Universal Relation between Entropy and Kinetics.

Relating thermodynamic and kinetic properties is a conceptual challenge with many practical benefits. Here, based on first principles, we derive a rigorous inequality relating the entropy and the dynamic propagator of particle configurations. It is universal and applicable to steady states arbitrarily far from thermodynamic equilibrium. Applying the general relation to diffusive dynamics yields a relation between the entropy and the (normal or anomalous) diffusion coefficient. The relation can be used to obtain useful bounds for the late-time diffusion coefficient from the calculated steady-state entropy or, conversely, to estimate the entropy based on measured diffusion coefficients. We demonstrate the validity and usefulness of the relation through several examples and discuss its broad range of applications, in particular, for systems far from equilibrium.

Detecting and characterizing phase transitions in active matter using entropy.

A major challenge in the study of active matter lies in quantitative characterization of phases and transitions between them. We show how the entropy of a collection of active objects can be used to classify regimes and spatial patterns in their collective behavior. Specifically, we estimate the contributions to the total entropy from correlations between the degrees of freedom of position and orientation. This analysis pin-points the flocking transition in the Vicsek model while clarifying the physical mechanism behind the transition. When applied to experiments on swarming Bacillus subtilis with different cell aspect ratios and overall bacterial area fractions, the entropy analysis reveals a rich phase diagram with transitions between qualitatively different swarm statistics. We discuss physical and biological implications of these findings.

Spontaneous and directed symmetry breaking in the formation of chiral nanocrystals.

Symmetry plays a crucial part in our understanding of the natural world. Mirror symmetry breaking is of special interest as it is related to life as we know it. Studying systems which display chiral amplification, therefore, could further our understanding of symmetry breaking in chemical systems, in general, and thus also of the asymmetry in Nature. Here, we report on strong chiral amplification in the colloidal synthesis of intrinsically chiral lanthanide phosphate nanocrystals, measured via circularly polarized luminescence. The amplification involves spontaneous symmetry breaking into either left- or right-handed nanocrystals below a critical temperature. Furthermore, chiral tartaric acid molecules in the solution direct the amplified nanocrystal handedness through a discontinuous transition between left- and right-handed excess. We analyze the observations based on the statistical thermodynamics of critical phenomena. Our results demonstrate how chiral minerals with high enantiopurity can form in a racemic aqueous environment.

Persistent collective motion of a dispersing membrane domain.

We study the Brownian motion of an assembly of mobile inclusions embedded in a fluid membrane. The motion includes the dispersal of the assembly, accompanied by the diffusion of its center of mass. Usually, the former process is much faster than the latter because the diffusion coefficient of the center of mass is inversely proportional to the number of particles. However, in the case of membrane inclusions, we find that the two processes occur on the same timescale, thus significantly prolonging the lifetime of the assembly as a collectively moving object. This effect is caused by the quasi-two-dimensional membrane flows, which couple the motions of even the most remote inclusions in the assembly. The same correlations also cause the diffusion coefficient of the center of mass to decay slowly with time, resulting in weak subdiffusion. We confirm our analytical results by Brownian dynamics simulations with flow-mediated correlations. The effect reported here should have implications for the stability of nanoscale membrane heterogeneities.

Parametric excitation of wrinkles in elastic sheets on elastic and viscoelastic substrates.

Thin elastic sheets supported on compliant media form wrinkles under lateral compression. Since the lateral pressure is coupled to the sheet's deformation, varying it periodically in time creates a parametric excitation. We study the resulting parametric resonance of wrinkling modes in sheets supported on semi-infinite elastic or viscoelastic media, at pressures smaller than the critical pressure of static wrinkling. We find distinctive behaviors as a function of excitation amplitude and frequency, including (a) a different dependence of the dynamic wrinkle wavelength on sheet thickness compared to the static wavelength; and (b) a discontinuous decrease in the dominant wrinkle wavelength upon increasing excitation frequency at sufficiently large pressures. In the case of a viscoelastic substrate, resonant wrinkling requires crossing a threshold of excitation amplitude. The frequencies for observing these phenomena in relevant experimental systems are of the order of a kilohertz and above. We discuss experimental implications of the results.

A review of shaped colloidal particles in fluids: anisotropy and chirality.

This review treats asymmetric colloidal particles moving through their host fluid under the action of some form of propulsion. The propulsion can come from an external body force or from external shear flow. It may also come from externally-induced stresses at the surface, arising from imposed chemical, thermal or electrical gradients. The resulting motion arises jointly from the driven particle and the displaced fluid. If the objects are asymmetric, every aspect of their motion and interaction depends on the orientation of the objects. This orientation in turn changes in response to the driving. The objects' shape can thus lead to a range of emergent anisotropic and chiral motion not possible with isotropic spherical particles. We first consider what aspects of a body's asymmetry can affect its drift through a fluid, especially chiral motion. We next discuss driving by injecting external force or torque into the particles. Then we consider driving without injecting force or torque. This includes driving by shear flow and driving by surface stresses, such as electrophoresis. We consider how time-dependent driving can induce collective orientational order and coherent motion. We show how a given particle shape can be represented using an assembly of point forces called a Stokeslet object. We next consider the interactions between anisotropic propelled particles, the symmetries governing the interactions, and the possibility of bound pairs of particles. Finally we show how the collective hydrodynamics of a suspension can be qualitatively altered by the particles' shapes. The asymmetric responses discussed here are broadly relevant also for swimming propulsion of active micron-scale objects such as microorganisms.

Surface Response of a Polymer Network: Semi-infinite Network.

We study theoretically the surface response of a semi-infinite viscoelastic polymer network using the two-fluid model. We focus on the overdamped limit and on the effect of the network's intrinsic length scales. We calculate the decay rate of slow surface fluctuations, and the surface displacement in response to a localized force. Deviations from the large-scale continuum response are found at length scales much larger than the network's mesh size. We discuss implications for surface scattering and microrheology. We provide closed-form expressions that can be used for surface microrheology: the extraction of viscoelastic moduli and intrinsic length scales from the motions of tracer particles lying on the surface without doping the bulk material.

Delayed nucleation in lipid particles.

Metastable states in first-order phase-transitions have been traditionally described by classical nucleation theory (CNT). However, recently an increasing number of systems displaying such a transition have not been successfully modelled by CNT. The delayed crystallization of phospholipids upon super-cooling is an interesting case, since the extended timescales allow access into the dynamics. Herein, we demonstrate the controllable behavior of the long-lived metastable liquid-crystalline phase of dilauroyl-phosphatidylethanolamine (DLPE), arranged in multi-lamellar vesicles, and the ensuing cooperative transition to the crystalline state. Experimentally, we find that the delay in crystallization is a bulk phenomenon, which is tunable and can be manipulated to span two orders of magnitude in time by changing the quenching temperature, solution salinity, or adding a secondary phospholipid. Our results reveal the robust persistence of the metastability, and showcase the apparent deviation from CNT. This distinctive suppression of the transition may be explained by the resistance of the multi-lamellar vesicle to deformations caused by nucleated crystalline domains. Since phospholipids are used as a platform for drug-delivery, a programmable design of cargo hold and release can be of great benefit.

Light-Controlled Selective Collection-and-Release of Biomolecules by an On-Chip Nanostructured Device.

The analysis of biosamples, e.g., blood, is a ubiquitous task of proteomics, genomics, and biosensing fields; yet, it still faces multiple challenges, one of the greatest being the selective separation and detection of target proteins from these complex biosamples. Here, we demonstrate the development of an on-chip light-triggered reusable nanostructured selective and quantitative protein separation and preconcentration platform for the direct analysis of complex biosamples. The on-chip selective separation of required protein analytes from raw biosamples is performed using antibody-photoacid-modified Si nanopillars vertical arrays (SiNPs) of ultralarge binding surface area and enormously high binding affinity, followed by the light-controlled rapid release of the tightly bound target proteins in a controlled liquid media. Two important experimental observations are presented: (1) the first demonstration on the control of biological reaction binding affinity by the nanostructuring of the capturing surface, leading to highly efficient protein collection capabilities, and (2) the light-triggered switching of the highly sticky binding surfaces into highly reflective nonbinding surfaces, leading to the rapid and quantitative release of the originally tightly bound protein species. Both of these two novel behaviors were theoretically and experimentally investigated. Importantly, this is the first demonstration of a three-dimensional (3D) SiNPs on-chip filter with ultralarge binding surface area and reversible light-controlled quantitative release of adsorbed biomolecules for direct purification of blood samples, able to selectively collect and separate specific low abundant proteins, while easily removing unwanted blood components (proteins, cells) and achieving desalting results, without the requirement of time-consuming centrifugation steps, the use of desalting membranes, or affinity columns.

Permeability of immobile rings of membrane inclusions to in-plane flow.

We study the flow of membranal fluid through a ring of immobile particles mimicking, for example, a fence around a membrane corral. We obtain a simple closed-form expression for the permeability coefficient of the ring as a function of the particles' line fraction. The analytical results agree with those of numerical calculations and are found to be robust against changes in particle number and corral shape. From the permeability results, we infer the collective diffusion coefficient of lipids through the ring and discuss possible implications for collective lipid transport in a crowded membrane.

Membrane undulations in a structured fluid: Universal dynamics at intermediate length and time scales.

The dynamics of membrane undulations inside a viscous solvent is governed by distinctive, anomalous, power laws. Inside a viscoelastic continuous medium these universal behaviors are modified by the specific bulk viscoelastic spectrum. Yet, in structured fluids the continuum limit is reached only beyond a characteristic correlation length. We study the crossover to this asymptotic bulk dynamics. The analysis relies on a recent generalization of the hydrodynamic interaction in structured fluids, which shows a slow spatial decay of the interaction toward the bulk limit. For membranes which are weakly coupled to the structured medium we find a wide crossover regime characterized by different, universal, dynamic power laws. We discuss various systems for which this behavior is relevant, and delineate the time regime over which it may be observed.

Many-particle mobility and diffusion tensors for objects in viscous sheets.

We derive a mobility tensor for many cylindrical objects embedded in a viscous sheet. This tensor guarantees a positive dissipation rate for any configuration of particles and forces, analogous to the Rotne-Prager-Yamakawa tensor for spherical particles in a three-dimensional viscous fluid. We test our result for a ring of radially driven particles, demonstrating the positive-definite property at all particle densities. The derived tensor can be utilized in Brownian dynamics simulations with hydrodynamic interactions for such systems as proteins in biomembranes and inclusions in free-standing liquid films.

Screening, Hyperuniformity, and Instability in the Sedimentation of Irregular Objects.

We study the overdamped sedimentation of non-Brownian objects of irregular shape using fluctuating hydrodynamics. The anisotropic response of the objects to flow, caused by their tendency to align with gravity, directly suppresses concentration and velocity fluctuations. This allows the suspension to avoid the anomalous fluctuations predicted for suspensions of symmetric spheroids. The suppression of concentration fluctuations leads to a correlated, hyperuniform structure. For certain object shapes, the anisotropic response may act in the opposite direction, destabilizing uniform sedimentation.

Pattern transitions in a compressible floating elastic sheet.

Thin rigid sheets floating on a liquid substrate appear, for example, in coatings and surfactant monolayers. Upon uniaxial compression the sheet undergoes transitions from a compressed flat state to a periodic wrinkled pattern to a localized folded pattern. The stability of these states is determined by the in-plane elasticity of the sheet, its bending rigidity, and the hydrostatics of the underlying liquid. Wrinkles and folds, and the wrinkle-to-fold transition, were previously studied for incompressible sheets. In the present work we extend the theory to include finite compressibility. We analyze the details of the flat-to-wrinkle transition, the effects of compressibility on wrinkling and folding, and the compression field associated with pattern formation. The state diagram of the floating sheet including all three states is presented.

Elasticity and Fluctuations of Frustrated Nanoribbons.

We derive a reduced quasi-one-dimensional theory of geometrically frustrated elastic ribbons. Expressed in terms of geometric properties alone, it applies to ribbons over a wide range of scales, allowing the study of their elastic equilibrium, as well as thermal fluctuations. We use the theory to account for the twisted-to-helical transition of ribbons with spontaneous negative curvature and the effect of fluctuations on the corresponding critical exponents. The persistence length of such ribbons changes nonmonotonically with the ribbon's width, dropping to zero at the transition. This and other statistical properties qualitatively differ from those of nonfrustrated fluctuating filaments.

Properties of compressible elastica from relativistic analogy.

Kirchhoff's kinetic analogy relates the deformation of an incompressible elastic rod to the classical dynamics of rigid body rotation. We extend the analogy to compressible filaments and find that the extension is similar to the introduction of relativistic effects into the dynamical system. The extended analogy reveals a surprising symmetry in the deformations of compressible elastica. In addition, we use known results for the buckling of compressible elastica to derive the explicit solution for the motion of a relativistic nonlinear pendulum. We discuss cases where the extended Kirchhoff analogy may be useful for the study of other soft matter systems.

Response of a polymer network to the motion of a rigid sphere.

In view of recent microrheology experiments we re-examine the problem of a rigid sphere oscillating inside a dilute polymer network. The network and its solvent are treated using the two-fluid model. We show that the dynamics of the medium can be decomposed into two independent incompressible flows. The first, dominant at large distances and obeying the Stokes equation, corresponds to the collective flow of the two components as a whole. The other, governing the dynamics over an intermediate range of distances and following the Brinkman equation, describes the flow of the network and solvent relative to one another. The crossover between these two regions occurs at a dynamic length scale which is much larger than the network's mesh size. The analysis focuses on the spatial structure of the medium's response and the role played by the dynamic crossover length. We examine different boundary conditions at the sphere surface. The large-distance collective flow is shown to be independent of boundary conditions and network compressibility, establishing the robustness of two-point microrheology at large separations. The boundary conditions that fit the experimental results for inert spheres in entangled F-actin networks are those of a free network, which does not interact directly with the sphere. Closed-form expressions and scaling relations are derived, allowing for the extraction of material parameters from a combination of one- and two-point microrheology. We discuss a basic deficiency of the two-fluid model and a way to bypass it when analyzing microrheological data.

Structure and dynamics of a layer of sedimented particles.

We investigate experimentally and theoretically thin layers of colloid particles held adjacent to a solid substrate by gravity. Epifluorescence, confocal, and holographic microscopy, combined with Monte Carlo and hydrodynamic simulations, are applied to infer the height distribution function of particles above the surface, and their diffusion coefficient parallel to it. As the particle area fraction is increased, the height distribution becomes bimodal, indicating the formation of a distinct second layer. In our theory, we treat the suspension as a series of weakly coupled quasi-two-dimensional layers in equilibrium with respect to particle exchange. We experimentally, numerically, and theoretically study the changing occupancies of the layers as the area fraction is increased. The decrease of the particle diffusion coefficient with concentration is found to be weakened by the layering. We demonstrate that particle polydispersity strongly affects the properties of the sedimented layer, because of particle size segregation due to gravity.

Drag of the cytosol as a transport mechanism in neurons.

Axonal transport is typically divided into two components, which can be distinguished by their mean velocity. The fast component includes steady trafficking of different organelles and vesicles actively transported by motor proteins. The slow component comprises nonmembranous materials that undergo infrequent bidirectional motion. The underlying mechanism of slow axonal transport has been under debate during the past three decades. We propose a simple displacement mechanism that may be central for the distribution of molecules not carried by vesicles. It relies on the cytoplasmic drag induced by organelle movement and readily accounts for key experimental observations pertaining to slow-component transport. The induced cytoplasmic drag is predicted to depend mainly on the distribution of microtubules in the axon and the organelle transport rate.

Resolving entropy contributions in nonequilibrium transitions.

We derive a functional for the entropy contributed by any microscopic degrees of freedom as arising from their measurable pair correlations. Applicable both in and out of equilibrium, this functional yields the maximum entropy which a system can have given a certain correlation function. When applied to different correlations, the method allows us to identify the degrees of freedom governing a certain physical regime, thus capturing and characterizing dynamic transitions. The formalism applies also to systems whose translational invariance is broken by external forces and whose number of particles may vary. We apply it to experimental results for jammed bidisperse emulsions, capturing the crossover of this nonequilibrium system from crystalline to disordered hyperuniform structures as a function of mixture composition. We discover that the cross-correlations between the positions and sizes of droplets in the emulsion play the central role in the formation of the disordered hyperuniform states. We discuss implications of the approach for entropy estimation out of equilibrium and for characterizing transitions in disordered systems.