arXiv subjects

Seth Fraden

Publications and source records attributed to Seth Fraden.

At least 37 records · Page 2Linked to original sources

arXiv2021

Effects of confinement on the dynamics and correlation scales in active fluids

We study the influence of solid boundaries on dynamics and structure of active fluids as the height of the container, $z$, changes. Along the varying dimension, the geometry systematically increases, therefore, the confinement ($z$) transits from "strong confinement", to "intermediate confinement" and to "weak confinement" (close to "unconfined"). In horizontal dimensions ($x,y$), the system remains "unconfined". Through tracking the tracers dispersed in the active fluids in three dimensions we observed that activity level, characterized by velocity fluctuations of flow tracers, increases as system size increases. Concomitantly, the velocity-velocity temporal correlation changes from weak correlation to strong positive correlation, indicating "memory" in active flows. We estimate the characteristic size of the flow structure by integrating the velocity-velocity spatial correlation function. The integral increases as confinement becomes weaker and saturates at approximately 400 microns as the system becomes "unconfined". This saturation indicates an intrinsic length scale which, along with the small-scale isotropy, demonstrates the multi-scale nature of this kinesin-driven bundled microtubule system.

cond-mat.soft↗

arXiv2021

The Symmetry Basis of Pattern Formation in Reaction-Diffusion Networks

In networks of nonlinear oscillators, symmetries place hard constraints on the system that can be exploited to predict universal dynamical features and steady-states, providing a rare generic organizing principle for far-from-equilibrium systems. However, the robustness of this class of theories to symmetry-disrupting imperfections is untested. Here, we develop a model experimental reaction-diffusion network of chemical oscillators to test applications of this theory in the context of self-organizing systems relevant to biology and soft robotics. The network is a ring of 4 identical microreactors containing the oscillatory Belousov-Zhabotinsky reaction coupled to nearest neighbors via diffusion. Assuming perfect symmetry, theory predicts 4 categories of stable spatiotemporal phase-locked periodic states and 4 categories of invariant manifolds that guide and structure transitions between phase-locked states. In our experiments, we observed the predicted symmetry-derived synchronous clustered transients that occur when the dynamical trajectories coincide with invariant manifolds. However, we observe only 3 of the 4 phase-locked states that are predicted for the idealized homogeneous system. Quantitative agreement between experiment and numerical simulations is found by accounting for the small amount of experimentally determined heterogeneity. This work demonstrates that a surprising degree of the network's dynamics are constrained by symmetry in spite of the breakdown of the assumption of homogeneity and raises the question of why heterogeneity destabilizes some symmetry predicted states, but not others.

nlin.PS↗

arXiv2020

Machine Learning Forecasting of Active Nematics

Active nematics are a class of far-from-equilibrium materials characterized by local orientational order of force-generating, anisotropic constitutes. Traditional methods for predicting the dynamics of active nematics rely on hydrodynamic models, which accurately describe idealized flows and many of the steady-state properties, but do not capture certain detailed dynamics of experimental active nematics. We have developed a deep learning approach that uses a Convolutional Long-Short-Term-Memory (ConvLSTM) algorithm to automatically learn and forecast the dynamics of active nematics. We demonstrate our purely data-driven approach on experiments of 2D unconfined active nematics of extensile microtubule bundles, as well as on data from numerical simulations of active nematics.

cond-mat.soft↗

arXiv2020

Optimal Control of Active Nematics

In this work we present the first systematic framework to sculpt active nematics systems, using optimal control theory and a hydrodynamic model of active nematics. We demonstrate the use of two different control fields, (1) applied vorticity and (2) activity strength, to shape the dynamics of an extensile active nematic that is confined to a disk. In the absence of control inputs, the system exhibits two attractors, clockwise and counterclockwise circulating states characterized by two co-rotating topological $+\frac{1}{2}$ defects. We specifically seek spatiotemporal inputs that switch the system from one attractor to the other; we also examine phase-shifting perturbations. We identify control inputs by optimizing a penalty functional with three contributions: total control effort, spatial gradients in the control, and deviations from the desired trajectory. This work demonstrates that optimal control theory can be used to calculate non-trivial inputs capable of restructuring active nematics in a manner that is economical, smooth, and rapid, and therefore will serve as a guide to experimental efforts to control active matter.

cond-mat.soft↗

arXiv2019

Dynamics of Reaction-Diffusion Oscillators in Star Networks

We experimentally and theoretically investigate the dynamics of inhibitory coupled self-driven oscillators on a star network in which a single central hub node is connected to $k$ peripheral arm nodes. The system consists of water-in-oil Belousov-Zhabotinsky $\sim$100$μ$m emulsion drops contained in storage wells etched in silicon wafers. We observed three dynamical attractors by varying the number of arms in the star graph and the coupling strength; ($i$) unlocked; uncorrelated phase shifts between all oscillators, ($ii$) locked; arm-hubs synchronized in-phase with a $k$-dependent phase shift between the arm and central hub, and ($iii$) center silent; central hub stopped oscillating and the arm-hubs oscillated without synchrony. We compare experiment to theory. For case ($ii$), we identified a logarithmic dependence of the phase shift on star degree, and were able to discriminate between contributions to the phase shift arising from star topology and oscillator chemistry.

nlin.AO↗

arXiv2019

Equation of State of Colloidal Membranes

In the presence of a non-adsorbing polymer, monodisperse rod-like colloids assemble into one-rod-length thick liquid-like monolayers, called colloidal membranes. The density of the rods within a colloidal membrane is determined by a balance between the osmotic pressure exerted by the enveloping polymer suspension and the repulsion between the colloidal rods. We developed a microfluidic device for continuously observing an isolated membrane while dynamically controlling the osmotic pressure of the polymer suspension. Using this technology we measured the membrane rod density over a range of osmotic pressures than is wider that what is accessible in equilibrium samples. With increasing density we observed a first-order phase transition, in which the in-plane membrane order transforms from a 2D fluid into a 2D solid. In the limit of low osmotic pressures, we measured the rate at which individual rods evaporate from the membrane. The developed microfluidic technique could have wide applicability for in situ investigation of various soft materials and how their properties depend on the solvent composition.

cond-mat.soft↗

arXiv2019

Self-organized dynamics and the transition to turbulence of confined active nematics

We study how confinement transforms the chaotic dynamics of bulk microtubule-based active nematics into regular spatiotemporal patterns. For weak confinements, multiple continuously nucleating and annihilating topological defects self-organize into persistent circular flows of either handedness. Increasing confinement strength leads to the emergence of distinct dynamics, in which the slow periodic nucleation of topological defects at the boundary is superimposed onto a fast procession of a pair of defects. A defect pair migrates towards the confinement core over multiple rotation cycles, while the associated nematic director field evolves from a distinct double spiral towards a nearly circularly symmetric configuration. The collapse of the defect orbits is punctuated by another boundary-localized nucleation event, that sets up long-term doubly-periodic dynamics. Comparing experimental data to a theoretical model of an active nematic, reveals that theory captures the fast procession of a pair of $+\frac{1}{2}$ defects, but not the slow spiral transformation nor the periodic nucleation of defect pairs. Theory also fails to predict the emergence of circular flows in the weak confinement regime. The developed confinement methods are generalized to more complex geometries, providing a robust microfluidic platform for rationally engineering two-dimensional autonomous flows.

cond-mat.soft↗

arXiv2017

Insensitivity of active nematic dynamics to topological constraints

Confining a liquid crystal imposes topological constraints on the orientational order, allowing global control of equilibrium systems by manipulation of anchoring boundary conditions. In this article, we investigate whether a similar strategy allows control of active liquid crystals. We study a hydrodynamic model of an extensile active nematic confined in containers, with different anchoring conditions that impose different net topological charges on the nematic director. We show that the dynamics are controlled by a complex interplay between topological defects in the director and their induced vortical flows. We find three distinct states by varying confinement and the strength of the active stress: a topologically minimal state, a circulating defect state, and a turbulent state. In contrast to equilibrium systems, we find that anchoring conditions are screened by the active flow, preserving system behavior across different topological constraints. This observation identifies a fundamental difference between active and equilibrium materials.

cond-mat.soft↗

arXiv2017

Engineering reaction-diffusion networks with properties of neural tissue

We present an experimental system of networks of coupled non-linear chemical reactors, which we theoretically model within a reaction-diffusion framework. The networks consist of patterned arrays of diffusively coupled nanoliter-scale reactors containing the Belousov- Zhabotinsky (BZ) reaction. Microfluidic fabrication techniques are developed that provide the ability to vary the network topology, the reactor coupling strength and offer the freedom to choose whether an arbitrary reactor is inhibitory or excitatory coupled to its neighbor. This versatile experimental and theoretical framework can be used to create a wide variety of chemical networks. Here we design, construct and characterize chemical networks that achieve the complexity of central pattern generators (CPGs), which are found in the autonomic nervous system of a variety of organisms.

nlin.PS↗

arXiv2017

Transition from turbulent to coherent flows in confined three-dimensional active fluids

Transport of fluid through a pipe is essential for the operation of macroscale machines and microfluidic devices. Conventional fluids only flow in response to external pressure. We demonstrate that an active isotropic fluid, comprised of microtubules and molecular motors, autonomously flows through meter-long three-dimensional channels. We establish control over the magnitude, velocity profile and direction of the self-organized flows, and correlate these to the structure of the extensile microtubule bundles. The inherently three-dimensional transition from bulk-turbulent to confined-coherent flows occurs concomitantly with a transition in the bundle orientational order near the surface, and is controlled by a scale-invariant criterion related to the channel profile. The non-equilibrium transition of confined isotropic active fluids can be used to engineer self-organized soft machines.

cond-mat.soft↗

arXiv2015

ATP consumption of eukaryotic flagella measured at a single-cell level

The motility of cilia and flagella is driven by thousands of dynein motors that hydrolyze adenosine triphosphate (ATP). Despite decades of genetic, biochemical, structural and biophysical studies, some aspects of ciliary motility remain elusive, such as the regulation of beating patterns and the energetic efficiency of these nanomachines. Here, we introduce an experimental method to measure ATP consumption of actively beating axonemes on a single-cell level. We encapsulated individual sea urchin sperm with demembranated flagellum inside water-in-oil emulsion droplets and measured the axonemes ATP consumption by monitoring fluorescence intensity of a fluorophore-coupled reporter system for ATP turnover in the droplet. Concomitant phase contrast imaging allowed us to extract a linear dependence between the ATP consumption rate and the flagellar beating frequency, with ~2.3e5 ATP molecules consumed per beat of a demembranated flagellum. Increasing the viscosity of the aqueous medium led to modified beating waveforms of the axonemes and to higher energy consumption per beat cycle. Our single-cell experimental platform provides both new insights into the beating mechanism of flagella and a powerful tool for future studies.

physics.bio-ph↗

arXiv2011

Interactions between colloids induced by a soft cross-linked polymer substrate

Using video-microscopy imaging we demonstrate the existence of a short-ranged equilibrium attraction between heavy silica colloids diffusing on soft surfaces of cross-linked polymer gels. The inter-colloid potential can be tuned by changing the gel stiffness or by coating the colloids with a polymer layer. On sufficiently soft substrates, the interaction induced by the polymer matrix leads to large-scale colloidal aggregation. We correlate the in-plane interaction with a colloid-surface attraction.

cond-mat.soft↗

arXiv2007

Smectic ordering in athermal systems of rod-like triblock copolymers

The phase behavior of the system of parallel rigid triblock copolymers is examined using the second-virial density functional theory. The triblock particle consists of two identical infinitely thin hard rods of finite lengths on the opposite ends of one central hard cylinder with nonzero length and diameter. Stability analyses and free energy calculations show that the system of parallel particles can form not only uniform nematic and smectic A phases, but a smectic-C phase too. The stability and structure of the tilted structure is controlled by only the diameter and the length of the central cylinder segment. Interestingly, the diameter effects only the layer tilting and the periodicity, but not the packing fraction of the nematic to smectic-C transition. For all values of cylinder length the usual smectic-A and smectic-C transitions compete with each other and no nematic-columnar transition is observed. At low and high cylinder length the smectic-A phase is stabilized first, while the smectic C is the most stable for intermediate length values.

cond-mat.soft↗

arXiv2006

The influence of charge and flexibility on smectic phase formation in filamentous virus suspensions

We present experimental measurements of the cholesteric-smectic phase transition of suspensions of charged semiflexible rods as a function of rod flexibility and surface charge. The rod particles consist of the bacteriophage M13 and closely related mutants, which are structurally identical to this virus, but vary either in contour length and therefore ratio of persistence length to contour length, or vary in surface charge. Surface charge is altered in two ways; by changing solution pH and by comparing M13 with {\it fd} virus, a mutant which differs from M13 only by the substitution of a single charged amino acid for a neutral one per viral coat protein. Phase diagrams are measured as a function of particle length, particle charge and ionic strength. The experimental results are compared with existing theoretical predictions for the phase behavior of flexible rods and charged rods. In contrast to the isotropic-cholesteric transition, where theory and experiment agree at high ionic strength, the nematic-smectic transition exhibits complex charge and ionic strength dependence significantly different from predicted phase behavior. Possible explanations for these unexpected results are discussed.

cond-mat.soft↗

arXiv2004

Nematic phase transitions in mixtures of thin and thick colloidal rods

We present the first experimental measurements of the isotropic and nematic phases of mixtures of thin, charged semiflexible fd virus, and thick, fd-PEG created by covalently grafting poly-(ethylene glycol) to the the surface of fd, rods. The fd-PEG is sterically stabilized and its phase behavior is independent of ionic strength. The fd is charged. Therefore, by varying the ionic strength of a mixture of fd and fd-PEG, only the effective diameter of the bare fd rods changes, subsequently varying the effective diameter ratio (d=D_fd-PEG/D_fd) from 3.7 to 1. In solution, binary mixtures of fd and fd-PEG are shown to exhibit isotropic-nematic, isotropic-nematic-nematic and nematic-nematic coexisting phases with increasing concentration. We measure the binary phase diagrams as a function of composition, total concentration, and ionic strength. We find a lower critical point in the nematic-nematic coexistence region which has not been observed previously. These experimental results resolve a controversy in the literature concerning the evolution of the nematic-nematic phase separation with concentration. The experimental results are qualitatively described by a rescaled Onsager-type theory for the phase behavior of binary rod mixtures.

cond-mat.soft↗

arXiv2004

The isotropic-cholesteric phase transition of filamentous virus suspensions as a function of rod length and charge

The viruses studied are genetically engineered, charged, semiflexible filamentous bacteriophages that are structurally identical to M13 virus, but differ either in contour length or surface charge. While varying contour length (L) we assume the persistence length (P) remains constant, and thus we alter the rod flexibility (L/P). Surface charge is altered both by changing solution pH and by comparing two viruses, fd and M13, which differ only by the substitution of one charged for one neutral amino acid per virus coat protein. We measure both the isotropic and cholesteric coexistence concentrations as well as the nematic order parameter after unwinding the cholesteric phase in a magnetic field. The isotropic-cholesteric transition experimental results agree semi-quantitatively with theoretical predictions for semiflexible, charged rods.

cond-mat.soft↗

arXiv2004

Isotropic-nematic phase transition in suspensions of filamentous virus and the neutral polymer Dextran

We present an experimental study of the isotropic-nematic phase transition in an aqueous mixture of charged semi-flexible rods (fd virus) and neutral polymer (Dextran). A complete phase diagram is measured as a function of ionic strength and polymer molecular weight. At high ionic strength we find that adding polymer widens the isotropic-nematic coexistence region with polymers preferentially partitioning into the isotropic phase, while at low ionic strength the added polymer has no effect on the phase transition. The nematic order parameter is determined from birefringence measurements and is found to be independent of polymer concentration (or equivalently the strength of attraction). The experimental results are compared with the existing theoretical predictions for the isotropic-nematic transition in rods with attractive interactions.

cond-mat.soft↗

arXiv2003

What is the origin of chirality in the cholesteric phase of virus suspensions ?

We report a study of the cholesteric phase in monodisperse suspensions of the rod-like virus fd sterically stabilized with the polymer polyethylene glycol (PEG). After coating the virus with neutral polymers, the phase diagram and nematic order parameter of the fd-PEG system then become independent of ionic strength. Surprisingly, the fd-PEG suspensions not only continue to exhibit a cholesteric phase, which means that the grafted polymer does not screen all chiral interactions between rods, but paradoxically the cholesteric pitch of this sterically stabilized fd-PEG system varies with ionic strength. Furthermore, we observe that the cholesteric pitch decreases with increasing viral contour length, in contrast to theories which predict the opposite trend. Different models of the origin of chirality in colloidal liquid crystals are discussed.

cond-mat.soft↗