Classic and contemporary approaches to modeling biochemical reactions

WW Chen, M Niepel, PK Sorger - Genes & development, 2010 - genesdev.cshlp.org
Recent interest in modeling biochemical networks raises questions about the relationship
between often complex mathematical models and familiar arithmetic concepts from classical …

Multisite protein phosphorylation–from molecular mechanisms to kinetic models

C Salazar, T Höfer - The FEBS journal, 2009 - Wiley Online Library
Multisite phosphorylation is an important mechanism for fine‐tuned regulation of protein
function. Mathematical models developed over recent years have contributed to elucidation …

Beyond the Michaelis-Menten equation: Accurate and efficient estimation of enzyme kinetic parameters

B Choi, GA Rempala, JK Kim - Scientific reports, 2017 - nature.com
Examining enzyme kinetics is critical for understanding cellular systems and for using
enzymes in industry. The Michaelis-Menten equation has been widely used for over a …

Modular cell biology: retroactivity and insulation

D Del Vecchio, AJ Ninfa, ED Sontag - Molecular systems biology, 2008 - embopress.org
Modularity plays a fundamental role in the prediction of the behavior of a system from the
behavior of its components, guaranteeing that the properties of individual components do …

[PDF][PDF] The meshless local Petrov-Galerkin (MLPG) method: a simple & less-costly alternative to the finite element and boundary element methods

S Shen, SN Atluri - Computer Modeling in Engineering & Sciences, 2002 - Citeseer
A comparison study of the efficiency and accuracy of a variety of meshless trial and test
functions is presented in this paper, based on the general concept of the meshless local …

Validity of the Michaelis–Menten equation–steady‐state or reactant stationary assumption: that is the question

S Schnell - The FEBS journal, 2014 - Wiley Online Library
The Michaelis–Menten equation is generally used to estimate the kinetic parameters, V and
KM, when the steady‐state assumption is valid. Following a brief overview of the derivation …

Internal coarse-graining of molecular systems

J Feret, V Danos, J Krivine, R Harmer… - Proceedings of the …, 2009 - pnas.org
Modelers of molecular signaling networks must cope with the combinatorial explosion of
protein states generated by posttranslational modifications and complex formation. Rule …

The cell cycle switch computes approximate majority

L Cardelli, A Csikász-Nagy - Scientific reports, 2012 - nature.com
Both computational and biological systems have to make decisions about switching from
one state to another. The 'Approximate Majority'computational algorithm provides the …

Misuse of the Michaelis–Menten rate law for protein interaction networks and its remedy

JK Kim, JJ Tyson - PLOS Computational Biology, 2020 - journals.plos.org
For over a century, the Michaelis–Menten (MM) rate law has been used to describe the rates
of enzyme-catalyzed reactions and gene expression. Despite the ubiquity of the MM rate …

[LIBRO][B] Modeling biomolecular networks in cells: structures and dynamics

L Chen, R Wang, C Li, K Aihara - 2010 - books.google.com
Taking ideas from nature has been a theme of humanity's technological progress but it is
only our newfound expertise in molecular manipulation and complex nonlinear dynamics …