Related papers: On Creativity of Slime Mould
This work introduces SwarmRL, a Python package designed to study intelligent active particles. SwarmRL provides an easy-to-use interface for developing models to control microscopic colloids using classical control and deep reinforcement…
We present a coarse-grained single-site potential for simulating chiral interactions, with adjustable strength, handedness, and preferred twist angle. As an application, we perform basin-hopping global optimisation to predict the favoured…
The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…
Filamentous cyanobacteria are one of the oldest and today still most abundant lifeforms on earth, with manifold implications in ecology and economics. Their flexible filaments, often several hundred cells long, exhibit gliding motility in…
Since the lipid raft model was developed at the end of the last century, it became clear that the specific molecular arrangements of phospholipid assemblies within a membrane have profound implications in a vast range of physiological…
Many biological and synthetic materials self-assemble into helical or twisted aggregates. The shape is determined by a complex interplay between elastic forces and the orientation and chirality of the constituent molecules. We study this…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
Recent experiments suggest that the interplay between cells and the mechanics of their substrate gives rise to a diversity of morphological and migrational behaviors. Here, we develop a Cellular Potts Model of polarizing cells on a…
Mycelium, a natural and sustainable material, possesses unique electrical, mechanical, and biological properties that make it a promising candidate for biosensor applications. These properties include its ability to conduct electrical…
The hydrodynamic interactions among bacterial cell bodies, flagella, and surrounding boundaries are essential for understanding bacterial motility in complex environments. In this study, we demonstrate that each slender flagellum can be…
Essentially all biology is active and dynamic. Biological entities autonomously sense, com- pute, and respond using energy-coupled ratchets that can produce force and do work. The cytoskeleton, along with its associated proteins and motors,…
We have built an open-source software system for the modeling of biomolecular reaction networks, SloppyCell, which is written in Python and makes substantial use of third-party libraries for numerics, visualization, and parallel…
The swarm intelligence of animals is a natural paradigm to apply to optimization problems. Ant colony, bee colony, firefly and bat algorithms are amongst those that have been demonstrated to efficiently to optimize complex constraints. This…
Soft slender structures are ubiquitous in natural and artificial systems and can be observed at scales that range from the nanometric to the kilometric, from polymers to space tethers. We present a practical numerical approach to simulate…
Natural groups of animals, such as swarms of social insects, exhibit astonishing degrees of task specialization, useful to address complex tasks and to survive. This is supported by phenotypic plasticity: individuals sharing the same…
The Physarum solver is an intuitive mechanism for solving optimisation problems based on the idea of an electrical network, whereby the conductivity is reinforced by the current. We show that the Physarum solver obtains the solution to the…
In this paper, we propose applying semantic embedding to learn the range of behaviors exhibited by molecular swarms, thereby providing a richer set of features to optimize such systems. Specifically, we consider a standard molecular swarm…
Mycelium bound composites are promising materials for a diverse range of applications including wearables and building elements. Their functionality surpasses some of the capabilities of traditionally passive materials, such as synthetic…
The aim of this work is to quantify the spatio-temporal dynamics of flow-driven amoeboid locomotion in small ($\sim$100 $\mu$m) fragments of the true slime mold \phys {\it polycephalum}. In this model organism, cellular contraction drives…
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…