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We present models and computational results which indicate that the spatial and temporal regularity seen in Proteus mirabilis swarm-colony development is largely an expression of a sharp age of dedifferentiation in the cell cycle from…
Molecular sorting is a fundamental process that allows eukaryotic cells to distill and concentrate specific chemical factors in appropriate cell membrane subregions, thus endowing them with different chemical identities and functional…
Many motile microorganisms react to environmental light cues with a variety of motility responses guiding cells towards better conditions for survival and growth. The use of spatial light modulators could help to elucidate the mechanisms of…
Reservoir computing is a novel machine learning algorithm that uses a nonlinear dynamical system to efficiently learn complex temporal patterns from data. The objective of this thesis is to investigate the principles of reservoir computing…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
Bacterial growth environment strongly influences the efficacy of antibiotic treatment, with slow growth often being associated with decreased susceptibility. Yet in many cases the connection between antibiotic susceptibility and pathogen…
Bacteria build multicellular communities termed biofilms, which are often encased in a self-secreted extracellular matrix that gives the community mechanical strength and protection against harsh chemicals. How bacteria assemble distinct…
Suitable asymmetric microstructures can be used to control the direction of motion in microorganism populations. This rectification process makes it possible to accumulate swimmers in a region of space or to sort different swimmers. Here we…
It is common for researchers to record long, multiple time series from experiments or calculations. But sometimes there are no good models for the systems or no applicable mathematical theorems that can tell us when there are basic…
Mechanical interactions among cells in a growing microbial colony can significantly influence the colony's spatial genetic structure and, thus, evolutionary outcomes such as the fates of rare mutations. Here, we computationally investigate…
Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of…
Feature selection is indispensable in microbiome data analysis, but it can be particularly challenging as microbiome data sets are high-dimensional, underdetermined, sparse and compositional. Great efforts have recently been made on…
We study the effect of discreteness on various models for patterning in bacterial colonies. In a bacterial colony with branching pattern, there are discrete entities - bacteria - which are only two orders of magnitude smaller than the…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
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…
Recent progress in diverse intelligence has shown simple learning capacities below the organism level - single cells and even molecular networks. However, there are still many knowledge gaps around learning capacity above the organism…
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new…
Memories are stored, retained, and recollected through complex, coupled processes operating on multiple timescales. To understand the computational principles behind these intricate networks of interactions we construct a broad class of…
The living cell expends energetic and material resources to reliably process information from its environment. To do so, it utilises unreliable molecular circuitry that is subject to thermal and other fluctuations. Here, we argue that…
Exploring nonlinear chemical dynamic systems for information processing has emerged as a frontier in chemical and computational research, seeking to replicate the brain's neuromorphic and dynamic functionalities. We have extensively…