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The neural dynamics of the nematode C. elegans are experimentally low-dimensional and correspond to discrete behavioral states, where previous modeling work has found neural proxies for some of these states. Experimental results further…

Understanding physical rules underlying collective motions requires perturbation of controllable parameters in self-propelled particles. However, controlling parameters in animals is generally not easy, which makes collective behaviours of…

Animals adjust their behavioral response to sensory input adaptively depending on past experiences. The flexible brain computation is crucial for survival and is of great interest in neuroscience. The nematode C. elegans modulates its…

We apply topological data analysis to the behavior of C. elegans, a widely-studied model organism in biology. In particular, we use topology to produce a quantitative summary of complex behavior which may be applied to high-throughput data.…

The dynamics of complex systems generally include high-dimensional, non-stationary and non-linear behavior, all of which pose fundamental challenges to quantitative understanding. To address these difficulties we detail a new approach based…

The nonlinearity of dynamics in systems biology makes it hard to infer them from experimental data. Simple linear models are computationally efficient, but cannot incorporate these important nonlinearities. An adaptive method based on the…

Dissipative environments are ubiquitous in nature, from microscopic swimmers in low-Reynolds-number fluids to macroscopic animals in frictional media. In this study, motivated by various behaviours of {\it Caenorhabditis elegans} during…

The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and…

Animals must integrate sensory cues with their current behavioral context to generate a suitable response. How this integration occurs is poorly understood. Previously we developed high throughput methods to probe neural activity in…

Neuronal networks provide living organisms with the ability to process information. They are also characterized by abundant recurrent connections, which give rise to strong feedback that dictates their dynamics and endows them with fading…

Walking animals, like stick insects, cockroaches or ants, demonstrate a fascinating range of locomotive abilities and complex behaviors. The locomotive behaviors can consist of a variety of walking patterns along with adaptation that allow…

When complex systems are driven to extinction by some external factor, their non-stationary dynamics can present an intermittent behaviour between relative tranquility and burst of activity whose consequences are often catastrophic. To…

Switching dynamical systems provide a powerful, interpretable modeling framework for inference in time-series data in, e.g., the natural sciences or engineering applications. Since many areas, such as biology or discrete-event systems, are…

We develop a biophysically realistic model of the nematode C. elegans that includes: (i) its muscle structure and activation, (ii) key connectomic activation circuitry, and (iii) a weighted and time-dynamic proprioception. In combination,…

Computer based models describing pedestrian behavior in an emergency evacuation play a vital role in the development of active strategies that minimize the evacuation time when a closed area must be evacuated. The reference model has a…

Many animals in their natural habitat exhibit collective motion and form complex patterns to tackle environmental difficulties. Several physical and biological factors, such as animal motility, population densities, and chemical cues, play…

Tracking a turbulent plume to locate its source is a complex control problem because it requires multi-sensory integration and must be robust to intermittent odors, changing wind direction, and variable plume statistics. This task is…

The bounded rationality plays a vital role in the collective behavior of the evacuation process. Also investigating human behavior in such an extreme situation is a continuing concern within social psychology. In this paper, we construct a…

Organisms move through the world by changing their shape, and here we explore the mapping from shape space to movements in the nematode C. elegans as it crawls on a planar agar surface. We characterize the statistics of the trajectories…

The dynamics of active particles is of interest at many levels and is the focus of theoretical and experimental research. There have been many attempts to describe the dynamics of particles affected by random active forces in terms of an…