arXiv subjects

Rae M. Robertson-Anderson

Publications and source records attributed to Rae M. Robertson-Anderson.

At least 19 recordsLinked to original sources

arXiv2025

Hacktive Matter: data-driven discovery through hackathon-based cross-disciplinary coding

The past decade has seen unprecedented growth in active matter and autonomous biomaterials research, yielding diverse classes of materials that promise revolutionary applications such as self-healing infrastructure and self-sensing tissue implants. However, inconsistencies in metrics, definitions, and analysis algorithms across research groups, as well as the high-dimension data streams, has hindered identification of performance intersections. Progress in this arena demands multi-disciplinary team approaches to discovery with scaffolded training and cross-pollination of ideas, and requires new learning and collaboration methods. To address this challenge, we have developed a hackathon platform to train future scientists and engineers in big data, interdisciplinary collaboration, and community coding; and to design and beta-test high-throughput (HTP) biomaterials analysis software and workflows. We enforce a flat hierarchy, pairing participants ranging from high school students to faculty with varied experiences and skills to collectively contribute to data acquisition and processing, ideation, coding, testing and dissemination. With clearly-defined goals and deliverables, participants achieve success through a series of tutorials, small group coding sessions, facilitated breakouts, and large group report-outs and discussions. These modules facilitate efficient iterative algorithm development and optimization; strengthen community and collaboration skills; and establish teams, benchmarks, and community standards for continued productive work. Our hackathons provide a powerful model for the soft matter community to educate and train students and collaborators in cutting edge data-driven analysis, which is critical for future innovation in complex materials research.

physics.ed-ph↗

arXiv2025

BARCODE: Biomaterial Activity Readouts to Categorize, Optimize, Design and Engineer for high throughput screening and characterization of dynamically restructuring soft materials

Active, responsive, nonequilibrium materials, at the forefront of materials engineering, offer dynamical restructuring, mobility and other complex life-like properties. Yet, this enhanced functionality comes with significant amplification of the size and complexity of the datasets needed to characterize their properties, thereby challenging conventional approaches to analysis. To meet this need, we present BARCODE (Biomaterial Activity Readouts to Categorize, Optimize, Design and Engineer), an open-access software that automates high throughput screening of microscopy video data to enable nonequilibrium material optimization and discovery. BARCODE produces a unique fingerprint or barcode of performance metrics that visually and quantitatively encodes dynamic material properties with minimal file size. Using three complementary material agnostic analysis branches, BARCODE significantly reduces data dimensionality and size, while providing rich, multiparametric outputs and rapid tractable characterization of activity and structure. We analyze a series of datasets of cytoskeleton networks and cell monolayers to demonstrate the ability of BARCODE to accelerate and streamline screening and analysis, reveal unexpected correlations and emergence, and enable broad non-expert data access, comparison, and sharing.

cond-mat.soft↗

arXiv2025

Kinesin-driven de-mixing of cytoskeleton composites drives emergent mechanical properties

The cytoskeleton is an active composite of filamentous proteins that dictates diverse mechanical properties and processes in eukaryotic cells by generating forces and autonomously restructuring itself. Enzymatic motors that act on the comprising filaments play key roles in this activity, driving spatiotemporally heterogeneous mechanical responses that are critical to cellular multifunctionality, but also render mechanical characterization challenging. Here, we couple optical tweezers microrheology and fluorescence microscopy with simulations and mathematical modeling to robustly characterize the mechanics of active composites of actin filaments and microtubules restructured by kinesin motors. We discover that composites exhibit a rich ensemble of force response behaviors, elastic, yielding, and stiffening, with their propensity and properties tuned by motor concentration and strain rate. Moreover, intermediate kinesin concentrations elicit emergent mechanical stiffness and resistance while higher and lower concentrations exhibit softer, more viscous dissipation. We further show that composites transition from well-mixed interpenetrating double-networks of actin and microtubules to de-mixed states of microtubule-rich aggregates surrounded by relatively undisturbed actin phases. It is this de-mixing that leads to the emergent mechanical response, offering an alternate route that composites can leverage to achieve enhanced stiffness through coupling of structure and mechanics.

cond-mat.soft↗

arXiv2024

DNA transport is topologically sculpted by active microtubule dynamics

The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments comprising the cytoskeleton often leads to anomalous subdiffusion, while active processes such as motor-driven restructuring can induce athermal superdiffusion. Understanding the interplay between these seemingly antagonistic contributions to intracellular dynamics remains a grand challenge. Here, we use single-molecule tracking to show that the transport of large linear and circular DNA through motor-driven microtubule networks can be non-gaussian and multi-modal, with the degree and spatiotemporal scales over which these features manifest depending non-trivially on the state of activity and DNA topology. For example, active network restructuring increases caging and non-Gaussian transport modes of linear DNA, while dampening these mechanisms for rings. We further discover that circular DNA molecules exhibit either markedly enhanced subdiffusion or superdiffusion compared to their linear counterparts, in the absence or presence of kinesin activity, indicative of microtubules threading circular DNA. This strong coupling leads to both stalling and directed transport, providing a direct route towards parsing distinct contributions to transport and determining the impact of coupling on the transport signatures. More generally, leveraging macromolecular topology as a route to programming molecular interactions and transport dynamics is an elegant yet largely overlooked mechanism that cells may exploit for intracellular trafficking, streaming, and compartmentalization. This mechanism could be harnessed for the design of self-regulating, sensing, and reconfigurable biomimetic matter.

cond-mat.soft↗

arXiv2024

Timed material self-assembly controlled by circadian clock proteins

Active biological molecules present a powerful, yet largely untapped, opportunity to impart autonomous regulation to materials. Because these systems can function robustly to regulate when and where chemical reactions occur, they have the ability to bring complex, life-like behavior to synthetic materials. Here, we achieve this design feat by using functionalized circadian clock proteins, KaiB and KaiC, to engineer time-dependent crosslinking of colloids. The resulting material self-assembles with programmable kinetics, producing macroscopic changes in material properties, via molecular assembly of KaiB-KaiC complexes. We show that colloid crosslinking depends strictly on the phosphorylation state of KaiC, with kinetics that are synced with KaiB-KaiC complexing. Our microscopic image analyses and computational models indicate that the stability of colloidal super-structures depends sensitively on the number of Kai complexes per colloid connection. Consistent with our model predictions, a high concentration stabilizes the material against dissolution after a robust self-assembly phase, while a low concentration allows circadian oscillation of material structure. This work introduces the concept of harnessing biological timers to control synthetic materials; and, more generally, opens the door to using protein-based reaction networks to endow synthetic systems with life-like functional properties.

cond-mat.soft↗

arXiv2023

Motor antagonism dictates emergent dynamics in active double networks tuned by crosslinkers

The cytoskeleton relies on diverse populations of motors, filaments, and binding proteins acting in concert to enable non-equilibrium processes ranging from mitosis to chemotaxis. Its versatile reconfigurability, programmed by interactions between its constituents, make the cytoskeleton foundational active matter. Yet, current active matter endeavors are limited largely to single force-generating components acting on a single substrate, far from the composite cytoskeleton in cells. Here, we engineer actin-microtubule double-networks, driven by kinesin and myosin motors and tuned by crosslinkers, to ballistically restructure and flow with speeds that span three orders of magnitude depending on the composite formulation and time relative to the onset of motor activity. Differential dynamic microscopy analyses reveal that kinesin and myosin compete to delay the onset of acceleration and suppress discrete restructuring events, while passive crosslinking of either actin or microtubules has an opposite effect. Our minimal advection-diffusion model and spatial correlation analyses correlate these dynamics to structure, with motor antagonism suppressing reconfiguration and de-mixing, while crosslinking enhances clustering. Despite the rich formulation space and emergent formulation-dependent structures, the non-equilibrium dynamics across all networks and timescales can be organized into three classes: slow isotropic reorientation, fast directional flow, and multimode restructuring. Moreover, our mathematical model demonstrates that diverse structural motifs can arise simply from the interplay between motor-driven advection and frictional drag. These general features of our platform facilitate applicability to other active matter systems, and shed light on diverse ways that cytoskeletal components can cooperate or compete to enable wide-ranging cellular processes.

physics.bio-ph↗

arXiv2023

Cooperative rheological state-switching of enzymatically-driven composites of circular DNA and dextran

Polymer topology, which plays a principal role in the rheology of polymeric fluids, and non-equilibrium materials, which exhibit time-varying rheological properties, are topics of intense investigation. Here, we push composites of circular DNA and dextran out-of-equilibrium via enzymatic digestion of DNA rings to linear fragments. Our time-resolved rheology measurements reveal discrete state-switching, with composites undergoing abrupt transitions between dissipative and elastic-like states. The gating time and lifetime of the elastic-like states, and the magnitude and sharpness of the transitions, are surprisingly decorrelated from digestion rates and non-monotonically depend on the DNA fraction. We model our results using sigmoidal two-state functions to show that bulk state-switching can arise from continuous molecular-level activity due to the necessity for cooperative percolation of entanglements to support macroscopic stresses. Our platform, coupling the tunability of topological composites with the power of enzymatic reactions, may be leveraged for diverse material applications from wound-healing to self-repairing infrastructure.

cond-mat.soft↗

arXiv2022

Polymer threadings and rigidity dictate the viscoelasticity and nonlinear relaxation dynamics of entangled ring-linear blends and their composites with rigid rod microtubules

Mixtures of polymers of varying topologies and stiffnesses display complex emergent rheological properties that often cannot be predicted from their single-component counterparts. For example, entangled blends of ring and linear polymers have been shown to exhibit enhanced shear thinning and viscosity, as well as prolonged relaxation timescales, compared to pure solutions of rings or linear chains. These emergent properties arise in part from the synergistic threading of rings by linear polymers. Topology has also been shown to play an important role in composites of flexible (e.g., DNA) and stiff (e.g., microtubules) polymers, whereby rings promote mixing while linear polymers induce de-mixing and flocculation of stiff polymers, with these topology-dependent interactions giving rise to highly distinct rheological signatures. To shed light on these intriguing phenomena, we use optical tweezers microrheology to measure the linear and nonlinear rheological properties of entangled ring-linear DNA blends and their composites with rigid microtubules. We show that the linear viscoelasticity is primarily dictated by the microtubules at lower frequencies, but their contributions become frozen out at frequencies above the DNA entanglement rate. In the nonlinear regime, we reveal that mechanical response features, such as shear thinning, stress softening and multi-modal relaxation dynamics are mediated by entropic stretching, threading, and flow alignment of entangled DNA, as well as forced de-threading, disentanglement, and clustering. The contributions of each of these mechanisms depend on the strain rate as well as the entanglement density and stiffness of the polymers, leading to non-monotonic rate dependences of mechanical properties that are most pronounced for highly concentrated ring-linear blends rather than DNA-MT composites.

cond-mat.soft↗

arXiv2022

Active restructuring of cytoskeleton composites leads to increased mechanical stiffness, memory, and heterogeneity

The composite cytoskeleton, comprising interacting networks of semiflexible actin and rigid microtubules, actively generates forces and restructures using motor proteins such as myosins to enable key mechanical processes including cell motility and mitosis. Yet, how motor-driven activity alters the mechanics of cytoskeleton composites remains an open challenge. Here, we perform optical tweezers microrheology on actin-microtubule composites driven by myosin II motors to show that motor activity increases the linear viscoelasticity and elastic storage of the composite by active restructuring to a network of tightly-packed filament clusters and bundles. Our nonlinear microrheology measurements performed hours after cessation of activity show that the motor-contracted structure is stable and robust to nonlinear forcing. Unique features of the nonlinear response include increased mechanical stiffness, memory and heterogeneity, coupled with suppressed filament bending following motor-driven restructuring. Our results shed important new light onto the interplay between viscoelasticity and non-equilibrium dynamics in active polymer composites such as the cytoskeleton.

cond-mat.soft↗

arXiv2022

OpTiDDM (Optical Tweezers integrating Differential Dynamic Microscopy) maps the spatiotemporal propagation of nonlinear stresses in polymer blends and composites

How local stresses propagate through polymeric fluids, and, more generally, how macromolecular dynamics give rise to viscoelasticity are open questions vital to wide-ranging scientific and industrial fields. Here, to unambiguously connect polymer dynamics to force response, and map stress propagation in macromolecular materials, we present a powerful approach-Optical Tweezers integrating Differential Dynamic Microscopy (OpTiDMM)-that simultaneously imposes local strains, measures resistive forces, and analyzes the motion of the surrounding polymers. Our measurements with blends of ring and linear polymers (DNA) and their composites with stiff polymers (microtubules) uncover a surprising resonant response, in which affine alignment, superdiffusivity, and elastic memory are maximized when the strain rate is comparable to the entanglement rate. Microtubules suppress this resonance, while substantially increasing elastic force and memory, due to varying degrees to which the polymers buildup, stretch and flow along the strain path, and configurationally dissipate stress. More broadly, the rich multi-scale coupling of mechanics and dynamics afforded by OpTiDDM, empowers its interdisciplinary use to elucidate non-trivial phenomena that sculpt stress propagation dynamics-critical to commercial applications and cell mechanics alike.

cond-mat.soft↗

arXiv2021

DNA topology dictates strength and flocculation in DNA-microtubule composites

Polymer composites are ubiquitous in biology and industry alike, owing to their emergent desirable mechanical properties not attainable in single-species systems. At the same time, polymer topology has been shown to play a key role in tuning the rheology of polymeric fluids. However, how topology impacts the rheology of composites remains poorly understood. Here, we create composites of rigid rods (microtubules) polymerized within entangled solutions of flexible linear and ring polymers (DNA). We couple linear and nonlinear optical tweezers microrheology with confocal microscopy and scaled particle theory to show that composites of linear DNA and microtubules exhibit a strongly non-monotonic dependence of elasticity and stiffness on microtubule concentration due to depletion-driven polymerization and flocculation of microtubules. In contrast, composites of ring DNA and microtubules show a much more modest monotonic increase in elastic strength with microtubule concentration, which we demonstrate arises from the increased ability of rings to mix with microtubules.

cond-mat.soft↗

arXiv2021

Active Cytoskeletal Composites Display Emergent Tunable Contractility and Restructuring

The cytoskeleton is a model active matter system that controls diverse cellular processes from division to motility. While both active actomyosin dynamics and actin-microtubule interactions are key to the cytoskeleton's versatility and adaptability, an understanding of their interplay is lacking. Here, we couple microscale experiments with mechanistic modeling to elucidate how connectivity, rigidity, and force-generation affect emergent material properties in in vitro composites of actin, tubulin, and myosin. We use time-resolved differential dynamic microscopy and spatial image autocorrelation to show that ballistic contraction occurs in composites with sufficient flexibility and motor density, but that a critical fraction of microtubules is necessary to sustain controlled dynamics. Our active double-network models reveal that percolated actomyosin networks are essential for contraction, but that networks with comparable actin and microtubule densities can uniquely resist mechanical stresses while simultaneously supporting substantial restructuring. Our findings provide a much-needed blueprint for designing cytoskeleton-inspired materials that couple tunability with resilience and adaptability.

cond-mat.soft↗

arXiv2021

Dynamics and Rheology of Ring-Linear Blend Semidilute Solutions in Extensional Flow: Single Molecule Experiments

Ring polymers exhibit unique flow properties due to their closed chain topology. Despite recent progress, we have not yet achieved a full understanding of the nonequilibrium flow behavior of rings in nondilute solutions where intermolecular interactions greatly influence chain dynamics. In this work, we directly observe the dynamics of DNA rings in semidilute ring-linear polymer blends using single molecule techniques. We systematically investigate ring polymer relaxation dynamics from high extension and transient and steady-state stretching dynamics in planar extensional flow for a series of ring-linear blends with varying ring fraction. Our results show multiple molecular sub-populations for ring relaxation in ring-linear blends, as well as large conformational fluctuations for rings in steady extensional flow, even long after the initial transient stretching process has subsided. We further quantify the magnitude and characteristic timescales of ring conformational fluctuations as a function of blend composition. Interestingly, we find that the magnitude of ring conformational fluctuations follows a non-monotonic response with increasing ring fraction, first increasing at low ring fraction and then substantially decreasing at large ring fraction in ring-linear blends. A unique set of ring polymer conformations are observed during the transient stretching process, which highlights the prevalence of molecular individualism and supports the notion of complex intermolecular interactions in ring-linear polymer blends. Together with results from molecular simulations, our results suggest that ring conformational fluctuations arise due to ring-linear threading and intermolecular hydrodynamic interactions (HI). Taken together, our results provide a new molecular understanding of ring polymer dynamics in ring-linear blends in nonequilibrium flow.

cond-mat.soft↗

arXiv2019

Unexpected entanglement dynamics in semidilute blends of supercoiled and ring DNA

Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of producing polymers of different topologies, the dynamics of topological polymer blends remains poorly understood. We address this void by using both passive and active microrheology to characterize the linear and nonlinear rheological properties of blends of relaxed circular and supercoiled DNA. We characterize the dynamics as we vary the concentration from below the overlap concentration c* to above (0.5c* to 2c*). Surprisingly, despite working at the dilute-semidilute crossover, entanglement dynamics, such as shear-thinning, elastic plateaus, and multiple relaxation modes, emerge. Finally, blends exhibit an unexpected sustained elastic response to nonlinear strains not previously observed even in well-entangled linear polymer solutions.

cond-mat.soft↗

arXiv2019

Optical tweezers microrheology maps the dynamics of strain-induced local inhomogeneities in entangled polymers

Optical tweezers microrheology (OTM) offers a powerful approach to probe the nonlinear response of complex soft matter systems, such as networks of entangled polymers, over wide-ranging spatiotemporal scales. OTM can also uniquely characterize the microstructural dynamics that lead to the intriguing nonlinear rheological properties that these systems exhibit. However, the strain in OTM measurements, applied by optically forcing a micro-probe through the material, induces network inhomogeneities in and around the strain path, and the resultant flow field complicates the measured response of the system. Through a robust set of custom-designed OTM protocols, coupled with modeling and analytical calculations, we characterize the time-varying inhomogeneity fields induced by OTM measurements. We show that post-strain homogenization does not interfere with the intrinsic stress relaxation dynamics of the system, rather it manifests as an independent component in the stress decay, even in highly nonlinear regimes such as with the microrheological-LAOS (mLAOS) protocols we introduce. Our specific results show that Rouse-like elastic retraction, rather than disentanglement and disengagement, dominates the nonlinear stress relaxation of entangled polymers at micro- and meso- scales. Thus, our study opens up possibilities of performing precision nonlinear microrheological measurements, such as mLAOS, on a wide range of complex macromolecular systems.

cond-mat.soft↗

arXiv2018

Synergistic interactions between DNA and actin trigger emergent viscoelastic behavior

Composites of flexible and rigid polymers are ubiquitous in biology and industry alike, yet the physical principles determining their mechanical properties are far from understood. Here, we couple force spectroscopy with large-scale Brownian Dynamics simulations to elucidate the unique viscoelastic properties of custom-engineered blends of entangled flexible DNA molecules and semiflexible actin filaments. We show that composites exhibit enhanced stress-stiffening and prolonged mechano-memory compared to systems of actin or DNA alone, and that these nonlinear features display a surprising non-monotonic dependence on the fraction of actin in the composite. Simulations reveal that these counterintuitive results arise from synergistic microscale interactions between the two biopolymers. Namely, DNA entropically drives actin filaments to form bundles that stiffen the network but reduce the entanglement density, while a percolating actin network is required to reinforce the DNA network against yielding and flow. The competition between bundling and percolation triggers an unexpected stress response that leads equal mass actin-DNA composites to exhibit the most pronounced stress-stiffening and the most long-lived entanglements.

cond-mat.soft↗

arXiv2018

Crowding induces entropically-driven changes to DNA dynamics that depend on crowder structure and ionic conditions

Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a topic of debate. To address this problem, we use single-molecule fluorescence microscopy and custom particle-tracking algorithms to investigate the impact of varying macromolecular crowding conditions on the transport and conformational dynamics of large DNA molecules. Specifically, we measure the mean-squared center-of-mass displacements, as well as the conformational size, shape, and fluctuations, of individual 115 kbp DNA molecules diffusing through various in vitro solutions of crowding polymers. We determine the role of crowder structure and concentration, as well as ionic conditions, on the diffusion and configurational dynamics of DNA. We find that branched, compact crowders (10 kDa PEG, 420 kDa Ficoll) drive DNA to compact, whereas linear, flexible crowders (10 kDa, 500 kDa dextran) cause DNA to elongate. Interestingly, the extent to which DNA mobility is reduced by increasing crowder concentrations appears largely insensitive to crowder structure (branched vs linear), despite the highly different configurations DNA assumes in each case. We also characterize the role of ionic conditions on crowding-induced DNA dynamics. We show that both DNA diffusion and conformational size exhibit an emergent non-monotonic dependence on salt concentration that is not seen in the absence of crowders.

physics.bio-ph↗

arXiv2017

Active Disassembly and Reassembly of Actin Networks Induces Distinct Biphasic Mechanics

Actin is a key component of the cytoskeleton, which plays central roles in cell motility, division, growth, and tensile strength. To enable this wide range of transient mechanical processes and properties, networks of actin filaments continuously disassemble and reassemble via active de/re-polymerization. However, the question remains as to how de/re-polymerization kinetics of individual actin filaments translate to time-varying mechanics of dis/re-assembling networks. To address this question, to ultimately elucidate the molecular mechanisms that enable cells to exhibit a myriad of transitory mechanical properties, we couple time-resolved active microrheology with microfluidics to measure the time-varying viscoelastic moduli of entangled and crosslinked actin networks during chemically-triggered network disassembly and reassembly. We also develop a corresponding mathematical model that relates the time-evolution of filament length to the resulting time-dependent storage moduli of evolving networks. During disassembly, we find that the moduli exhibit two distinct exponential decays, with experimental time constants of $\sim$169 and $\sim$47 min, which we show arises from a phase transition from a rigid percolated network to a non-rigid regime occurring after $\sim$90 min. During reassembly, measured moduli exhibit linear increase with time for $\sim$90 min, after which steady-state values are achieved. Our theoretical model shows that reassembly mechanics are dominated by elongation kinetics, and that elongation rates are much slower than has been recently assumed. Our measurements shed much needed light onto how polymerization kinetics map to time-varying mechanics of actively evolving cytoskeleton networks, and provide a powerful platform for studying other active and dynamic systems currently under intense investigation.

physics.bio-ph↗