Related papers: Optimal metabolic pathway activation
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
Molecular dynamics simulations have become essential in many areas of atomistic modelling from drug discovery to materials science. They provide critical atomic-level insights into key dynamical events experiments cannot easily capture.…
The presented previously indirect optimization method (IOM) developed within biochemical systems theory (BST) provides a versatile and mathematically tractable optimization strategy for biochemical systems. However, due to the local…
In this work, a machine learning approach for identifying the multi-omics metabolic regulatory control circuits inside the pathways is described. Therefore, the identification of bacterial metabolic pathways that are more regulated than…
Active matter systems comprise self-propelled particles that move on a substrate while leaving chemical trails that influence other particles through chemotaxis (e.g., slime-depositing bacteria). Orientational chemotaxis manifests as a…
Designing reaction pathways that maximize the production of a target compound in a given metabolic network is a fundamental problem in systems biology. In this study, we systematically explore the non-oxidative glycolysis metabolic network,…
Living organisms are not just random collections of organic molecules. There is continuous information processing going on in the apparent bouncing around of molecules of life. Optimisation criteria in this information processing can be…
A class of semilinear parabolic reaction diffusion equations with multiple time delays is considered. These time delays and corresponding weights are to be optimized such that the associated solution of the delay equation is the best…
The Bell-Evans-Polanyi principle that is valid for a chemical reaction that proceeds along the reaction coordinate over the transition state is extended to molecular dynamics trajectories that in general do not cross the dividing surface…
It was hypothesized that the structures of biological transport networks are the result of either energy consumption or adaptation dynamics. Although approaches based on these hypotheses can produce optimal network and form loop structures,…
Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions,…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
Many processes in chemistry, physics, and biology involve rare events in which the system escapes from a metastable state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation events…
The emerging field of immunometabolism has underscored the central role of metabolic pathways in orchestrating immune cell function. Far from being passive background processes, metabolic activities actively regulate key immune responses.…
We study an ancient problem that in a static or dynamical system, sought an optimal path, which the context always means within an extremal condition. In fact, through those discussions about this theme, we established a universal essential…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
Any process in which competing solutions replicate with errors and numbers of their copies depend on their respective fitnesses is the evolutionary optimization process. As during carcinogenesis mutated genomes replicate according to their…
Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fluctuations in their expression can affect the levels of…
In this work we present a novel methodology to deal with the optimal performance of raceways (open-channel ponds where the circulating wastewater, during its purification process, is used to grow algae that will be used as a source for the…
This paper addresses optimal battery thermal management (BTM), charging, and eco-driving of a battery electric vehicle (BEV) with the goal of improving its grid-to-meter energy efficiency. Thus, an optimisation problem is formulated, aiming…