Related papers: Optimal metabolic pathway activation
How do single cell fate decisions induced by activation of key signaling proteins above threshold concentrations within a time interval are affected by stochastic fluctuations in biochemical reactions? We address this question using minimal…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
Signal transduction pathways recover a crucial role in cellular processes: they represent a connection between environmental conditions and cellular reactions. There are many pathways and they all are related to create a network. But how…
Biochemical signalling cascades transduce extracellular stimuli into cellular responses through sequences of discrete, node-to-node activations. While signal fidelity depends critically on local interaction kinetics, the mechanisms…
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the…
The connection between optimal biological function and energy use, measured for example by the rate of metabolite consumption, is a current topic of interest in the systems biology literature which has been explored in several different…
Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
Biological molecular machines convert free energy between different forms in cells, often at high efficiency. Optimal control theory provides a framework to elucidate design principles governing energetically efficient driving. Here, we use…
Enzyme costs play a major role in the choice of metabolic routes, both in evolution and bioengineering. Given desired fluxes, necessary enzyme levels can be estimated based on known rate laws and on a principle of minimal enzyme cost. With…
Chemical reactions can be modelled via diffusion processes conditioned to make a transition between specified molecular configurations representing the state of the system before and after the chemical reaction. In particular the model of…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
Extinction appears ubiquitously in many fields, including chemical reactions, population biology, evolution, and epidemiology. Even though extinction as a random process is a rare event, its occurrence is observed in large finite…
The optimal control of epidemic-like stochastic processes is important both historically and for emerging applications today, where it can be especially important to include time-varying parameters that impact viral epidemic-like…
Models in systems biology are mathematical descriptions of biological processes that are used to answer questions and gain a better understanding of biological phenomena. Dynamic models represent the network through rates of the production…
Background: Mechanotransduction in bone cells plays a pivotal role in osteoblast differentiation and bone remodelling. Mechanotransduction provides the link between modulation of the extracellular matrix and intracellular actions. By…
The least action principle is exploited as a simulation tool to find the optimal dynamic path for spatially extended systems driven by a small noise. Applications are presented for thermally activated switching of a spatially-extended…
Many biological molecular motors and machines are driven by chemical reactions that occur in specific catalytic sites. We study whether the arrival of molecules to such an active site can be accelerated by the presence of a nearby inactive…