Related papers: Modeling Metabolic State Transitions in Obesity Us…
Objective: As metabolic cost is a primary factor influencing humans' gait, we want to deepen our understanding of metabolic energy expenditure models. Therefore, this paper identifies the parameters and input variables, such as muscle or…
Adiabatic passage employs a slowly varying time-dependent Hamiltonian to control the evolution of a quantum system along the Hamiltonian eigenstates. For processes of finite duration, the exact time evolving state may deviate from the…
We introduce two time-delay models of metabolic oscillations in yeast cells. Our model tests a hypothesis that the oscillations occur as multiple pathways share a limited resource which we equate to the number of available ribosomes. We…
Metabolomic based approaches have gained much attention in recent years due to their promising potential to deliver objective tools for assessment of food intake. In particular, multiple biomarkers have emerged for single foods. However,…
We revisit the modeling of the diauxic growth of a pure microorganism on two distinct sugars which was first described by Monod. Most available models are deterministic and make the assumption that all cells of the microbial ecosystem…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Integrated global food system analysis is hampered by the fragmentation of data among food types, processes, and scales. Studies also often neglect the connection to human metabolism -- the ultimate driver of food demand. Here we use a…
We study dynamical phase transitions in a model supercooled liquid. These transitions occur in ensembles of trajectories that are biased towards low (or high) dynamical activity. We compare two different measures of activity that were…
Analysis of mathematical models in ecology and epidemiology often focuses on asymptotic dynamics, such as stable equilibria and periodic orbits. However, many systems exhibit long transient behaviors where certain aspects of the dynamics…
Representation of cities as organisms with metabolic processes is a useful analogy for urban design, development and sustainability. Urban metabolism can be modeled by representing urban systems as networks. The various networks included in…
A classic problem in metabolism is that fast-proliferating cells use seemingly wasteful fermentation for energy biogenesis in the presence of sufficient oxygen. This counterintuitive phenomenon, known as overflow metabolism or the Warburg…
Despite their topological complexity almost all functional properties of metabolic networks can be derived from steady-state dynamics. Indeed, many theoretical investigations (like flux-balance analysis) rely on extracting function from…
The traditional dynamical phase transition refers to the appearance of singularities in an observable with respect to a control parameter for a late-time state or singularities in the rate function of the Loschmidt echo with respect to…
The metabolic state of a cell, comprising fluxes, metabolite concentrations and enzyme levels, is shaped by a compromise between metabolic benefit and enzyme cost. This hypothesis and its consequences can be studied by computational models…
We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation matrix, and stochastic force. These four elements are…
Intercellular exchange networks are essential for the adaptive capabilities of populations of cells. While diffusional exchanges have traditionally been difficult to map, recent advances in nanotechnology enable precise probing of exchange…
We consider two minimal mathematical models for cancer dynamics and self-adaptation. We aim to capture the interplay between the rapid progression of cancer growth and the possibility to leverage and enhance self-adaptive defense mechanisms…
We study the qualitative behavior of a model to represent local regulation in a metabolic network. The model is based on the end-product control structure introduced in [A. Goelzer, F. Bekkal Brikci, I. Martin-Verstraete et al., BMC Syst…
Biological organisms are adaptive, able to function in unpredictably changing environments. Drawing on recent nonequilibrium physics, we show that in adaptation, fitness has two components parameterized by observable coordinates: a static…
In earlier work, we introduced a discrete Fibonacci-based ontogenetic model in which the metabolic scaling exponent $b(n)$ is treated as a dynamic function of an organism's developmental stage, and we estimated $b(n)$ for selected mammalian…