Related papers: Theory for transitions between log and stationary …
Prolonged lag time can be induced by starvation contributing to the antibiotic tolerance of bacteria. We analyze the optimal lag time to survive and grow the iterative and stochastic application of antibiotics. A simple model shows that the…
A simple cell model consisting of a catalytic reaction network with intermediate complex formation is numerically studied. As nutrients are depleted, the transition from the exponential growth phase to the growth-arrested dormant phase…
Monod's law is a widely accepted phenomenology for bacterial growth. Since it has the same functional form as the Michaelis--Menten equation for enzyme kinetics, cell growth is often considered to be locally constrained by a single…
In this paper, experimental data is presented and a simple model is developed for the time evolution of a F-amp \textit{E. Coli} culture population. In general, the bacteria life cycle as revealed by monitoring a culture's population…
An important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell, where a crowded cytoplasm as…
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…
The discovery of two fundamental laws concerning cellular dynamics with recursive growth is reported. First, the chemical abundances measured over many cells are found to obey a log-normal distribution and second, the relationship between…
We propose a neo-logistic model that can describe bacterial growth data precisely. This model is not derived by modifying the logistic model formally, but by incorporating the synthesis of inducible enzymes into the logistic model…
We study nonequilibrium phase transitions in a mass-aggregation model which allows for diffusion, aggregation on contact, dissociation, adsorption and desorption of unit masses. We analyse two limits explicitly. In the first case mass is…
We propose new analytical tools for describing growth-rate distributions generated by stationary time-series. Our analysis shows how deviations from normality are not pathological behaviour, as suggested by some traditional views, but…
A new delay equation is introduced to describe the punctuated evolution of complex nonlinear systems. A detailed analytical and numerical investigation provides the classification of all possible types of solutions for the dynamics of a…
This thesis investigates critical phenomena and equilibrium states in various stochastic models through three interconnected studies. In the first chapter, we analyze the Activated Random Walk model on a one-dimensional ring in the…
Recently discovered simple quantitative relations, known as bacterial growth laws, hint on the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture on how these known…
Cell colonies of bacteria, tumour cells and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell…
Dynamic logit models are popular tools in economics to measure state dependence. This paper introduces a new method to derive moment restrictions in a large class of such models with strictly exogenous regressors and fixed effects. We…
Cellular differentiation and evolution are stochastic processes that can involve multiple types (or states) of particles moving on a complex, high-dimensional state-space or "fitness" landscape. Cells of each specific type can thus be…
Measurements of cell size dynamics have established the adder principle as a robust mechanism of cell size homeostasis. In this framework, cells add a nearly constant amount of size during each cell cycle, independent of their size at…
Predicting cellular metabolic states is a central problem in biophysics. Conventional approaches, however, sensitively depend on the microscopic details of individual metabolic systems. In this Letter, we derived a universal linear…
We introduce a new model of aggregation of particles where in addition to diffusion and aggregation upon contact, a single unit of mass can dissociate from a conglomerate. This dissociation move conserves the total mass and leads to a…
Self-assembly of proteins into amyloid aggregates is an important biological phenomenon associated with human diseases such as Alzheimer's disease. Amyloid fibrils also have potential applications in nano-engineering of biomaterials. The…