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preprint2014arXiv

Electric-field-induced turbulent energy cascade in an oil-in-oil emulsion

We observe electro-hydrodynamically driven turbulent flows at low Reynolds numbers in a two-fluid emulsion consisting of micron-scale droplets. In the presence of electric fields, the droplets produce interacting hydrodynamic flows which result in a dynamical organization at a spatial scale much larger than the size of the individual droplets. We characterize the dynamics associated with these structures by both video imaging and a simultaneous, in situ, measurement of the time variation of the bulk Reynolds stress with a rheometer. The results display scale invariance in the energy spectra in both space and time.

preprint1998arXiv

Dynamics of spherical particles on a surface: About collision induced sliding and other effects

We present a model for the motion of hard spherical particles on a two dimensional surface. The model includes both the interaction between the particles via collisions, as well as the interaction of the particles with the substrate. We analyze in details the effects of sliding and rolling friction, that are usually overlooked. It is found that the properties of this particulate system are influenced significantly by the substrate-particle interactions. In particular, sliding of the particles relative to the substrate after a collision leads to considerable energy loss for common experimental conditions. The presented results provide a basis, that can be used to realistically model the dynamical properties of the system, and provide further insight into density fluctuations and related phenomena of clustering, structure formations, and inelastic collapse.

preprint2013arXiv

The syncytial Drosophila embryo as a mechanically excitable medium

Mitosis in the early syncytial Drosophila embryo is highly correlated in space and time, as manifested in mitotic wavefronts that propagate across the embryo. In this paper we investigate the idea that the embryo can be considered a mechanically-excitable medium, and that mitotic wavefronts can be understood as nonlinear wavefronts that propagate through this medium. We study the wavefronts via both image analysis of confocal microscopy videos and theoretical models. We find that the mitotic waves travel across the embryo at a well-defined speed that decreases with replication cycle. We find two markers of the wavefront in each cycle, corresponding to the onsets of metaphase and anaphase. Each of these onsets is followed by displacements of the nuclei that obey the same wavefront pattern. To understand the mitotic wavefronts theoretically we analyze wavefront propagation in excitable media. We study two classes of models, one with biochemical signaling and one with mechanical signaling. We find that the dependence of wavefront speed on cycle number is most naturally explained by mechanical signaling, and that the entire process suggests a scenario in which biochemical and mechanical signaling are coupled.

preprint2014arXiv

Neutron diffraction of hydrogenous materials: measuring incoherent and coherent intensities separately from liquid water - a 40-year-old puzzle solved

(short version) Accurate determination of the coherent static structure factor of disordered materials containing proton nuclei is prohibitively difficult by neutron diffraction, due to the large incoherent cross section of $^1$H. This notorious problem has set severe obstacles to the structure determination of hydrogenous materials up to now, via introducing large uncertainties into neutron diffraction data processing. Here we present the first accurate separate measurements, using polarized neutron diffraction, of the coherent and incoherent contributions to the total static structure factor of 5 mixtures of light and heavy water, over an unprecedentedly wide momentum transfer range. The structure factors of H$_2$O and D$_2$O mixtures derived in this work may signify the beginning of a new era in the structure determination of hydrogenous materials, using neutron diffraction.

preprint2010arXiv

Discrete Nonlinear Schrodinger Equation, Solitons and Organizing Principles for Protein Folding

We introduce a novel generalization of the discrete nonlinear Schrödinger equation. It supports solitons that describe how proteins fold. As an example we scrutinize the villin headpiece HP35, an archetypal protein for testing both experimental and theoretical approaches to protein folding. Using explicit soliton profiles we construct its carbon backbone with an unprecedented accuracy.

preprint2015arXiv

Oscillatory elastic instabilities in an extensional viscoelastic flow

Dilute polymer solutions are known to exhibit purely elastic instabilities even when the fluid inertia is negligible. Here we report the quantitative evidence of two consecutive oscillatory elastic instabilities in an elongation flow of a dilute polymer solution as realized in a T-junction geometry with a long recirculating cavity. The main result reported here is the observation and characterization of the first transition as a forward Hopf bifurcation resulted in a uniformly oscillating state due to breaking of time translational invariance. This unexpected finding is in contrast with previous experiments and numerical simulations performed in similar ranges of the $Wi$ and $Re$ numbers, where the forward fork-bifurcation into a steady asymmetric flow due to the broken spatial inversion symmetry was reported. We discuss the plausible discrepancy between our findings and previous studies that could be attributed to the long recirculating cavity, where the length of the recirculating cavity plays a crucial role in the breaking of time translational invariance instead of the spatial inversion. The second transition is manifested via time aperiodic transverse fluctuations of the interface between the dyed and undyed fluid streams at the channel junction and advected downstream by the mean flow. Both instabilities are characterized by fluid discharge-rate and simultaneous imaging of the interface between the dyed and undyed fluid streams in the outflow channel.

preprint2016arXiv

Effect of Energy Polydispersity on the Nature of Lennard-Jones Liquids

In the companion paper [T. S. Ingebrigtsen and H. Tanaka, J. Phys. Chem. B 119, 11052 (2015)] the effect of size polydispersity on the nature of Lennard-Jones (LJ) liquids, which represent most molecular liquids without hydrogen bonds, was studied. More specifically, it was shown that even highly size polydisperse LJ liquids are Roskilde-simple (RS) liquids. RS liquids are liquids with strong correlation between constant volume equilibrium fluctuations of virial and potential energy and are simpler than other types of liquids. Moreover, it was shown that size polydisperse LJ liquids have isomorphs to a good approximation. Isomorphs are curves in the phase diagram of RS liquids along which structure, dynamics, and some thermodynamic quantities are invariant in dimensionless (reduced) units. In this paper, we study the effect of energy polydispersity on the nature of LJ liquids. We show that energy polydisperse LJ liquids are RS liquids. However, a tendency of particle segregation which increases with the degree of polydispersity leads to a loss of strong virial-potential energy correlation, but is mitigated with increasing temperature and/or density. Isomorphs are a good approximation also for energy polydisperse LJ liquids, although particle-resolved quantities display a somewhat poorer scaling compared to the mean quantities along the isomorph.

preprint2016arXiv

Microphase Separation in Random Multiblock Copolymers

Microphase separation in random multiblock copolymers is studied with mean-field theory assuming that long blocks of a copolymer are strongly segregated, whereas short blocks are able to penetrate into "alien" domains and exchange between the domains and interfacial layer. A bidisperse copolymer with blocks of only two sizes (long and short) is considered as a model of multiblock copolymers with high polydispersity in the block size. Short blocks of the copolymer play an important role in microphase separation. First, their penetration into the "alien" domains leads to the formation of joint long blocks in their own domains. Second, short blocks localized at the interface considerably change the interfacial tension. The possibility of penetration of short blocks into the "alien" domains is controlled by the product chi*Nsh (chi is the Flory-Huggins interaction parameter, Nsh is the short block length). At not very large chi*Nsh, the domain size is larger than that for a regular copolymer consisting of the same long blocks as in the considered random copolymer. At a fixed mean block size, the domain size grows with an increase in the block size dispersity, the rate of the growth being dependent of the more detailed parameters of the block size distribution.

preprint2016arXiv

Equilibrium binding energies from fluctuation theorems and force spectroscopy simulations

Brownian dynamics simulations are used to study the detachment of a particle from a substrate. Although the model is simple and generic, we attempt to map its energy, length and time scales onto a specific experimental system, namely a bead that is weakly bound to a cell and then removed by an optical tweezer. The external driving force arises from the combined optical tweezer and substrate potentials, and thermal fluctuations are taken into account by a Brownian force. The Jarzynski equality and Crooks' fluctuation theorem are applied to obtain the equilibrium free energy difference between the final and initial states. To this end, we sample non--equilibrium work trajectories for various tweezer pulling rates. We argue that this methodology should also be feasible experimentally for the envisioned system. Furthermore, we outline how the measurement of a whole free energy profile would allow the experimentalist to retrieve the unknown substrate potential by means of a suitable deconvolution. The influence of the pulling rate on the accuracy of the results is investigated, and umbrella sampling is used to obtain the equilibrium probability of particle escape for a variety of trap potentials.

preprint2017arXiv

Rheology of hydrating cement paste: crossover between two aging processes

The roles of applied strain and temperature on the hydration dynamics of cement paste are uncovered in the present study. We find that the system hardens over time through two different aging processes. The first process dominates the initial period of hydration and is characterized by the shear stress $σ$ varying sub-linearly with the strain-rate $\dotγ$; during this process the system is in a relatively low-density state and the inter-particle interactions are dominated by hydrodynamic lubrication. At a later stage of hydration the system evolves to a high-density state where the interactions become frictional, and $σ$ varies super-linearly with $\dotγ$; this is identified as the second process. An instability, indicated by a drop in $σ$, that is non-monotonic with $\dotγ$ and can be tuned by temperature, separates the two processes. Both from rheology and microscopy studies we establish that the observed instability is related to fracture mechanics of space-filling structure.

preprint2019arXiv

The behaviour of information flow near criticality

Recent experiments have indicated that many biological systems self-organise near their critical point, which hints at a common design principle. While it has been suggested that information transmission is optimized near the critical point, it remains unclear how information transmission depends on the dynamics of the input signal, the distance over which the information needs to be transmitted, and the distance to the critical point. Here we employ stochastic simulations of a driven 2D Ising system and study the instantaneous mutual information and the information transmission rate between a driven input spin and an output spin. The instantaneous mutual information varies non-monotonically with the temperature, but increases monotonically with the correlation time of the input signal. In contrast, the information transmission rate exhibits a maximum as a function of the input correlation time. Moreover, there exists an optimal temperature that maximizes this maximum information transmission rate. It arises from a tradeoff between the necessity to respond fast to changes in the input so that more information per unit amount of time can be transmitted, and the need to respond to reliably. The optimal temperature lies above the critical point, but moves towards it as the distance between the input and output spin is increased.

preprint2019arXiv

Stokes flow analogous to viscous electron current in graphene

Electron transport in two-dimensional conducting materials such as graphene, with dominant electron-electron interaction, exhibits unusual vortex flow that leads to a nonlocal current-field relation (negative resistance), distinct from the classical Ohm's law. The transport behavior of these materials is best described by low Reynolds number hydrodynamics, where the constitutive pressure-speed relation is Stoke's law. Here we report evidence of such vortices observed in a viscous flow of Newtonian fluid in a microfluidic device consisting of a rectangular cavity$-$analogous to the electronic system. We extend our experimental observations to elliptic cavities of different eccentricities, and validate them by numerically solving bi-harmonic equation obtained for the viscous flow with no-slip boundary conditions. We verify the existence of a predicted threshold at which vortices appear. Strikingly, we find that a two-dimensional theoretical model captures the essential features of three-dimensional Stokes flow in experiments.

preprint2019arXiv

Modelling ternary fluids in contact with elastic membranes

We present a thermodynamically consistent model of a ternary fluid interacting with elastic membranes. Following a free-energy modelling approach and taking into account the thermodynamics laws, we derive the equations governing the ternary fluid flow and dynamics of the membranes. We also provide the numerical framework for simulating such fluid-structure interaction problems. It is based on the lattice Boltzmann method, employed for resolving the evolution equations of the ternary fluid in an Eulerian description, coupled to the immersed boundary method, allowing for the membrane equations of motion to be solved in a Lagrangian system. The configuration of an elastic capsule placed at a fluid-fluid interface is considered for validation purposes. Systematic simulations are performed for a detailed comparison with reference numerical results obtained by Surface Evolver, and the Galilean invariance of the proposed model is also proven. The proposed approach is versatile, and a wide range of geometries can be simulated. To demonstrate this, the problem of a capillary bridge formed between two deformable capsules is investigated here.

preprint2019arXiv

Numerical insights on ionic microgels: structure and swelling behaviour

Recent progress has been made in the numerical modelling of neutral microgel particles with a realistic, disordered structure. In this work we extend this approach to the case of co-polymerised microgels where a thermoresponsive polymer is mixed with acidic groups. We compare the cases where counterions directly interact with microgel charges or are modelled implicitly through a Debye-Hückel description. We do so by performing extensive numerical simulations of single microgels across the volume phase transition (VPT) varying the temperature and the fraction of charged monomers. We find that the presence of charges considerably alters the microgel structure, quantified by the monomer density profiles and by the form factors of the microgels, particularly close to the VPT. We observe significant deviations between the implicit and explicit models, with the latter comparing more favourably to available experiments. In particular, we observe a shift of the VPT temperature to larger values as the amount of charged monomers increases. We also find that below the VPT the microgel-counterion complex is almost neutral, while it develops a net charge above the VPT. Interestingly, under these conditions the collapsed microgel still retains a large amount of counterions inside its structure. Since these interesting features cannot be captured by the implicit model, our results show that it is crucial to explicitly include the counterions in order to realistically model ionic thermoresponsive microgels.

preprint2019arXiv

A particle-field representation unifies paradigms in active matter

Active matter research focuses on the emergent behavior among interacting self-propelled particles. Unification of seemingly disconnected paradigms -- active phase-separation of repulsive discs and collective motion of self-propelled rods -- is a major challenge in contemporary active matter. Inspired by the quanto-mechanical wave-particle duality, we develop an approach based on the representation of active particles by smoothed continuum fields. On the basis of the collision kinetics, we demonstrate analytically and numerically how nonequilibrium stresses acting among self-driven, anisotropic objects hinder the formation of phase-separated states as observed for self-propelled discs and facilitate the emergence of orientational order. Besides particle shape, the rigidity of self-propelled objects controlling the symmetry of emergent ordered states is as a crucial parameter: impenetrable, anisotropic rods are found to form polar, moving clusters, whereas large-scale nematic structures emerge for soft rods, notably separated by a bistable coexistence regime. These results indicate that the symmetry of the ordered state is not dictated by the symmetry of the interaction potential but is rather a dynamical, emergent property of active systems. This unifying theoretical framework can represent a variety of active systems: living cell tissues, bacterial colonies, cytoskeletal extracts as well as shaken granular media.

preprint2019arXiv

Self-Propelled Rods: Insights and Perspectives for Active Matter

A wide range of experimental systems including gliding, swarming and swimming bacteria, in-vitro motility assays as well as shaken granular media are commonly described as self-propelled rods. Large ensembles of those entities display a large variety of self-organized, collective phenomena, including formation of moving polar clusters, polar and nematic dynamic bands, mobility-induced phase separation, topological defects and mesoscale turbulence, among others. Here, we give a brief survey of experimental observations and review the theoretical description of self-propelled rods. Our focus is on the emergent pattern formation of ensembles of dry self-propelled rods governed by short-ranged, contact mediated interactions and their wet counterparts that are also subject to long-ranged hydrodynamic flows. Altogether, self-propelled rods provide an overarching theme covering many aspects of active matter containing well-explored limiting cases. Their collective behavior not only bridges the well-studied regimes of polar self-propelled particles and active nematics, and includes active phase separation, but also reveals a rich variety of new patterns.

preprint2019arXiv

Propagation of active nematic-isotropic interfaces on substrates

Motivated by results for the propagation of active-passive interfaces of bacterial Serratia marcescens swarms [Nat. Comm., 9, 5373 (2018)] we use a hydrodynamic multiphase model to investigate the propagation of interfaces of active nematics on substrates. We characterize the active nematic phase of the model and discuss its description of the statistical dynamics of the swarms. We show that the velocicity correlation functions and the energy spectrum of the active turbulent phase of the model scale with the active length, for a range of activities. In addition, the energy spectrum exhibits two power-law regimes with exponents close to those reported for other models and bacterial swarms. Although the exponent of the rising branch of the spectrum (small wavevector) appears to be independent of the activity, the exponent of the decay changes with activity systematically, albeit slowly. We characterize also the propagation of circular and flat active-passive interfaces. We find that the closing time of the circular passive domain decays quadratically with the activity and that the structure factor of the flat interface is similar to that reported for swarms, with an activity dependent exponent. Finally, the effect of the substrate friction was investigated. We found an activity dependent threshold, above which the turbulent active nematic forms isolated islands that shrink until the system becomes isotropic and below which the active nematic expands, with a well defined propagating interface. The interface may be stopped by a fricion gradient.

preprint2019arXiv

Collective cell migration of epithelial cells driven by chiral torque generation

Various multicellular tissues show chiral morphology. Experimental studies have shown this can originate from cell chirality. However, no theory has been proposed to connect the cellular chiral torque and multicellular chiral morphogenesis. We propose a model of confluent tissue dynamics with cellular chiral torque. We found that cells migrate unidirectionally under a gradient of cellular chiral torque. While the migration speed varies depending on the tissue's mechanical parameters, it is scaled solely by a structural order parameter for liquid-to-solid transition in confluent tissues.

preprint2019arXiv

Lattice-Boltzmann simulation of free nematic-isotropic interfaces

We use a hybrid method of lattice Boltzmann and finite differences to simulate flat and curved interfaces between the nematic and isotropic phases of a liquid crystal described by the Landau-de Gennes theory. For the flat interface, we measure the interfacial velocity at different temperatures around the coexistence. We show that the interface is completely static at the coexistence temperature and that the profile width is in line with the theoretical predictions. The interface is stable in a range of temperatures around coexistence and disappears when one of the two phases becomes mechanically unstable. We stabilize circular nematic domains by a shift in temperature, related to the Laplace pressure, and estimate the spurious velocities of these lattice Boltzmann simulations.

preprint2019arXiv

Crumpling an elasto-plastic thin sphere

The phenomenon of crumpling is common in our daily life and nature. It exhibits many interesting properties, such as ultra-tough resistance to pressure with less than 30$\%$ of volume density, power-law relation for pressure vs density, and crackling noises with occurrence frequency vs intensity mimicking that of earthquakes. These results are mainly obtained by using flat thin sheets. But, in reality the majority of crumpled objects exhibit nonzero intrinsic curvatures. Notable examples are crushed aluminum cans, car wreckage, and cells move in and out of blood vessels. In this work we concentrate on establishing the fact that they behave very differently from flat sheets by employing both experiments and molecular dynamics simulations.

preprint2019arXiv

Differences in mechanical properties lead to anomalous phase separation in a model cell co-culture

During the morphogenesis of tissues and tumors, cells often interact with neighbors with different mechanical properties, but the understanding of its role is lacking. We use active Brownian Dynamics simulations to study a model co-culture consisting of two types of cells with the same size and self-propulsion speed, but different mechanical stiffness and cell-cell adhesion. As time evolves, the system phase separates out into clusters with distinct morphologies and transport properties for the two cell types. The density structure functions and the growth of cell clusters deviate from behavior characteristic of the phase separation in binary fluids. Our results capture emergent structure and motility previously observed in co-culture experiments and provide mechanistic insights into intercellular phase separation during development and disease.

preprint2019arXiv

Droplet leaping governs microstructured surface wetting

Microstructured surfaces that control the direction of liquid transport are not only ubiquitous in nature, but they are also central to technological processes such as fog/water harvesting, oil-water separation, and surface lubrication. However, a fundamental understanding of the initial wetting dynamics of liquids spreading on such surfaces is lacking. Here, we show that three regimes govern microstructured surface wetting on short time scales: spread, stick, and contact line leaping. The latter involves establishing a new contact line downstream of the wetting front as the liquid leaps over specific sections of the solid surface. Experimental and numerical investigations reveal how different regimes emerge in different flow directions during wetting of periodic asymmetrically microstructured surfaces. These insights improve our understanding of rapid wetting in droplet impact, splashing, and wetting of vibrating surfaces and may contribute to advances in designing structured surfaces for the mentioned applications.

preprint2019arXiv

Structural, Rheological and Dynamic Aspects of Hydrogen-Bonding Molecular Liquids: Aqueous Solutions of Hydrotropic tert-Butyl Alcohol

Hypothesis: The structural details, viscosity trends and dynamic phenomena in t-butanol/water solutions are closely related on the molecular scales across the entire composition range. Utilizing the experimental small- and wide-angle x-ray scattering (SWAXS) method, molecular dynamics (MD) simulations and the complemented-system approach method developed in our group it is possible to comprehensively describe the structure-viscosity-dynamics relationship in such structurally versatile hydrogen-bonded molecular liquids, as well as in similar, self-assembling systems with pronounced molecular and supramolecular structures at the intra-, inter-, and supra-molecular scales. Experiments: The SWAXS and x-ray diffraction experiments and MD simulations were performed for aqueous t-butanol solutions at 25 °C. Literature viscosity and self-diffusion data were also used. Findings: The interpretive power of the proposed scheme was demonstrated by the extensive and diverse results obtained for aqueous t-butanol solutions across the whole concentration range. Four composition ranges with qualitatively different structures and viscosity trends were revealed. The experimental and calculated zero-shear viscosities and molecular self-diffusion coefficients were successfully related to the corresponding structural details. The hydrogen bonds, that were, along with hydrophobic effects, recognized as the most important driving force for the formation of t-butanol aggregates, show intriguing lifetime trends and thermodynamic properties of their formation.

preprint2019arXiv

Active nematic-isotropic interfaces in channels

We use numerical simulations to investigate the hydrodynamic behavior of the interface between nematic (N) and isotropic (I) phases of a confined active liquid crystal. At low activities, a stable interface with constant shape and velocity is observed separating the two phases. For nematics in homeotropic channels, the velocity of the interface at the NI transition increases from zero (i) linearly with the activity for contractile systems and (ii) quadratically for extensile ones. Interestingly, the nematic phase expands for contractile systems while it contracts for extensile ones, as a result of the active forces at the interface. Since both activity and temperature affect the stability of the nematic, for active nematics in the stable regime the temperature can be tuned to observe static interfaces, providing an operational definition for the coexistence of active nematic and isotropic phases. At higher activities, beyond the stable regime, an interfacial instability is observed for extensile nematics. In this regime defects are nucleated at the interface and move away from it. The dynamics of these defects is regular and persists asymptotically for a finite range of activities. We used an improved hybrid model of finite differences and lattice Boltzmann method with multi-relaxation-time collision operator, the accuracy of which allowed us to characterize the dynamics of the distinct interfacial regimes.