Related papers: A Markovian dynamics for C. elegans behavior acros…
The nematode Caenorhabditis elegans (C. elegans) serves as an important model organism in a wide variety of biological studies. In this paper we introduce a pipeline for automated analysis of C. elegans imagery for the purpose of studying…
The movement of intracellular cargo transported by molecular motors is commonly marked by switches between directed motion and stationary pauses. The predominant measure for assessing movement is effective diffusivity, which predicts the…
Mechanistic modelling of animal movement is often formulated in discrete time despite problems with scale invariance, such as handling irregularly timed observations. A natural solution is to formulate in continuous time, yet uptake of this…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
Stochastic modeling of movement behavior provides a valuable way to understand how complex motion can be generated from relatively simple building blocks. Ants demonstrate sophisticated social behavior ranging from foraging to nest…
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 stochastic exploration of the configuration space and the exploitation of functional states underlie many biological processes. The evolutionary dynamics stands out as a remarkable example. Here, we introduce a novel formalism that…
The ability to acquire large-scale recordings of neuronal activity in awake and unrestrained animals poses a major challenge for studying neural coding of animal behavior. We present a new instrument capable of recording intracellular…
Rapid advances in genetics, genomics, and imaging have given insight into the molecular and cellular basis of behaviour in a variety of model organisms with unprecedented detail and scope. It is increasingly routine to isolate behavioural…
Free-living nematode Caenorhabditis elegans is a powerful genetic model, essential for investigations ranging from behavior to neuroscience to aging, and locomotion is a key observable used in these studies. However, despite the fact that…
Spatially-embedded complex networks, such as nervous systems, the Internet and transportation networks, generally have non-trivial topological patterns of connections combined with nearly minimal wiring costs. However the growth rules…
Markov chains are simple yet powerful mathematical structures to model temporally dependent processes. They generally assume stationary data, i.e., fixed transition probabilities between observations/states. However, live, real-world…
We study the stochastic motion of active particles that undergo spontaneous transitions between two distinct modes of motion. Each mode is characterized by a velocity distribution and an arbitrary (anti-)persistence. We present an…
1. Movement is the primary means by which animals obtain resources and avoid hazards. Most movement exhibits directional bias that is related to environmental features (taxis), such as the location of food patches, predators, ocean…
Deep phenotyping is an emerging conceptual paradigm and experimental approach that seeks to measure many aspects of phenotypes and link them to understand the underlying biology. Successful deep phenotyping has mostly been applied in…
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,…
Undulatory swimming is a widespread propulsion strategy adopted by many small-scale organisms including various single-cell eukaryotes and nematodes. In this work, we report a comprehensive study of undulatory locomotion of a finite…
C. elegans is commonly used in neuroscience for behaviour analysis because of it's compact nervous system with well-described connectivity. Localizing the animal and distinguishing between its head and tail are important tasks to track the…
Animals chain movements into long-lived motor strategies, exhibiting variability across scales that reflects the interplay between internal states and environmental cues. To reveal structure in such variability, we build Markov models of…
A large number of biological systems - from bacteria to sheep - can be described as ensembles of self-propelled agents (active particles) with a complex internal dynamic that controls the agent's behavior: resting, moving slow, moving fast,…