Related papers: The Quasi-Steady State Assumption in an Enzymatica…
Consider a mathematical model of evolutionary adaptation of fitness landscape and mutation matrix as a reaction to population changes. As a basis, we use an open quasispecies model, which is modified to include explicit death flow. We…
We demonstrate that the Michaelis-Menten reaction mechanism can be accurately approximated by a linear system when the initial substrate concentration is low. This leads to pseudo-first-order kinetics, simplifying mathematical calculations…
In this work, we revisit the scaling analysis and commonly accepted conditions for the validity of the standard, reverse and total quasi-steady-state approximations through the lens of dimensional Tikhonov-Fenichel parameters and their…
The Quasi Steady-State (QSS) model of long-term dynamics relies on the idea of time-scale decomposition. Assuming that the fast variables are infinitely fast and are stable in the long-term, the QSS model replaces the differential equations…
We introduce a reaction-path statistical mechanics formalism based on the principle of large deviations to quantify the kinetics of single-molecule enzymatic reaction processes under the Michaelis-Menten mechanism, which exemplifies an…
A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models…
"Quantum mechanics must be regarded as open systems. On one hand, this is due to the fact that, like in classical physics, any realistic system is subjected to a coupling to an uncontrollable environment which influences it in a…
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…
In recent work, Baez, Fong and the author introduced a framework for describing Markov processes equipped with a detailed balanced equilibrium as open systems of a certain type. These `open Markov processes' serve as the building blocks for…
The problem of the microscopic description of excited states of the even-even open-shell atomic nuclei is considered. A model is formulated which allows one to go beyond the quasiparticle random phase approximation. The physical content of…
Deterministic approximations to stochastic Susceptible-Infectious-Susceptible models typically predict a stable endemic steady-state when above threshold. This can be hard to relate to the underlying stochastic dynamics, which has no…
Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a…
To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves…
We consider quasi maximum likelihood (QML) estimation for general non-Gaussian discrete-ime linear state space models and equidistantly observed multivariate L\'evy-driven continuoustime autoregressive moving average (MCARMA) processes. In…
We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under1 quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady…
Glycosylation is a critical quality attribute for monoclonal antibody (mAb) production, influenced by both process conditions and cellular mechanisms. Multiscale mechanistic models, spanning from the bioreactor to the Golgi apparatus, have…
The estimation of the kinetic parameters requires the careful design of experiments under a constrained set of conditions. Many estimates reported in the literature incorporate protocols that leverage simplified mathematical models known as…
The Quasi-Steady State Approximation (QSSA) can be an effective tool for reducing the size and stiffness of chemical mechanisms for implementation in computational reacting flow solvers. However, for many applications, stiffness remains,…
For a large class of processes with an absorbing state, statistical properties of the surviving sample attain time-independent values in the quasi-stationary (QS) regime. We propose a practical simulation method for studying…
A preceding paper demonstrated that explicit asymptotic methods generally work much better for extremely stiff reaction networks than has previously been shown in the literature. There we showed that for systems well removed from…