4.4 Article

Effects of quasi-steady-state reduction on biophysical models with oscillations

Journal

JOURNAL OF THEORETICAL BIOLOGY
Volume 393, Issue -, Pages 16-31

Publisher

ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jtbi.2015.12.011

Keywords

Quasi-steady-state reduction; Multiple timescales; Biological oscillators; Dimension reduction

Funding

  1. Marsden Fund

Ask authors/readers for more resources

Many biophysical models have the property that some variables in the model evolve much faster than others. A common step in the analysis of such systems is to simplify the model by assuming that the fastest variables equilibrate instantaneously, an approach that is known as quasi-steady state reduction (QSSR). QSSR is intuitively satisfying but is not always mathematically justified, with problems known to arise, for instance, in some cases in which the full model has oscillatory solutions; in this case, the simplified version of the model may have significantly different dynamics to the full model. This paper focusses on the effect of QSSR on models in which oscillatory solutions arise via one or more Hopf bifurcations. We first illustrate the problems that can arise by applying QSSR to a selection of well-known models. We then categorize Hopf bifurcations according to whether they involve fast variables, slow variables or a mixture of both, and show that Hopf bifurcations that involve only slow variables are not affected by QSSR, Hopf bifurcations that involve fast and slow variables (i.e., singular Hopf bifurcations) are generically preserved under QSSR so long as a fast variable is kept in the simplified system, and Hopf bifurcations that primarily involve fast variables may be eliminated by QSSR. Finally, we present some guidelines for the application of QSSR if one wishes to use the method while minimising the risk of inadvertently destroying essential features of the original model. (c) 2015 Elsevier Ltd. All rights reserved.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.4
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Neurosciences

Olfactory Navigation and the Receptor Nonlinearity

Jonathan D. Victor, Sebastian D. Boie, Erin G. Connor, John P. Crimaldi, G. Bard Ermentrout, Katherine Nagel

JOURNAL OF NEUROSCIENCE (2019)

Article Mathematics, Applied

Two-stroke relaxation oscillators

Samuel Jelbart, Martin Wechselberger

NONLINEARITY (2020)

Article Mathematics, Applied

Slow Unfoldings of Contact Singularities in Singularly Perturbed Systems Beyond the Standard Form

Ian Lizarraga, Robert Marangell, Martin Wechselberger

JOURNAL OF NONLINEAR SCIENCE (2020)

Article Mathematics

Singularly perturbed boundary-focus bifurcations

Samuel Jelbart, Kristian Uldall Kristiansen, Martin Wechselberger

Summary: We study the transition of smooth systems to piecewise-smooth systems with a boundary-focus bifurcation as epsilon -> 0, and identify different bifurcation structures. We uncover the evolution characteristics of cycles associated with BF bifurcations in the smooth system, and prove the existence of a family of stable limit cycles.

JOURNAL OF DIFFERENTIAL EQUATIONS (2021)

Article Mathematics, Applied

Singularly Perturbed Oscillators with Exponential Nonlinearities

S. Jelbart, K. U. Kristiansen, P. Szmolyan, M. Wechselberger

Summary: This paper investigates two prototypical singularly perturbed oscillators with exponential nonlinearities, normalizing both systems to a piecewise smooth system in the limit is an element of -> 0, showing exponential convergence due to the nonlinearities studied. By extending spatial dimensions, degeneracies caused by exponentially small terms are tackled for the second model system, with (unique) limit cycles proven to exist for both systems by perturbing away from singular cycles with desirable hyperbolicity properties.

JOURNAL OF DYNAMICS AND DIFFERENTIAL EQUATIONS (2022)

Article Mathematics, Applied

Singularly perturbed boundary-equilibrium bifurcations

S. Jelbart, K. U. Kristiansen, M. Wechselberger

Summary: This work completes a classification of codimension-1 singularly perturbed boundary equilibria bifurcation (BEB) in the plane, utilizing tools from PWS theory, geometric singular perturbation theory, and the method of geometric desingularization known as blow-up. Local normal forms for generating all 12 singularly perturbed BEBs are derived, and the unfolding in each case is described. Detailed quantitative results on various bifurcations involved in the unfoldings and classification are presented, including saddle-node, Andronov-Hopf, homoclinic, and codimension-2 Bogdanov-Takens bifurcations.

NONLINEARITY (2021)

Article Mathematics, Applied

Multiple timescales and the parametrisation method in geometric singular perturbation theory

Ian Lizarraga, Bob Rink, Martin Wechselberger

Summary: The novel method presented in this study computes slow manifolds and fast fibre bundles in geometric singular perturbation problems with high degrees of accuracy, making it suitable for systems with multiple timescales. This top-down approach highlights the emergence of hidden timescales and can uncover surprising multiple timescale structures. It has been successfully applied to various reaction network problems.

NONLINEARITY (2021)

Article Mathematics, Applied

Shock-fronted travelling waves in a reaction-diffusion model with nonlinear forward-backward-forward diffusion

Yifei Li, Peter van Heijster, Matthew J. Simpson, Martin Wechselberger

Summary: Reaction-diffusion equations (RDEs) are derived from lattice-based discrete models, with recent developments allowing for negative diffusion terms. Numerical simulations support shock-fronted travelling waves in RDEs with Allee effects. By embedding RDEs in a larger class of PDEs, the existence of shock-fronted travelling waves has been proven, with different embeddings leading to waves with varying properties.

PHYSICA D-NONLINEAR PHENOMENA (2021)

Article Astronomy & Astrophysics

On the stability of shocks in isothermal black hole accretion discs

Eric W. Hester, Geoffrey M. Vasil, Martin Wechselberger

Summary: This study investigates shocks in a thin isothermal black hole accretion flow and finds that the inner shock is always unstable while the outer shock is always stable. The growth/decay rates of perturbations depend on an effective potential and the incoming-outgoing flow difference at the shock location. A prescription of accretion regimes in terms of angular momentum and black hole radius is provided, with unstable outer shocks being implied in much of the parameter space when accounting for viscous angular momentum dissipation.

MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY (2022)

Article Mathematics, Applied

Process-Oriented Geometric Singular Perturbation Theory and Calcium Dynamics

Samuel Jelbart, Nathan Pages, Vivien Kirk, James Sneyd, Martin Wechselberger

Summary: This article discusses ordinary differential equations (ODEs) used to model phenomena in chemistry, biology, and neuroscience, and presents a heuristic procedure for identifying small parameters in these ODE models. The procedure is applied to a model of intracellular calcium dynamics characterized by switching and multiple time-scale dynamics. Using geometric singular perturbation theory, the existence and uniqueness of stable relaxation oscillations with three distinct time scales are proven, and an estimate for the period of the oscillations is provided.

SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS (2022)

Article Medical Informatics

A Recurrent Neural Network Model for Predicting Activated Partial Thromboplastin Time After Treatment With Heparin: Retrospective Study

Sebastian Daniel Boie, Lilian Jo Engelhardt, Nicolas Coenen, Niklas Giesa, Kerstin Rubarth, Mario Menk, Felix Balzer

Summary: This study evaluates the capability of different machine learning algorithms to predict patients' response to heparin treatment. The results show that a recurrent neural network that uses time series features has the highest performance in predicting aPTT after heparin treatment.

JMIR MEDICAL INFORMATICS (2022)

Article Mathematics, Applied

The Dynamics of Bilateral Olfactory Search and Navigation

Nour Riman, Jonathan D. Victor, Sebastian D. Boie, Bard Ermentrout

Summary: The text discusses the importance of odor concentration for animals in localizing sources and following trails, analyzing a bilateral model and different types of odor landscapes with corresponding animal behaviors.

SIAM REVIEW (2021)

Article Mathematics, Applied

LOCAL THEORY FOR SPATIO-TEMPORAL CANARDS AND DELAYED BIFURCATIONS

Daniele Avitabile, Mathieu Desroches, Romain Veltz, Martin Wechselberger

SIAM JOURNAL ON MATHEMATICAL ANALYSIS (2020)

Article Mathematics, Applied

(IN)STABILITY OF TRAVELLING WAVES IN A MODEL OF HAPTOTAXIS

Kristen E. Harley, Peter van Heijster, Robert Marangell, Graeme J. Pettet, Timothy Roberts, Martin Wechselberger

SIAM JOURNAL ON APPLIED MATHEMATICS (2020)

Article Mathematics, Applied

Computational Singular Perturbation Method for Nonstandard Slow-Fast Systems

Ian Lizarraga, Martin Wechselberger

SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS (2020)

Article Biology

A framework for relating natural movement to length and quality of life in human and non-human animals

Iain Hunter, Raz Leib

Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

A geometric approach to the evolution of altruism

Andy Gardner

Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

A mathematical framework for the emergence of winners and losers in cell competition

Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker

Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

The eco-evolutionary dynamics of Batesian mimicry

Haruto Tomizuka, Yuuya Tachiki

Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Gene drives for the extinction of wild metapopulations

Jason W. Olejarz, Martin A. Nowak

Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Intelligent phenotype-detection and gene expression profile generation with generative adversarial networks

Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti

Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Network-based uncertainty quantification for mathematical models in epidemiology

Beatrix Rahnsch, Leila Taghizadeh

Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Dynamics of cell-type transition mediated by epigenetic modifications

Rongsheng Huang, Qiaojun Situ, Jinzhi Lei

Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Comparative analysis of kinetic realizations of insulin signaling

Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao

Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Simulating tumor volume dynamics in response to radiotherapy: Implications of model selection

Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid

Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.

JOURNAL OF THEORETICAL BIOLOGY (2024)

Article Biology

Pillars of theoretical biology: Biochemical systems analysis, I, II and III

Armindo Salvador

Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.

JOURNAL OF THEORETICAL BIOLOGY (2024)