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The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
In this work we focus on how noise propagates in biochemical reaction networks and affects sensitivities of the system. We discover that the stochastic fluctuations can enhance sensitivities in one region of the value of control parameters…
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…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
The chemotaxis pathway of the bacterium Rhodobacter sphaeroides has many similarities to the well-studied pathway in Escherichia coli. It exhibits robust adaptation and has several homologues of the latter's chemotaxis proteins. Recent…
Transcription factor concentrations provide signals to cells that allow them to regulate gene expression to make correct cell fate decisions. Calculations for noise bounds in gene regulation suggest that clustering or cooperative binding of…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
Living systems adapt to various environmental conditions by changing their internal states. Inspired by gene expression and epigenetic modification dynamics, we herein propose a generic mechanism for adaptation by combining fast oscillatory…
Intracellular signaling often arises from ligand-induced oligomerization of cell surface receptors. This oligomerization or clustering process is fundamentally a cooperative behavior between near-neighbor receptor molecules; the properties…
Organisms use specialized sensors to measure their environments, but the fundamental principles that determine their accuracy remain largely unknown. In Escherichia coli chemotaxis, we previously found that gradient-climbing speed is…
A model of clustering dynamics is proposed for a population of spatially distributed active rotators. A transition from excitable to oscillatory dynamics is induced by the increase of the local density of active rotators. It is interpreted…
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…
A variety of biomolecular systems rely on exploratory dynamics to reach target locations or states within a cell. Without a mechanism to remotely sense and move directly towards a target, the system must sample over many paths, often…
Response time-delay is an ubiquitous phenomenon in biological systems. Here we use a simple stochastic population model with time-delayed switching-rate conversion to quantitatively study the biological influence of the response time-delay…
Cell growth is determined by substrate availability and the cell's metabolic capacity to assimilate substrates into building blocks. Metabolic genes that determine growth rate may interact synergistically or antagonistically, and can…
Cells are constantly exposed to fluctuating environmental conditions. External signals are sensed, processed and integrated by cellular signal transduction networks, which translate input signals into specific cellular responses by means of…
Packing and crowding are used in biology as mechanisms to (self-)regulate internal molecular or cellular processes based on collective signalling. Here, we study how the transition kinetics of an internal switch of responsive macromolecules…
Over the past few decades, the research community has been interested in the study of multi-agent systems and their emerging collective dynamics. These systems are all around us in nature, like bacterial colonies, fish schools, bird flocks,…
Oscillatory chemical reactions often serve as a timing clock of cellular processes in living cells. The temporal dynamics of protein concentration levels is thus of great interest in biology. Here we propose a theoretical framework to…