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We show that stable, freely suspended liquid crystal films can be made from the ferroelectric nematic ($\mathrm{N_F}$) phase and from the recently discovered polar, lamellar $\mathrm{SmZ_A}$ and $\mathrm{SmA_F}$ phases. The $\mathrm{N_F}$ films display two-dimensional, smectic-like parabolic focal conic textures comprising director/polarization bend that are a manifestation of the electrostatic suppression of director splay in the film plane. In the $\mathrm{SmZ_A}$ and $\mathrm{SmA_F}$ phases, the smectic layers orient preferentially normal to the film surfaces, a condition never found in typical thermotropic or lyotropic lamellar LC phases, with the $\mathrm{SmZ_A}$ films exhibiting focal-conic fan textures mimicking the appearance of typical smectics in glass cells when the layers are oriented normal to the plates, and the $\mathrm{SmA_F}$ films showing a texture of plaquettes of uniform in-plane orientation where both bend and splay are suppressed, separated by grain boundaries. The $\mathrm{SmA_F}$ phase can also be drawn into thin filaments, in which X-ray scattering reveals that the smectic layer planes are normal to the filament axis. Remarkably, the filaments are mechanically stable even if they break, forming free-standing, fluid filaments supported only at one end. The unique architectures of these films and filaments are stabilized by the electrostatic self-interaction of the liquid crystal polarization field, which enables the formation of confined, fluid structures that are fundamentally different from those of their counterparts made using previously known liquid crystal phases., Comment: Main paper 25 pages (5 figures); Supplement: 7 pages (7 figures)

The current intense study of ferroelectric nematic liquid crystals was initiated by the observation of the same ferroelectric nematic phase in two independently discovered organic rod-shaped mesogenic compounds, RM734 and DIO. We recently reported that the compound RM734 also exhibits a monotropic, low-temperature, antiferroelectric phase having reentrant isotropic symmetry (the $I_A$ phase), the formation of which is facilitated to a remarkable degree by doping with small (below $1\%$) amounts of the ionic liquid ${\rm BMIM-PF}_6$. Here we report similar phenomenology in DIO, showing that this reentrant isotropic behavior is not only a property of RM734 but is rather a more general, material-independent feature of ferroelectric nematic mesogens. We find that the reentrant isotropic phases observed in RM734 and DIO are similar but not identical, adding two new phases to the ferroelectric nematic realm. The two $I_A$ phases exhibit similar, strongly peaked, diffuse x-ray scattering in the WAXS range $(1

We report a transition from the ferroelectric nematic liquid crystal ($N_F$) phase to a lower-temperature, antiferroelectric fluid phase having reentrant isotropic symmetry ($I_A$), in the liquid crystal compound RM734 doped with small concentrations of the ionic liquids BMIM or EMIM. Even a trace amount of ionic liquid dopant facilitates the kinetic pathway for the transition from the $N_F$ to the $I_A$, enabling simple cooling to produce this isotropic fluid phase rather than resulting in crystallization. The $I_A$ was also obtained in the absence of specific ionic liquid doping by appropriate temperature cycling in three distinct, as-synthesized-and-purified batches of RM734, two commercial and one from our laboratory. An additional birefringent, lamellar-modulated, antiferroelectric phase with the director parallel to the layers, resembling the smectic $Z_A$, is found between the paraelectric and ferroelectric nematic phases in RM734/BMIM mixtures., Comment: 45 pages, including Supplementary Information

The combination of large spontaneous polarization and fluidity makes the newly discovered ferroelectric nematic liquid crystalline phase (NF) responsive to electric fields in ways that have no counterpart in other materials. We probe this sensitive field response by confining a NF fluid in microchannels that connect electrodes through straight and curved paths. We find that by applying electric fields as low as E c.a. 0.5 V/mm, the NF phase orders with its polarization smoothly following the winding paths of the channels even when oriented antiparallel to the line connecting positive to negative electrodes, implying analogous behavior of the electric field. Upon inversion of E, the polar order undergoes a complex multistage switching process dominated by electrostatic interactions. Multistage polarization switching dynamics is also found in numerical simulations of a quasi-2D continuum model of NF liquid crystals in microchannels, which also clarify the conditions under which the electric field is guided by the microchannels. Experiments and theory indicate that all observations are direct consequences of the prompt effective screening of electric field components normal to the channel walls. This electric "superscreening" effect emerges as a distinctive property of the NF phase, capable of inducing conditions in which both the polarization and the electric field are guided by microchannels., Comment: Paper Submitted

Numerous measurements of the dielectric constant $\epsilon$ of the recently discovered ferroelectric nematic ($N_F$) liquid crystal (LC) phase report extraordinarily large values of $\epsilon^\prime$ (up to ~30,000). We show that what is in fact being measured in such experiments is the high capacitance of the non-ferroelectric, interfacial, insulating layers of nanoscale thickness that bound the $N_F$ material in typical cells. We analyze a parallel-plate cell filled with $N_F$ material of high-polarization $\mathbf{P}$, oriented parallel to the plates at zero applied voltage. Minimization of the dominant electrostatic energy renders $\mathbf{P}$ spatially uniform and orients it to make the electric field in the $N_F$ as small as possible, a condition under which the voltage applied to the cell appears almost entirely across the high-capacity interfacial layers. This coupling of orientation and charge creates a combined polarization-external capacitance (PCG) Goldstone reorientation mode requiring applied voltages orders of magnitude smaller than that of the $N_F$ layer alone to effectively transport charge across the $N_F$ layer. The $N_F$ layer acts as a low-value resistor and the interfacial capacitors as reversible energy storage reservoirs, lowering the restoring force (mass) of the PCG mode and producing strong reactive dielectric behavior. Analysis of data from several experiments on ferroelectric liquid crystals (chiral smectics C, bent-core smectics, and the $N_F$ phase supports the PCG model, showing that deriving dielectric constants from electrical impedance measurements of high-polarization ferroelectric LCs, without properly accounting for the self-screening effects of polarization charge and the capacitive contributions of interfacial layers, can result in overestimation of the $\epsilon^\prime$ values of the LC by many orders of magnitude., Comment: 30 pages of text, 11 figures, 59 references (47 pages total)

We report the smectic $A_F$, a new liquid crystal phase of the ferroelectric nematic realm. The smectic $A_F$ is a phase of small polar, rod-shaped molecules which form two-dimensional fluid layers spaced by approximately the mean molecular length. The phase is uniaxial, with the molecular director, the local average long-axis orientation, normal to the layer planes, and ferroelectric, with a spontaneous electric polarization parallel to the director. Polarization measurements indicate almost complete polar ordering of the $\sim 10$ Debye longitudinal molecular dipoles, and hysteretic polarization reversal with a coercive field of about $2 \times 10^5$ V/m is observed. The smectic $A_F$ phase appears upon cooling in two binary mixtures of partially fluorinated mesogens: 2N/DIO, exhibiting a nematic ($N$) -- smectic $Z_A$ (Sm$Z_A$) -- ferroelectric nematic ($N_F$) -- smectic $A_F$ (Sm$A_F$) phase sequence; and 7N/DIO, exhibiting an $N$ -- Sm$Z_A$ -- Sm$A_F$ phase sequence. The latter presents an opportunity to study a transition between two smectic phases having orthogonal systems of layers., Comment: 26 pages, 6 figures

We have structurally characterized the liquid crystal phase that appears as an intermediate state when a dielectric nematic, having polar disorder of its molecular dipoles, transitions to the almost perfectly polar-ordered ferroelectric nematic. This intermediate phase, which fills a 100-year-old void in the taxonomy of smectics and which we term the "smectic $Z_A$", is antiferroelectric, with the nematic director and polarization oriented parallel to smectic layer planes, and the polarization alternating in sign from layer to layer. The period of this polarization wave ($\sim$180 A) is mesoscopic, corresponding to $\sim$40 molecules side-by-side, indicating that this lamellar structure is collectively stabilized. A Landau free energy, originally formulated to model incommensurate antiferroelectricity in crystals, describes the key features of the nematic-Sm$Z_A$-ferroelectric nematic phase sequence., Comment: main paper (with 7 figures) and supplement (with 12 figures) comprise 65 pages

The organic mesogens RM734 and DIO are members of separate molecular families featuring distinct molecular structures. These families, at the present time, are the only ones known to exhibit a ferroelectric nematic liquid crystal (LC) phase. Here we present an experimental investigation of the phase diagram and electro-optics of binary mixtures of RM734 and DIO. We observe paraelectric nematic (N) and ferroelectric nematic (NF) phases in both materials, each of which exhibits complete miscibility across the phase diagram, showing that the paraelectric and ferroelectric are the same phases in RM734 as in DIO. Remarkably, these molecules form ideal mixtures with respect to both the paraelectric-ferroelectric nematic phase behavior and the ferroelectric polarization density of the mixtures, the principal order parameter of the transition. Ideal mixing is also manifested in the orientational viscosity, and the onset of glassy dynamics at low temperature. This behavior is attributable in part to the similarity of their overall molecular shape and net longitudinal dipole moment (~ 11 Debye), and to a common tendency for head-to-tail molecular association. In contrast, the significant difference in molecular structures leads to poor solubility in the crystal phases, enhancing the stability of the ferroelectric nematic phase at low temperature in the mixtures and making possible room temperature electro-optic effects. In the mixtures with excess DIO, an intermediate phase appears via an ultraweak, first-order transition from the N phase, in a narrow temperature range between the paraelectric and ferroelectric nematics., Comment: main paper has 24 pages with 5 figures; supplementary information has 14 pages with 8 figures

The cytoskeleton -- a collection of polymeric filaments, molecular motors, and crosslinkers -- is a foundational example of active matter, and in the cell assembles into organelles that guide basic biological functions. Simulation of cytoskeletal assemblies is an important tool for modeling cellular processes and understanding their surprising material properties. Here we present aLENS, a novel computational framework to surmount the limits of conventional simulation methods. We model molecular motors with crosslinking kinetics that adhere to a thermodynamic energy landscape, and integrate the system dynamics while efficiently and stably enforcing hard-body repulsion between filaments -- molecular potentials are entirely avoided in imposing steric constraints. Utilizing parallel computing, we simulate different mixtures of tens to hundreds of thousands of cytoskeletal filaments and crosslinking motors, recapitulating self-emergent phenomena such as bundle formation and buckling, and elucidating how motor type, thermal fluctuations, internal stresses, and confinement determine the evolution of active matter aggregates.

We show that surface interactions can vectorially structure the three-dimensional polariza-tion field of a ferroelectric fluid. The contact between a ferroelectric nematic liquid crystal and a surface with in-plane polarity generates a preferred in-plane orientation of the polarization field at that interface. This is a route to the formation of fluid or glassy monodomains of high polarization without the need for electric field poling. For example, unidirectional buffing of polyimide films on planar surfaces to give quadrupolar in-plane anisotropy also induces mac-roscopic in-plane polar order at the surfaces, enabling the formation of a variety of azimuthal polar director structures in the cell interior, including uniform and twisted states. In a {\pi}-twist cell, obtained with antiparallel, unidirectional buffing on opposing surfaces, we demonstrate three distinct modes of ferroelectric nematic electro-optic response: intrinsic, viscosity-limited, field-induced molecular reorientation; field-induced motion of domain walls separating twist-ed states of opposite chirality; and propagation of polarization reorientation solitons from the cell plates to the cell center upon field reversal. Chirally doped ferroelectric nematics in anti-parallel-rubbed cells produce Grandjean textures of helical twist that can be unwound via field-induced polar surface reorientation transitions. Fields required are in the 3 V/mm range, indicating an in-plane polar anchoring energy of wP ~ 3x10-3 J/m2., Comment: 34 pages, including 5 figures and bibliography

In cells, cytoskeletal filament networks are responsible for cell movement, growth, and division. Filaments in the cytoskeleton are driven and organized by crosslinking molecular motors. In reconstituted cytoskeletal systems, motor activity is responsible for far-from-equilibrium phenomena such as active stress, self-organized flow, and spontaneous nematic defect generation. How microscopic interactions between motors and filaments lead to larger-scale dynamics remains incompletely understood. To build from motor-filament interactions to predict bulk behavior of cytoskeletal systems, more computationally efficient techniques for modeling motor-filament interactions are needed. Here we derive a coarse-graining hierarchy of explicit and continuum models for crosslinking motors that bind to and walk on filament pairs. We compare the steady-state motor distribution and motor-induced filament motion for the different models and analyze their computational cost. All three models agree well in the limit of fast motor binding kinetics. Evolving a truncated moment expansion of motor density speeds the computation by $10^3$--$10^6$ compared to the explicit or continuous-density simulations, suggesting an approach for more efficient simulation of large networks. These tools facilitate further study of motor-filament networks on micrometer to millimeter length scales., Comment: 54 pages, 7 figures, 1 table

Many-body interactions in systems of active matter can cause particles to move collectively and self-organize into dynamic structures with long-range order. In cells, the self-assembly of cytoskeletal filaments is critical for cellular motility, structure, intracellular transport, and division. Semiflexible cytoskeletal filaments driven by polymerization or motor-protein interactions on a two-dimensional substrate, such as the cell cortex, can induce filament bending and curvature leading to interesting collective behavior. For example, the bacterial cell-division filament FtsZ is known to have intrinsic curvature that causes it to self-organize into rings and vortices, and recent experiments reconstituting the collective motion of microtubules driven by motor proteins on a surface have observed chiral symmetry breaking of the collective behavior due to motor-induced curvature of the filaments. Previous work on the self-organization of driven filament systems have not studied the effects of curvature and filament structure on collective behavior. In this work, we present Brownian dynamics simulation results of driven semiflexible filaments with intrinsic curvature and investigate how the interplay between filament rigidity and radius of curvature can tune the self-organization behavior in homochiral systems and heterochiral mixtures. We find a curvature-induced phase transition from polar flocks to self-sorted chiral clusters, which is modified by filament flexibility. This phase transition changes filament transport from ballistic to diffusive at long timescales.

We report the experimental determination of the structure and response to applied electric field of the lower-temperature nematic phase of the previously reported calamitic compound 4-[(4-nitrophenoxy)carbonyl]phenyl2,4-dimethoxybenzoate (RM734). We exploit its electro-optics to visualize the appearance, in the absence of applied field, of a permanent electric polarization density, manifested as a spontaneously broken symmetry in distinct domains of opposite polar orientation. Polarization reversal is mediated by field-induced domain wall movement, making this phase ferroelectric, a 3D uniaxial nematic having a spontaneous, reorientable, polarization locally parallel to the director. This polarization density saturates at a low temperature value of ~ 6 microcoulombs/cm-sqd, the largest ever measured for an organic material or for any fluid. This polarization is comparable to that of solid state ferroelectrics, and is close to the average value obtained by assuming perfect, polar alignment of molecular long axes in the nematic. We find a host of spectacular optical and hydrodynamic effects driven by ultra-low applied field (E~1V/cm), produced by the coupling of the large polarization to nematic birefringence and flow. Electrostatic self-interaction of the polarization charge renders the transition from the nematic phase mean-field-like and weakly first-order, and controls the director field structure of the ferroelectric phase. Atomistic molecular dynamics simulation reveals short-range polar molecular interactions that favor ferroelectric ordering, including a tendency for head-to-tail association into polar, chain-like assemblies having polar lateral correlations. These results indicate a significant potential for transformative new nematic science and technology based on the enhanced understanding, development, and exploitation of molecular electrostatic interaction., Comment: main paper: 23 pages; SI 34 pages

In active matter systems, self-propelled particles can self-organize to undergo collective motion, leading to persistent dynamical behavior out of equilibrium. In cells, cytoskeletal filaments and motor proteins self-organize into complex structures important for cell mechanics, motility, and division. Collective dynamics of cytoskeletal systems can be reconstituted using filament gliding experiments, in which cytoskeletal filaments are propelled by surface-bound motor proteins. These experiments have observed diverse dynamical states, including flocks, polar streams, and single-filament spirals. Recent experiments with microtubules and kinesin motor proteins found that the collective behavior of filaments can be tuned by altering the concentration of the crowding macromolecule methylcellulose in solution. Increasing the methycellulose concentration reduced filament crossing, promoted alignment, and led to a transition from active, isotropically oriented filaments to locally aligned polar streams. This emergence of collective motion is typically explained as an increase in alignment interactions by Vicsek-type models of active polar particles. However, it is not yet understood how steric interactions and bending stiffness modify the collective behavior of active filaments. We use simulations of driven filaments with tunable soft repulsion and rigidity in order to better understand how the interplay between filament flexibility and steric effects can lead to different active dynamic states. We find that increasing filament stiffness decreases the probability of filament alignment, yet increases collective motion and long-range order, in contrast to the assumptions of a Vicsek-type model. In addition to repulsion and driving, tuning filament stiffness can promote collective behavior, and controls the transition between active isotropic filaments, locally aligned flocks, and polar streams.

Two dimensional (2D) laminar jet-----a stream of fluid that projected into a surrounding medium with the flow confined in 2D-----has both theoretical and experimental significance. We carried out 2D laminar jet experiments in freely suspended liquid crystal films (FSLCFs) of nanometers thick and centimeters in size, in which individual molecules are confined to single layers thus enable film flows with two degrees of freedom. The experimental observations are found in good agreement with the classic 2D laminar jet theory of ideal cases that assume no external coupling effects, even in fact there exist strong coupling force from the ambient air. We further investigated this air coupling effect in computer simulations, with the results indicated air has little influence on the velocity maps of flow near the nozzle. This astonishing results could be intuitively understood by considering 2D incompressibility of the films. This experiment, together with a series of our previous experiments, show for a wide range of Reynolds number, FSLCFs are excellent testing beds for 2D hydrodynamics., Comment: 6 pages, 8 figures

Freely suspended films of smectic liquid crystals are unique examples of quasi two-dimensional fluids. Mechanically stable and with quantized thickness of the order of only a few molecular layers, smectic films are ideal systems for studying fundamental fluid physics, such as collective molecular ordering, defect and fluctuation phenomena, hydrodynamics, and nonequilibrium behavior in two dimensions (2D), including serving as models of complex biological membranes. Smectic films can be drawn across openings in planar supports resulting in thin, meniscus-bounded membranes, and can also be prepared as bubbles, either supported on an inflation tube or floating freely. The quantized layering renders smectic films uniquely useful in 2D fluid physics. The OASIS team has pursued a variety of ground-based and microgravity applications of thin liquid crystal films to fluid structure and hydrodynamic problems in 2D and quasi-2D systems. Parabolic flights and sounding rocket experiments were carried out in order to explore the shape evolution of free floating smectic bubbles, and to probe Marangoni effects in flat films. The dynamics of emulsions of smectic islands (thicker regions on thin background films) and of microdroplet inclusions in spherical films, as well as thermocapillary effects, were studied over extended periods within the OASIS (Observation and Analysis of Smectic Islands in Space) project on the International Space Station. We summarize the technical details of the OASIS hardware and give preliminary examples of key observations.

The twist-bend nematic liquid crystal phase is a three-dimensional fluid in which achiral bent molecules spontaneously form an orientationally ordered macroscopically chiral heliconical winding of molecular scale pitch, in absence of positional ordering. Here we characterize the structure of the ground state of the twist-bend phase of the bent dimer CB7CB and its mixtures with 5CB over a wide range of concentrations and temperatures, showing that the contour length along the molecular direction for a single turn of the helix is approximately equal to 2{\pi}Rmol, where Rmol is the radius of bend curvature of a single all-trans CB7CB molecule. This relation emerges from a model which simply relates the macroscopic characteristics of the helical structure, which is mostly biaxial twist and has little bend, to the bent molecular shape. This connection comes about through the presence in the fluid of self-assembled oligomer-like correlations of interlocking molecules, arising from the nanosegregation of rigid and flexible molecular subcomponents, forming a brickwork tiling of pairs of molecular strands into a duplex double-helical chain., Comment: Supplementary Information included

Microtubule dynamic instability allows search and capture of kinetochores during spindle formation, an important process for accurate chromosome segregation during cell division. Recent work has found that microtubule rotational diffusion about minus-end attachment points contributes to kinetochore capture in fission yeast, but the relative contributions of dynamic instability and rotational diffusion are not well understood. We have developed a biophysical model of kinetochore capture in small fission-yeast nuclei using hybrid Brownian dynamics/kinetic Monte Carlo simulation techniques. With this model, we have studied the importance of dynamic instability and microtubule rotational diffusion for kinetochore capture, both to the lateral surface of a microtubule and at or near its end. Over a range of biologically relevant parameters, microtubule rotational diffusion decreased capture time, but made a relatively small contribution compared to dynamic instability. At most, rotational diffusion reduced capture time by 25%. Our results suggest that while microtubule rotational diffusion can speed up kinetochore capture, it is unlikely to be the dominant physical mechanism. In addition, we found that when microtubules undergo dynamic instability, lateral captures predominate even in the absence of rotational diffusion. Counterintuitively, adding rotational diffusion to a dynamic microtubule increases the probability of end-on capture.

Binary mixtures of the twist-bend nematic-forming liquid crystal CB7CB with the prototypical rod-like liquid crystal 5CB exhibit a twist-bend nematic phase with properties similar to those reported for neat CB7CB. The mixtures appear homogeneous, with no micron- or nano-scale segregation evident at any concentration. The linear dependence of the phase transition temperature on concentration indicates that these binary mixtures are nearly ideal. However, a decrease in the viscosity with the addition of 5CB allows the characteristic twist-bend stripe textures to relax into a state of uniform birefringence. We confirm the presence of nanoscale modulations of the molecular orientation in the mixtures by freeze-fracture transmission electron microscopy (FFTEM), further evidence of their twist-bend nature. We devise and implement a statistical approach to quantitatively measure the ground state pitch of the twist-bend phase and its mixtures using FFTEM. The addition of 5CB generally shifts the measured ground-state pitch distributions towards larger pitch. Interestingly, the pitch appears to increase discontinuously by ~10 nm at the 50 wt% concentration of 5CB, indicating that the twist-bend phase undergoes a structural transition at higher 5CB concentrations., Comment: Supplementary information included

Using atomistic molecular dynamics simulation we study the discotic columnar liquid crystalline (LC) phases formed by a new organic compound having Hexa-peri-Hexabenzocoronene (HBC) core with six pendant oligothiophene units recently synthesized by Nan Hu et al. (N. Hu, R. Shao, Y. Shen, D. Chen, N. A. Clark and D. M. Walba, Adv. Mater. 26, 2066, 2014). This HBC core based LC phase was shown to have electric field responsive behavior and has important application in organic electronics. Our simulation results confirm the hexagonal arrangement of columnar LC phase with a lattice spacing consistent with that obtained from small angle X-ray diffraction data. We have also calculated various positional and orientational correlation functions to characterize the ordering of the molecules in the columnar arrangement. The molecules in a column are arranged with an average twist of 25 degrees having an average inter-molecular separation of ~5 {\AA}. Interestingly, we find an overall tilt angle of 43 degrees between the columnar axis and HBC core. We also simulate the charge transport through this columnar phase and report the numerical value of charge carrier mobility for this liquid crystal phase. The charge carrier mobility is strongly influenced by the twist angle and average spacing of the molecules in the column.

Microtubules and motor proteins self organize into biologically important assemblies including the mitotic spindle and the centrosomal microtubule array. Outside of cells, microtubule-motor mixtures can form novel active liquid-crystalline materials driven out of equilibrium by ATP-consuming motor proteins. Microscopic motor activity causes polarity-dependent interactions between motor proteins and microtubules, but how these interactions yield such larger-scale dynamical behavior such as complex flows and defect dynamics is not well understood. We develop a multiscale theory for microtubule-motor systems in which Brownian dynamics simulations of polar microtubules driven by motors are used to study microscopic organization and stresses created by motor-mediated microtubule interactions. We identify polarity-sorting and crosslink tether relaxation as two polar-specific sources of active destabilizing stress. We then develop a continuum Doi-Onsager model that captures polarity sorting and the hydrodynamic flows generated by these polar-specific active stresses. In simulations of active nematic flows on immersed surfaces, the active stresses drive turbulent flow dynamics and continuous generation and annihilation of disclination defects. The dynamics follow from two instabilities, and accounting for the immersed nature of the experiment yields unambiguous characteristic length and time scales. When turning off the hydrodynamics in the Doi-Onsager model, we capture formation of polar lanes as observed in the Brownian dynamics simulation., Comment: arXiv admin note: substantial text overlap with arXiv:1401.8059

Ferrofluids are familiar as colloidal suspensions of ferromagnetic nanoparticles in aqueous or organic solvents. The dispersed particles are randomly oriented but their moments become aligned if a magnetic field is applied, producing a variety of exotic and useful magneto-mechanical effects. A longstanding interest and challenge has been to make such suspensions macroscopically ferromagnetic, that is having uniform magnetic alignment in absence of a field. Here we report a fluid suspension of magnetic nanoplates which spontaneously aligns into an equilibrium nematic liquid crystal phase that is also macroscopically ferromagnetic. Its zero-field magnetization produces distinctive magnetic self-interaction effects, including liquid crystal textures of fluid block domains arranged in closed flux loops, and makes this phase highly sensitive, with it dramatically changing shape even in the Earth's magnetic field.

The Brownian diffusion of micron-scale inclusions in freely suspended smectic A liquid crystal films a few nanometers thick and several millimeters in diameter depends strongly on the air surrounding the film. Near atmospheric pressure, the three-dimensionally coupled film/gas system is well described by Hughes/Pailthorpe/White hydrodynamic theory but at lower pressure (p < 70 torr), the diffusion coefficient increases substantially, tending in high vacuum toward the two-dimensional limit where it is determined by film size. In the absence of air, the films are found to be a nearly ideal physical realization of a two-dimensional, incompressible Newtonian fluid., Comment: 5 pages, 3 figures

Non-equilibrium active matter made up of self-driven particles with short-range repulsive interactions is a useful minimal system to study active matter as the system exhibits collective motion and nonequilibrium order-disorder transitions. We studied high-aspect-ratio self-propelled rods over a wide range of packing fraction and driving to determine the nonequilibrium state diagram and dynamic properties. Flocking and nematic-laning states occupy much of the parameter space. In the flocking state the average internal pressure is high and structural and mechanical relaxation times are long, suggesting that rods in flocks are in a translating glassy state despite overall flock motion. In contrast, the nematic-laning state shows fluid-like behavior. The flocking state occupies regions of the state diagram at both low and high packing fraction separated by nematic-laning at low driving and a history-dependent region at higher driving; the nematic-laning state transitions to the flocking state for both compression and expansion. We propose that the laning-flocking transitions are a type of glass transition which, in contrast to other glass-forming systems, can show fluidization as density increases. The fluid internal dynamics and ballistic transport of the nematic-laning state may promote collective dynamics of rod-shaped microorganisms.

Microtubules and motor proteins are building blocks of self-organized subcellular biological structures such as the mitotic spindle and the centrosomal microtubule array. These same ingredients can form new "bioactive" liquid-crystalline fluids that are intrinsically out of equilibrium and which display complex flows and defect dynamics. It is not yet well understood how microscopic activity, which involves polarity-dependent interactions between motor proteins and microtubules, yields such larger scale dynamical structures. In our multiscale theory, Brownian dynamics simulations of polar microtubule ensembles driven by crosslinking motors allow us to study microscopic organization and stresses. Polarity sorting and crosslink relaxation emerge as two polar-specific sources of active destabilizing stress. On larger length scales, our continuum Doi-Onsager theory captures the hydrodynamic flows generated by polarity-dependent active stresses. The results connect local polar structure to flow structures and defect dynamics.

We study experimentally and theoretically the hydrodynamic interaction of pairs of circular inclusions in two-dimensional, fluid smectic membranes suspended in air. By analyzing their Brownian motion, we find that the radial mutual mobilities of identical inclusions are independent of their size but that the angular coupling becomes strongly size-dependent when their radius exceeds a characteristic hydrodynamic length. The observed dependence of the mutual mobilities on inclusion size is described well for arbitrary separations by a model that generalizes the Levine/MacKintosh theory of point-force response functions and uses a boundary-element approach to calculate the mobility matrix.

The chiral, heliconical (twist-bend) nematic ground state is reported in an achiral, rigid, bent-core mesogen (UD68). Similar to the nematic twist-bend (NTB) phase observed in bent molecular dimers, the NTB phase of UD68 forms macroscopic, smectic-like focal-conic textures and exhibits nanoscale, periodic modulation with no associated modulation of the electron density, i.e., without a detectable lamellar x-ray reflection peak. The NTB helical pitch is pTB ~ 14 nm. When an electric field is applied normal to the helix axis, a weak electroclinic effect is observed, revealing 50 um-scale left- and right-handed domains in a chiral conglomerate., Comment: 19 pages, 4 figures

Freeze Fracture Transmission Electron Microscopy (FFTEM) study of the nanoscale structure of the so-called "twist-bend" nematic (NX) phase of the cyanobiphenyl (CB) dimer molecule CB(CH2)7CB reveals a stripe texture of fluid layers periodically arrayed with a bulk spacing of d ~ 8.3 nm. Fluidity and a rigorously maintained spacing produce long-range-ordered fluid layered focal conic domains. Absence of a lamellar x-ray reflection at wavevector q ~ 2{\pi}/8 nm-1 or its harmonics in synchrotron-based scattering experiments indicates that this periodic structure is achieved with no detectable associated modulation of the electron density, and thus has nematic molecular ordering. A search for periodic ordering with d ~ 8nm in CB(CH2)7CB using atomistic molecular dynamic computer simulation yielded equilibration of a conical twist-bend helixed nematic ground state, of the sort first proposed by Meyer, and envisioned in systems of bent molecules by Dozov and Memmer, We identify {\theta} ~ 33 degree as the cone angle, and p ~ 8nm as the full pitch of the helix, the shortest ever found in a nematic fluid., Comment: 21 pages, 6 figures

Many soft-matter and biophysical systems are composed of monomers which reversibly assemble into rod-like aggregates. The aggregates can then order into liquid-crystal phases if the density is high enough, and liquid-crystal ordering promotes increased growth of aggregates. Systems that display coupled aggregation and liquid-crystal ordering include wormlike micelles, chromonic liquid crystals, DNA and RNA, and protein polymers and fibrils. Coarse-grained molecular models that capture key features of coupled aggregation and liquid-crystal ordering common to many different systems are lacking; in particular, the role of monomer aspect ratio and aggregate flexibility in controlling the phase behavior are not well understood. Here we study a minimal system of sticky cylinders using Monte Carlo simulations and analytic theory. Cylindrical monomers interact primarily by hard-core interactions but can stack and bind end to end. We present results for several different cylinder aspect ratios and a range of end-to-end binding energies. The phase diagrams are qualitatively similar to those of chromonic liquid crystals, with an isotropic-nematic-columnar triple point. The location of the triple point is sensitive to the monomer aspect ratio.We find that the aggregate persistence length varies with temperature in a way that is controlled by the interaction potential; this suggests that the form of the interaction potential affects the phase behavior of the system. Our analytic theory shows improvement compared to previous theory in quantitatively predicting the I-N transition for relatively stiff aggregates, but requires a better treatment of aggregate flexibility., Comment: 21 pages, 16 figures

Proteins from the kinesin-8 family promote microtubule (MT) depolymerization, a process thought to be important for the control of microtubule length in living cells. In addition to this MT shortening activity, kinesin 8s are motors that show plus-end directed motility on MTs. Here we describe a simple model that incorporates directional motion and destabilization of the MT plus end by kinesin 8. Our model quantitatively reproduces the key features of length-vs-time traces for stabilized MTs in the presence of purified kinesin 8, including length-dependent depolymerization. Comparison of model predictions with experiments suggests that kinesin 8 depolymerizes processively, i.e., one motor can remove multiple tubulin dimers from a stabilized MT. Fluctuations in MT length as a function of time are related to depolymerization processivity. We have also determined the parameter regime in which the rate of MT depolymerization is length dependent: length-dependent depolymerization occurs only when MTs are sufficiently short; this crossover is sensitive to the bulk motor concentration., Comment: 34 pages, 11 figures

This paper has been withdrawn because it is a duplicate of arXiv:cond-mat/0609570., Comment: This paper has been withdrawn because it is a duplicate of arXiv:cond-mat/0609570

Our previous molecular dynamic simulation studies of simple two-dimensional (2D) systems \cite{matt_big} suggested that both geometrical defects (localized, large-amplitude deviations from hexagonal ordering) and topological defects (dislocations and disclinations) play a role in 2D melting. To capture the main features of the 2D melting transition and investigate the respective roles of these two classes of defects, we study a discrete elastic model consisting of an array of nodes connected by springs, for which the relative number of geometrical defects (modeled as broken springs) and topological defects (nodes having a coordination number different from 6) may be precisely controlled. We preform Monte Carlo simulations of this model in the isobaric-isothermal ensemble, and present the phase diagram as well as various thermodynamic, statistical and structural quantities as a function of the relative populations of geometrical and topological defects. The model exhibits a rich phase behavior including hexagonal and square crystals, expanded crystal, dodecagonal quasicrystal, and liquid structure. We found that the solid--liquid transition temperature is lowered by a factor 3 to 4, with respect to the case when only topological defects are allowed, when both topological and geometrical defects are permitted, supporting our hypothesis concerning the central role played by the geometrical defects in the melting. The microscopic structure of the dense liquid has been investigated and the results are compared to those from simulations of 2D particle systems., Comment: 20 pages Revtex, 9 jpeg figures

We have carried out Monte Carlo simulations of zig-zag shaped molecules where the the molecules is composed of three rigidly linked hard spherocylinder arranged in a zigzag fashion. By varying zigzag angle we have mapped out the whole phase diagram as a function of pressure, molecular density and zigzag angle $\Psi$. For $\Psi$ between $35^0$ and $80^0$ our model simulation exhibits SmC phase. This is the first conclusive evidence where steric interaction arising out of molecular shape alone induce the occurrence of SmC phase for a wide range of zigzag angle. For smaller $\Psi$, a transition from tilted crystal (XT) to nontlted crystal is observed., Comment: 4 pages Revtex, 4 eps figures

The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried out a molecular dynamics simulation study of electrophoretic translocation of a charged polymer through an artificial nanopore to explore the feasibility of semiconductor--based nanopore devices for ultra--fast DNA sequencing. The polymer is represented by a simple bead--spring model designed to yield an appropriate coarse-grained description of the phosphate backbone of DNA in salt--free aqueous solution. A detailed analysis of single translocation event is presented to assess whether the passage of individual ions through the pore can be detected by a nanoscale field--effect transistor by measuring variations in electrostatic potential during polymer translocation. We find that it is possible to identify single events corresponding to the passage of counterions through the pore, but that discrimination of individual ions on the polymer chain based on variations in electrostatic potential is problematic. Several distinct stages in the translocation process are identified, characterized by changes in polymer conformation and by variations in the magnitude and direction of the internal electric field induced by the fluctuating charge distribution. The dependence of the condensed fraction of counterions on Bjerrum length leads to significant changes in polymer conformation, which profoundly affect the dynamics of electrophoresis and translocation., Comment: 37 pages Revtex, 11 postscript figures

Recently, a new class of smectic liquid crystal phases (SmCP phases) characterized by the spontaneous formation of macroscopic chiral domains from achiral bent-core molecules has been discovered. We have carried out Monte Carlo simulations of a minimal hard spherocylinder dimer model to investigate the role of excluded volume interations in determining the phase behavior of bent-core materials and to probe the molecular origins of polar and chiral symmetry breaking. We present the phase diagram as a function of pressure or density and dimer opening angle $\psi$. With decreasing $\psi$, a transition from a nonpolar to a polar smectic phase is observed near $\psi = 167^{\circ}$, and the nematic phase becomes thermodynamically unstable for $\psi < 135^{\circ}$. No chiral smectic or biaxial nematic phases were found., Comment: 4 pages Revtex, 3 eps figures (included)

Recent experiments indicate that doping low concentrations of bent-core molecules into calamitic smectic solvents can induce anticlinic and biaxial smectic phases. We have carried out Monte Carlo (MC) simulations of mixtures of rodlike molecules (hard spherocylinders with length/breadth ratio $L_{\rm rod}/D = 5$) and bow- or banana-shaped molecules (hard spherocylinder dimers with length/breadth ratio $L_{ban}/D = 5$ or 2.5 and opening angle $\psi$) to probe the molecular-scale organization and phase behavior of rod/banana mixtures. We find that a low concentration (3%) of $L_{ban}/D = 5$ dimers induces anticlinic (SmC$_A$) ordering in an untilted smectic (SmA) phase for $100^\circ \le \psi < 150^\circ$. For smaller $\psi$, half of each bow-shaped molecule is nanophase segregated between smectic layers, and the smectic layers are untilted. For $L_{ban}/D = 2.5$, no tilted phases are induced. However, with decreasing $\psi$ we observe a sharp transition from {\sl intralamellar} nanophase segregation (bow-shaped molecules segregated within smectic layers) to {\sl interlamellar} nanophase segregation (bow-shaped molecules concentrated between smectic layers) near $\psi = 130^\circ$. These results demonstrate that purely entropic effects can lead to surprisingly complex behavior in rod/banana mixtures., Comment: 5 pages Revtex, 7 postscript figures

We have developed a class of idealized models of chromonic molecules which are miscible in water, but which can form aggregates which in turn organize into lyotropic liquid crystal (LC) phases. By carrying out Monte Carlo simulation in a binary mixture of model chromonic and water molecules, we have studied the effect of concentration and molecular shape on the nature of resulting mesophases. We have also computed the free energy associated with the formation of chromonic columnar aggregates by umbrella sampling. Our free energy computation helps us to verify the isodesmic behavior which is characteristic of chromonic systems. For isodesmic behavior the addition of each chromonic molecule to the columnar aggregates is accompanied by a constant free energy increment and the net free energy decreases with increasing column length., Comment: 27 pages Revtex, 15 postscript figures (4 color figures). High resolution color figures available upon request