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We derive a single-cell level understanding of metabolism in an isogenic cyanobacterial population by integrating secondary ion mass spectrometry (SIMS) derived multi-isotope uptake measurements of Synechocystis sp. PCC6803 with a…
The complexity of gene regulatory networks in multicellular organisms makes interpretable low-dimensional models highly desirable. An attractive geometric picture, attributed to Waddington, visualizes the differentiation of a cell into…
During overflow metabolism, cells excrete glycolytic byproducts when growing under aerobic conditions in a seemingly wasteful fashion. While potentially advantageous for microbes with finite oxidative capacity, its role in higher organisms…
To successfully navigate chemical gradients, microorganisms need to predict how the ligand concentration changes in space. Due to their limited size, they do not take a spatial derivative over their body length but rather a temporal…
We study the average asymptotic growth rate of cells in randomly fluctuating environments, with multiple viable phenotypes per environment. We show that any information processing strategy has an asymptotic growth rate, which is the sum of:…
A methodology is introduced which uses three simple objective function features to predict effective control parameters for differential evolution. This is achieved using cluster analysis techniques to classify objective functions using…
The variability in cell size of an isogenic population of Escherichia coli has been widely reported in experiment. The probability density function (PDF) of cell lengths has been variously described by exponential and lognormal functions.…
The analysis of biological networks is characterized by the definition of precise linear constraints used to cumulatively reduce the solution space of the computed states of a multi-omic (for instance metabolic, transcriptomic and…
Biological systems operate under simultaneous energetic and informational constraints, yet direct evidence that such constraints shape real metabolic networks is limited. The Network-Weighted Action Principle predicts that networks under…
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…
Saccharomyces cerevisiae is increasingly recognised as a key source for single-cell protein (SCP) production, a rising solution to global protein-supply challenges. This study presents a computational framework combining the Yeast9…
Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities,…
In the subtropical gyres, phytoplankton rely on eddies for transporting nutrients from depth to the euphotic zone. But, what controls the rate of nutrient supply for new production? We show that vertical nutrient flux depends both on the…
The dynamics of growth of bacterial populations has been extensively studied for planktonic cells in well-agitated liquid culture, in which all cells have equal access to nutrients. In the real world, bacteria are more likely to live in…
Chemotaxis of the bacterium Escherichia coli is well understood in shallow chemical gradients, but its swimming behavior remains difficult to interpret in steep gradients. By focusing on single-cell trajectories from simulations, we…
The metabolism of cells is the most basic and important part of human function. Neural networks in deep learning stem from neuronal activity. It is self-evident that the significance of metabolize neuronal network(MetaNet) in model…
High energy efficiency is critical for enabling massive machine-type communications (MTC) over cellular networks. This work is devoted to energy consumption modeling, battery lifetime analysis, lifetime-aware scheduling and transmit power…
Theoretical frameworks to estimate the tolerance of metabolic networks to various failures are important to evaluate the robustness of biological complex systems in systems biology. In this paper, we focus on a measure for robustness in…
Optimal experimental design for parameter precision attempts to maximize the information content in experimental data for a most effective identification of parametric model. With the recent developments in miniaturization and…
Sessile ciliates attach to substrates and generate feeding currents to capture passing particulates and dissolved nutrients. Optimal ciliary activity that maximizes nutrient flux at the cell surface while minimizing the rate of hydrodynamic…