Engineering synthetic phosphorylation signaling networks in human cells.

Protein phosphorylation signaling networks have a central role in how cells sense and respond to their environment. We engineered artificial phosphorylation networks in which reversible enzymatic phosphorylation cycles were assembled from modular protein domain parts and wired together to create synthetic phosphorylation circuits in human cells. Our design scheme enabled model-guided tuning of circuit function and the ability to make diverse network connections; synthetic phosphorylation circuits can be coupled to upstream cell surface receptors to enable fast-timescale sensing of extracellular ligands, and downstream connections can regulate gene expression.

A universal niche geometry governs the response of ecosystems to environmental perturbations.

How ecosystems respond to environmental perturbations is a fundamental question in ecology, made especially challenging due to the strong coupling between species and their environment. Here, we introduce a theoretical framework for calculating the steady-state response of ecosystems to environmental perturbations in generalized consumer-resource. Our construction is applicable to a wide class of systems, including models with non-reciprocal interactions, cross-feeding, and non-linear growth/consumption rates.

Integrating local energetics into Maxwell-Calladine constraint counting to design mechanical metamaterials.

The Maxwell-Calladine index theorem plays a central role in our current understanding of the mechanical rigidity of discrete materials. By considering the geometric constraints each material component imposes on a set of underlying degrees of freedom, the theorem relates the emergence of rigidity to constraint counting arguments. However, the Maxwell-Calladine paradigm is significantly limited-its exclusive reliance on the geometric relationships between constraints and degrees of freedom completely neglects the actual energetic costs of deforming individual components.

Phase Transition to Chaos in Complex Ecosystems with Nonreciprocal Species-Resource Interactions.

Nonreciprocal interactions between microscopic constituents can profoundly shape the large-scale properties of complex systems. Here, we investigate the effects of nonreciprocity in the context of theoretical ecology by analyzing a generalization of MacArthur's consumer-resource model with asymmetric interactions between species and resources. Using a mixture of analytic cavity calculations and numerical simulations, we show that such ecosystems generically undergo a phase transition to chaotic dynamics as the amount of nonreciprocity is increased.

A universal niche geometry governs the response of ecosystems to environmental perturbations.

How ecosystems respond to environmental perturbations is a fundamental question in ecology, made especially challenging due to the strong coupling between species and their environment. Here, we introduce a theoretical framework for calculating the linear response of ecosystems to environmental perturbations in generalized consumer-resource models. Our construction is applicable to a wide class of systems, including models with non-reciprocal interactions, cross-feeding, and non-linear growth/consumption rates.