arXiv subjects

Seth Fraden

Publications and source records attributed to Seth Fraden.

At least 19 recordsLinked to original sources

arXiv2026

ARTGEL: A temperature-regulated electrophoresis platform for quantitative studies of reversible association in gels

Here we present ARTGEL, an actively regulated-temperature gel electrophoresis platform designed for long-duration experiments under independently controlled thermal and electrical conditions. ARTGEL combines thermoelectric regulation of the gel temperature, a large heated and circulated buffer reservoir, and an automated electrode-wiping mechanism that stabilizes the voltage across the gel during runs exceeding 24 h. The platform was developed to address a limitation of conventional electrophoretic mobility shift assays, which are commonly used to analyze reversible biomolecular association but usually aim to suppress reaction during electrophoresis by dilution, competitors, or reduced temperature so that the gel reports a pre-equilibrated bulk solution. For temperature-sensitive systems, these strategies can alter the chemical state during loading and migration and obscure whether the measured band pattern reflects the original bulk sample or a re-equilibrated state inside the porous gel. Rather than attempting to quench reactions, ARTGEL enables electrophoresis to be performed at the same temperature as complementary bulk measurements, so that reversible association can be quantified directly in the gel and compared with matched measurements in solution. Using DNA origami assemblies, we show that ARTGEL preserves distinct temperature-dependent association states, resolves reaction-dependent distortions of migrating bands, and supports extraction of in-gel kinetic and thermodynamic parameters from reaction-diffusion-advection modeling.

cond-mat.soft↗

arXiv2025

From toroids to helical tubules: Kirigami-inspired programmable assembly of two-periodic curved crystals

Biology is full of intricate molecular structures whose geometries are inextricably linked to their function. Many of these structures exhibit varying curvature, such as the helical structure of the bacterial flagellum, which is critical for their motility. Because synthetic analogues of these shapes could be valuable platforms for nanotechnologies, including drug delivery and plasmonics, controllable synthesis of variable-curvature structures of various material systems, from fullerenes to supramolecular assemblies, has been a long-standing goal. Like two-dimensional crystals, these structures have a two-periodic symmetry, but unlike standard two-dimensional crystals, they are embedded in three dimensions with complex, spatially-varying curvatures that cause the structures to close upon themselves in one or more dimensions. Here, we develop and implement a design strategy to program the self-assembly of a complex spectrum of two-periodic curved crystals with variable periodicity, spatial dimension, and topology, spanning from toroids to achiral serpentine tubules to both left- and right-handed helical tubules. Our design strategy uses a kirigami-based mapping of 2D planar tilings to 3D curved crystals that preserves the periodicity, two-fold rotational symmetries, and subunit dimensions via the arrangement of disclination defects. We survey the modular geometry of these curved crystals and infer the addressable subunit interactions required to assemble them from triangular subunits. To demonstrate this design strategy, we program the self-assembly of toroids, helical- and serpentine-tubules from DNA origami subunits. A simulation model of the assembly pathways reveals physical considerations for programming the geometric specificity of angular folds in the curved crystal required to avoid defect-mediated misassembly.

cond-mat.soft↗

arXiv2025

Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures

We present a modular DNA origami design approach to address the challenges of assembling geometrically complex nanoscale structures, including those with nonuniform Gaussian curvature. This approach features a core structure that completely conserves the scaffold routing across different designs and preserves more than 70% of the DNA staples between designs, dramatically reducing both cost and effort, while enabling precise and independent programming of subunit interactions and binding angles through adjustable overhang lengths and sequences. Using cryogenic electron microscopy, gel electrophoresis, and coarse-grained molecular dynamics simulations, we validate a set of robust design rules. We demonstrate the method's utility by assembling a variety of self-limiting structures, including anisotropic shells with controlled inter-subunit interactions and curvature, and a toroid with globally varying curvature. Our strategy is both cost-effective and versatile, providing a promising and efficient solution for the synthetic fabrication of complex nanostructures.

cond-mat.soft↗

arXiv2025

Measuring multisubunit mechanics of geometrically-programmed colloidal assemblies via cryo-EM multi-body refinement

Programmable self-assembly has recently enabled the creation of complex structures through precise control of the interparticle interactions and the particle geometries. Targeting ever more structurally complex, dynamic, and functional assemblies necessitates going beyond the design of the structure itself, to the measurement and control of the local flexibility of the inter-subunit connections and its impact on the collective mechanics of the entire assembly. In this study, we demonstrate a method to infer the mechanical properties of multisubunit assemblies using cryogenic electron microscopy (cryo-EM) and RELION's multi-body refinement. Specifically, we analyze the fluctuations of pairs of DNA-origami subunits that self-assemble into tubules. By measuring the fluctuations of dimers using cryo-EM, we extract mechanical properties such as the bending modulus and interparticle spring constant. These properties are then applied to elastic models to predict assembly outcomes, which align well with experimental observations. This approach not only provides a deeper understanding of nanoparticle mechanics, but also opens new pathways to refining subunit designs to achieve precise assembly behavior. This methodology could have broader applications in the study of nanomaterials, including protein assemblies, where understanding the interplay of mechanical properties and subunit geometry is essential for controlling complex self-assembled structures.

cond-mat.soft↗

arXiv2024

Economical and versatile subunit design principles for self-assembled DNA origami structures

Self-assembly of nanoscale synthetic subunits is a promising bottom-up strategy for fabrication of functional materials. Here, we introduce a design principle for DNA origami nanoparticles of 50-nm size, exploiting modularity, to make a family of versatile subunits that can target an abundant variety of self-assembled structures. The subunits are based on a core module that remains constant among all the subunits. Variable bond modules and angle modules are added to the exterior of the core to control interaction specificity, strength and structural geometry. A series of subunits with designed bond/angle modules are demonstrated to self-assemble into a rich variety of structures with different Gaussian curvatures, exemplified by sheets, spherical shells, and tubes. The design features flexible joints implemented using single-stranded angle modules between adjacent subunits whose mechanical properties, such as bending elastic moduli, are inferred from cryo-EM. Our findings suggest that incorporating a judicious amount of flexibility in the bond provides error tolerances in design and fabrication while still guaranteeing target fidelity. Lastly, while increasing flexibility could introduce greater variability and potential errors in assembly, these effects can be counterbalanced by increasing the number of distinct bonds, thereby allowing for precise targeting of specific structural binding angles within a broad range of configurations.

cond-mat.soft↗

arXiv2024

Active assembly and non-reciprocal dynamics of elastic membranes

Equilibrium self-assembly and conventional materials processing techniques fall far short of mimicking dynamic self-actuating processes that are commonplace throughout biology. To bridge the gap between living and synthetic matter, we study adhesive non-thermal fibers immersed in an active fluid. Autonomous chaotic flows power non-equilibrium fiber dynamics, inducing their collisions, generating connections, and weaving a membrane-shaped elastic network. This active assembly generates a hierarchy of shapes, structures, and dynamical processes spanning nanometers to centimeters. Ultimately, it generates an active membrane that exhibits global limit cycles induced by a non-reciprocal coupling between the elastic membrane deformations and the alignment axis of the polar active fluid. Our work merges self-assembly with active matter, demonstrating self-processing materials wherein hierarchical life-like structures and dynamics emerge from an initially structureless suspension.

cond-mat.soft↗

arXiv2024

Closed-loop control of active nematic flows

Living things enact control of non-equilibrium, dynamical structures through complex biochemical networks, accomplishing spatiotemporally-orchestrated physiological tasks such as cell division, motility, and embryogenesis. While the exact minimal mechanisms needed to replicate these behaviors using synthetic active materials are unknown, controlling the complex, often chaotic, dynamics of active materials is essential to their implementation as engineered life-like materials. Here, we demonstrate the use of external feedback control to regulate and control the spatially-averaged speed of a model active material with time-varying actuation through applied light. We systematically vary the controller parameters to analyze the steady-state flow speed and temporal fluctuations, finding the experimental results in excellent agreement with predictions from both a minimal coarse-grained model and full nematohydrodynamic simulations. Our findings demonstrate that proportional-integral control can effectively regulate the dynamics of active nematics in light of challenges posed by the constituents, such as sample aging, protein aggregation, and sample-to-sample variability. As in living things, deviations of active materials from their steady-state behavior can arise from internal processes and we quantify the important consequences of this coupling on the controlled behavior of the active nematic. Finally, the interaction between the controller and the intrinsic timescales of the active material can induce oscillatory behaviors in a regime of parameter space that qualitatively matches predictions from our model. This work underscores the potential of feedback control in manipulating the complex dynamics of active matter, paving the way for more sophisticated control strategies in the design of responsive, life-like materials.

cond-mat.soft↗

arXiv2023

Economical routes to size-specific assembly of self-closing structures

Self-assembly is one of the prevalent strategies used by living systems to fabricate ensembles of precision nanometer-scale structures and devices. The push for analogous approaches to create synthetic nanomaterials has led to the development of a large class of programmable crystalline structures. However, many applications require `self-limiting' assemblies, which autonomously terminate growth at a well-defined size and geometry. For example, curved architectures such as tubules, vesicles, or capsids can be designed to self-close at a particular size, symmetry, and topology. But developing synthetic strategies for self-closing assembly has been challenging, in part because such structures are prone to polymorphism that arises from thermal fluctuations of their local curvature, a problem that worsens with increased target size. Here we demonstrate a strategy to eliminate this source of polymorphism in self-closing assembly of tubules by increasing the assembly complexity. In the limit of single-component assembly, we find that thermal fluctuations allow the system to assemble nearby, off-target structures with varying widths, helicities, and chirality. By increasing the number of distinct components, we reduce the density of off-target states, thereby increasing the selectivity of a user-specified target structure to nearly 100%. We further show that by reducing the design constraints by targeting either the pitch or the width of tubules, fewer components are needed to reach complete selectivity. Combining experiments with theory, our results reveal an economical limit, which determines the minimum number of components that are required to create arbitrary assembly sizes with full selectivity. In the future, this approach could be extended to more complex self-limited structures, such as shells or triply periodic surfaces.

cond-mat.soft↗

arXiv2023

Hierarchical assembly is more robust than egalitarian assembly in synthetic capsids

Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and concentrations of subunits. By contrast, we introduce an assembly paradigm that allows large error-tolerance in the subunit affinity and helps avoid kinetic traps. Our combined experimental and computational approach uses a model system of triangular subunits programmed to assemble into T=3 icosahedral capsids comprising 60 units. The experimental platform uses DNA origami to create monodisperse colloids whose 3D geometry is controlled to nanometer precision, with two distinct bonds whose affinities are controlled to kBT precision, quantified in situ by static light scattering. The computational model uses a coarse-grained representation of subunits, short-ranged potentials, and Langevin dynamics. Experimental observations and modeling reveal that when the bond affinities are unequal, two distinct hierarchical assembly pathways occur, in which the subunits first form dimers in one case, and pentamers in another. These hierarchical pathways produce complete capsids faster and are more robust against affinity variation than egalitarian pathways, in which all binding sites have equal strengths. This finding suggests that hierarchical assembly may be a general engineering principle for optimizing self-assembly of complex target structures.

cond-mat.soft↗

arXiv2023

A Machine Learning Approach to Robustly Determine Director Fields and Analyze Defects in Active Nematics

Active nematics are dense systems of rodlike particles that consume energy to drive motion at the level of the individual particles. They exist in natural systems like biological tissues and artificial materials such as suspensions of self-propelled colloidal particles or synthetic microswimmers. Active nematics have attracted significant attention in recent years due to their spectacular nonequilibrium collective spatiotemporal dynamics, which may enable applications in fields such as robotics, drug delivery, and materials science. The director field, which measures the direction and degree of alignment of the local nematic orientation, is a crucial characteristic of active nematic and is essential for studying topological defects. However, determining the director field is a significant challenge in many experimental systems. Although director fields can be derived from images of active nematics using traditional imaging processing methods, the accuracy of such methods are highly sensitive to the settings of the algorithms. These settings must be tuned from image-to-image due to experimental noise, intrinsic noise of the imaging technology, and perturbations caused by changes in experimental conditions. This sensitivity currently limits automatic analysis of active nematics. To address this, we developed a machine learning model for extracting reliable director fields from raw experimental images, which enables accurate analysis of topological defects. Application of the algorithm to experimental data demonstrates that the approach is robust and highly generalizable to experimental settings that are different from those in the training data. It could be a promising tool for investigating active nematics and may be generalized to other active matter systems.

cond-mat.soft↗

arXiv2023

From Disks to Channels: Dynamics of Active Nematics Confined to an Annulus

Confinement can be used to systematically tame turbulent dynamics occurring in active fluids. Although periodic channels are the simplest geometries to study confinement numerically, the corresponding experimental realizations require closed racetracks. Here, we computationally study 2D active nematics confined to such a geometry -- an annulus. By systematically varying the annulus inner radius and channel width, we bridge the behaviors observed in the previously studied asymptotic limits of the annulus geometry: a disk and an infinite channel. We identify new steady-state behaviors, which reveal the influence of boundary curvature and its interplay with confinement. We also show that, below a threshold inner radius, the dynamics are insensitive to topological constraints imposed by boundary conditions. We explain this insensitivity through a simple scaling analysis. Our work sheds further light on design principles for using confinement to control the dynamics of active nematics.

cond-mat.soft↗

arXiv2023

Light-activated microtubule-based 2D active nematic

We characterize two-dimensional (2D) microtubule-based active nematics driven by light-responsive kinesin motor clusters. We assess two constructs of optogenetic kinesin: opto-K401, a processive motor, and opto-K365, a non-processive motor. Measurements reveal an order of magnitude improvement in the contrast of nematic flow speeds between maximally- and minimally-illuminated states for opto-K365 motors. Focusing on opto-K365 nematics, we characterize both the steady-state flow and defect density as a function of applied light and examine the transient behavior between steady-states. The steady-state nematic flow and defect densities are set by the applied light intensity across centimeter-sized samples, independent of initial conditions. Although nematic flow reaches steady-state within tens of seconds, the defect density exhibits transient behavior for 4 to 10 minutes, showing a separation between small-scale active reorganization and system-scale structural states. This work establishes an experimental platform to test theoretical frameworks which exploit spatiotemporally-heterogeneous patterns of activity to generate targeted dynamical states.

cond-mat.soft↗

arXiv2023

Numerical analysis of the propagation modes of photo-switching PDMS-arylazopyrazole optical waveguide and thin-film spectroscopic characterization

A new light responsive arylazopyrazole (AAP) containing polymer matrix thin film is fabricated by spin-coating of different concentrations of the AAP azo dye into the polydimethylsiloxane (PDMS) polymer at 150C. The new AAP molecular switch was also used to fabricate a solid-state PDMS-AAP waveguide by contact lithography and soft replica modeling methods in the micrometer scale. The refractive index of the spin-coated photoswitchable material can be modulated via the reversible trans-to-cis photoisomerization behavior of the AAP unit using different concentrations. When 0.01 M solution of the AAP unit was used, the refractive of the composite was 2.32 in the trans state and dropped to 1.85 in the cis state in the operating wavelength of 340 nm. At higher concentrations of 0.020 and 0.03 M, a wide refractive index tuning is achieved under the same wavelength. In 0.030 M the refractive index was 2.65 for the trans state and 2.0 for the cis state. The results suggest that the increase in refractive index tuning is related to the concentration of the AAP unit of the composite film. Theoretically, the spectral properties of the composite film are also simulated with two methods: 1) the Maxwell Equations; and 2) the frequency dependent finite element, showing excellent agreement for the different propagation modes of the proposed waveguide for regulated signals of 365/525 nm wavelengths. Furthermore, the photoisomerization of the PDMS-AAP thin film is analyzed with UV-vis spectroscopy to demonstrate the isomerization responses of the AAP moiety in the solid state. Additionally, preliminary photomechanical actuation properties of the composite film have been investigated. The PDMS-AAP waveguide described in this study provides a new approach for optically tunable photonics applications in the Visible-IR region.

physics.optics↗

arXiv2022

Geometrically programmed self-limited assembly of tubules using DNA origami colloids

Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are needed. To address this challenge, we explore the trade-offs between addressable assembly and self-closing assembly of a specific class of self-limiting structures: cylindrical tubules. We make triangular subunits using DNA origami that have specific, valence-limited interactions and designed binding angles, and study their assembly into tubules that have a self-limited width that is much larger than the size of an individual subunit. In the simplest case, the tubules are assembled from a single component by geometrically programming the dihedral angles between neighboring subunits. We show that the tubules can reach many micrometers in length and that their average width can be prescribed through the dihedral angles. We find that there is a distribution in the width and the chirality of the tubules, which we rationalize by developing a model that considers the finite bending rigidity of the assembled structure as well as the mechanism of self-closure. Finally, we demonstrate that the distributions of tubules can be further sculpted by increasing the number of subunit species, thereby increasing the assembly complexity, and demonstrate that using two subunit species successfully reduces the number of available end states by half. These results help to shed light on the roles of assembly complexity and geometry in self-limited assembly and could be extended to other self-limiting architectures, such as shells, toroids, or triply-periodic frameworks.

cond-mat.soft↗

arXiv2022

Active pulsatile gels: from chemical microreactor to polymeric actuator

We report on a synthesis protocol, experimental characterization and theoretical modeling of active pulsatile Belousov-Zhabotinsky (BZ) hydrogels. Our two-step synthesis technique allows independent optimization of the geometry, the chemical, and the mechanical properties of BZ gels. We identify the role of the surrounding medium chemistry and gel radius for the occurrence of BZ gel oscillations, quantified by the Damkohler number, ratio of chemical reaction to diffusion rates. Tuning the BZ gel size to maximize its chemomechanical oscillation amplitude, we find that its oscillatory strain amplitude is limited by the timescale of gel swelling relative to the chemical oscillation period. Our experimental findings are in good agreement with a Vanag-Epstein model of BZ chemistry and a Tanaka Fillmore theory of gel swelling dynamics.

cond-mat.soft↗

arXiv2021

Extensile to contractile transition in active microtubule-actin composites generates layered asters with programmable lifetimes

We study a reconstituted composite system consisting of an active microtubule network interdigitated with a passive network of entangled F-actin filaments. Increasing viscoelasticity of the F-actin network controls the emergent dynamics, inducing a transition from turbulent-like flows to bulk contractions. At intermediate F-actin concentrations, where the active stresses change their symmetry from anisotropic extensile to isotropic contracting, the composite separates into layered asters that coexist with the background turbulent fluid. Contracted onion-like asters have a radially extending microtubule-rich cortex that envelops alternating layers of microtubules and F-actin. The self-regulating layered organization survives aster merging events, which are reminiscent of droplet coalescence, and suggest the presence of effective surface tension. Finally, the layered asters are metastable structures. Their lifetime, which ranges from minutes to hours, is encoded in the material properties of the composite. Taken together, these results challenge the current models of active matter. They demonstrate that the self-organized dynamical states and patterns, which are evocative of those observed in the cytoskeleton, do not require precise biochemical regulation but can arise due to purely mechanical interactions of actively driven filamentous materials.

cond-mat.soft↗

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↗