Results 1 to 10 of about 13,577 (95)

Nonequilibrium thermodynamics of glycolytic traveling wave: Benjamin-Feir instability [PDF]

journal = {Phys. Rev. E}, volume = {104}, pages = {014221}, numpages = {16}, year = {2021}, publisher = {American Physical Society}, 2021
Evolution of the nonequilibrium thermodynamic entities corresponding to dynamics of the Hopf instabilities and traveling waves at a nonequilibrium steady state of a spatially extended glycolysis model is assessed here by implementing an analytically tractable scheme incorporating a complex Ginzburg-Landau equation (CGLE).
arxiv   +1 more source

Self-Organization and Fractality in the Metabolic Process of Glycolysis [PDF]

Ukr. J. Phys., Vol. 59, N 12, p.1251-1262 (2015), 2017
Within a mathematical model, the metabolic process of glycolysis is studied. The general scheme of glycolysis is considered as a natural result of the biochemical evolution. By using the theory of dissipative structures, the conditions of self-organization of the given process are sought.
arxiv   +1 more source

Lower glycolysis carries a higher flux than any biochemically possible alternative [PDF]

Nature Communications 6, 8427 (2015), 2014
The universality of many pathways of core metabolism suggests a strong role for evolutionary selection, but it remains unclear whether existing pathways have been selected from a large or small set of biochemical possibilities. To address this question, we construct "in silico" all possible biochemically feasible alternatives to the trunk pathway of ...
arxiv   +1 more source

Model evaluation for glycolytic oscillations in yeast biotransformations of xenobiotics [PDF]

Biophysical Chemistry 109, 413-426 (2004), 2004
Anaerobic glycolysis in yeast perturbed by the reduction of xenobiotic ketones is studied numerically in two models which possess the same topology but different levels of complexity. By comparing both models' predictions for concentrations and fluxes as well as steady or oscillatory temporal behavior we answer the question what phenomena require what ...
arxiv   +1 more source

A machine learning approach to investigate regulatory control circuits in bacterial metabolic pathways [PDF]

, 2020
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 others in term of their multi-omics follows from the analysis of these circuits .
arxiv   +1 more source

Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression [PDF]

, 2014
The nonlinearity of dynamics in systems biology makes it hard to infer them from experimental data. Simple linear models are computationally efficient, but cannot incorporate these important nonlinearities. An adaptive method based on the S-system formalism, which is a sensible representation of nonlinear mass-action kinetics typically found in ...
arxiv   +1 more source

Energy-based Analysis of Biomolecular Pathways [PDF]

Proc. R. Soc. A 2017 473 20160825, 2016
Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about steady-state mass flows (reaction rates) through the network.
arxiv   +1 more source

Unbounded solutions of models for glycolysis [PDF]

arXiv, 2020
The Selkov oscillator, a simple description of glycolysis, is a system of two ordinary differential equations with mass action kinetics. In previous work the authors established several properties of the solutions of this system. In the present paper we extend this to prove that this system has solutions which diverge to infinity in an oscillatory ...
arxiv  

Warburg Effect due to Exposure to Different Types of Radiation [PDF]

arXiv, 2013
Cancer cells maintain a high level of aerobic glycolysis (the Warburg effect), which is associated with their rapid proliferation. Many studies have reported that the suppression of glycolysis and activation of oxidative phosphorylation can repress the growth of cancer cells through regulation of key regulators.
arxiv  

When Hopf meets saddle: bifurcations in the diffusive Selkov model for glycolysis [PDF]

arXiv, 2020
We study the linear instabilities and bifurcations in the Selkov model for glycolysis with diffusion. We show that this model has a zero wave-vector, finite frequency Hopf bifurcation to a growing oscillatory but spatially homogeneous state and a saddle-node bifurcation to a growing inhomogeneous state with a steady pattern with a finite wavevector. We
arxiv