Related papers: Scaling and optimal synergy: Two principles determ…
Life presents fascinating examples of self-organization and emergent phenomena. In multi-cellular organisms, a multitude of cells interact to form and maintain highly complex body plans of well-defined size. In this thesis, we investigate…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
Hypotheses: Quantitative molecular-thermodynamic theory of the growth of giant wormlike micelles in mixed nonionic surfactant solutions can be developed on the basis of a generalized model, which includes the classical phase separation and…
Real-world growth processes and scalings have been broadly categorized into three growth regimes with distinctly different properties and driving forces. The first two are characterized by a positive and constant feedback between growth and…
For the problem of efficiently supplying material to a spatial region from a single source, we present a simple scaling argument based on branching network volume minimization that identifies limits to the scaling of sink density. We…
The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide the first deep investigation of the predictive potential of machine…
Experimental studies of microbial communities routinely reveal that they have multiple stable states. While each of these states is generally resilient, certain perturbations such as antibiotics, probiotics and diet shifts, result in…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Biofilms are bacterial aggregates that grow on moist surfaces. Thin homogeneous biofilms naturally formed on the walls of conducts may serve as biosensors, providing information on the status of microsystems (MEMS) without disrupting them.…
Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with…
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…
Metabolism of living organisms is a foundation of life. The metabolic rate (energy production per unit time) increases slower than organisms' mass. When this phenomenon is considered across different species, it is called interspecific…
We consider the logistic metapopulation model over a stream network and use the metapopulation growth rate and the total biomass (of the positive equilibrium) as metrics for different aspects of population persistence. Our objective is to…
Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been…
For biological experiments aiming at calibrating models with unknown parameters, a good experimental design is crucial, especially for those subject to various constraints, such as financial limitations, time consumption and physical…
Highly-optimized complex transport networks serve crucial functions in many man-made and natural systems such as power grids and plant or animal vasculature. Often, the relevant optimization functional is non-convex and characterized by…
In this brief, we study epidemic spreading dynamics taking place in complex networks. We specifically investigate the effect of synergy, where multiple interactions between nodes result in a combined effect larger than the simple sum of…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
Regardless of a system's complexity or scale, its growth can be considered to be a spontaneous thermodynamic response to a local convergence of down-gradient material flows. Here it is shown how growth can be constrained to a few distinct…
We developed a simulator to quantify the effect of changes in environmental parameters on plant growth in precision farming. Our approach combines the processing of plant images with deep convolutional neural networks (CNN), growth curve…