Related papers: An ensemble approach to the structure-function pro…
The dynamics of many microbial ecosystems are driven by cross-feeding interactions, in which metabolites excreted by some species are metabolised further by others. The population dynamics of such ecosystems are governed by…
A classic problem in microbiology is that bacteria display two types of growth behavior when cultured on a mixture of two carbon sources: the two sources are sequentially consumed one after another (diauxie) or they are simultaneously…
Our planet is roughly closed to matter, but open to energy input from the sun. However, to harness this energy, organisms must transform matter from one chemical (redox) state to another. For example, photosynthetic organisms can capture…
We examine the modular structure of the metabolic network when combined with the regulatory network representing direct regulation of enzymes by small metabolites in E.coli. In order to identify the modular structure we introduce clustering…
From flocking birds to schooling fish, organisms interact to form collective dynamics across the natural world. Self-organization is present at smaller scales as well: cells interact and move during development to produce patterns in fish…
Metabolic pathways are fundamental maps in biochemistry that detail how molecules are transformed through various reactions. The complexity of metabolic network, where a single compound can play a part in multiple pathways, poses a…
Collective cell migration is a key driver of embryonic development, wound healing, and some types of cancer invasion. Here we provide a physical perspective of the mechanisms underlying collective cell migration. We begin with a catalogue…
Until recently, much of the microbial world was hidden from view. A global research effort has changed this, unveiling and quantifying microbial diversity across enormous range of critically-important contexts, from the human microbiome, to…
The large-scale shape and function of metabolic networks are intriguing topics of systems biology. Such networks are on one hand commonly regarded as modular (i.e. built by a number of relatively independent subsystems), but on the other…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences.…
Bacteria can spontaneously develop collective motions by aligning their motions in dense systems. Here, we show that bacteria can also respond collectively to an alternating electrical field and form dynamic clusters oscillating at the same…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
This study investigates the role of spatial segregation, prompted by competition avoidance, as a key mechanism for emergent coexistence within microbial communities. Recognizing these communities as complex adaptive systems, we challenge…
Modularity maximization has been one of the most widely used approaches in the last decade for discovering community structure in networks of practical interest in biology, computing, social science, statistical mechanics, and more.…
Collective phenomena emerge from the interaction of natural or artificial units with a complex organization. The interplay between structural patterns and dynamics might induce functional clusters that, in general, are different from…
Many networks are important because they are substrates for dynamical systems, and their pattern of functional connectivity can itself be dynamic -- they can functionally reorganize, even if their underlying anatomical structure remains…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
The diverse metabolic pathways are fundamental to all living organisms, as they harvest energy, synthesize biomass components, produce molecules to interact with the microenvironment, and neutralize toxins. While discovery of new…
Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive mechanism are expected to speculate a novel rule in wood biomass…