1967 Publications

Sculpting the Sphinx

Samuel Boury, S. Weady, Leif Ristroph

This paper is associated with a poster winner of a 2022 American Physical Society's Division of Fluid Dynamics (DFD) Milton van Dyke Award for work presented at the DFD Gallery of Fluid Motion. The original poster is available online at the Gallery of Fluid Motion.

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A model of replicating coupled oscillators generates naturally occurring cell networks

When a founder cell and its progeny divide with incomplete cytokinesis, a network forms in which each intercellular bridge corresponds to a past mitotic event. Such networks are required for gamete production in many animals, and different species have evolved diverse final network topologies. Although mechanisms regulating network assembly have been identified in particular organisms, we lack a quantitative framework to understand network assembly and inter-species variability. Motivated by cell networks responsible for oocyte production in invertebrates, where the final topology is typically invariant within each species, we devised a mathematical model for generating cell networks, in which each node is an oscillator and, after a full cycle, the node produces a daughter to which it remains connected. These cell cycle oscillations are transient and coupled via diffusion over the edges of the network. By variation of three biologically motivated parameters, our model generates nearly all such networks currently reported across invertebrates. Furthermore, small parameter variations can rationalize cases of intra-species variation. Because cell networks outside of the ovary often form less deterministically, we propose model generalizations to account for sources of stochasticity.

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Cytoplasmic stirring by active carpets

Large cells often rely on cytoplasmic flows for intracellular transport, maintaining homeostasis, and positioning cellular components. Understanding the mechanisms of these flows is essential for gaining insights into cell function, developmental processes, and evolutionary adaptability. Here, we focus on a class of self-organized cytoplasmic stirring mechanisms that result from fluid-structure interactions between cytoskeletal elements at the cell cortex. Drawing inspiration from streaming flows in late-stage fruit fly oocytes, we propose an analytically tractable active carpet theory. This model deciphers the origins and three-dimensional spatio-temporal organization of such flows. Through a combination of simulations and weakly nonlinear theory, we establish the pathway of the streaming flow to its global attractor: a cell-spanning vortical twister. Our study reveals the inherent symmetries of this emergent flow, its low-dimensional structure, and illustrates how complex fluid-structure interaction aligns with classical solutions in Stokes flow. This framework can be easily adapted to elucidate a broad spectrum of self-organized, cortex-driven intracellular flows.

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November 8, 2023

IIM2FieldII: A Framework for Validating Ultrasound Measurements of Volumetric Flow and WSS in Complex Carotid Plaque Geometries

Keerthi S. Anand, E. Kolahdouz, Boyce E. Griffith, Caterina M. Gallippi

High wall shear stress (WSS) is associated with risk of atherosclerotic plaque rupture, but there are numerous gaps in validating ultrasound-derived measurements of the parameter. Two major challenges are using simple models of stenosis and only evaluating WSS along a single 2D plane. To overcome these limitations, a novel simulation framework is herein demonstrated. The framework first models volumetric blood flow in actual stenosed human carotid artery geometries (using an immersed interface method (IIM) fluid structure interaction solver) and calculates the associated WSS. Then, the framework projects the modeled blood flow onto scatterers in Field II simulations of its ultrasonic interrogation. Volumetric ultrasound vector Doppler (VD) imaging using an elevationally swept L7-4 linear array was simulated in Field II, with variations in transmit sequences and flow conditions. In a ~55% stenosed human carotid artery under 600 mL/min flow, Bland-Altman analysis showed that a 3-angle plane wave (PW) transmit scheme estimated WSS with 0.04±0.64 Pa error (bias ± 95% CI) relative to the IIM ground truth, whereas transmitting with 5 angles increased accuracy, but decreased precision to -0.01±1.07 Pa, due to aliasing. These findings illustrate that the simulation framework enables direct comparison of data acquisition and processing methods for efficient development, validation, and refinement of WSS estimation methods in realistic clinical environments.

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Equilibrium quantum impurity problems via matrix product state encoding of the retarded action

B. Kloss, Julian Thoenniss, Michael Sonner, Alessio Lerose, M. Fishman, M. Stoudenmire, O. Parcollet, A. Georges, Dmitry A. Abanin

In the 0 + 1 -dimensional imaginary-time path integral formulation of quantum impurity problems, the retarded action encodes the hybridization of the impurity with the bath. In this article, we explore the computational power of representing the retarded action as matrix product state (RAMPS). We focus on the challenging Kondo regime of the single-impurity Anderson model, where nonperturbative strong-correlation effects arise at very low energy scales. We demonstrate that the RAMPS approach reliably reaches the Kondo regime for a range of interaction strengths U, with a numerical error scaling as a weak power law with inverse temperature. We investigate the convergence behavior of the method with respect to bond dimension and time discretization by analyzing the error of local observables in the full interacting problem and find polynomial scaling in both parameters. Our results suggest that the RAMPS approach offers an alternative avenue for exploring quantum impurity problems, thereby setting the stage for future advancements in the method's capability to address more complex quantum impurity scenarios. Overall, our study contributes to the development of efficient and accurate non-wave-function-based tensor-network methods for quantum impurity problems.

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Protein-Engineered Fibers For Drug Encapsulation Traceable via 19F Magnetic Resonance

Dustin Britton, Jakub Legocki, D. Renfrew, et al.

Theranostic materials research is experiencing rapid growth driven by the interest in integrating both therapeutic and diagnostic modalities. These materials offer the unique capability to not only provide treatment but also track the progression of a disease. However, to create an ideal theranostic biomaterial without compromising drug encapsulation, diagnostic imaging must be optimized for improved sensitivity and spatial localization. Herein, we create a protein-engineered fluorinated coiled-coil fiber, Q2TFL, capable of improved sensitivity to 19F magnetic resonance spectroscopy (MRS) detection. Leveraging residue-specific noncanonical amino acid incorporation of trifluoroleucine (TFL) into the coiled-coil, Q2, which self-assembles into nanofibers, we generate Q2TFL. We demonstrate that fluorination results in a greater increase in thermostability and 19F magnetic resonance detection compared to the nonfluorinated parent, Q2. Q2TFL also exhibits linear ratiometric 19F MRS thermoresponsiveness, allowing it to act as a temperature probe. Furthermore, we explore the ability of Q2TFL to encapsulate the anti-inflammatory small molecule, curcumin (CCM), and its impact on the coiled-coil structure. Q2TFL also provides hyposignal contrast in 1H MRI, echogenic signal with high-frequency ultrasound and sensitive detection by 19F MRS in vivo illustrating fluorination of coiled-coils for supramolecular assembly and their use with 1H MRI, 19F MRS and high frequency ultrasound as multimodal theranostic agents.

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Laser ablation and fluid flows reveal the mechanism behind spindle and centrosome positioning

Hai-Yin Wu, Gökberk Kabacaoğlu,, M. Shelley, D. Needleman

Few techniques are available for studying the nature of forces that drive subcellular dynamics. Here we develop two complementary ones. The first is femtosecond stereotactic laser ablation, which rapidly creates complex cuts of subcellular structures and enables precise dissection of when, where and in what direction forces are generated. The second is an assessment of subcellular fluid flows by comparison of direct flow measurements using microinjected fluorescent nanodiamonds with large-scale fluid-structure simulations of different force transduction models. We apply these techniques to study spindle and centrosome positioning in early Caenorhabditis elegans embryos and to probe the contributions of microtubule pushing, cytoplasmic pulling and cortical pulling upon centrosomal microtubules. Based on our results, we construct a biophysical model to explain the dynamics of centrosomes. We demonstrate that cortical pulling forces provide a general explanation for many behaviours mediated by centrosomes, including pronuclear migration and centration, rotation, metaphase spindle positioning, asymmetric spindle elongation and spindle oscillations. This work establishes methodologies for disentangling the forces responsible for cell biological phenomena.

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November 2, 2023

Extracting thermodynamic properties from van ’t Hoff plots with emphasis on temperature-sensing ion channels

Jakob T. Bullerjahn, S. Hanson

Transient receptor potential (TRP) ion channels are among the most well-studied classes of temperature-sensing molecules. Yet, the molecular mechanism and thermodynamic basis for the temperature sensitivity of TRP channels remains to this day poorly understood. One hypothesis is that the temperature-sensing mechanism can simply be described by a difference in heat capacity between the closed and open channel states. While such a two-state model may be simplistic it nonetheless has descriptive value, in the sense that it can be used to compare overall temperature sensitivity between different channels and mutants. Here, we introduce a mathematical framework based on the two-state model to reliably extract temperature-dependent thermodynamic potentials and heat capacities from measurements of equilibrium constants at different temperatures. Our framework is implemented in an open-source data analysis package that provides a straightforward way to fit both linear and nonlinear van ’t Hoff plots, thus avoiding some of the previous, potentially erroneous, assumptions when extracting thermodynamic variables from TRP channel electrophysiology data.

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November 2, 2023

Phase plane dynamics of ERK phosphorylation

S. Shvartsman, Sarah McFann, Martin Wühr , Boris Y. Rubinstein

The extracellular signal–regulated kinase (ERK) controls multiple critical processes in the cell and is deregulated in human cancers, congenital abnormalities, immune diseases, and neurodevelopmental syndromes. Catalytic activity of ERK requires dual phosphorylation by an upstream kinase, in a mechanism that can be described by two sequential Michaelis-Menten steps. The estimation of individual reaction rate constants from kinetic data in the full mechanism has proved challenging. Here, we present an analytically tractable approach to parameter estimation that is based on the phase plane representation of ERK activation and yields two combinations of six reaction rate constants in the detailed mechanism. These combinations correspond to the ratio of the specificities of two consecutive phosphorylations and the probability that monophosphorylated substrate does not dissociate from the enzyme before the second phosphorylation. The presented approach offers a language for comparing the effects of mutations that disrupt ERK activation and function in vivo. As an illustration, we use phase plane representation to analyze dual phosphorylation under heterozygous conditions, when two enzyme variants compete for the same substrate.

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Direct stellarator coil design using global optimization: application to a comprehensive exploration of quasi-axisymmetric devices

Many stellarator coil design problems are plagued by multiple minima, where the locally optimal coil sets can sometimes vary substantially in performance. As a result, solving a coil design problem a single time with a local optimization algorithm is usually insufficient and better optima likely do exist. To address this problem, we propose a global optimization algorithm for the design of stellarator coils and outline how to apply box constraints to the physical positions of the coils. The algorithm has a global exploration phase that searches for interesting regions of design space and is followed by three local optimization algorithms that search in these interesting regions (a "global-to-local" approach). The first local algorithm (phase I), following the globalization phase, is based on near-axis expansions and finds stellarator coils that optimize for quasisymmetry in the neighborhood of a magnetic axis. The second local algorithm (phase II) takes these coil sets and optimizes them for nested flux surfaces and quasisymmetry on a toroidal volume. The final local algorithm (phase III) polishes these configurations for an accurate approximation of quasisymmetry. Using our global algorithm, we study the trade-off between coil length, aspect ratio, rotational transform, and quality of quasi-axisymmetry. The database of stellarators, which comprises almost 140,000 coil sets, is available online and is called QUASR, for "QUAsi-symmetric Stellarator Repository".

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