Self-diffusion of rodlike viruses through smectic layers

Preferential ordering of incommensurate-length guest particles in a smectic host

Using density functional theory, we study the preferential ordering of rod-like guest particles immersed in a smectic host fluid. Within a model of perfectly aligned rods and assuming that the guest particles do not perturb the smectic host fluid, simple excluded-volume arguments explain that guest particles that are comparable in length to the host particles order in phase with the smectic host density layering, whereas guest particles that are considerably shorter or longer order in antiphase. The corresponding free-energy minima are separated by energetic barriers on the order of the thermal energy kBT, suggesting that guest particles undergo hopping-type diffusion between adjacent smectic layers. Upon introducing a slight orientational mismatch between the guest particles and the perfectly aligned smectic host, an additional, smaller free-energy barrier emerges for a range of intermediate guest-to-host length ratios, which splits the free-energy minimum into two. Guest particles in this range occupy positions intermediate between in-phase ordering and in-antiphase ordering. Finally, we use Kramers' theory to identify slow, fast, and intermediate diffusive regimes for the guest particles as a function of their length. Our model is in qualitative agreement with experiment and simulation and provides an alternative, complementary explanation in terms of a free-energy landscape for the intermediate diffusive regime, which was previously hypothesized to result from temporary caging effects [M. Chiappini, E. Grelet, and M. Dijkstra, Phys. Rev. Lett. 124, 087801 (2020)]. We argue that our simple model of aligned rods captures the salient features of incommensurate-length guest particles in a smectic host if a slight orientational mismatch is introduced.

Insight into the Viscoelasticity of Self-Assembling Smectic Liquid Crystals of Colloidal Rods from Active Microrheology Simulations

The rheology of colloidal suspensions is of utmost importance in a wide variety of interdisciplinary applications in formulation technology, determining equally interesting questions in fundamental science. This is especially intriguing when colloids exhibit a degree of long-range positional or orientational ordering, as in liquid crystals (LCs) of elongated particles. Along with standard methods, microrheology (MR) has emerged in recent years as a tool to assess the mechanical properties of materials at the microscopic level. In particular, by active MR one can infer the viscoelastic response of a soft material from the dynamics of a tracer particle being dragged through it by external forces. Although considerable efforts have been made to study the diffusion of guest particles in LCs, little is known about the combined effect of tracer size and directionality of the dragging force on the system's viscoelastic response. By dynamic Monte Carlo simulations, we apply active MR to investigate the viscoelasticity of self-assembling smectic (Sm) LCs consisting of rodlike particles. In particular, we track the motion of a spherical tracer whose size is varied within a range of values matching the system's characteristic length scales and being dragged by constant forces that are parallel, perpendicular, or at 45° to the nematic director. Our results reveal a uniform value of the effective friction coefficient as probed by the tracer at small and large forces, whereas a nonlinear, force-thinning regime is observed at intermediate forces. However, at relatively weak forces the effective friction is strongly determined by correlations between the tracer size and the structure of the host fluid. Moreover, we also show that external forces forming an angle with the nematic director provide additional details that cannot be simply inferred from the mere analysis of parallel and perpendicular forces. Our results highlight the fundamental interplay between tracer size and force direction in assessing the MR of Sm LC fluids.

Universal to nonuniversal transition of the statistics of rare events during the spread of random walks

Through numerous experiments that analyzed rare event statistics in heterogeneous media, it was discovered that in many cases the probability density function for particle position, P(X,t), exhibits a slower decay rate than the Gaussian function. Typically, the decay behavior is exponential, referred to as Laplace tails. However, many systems exhibit an even slower decay rate, such as power-law, log-normal, or stretched exponential. In this study, we utilize the continuous-time random walk method to investigate the rare events in particle hopping dynamics and find that the properties of the hop size distribution induce a critical transition between the Laplace universality of rare events and a more specific, slower decay of P(X,t). Specifically, when the hop size distribution decays slower than exponential, such as e^{-|x|^{β}} (β>1), the Laplace universality no longer applies, and the decay is specific, influenced by a few large events, rather than by the accumulation of many smaller events that give rise to Laplace tails.

Elastic response of colloidal smectic liquid crystals: Insights from microscopic theory

Elongated colloidal rods at sufficient packing conditions are known to form stable lamellar or smectic phases. Using a simplified volume-exclusion model, we propose a generic equation of state for hard-rod smectics that is robust against simulation results and is independent of the rod aspect ratio. We then extend our theory by exploring the elastic properties of a hard-rod smectic, including the layer compressibility (B) and bending modulus (K_{1}). By introducing weak backbone flexibility we are able to compare our predictions with experimental results on smectics of filamentous virus rods (fd) and find quantitative agreement between the smectic layer spacing, the out-of-plane fluctuation strength, as well as the smectic penetration length λ=sqrt[K_{1}/B]. We demonstrate that the layer bending modulus is dominated by director splay and depends sensitively on lamellar out-of-plane fluctuations that we account for on the single-rod level. We find that the ratio between the smectic penetration length and the lamellar spacing is about two orders of magnitude smaller than typical values reported for thermotropic smectics. We attribute this to the fact that colloidal smectics are considerably softer in terms of layer compression than their thermotropic counterparts while the cost of layer bending is of comparable magnitude.

Long-time relaxation dynamics in nematic and smectic liquid crystals of soft repulsive colloidal rods

Understanding the relaxation dynamics of colloidal suspensions is crucial to identifying the elements that influence the mobility of their constituents, assessing their macroscopic response across the relevant time and length scales, and thus disclosing the fundamentals underpinning their exploitation in formulation engineering. In this work, we specifically assess the impact of long-ranged ordering on the relaxation dynamics of suspensions of soft repulsive rodlike particles, which are able to self-organize into nematic and smectic liquid-crystalline phases. Rods are modeled as soft repulsive spherocylinders with a length-to-diameter ratio L^{★}=5, interacting via the truncated and shifted Kihara potential. By performing dynamic Monte Carlo simulations, we analyze the effect of translational and orientational order on the diffusion of the rods along the relevant directions imposed by the morphology of the background phases. To provide a clear picture of the resulting dynamics, we assess its dependence on temperature, which can dramatically determine the response time of the system relaxation and the self-diffusion coefficients of the rods. The computation of the van Hove correlation functions allows us to identify the existence of rods that diffuse significantly faster than the average and whose concentration can be accurately adjusted by a suitable choice of temperature.

Phase behavior of hard circular arcs

By using Monte Carlo numerical simulation, this work investigates the phase behavior of systems of hard infinitesimally thin circular arcs, from an aperture angle θ→0 to an aperture angle θ→2π, in the two-dimensional Euclidean space. Except in the isotropic phase at lower density and in the (quasi)nematic phase, in the other phases that form, including the isotropic phase at higher density, hard infinitesimally thin circular arcs autoassemble to form clusters. These clusters are either filamentous, for smaller values of θ, or roundish, for larger values of θ. Provided the density is sufficiently high, the filaments lengthen, merge, and straighten to finally produce a filamentary phase while the roundels compact and dispose themselves with their centers of mass at the sites of a triangular lattice to finally produce a cluster hexagonal phase.

When bigger is faster: A self-Van Hove analysis of the enhanced self-diffusion of non-commensurate guest particles in smectics

We investigate the anomalous dynamics in smectic phases of short host rods where, counter-intuitively, long guest rod-shaped particles diffuse faster than the short host ones due to their precise size mismatch. In addition to the previously reported mean-square displacement, we analyze the time evolution of the self-Van Hove functions G(r, t), as this probability density function uncovers intrinsic heterogeneous dynamics. Through this analysis, we show that the dynamics of the host particles parallel to the director becomes non-Gaussian and therefore heterogeneous after the nematic-to-smectic-A phase transition, even though it exhibits a nearly diffusive behavior according to its mean-squared displacement. In contrast, the non-commensurate guest particles display Gaussian dynamics of the parallel motion, up to the transition to the smectic-B phase. Thus, we show that the self-Van Hove function is a very sensitive probe to account for the instantaneous and heterogeneous dynamics of our system and should be more widely considered as a quantitative and complementary approach of the classical mean-squared displacement characterization in diffusion processes.

Diffusion of Anisotropic Colloids in Periodic Arrays of Obstacles

Colloidal suspensions in confined geometries exhibit rich diffusion dynamics governed by particle shapes and particle-confinement interactions. Here, we propose a colloidal system, consisting of ellipsoids in periodic array of obstacles, to investigate the confined diffusion of anisotropic colloids. From the obstacle density-dependent diffusion, we discover a decoupling of translational and rotational diffusion in which only rotational motion is localized while translational motion remains diffusive. Moreover, by evaluating the probability distributions of displacements, we found Brownian but non-Gaussian diffusion behaviors with increasing the obstacle densities, which originates from the shape anisotropy of the colloid and the multiplicity of the local configurations of the ellipsoids with respect to the obstacle. Our results suggest that the shape anisotropy and spatial confinements play a vital role in the diffusion dynamics. It is important for understanding the transportations of anisotropic objects in complex environments.

Speeding up Dynamics by Tuning the Noncommensurate Size of Rodlike Particles in a Smectic Phase

Using simulations, we study the diffusion of rodlike guest particles in a smectic environment of rodlike host particles. We find that the dynamics of guest rods across smectic layers changes from a fast nematiclike diffusion to a slow hopping-type dynamics via an intermediate switching regime by varying the length of the guest rods with respect to the smectic layer spacing. We determine the optimal rod length that yields the fastest and the slowest diffusion in a lamellar environment. We show that this behavior can be rationalized by a complex 1D effective periodic potential exhibiting two energy barriers, resulting in a varying preferred mean position of the guest particle in the smectic layer. The interplay of these two barriers controls the dynamics of the guest particles yielding a slow, an intermediate, and a fast diffusion regime depending on the particle length.

Short and Soft: Multidomain Organization, Tunable Dynamics, and Jamming in Suspensions of Grafted Colloidal Cylinders with a Small Aspect Ratio

The yet virtually unexplored class of soft colloidal rods with a small aspect ratio is investigated and shown to exhibit a very rich phase and dynamic behavior, spanning from liquid to nearly melt state. Instead of the nematic order, these short and soft nanocylinders alter their organization with increasing concentration from isotropic liquid with random orientation to small domains with preferred local orientation and eventually a multidomain arrangement with a local orientational order. The latter gives rise to a kinetically suppressed state akin to structural glass with detectable terminal relaxation, which, on further increasing concentration, reveals features of hexagonally packed order as in ordered block copolymers. The respective dynamic response comprises four regimes, all above the overlapping concentration of 0.02 g/mL:(I) from 0.03 to 0.1 g/mol, the system undergoes a liquid-to-solidlike transition with a structural relaxation time that grows by 4 orders of magnitude. (II) From 0.1 to 0.2 g/mL, a dramatic slowing-down is observed and is accompanied by an evolution from isotropic to a multidomain structure. (III) Between 0.2 and 0.6 g/mol, the suspensions exhibit signatures of shell interpenetration and jamming, with the colloidal plateau modulus depending linearly on concentration. (IV) At 0.74 g/mL, in the densely jammed state, the viscoelastic signature of hexagonally packed cylinders from microphase-separated block copolymers is detected. These properties set short and soft nanocylinders apart from long colloidal rods (with a large aspect ratio) and provide insights for fundamentally understanding the physics in this intermediate soft colloidal regime and for tailoring the flow properties of nonspherical soft colloids.

Structure, dynamics and phase behavior of short rod inclusions dissolved in a colloidal membrane

Inclusions dissolved in an anisotropic quasi-2D membrane acquire new types of interactions that can drive assembly of complex structures and patterns. We study colloidal membranes composed of a binary mixture of long and short rods, such that the length ratio of the long to short rods is approximately two. At very low volume fractions, short rods dissolve in the membrane of long rods by strongly anchoring to the membrane polymer interface. At higher fractions, the dissolved short rods phase separate from the background membrane, creating a composite structure comprised of bilayer droplets enriched in short rods that coexist with the background monolayer membrane. These results demonstrate that colloidal membranes serve as a versatile platform for assembly of soft materials, while simultaneously providing new insight into universal membrane-mediated interactions.

Energy landscape of colloidal dumbbells in a periodic distribution of light

Using a ray tracing calculation, the energy landscape of dumbbells, made of spherical colloidal particles, interacting with a periodic distribution of light is calculated. As shown previously [E. Sarmiento-Gomez, J. A. Rivera-Moran and J. L. Aruaz-Lara, Soft Matter, 2018, 14, 3684], planar aggregates of spherical particles adopt discrete configurations in such light distribution. Here we focus on the case of colloidal dumbbells both symmetric and asymmetric from an experimental and theoretical point of view. It has been shown that the direct calculation using the ray tracing approximation is in excellent agreement with the experiment in spite of the fact that the particles size and the wavelength of the trapping light are comparable. We also corroborate, at least for the more simple case of a single particle in a parabolic light distribution, that the simple method used here provides the same results as the more complex and general Lorenz-Mie approach giving a more simple yet reliable method for the calculation of the energy landscape of colloidal aggregates in periodic light distributions.

Synthesis of Colloidal SU-8 Polymer Rods Using Sonication

The bulk synthesis of fluorescent colloidal SU-8 polymer rods with tunable dimensions is described. The colloidal SU-8 rods are prepared by shearing an emulsion of SU-8 polymer droplets and then exposing the resulting non-Brownian rods to ultrasonic waves, which breaks them into colloidal rods with typical lengths of 3.5-10 µm and diameters of 0.4-1 µm. The rods are stable in both aqueous and apolar solvents, and by varying the composition of apolar solvent mixtures both the difference in refractive index and mass density between particles and solvent can be independently controlled. Consequently, these colloidal SU-8 rods can be used in both 3D confocal microscopy and optical trapping experiments while carefully tuning the effect of gravity. This is demonstrated by using confocal microscopy to image the liquid crystalline phases and the isotropic-nematic interface formed by the colloidal SU-8 rods and by optically trapping single rods in water. Finally, the simultaneous confocal imaging and optical manipulation of multiple SU-8 rods in the isotropic phase is shown.

Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales

Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.

Dynamically crowded solutions of infinitely thin Brownian needles

We study the dynamics of solutions of infinitely thin needles up to densities deep in the semidilute regime by Brownian dynamics simulations. For high densities, these solutions become strongly entangled and the motion of a needle is essentially restricted to a one-dimensional sliding in a confining tube composed of neighboring needles. From the density-dependent behavior of the orientational and translational diffusion, we extract the long-time transport coefficients and the geometry of the confining tube. The sliding motion within the tube becomes visible in the non-Gaussian parameter of the translational motion as an extended plateau at intermediate times and in the intermediate scattering function as an algebraic decay. This transient dynamic arrest is also corroborated by the local exponent of the mean-square displacements perpendicular to the needle axis. Moreover, the probability distribution of the displacements perpendicular to the needle becomes strongly non-Gaussian; rather, it displays an exponential distribution for large displacements. On the other hand, based on the analysis of higher-order correlations of the orientation we find that the rotational motion becomes diffusive again for strong confinement. At coarse-grained time and length scales, the spatiotemporal dynamics of the needle for the high entanglement is captured by a single freely diffusing phantom needle with long-time transport coefficients obtained from the needle in solution. The time-dependent dynamics of the phantom needle is also assessed analytically in terms of spheroidal wave functions. The dynamic behavior of the needle in solution is found to be identical to needle Lorentz systems, where a tracer needle explores a quenched disordered array of other needles.

Fast Diffusion of Long Guest Rods in a Lamellar Phase of Short Host Particles

We investigate the dynamic behavior of long guest rodlike particles immersed in liquid crystalline phases formed by shorter host rods, tracking both guest and host particles by fluorescence microscopy. Counterintuitively, we evidence that long rods diffuse faster than short rods forming the one-dimensional ordered smectic-A phase. This results from the larger and noncommensurate size of the guest particles as compared to the wavelength of the energy landscape set by the lamellar stack of liquid slabs. The long guest particles are also shown to be still mobile in the crystalline smectic-B phase, as they generate their own voids in the adjacent layers.

Colloidal liquid crystals in square confinement: isotropic, nematic and smectic phases

We report on the confinement of colloidal liquid crystals in three dimensional chambers with a square footprint. To this end we use colloidal silica rods and exploit their relatively large density difference with respect to the dispersing solvent to study isotropic, nematic and smectic phases confined into a single chamber. Combining laser scanning confocal microscopy and soft-lithography techniques enables us to characterize the configurations down to the single particle level. We will focus on the smectic phase and compare to recent theories and simulations.

Chiral twist drives raft formation and organization in membranes composed of rod-like particles

Lipid rafts are hypothesized to facilitate protein interaction, tension regulation, and trafficking in biological membranes, but the mechanisms responsible for their formation and maintenance are not clear. Insights into many other condensed matter phenomena have come from colloidal systems, whose micron-scale particles mimic basic properties of atoms and molecules but permit dynamic visualization with single-particle resolution. Recently, experiments showed that bidisperse mixtures of filamentous viruses can self-assemble into colloidal monolayers with thermodynamically stable rafts exhibiting chiral structure and repulsive interactions. We quantitatively explain these observations by modeling the membrane particles as chiral liquid crystals. Chiral twist promotes the formation of finite-sized rafts and mediates a repulsion that distributes them evenly throughout the membrane. Although this system is composed of filamentous viruses whose aggregation is entropically driven by dextran depletants instead of phospholipids and cholesterol with prominent electrostatic interactions, colloidal and biological membranes share many of the same physical symmetries. Chiral twist can contribute to the behavior of both systems and may account for certain stereospecific effects observed in molecular membranes.

Tube Concept for Entangled Stiff Fibers Predicts Their Dynamics in Space and Time

We study dynamically crowded solutions of stiff fibers deep in the semidilute regime, where the motion of a single constituent becomes increasingly confined to a narrow tube. The spatiotemporal dynamics for wave numbers resolving the motion in the confining tube becomes accessible in Brownian dynamics simulations upon employing a geometry-adapted neighbor list. We demonstrate that in such crowded environments the intermediate scattering function, characterizing the motion in space and time, can be predicted quantitatively by simulating a single freely diffusing phantom needle only, yet with very unusual diffusion coefficients.

Filamentous Phages As a Model System in Soft Matter Physics

Filamentous phages have unique physical properties, such as uniform particle lengths, that are not found in other model systems of rod-like colloidal particles. Consequently, suspensions of such phages provided powerful model systems that have advanced our understanding of soft matter physics in general and liquid crystals in particular. We described some of these advances. In particular we briefly summarize how suspensions of filamentous phages have provided valuable insight into the field of colloidal liquid crystals. We also describe recent experiments on filamentous phages that have elucidated a robust pathway for assembly of 2D membrane-like materials. Finally, we outline unique structural properties of filamentous phages that have so far remained largely unexplored yet have the potential to further advance soft matter physics and material science.

Finite particle size drives defect-mediated domain structures in strongly confined colloidal liquid crystals

When liquid crystals are confined to finite volumes, the competition between the surface anchoring imposed by the boundaries and the intrinsic orientational symmetry-breaking of these materials gives rise to a host of intriguing phenomena involving topological defect structures. For synthetic molecular mesogens, like the ones used in liquid-crystal displays, these defect structures are independent of the size of the molecules and well described by continuum theories. In contrast, colloidal systems such as carbon nanotubes and biopolymers have micron-sized lengths, so continuum descriptions are expected to break down under strong confinement conditions. Here, we show, by a combination of computer simulations and experiments with virus particles in tailor-made disk- and annulus-shaped microchambers, that strong confinement of colloidal liquid crystals leads to novel defect-stabilized symmetrical domain structures. These finite-size effects point to a potential for designing optically active microstructures, exploiting the as yet unexplored regime of highly confined liquid crystals.

Liquid crystals confined to micrometre-sized geometries can be well described by a continuum theory, where the size effect of constituent mesogens is negligible. Here, the authors show how the continuum theory breaks down in colloidal liquid crystal, leading to the formation of defect-mediated domains.

Diffusion of a nanowire rod through an obstacle field

We report the experimental realization of a rod diffusing in a two-dimensional obstacle field following the single rod dynamics. We use a silver nanowire as our rod and two types of obstacles: repelling light beams and polymer pillars. We study the effect of hydrodynamic interactions on the transport of the rod, comparing both experimental realizations and recent simulations. We propose a framework for analyzing the transport through such systems, and we predict a new superdiffusive regime of rod transport at high obstacle concentration and short times.

Analysis of single particle diffusion with transient binding using particle filtering

Diffusion with transient binding occurs in a variety of biophysical processes, including movement of transmembrane proteins, T cell adhesion, and caging in colloidal fluids. We model diffusion with transient binding as a Brownian particle undergoing Markovian switching between free diffusion when unbound and diffusion in a quadratic potential centered around a binding site when bound. Assuming the binding site is the last position of the particle in the unbound state and Gaussian observational error obscures the true position of the particle, we use particle filtering to predict when the particle is bound and to locate the binding sites. Maximum likelihood estimators of diffusion coefficients, state transition probabilities, and the spring constant in the bound state are computed with a stochastic Expectation-Maximization (EM) algorithm.

Spreading of triboelectrically charged granular matter

We report on the spreading of triboelectrically charged glass particles on an oppositely charged surface of a plastic cylindrical container in the presence of a constant mechanical agitation. The particles spread via sticking, as a monolayer on the cylinder's surface. Continued agitation initiates a sequence of instabilities of this monolayer, which first forms periodic wavy-stripe-shaped transverse density modulation in the monolayer and then ejects narrow and long particle-jets from the tips of these stripes. These jets finally coalesce laterally to form a homogeneous spreading front that is layered along the spreading direction. These remarkable growth patterns are related to a time evolving frictional drag between the moving charged glass particles and the countercharges on the plastic container. The results provide insight into the multiscale time-dependent tribolelectric processes and motivates further investigation into the microscopic causes of these macroscopic dynamical instabilities and spatial structures.

Phase equilibria, fluid structure, and diffusivity of a discotic liquid crystal

Molecular Dynamics simulations were performed for the Gay-Berne discotic fluid parameterized by GB(0.345, 0.2, 1.0, 2.0). The volumetric phase diagram exhibits isotropic (IL), nematic (ND), and two columnar phases characterized by radial distribution functions: the transversal fluid structure varies between a hexagonal columnar (CD) phase (at higher temperatures and pressures) and a rectangular columnar (CO) phase (at lower temperatures and pressures). The slab-wise analysis of fluid dynamics suggests the formation of grain-boundary defects in the CO phase. Longitudinal fluid structure is highly periodic with narrow peaks for the CO phase, suggestive of a near-crystalline (yet diffusive) system, but is only short-ranged for the CD phase. The IL phase does not exhibit anisotropic diffusion. Transversal diffusion is more favorable in the ND phase at all times, but only favorable at short times for the columnar phases. In the columnar phases, a crossover occurs where longitudinal diffusion is favored over transversal diffusion at intermediate-to-long timescales. The anomalous diffusivity is pronounced in both columnar phases, with three identifiable contributions: (a) the rattling of discogens within a transient "interdigitation" cage, (b) the hopping of discogens across columns, and (c) the drifting motion of discogens along the orientation of the director.

Size and boundary effects on the diffusive behavior of elongated colloidal particles in a strongly confined dense dispersion

In very recent experimental work, diffusive motion of individual particles in a dense columnar phase of colloidal suspension of filamentous virus particles probed by means of fluorescence video microscopy [S. Naderi, E. Pouget, P. Ballesta, P. van der Schoot, M. P. Lettinga, and E. Grelet, Phys. Rev. Lett. 111, 037801 (2013)]. Rare events were observed in which the minority fluorescently labeled particles engage in sudden, jump-like motion along the director. The jump length distribution turned out to be biased towards a half and a full particle length. We suggest these events may be indicative of two types of particle motion, one in which particles overtake other particles in the same column and the other where a column re-equilibrates after a particle leaves a column either to enter into another column or into a void defect on the lattice. Our Brownian dynamics simulations of a quasi one-dimensional system of semi-flexible particles, subject to a Gaussian confinement potentials mimicking the effects of the self-consistent molecular field in the columnar phase, support this idea. We find that the frequency of overtaking depends on the linear fraction of particles and the steepness of the confining potential. The re-equilibration time of a column after a particle is removed from it is much shorter than the self-diffusion timescale. For the case of large system sizes and periodic boundary conditions, overtaking events do not present themselves as full-length jumps. Only if the boundary conditions are reflecting and the system is sufficiently small, full length jumps are observed in particle trajectories. The reason is that only then the amplitude of the background fluctuations is smaller than a particle length. Increasing the bending flexibility of the particles on the one hand enhances the ability of particles to overtake each other but on the other it enhances fluctuations that wash out full jumps in particle trajectories.

Collective stringlike motion of semiflexible filamentous particles in columnar liquid crystalline phases

We study, by means of Brownian dynamics simulations, heterogeneous dynamics in a dense columnar phase of monodisperse hard filamentous particles, and find that in a background of barely moving particles, some particles occasionally engage in a fast coherent string-type motion similar to what is observed in glassy states of isometric particles. This fast motion is triggered by the exchange of particles between two or more columns at different positions in the columns, which leads to sudden displacement of particles between these positions. The distribution of particle displacements shows a pronounced peak at one particle length. We perform our simulations with particles of different persistence lengths and find that for more flexible particles, the number of jump events increases. As the number of particles in the columns increases with system size for a given linear fraction of particles in the columns, the peak in the distribution becomes wider and, for sufficiently large systems, the peak disappears completely. This is associated with the increase in the magnitude of fluctuations in the motion of particles as the system size increases. Our simulation results explain recent experimental observations on single-particle motion in dense columnar phases in aqueous dispersions of filamentous virus particles.

Fractional hoppinglike motion in columnar mesophases of semiflexible rodlike particles

We report on single-particle dynamics of strongly interacting filamentous fd virus particles in the liquid-crystalline columnar state in aqueous solution. From fluorescence microscopy, we find that rare, discrete events take place, in which individual particles engage in sudden, jumplike motion along the main rod axis. The jump length distribution is bimodal and centered at half- and full-particle lengths. Our Brownian dynamics simulations of hard semiflexible particles mimic our experiments and indicate that full-length jumps must be due to collective dynamics in which particles move in stringlike fashion in and between neighboring columns, while half jumps arise as a result of particles moving into defects. We find that the finite domain structure of the columnar phase strongly influences the observed dynamics.

Dual translocation pathways in smectic liquid crystals facilitated by molecular flexibility

We investigate translocation mechanisms in smectic A liquid crystals (LCs) by a realistic, coarse-grained model of a LC compound comprising a stiff azobenzene core with flexible tails. We observe that the molecules can permeate from one smectic layer to the next via two different mechanisms, with and without significant reorientation, the former being facilitated through transverse interlayer intermediates. This is possible due to the intrinsic flexibility of the molecules. The two processes lead to characteristic signatures in the Van Hove self-correlation function, which can also be observed experimentally.

Confinement induced splay-to-bend transition of colloidal rods

We study the nematic phase of rodlike f d-virus particles confined to channels with wedge-structured walls. Using laser scanning confocal microscopy we observe a splay-to-bend transition at the single particle level as a function of the wedge opening angle. Lattice Boltzmann simulations reveal the underlying origin of the transition and its dependence on nematic elasticity and wedge geometry. Our combined work provides a simple method to estimate the splay-to-bend elasticity ratios of the virus and offers a way to control the position of defects through the confining boundary conditions.

Brownian dynamics and dynamic Monte Carlo simulations of isotropic and liquid crystal phases of anisotropic colloidal particles: a comparative study

We report on the diffusion of purely repulsive and freely rotating colloidal rods in the isotropic, nematic, and smectic liquid crystal phases to probe the agreement between Brownian and Monte Carlo dynamics under the most general conditions. By properly rescaling the Monte Carlo time step, being related to any elementary move via the corresponding self-diffusion coefficient, with the acceptance rate of simultaneous trial displacements and rotations, we demonstrate the existence of a unique Monte Carlo time scale that allows for a direct comparison between Monte Carlo and Brownian dynamics simulations. To estimate the validity of our theoretical approach, we compare the mean square displacement of rods, their orientational autocorrelation function, and the self-intermediate scattering function, as obtained from Brownian dynamics and Monte Carlo simulations. The agreement between the results of these two approaches, even under the condition of heterogeneous dynamics generally observed in liquid crystalline phases, is excellent.

Microdiffusion in (2 + 1)-dimensional chain-bundle dusty-plasma liquids

Microdiffusion in a (2 + 1)-dimensional liquid with flexible long longitudinal chain bundles, formed by negatively charged dusts suspended in a low-pressure Ar gaseous discharge, is investigated. With increasing time scale τ, the transverse hopping dominated displacement induces the transition from the sub- to the superdiffusion of the single dust, and the growth of spatial displacement correlation of two dusts, which suppresses their relative diffusion. The rise time of displacement correlation increases with dust separation. The bond breaking around the hopping cluster boundary is the main source for long time relative diffusion and causes the presence of the multiple shoulders in the fat tails of the non-Gaussian relative displacement histograms. The stronger longitudinal coupling than the transverse coupling strongly enhances the motion correlation over much larger separation, and suppresses the bond-breaking rate and the relative diffusion of the longitudinal dust pairs.

Dynamics in the smectic phase of stiff viral rods

We report on the dynamics in colloidal suspensions of stiff viral rods, called fd-Y21M. This mutant filamentous virus exhibits a persistence length 3.5 times larger than the wild-type fd-wt. Such a virus system can be used as a model system of rodlike particles for studying their self-diffusion. In this paper, the physical features, such as rod contour length and polydispersity have been determined for both viruses. The effect of viral rod flexibility on the location of the nematic-smectic phase transition has been investigated, with a focus on the underlying dynamics studied more specifically in the smectic phase. Direct visualization of the stiff fd-Y21M at the scale of a single particle has shown the mass transport between adjacent smectic layers, as found earlier for the more flexible rods. We could relate this hindered diffusion with the smectic ordering potentials for varying rod concentrations. The self-diffusion within the layers is far more pronounced for the stiff rods as compared to the more flexible fd-wt viral rod.

Hybrid macroscopic fibers from the synergistic assembly between silica and filamentous viruses

In this work, we report the elaboration of macroscopic hybrid virus-silica fibers. By using a silicate sol as inorganic precursor combined with the filamentous fd virus, well-dispersed hybrid fibers are obtained in solution. These macroscopic fd-silica fibers exhibit a narrow distribution of their diameter, while their length is at the millimeter scale. A scenario of the morphosynthesis is proposed to account for the formation of these high aspect ratio hybrid fibers.

Crossover from normal to anomalous diffusion in systems of field-aligned dipolar particles

Using molecular dynamics simulations we investigate the translational dynamics of particles with dipolar interactions in homogenous external fields. For a broad range of concentrations, we find that the anisotropic, yet normal diffusive behavior characterizing weakly coupled systems becomes anomalous both parallel and perpendicular to the field at sufficiently high dipolar coupling and field strength. After the ballistic regime, chain formation first yields cagelike motion in all directions, followed by transient, mixed diffusive-superdiffusive behavior resulting from cooperative motion of the chains. The enhanced dynamics disappears only at higher densities close to crystallization.

Charge reversal of the rodlike colloidal fd virus through surface chemical modification

There is increasing interest in the use of viruses as model systems for fundamental research and as templates for nanomaterials. In this work, the rodlike fd virus was subjected to chemical modifications targeting different solvent-exposed functional groups in order to tune its surface properties, especially reversing the surface charge from negative to positive. The carboxyl groups of fd were coupled with different kinds of organic amines by carbodiimide chemistry, resulting in modified viruses that are positively charged over a wide range of pH. Care was taken to minimize intervirus cross linking, which often occurs because of such modifications. The surface amino groups were also grafted with poly(ethylene glycol) (PEG) end-functionalized with an active succinimidyl ester in order to introduce a steric stabilization effect. By combining charge reversal with PEG grafting, a reversible attraction between positively and negatively charged PEG-grafted fd viruses could be realized, which was tuned by the ionic strength of the solution. In addition, a charge-reversed fd virus forms only a pure nematic phase in contrast to the cholesteric phase of the wild type. These modified viruses might be used as model systems in soft condensed matter physics, for example, in the study of polyelectrolyte complexes or lyotropic liquid-crystalline phase behavior.

Entropy driven self-assembly of nonamphiphilic colloidal membranes

We demonstrate that homogeneous monodisperse rods in the presence of attractive interactions assemble into equilibrium 2D fluid-like membranes composed of a one-rod length thick monolayer of aligned rods. Unique features of our system allow us to simultaneously investigate properties of these membranes at both continuum and molecular lengthscales. Analysis of thermal fluctuations at continuum lengthscales yields the membranes' lateral compressibility and bending rigidity and demonstrates that the properties of colloidal membranes are comparable to those of traditional lipid bilayers. Fluctuations at molecular lengthscales, in which single rods protrude from the membrane surface, are directly measured by comparing the positions of individual fluorescently labeled rods within a membrane to that of the membrane's continuum conformation. As two membranes approach each other in suspension, protrusion fluctuations are suppressed leading to effective repulsive interactions. Motivated by these observations, we propose an entropic mechanism that explains the stability of colloidal membranes and offers a general design principle for the self-assembly of 2D nanostructured materials from rod-like molecules.