particles (length-to-width ratio) was varied within the range ε=1−12 . At ɛ < 10 the relaxation into the isotropic state was always observed. In the intermediate range, 10⩽ε⩽11 , the relaxation transition into the states with ordered domains was observed. Particularly, for ɛ = 10 this transition was related with significant finite size scaling effects. For particles with ɛ = 12 formation of the large scale quasi-nematic domains and unlimited domain growth was observed. The impact of the relaxation on the domain structure, porosity, percolation connectivity and tracer particle diffusion in such barrier systems was also discussed.

A geometric formulation of Schaefer’s theory of Cosserat solids

The Cosserat solid is a theoretical model of a continuum whose elementary constituents are notional rigid bodies, having both positional and orientational degrees of freedom. In this article, we present a differential geometric formulation of the mechanics of a Cosserat solid, motivated by Schaefer’s “motor field” theory. The solid is modeled as a special principal fiber bundle (a Cartan space) and its configurations are related by bundle maps. We show that the classical Lagrangian strain measure of a Cosserat solid is the difference of two Cartan connections on the bundle. The infinitesimal strain is derived by a rigorous linearization and is revealed to be the Lie derivative of a Cartan connection along the vector field representing the infinitesimal deformation. Incompatibilities in a Cosserat solid are characterised by a non-flat Cartan connection whose curvature is recognized as the density of topological defects. Stresses are defined as vector bundle-valued differential forms that are work-dual to strains and balance laws in the limit of vanishing inertia are obtained via a d’Alembert principle. Constitutive equations, with an emphasis on recent applications to active oriented solids, are briefly discussed.

Atomic Structure and Dynamics of Organic-Inorganic Hybrid Perovskite Formamidinium Lead Iodide.

The atomic dynamic behaviors of formamidinium lead iodide [HC(NH2)2PbI3] are critical for understanding and improving photovoltaic performances. However, they remain unclear. Here, we investigate the structural phase transitions and the reorientation dynamics of the formamidinium cation [HC(NH2)2+, FA+] of FAPbI3 using neutron scattering techniques. Two structural phase transitions occur with decreasing temperature, from cubic to tetragonal phase at 285 K and then to another tetragonal at 140 K, accompanied by gradually frozen reorientation of FA cations. The nearly isotropic reorientation in the cubic phase is suppressed to reorientation motions involving a two-fold (C2) rotation along the N···N axis and a four-fold (C4) rotation along the C-H axis in the tetragonal phase, and eventually to local disordered motion as a partial C4 along the C-H axis in another tetragonal phase, thereby indicating an intimate interplay between lattice and orientation degrees of freedom in the hybrid perovskite materials. The present complete atomic structure and dynamics provide a solid standing point to understand and then improve photovoltaic properties of organic-inorganic hybrid perovskites in the future.

Theory of melting of glasses

ABSTRACT Glassy matter like crystals resists change in shape. Therefore a theory for their continuous melting should show how the shear elastic constant μ goes to zero. Since viscosity is the long wave-length low frequency limit of shear correlations, the same theory should give phenomena like the Volger-Fulcher dependence of the viscosity on temperature near the transition. A continuum model interrupted randomly by asymmetric rigid defects with orientational degrees of freedom is considered. Such defects are orthogonal to the continuum excitations, and are required to be imprisoned by rotational motion of the nearby atoms of the continuum. The defects interact with an angle dependent potential. A renormalisation group for the elastic constants, and the fugacity of the defects in 3D is constructed. The principal results are that there is a scale-invariant reduction of μ as a function of length at any temperature , above which it is 0 macrosopically but has a finite correlation length which diverges as . Viscosity is shown to be proportional to and has the Vogel-Fulcher form. The specific heat is . As , the Kauzman temperature from above, the configuration entropy of the liquid is exhausted. The theory also gives the ‘fragility’ of glasses in terms of their .

Fission dynamics of excited compound nuclei in a wide range of fissile parameters produced in O16,18+X reactions within a stochastic approach

A stochastic approach based on four-dimensional Langevin equations has been used to simulate the fission dynamics of the excited compound nuclei $^{256}\mathrm{Fm}, ^{254}\mathrm{Fm}, ^{224}\mathrm{Th}, ^{215}\mathrm{Fr}, ^{213}\mathrm{Fr}, ^{200}\mathrm{Pb}, ^{187}\mathrm{Ir}, ^{172}\mathrm{Yb}, ^{170}\mathrm{Yb}, ^{162}\mathrm{Yb}, ^{142}\mathrm{Ce}$, and $^{125}\mathrm{Cs}$ produced in ${}^{16,18}\mathrm{O}+X$ reactions with projectile energies 158.8 and 288 MeV. The effect of nuclear dissipation was investigated in the dynamical simulation of fission process of these nuclei. The average prescission neutron multiplicity, the fission time, the average total kinetic energy of fission fragments, the mass and energy distribution of fission fragments, and the variation of the prescission neutron multiplicity with total kinetic energy of fission fragments have been calculated for these nuclei. The dynamical calculations have taken into account not only three shape collective coordinates introduced on the basis of the ``funny hills'' shape parameters but also orientation degree of freedom (spin about the symmetry axis), and in the dynamical calculations dissipation generated through the chaos-weighted wall and window friction formula and also the sum of the chaos-weighted wall and window friction formula with the two-body nuclear friction. Furthermore, the effect of dissipation coefficient of $K, {\ensuremath{\gamma}}_{K}$, were also considered in the dynamical calculations. Comparison of the theoretical results with the experimental data shows that the experimental data for compound nuclei produced with the projectile energy 158.8 MeV can be reproduced satisfactorily with the results of calculations by using the chaos-weighted wall and window friction formula, although the results of calculations of the average prescission neutron multiplicity, the fission time, and the variation of the pre-scission neutron multiplicity with total kinetic energy of fission fragments lie somewhat below the experimental data for heavy nuclei produced in reactions with projectile energy ${E}_{\mathrm{lab}}=158.8\phantom{\rule{0.28em}{0ex}}\mathrm{MeV}$ and also for compound nuclei produced with the projectile energy 288 MeV. It was also shown that for reproducing experimental data for heavy nuclei produced in reactions with projectile energy ${E}_{\mathrm{lab}}=158.8\phantom{\rule{0.16em}{0ex}}\mathrm{MeV}$ and also for nuclei produced with projectile energy ${E}_{\mathrm{lab}}=288\phantom{\rule{0.16em}{0ex}}\mathrm{MeV}$ is suitable to use the sum of the chaos-weighted wall and window friction formula with the two-body nuclear friction in the Langevin equations. In other words, for simulations of fission dynamics of nuclei at high excitation energies and also for heavy nuclei it is suitable to use the sum of the chaos-weighted wall and window friction formula with the two-body nuclear friction in the Langevin equations.

Elasticity of Semiflexible ZigZag Nanosprings with a Point Magnetic Moment.

Kinks can appear along the contour of semiflexible polymers (biopolymers or synthetic ones), and they affect their elasticity and function. A regular sequence of alternating kink defects can form a semiflexible nanospring. In this article, we theoretically analyze the elastic behavior of such a nanospring with a point magnetic dipole attached to one end while the other end is assumed to be grafted to a rigid substrate. The rod-like segments of the nanospring are treated as weakly bending wormlike chains, and the propagator (Green's function) method is used in order to calculate the conformational and elastic properties of this system. We analytically calculate the distribution of orientational and positional fluctuations of the free end, the force-extension relation, as well as the compressional force that such a spring can exert on a planar wall. Our results show how the magnetic interaction affects the elasticity of the semiflexible nanospring. This sensitivity, which is based on the interplay of positional and orientational degrees of freedom, may prove useful in magnetometry or other applications.

Davydov–Kyslukha model as the starting point in the development of integrable multi-component nonlinear dynamical systems on quasi-one-dimensional lattices

The Davydov–Kyslukha nonlinear exciton-phonon model on a regular one-dimensional lattice is asserted to be the driving force for the development of integrable multi-component nonlinear dynamical systems encompassing excitonic, vibrational and orientational degrees of freedom. The two most representative quasi-one-dimensional integrable multi-component nonlinear systems inspired by the Davydov–Kyslukha model are presented explicitly in their concise Hamiltonian forms. The new six-subsystem integrable nonlinear model on a regular quasi-one-dimensional lattice is proposed and its derivation based upon the appropriate zero-curvature representation is presented. The constructive aspect of the famous Davydov motto is illustrated by the examples of semi-discrete integrable nonlinear dynamical systems canonicalizeable via the proper point transformations to the physically motivated field variables.

Zwitterionic Polymers toward the Development of Orientation-Sensitive Bioprobes

Dynamics with an orientational degree of freedom are fundamental in biological events. Probes with polarized luminescence enable a determination of the orientation. Lanthanide-doped nanocrystals can provide more precise analysis than quantum dots due to the nonphotoblinking/bleaching nature and the multiple line-shaped emission. However, the intrinsic polarization property of the original nanocrystals often deteriorates in complex physiological environments because the colloidal stability easily breaks and the probes aggregate in the media with abundant salts and macromolecules. Engineering the surface chemistry of the probes is thus essential to be compatible with biosystems, which has remained a challenging task that should be exclusively addressed for each specific probe. Here, we demonstrate a facile and efficient surface functionalization of lanthanide-doped nanorods by zwitterionic block copolymers. Due to the steric interaction and the intrinsic zwitterionic nature of the polymers, high colloidal stability of the zwitterionic nanorod suspension is achieved over wide ranges of pH and concentration of salts, even giving rise to the lyotropic liquid crystalline behavior of the nanorods in physiological media. The shear-aligned ability is shown to be unaltered by the coated polymers, and thus, the strongly polarized emission of Eu3+ is preserved. Besides, biological experiments reveal good biocompatibility of the zwitterionic nanorods with negligible nonspecific binding. This study is a stepping stone for the use of the nanorods as orientation probes in biofluids and validates the strategy of coupling zwitterions to lanthanide-doped nanocrystals for various bioapplications.

Thermodynamic perturbation theory coefficients for hard spherocylinders and cylinders

Thermodynamic perturbation theories are indispensable in the development of equations of state based on Statistical Mechanics. Recently, a new statistical thermodynamic model has been proposed in which molecules are represented as cylindrically symmetric hard bodies (ellipsoids of revolution, spherocylinders, and cylinders) interacting with identical neighboring molecules through a spherically symmetric square-well potential. This novel equation of state embeds at least two approximations to the Onsager’s second virial theory: one restrains the equation of state to systems with an isotropic (disordered) orientation distribution, while the other decouples the translational and orientational degrees of freedom, being only valid at low densities. Using canonical Monte Carlo simulations, we investigated the feasibility of such approximations by determining the uniaxial nematic order parameter of the systems and calculating the first- and second-order perturbation coefficients of the high-temperature series expansion (HTSE) of the Helmholtz free energy. Our results indicate that both approximations are reasonable for a certain range of packing fractions and molecular anisotropies. We have also calculated the full Helmholtz free energy of the perturbed system, which can be used for determining high-order perturbation terms to improve the predictive capability of the equation of state.

A one-dimensional high-order commensurate phase of tilted molecules.

We report on the formation of a high-order commensurate (HOC) structure of 5,14-dihydro-5,7,12,14-tetraazapentacene (DHTAP) molecules on the highly corrugated Cu(110)–(2 × 1)O surface. Scanning tunnelling microscopy shows that the DHTAP molecules form a periodic uniaxial arrangement in which groups of seven molecules are distributed over exactly nine substrate lattice spacings along the [1̄10] direction. DFT-calculations reveal that this peculiar arrangement is associated with different tilting of the seven DHTAP molecules within the quasi one-dimensional HOC unit cell. The orientational degree of freedom thus adds a new parameter, which can efficiently stabilize complex molecular structures on corrugated surfaces.

High accuracy ab initio potential energy surface for the H2O-H van der Waals dimer.

A representation of the three-dimensional potential energy surface (PES) of the H2O-H van der Waals dimer is presented. The H2O molecule is treated as a rigid body held at its experimentally determined equilibrium geometry, with the OH bond length set to 1.809 650 34 a0 and the HOH bond angle set to 1.824 044 93 radians. Ab initio calculations are carried out at the coupled-cluster single, double, and perturbative triple level, with scalar relativistic effects included using the second-order Douglas-Kroll-Hess approximation. The ab initio calculations employ the aug-cc-pVnZ-DK series of basis sets (n = D, T, Q), which are recontracted versions of the aug-cc-pVnZ basis sets that are appropriate for relativistic calculations. The counterpoise method is used to reduce the basis set superposition error; in addition, results obtained using the aug-cc-pVTZ-DK and aug-cc-pVQZ-DK basis sets were extrapolated to the complete basis set (CBS) limit. The PES is based on calculations carried out at 1054 symmetry-unique H2O-H geometries for which the distance R between the H-atom and the H2O center of mass ranges from R = 2.5-9.0 Å. The reproduction of the PES along the orientational degrees of freedom was performed using Lebedev quadrature and an expansion in spherical harmonics. The mean absolute error of the reproduced PES is <0.02cm-1 for R ≥ 3.0 Å and <0.21cm-1 for R between 2.5 and 3.0 Å. The global minimum for the CBS PES is a coplanar H2O-H geometry, with R = 3.41 Å, in which the angle formed between the H2O C2 symmetry axis and the H-atom is 122.25°; the CBS binding energy for this geometry is 61.297cm-1. In addition, by utilizing the symmetry of the H2O molecule, the spherical harmonic expansion was simplified with no loss in accuracy and a speedup of ∼1.8 was achieved. The reproduced PES can be used in future molecular dynamics simulations.

Jerky active matter: a phase field crystal model with translational and orientational memory

Most field theories for active matter neglect effects of memory and inertia. However, recent experiments have found inertial delay to be important for the motion of self-propelled particles. A major challenge in the theoretical description of these effects, which makes the application of standard methods very difficult, is the fact that orientable particles have both translational and orientational degrees of freedom which do not necessarily relax on the same time scale. In this work, we derive the general mathematical form of a field theory for soft matter systems with two different time scales. This allows to obtain a phase field crystal model for active particles with translational and orientational memory. Notably, this theory is of third order in temporal derivatives and can thus be seen as a spatiotemporal jerky dynamics. We obtain the phase diagram of this model, which shows that, unlike in the passive case, the linear stability of the liquid state depends on the damping coefficients. Moreover, we investigate sound waves in active matter. It is found that, in active fluids, there are two different mechanisms for sound propagation. For certain parameter values and sufficiently high frequencies, sound mediated by polarization waves experiences less damping than usual passive sound mediated by pressure waves of the same frequency. By combining the different modes, acoustic frequency filters based on active fluids could be realized.

Connectedness percolation in the random sequential adsorption packings of elongated particles.

Connectedness percolation phenomena in the two-dimensional packing of elongated particles (discorectangles) were studied numerically. The packings were produced using random sequential adsorption off-lattice models with preferential orientations of the particles along a given direction. The partial ordering was characterized by the order parameter S, with S=0 for completely disordered films (random orientation of particles) and S=1 for completely aligned particles along the horizontal direction x. The aspect ratio (length-to-width ratio) of the particles was varied within the range ɛ∈[1;100]. Analysis of connectivity was performed assuming a core-shell structure of the particles. The value of S affected the structure of the packings, the formation of long-range connectivity, and the behavior of the electrical conductivity. The effects can be explained by taking accounting of the competition between the particles' orientational degrees of freedom and excluded volume effects. For aligned deposition, anisotropy in the electrical conductivity was observed with the values along the alignment direction σ_{x} being larger than the values in the perpendicular direction σ_{y}. Anisotropy in the localization of the percolation threshold was also observed in finite-sized packings, but it disappeared in the limit of infinitely large systems.

Concentration banding instability of a sheared bacterial suspension

Abstract

Density Functional Approach to the Molecular Theory of Rod-Coil Diblock Copolymers

The general density functional approach is used to develop a molecular-statistical theory of rod-coil diblock copolymers which is valid in the case of both weak and strong segregation. The free energy of the rod-coil copolymer is expressed as a functional of the number densities of rod and coil monomers which depend on the translational and orientational degrees of freedom. The equilibrium densities are determined by minimization of the free energy functional and depend on the orientational and translational order parameters of the monomers. The order parameters are calculated numerically by minimization of the free energy taking into account the incompressibility condition within the formalism of Lagrange multipliers. Phase diagrams are obtained and the profiles of orientational and translational order parameters are presented as functions of temperature and the fraction of coil fragments. It is shown that the lamellar phase possesses strong orientational order and the stability of the phase is increasing with the increasing fraction of rod monomers.

Paris car parking problem for partially oriented discorectangles on a line.

The random sequential adsorption (RSA) of identical elongated particles (discorectangles) on a line ("Paris car parking problem") was studied numerically. An off-lattice model with continuous positional and orientational degrees of freedom was considered. The possible orientations of the discorectanles were restricted between θ∈[-θ_{m};θ_{m}] while the aspect ratio (length-to-width ratio) for the discorectangles was varied within the range ɛ∈[1;100]. Additionally, the limiting case ɛ=∞ (i.e., widthless sticks) was considered. We observed that the RSA deposition for the problem under consideration was governed by the formation of rarefied holes (containing particles oriented along a line) surrounded by comparatively dense stacks (filled with almost parallel particles oriented in the vertical direction). The kinetics of the changes of the order parameter and the packing density are discussed. Partial ordering of the discorectangles significantly affected the packing density at the jamming state, φ_{j}, and shifted the cusps in the φ_{j}(ɛ) dependencies. This can be explained by the effects on the competition between the particles' orientational degrees of freedom and the excluded volume effects.

Manipulating Hybrid Nanostructures by the Cooperative Assembly of Amphiphilic Oligomers and Triblock Janus Nanoparticles.

The cooperative assembly of nanoparticles and amphiphilic molecules has emerged as an appealing strategy for fabricating hybrid nanomaterials for a wide range of potential applications. However, it is challenging to precisely manipulate hybrid nanostructures. In this study, extensive dissipative particle dynamics simulations are carried out to investigate the cooperative assembly of amphiphilic oligomers and triblock Janus nanoparticles with different hydrophobic-hydrophilic patches. Three different hybrid nanostructures (networks, disks, and vesicles) are observed from the simulations. The structural characteristics and kinetic pathways are analyzed in detail. We reveal that the hydrophobic-hydrophilic patches in the triblock Janus nanoparticles significantly affect the arrangement of amphiphiles and nanoparticles, as well as the orientational degree of freedom between nanoparticles; therefore, the triblock Janus nanoparticles can function as a robust structure-directing agent to regulate the spatial organization of nanoparticles in networks, the curvature of disks, and the size of vesicles. This study demonstrates the cooperative assembly can serve as an efficient platform for the engineering of hybrid nanomaterials with tailored nanostructures.

Properties of surface Landau-de Gennes Q-tensor models.

Uniaxial nematic liquid crystals whose molecular orientation is subjected to tangential anchoring on a curved surface offer a non trivial interplay between the geometry and the topology of the surface and the orientational degree of freedom. We consider a general thin film limit of a Landau-de Gennes Q-tensor model which retains the characteristics of the 3D model. From this, previously proposed surface models follow as special cases. We compare fundamental properties, such as the alignment of the orientational degrees of freedom with principle curvature lines, order parameter symmetry and phase transition type for these models, and suggest experiments to identify suitable model assumptions.

Patchy particles at a hard wall: Orientation-dependent bonding.

The well-known and widely used Wertheim thermodynamic perturbation theory (TPT) of associating fluids averages over the orientational dependence of the bonding interactions. For this reason, density functional theories based on the otherwise very successful TPT have been unable to describe the structure of patchy particle fluids at hard walls, when the coupling of positional and orientational degrees of freedom becomes important at low temperatures [N. Gnan et al., J. Chem. Phys. 137, 084704 (2012)]. As a first attempt at remedying this, we propose to introduce into the theory an additional, nonbonding, anisotropic interparticle potential that enforces end-to-end alignment of two-patch particles. Within the simplest mean-field approximation, this additional potential does not change the thermodynamics of the bulk system and hence preserves its phase diagram but has the qualitatively correct effect on the order parameter and density profiles at a hard wall, as determined from computer simulation.