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We propose a method to decompose dynamical systems based on the idea that modules constrain the spread of perturbations. We find partitions of system variables that maximize 'perturbation modularity', defined as the autocovariance of…

Bacteria and plankton populations living in oceans and lakes reproduce and die under the in- fluence of turbulent currents. Turbulent transport interacts in a complex way with the dynamics of populations because the typical reproduction…

Many organisms form colonies for a transient period of time to withstand environmental pressure. Bacterial biofilms are a prototypical example of such behavior. Despite significant interest across disciplines, physical mechanisms governing…

Active systems comprised of self-propelled units show fascinating transitions from Brownian-like dynamics to collective coherent motion. Swirling of swimming bacteria is a spectacular example. This study demonstrates that a nematic liquid…

We study the spreading of a bacterial colony undergoing turbulent like collective motion. We present two minimalistic models to investigate the interplay between population growth and coherent structures arising from turbulence. Using…

From intracellular protein trafficking to large scale motion of animal groups, the physical concepts driving the self-organization of living systems are still largely unraveled. Selforganization of active entities, leading to novel phases…

Run-and-tumble is a common but vital strategy that bacteria employ to explore environment suffused with boundaries, as well as to escape from entrapment. In this study we reveal how this strategy and the resulting dynamical behavior can be…

Recent studies have shown that packings of cells, both eukaryotic cellular tissues and growing or swarming bacterial colonies, can often be understood as active nematic fluids. A key property of volume-conserving active nematic model…

Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…

There has been a long-standing and at times fractious debate whether complex and large systems can be stable. In ecology, the so-called `diversity-stability debate' arose because mathematical analyses of ecosystem stability were either…

Stability is a desirable property of complex ecosystems. If a community of interacting species is at a stable equilibrium point then it is able to withstand small perturbations to component species' abundances without suffering adverse…

The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can…

The composition of ecological communities varies not only between different locations but also in time. Understanding the fundamental processes that drive species towards rarity or abundance is crucial to assessing ecosystem resilience and…

Populations of species in ecosystems are often constrained by availability of resources within their environment. In effect this means that a growth of one population, needs to be balanced by comparable reduction in populations of others.…

Complex evolving systems such as the biosphere, ecosystems and societies exhibit sudden collapses, for reasons that are only partially understood. Here we study this phenomenon using a mathematical model of a system that evolves under…

We numerically study the dynamics of run-and-tumble particles confined in two chambers connected by thin channels. Two dominant dynamical behaviors emerge: (i) an oscillatory pumping state, in which particles periodically fill the two…

Colonies of bacteria grown on thin agar plate exhibit fractal patterns as a result of adaptation to their environments. The bacterial colony pattern formation is regulated crucially by chemotaxis, the movement of cells along a chemical…

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…

Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types…

A key unresolved question in microbial ecology is how the extraordinary diversity of microbiomes emerges from the behaviour of individual populations. This process is driven by the cross-feeding networks that structure these communities,…