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Charles M. Schroeder

Publications and source records attributed to Charles M. Schroeder.

16 recordsLinked to original sources

Range-Aware Bayesian Optimization for Discovering Diverse Designs within Target Property Windows

In many materials and product design problems, desirable candidates exhibit properties that fall within an acceptable range rather than achieve a single optimum. Recovering multiple, distinct solutions that satisfy such specifications is also practically valuable, as some candidates may be preferred for reasons of cost, processability, or robustness that are difficult to encode directly in an objective function. Here, we develop a range-aware Bayesian optimization (BO) framework in which the acquisition function directly scores the posterior probability that a candidate satisfies a target range. The framework naturally extends to parallel pursuit of multiple distinct specifications over a shared candidate space. Across benchmark tasks, range-aware acquisition consistently recovers larger and more diverse sets of valid designs than standard BO baselines and recent goal-seeking methods. Its utility is further demonstrated in two practically motivated design case studies involving optimizing reaction conditions for polymer synthesis and sequence-defined oligomer discovery for prescribed optical absorption bands, supported by quantum chemical calculations. These results suggest that range-aware BO can provide a practical and sample-efficient foundation for specification-driven design, particularly when design flexibility and solution diversity are important considerations.

cs.LG↗

DNA Tails for Molecular Flash Memory

DNA-based data storage systems face practical challenges due to the high cost of DNA synthesis. A strategy to address the problem entails encoding data via topological modifications of the DNA sugar-phosphate backbone. The DNA Punchcards system, which introduces nicks (cuts) in the DNA backbone, encodes only one bit per nicking site, limiting density. We propose \emph{DNA Tails,} a storage paradigm that encodes nonbinary symbols at nicking sites by growing enzymatically synthesized single-stranded DNA of varied lengths. The average tail lengths encode multiple information bits and are controlled via a staggered nicking-tail extension process. We demonstrate the feasibility of this encoding approach experimentally and identify common sources of errors, such as calibration errors and stumped tail growth errors. To mitigate calibration errors, we use rank modulation proposed for flash memory. To correct stumped tail growth errors, we introduce a new family of rank modulation codes that can correct ``stuck-at'' errors. Our analytical results include constructions for order-optimal-redundancy permutation codes and accompanying encoding and decoding algorithms.

cs.ET↗

Visualizing Energy Transfer Between Redox-Active Colloids

Redox-based electrical conduction in nonconjugated polymers has been explored less than a decade, yet is already showing promise as a new concept for electrical energy transport. Here using monolayers and sub-monolayers of touching micron-sized redox active colloids (RAC) containing high densities of ethyl-viologen (EV) side groups, intercolloid redox-based electron transport was directly observed via fluorescence microscopy. This observation was enabled by the discovery that these RAC exhibit a highly non-linear electrofluorochromism which can be quantitatively coupled to the colloid redox state. By evaluating the quasi-Fickian nature of the charge transfer (CT) kinetics, the apparent CT diffusion coefficient DCT was extracted. Along with addressing more fundamental questions regarding energy transport in colloidal materials, this first real-time real-space imaging of energy transport within monolayers of redox-active colloids may provide insights into energy transfer in flow batteries, and enable design of new forms of conductive polymers for applications including organic electronics.

cond-mat.soft↗

Dynamics of Meniscus-Bound Particle Clusters in Extensional Flow

Capillary suspensions are three-phase mixtures containing a solid particulate phase, a continuous liquid phase, and a second immiscible liquid forming capillary bridges between particles. Capillary suspensions are encountered in a wide array of applications including 3D printing, porous materials, and food formulations, but despite recent progress, the micromechanics of particle clusters in flow is not fully understood. In this work, we study the dynamics of meniscus-bound particle clusters in planar extensional flow using a Stokes trap, which is an automated flow control technique that allows for precise manipulation of freely suspended particles or particle clusters in flow. Focusing on the case of a two-particle doublet, we use a combination of experiments and analytical modeling to understand how particle clusters rearrange, deform, and ultimately break up in extensional flow. The time required for cluster breakup is quantified as a function of capillary number $Ca$ and meniscus volume $V$. Importantly, a critical capillary number $Ca_{crit}$ for cluster breakup is determined using a combination of experiments and modeling. Cluster relaxation experiments are also performed by deforming particle clusters in flow, followed by flow cessation prior to breakup and observing cluster relaxation dynamics under zero-flow conditions. In all cases, experiments are complemented by an analytical model that accounts for capillary forces, lubrication forces, hydrodynamic drag forces, and hydrodynamic interactions acting on the particles. Results from the analytical models are found to be in good agreement with experiments. Overall, this work provides a new quantitative understanding of the deformation dynamics of capillary clusters in extensional flow.

physics.flu-dyn↗

Dynamics and Rheology of Ring-Linear Blend Semidilute Solutions in Extensional Flow: Modeling and Molecular Simulations

We use Brownian dynamics (BD) simulations and single molecule experiments to investigate the influence of topological constraints and hydrodynamic interactions on the dynamics and rheology of solutions of ring-linear polymer blends at the overlap concentration. We find agreement between simulation and experiment in that rings in solution blends exhibit large conformational fluctuations, including extension overshoots in the startup of flow and tumbling and tank-treading at steady state. Ring polymer fluctuations increase with blend fraction of linear polymers and are peaked at a ring Weissenberg number $\textrm{Wi}_R \approx 1.5$. On the contrary, linear and ring polymers in pure solutions show a peak in fluctuations at the critical coil-stretch Weissenberg number $\textrm{Wi} = 0.5$. BD simulations show that extension overshoots on startup of flow are due to flow-induced intermolecular ring-linear polymer hooks, whereas fluctuations at steady state are dominated by intermolecular hydrodynamic interactions (HI). This is supported by simulations of bidisperse linear polymer solution blends, which show similar trends in conformational dynamics between rings and linear polymers with a matched contour length. Compared to BD simulations, single molecule experiments show quantitatively larger fluctuations, which could arise because experiments are performed on higher molecular weight polymers with stronger topological constraints. To this end, we have advanced the understanding of the effects of topological interactions and intermolecular HI on the dynamics of semidilute ring-linear polymer blend solutions.

cond-mat.soft↗

Vesicle dynamics in large amplitude oscillatory extensional flow

Although the behavior of fluid-filled vesicles in steady flows has been extensively studied, far less is understood regarding the shape dynamics of vesicles in time-dependent oscillatory flows. Here, we investigate the nonlinear dynamics of vesicles in large amplitude oscillatory extensional (LAOE) flows using both experiments and boundary integral (BI) simulations. Our results characterize the transient membrane deformations, dynamical regimes, and stress response of vesicles in LAOE in terms of reduced volume (vesicle asphericity), capillary number ($\Ca$, dimensionless flow strength), and Deborah number ($\De$, dimensionless flow frequency). Results from single vesicle experiments are found to be in good agreement with BI simulations across a wide range of parameters. Our results reveal three distinct dynamical regimes based on vesicle deformation: pulsating, reorienting, and symmetrical regimes. We construct phase diagrams characterizing the transition of vesicle shapes between pulsating, reorienting, and symmetrical regimes within the two-dimensional Pipkin space defined by $\De$ and $\Ca$. Contrary to observations on clean Newtonian droplets, vesicles do not reach a maximum length twice per strain rate cycle in the reorienting and pulsating regimes. The distinct dynamics observed in each regime result from a competition between the flow frequency, flow time scale, and membrane deformation timescale. By calculating the particle stresslet, we quantify the nonlinear relationship between average vesicle stress and strain rate. Additionally, we present results on tubular vesicles that undergo shape transformation over several strain cycles. Broadly, our work provides new information regarding the transient dynamics of vesicles in time-dependent flows that directly informs bulk suspension rheology.

cond-mat.soft↗

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↗

Double-mode relaxation of highly deformed vesicles

Lipid vesicles are known to undergo complex conformational transitions, but it remains challenging to systematically characterize non-equilibrium membrane shape dynamics. Here, we report the direct observation of lipid vesicle relaxation from highly deformed shapes using a Stokes trap. Vesicle shape relaxation is described by two distinct characteristic time scales governed by the bending modulus and membrane tension. Interestingly, experimental results are consistent with a viscoelastic model of a deformed membrane. Overall, these results show that vesicle relaxation is governed by an interplay between membrane elastic moduli, surface tension, and vesicle deflation.

cond-mat.soft↗

Conformational dynamics and phase behavior of lipid vesicles in a precisely controlled extensional flow

Lipid vesicles play a key role in fundamental biological processes. Despite recent progress, we lack a complete understanding of the non-equilibrium dynamics of vesicles due to challenges associated with long-time observation of shape fluctuations in strong flows. In this work, we present a flow-phase diagram for vesicle shape and conformational transitions in planar extensional flow using a Stokes trap, which enables control over the center-of-mass position of single or multiple vesicles in precisely defined flows [Shenoy, Rao, Schroeder, \textit{PNAS}, 113(15):3976-3981, 2016]. In this way, we directly observe the non-equilibrium conformations of lipid vesicles as a function of reduced volume $ν$, capillary number $Ca$, and viscosity contrast $λ$. Our results show that vesicle dynamics in extensional flow are characterized by the emergence of three distinct shape transitions, including a tubular to symmetric dumbbell transition, a spheroid to asymmetric dumbbell transition, and quasi-spherical to ellipsoid transition. The experimental phase diagram is in good agreement with recent predictions from simulations [Narsimhan, Spann, Shaqfeh, \textit{J. Fluid Mech.}, 2014, \textbf{750}, 144]. We further show that the phase boundary of vesicle shape transitions is independent of the viscosity contrast. Taken together, our results demonstrate the utility of the Stokes trap for the precise quantification of vesicle stretching dynamics in precisely defined flows.

physics.bio-ph↗

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↗

Flow topology during multiplexed particle manipulation using a Stokes Trap

Trapping and manipulation of small particles underlies many scientific and technological applications. Recently, the precise manipulation of multiple small particles was demonstrated using a Stokes trap that relies only on fluid flow without the need for optical or electric fields. Active flow control generates complex flow topologies around suspended particles during the trapping process, yet the relationship between the control algorithm and flow structure is not well understood. In this work, we characterize the flow topology during active control of particle trajectories using a Stokes trap. Our results show that optimal control of two particles unexpectedly relies on flow patterns with zero or one stagnation points, as opposed to positioning two particles using two distinct stagnation points. We characterize the sensitivity of the system with respect to the parameters in the control objective function, thereby providing a systematic understanding of the trapping process. Overall, these results will be useful in guiding applications involving the controlled manipulation of multiple colloidal particles and the precise deformation of soft particles in defined flow fields.

physics.flu-dyn↗

Orientation control and nonlinear trajectory tracking of colloidal particles using microfluidics

Suspensions of anisotropic Brownian particles are commonly encountered in a wide array of applications such as drug delivery and manufacturing of fiber-reinforced composites. Technological applications and fundamental studies of small anisotropic particles critically require precise control of particle orientation over defined trajectories and paths. In this work, we demonstrate robust control over the two-dimensional (2D) center-of-mass position and orientation of anisotropic Brownian particles using only fluid flow. We implement a path-following model predictive control scheme to manipulate colloidal particles over defined trajectories in position space, where the speed of movement along the path is a degree of freedom in the controller design. We further explore how the external flow field affects the orientation dynamics of anisotropic particles in steady and transient extensional flow using a combination of experiments and analytical modeling. Overall, this technique offers new avenues for fundamental studies of anisotropic colloidal particles using only fluid flow, without the need for external electric or optical fields.

cond-mat.soft↗

Dynamically Heterogeneous Relaxation of Entangled Polymer Chains

Stress relaxation following deformation of an entangled polymeric liquid is thought to be affected by transient reforming of chain entanglements. In this work, we use single molecule techniques to study the relaxation of individual polymers in the transition regime from unentangled to entangled solutions. Our results reveal the emergence of dynamic heterogeneity underlying polymer relaxation behavior, including distinct molecular sub-populations described by a single-mode and a double-mode exponential relaxation process. The slower double-mode timescale $τ_{d,2}$ is consistent with a characteristic reptation time, whereas the single-mode timescale $τ_s$ and the fast double-mode timescale $τ_{d,1}$ are attributed to local regions of transient disentanglement due to deformation.

cond-mat.soft↗

Single Polymer Dynamics for Molecular Rheology

Single polymer dynamics offers a powerful approach to study molecular-level interactions and dynamic microstructure in materials. Direct visualization of single chain dynamics has uncovered new ideas regarding the rheology and non-equilibrium dynamics of macromolecules, including the importance of molecular individualism, dynamic heterogeneity, and molecular sub-populations that govern macroscale behavior. In recent years, the field of single polymer dynamics has been extended to increasingly complex materials, including architecturally complex polymers such as combs, bottlebrushes, and ring polymers and entangled solutions of long chain polymers in flow. Single molecule visualization, complemented by modeling and simulation techniques such as Brownian dynamics and Monte Carlo methods, allow for unparalleled access to the molecular-scale dynamics of polymeric materials. In this review, recent progress in the field of single polymer dynamics is examined by highlighting major developments and new physics to emerge from these techniques. The molecular properties of DNA as a model polymer are examined, including the role of flexibility, excluded volume interactions, and hydrodynamic interactions in governing behavior. Recent developments in studying polymer dynamics in time-dependent flows, new chemistries and new molecular topologies, and the role of intermolecular interactions in concentrated solutions are considered. Moreover, cutting-edge methods in simulation techniques are further reviewed as an ideal complementary method to single polymer experiments. Future work aimed at extending the field of single polymer dynamics to new materials promises to uncover original and unexpected information regarding the flow dynamics of polymeric systems.

cond-mat.soft↗

Direct observation of DNA dynamics in semi-dilute solutions in extensional flow

The dynamic behavior of semi-dilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semi-dilute solutions are characterized by large fluctuations in concentration, wherein polymer coils interpenetrate but may not be topologically entangled at equilibrium. In non-equilibrium flows, it is generally thought that polymer chains can self-entangle in semi-dilute solutions, thereby leading to entanglements in solutions that are nominally unentangled at equilibrium. Despite recent progress, we still lack a complete molecular-level understanding of these dynamics. In this work, we use single molecule techniques to study the dynamics of semi-dilute solutions of DNA in planar extensional flow, including polymer relaxation from high stretch, transient stretching dynamics in step-strain experiments, and steady-state stretching in flow. Our results are consistent with a power-law scaling of the longest polymer relaxation time in semi-dilute solutions, revealing an effective excluded volume exponent $ν$ = 0.56. We further studied the non-equilibrium stretching dynamics in extensional flow, with results showing a decrease in transient polymer stretch at moderate Weissenberg number and a milder coil-to-stretch transition in semi-dilute solutions compared to dilute solutions. Interestingly, a unique set of molecular conformations during the transient stretching process for single polymers in semi-dilute solutions is observed, which suggests transient stretching pathways for polymer chains in semi-dilute solutions are qualitatively different than dilute solutions due to intermolecular interactions. Taken together, this work provides a molecular framework for understanding the non-equilibrium stretching dynamics of semi-dilute solutions in strong flows.

cond-mat.soft↗

Parameter-free prediction of DNA dynamics in planar extensional flow of semidilute solutions

The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the context of a coarse-grained bead-spring chain model for DNA. The successive fine-graining protocol [1, 2], in which simulation data acquired for bead-spring chains with increasing values of the number of beads $N_b$, is extrapolated to the number of Kuhn steps $N_\text{K}$ in DNA (while keeping key physical parameters invariant), is used to obtain parameter-free predictions for a range of Weissenberg numbers and Hencky strain units. A systematic comparison of simulation predictions is carried out with the experimental observations of [3], who have recently used single molecule techniques to investigate the dynamics of dilute and semidilute solutions of $λ$-phage DNA in planar extensional flow. In particular, they examine the response of individual chains to step-strain deformation followed by cessation of flow, thereby capturing both chain stretch and relaxation in a single experiment. The successive fine-graining technique is shown to lead to quantitatively accurate predictions of the experimental observations in the stretching and relaxation phases. Additionally, the transient chain stretch following a step strain deformation is shown to be much smaller in semidilute solutions than in dilute solutions, in agreement with experimental observations.

cond-mat.soft↗