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The composition of cellular metabolism is different across species. Empirical data reveal that bacterial species contain similar numbers of metabolic reactions but that the cross-species popularity of reactions is so heterogenous that some…
We have discovered a novel transition rule for binary cellular automata (CA) that yields self-replicating structures across two spatial and temporal scales from sparsely populated random initial conditions. Lower-level, shapeshifting…
A poorly understood step in the transition from a chemical to a biological world is the emergence of self-replicating molecular systems. We study how a precursor for such a replicator might arise in a hydrothermal RNA reactor, which…
The emergence of membranous compartments (protocells) with encapsulated genetic material was a crucial step life's origin and evolution. The hot spring hypothesis for the origin of life suggests that protocells could have formed in hot…
Large language models can perform various reasoning tasks by using chain-of-thought prompting, which guides them to find answers through step-by-step demonstrations. However, the quality of the prompts depends on the demonstrations given to…
We consider catalytic branching populations. They consist of a catalyst population evolving according to a critical binary branching process in continuous time with a constant branching rate and a reactant population with a branching rate…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
Artificial chemistry simulations produce many intriguing emergent behaviors, but they are often difficult to steer or control. This paper proposes a method for steering the dynamics of a classic artificial chemistry model, known as AlChemy…
The mechanics of crawling cells on a substrate is investigated by using a minimal model that satisfies the force-free condition. A cell is described by two subcellular elements connected by a linear actuator that changes the length of the…
Active systems across scales, ranging from molecular machines to human crowds, are usually modeled as assemblies of self-propelled particles driven by internally generated forces. However, these models often assume memoryless dynamics and…
Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular…
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from molecular to mesoscopic level. Herein we report an example of using fully synthetic systems that mimic two levels of…
The origin of life is often approached through the lens of replication, heredity, or molecular specificity. This paper proposes a thermodynamic framework in which the emergence of life is driven by the persistence of reaction pathways that…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
Transitions between metabasins in supercooled liquids seem to occur through rapid "democratic" collective particle rearrangements. Here we show that this apparent homogeneous particle motion is a direct consequence of dynamic facilitation.…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
Cells of the human body have nearly identical genome but exhibit very different phenotypes that allow them to carry out specific functions and react to changes in their surrounding environment. This division of labour is achieved by…
An explanatory model for the emergence of evolvable units must display emerging structures that (1) preserve themselves in time (2) self-reproduce and (3) tolerate a certain amount of variation when reproducing. To tackle this challenge,…
Emergence of regular spatial patterns is a hallmark in living matter ranging from subcellular organelles to developing embryos and to ecosystems. Mechanisms for the formation of ordered spatial patterns in biology often require chemical…