Related papers: Mapping high-growth phenotypes in the flux space o…
Biological populations are subject to fluctuating environmental conditions. Different adaptive strategies can allow them to cope with these fluctuations: specialization to one particular environmental condition, adoption of a generalist…
The metabolic networks are very well characterized for a large set of organisms, a unique case in within the large-scale biological networks. For this reason they provide a a very interesting framework for the construction of analytically…
The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular…
Flow-matching generative models are increasingly used to simulate cell responses to biological perturbations. However, the design space for building such models is large and underexplored. We systematically analyse the design space of flow…
We study an optimal control problem arising from a resource allocation problem in cellular metabolism. A minimalistic model that describes the production of enzymatic vs. non-enzymatic biomass components from a single nutrient source is…
Feed-forward loops (FFLs) are among the most ubiquitously found motifs of reaction networks in nature. However, little is known about their stochastic behavior and the variety of network phenotypes they can exhibit. In this study, we…
Biofilm infections on medical implants are difficult to eradicate because insufficient nutrient availability promotes antibiotic-tolerant persister cells that survive treatment and reseed growth. Existing mathematical models usually omit…
Constraint-based modeling has been widely used on metabolic networks analysis, such as biosynthetic prediction and flux optimization. The linear constraints, like mass conservation constraint, reversibility constraint, biological capacity…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…
Modeling of growth (or decay) curves arises in many fields such as microbiology, epidemiology, marketing, and econometrics. Parametric forms like Logistic and Gompertz are often used for modeling such monotonic patterns. While useful for…
We measure different contributions to entropy production in a living functional epithelial tissue. We do this by extracting the functional dynamics of development while at the same time quantifying fluctuations. Using the translucent…
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…
We introduce a methodology to study the possible matter flows of an ecosystem defined by observational biomass data and realistic biological constraints. The flows belong to a polyhedron in a multi dimensional space making statistical…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform…
Phase-field models of tumour growth have proved useful as theoretical tools to investigate cancer invasion. A key implicit assumption underlying mathematical models of this type which have so far been proposed, though, is that cells in the…
The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a…
Collective cell migration plays a crucial role in numerous biological processes, including tumour growth, wound healing, and the immune response. Often, the migrating population consists of cells with various different phenotypes. This…
Production of chemicals from engineered organisms in a batch culture involves an inherent trade-off between productivity, yield, and titer. Existing strategies for strain design typically focus on designing mutations that achieve the…
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…