arXiv subjects

James Clarke

Publications and source records attributed to James Clarke.

7 recordsLinked to original sources

arXiv2026

Pinned Boundaries Delay Contraction and Shape Stress Relaxation in Active Gels

Cells dynamically generate, transmit, and dissipate stress. Central to these processes is the actomyosin cortex, an active contractile material that drives cellular mechanical behavior. While prior studies have focused on freely contracting actomyosin systems, the role of mechanical constraints such as adhesion to boundaries remains less explored. To address this, we employ reconstituted actomyosin gels to investigate cellular contractility. We study contraction dynamics under pinned boundary conditions, where the gel is adhered transversely to two opposing surfaces, mimicking supracellular actomyosin networks in tissues and embryos. We find that pinned contraction leads to stress buildup, delaying contraction, producing intermittent dynamics, and generating spatially nonuniform strain fields. Stress is relieved through several pathways, including active-stress-driven symmetric constriction and defect-driven processes such as boundary detachment and internal rupture. We develop a hydrodynamic model incorporating elastic, viscous, and active stress contributions that distinguishes between stress-accumulation and stress-release phases and links variations in active stress to the observed intermittent dynamics. The model predicts distinct energy relaxation rates before and after detachment events, providing insight into stress dissipation. We compare experiments with numerical simulations, which reproduce the observed behavior and reveal how internal energy is generated and dissipated during stress buildup and relaxation. Together, our results demonstrate how boundary conditions and spatial heterogeneity govern the mechanical behavior of contractile active gels. These findings provide insight into stress regulation in cellular and tissue-scale systems and may inform the design of adaptive soft materials and bioinspired robotic systems.

cond-mat.soft↗

arXiv2025

Experimental methods to control pinned and coupled actomyosin contraction events

Actin and myosin drive many instances of force generation, deformation, and shape change in cells, tissues, and organisms. In particular, cytoskeletal actomyosin is remarkable in its adaptive architecture, responding to a host of actin-binding proteins. Equally important, however, is actomyosin's interaction with its mechanical environment. Actomyosin contractility and environmental properties, such as geometry and stiffness, are inherently coupled. To understand this coupling, novel experimental techniques are needed. Here we describe methods to spatially control the anchoring of reconstituted contractile actomyosin networks to two, opposing surfaces ("transverse anchoring"). The two surfaces can be either rigid ("pinned contraction"), or one of the surfaces may be compliant ("coupled contraction"). We introduce compliance by manufacturing flexure hinges, and describe their calibration. Calibration permits a direct measurement of the contractile force and mechanical work that actomyosin exerts on the environment. The methods described here provide an avenue toward a more complete characterization of actomyosin's role as an actuator, an essential property in its context of driving deformation and shape change in living systems.

cond-mat.soft↗

arXiv2025

Control across scales: signals, information, and adaptive biological mechanical function

Biological systems perform an astonishing array of dynamical processes -- including development and repair, regulation, behavior and motor control, sensing and signaling, and adaptation, among others. Powered by the transduction of stored energy resources, these behaviors enable biological systems to regulate functions, achieve specific outcomes, and maintain stability far from thermodynamic equilibrium. These behaviors span orders of magnitude in length and time: from nanometer-scale molecular motors driving morphogenesis to kilometer-scale seasonal migrations, and from millisecond reflexes to millennia of evolutionary adaptations. While physical laws govern the dynamics of biological systems, they alone are insufficient to fully explain how living systems sense, decide, adapt, and, ultimately, control their dynamics. In this article, we argue that control theory provides a powerful, unifying framework for understanding how biological systems regulate dynamics to maintain stability across length and time scales far from equilibrium.

cond-mat.soft↗

arXiv2025

Nonlinear contractile response of actomyosin active gels to control signals

Biological systems tightly regulate their physiological state using control signals. This includes the actomyosin cytoskeleton, a contractile active gel that consumes chemical free energy to drive many examples of cellular mechanical behavior. Upstream regulatory pathways activate or inhibit actomyosin activity. However, the contractile response of the actomyosin cytoskeleton to control signals remains poorly characterized. Here we employ reconstituted actomyosin active gels and subject them to step and pulsatile activation inputs. We find evidence for a nonlinear impulse response, which we quantify via a transfer function $\delta \varepsilon / \delta g$ that relates input free-energy pulses $\delta g$ to output strain pulses $\delta \varepsilon$. We find a scaling relation $\delta \varepsilon / \delta g \sim g^{-0.3}$. The negative sign of the exponent represents a decreased effectiveness of a contracting gel in converting energy to strain. We ascribe nonlinearity in our system to a density-dependent mechanism, which contrasts strain-stiffening nonlinear responses to external stresses. Contractile response to control signals is an essential step toward understanding how information from mechanical signaling processes flow through actomyosin networks in living, and likely also synthetic, cells.

cond-mat.soft↗

arXiv2023

Morphological Control of Bundled Actin Networks Subject to Fixed-Mass Depletion

Depletion interactions are thought to significantly contribute to the organization of intracellular structures in the crowded cytosol. The strength of depletion interactions depends on physical parameters like the depletant number density and the depletant size ratio. Cells are known to dynamically regulate these two parameters by varying the copy number of proteins of a wide distribution of sizes. However, mammalian cells are also known to keep the total protein mass density remarkably constant, to within 0.5% throughout the cell cycle. We thus ask how the strength of depletion interactions varies when the total depletant mass is held fixed, a.k.a. fixed-mass depletion. We answer this question via scaling arguments, as well as by studying depletion effects on networks of reconstituted semiflexible actin $\textit{in silico}$ and $\textit{in vitro}$. We examine the maximum strength of the depletion interaction potential $U^*$ as a function of $q$, the size ratio between the depletant and the matter being depleted. We uncover a scaling relation $U^* \sim q^{-\zeta}$ for two cases: fixed volume fraction $\phi$ and fixed mass density $\rho$. For fixed volume fraction, we report $\zeta < 0$. For the fixed mass density case, we report $\zeta > 0$, which suggests the depletion interaction strength increases as the depletant size ratio is increased. To test this prediction, we prepared our filament networks at fixed mass concentrations with varying sizes of the depletant molecule poly(ethylene glycol) (PEG). We characterize the depletion interaction strength in our simulations via the mesh size. In experiments, we observe two distinct actin network morphologies, which we call weakly bundled and strongly bundled. We identify a mass concentration where different PEG depletant sizes leads to weakly bundled or strongly bundled morphologies...[more in main text].

cond-mat.soft↗

arXiv2022

Depletion-Driven Morphological Control of Bundled Actin Networks

The actin cytoskeleton is a semiflexible biopolymer network whose morphology is controlled by a wide range of biochemical and physical factors. Actin is known to undergo a phase transition from a single-filament state to a bundled state by the addition of polyethylene glycol (PEG) molecules in sufficient concentration. While the depletion interaction experienced by these biopolymers is well-known, the effect of changing the molecular weight of the depletant is less well understood. Here, we experimentally identify a phase transition in solutions of actin from networks of filaments to networks of bundles by varying the molecular weight of PEG polymers, while holding the concentration of these PEG polymers constant. We examine the states straddling the phase transition in terms of micro and macroscale properties. We find that the mesh size, bundle diameter, persistence length, and intra-bundle spacing between filaments across the line of criticality do not show significant differences, while the relaxation time, storage modulus, and degree of bundling change between the two states do show significant differences. Our results demonstrate the ability to tune actin network morphology and mechanics by controlling depletant size, a property which could be exploited to develop actin-based materials with switchable rigidity.

cond-mat.soft↗

arXiv2013

The Kinematic Age of the Coolest T Dwarfs

Surprisingly, current atmospheric models suggest that the coolest T dwarfs (T8.5 to T10) are young and very low mass (0.06-2Gyr, 5-20Mjup, Leggett et al.2009, 2010, 2012). Studies of population kinematics offer an independent constraint on the age of the population. We present kinematic data of a sample of 75 mid to late T dwarfs drawn from a variety of sources. We define our samples, T5.5 to T8 and T8.5 to T10, as mid and late T respectively. UKIDSS LAS kinematics were derived from our automated LAS proper motion pipeline and distance estimates derived from spectral types and photometry for the minority of sources that lack parallaxes. Our results show that the mid and late T populations do not have distinctly separate tangential velocity distributions to 95% probability. They also give an approximate mean kinematic age equal to that of a population with B-V colour 0.51-0.54, and a spectral type late F, which corresponds to an age of about 2 Gyr. However the median and modal ages are greater. This indicates that while model atmospheres correctly predict some trends in colour with gravity and age, reliable ages cannot yet be inferred from them. More benchmark objects are needed to anchor the models.

astro-ph.SR↗