Fishnet mesh of centrin-Sfi1 drives ultrafast calcium-activated contraction of the giant cell .

is a unicellular ciliate capable of contracting to a quarter of its body length in less than five milliseconds. When measured as fractional shortening, this is an order of magnitude faster than motion powered by actomyosin. Myonemes, which are protein networks found near the cortex of many protists, are believed to power contraction.

Limits on the computational expressivity of non-equilibrium biophysical processes.

Many biological decision-making processes can be viewed as performing a classification task over a set of inputs, using various chemical and physical processes as "biological hardware." In this context, it is important to understand the inherent limitations on the computational expressivity of classification functions instantiated in biophysical media. Here, we model biochemical networks as Markov jump processes and train them to perform classification tasks, allowing us to investigate their computational expressivity.

Motor crosslinking augments elasticity in active nematics.

In active materials, uncoordinated internal stresses lead to emergent long-range flows. An understanding of how the behavior of active materials depends on mesoscopic (hydrodynamic) parameters is developing, but there remains a gap in knowledge concerning how hydrodynamic parameters depend on the properties of microscopic elements. In this work, we combine experiments and multiscale modeling to relate the structure and dynamics of active nematics composed of biopolymer filaments and molecular motors to their microscopic properties, in particular motor processivity, speed, and valency.

Motor crosslinking augments elasticity in active nematics.

In active materials, uncoordinated internal stresses lead to emergent long-range flows. An understanding of how the behavior of active materials depends on mesoscopic (hydrodynamic) parameters is developing, but there remains a gap in knowledge concerning how hydrodynamic parameters depend on the properties of microscopic elements. In this work, we combine experiments and multiscale modeling to relate the structure and dynamics of active nematics composed of biopolymer filaments and molecular motors to their microscopic properties, in particular motor processivity, speed, and valency.

A unified model for the dynamics of ATP-independent ultrafast contraction.

In nature, several ciliated protists possess the remarkable ability to execute ultrafast motions using protein assemblies called myonemes, which contract in response to Ca ions. Existing theories, such as actomyosin contractility and macroscopic biomechanical latches, do not adequately describe these systems, necessitating development of models to understand their mechanisms. In this study, we image and quantitatively analyze the contractile kinematics observed in two ciliated protists ( sp.

Simulating structured fluids with tensorial viscoelasticity.

We consider an immersed elastic body that is actively driven through a structured fluid by a motor or an external force. The behavior of such a system generally cannot be solved analytically, necessitating the use of numerical methods. However, current numerical methods omit important details of the microscopic structure and dynamics of the fluid, which can modulate the magnitudes and directions of viscoelastic restoring forces.

On Stretching, Bending, Shearing, and Twisting of Actin Filaments I: Variational Models.

Mechanochemical simulations of actomyosin networks are traditionally based on one-dimensional models of actin filaments having zero width. Here, and in the follow up paper (, DOI 10.48550/arXiv.

Understanding cytoskeletal avalanches using mechanical stability analysis.

Eukaryotic cells are mechanically supported by a polymer network called the cytoskeleton, which consumes chemical energy to dynamically remodel its structure. Recent experiments in vivo have revealed that this remodeling occasionally happens through anomalously large displacements, reminiscent of earthquakes or avalanches. These cytoskeletal avalanches might indicate that the cytoskeleton's structural response to a changing cellular environment is highly sensitive, and they are therefore of significant biological interest.

Gibbs free energy change of a discrete chemical reaction event.

In modeling the interior of cells by simulating a reaction-diffusion master equation over a grid of compartments, one employs the assumption that the copy numbers of various chemical species are small, discrete quantities. We show that, in this case, textbook expressions for the change in Gibbs free energy accompanying a chemical reaction or diffusion between adjacent compartments are inaccurate. We derive exact expressions for these free energy changes for the case of discrete copy numbers and show how these expressions reduce to traditional expressions under a series of successive approximations leveraging the relative sizes of the stoichiometric coefficients and the copy numbers of the solutes and solvent.

Quantifying dissipation in actomyosin networks.

Quantifying entropy production in various active matter phases will open new avenues for probing self-organization principles in these far-from-equilibrium systems. It has been hypothesized that the dissipation of free energy by active matter systems may be optimized, leading to system trajectories with histories of large dissipation and an accompanying emergence of ordered dynamical states. This interesting idea has not been widely tested.

Accurate quantification of brown adipose tissue mass by xenon-enhanced computed tomography.

Detection and quantification of brown adipose tissue (BAT) mass remains a major challenge, as current tomographic imaging techniques are either nonspecific or lack the necessary resolution to quantify BAT mass, especially in obese phenotypes, in which this tissue may be present but inactive. Here, we report quantification of BAT mass by xenon-enhanced computed tomography. We show that, during stimulation of BAT thermogenesis, the lipophilic gas xenon preferentially accumulates in BAT, leading to a radiodensity enhancement comparable to that seen in the lungs.

Detection of brown adipose tissue and thermogenic activity in mice by hyperpolarized xenon MRI.

The study of brown adipose tissue (BAT) in human weight regulation has been constrained by the lack of a noninvasive tool for measuring this tissue and its function in vivo. Existing imaging modalities are nonspecific and intrinsically insensitive to the less active, lipid-rich BAT of obese subjects, the target population for BAT studies. We demonstrate noninvasive imaging of BAT in mice by hyperpolarized xenon gas MRI.