Related papers: A Markovian dynamics for C. elegans behavior acros…
Motivated by applications in movement ecology, in this paper I propose a new class of integrated continuous-time hidden Markov models in which each observation depends on the underlying state of the process over the whole interval since the…
Worm-inspired robots provide an effective locomotion strategy for constrained environments by combining cyclic body deformation with alternating anchoring. For compliant robots, however, the interaction between deformable anchoring…
In this paper, we present a theory to efficiently deal with mechanical properties of heterogeneous polymer chain in free space and the central problem is to evaluate the diffusion equation and orientation-orientation correlation function,…
Computational approaches which emulate in-vivo nervous system are needed to investigate mechanisms of the brain to orchestrate behavior. Such approaches must integrate a series of biophysical models encompassing the nervous system, muscles,…
Behaviors of several laboratory animals can be modeled as sequences of stereotyped behaviors, or behavioral motifs. However, identifying such motifs is a challenging problem. Behaviors have a multi-scale structure: the animal can be…
The use of accelerometers in wildlife tracking provides a fine-scale data source for understanding animal behavior and decision-making. Current methods in movement ecology focus on behavior as a driver of movement mechanisms. Our Markov…
We study the critical behavior of the nonequilibrium dynamics and of the steady states emerging from the competition between coherent and dissipative dynamics close to quantum phase transitions. The latter is induced by the coupling of the…
Like ants, some microorganisms are known to leave trails on surfaces to communicate. We explore how trail-mediated self-interaction could affect the behavior of individual microorganisms when diffusive spreading of the trail is negligible…
Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…
We study the distribution of lengths and other statistical properties of worms constructed by Monte Carlo worm algorithms in the power-law three-sublattice ordered phase of frustrated triangular and kagome lattice Ising antiferromagnets.…
In this paper we study the long term evolution of a continuous time Markov chain formed by two interacting birth-and-death processes. The interaction between the processes is modelled by transition rates which are functions with suitable…
Several stochastic processes modeling molecular motors on a linear track are given by random walks (not necessarily Markovian) on quasi 1d lattices and share a common regenerative structure. Analyzing this abstract common structure, we…
A major challenge in biology is to understand how molecular processes determine phenotypic features. We address this fundamental problem in a class of model systems by developing a general mathematical framework that allows the calculation…
The formation and dynamics of swarms is wide spread in living systems, from bacterial bio-films to schools of fish and flocks of birds. We study this emergent collective behavior in a model of active Brownian particles with…
1. The utilisation distribution describes the relative probability of use of a spatial unit by an animal. It is natural to think of it as the long-term consequence of the animal's short-term movement decisions: it is the accumulation of…
Limbless crawling is ubiquitous in biology, from cells to organisms. We develop and analyze a model for the dynamics of one-dimensional elastic crawlers, subject to active stress and deformation-dependent friction with the substrate. We…
Recordings of whole brain activity with single neuron resolution are now feasible in simple organisms. Yet, it is still challenging to appropriately simplify such complex, noisy, and multivariate data in order to reveal general principles…
Animal movements have been related to optimal foraging strategies where self-similar trajectories are central. Most of the experimental studies done so far have focused mainly on fitting statistical models to data in order to test for…
We propose a minimal model to simulate long waiting times followed by evolutionary bursts on rugged landscapes. It combines point and inversions-like mutations as sources of genetic variation. The inversions are intended to simulate one of…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…